Modified Short Interfering Nucleic Acid (siNA) Molecules and Uses Thereof

- Aligos Therapeutics, Inc.

Disclosed herein are short interfering nucleic acid (siNA) molecules comprising modified nucleotides and uses thereof. The siNA molecules may be double stranded and comprise modified nucleotides selected from 2′-O-methyl nucleotides and 2′-fluoro nucleotides. Further disclosed herein are siNA molecules comprising (a) a phosphorylation blocker, conjugated moiety, or 5′-stabilized end cap; and (b) a short interfering nucleic acid (siNA).

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Description
CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a Divisional of U.S. application Ser. No. 17/672,268, filed Feb. 15, 2022, which is a Continuation of U.S. application Ser. No. 17/194,079, filed Mar. 5, 2021, which claims priority to U.S. Provisional Application No. 62/986,150, filed Mar. 6, 2020, and U.S. Provisional Application No. 63/109,196, filed Nov. 3, 2020, the disclosures of which are hereby incorporated by reference in their entireties.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted electronically in XML. format and is hereby incorporated by reference in its entirety. Said XML. copy, created on 15 Nov., 2022, is named 122400-0307_SL.XML. and is 768000 bytes in size.

FIELD OF THE INVENTION

Described are short interfering nucleic acid (siNA) molecules comprising modified nucleotides, compositions, and uses thereof.

BACKGROUND OF THE INVENTION

RNA interference (RNAi) is a biological response to double-stranded RNA that mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes. The short interfering nucleic acids (siNA), such as siRNA, have been developed for RNAi therapy to treat a variety of diseases. For instance, RNAi therapy has been proposed for the treatment of metabolic diseases, neurodegenerative diseases, cancer, and pathogenic infections (See e.g., Rondindone, Biotechniques, 2018, 40(4S), doi.org/10.2144/000112163, Boudreau and Davidson, Curr Top Dev Biol, 2006, 75:73-92, Chalbatani et al., Int J Nanomedicine, 2019, 14:3111-3128, Arbuthnot, Drug News Perspect, 2010, 23(6):341-50, and Chernikov et. al., Front. Pharmacol., 2019, doi.org/10.3389/fphar.2019.00444, each of which are incorporated by reference in their entirety). However, major limitations of RNAi therapy are the ability to effectively deliver siRNA to target cells and the degradation of the siRNA.

The present disclosure improves the delivery and stability of siNA molecules by providing siNA molecules comprising modified nucleotides. The siNA molecules of the present disclosure provide optimized combinations and numbers of modified nucleotides, nucleotide lengths, design (e.g., blunt ends or overhangs, internucleoside linkages, conjugates), and modification patterns for improving the delivery and stability of siNA molecules.

SUMMARY OF THE INVENTION

Disclosed herein is a short interfering nucleic acid (siNA) molecule comprising: (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and the nucleotide at position 3, 5, 7, 8, 9, 10, 11, 12, 14, 17, and/or 19 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide; and (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide.

Disclosed herein is a short interfering nucleic acid (siNA) molecule comprising: (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide; and (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and the nucleotide at position 2, 5, 6, 8, 10, 14, 16, 17, and/or 18 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide.

In some embodiments, the first nucleotide sequence comprises 16, 17, 18, 19, 20, 21, 22, 23, or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide. In some embodiments, 70%, 75%, 80%, 85%, 90%, 95% or 100% of the nucleotides in the first nucleotide sequence are modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide. In some embodiments, between 2 to 15 modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, between 2 to 10 modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, between 2 to 6 modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least 2, 3, 4, 5, or 6 modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, less than or equal to 10, 9, 8, 7, 6, 5, 4, 3, or 2 modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, between about 2 to 25 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, between about 2 to 20 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, between about 5 to 25 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, between about 10 to 25 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, between about 12 to 25 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or 22 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, or 2 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides.

In some embodiments, the second nucleotide sequence comprises 16, 17, 18, 19, 20, 21, 22, 23, or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide. In some embodiments, 70%, 75%, 80%, 85%, 90%, 95% or 100% of the nucleotides in the second nucleotide sequence are modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide. In some embodiments, between 2 to 15 modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, between 2 to 10 modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, between 2 to 6 modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least 2, 3, 4, 5, or 6 modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, less than or equal to 10, 9, 8, 7, 6, 5, 4, 3, or 2 modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, between about 2 to 25 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, between about 2 to 20 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, between about 5 to 25 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, between about 10 to 25 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, between about 12 to 25 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or 22 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3,or 2 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides.

Disclosed herein is a short interfering nucleic acid (siNA) molecule comprising: (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence: (i) is 15 to 30 nucleotides in length; (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide; and (iii) comprises 1 or more phosphorothioate internucleoside linkage; and (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence: (i) is 15 to 30 nucleotides in length; (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide; and (iii) comprises 1 or more phosphorothioate internucleoside linkage.

Disclosed herein is a short interfering nucleic acid (siNA) molecule comprising: (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide; and (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide, wherein the siNA further comprises a phosphorylation blocker, a galactosamine, or 5′-stabilized end cap.

In some embodiments, at least 1, 2, 3, 4, 5, 6, or 7 nucleotides at position 3, 5, 7, 8, 9, 10, 11, 12, and/or 17 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 3 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 5 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 7 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 8 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 9 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 12 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 17 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, nucleotide at position 10 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 11 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide.

In some embodiments, at least 1, 2, 3, 4, 5, 6, 7, 8, or 9 nucleotides at position 2, 5, 6, 8, 10, 14, 16, 17, and/or 18 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 2 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 5 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 6 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 8 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 10 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 14 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotides at position 16 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 17 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 18 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide.

In some embodiments, the nucleotides in the second nucleotide sequence are arranged in an alternating 1:3 modification pattern, and wherein 1 nucleotide is a 2′-fluoro nucleotide and 3 nucleotides are 2′-O-methyl nucleotides. In some embodiments, the alternating 1:3 modification pattern occurs 2-5 times. In some embodiments, at least two of the alternating 1:3 modification pattern occur consecutively. In some embodiments, at least two of the alternating 1:3 modification pattern occurs nonconsecutively. In some embodiments, at least 1, 2, 3, 4, or 5 alternating 1:3 modification pattern begins at nucleotide position 2, 6, 10, 14, and/or 18 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 2 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 6 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 10 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 14 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 18 from the 5′ end of the antisense strand.

In some embodiments, the nucleotides in the second nucleotide sequence are arranged in an alternating 1:2 modification pattern, and wherein 1 nucleotide is a 2′-fluoro nucleotide and 2 nucleotides are 2′-O-methyl nucleotides. In some embodiments, the alternating 1:2 modification pattern occurs 2-5 times. In some embodiments, at least two of the alternating 1:2 modification pattern occurs consecutively. In some embodiments, at least two of the alternating 1:2 modification pattern occurs nonconsecutively. In some embodiments, at least 1, 2, 3, 4, or 5 alternating 1:2 modification pattern begins at nucleotide position 2, 5, 8, 14, and/or 17 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:2 modification pattern begins at nucleotide position 2 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:2 modification pattern begins at nucleotide position 5 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:2 modification pattern begins at nucleotide position 8 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:2 modification pattern begins at nucleotide position 14 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:2 modification pattern begins at nucleotide position 17 from the 5′ end of the antisense strand.

Disclosed herein is a short interfering nucleic acid (siNA) molecule represented by Formula (VIII):

5′-An1Bn2An3Bn4An5Bn6An7Bn8An9-3′ 3′-Cq1Aq2Bq3Aq4Bq5Aq6Bq7Aq8Bq9Aq10Bq1lAq12-5′

wherein:
    • the top strand is a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence comprises 15 to 30 nucleotides; the bottom strand is an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence comprises 15 to 30 nucleotides;
    • each A is independently a 2′-O-methyl nucleotide or a nucleotide comprising a 5′-stabilized
    • end cap or a phosphorylation blocker;
    • B is a 2′-fluoro nucleotide;
    • C represents overhanging nucleotides and is a 2′-O-methyl nucleotide;
    • n1=1-4 nucleotides in length;
    • each n2, n6, n8, q3, q5, q7, q9, q11, and q12 is independently 0-1 nucleotides in length; each n3 and n4 is independently 1-3 nucleotides in length;
    • n5 is 1-10 nucleotides in length;
    • n7 is 0-4 nucleotides in length;
    • each n9, q1, and q2 is independently 0-2 nucleotides in length;
    • q4 is 0-3 nucleotides in length;
    • q6 is 0-5 nucleotides in length;
    • q8 is 2-7 nucleotides in length; and
    • q10 is 2-11 nucleotides in length.

Disclosed herein is a short interfering nucleic acid (siNA) molecule represented by Formula (IX):

5′-A2-4B1A1-3B2-3A2-10B0-1A0-4B0-1A0-2-3′ 3′-C2A0-2B0-1A0-3B0-1A0-5B0-1A2-7B1A2-11B1A1-5′

wherein:
    • the top strand is a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence comprises 15 to 30 nucleotides; the bottom strand is an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence comprises 15 to 30 nucleotides;
    • each A is independently a 2′-O-methyl nucleotide or a nucleotide comprising a 5′-stabilized end cap or a phosphorylation blocker;
    • B is a 2′-fluoro nucleotide;
    • C represents overhanging nucleotides and is a 2′-O-methyl nucleotide.

Disclosed herein is a short interfering nucleic acid (siNA) molecule comprising (a) a sense strand comprising a first nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 3, 7-9, 12, and 17 from the 5′ end of the first nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1, 2, 4-6, 10, 11, and 13-16 from the 5′ end of the first nucleotide sequence; and (b) an antisense strand comprising a second nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 2 and 14 from the 5′ end of the second nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1, 3-13, and 15-17 from the 5′ end of the second nucleotide sequence. In some embodiments, the first nucleotide sequence consists of 19 nucleotides. In some embodiments, 2′-O-methyl nucleotides are at positions 18 and 19 from the 5′ end of the first nucleotide sequence. In some embodiments, the second nucleotide sequence consists of 21 nucleotides. In some embodiments, 2′-O-methyl nucleotides are at positions 18-21 from the 5′ end of the second nucleotide sequence.

Disclosed herein is a short interfering nucleic acid (siNA) molecule comprising (a) a sense strand comprising a first nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 3, 7, 8, and 17 from the 5′ end of the first nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1, 2, 4-6, and 9-16 from the 5′ end of the first nucleotide sequence; and (b) an antisense strand comprising a second nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 2 and 14 from the 5′ end of the first nucleotide sequence; and wherein 2′-O-methyl nucleotides are at positions 1, 3-13, and 15-17 from the 5′ end of the first nucleotide sequence. In some embodiments, the first nucleotide sequence consists of 19 nucleotides. In some embodiments, 2′-O-methyl nucleotides are at positions 18 and 19 from the 5′ end of the first nucleotide sequence. In some embodiments, the second nucleotide sequence consists of 21 nucleotides. In some embodiments, 2′-O-methyl nucleotides are at positions 18-21 from the 5′ end of the second nucleotide sequence.

Disclosed herein is a short interfering nucleic acid (siNA) molecule comprising (a) a sense strand comprising a first nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 3, 7-9, 12 and 17 from the 5′ end of the first nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1, 2, 4-6, 10, 11, and 13-16 from the 5′ end of the first nucleotide sequence; and (b) an antisense strand comprising a second nucleotide sequence consisting of 17 to 23 nucleotides, wherein the nucleotides in the second nucleotide sequence are arranged in an alternating 1:3 modification pattern, and wherein 1 nucleotide is a 2′-fluoro nucleotide and 3 nucleotides are 2′-O-methyl nucleotides. In some embodiments, the first nucleotide sequence consists of 19 nucleotides. In some embodiments, 2′-O-methyl nucleotides are at positions 18 and 19 from the 5′ end of the first nucleotide sequence. In some embodiments, the second nucleotide sequence consists of 21 nucleotides. In some embodiments, 2′-O-methyl nucleotides are at positions 19-21 from the 5′ end of the second nucleotide sequence. In some embodiments, the alternating 1:3 modification pattern occurs 2-5 times. In some embodiments, at least two of the alternating 1:3 modification pattern occur consecutively. In some embodiments, at least two of the alternating 1:3 modification pattern occurs nonconsecutively. In some embodiments, at least 1, 2, 3, 4, or 5 alternating 1:3 modification pattern begins at nucleotide position 2, 6, 10, 14, and/or 18 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 2 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 6 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 10 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 14 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 18 from the 5′ end of the antisense strand.

Disclosed herein is a short interfering nucleic acid (siNA) molecule comprising (a) a sense strand comprising a first nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 5 and 7-9 from the 5′ end of the first nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1-4, 6, and 10-17 from the 5′ end of the first nucleotide sequence; and (b) an antisense strand comprising a second nucleotide sequence consisting of 17 to 23 nucleotides, wherein the nucleotides in the second nucleotide sequence are arranged in an alternating 1:3 modification pattern, and wherein 1 nucleotide is a 2′-fluoro nucleotide and 3 nucleotides are 2′-O-methyl nucleotides. In some embodiments, the first nucleotide sequence consists of 19 nucleotides. In some embodiments, 2′-O-methyl nucleotides are at positions 18 and 19 from the 5′ end of the first nucleotide sequence. In some embodiments, the second nucleotide sequence consists of 21 nucleotides. In some embodiments, 2′-O-methyl nucleotides are at positions 19-21 from the 5′ end of the second nucleotide sequence. In some embodiments, the alternating 1:3 modification pattern occurs 2-5 times. In some embodiments, at least two of the alternating 1:3 modification pattern occur consecutively. In some embodiments, at least two of the alternating 1:3 modification pattern occurs nonconsecutively. In some embodiments, at least 1, 2, 3, 4, or 5 alternating 1:3 modification pattern begins at nucleotide position 2, 6, 10, 14, and/or 18 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 2 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 6 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 10 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 14 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 18 from the 5′ end of the antisense strand.

Disclosed herein is a short interfering nucleic acid (siNA) molecule comprising (a) a sense strand comprising a first nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 5 and 7-9 from the 5′ end of the first nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1-4, 6, and 10-17 from the 5′ end of the first nucleotide sequence; and (b) an antisense strand comprising a second nucleotide sequence consisting of 17 to 23 nucleotides, wherein the nucleotides in the second nucleotide sequence are arranged in an alternating 1:2 modification pattern, and wherein 1 nucleotide is a 2′-fluoro nucleotide and 2 nucleotides are 2′-O-methyl nucleotides. In some embodiments, the first nucleotide sequence consists of 19 nucleotides. In some embodiments, 2′-O-methyl nucleotides are at positions 18 and 19 from the 5′ end of the first nucleotide sequence. In some embodiments, the second nucleotide sequence consists of 21 nucleotides. In some embodiments, 2′-O-methyl nucleotides are at positions 18-21 from the 5′ end of the second nucleotide sequence. In some embodiments, the alternating 1:2 modification pattern occurs 2-5 times. In some embodiments, at least two of the alternating 1:2 modification pattern occur consecutively. In some embodiments, at least two of the alternating 1:2 modification pattern occurs nonconsecutively. In some embodiments, at least 1, 2, 3, 4, or 5 alternating 1:2 modification pattern begins at nucleotide position 2, 5, 8, 14, and/or 17 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:2 modification pattern begins at nucleotide position 2 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:2 modification pattern begins at nucleotide position 5 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:2 modification pattern begins at nucleotide position 8 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:2 modification pattern begins at nucleotide position 14 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:2 modification pattern begins at nucleotide position 17 from the 5′ end of the antisense strand.

Disclosed herein is a short interfering nucleic acid (siNA) molecule comprising (a) a sense strand comprising a first nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 5 and 7-9 from the 5′ end of the first nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1-4, 6, and 10-17 from the 5′ end of the first nucleotide sequence; and (b) an antisense strand comprising a second nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 2, 6, 14, and 16 from the 5′ end of the second nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1, 3-5, 7-13, 15, and 17 from the 5′ end the second nucleotide sequence. In some embodiments, the first nucleotide sequence consists of 19 nucleotides. In some embodiments, 2′-O-methyl nucleotides are at positions 18 and 19 from the 5′ end of the first nucleotide sequence. In some embodiments, the second nucleotide sequence consists of 21 nucleotides. In some embodiments, 2′-O-methyl nucleotides are at positions 18-21 from the 5′ end of the second nucleotide sequence.

Disclosed herein is a short interfering nucleic acid (siNA) molecule comprising: (a) a sense strand comprising a first nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 5, 9-11, and 14 from the 5′ end of the first nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1-4, 6-8, and 12-17 from the 5′ end of the first nucleotide sequence; and (b) an antisense strand comprising a second nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 2 and 14 from the 5′ end of the second nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1, 3-13, and 15-17 from the 5′ end the second nucleotide sequence. In some embodiments, the first nucleotide sequence consists of 21 nucleotides. In some embodiments, 2′-O-methyl nucleotides are at positions 18-21 from the 5′ end of the first nucleotide sequence. In some embodiments, the second nucleotide sequence consists of 23 nucleotides. In some embodiments, 2′-O-methyl nucleotides are at positions 18-23 from the 5′ end of the second nucleotide sequence.

In some embodiments, any of the sense strands disclosed herein further comprise a TT sequence adjacent to the first nucleotide sequence.

In some embodiments, any of the sense strands disclosed herein further comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more phosphorothioate internucleoside linkages. In some embodiments, at least one phosphorothioate internucleoside linkage is between the nucleotides at positions 1 and 2 from the 5′ end of the first nucleotide sequence. In some embodiments, at least one phosphorothioate internucleoside linkage is between the nucleotides at positions 2 and 3 from the 5′ end of the first nucleotide sequence.

In some embodiments, any of the antisense strands disclosed herein further comprise TT sequence adjacent to the second nucleotide sequence. In some embodiments, the antisense strand further comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more phosphorothioate internucleoside linkages. In some embodiments, at least one phosphorothioate internucleoside linkage is between the nucleotides at positions 1 and 2 from the 5′ end of the second nucleotide sequence. In some embodiments, at least one phosphorothioate internucleoside linkage is between the nucleotides at positions 2 and 3 from the 5′ end of the second nucleotide sequence. In some embodiments, at least one phosphorothioate internucleoside linkage is between the nucleotides at positions 1 and 2 from the 3′ end of the second nucleotide sequence. In some embodiments, at least one phosphorothioate internucleoside linkage is between the nucleotides at positions 2 and 3 from the 3′ end of the second nucleotide sequence.

In some embodiments, the first nucleotide from the 5′ end of any of the first nucleotide sequences disclosed herein comprises a 5′ stabilizing end cap.

In some embodiments, the first nucleotide from the 5′ end of any of the second nucleotide sequences disclosed herein comprise a 5′ stabilizing end cap.

In some embodiments, the first nucleotide from the 5′ end of any of the first nucleotide sequences disclosed herein comprises a phosphorylation blocker.

In some embodiments, the first nucleotide from the 5′ end of any of the second nucleotide sequences disclosed herein comprises a phosphorylation blocker.

In some embodiments, any of the first nucleotide sequences or second nucleotide sequences disclosed herein comprise at least one modified nucleotide selected from

R is H or alkyl (or AmNA(N-Me)) when R is alkyl);

wherein B is a nucleobase.

Disclosed herein is a short-interfering nucleic acid (siNA) molecule comprising:

    • (a) a phosphorylation blocker of Formula (IV):

    • wherein
    • R1 is a nucleobase,
    • R4 is —O—R30 or —NR31R32,
    • R30 is C1-C8 substituted or unsubstituted alkyl; and
    • R31 and R32 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring; and
    • (b) a short interfering nucleic acid (siNA). In some embodiments, the siNA is any of the siNAs disclosed herein. In some embodiments, the siNA comprises any of the sense strands, first nucleotide sequences, antisense strands, or second nucleotide sequences disclosed herein. In some embodiments, the siNA comprises any of the the sense strands disclosed herein. In some embodiments, the siNA comprises any of the antisense strand disclosed herein. In some embodiments, the siNA comprises a first nucleotide sequence selected from any one of SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the siNA comprises a second nucleotide sequence selected from any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the siNA comprises a sense sequence selected from any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the siNA comprises an antisense sequence selected from any one of SEQ ID NOs: 363-409, 445-533, and 536-539. In some embodiments, the siNA comprises a ds-siNA sequence selected from any one of ds-siNA-001 to ds-siNA-0178. In some embodiments, the siNA further comprises any of the 5′ end caps disclosed herein. In some embodiments, the siNA further comprises any of the conjugated moieties disclosed herein. In some embodiments, the siNA further comprises any of the destabilizing nucleotides disclosed herein. In some embodiments, the siNA further comprises any of the modified nucleotides disclosed herein.

Disclosed herein is a short-interfering nucleic acid (siNA) molecule comprising:

    • (a) a 5′-stabilized end cap of Formula (Ia):

    • wherein
    • R1 is a nucleobase, aryl, heteroaryl, or H,
    • R2 is

—CH═CD-Z, —CD=CH-Z, —CD=CD-Z, —(CR21R22)—Z, or —(C2-C6 alkenylene)-Z and R20 is hydrogen; or

    • R2 and R20 together form a 3- to 7-membered carbocyclic ring substituted with —(CR21R22)n—
    • Z or —(C2-C6 alkenylene)-Z;
    • n is 1, 2, 3, or 4;
    • Z is —ONR21R24, —OP(O)OH(CH2)mCO2R23, —OP(S)OH(CH2)mCO2R23, —P(O)(OH)2, —P(O)(OH)(OCH3), —P(O)(OH)(OCD3), —SO2(CH2)mP(O)(OH)2, —SO2NR23R25, —NR23R24,
    • R21 and R22 are independently hydrogen or C1-C6 alkyl; R21 and R22 together form an oxo group;
    • R23 is hydrogen or C1-C6 alkyl;
    • R24 is —SO2R25 or —C(O)R25; or
    • R23 and R24 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring;
    • R25 is C1-C6 alkyl; and
    • m is 1, 2, 3, or 4; and
    • (b) a short interfering nucleic acid (siNA). In some embodiments, the siNA comprises any of the the sense strands disclosed herein. In some embodiments, the siNA comprises any of the antisense strand disclosed herein. In some embodiments, the siNA comprises a first nucleotide sequence selected from any one of SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the siNA comprises a second nucleotide sequence selected from any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the siNA comprises a sense sequence selected from any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the siNA comprises an antisense sequence selected from any one of SEQ ID NOs: 363-409, 445-533, and 536-539. In some embodiments, the siNA comprises a ds-siNA sequence selected from any one of ds-siNA-001 to ds-siNA-0178. In some embodiments, the siNA further comprises any of the phosphorylation blockers disclosed herein. In some embodiments, the siNA further comprises any of the conjugated moieties disclosed herein. In some embodiments, the siNA further comprises any of the destabilizing nucleotides disclosed herein. In some embodiments, the siNA further comprises any of the modified nucleotides disclosed herein.

Disclosed herein is a short-interfering nucleic acid (siNA) molecule comprising:

    • (a) a 5′-stabilized end cap of Formula (Ib):

wherein

    • R1 is a nucleobase, aryl, heteroaryl, or H,
    • R2 is

—CH═CD-Z, —CD=CH-Z, —CD=CD-Z, —(CR211R22)n-Z, or —(C2-C6 alkenylene)-Z and R30 is hydrogen; or

    • R2 and R20 together form a 3- to 7-membered carbocyclic ring substituted with —(CR21R22)n—
    • Z or —(C2-C6 alkenylene)-Z;
    • n is 1, 2, 3, or 4;
    • Z is —ONR23R24, —OP(O)OH(CH2)mCO2R23, —OP(S)OH(CH2)mCO2R23, —P(O)(OH)2, —P(O)(OH)(OCH3), —P(O)(OH)(OCD3), —SO2(CH2)mP(O)(OH)2, —SO2NR23R25, —NR23R24,
    • R21 and R22 are independently hydrogen or C1-C6 alkyl; R21 and R22 together form an oxo group;
    • R23 is hydrogen or C1-C6 alkyl;
    • R24 is —SO2R25 or —C(O)R25; or
    • R23 and R24 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring;
    • R25 is C1-C6 alkyl; and
    • m is 1, 2, 3, or 4; and
    • (b) a short interfering nucleic acid (siNA). In some embodiments, the siNA comprises any of the the sense strands disclosed herein. In some embodiments, the siNA comprises any of the antisense strand disclosed herein. In some embodiments, the siNA comprises a first nucleotide sequence selected from any one of SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the siNA comprises a second nucleotide sequence selected from any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the siNA comprises a sense sequence selected from any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the siNA comprises an antisense sequence selected from any one of SEQ ID NOs: 363-409, 445-533, and 536-539. In some embodiments, the siNA comprises a ds-siNA sequence selected from any one of ds-siNA-001 to ds-siNA-0178. In some embodiments, the siNA further comprises any of the phosphorylation blockers disclosed herein. In some embodiments, the siNA further comprises any of the conjugated moieties disclosed herein. In some embodiments, the siNA further comprises any of the destabilizing nucleotides disclosed herein. In some embodiments, the siNA further comprises any of the modified nucleotides disclosed herein.

Disclosed herein is a short-interfering nucleic acid (siNA) molecule comprising: (a) a 5′-stabilized end cap selected from the group consisting of Formula (1) to Formula (15), Formula (9X) to Formula (12X), and Formula (9Y) to Formula (12Y):

wherein R1 is a nucleobase, aryl, heteroaryl, or H; and (b) a short interfering nucleic acid (siNA). In some embodiments, the siNA comprises any of the the sense strands disclosed herein. In some embodiments, the siNA comprises any of the antisense strand disclosed herein. In some embodiments, the siNA comprises a first nucleotide sequence selected from any one of SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the siNA comprises a second nucleotide sequence selected from any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the siNA comprises a sense sequence selected from any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the siNA comprises an antisense sequence selected from any one of SEQ ID NOs: 363-409, 445-533, and 536-539. In some embodiments, the siNA comprises a ds-siNA sequence selected from any one of ds-siNA-001 to ds-siNA-0178. In some embodiments, the siNA further comprises any of the phosphorylation blockers disclosed herein. In some embodiments, the siNA further comprises any of the conjugated moieties disclosed herein. In some embodiments, the siNA further comprises any of the destabilizing nucleotides disclosed herein. In some embodiments, the siNA further comprises any of the modified nucleotides disclosed herein.

Disclosed herein is a short-interfering nucleic acid (siNA) molecule comprising: (a) a 5′-stabilized end cap selected from the group consisting of Formulas (1A)-(15A), Formulas (9B)-(12B), Formulas (9AX)-(12AX), Formulas (9AY)-(12AY), Formulas (9BX)-(12BX), and Formulas (9BY)-(12BY):

and (b) a short interfering nucleic acid (siNA). In some embodiments, the siNA comprises any of the the sense strands disclosed herein. In some embodiments, the siNA comprises any of the antisense strand disclosed herein. In some embodiments, the siNA comprises a first nucleotide sequence selected from any one of SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the siNA comprises a second nucleotide sequence selected from any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the siNA comprises a sense sequence selected from any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the siNA comprises an antisense sequence selected from any one of SEQ ID NOs: 363-409, 445-533, and 536-539. In some embodiments, the siNA comprises a ds-siNA sequence selected from any one of ds-siNA-001 to ds-siNA-0178. In some embodiments, the siNA further comprises any of the phosphorylation blockers disclosed herein. In some embodiments, the siNA further comprises any of the conjugated moieties disclosed herein. In some embodiments, the siNA further comprises any of the destabilizing nucleotides disclosed herein. In some embodiments, the siNA further comprises any of the modified nucleotides disclosed herein.

Disclosed herein is a short-interfering nucleic acid (siNA) molecule comprising:

    • (a) a 5′-stabilized end cap of Formula (Ic):

wherein

    • R1 is a nucleobase, aryl, heteroaryl, or H,

R2 is

—CH═CD-Z, —CD=CH-Z, —CD=CD-Z, —(CR21R22)-Z, or —(C2-C6 alkenylene)-Z and R30 is hydrogen; or

    • R2 and R20 together form a 3- to 7-membered carbocyclic ring substituted with —(CR21R22)n—
    • Z or —(C2-C6 alkenylene)-Z;
    • n is 1, 2, 3, or 4;
    • Z is —ONR21R24, —OP(O)OH(CH2)mCO2R23, —OP(S)OH(CH2)mCO2R23, —P(O)(OH)2, —P(OOH)(OCH3), —P(O)(OH)(OCD3), —SO2(CH2)mP(O)(OH)2, —SO2NR23R25, —NR23R24, or —NR23SO2R24;
    • R21 and R22 either are independently hydrogen or C1-C6 alkyl, or R21 and R22 together form an oxo group;
    • R23 is hydrogen or C1-C6 alkyl;
    • R24 is —SO2R25 or —C(O)R25; or
    • R23 and R24 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring;
    • R25 is C1-C6 alkyl; and
    • m is 1, 2, 3, or 4; and
    • (b) a short interfering nucleic acid (siNA). In some embodiments, the siNA comprises any of the the sense strands disclosed herein. In some embodiments, the siNA comprises any of the antisense strand disclosed herein. In some embodiments, the siNA comprises a first nucleotide sequence selected from any one of SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the siNA comprises a second nucleotide sequence selected from any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the siNA comprises a sense sequence selected from any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the siNA comprises an antisense sequence selected from any one of SEQ ID NOs: 363-409, 445-533, and 536-539. In some embodiments, the siNA comprises a ds-siNA sequence selected from any one of ds-siNA-001 to ds-siNA-0178. In some embodiments, the siNA further comprises any of the phosphorylation blockers disclosed herein. In some embodiments, the siNA further comprises any of the conjugated moieties disclosed herein. In some embodiments, the siNA further comprises any of the destabilizing nucleotides disclosed herein. In some embodiments, the siNA further comprises any of the modified nucleotides disclosed herein.

Disclosed herein is a short-interfering nucleic acid (siNA) molecule comprising: (a) a 5′-stabilized end cap selected from the group consisting of Formula (21) to Formula (35):

wherein R1 is a nucleobase, aryl, heteroaryl, or H; and (b) a short interfering nucleic acid (siNA). In some embodiments, the siNA comprises any of the the sense strands disclosed herein. In some embodiments, the siNA comprises any of the antisense strand disclosed herein. In some embodiments, the siNA comprises a first nucleotide sequence selected from any one of SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the siNA comprises a second nucleotide sequence selected from any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the siNA comprises a sense sequence selected from any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the siNA comprises an antisense sequence selected from any one of SEQ ID NOs: 363-409, 445-533, and 536-539. In some embodiments, the siNA comprises a ds-siNA sequence selected from any one of ds-siNA-001 to ds-siNA-0178. In some embodiments, the siNA further comprises any of the phosphorylation blockers disclosed herein. In some embodiments, the siNA further comprises any of the conjugated moieties disclosed herein. In some embodiments, the siNA further comprises any of the destabilizing nucleotides disclosed herein. In some embodiments, the siNA further comprises any of the modified nucleotides disclosed herein.

Disclosed herein is a short-interfering nucleic acid (siNA) molecule comprising: (a) a 5′-stabilized end cap selected from the group consisting of Formulas (21A)-(35A), Formulas (29B)-(32B), Formulas (29AX)-(32AX), Formulas (29AY)-(32AY), Formulas (29BX)-(32BX), and Formulas (29BY)-(32BY):

and (b) a short interfering nucleic acid (siNA). In some embodiments, the siNA comprises any of the the sense strands disclosed herein. In some embodiments, the siNA comprises any of the antisense strand disclosed herein. In some embodiments, the siNA comprises a first nucleotide sequence selected from any one of SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the siNA comprises a second nucleotide sequence selected from any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the siNA comprises a sense sequence selected from any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the siNA comprises an antisense sequence selected from any one of SEQ ID NOs: 363-409, 445-533, and 536-539. In some embodiments, the siNA comprises a ds-siNA sequence selected from any one of ds-siNA-001 to ds-siNA-0178. In some embodiments, the siNA further comprises any of the phosphorylation blockers disclosed herein. In some embodiments, the siNA further comprises any of the conjugated moieties disclosed herein. In some embodiments, the siNA further comprises any of the destabilizing nucleotides disclosed herein. In some embodiments, the siNA further comprises any of the modified nucleotides disclosed herein.

Disclosed herein is a short interfering nucleic acid (siNA) molecule comprising: (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence comprises a nucleotide sequence of any one SEQ ID NOs: 1-56, 103-158, and 205-260; and (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence comprises a nucleotide sequence of any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the siNA further comprises any of the 5′ end caps disclosed herein. In some embodiments, the siNA further comprises any of the phosphorylation blockers disclosed herein. In some embodiments, the siNA further comprises any of the conjugated moieties disclosed herein. In some embodiments, the siNA further comprises any of the destabilizing nucleotides disclosed herein. In some embodiments, the siNA further comprises any of the modified nucleotides disclosed herein.

Disclosed herein is a interfering nucleic acid (siNA) molecule comprising: (a) a sense strand comprising a nucleotide sequence of any one of SEQ ID NOs: 307-362 and 415-444; and (b) an antisense strand comprising a nucleotide sequence of any one of SEQ ID NOs: 363-409, 445-533, and 536-539.

In some embodiments, any of the siNA disclosed herein further comprise a phosphorylation blocker.

In some embodiments, the phosphorylation blocker has the structure of Formula (IV):

wherein

    • R1 is a nucleobase,
    • R4 is —O—R30 or —NR31R32, R30 is C1-C8 substituted or unsubstituted alkyl; and
    • R31 and R32 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring.

In some embodiments, R4 is —OCH3 or —N(CH2CH2)2O.

In some embodiments, the phosphorylation blocker is attached to the 5′ end of the sense strand.

In some embodiments, the phosphorylation blocker is attached to the 5′ end of the sense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, and phosphorodithioate linker.

In some embodiments, the phosphorylation blocker is attached to the 3′ end of the sense strand.

In some embodiments, the phosphorylation blocker is attached to the 3′ end of the sense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, and phosphorodithioate linker.

In some embodiments, the phosphorylation blocker is attached to the 5′ end of the antisense strand. In some embodiments, the phosphorylation blocker is attached to the 5′ end of the antisense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, and phosphorodithioate linker. In some embodiments, the phosphorylation blocker is attached to the 3′ end of the antisense strand. In some embodiments, the phosphorylation blocker is attached to the 3′ end of the antisense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, and phosphorodithioate linker.

In some embodiments, any of the siNAs disclosed herein further comprise a conjugated moiety. In some embodiments, the conjugated moiety comprises a galactosamine. In some embodiments, the galactosamine is N-acetylgalactosamine (GalNAc) of Formula (VII):

wherein each n is independently 1 or 2. In some embodiments, the galactosamine is N-acetylgalactosamine (GalNAc) of Formula (VI):

wherein

    • m is 1, 2, 3, 4, or 5;
    • each n is independently 1 or 2;
    • p is 0 or 1;
    • each R is independently H;
    • each Y is independently selected from —O—P(═O)(SH)—, —O—P(═O)(O))—, —O—P(═O)(OH)—, and —O—P(S)S—;
    • Z is H or a second protecting group;
    • either L is a linker or L and Y in combination are a linker; and
    • A is H, OH, a third protecting group, an activated group, or an oligonucleotide. In some embodiments, wherein A is an oligonucleotide. In some embodiments, A is 1-2 oligonucleotides. In some embodiments, the oligonucleotide is dTdT. In some embodiments, the galactosamine is attached to the 3′ end of the sense strand. In some embodiments, the galactosamine is attached to the 3′ end of the sense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, or phosphorodithioate linker. In some embodiments, the galactosamine is attached to the 5′ end of the sense strand. In some embodiments, the galactosamine is attached to the 5′ end of the sense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, or phosphorodithioate linker. In some embodiments, the galactosamine is attached to the 3′ end of the antisense strand. In some embodiments, the galactosamine is attached to the 3′ end of the atnisense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, or phosphorodithioate linker. In some embodiments, the galactosamine is attached to the 5′ end of the antisense strand. In some embodiments, the galactosamine is attached to the 5′ end of the atnisense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, or phosphorodithioate linker.

In some embodiments, any of the siNAs disclosed herein further comprise a 5′-stabilized end cap. In some embodiments, the 5′-stabilized end cap is a 5′ vinyl phosphonate or deuterated 5′ vinyl phosphonate. In some embodiments, the 5′-stabilized end cap has the structure of Formula (Ia):

wherein

    • R1 is a nucleobase, aryl, heteroaryl, or H,
    • R2 is

—CH═CD-Z, —CD=CH-Z, —CD=CD-Z, —(CR21R22)—Z, or —(C2-C6 alkenylene)-Z and R20 is hydrogen; or

    • R2 and R20 together form a 3- to 7-membered carbocyclic ring substituted with —(CR21R22)n—
    • Z or —(C2-C6 alkenylene)-Z;
    • n is 1, 2, 3, or 4;
    • Z is —ONR23R24, —OP(O)OH(CH2)mCO2R23, —OP(S)OH(CH2)mCO2R23, —P(O)(OH)2, —P(O)(OH)(OCH3), —P(O)(OH)(OCD3), —SO2(CH2)mP(O)(OH)2, —SO2NR23R25, —NR23R24, or —NR23SO2R24;
    • R21 and R22 either are independently hydrogen or C1-C6 alkyl, or R21 and R22 together form an oxo group;
    • R23 is hydrogen or C1-C6 alkyl;
    • R24 is —SO2R25 or —C(O)R25; or
    • R23 and R24 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring;
    • R25 is C1-C6 alkyl; and
    • m is 1, 2, 3, or 4. In some embodiments, the 5′-stabilized end cap has the structure of
    • Formula (Ib):

wherein

    • R1 is a nucleobase, aryl, heteroaryl, or H,
    • R2 is

—CH═CD-Z, —CD=CH-Z, —CD=CD-Z, —(CR21R22)n-Z, or —(C2-C6 alkenylene)-Z and R20 is hydrogen; or

    • R2 and R20 together form a 3- to 7-membered carbocyclic ring substituted with —(CR21R22)n—
    • Z or —(C2-C6 alkenylene)-Z;
    • n is 1, 2, 3, or 4;
    • Z is —ONR23R24, —OP(O)OH(CH2)mCO2R23, —OP(S)OH(CH2)mCO2R23, —P(O)(OH)2, —P(O)(OH)(OCH3), —P(O)(OH)(OCD3), —SO2(CH2)mP(O)(OH)2, —SO2NR23R25, —NR23R24, or —NR23SO2R24;
    • R21 and R22 either are independently hydrogen or C1-C6 alkyl, or R21 and R22 together form an oxo group;
    • R23 is hydrogen or C1-C6 alkyl;
    • R24 is —SO2R25 or —C(O)R25; or
    • R23 and R24 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring;
    • R25 is C1-C6 alkyl; and
    • m is 1, 2, 3, or 4. In some embodiments, the 5′-stabilized end cap has the structure of
    • Formula (Ic):

wherein

    • R1 is a nucleobase, aryl, heteroaryl, or H,
    • R2 is

—CH═CD-Z, —CD=CH-Z, —CD=CD-Z, —(CR21R22)n-Z, or —(C2-C6 alkenylene)-Z and R20 is hydrogen; or

    • R2 and R20 together form a 3- to 7-membered carbocyclic ring substituted with —(CR21R22)n—
    • Z or —(C2-C6 alkenylene)-Z;
    • n is 1, 2, 3, or 4;
    • Z is —ONR23R24, —OP(O)OH(CH2)mCO2R23, —OP(S)OH(CH2)mCO2R23, —P(O)(OH)2, —P(O)(OH)(OCH3), —P(O)(OH)(OCD3), —SO2(CH2)mP(O)(OH)2, —SO2NR23R24, —NR23R24, or —NR23SO2R24;
    • R21 and R22 either are independently hydrogen or C1-C6 alkyl, or R21 and R22 together form an oxo group;
    • R23 is hydrogen or C1-C6 alkyl;
    • R24 is —SO2R25 or —C(O)R25; or
    • R23 and R24 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring;
    • R25 is C1-C6 alkyl; and
    • m is 1, 2, 3, or 4. In some embodiments, R1 is an aryl. In some embodiments, the aryl is a phenyl. In some embodiments, the 5′-stabilized end cap is selected from the group consisting of Formula (1) to Formula (15), Formula (9X) to Formula (12X), and Formula (9Y) to Formula (12Y):

wherein R1 independently is a nucleobase, aryl, heteroaryl, or H. In some embodiments, the 5′-stabilized end cap is selected from the group consisting of Formulas (1A)-(15A), Formulas (9B)-(12B), Formulas (9AX)-(12AX), Formulas (9AY)-(12AY), Formulas (9BX)-(12BX), and Formulas (9BY)-(12BY):

In some embodiments, the 5′-stabilized end cap is selected from the group consisting of Formula (21) to Formula (35):

wherein R1 is a nucleobase, aryl, heteroaryl, or H. In some embodiments, the 5′-stabilized end cap is selected from the group consisting of Formulas (21A)-(35A), Formulas (29B)-(32B), Formulas (29AX)-(32AX), Formulas (29AY)-(32AY), Formulas (29BX)-(32BX), and Formulas (29BY)-(32BY):

In some embodiments, the 5′-stabilized end cap is attached to the 5′ end of the antisense strand. In some embodiments, the 5′-stabilized end cap is attached to the 5′ end of the antisense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, or phosphorodithioate linker. In some embodiments, the 5′-stabilized end cap is attached to the 5′ end of the sense strand. In some embodiments, the 5′-stabilized end cap is attached to the 5′ end of the sense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, or phosphorodithioate linker.

In some embodiments, any of the siNAs, sense strands, first nucleotide sequences, antisense strands, or second nucleotide sequences disclosed herein further comprise at least one thermally destabilizing nucleotides. In some embodiments, any of the antisense strands disclosed herein further comprise at least one thermally destabilizing nucleotide selected from:

In some embodiments, any of the sense strands disclosed herein comprise at least one thermally destabilizing nucleotide selected from:

In some embodiments, any of the first nucleotide sequences disclosed herein further comprise at least one thermally destabilizing nucleotide selected from:

In some embodiments, any of the second nucleotide sequences disclosed herein further comprise at least one thermally destabilizing nucleotide selected from:

In some embodiments, any of the modified nucleotides disclosed herein is a thermally destabilizing nucleotide.

In some embodiments, any of the siNAs disclosed herein specifically downregulate or reduce expression of a target gene. In some embodiments, the target gene is a viral gene. In some embodiments, the viral gene is from a DNA virus. In some embodiments, the DNA virus is a double-stranded DNA (dsDNA) virus. In some embodiments, the dsDNA virus is a hepadnavirus. In some embodiments, the hepadnavirus is a hepatitis B virus (HBV). In some embodiments, the HBV is selected from HBV genotypes A-J. In some embodiments, the target gene is selected from the S gene or X gene of the HBV.

In some embodiments, the second nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to 15 to 30 nucleotides within positions 200-720 or 1100-1700 of SEQ ID NO: 410. In some embodiments, the second nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to 15 to 30 nucleotides within positions 200-280, 300-445, 460-510, 650-720, 1170-1220, 1250-1300, or 1550-1630 of SEQ ID NO: 410. In some embodiments, the second nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to 15 to 30 nucleotides within positions 200-230, 250-280, 300-330, 370-400, 405-445, 460-500, 670-700, 1180-1210, 1260-1295, 1520-1550, or 1570-1610 of SEQ ID NO: 410. In some embodiments, the second nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to 15 to 30 nucleotides starting at position 203, 206, 254, 305, 375, 409, 412, 415, 416, 419, 462, 466, 467, 674, 676, 1182, 1262, 1263, 1268, 1526, 1577, 1578, 1580, 1581, 1583, or 1584 of SEQ ID NO: 410.

In some embodiments, the first nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to 15 to 30 nucleotides within positions 200-720 or 1100-1700 of SEQ ID NO: 410. In some embodiments, the first nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to 15 to 30 nucleotides within positions 200-280, 300-445, 460-510, 650-720, 1170-1220, 1250-1300, or 1550-1630 of SEQ ID NO: 410. In some embodiments, the first nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to 15 to 30 nucleotides within positions 200-230, 250-280, 300-330, 370-400, 405-445, 460-500, 670-700, 1180-1210, 1260-1295, 1520-1550, or 1570-1610 of SEQ ID NO: 410. In some embodiments, the first nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to 15 to 30 nucleotides starting at position 203, 206, 254, 305, 375, 409, 412, 415, 416, 419, 462, 466, 467, 674, 676, 1182, 1262, 1263, 1268, 1526, 1577, 1578, 1580, 1581, 1583, or 1584 of SEQ ID NO: 410.

In some embodiments, the first nucleotide sequence comprises a nucleotide sequence of any one SEQ ID NOs: 1-56, 103-158, and 205-260.

In some embodiments, the second nucleotide sequence comprises a nucleotide sequence of any one of SEQ ID NOs: 57-102, 159-204, and 261-306.

In some embodiments, the sense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 307-362 and 415-444.

In some embodiments, the antisense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 363-409, 445-533, and 536-539.

In some embodiments, at least one end of the siNA is a blunt end.

In some embodiments, at least one end of the siNA comprises an overhang, wherein the overhang comprises at least one nucleotide.

In some embodiments, both ends of the siNA comprise an overhang, wherein the overhang comprises at least one nucleotide.

In some embodiments, the siNA is selected from ds-siNA-001 to ds-siNA-0178.

In some embodiments, at least one 2′-fluoro nucleotide or 2′-O-methyl nucleotide is a 2′-fluoro or 2-O-methyl nucleotide mimic of Formula (V):

wherein

    • R1 is independently a nucleobase, aryl, heteroaryl, or H, Q1 and Q2 are independently S or O,
    • R5 is independently —OCD3, —F, or —OCH3, and
    • R6 and R7 are independently H, D, or CD3.

In some embodiments, the 2′-fluoro or 2′-O-methyl nucleotide mimic is a nucleotide mimic of Formula (16)-Formula (20):

wherein R1 is a nucleobase and R2 is independently F or —OCH3.

Further disclosed herein are compositions comprising any of the siNAs disclosed herein. In some embodiments, the siNA targets an S gene of HBV. In some embodiments, the siNA specifically downregulates or reduces expression of the S gene of HBV. In some embodiments, the siNA targets an X gene of HBV. In some embodiments, the siNA specifically downregulates or reduces expression of the X gene of HBV. In some embodiments, the siNA comprises a first nucleotide sequence. In some embodiments, the first nucleotide sequence comprises a nucleotide sequence of any one SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the siNA comprises a second nucleotide sequence. In some embodiments, the second nucleotide sequence comprises a nucleotide sequence of any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the siNA comprises a sense strand. In some embodiments, the sense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the siNA comprises an antisense strand. In some embodiments, the antisense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 363-409, 445-533, and 536-539. In some embodiments, the siNA further comprises any of the 5′ end caps disclosed herein. In some embodiments, the siNA further comprises any of the phosphorylation blockers disclosed herein. In some embodiments, the siNA further comprises any of the conjugated moieties disclosed herein. In some embodiments, the siNA further comprises any of the destabilized nucleotides disclosed herein. In some embodiments, the siNA further comprises any of the modified nucleotides disclosed herein.

Further disclosed herein are compositions comprising 2, 3, 4, 5, 6, 7, 8, 9, 10 or more of any of the siNAs disclosed herein. In some embodiments, at least 1, 2, 3, 4, 5, or more siNAs target an S gene of HBV. In some embodiments, at least 1, 2, 3, 4, 5, or more siNAs specifically downregulate or reduce expression of the S gene of HBV. In some embodiments, at least 1, 2, 3, 4, 5, or more siNAs target an X gene of HBV. In some embodiments, at least 1, 2, 3, 4, 5, or more siNAs specifically downregulate or reduce expression of the X gene of HBV. In some embodiments, the siNA comprises a first nucleotide sequence. In some embodiments, the first nucleotide sequence comprises a nucleotide sequence of any one SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the siNA comprises a second nucleotide sequence. In some embodiments, the second nucleotide sequence comprises a nucleotide sequence of any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the siNA comprises a sense strand. In some embodiments, the sense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the siNA comprises an antisense strand. In some embodiments, the antisense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 363-409, 445-533, and 536-539. In some embodiments, the siNA further comprises any of the 5′ end caps disclosed herein. In some embodiments, the siNA further comprises any of the phosphorylation blockers disclosed herein. In some embodiments, the siNA further comprises any of the conjugated moieties disclosed herein. In some embodiments, the siNA further comprises any of the destabilized nucleotides disclosed herein. In some embodiments, the siNA further comprises any of the modified nucleotides disclosed herein.

In some embodiments, any of the compositions disclosed herein further comprise an additional HBV treatment agent. In some embodiments, the additional HBV treatment agent is selected from a nucleotide analog, nucleoside analog, a capsid assembly modulator (CAM), a recombinant interferon, an entry inhibitor, a small molecule immunomodulator and oligonucleotide therapy. In some embodiments, the oligonucleotide therapy is an additional siNA. In some embodiments, the additional siNA is selected from any of ds-siNA-001 to ds-siNA-0178. In some embodiments, the oligonucleotide therapy is an antisense oligonucleotide (ASO), NAPs, or STOPs. In some embodiments, the ASO is ASO 1 or ASO 2. In some embodiments, the ASO specifically targets the S gene of HBV. In some embodiments, the ASO specifically targets the X gene of HBV. In some embodiments, the additional HBV treatment agent is selected from HBV STOPS™ ALG-010133, HBV CAM ALG-000184, ASO 1, recombinant interferon alpha 2b, IFN-α, PEG-IFN-α-2a, lamivudine, telbivudine, adefovir dipivoxil, clevudine, entecavir, tenofovir alafenamide, tenofovir disoproxil, NVR3-778, BAY41-4109, JNJ-632, JNJ-3989 (ARO-HBV), RG6004, GSK3228836, REP-2139, REP-2165, AB-729, VIR-2218, RG6346 (DCR-HBVS), JNJ-6379, GLS4, ABI-HO731, JNJ-440, NZ-4, RG7907, EDP-514, AB-423, AB-506, ABI-H03733 and ABI-H2158.

In some embodiments, any of the compositions disclosed herein further comprise a liver disease treatment agent. In some embodiments, the liver disease treatment agent is selected from a peroxisome proliferator-activator receptor (PPAR) agonist, farnesoid X receptor (FXR) agonist, lipid-altering agent, and incretin-based therapy. In some embodiments, the PPAR agonist is selected from a PPARα agonist, dual PPARα/δ agonist, PPARγ agonist, and dual PPARα/γ agonist. In some embodiments, the dual PPARα agonist is a fibrate. In some embodiments, the PPARα/δ agonist is elafibranor. In some embodiments, the PPARγ agonist is a thiazolidinedione (TZD). In some embodiments, TZD is pioglitazone. In some embodiments, the dual PPARα/γ agonist is saroglitazar. In some embodiments, the FXR agonist is obeticholic acis (OCA). In some embodiments, the lipid-altering agent is aramchol. In some embodiments, the incretin-based therapy is a glucagon-like peptide 1 (GLP-1) receptor agonist or dipeptidyl peptidase 4 (DPP-4) inhibitor. In some embodiments, the GLP-1 receptor agonist is exenatide or liraglutide. In some embodiments, the DPP-4 inhibitor is sitagliptin or vildapliptin.

Further disclosed herein are methods of treating a disease in a subject in need thereof, comprising administering to the subject any of the siNAs disclosed herein. In some embodiments, the siNA comprises a first nucleotide sequence. In some embodiments, the first nucleotide sequence comprises a nucleotide sequence of any one SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the siNA comprises a second nucleotide sequence. In some embodiments, the second nucleotide sequence comprises a nucleotide sequence of any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the siNA comprises a sense strand. In some embodiments, the sense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the siNA comprises an antisense strand. In some embodiments, the antisense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 363-409, 445-533, and 536-539. In some embodiments, the siNA further comprises any of the 5′ end caps disclosed herein. In some embodiments, the siNA further comprises any of the phosphorylation blockers disclosed herein. In some embodiments, the siNA further comprises any of the conjugated moieties disclosed herein. In some embodiments, the siNA further comprises any of the destabilized nucleotides disclosed herein. In some embodiments, the siNA further comprises any of the modified nucleotides disclosed herein.

Further disclosed herein are methods of treating a disease in a subject in need thereof, comprising administering to the subject any of the compositions disclosed herein. In some embodiments, the composition comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more of any of the siNAs disclosed herein. In some embodiments, the siNA comprises a first nucleotide sequence. In some embodiments, the first nucleotide sequence comprises a nucleotide sequence of any one SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the siNA comprises a second nucleotide sequence. In some embodiments, the second nucleotide sequence comprises a nucleotide sequence of any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the siNA comprises a sense strand. In some embodiments, the sense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the siNA comprises an antisense strand. In some embodiments, the antisense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 363-409, 445-533, and 536-539. In some embodiments, the siNA further comprises any of the 5′ end caps disclosed herein. In some embodiments, the siNA further comprises any of the phosphorylation blockers disclosed herein. In some embodiments, the siNA further comprises any of the conjugated moieties disclosed herein. In some embodiments, the siNA further comprises any of the destabilized nucleotides disclosed herein. In some embodiments, the siNA further comprises any of the modified nucleotides disclosed herein. In some embodiments, the composition further comprises any of the additional HBV treatment agents disclosed herein. In some embodiments, the disease is a viral disease. In some embodiments, the viral disease is caused by a DNA virus. In some embodiments, the DNA virus is a double stranded DNA (dsDNA) virus. In some embodiments, the dsDNA virus is a hepadnavirus. In some embodiments, the hepadnavirus is a hepatitis B virus (HBV). In some embodiments, the HBV is selected from HBV genotypes A-J. In some embodiments, the method further comprises administering an additional HBV treatment agent. In some embodiments, the siNA or the composition and the additional HBV treatment agent are administered concurrently. In some embodiments, the siNA or the composition and the additional HBV treatment agent are administered sequentially. In some embodiments, the siNA or the composition is administered prior to administering the additional HBV treatment agent. In some embodiments, the siNA or the composition is administered after administering the additional HBV treatment agent. In some embodiments, the additional HBV treatment agent is selected from a nucleotide analog, nucleoside analog, a capsid assembly modulator (CAM), a recombinant interferon, an entry inhibitor, a small molecule immunomodulator and oligonucleotide therapy. In some embodiments, the oligonucleotide therapy is an additional siNA. In some embodiments, the additional siNA is selected from any of ds-siNA-001 to ds-siNA-0178. In some embodiments, the oligonucleotide therapy is an antisense oligonucleotide (ASO), NAPs, or STOPs. In some embodiments, the ASO is ASO 1 or ASO 2. In some embodiments, the additional HBV treatment agent is selected from HBV STOPS' ALG-010133, HBV CAM ALG-000184, ASO 1, recombinant interferon alpha 2b, IFN-α, PEG-IFN-α-2a, lamivudine, telbivudine, adefovir dipivoxil, clevudine, entecavir, tenofovir alafenamide, tenofovir disoproxil, NVR3-778, BAY41-4109, JNJ-632, JNJ-3989 (ARO-HBV), RG6004, GSK3228836, REP-2139, REP-2165, AB-729, VIR-2218, RG6346 (DCR-HBVS), JNJ-6379, GLS4, ABI-HO731, JNJ-440, NZ-4, RG7907, EDP-514, AB-423, AB-506, ABI-H03733 and ABI-H2158.

In some embodiments, the disease is a liver disease. In some embodiments, the liver disease is a nonalcoholic fatty liver disease (NAFLD) or hepatocellular carcinoma (HCC). In some embodiments, the NAFLD is nonalcoholic steatohepatitis (NASH). In some embodiments, the method further comprises administering to the subject a liver disease treatment agent. In some embodiments, the liver disease treatment agent is selected from a peroxisome proliferator-activator receptor (PPAR) agonist, farnesoid X receptor (FXR) agonist, lipid-altering agent, and incretin-based therapy. In some embodiments, the PPAR agonist is selected from a PPARα agonist, dual PPARα/δ agonist, PPARγ agonist, and dual PPARα/γ agonist. In some embodiments, the dual PPARα agonist is a fibrate. In some embodiments, the PPARα/δ agonist is elafibranor. In some embodiments, the PPARγ agonist is a thiazolidinedione (TZD). In some embodiments, TZD is pioglitazone. In some embodiments, the dual PPARα/γ agonist is saroglitazar. In some embodiments, the FXR agonist is obeticholic acis (OCA). In some embodiments, the lipid-altering agent is aramchol. In some embodiments, the incretin-based therapy is a glucagon-like peptide 1 (GLP-1) receptor agonist or dipeptidyl peptidase 4 (DPP-4) inhibitor. In some embodiments, the GLP-1 receptor agonist is exenatide or liraglutide. In some embodiments, the DPP-4 inhibitor is sitagliptin or vildapliptin. In some embodiments, the siNA or composition and the liver disease treatment agent are administered concurrently. In some embodiments, the siNA or composition and the liver disease treatment agent are administered sequentially. In some embodiments, the siNA or composition is administered prior to administering the liver disease treatment agent. In some embodiments, the siNA or composition is administered after administering the liver disease treatment agent.

In some embodiments, the siNA or the composition is administered at a dose of at least 1 mg/kg, 2 mg/kg, 3 mg/kg, 4 mg/kg, 5 mg/kg, 6 mg/kg, 7 mg/kg, 8 mg/kg, 9 mg/kg, 10 mg/kg, 11 mg/kg, 12 mg/kg, 13 mg/kg 14 mg/kg, or 15 mg/kg. In some embodiments, the siNA or the composition is administered at a dose of between 0.5 mg/kg to 50 mg/kg, 0.5 mg/kg to 40 mg/kg 0.5 mg/kg to 30 mg/kg, 1 mg/kg to 50 mg/kg, 1 mg/kg to 40 mg/kg, 1 mg/kg to 30 mg/kg, 1 mg/kg to 20 mg/kg, 3 mg/kg to 50 mg/kg, 3 mg/kg to 40 mg/kg, 3 mg/kg to 30 mg/kg, 3 mg/kg to 20 mg/kg, 3 mg/kg to 15 mg/kg, 3 mg/kg to 10 mg/kg, 4 mg/kg to 50 mg/kg, 4 mg/kg to 40 mg/kg, 4 mg/kg to 30 mg/kg, 4 mg/kg to 20 mg/kg, 4 mg/kg to 15 mg/kg, 4 mg/kg to 10 mg/kg, 5 mg/kg to 50 mg/kg, 5 mg/kg to 40 mg/kg, 5 mg/kg to 30 mg/kg, 5 mg/kg to 20 mg/kg, 5 mg/kg to 15 mg/kg, or 5 mg/kg to 10 mg/kg.

In some embodiments, the siNA or the composition is administered at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times. In some embodiments, the siNA or the composition is administered at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times a day, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times a week, or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times a month. In some embodiments, the siNA or the composition are administered at least once every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 days. In some embodiments, the siNA or the composition is administered for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 days, or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 51, 52, 53, 54, or 55 weeks.

In some embodiments, the siNA or the composition is administered at a single dose of 5 mg/kg. In some embodiments, the siNA or the composition is administered at a single dose of 10 mg/kg. In some embodiments, the siNA or the composition is administered at three doses of 10 mg/kg once a week. In some embodiments, the siNA or the composition is administered at three doses of 10 mg/kg once every three days. In some embodiments, the siNA or the composition is administered at five doses of 10 mg/kg once every three days. In some embodiments, the siNA or the composition is administered at six doses of ranging from 1 mg/kg to 15 mg/kg, 1 mg/kg to 10 mg/kg, 2 mg/kg to 15 mg/kg, 2 mg/kg to 10 mg/kg, 3 mg/kg to 15 mg/kg, or 3 mg/kg to 10 mg/kg. In some embodiments, the first dose and second dose are administered at least 3 days apart. In some embodiments, the second dose and third dose are administered at least 4 days apart. In some embodiments, the third dose and fourth dose, fourth dose and fifth dose, or fifth dose and sixth dose are administered at least 7 days apart.

In some embodiments, any of the siNAs or the compositions disclosed herein are formulated as a particle or viral vector. In some embodiments, the siNA or the composition are administered in a particle or viral vector. In some embodiments, the viral vector is a vector of adenovirus, adeno-associated virus (AAV), alphavirus, flavivirus, herpes simplex virus, lentivirus, measles virus, picornavirus, poxvirus, retrovirus, or rhabdovirus. In some embodiments, the viral vector is a recombinant viral vector. In some embodiments, the viral vector is selected from AAVrh.74, AAVrh.10, AAVrh.20, AAV-1, AAV-2, AAV-3, AAV-4, AAV-5, AAV-6, AAV-7, AAV-8, AAV-9, AAV-10, AAV-11, AAV-12 and AAV-13. In some embodiments, the siNA or the composition is administered systemically. In some embodiments, the siNA or the composition is administered locally. In some embodiments, the siNA or the composition is administered intravenously, subcutaneously, or intramuscularly.

In some embodiments, any of the siRNAs or compositions disclosed herein are used in the manufacture of a medicament for treating a disease. In some embodiments, the disease is a viral disease. In some embodiments, the viral disease is caused by a DNA virus. In some embodiments, the DNA virus is a double stranded DNA (dsDNA virus). In some embodiments, the dsDNA virus is a hepadnavirus. In some embodiments, the hepadnavirus is a hepatitis B virus (HBV). In some embodiments, the HBV is selected from HBV genotypes A-J. In some embodiments, an additional HBV treatment agent is further used in the manufacture of the medicament. In some embodiments, the additional HBV treatment agent is selected from a nucleotide analog, nucleoside analog, a capsid assembly modulator (CAM), a recombinant interferon, an entry inhibitor, a small molecule immunomodulator and oligonucleotide therapy. In some embodiments, the oligonucleotide therapy is an additional siNA. In some embodiments, the additional siNA is selected from any of ds-siNA-001 to ds-siNA-0178. In some embodiments, the oligonucleotide therapy is an antisense oligonucleotide (ASO), NAPs, or STOPs. In some embodiments, the ASO is ASO 1 or ASO 2. In some embodiments, the additional HBV treatment agent is selected from HBV STOPS™ ALG-010133, HBV CAM ALG-000184, ASO 1, recombinant interferon alpha 2b, IFN-α, PEG-IFN-α-2a, lamivudine, telbivudine, adefovir dipivoxil, clevudine, entecavir, tenofovir alafenamide, tenofovir disoproxil, NVR3-778, BAY41-4109, JNJ-632, JNJ-3989 (ARO-HBV), RG6004, GSK3228836, REP-2139, REP-2165, AB-729, VIR-2218, RG6346 (DCR-HBVS), JNJ-6379, GLS4, ABI-HO731, JNJ-440, NZ-4, RG7907, EDP-514, AB-423, AB-506, ABI-H03733 and ABI-H2158.

In some embodiments, any of the siRNAs or compositions disclosed herein are used in the manufacture of a medicament for treating a disease. In some embodiments, the disease is a liver disease. In some embodiments, the liver disease is a nonalcoholic fatty liver disease (NAFLD) or hepatocellular carcinoma (HCC). In some embodiments, the NAFLD is nonalcoholic steatohepatitis (NASH). In some embodiments, the siNA comprises a first nucleotide sequence. In some embodiments, the first nucleotide sequence comprises a nucleotide sequence of any one SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the siNA comprises a second nucleotide sequence. In some embodiments, the second nucleotide sequence comprises a nucleotide sequence of any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the siNA comprises a sense strand. In some embodiments, the sense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the siNA comprises an antisense strand. In some embodiments, the antisense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 363-409, 445-533, and 536-539. In some embodiments, the siNA further comprises any of the 5′ end caps disclosed herein. In some embodiments, the siNA further comprises any of the phosphorylation blockers disclosed herein. In some embodiments, the siNA further comprises any of the conjugated moieties disclosed herein. In some embodiments, the siNA further comprises any of the destabilized nucleotides disclosed herein. In some embodiments, the siNA further comprises any of the modified nucleotides disclosed herein. In some embodiments, a liver disease treatment agent is further used in the manufacture of the medicament. In some embodiments, the liver disease treatment agent is selected from a peroxisome proliferator-activator receptor (PPAR) agonist, farnesoid X receptor (FXR) agonist, lipid-altering agent, and incretin-based therapy. In some embodiments, the PPAR agonist is selected from a PPARα agonist, dual PPARα/δ agonist, PPARγ agonist, and dual PPARα/γ agonist. In some embodiments, the dual PPARα agonist is a fibrate. In some embodiments, the PPARα/S agonist is elafibranor. In some embodiments, the PPARγ agonist is a thiazolidinedione (TZD). In some embodiments, TZD is pioglitazone. In some embodiments, the dual PPARα/γ agonist is saroglitazar. In some embodiments, the FXR agonist is obeticholic acis (OCA). In some embodiments, the lipid-altering agent is aramchol. In some embodiments, the incretin-based therapy is a glucagon-like peptide 1 (GLP-1) receptor agonist or dipeptidyl peptidase 4 (DPP-4) inhibitor. In some embodiments, the GLP-1 receptor agonist is exenatide or liraglutide. In some embodiments, the DPP-4 inhibitor is sitagliptin or vildapliptin.

In some embodiments, any of the siNAs disclosed herein is used as a medicament. In some embodiments, the siNA comprises a first nucleotide sequence. In some embodiments, the first nucleotide sequence comprises a nucleotide sequence of any one SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the siNA comprises a second nucleotide sequence. In some embodiments, the second nucleotide sequence comprises a nucleotide sequence of any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the siNA comprises a sense strand. In some embodiments, the sense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the siNA comprises an antisense strand. In some embodiments, the antisense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 363-409, 445-533, and 536-539. In some embodiments, the siNA further comprises any of the 5′ end caps disclosed herein. In some embodiments, the siNA further comprises any of the phosphorylation blockers disclosed herein. In some embodiments, the siNA further comprises any of the conjugated moieties disclosed herein. In some embodiments, the siNA further comprises any of the destabilized nucleotides disclosed herein. In some embodiments, the siNA further comprises any of the modified nucleotides disclosed herein.

In some embodiments, any of the compositions disclosed herein are used as a medicament. In some embodiments, the composition comprises any of the siNAs disclosed herein. In some embodiments, the siNA comprises a first nucleotide sequence. In some embodiments, the first nucleotide sequence comprises a nucleotide sequence of any one SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the siNA comprises a second nucleotide sequence. In some embodiments, the second nucleotide sequence comprises a nucleotide sequence of any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the siNA comprises a sense strand. In some embodiments, the sense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the siNA comprises an antisense strand. In some embodiments, the antisense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 363-409, 445-533, and 536-539. In some embodiments, the siNA further comprises any of the 5′ end caps disclosed herein. In some embodiments, the siNA further comprises any of the phosphorylation blockers disclosed herein. In some embodiments, the siNA further comprises any of the conjugated moieties disclosed herein. In some embodiments, the siNA further comprises any of the destabilized nucleotides disclosed herein. In some embodiments, the siNA further comprises any of the modified nucleotides disclosed herein.

In some embodiments, any of the siNAs disclosed herein are used in the treatment of a disease. In some embodiments, the siNA comprises a first nucleotide sequence. In some embodiments, the first nucleotide sequence comprises a nucleotide sequence of any one SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the siNA comprises a second nucleotide sequence. In some embodiments, the second nucleotide sequence comprises a nucleotide sequence of any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the siNA comprises a sense strand. In some embodiments, the sense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the siNA comprises an antisense strand. In some embodiments, the antisense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 363-409, 445-533, and 536-539. In some embodiments, the siNA further comprises any of the 5′ end caps disclosed herein. In some embodiments, the siNA further comprises any of the phosphorylation blockers disclosed herein. In some embodiments, the siNA further comprises any of the conjugated moieties disclosed herein. In some embodiments, the siNA further comprises any of the destabilized nucleotides disclosed herein. In some embodiments, the siNA further comprises any of the modified nucleotides disclosed herein. In some embodiments, the disease is a viral disease. In some embodiments, the viral disease is caused by a DNA virus. In some embodiments, the DNA virus is a double stranded DNA (dsDNA virus). In some embodiments, the dsDNA virus is a hepadnavirus. In some embodiments, the hepadnavirus is a hepatitis B virus (HBV). In some embodiments, the HBV is selected from HBV genotypes A-J. In some embodiments, the disease is a liver disease. In some embodiments, the liver disease is a nonalcoholic fatty liver disease (NAFLD) or hepatocellular carcinoma (HCC). In some embodiments, the NAFLD is nonalcoholic steatohepatitis (NASH).

In some embodiments, any of the compositions disclosed herein are used in the treatment of a disease. In some embodiments, the composition comprises any of the siNAs disclosed herein. In some embodiments, the siNA comprises a first nucleotide sequence. In some embodiments, the first nucleotide sequence comprises a nucleotide sequence of any one SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the siNA comprises a second nucleotide sequence. In some embodiments, the second nucleotide sequence comprises a nucleotide sequence of any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the siNA comprises a sense strand. In some embodiments, the sense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the siNA comprises an antisense strand. In some embodiments, the antisense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 363-409, 445-533, and 536-539. In some embodiments, the siNA further comprises any of the 5′ end caps disclosed herein. In some embodiments, the siNA further comprises any of the phosphorylation blockers disclosed herein. In some embodiments, the siNA further comprises any of the conjugated moieties disclosed herein. In some embodiments, the siNA further comprises any of the destabilized nucleotides disclosed herein. In some embodiments, the siNA further comprises any of the modified nucleotides disclosed herein. In some embodiments, the disease is a viral disease. In some embodiments, the viral disease is caused by a DNA virus. In some embodiments, the DNA virus is a double stranded DNA (dsDNA virus). In some embodiments, the dsDNA virus is a hepadnavirus. In some embodiments, the hepadnavirus is a hepatitis B virus (HBV). In some embodiments, the HBV is selected from HBV genotypes A-J. In some embodiments, the disease is a liver disease. In some embodiments, the liver disease is a nonalcoholic fatty liver disease (NAFLD) or hepatocellular carcinoma (HCC). In some embodiments, the NAFLD is nonalcoholic steatohepatitis (NASH).

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates an exemplary siNA molecule.

FIG. 2 illustrates an exemplary siNA molecule.

FIGS. 3A-3G illustrate exemplary double-stranded siNA molecules.

FIG. 4 shows a graph of the change in serum HBsAg from AAV-HBV mice treated with ds-siNA-0160, ds-siNA-0165, ds-siNA-0163, or ds-siNA-0166.

FIG. 5A shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01) or ds-siNA-0160 (G03).

FIG. 5B shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01) or ds-siNA-0160 (G15).

FIG. 5C shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01) or ds-siNA-0160 (G03).

FIG. 5D shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0160 (G03), or ds-siNA-0109 (G09).

FIGS. 5E-5F show a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01) or ds-siNA-0169 (G18).

FIG. 5G shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01) or ds-siNA-0169 (G04).

FIG. 5H shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01) or ds-siNA-0169 (G04).

FIG. 5I shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0169 (G04), or ds-siNA-0147 (G08).

FIG. 5J shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0166 (G06), or ds-siNA-0153 (G14).

FIG. 5K shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0163 (G05), or ds-siNA-0119 (G13).

FIG. 6A shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0160 (G15), or ds-siNA-080 (G14).

FIG. 6B shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0169 (G16), or ds-siNA-081 (G13).

FIG. 7A shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0165 (G18), or ds-siNA-0127 (G17).

FIG. 7B shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0168 (G20), or ds-siNA-0150 (G19).

FIG. 8A shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0160 (G06), ASO 1 (G18), or a combination of ds-siNA-0160 and ASO 1 (G20).

FIG. 8B shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0160 (G06), ASO 1 (G18), or a combination of ds-siNA-0160 and ASO 1 (G20).

FIG. 8C shows a graph of a synergy analysis of a combination therapy with unconjugated forms of ds-siNA-0164 and ASO 2 (e.g., ds-siNA-0160 and ASO 1 without GalNac).

FIG. 9 shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0166 (G03), ds-siNA-0155 (G08), or ds-siNA-0157.

FIG. 10 shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0165 (G10), ds-siNA-0160 (G06), or a combination therapy with ds-siNA-0160 and ds-siNA-0165 (G14).

FIG. 11 shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0165 (G05), or ds-siNA-0144 (G11).

FIG. 12 shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0163 (G04), ds-siNA-0122 (G09), or ds-siNA-0123 (G13).

FIG. 13 shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G 15) or ds-siNA-0147 (G 19).

FIG. 14 shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G 15, square), ds-siNA-0109 (G 21, circle), or ds-siNA-0172 (G 27, diamond).

FIG. 15 shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G 01, circle), ds-siNA-0109 (G 07, square), ds-siNA-0119 (G 11, triangle), or ds-siNA-0153 (G 13, diamond).

FIG. 16 shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G 01, circle), ASO 1 (G 20, square), ds-siNA-0147 (G 24, diamond), or a combination of ASO 1 and ds-siNA-0147 (G 25, triangle).

FIG. 17 shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G 01, circle), ASO 1 (G 20, square), ds-siNA-0109 (G 26, diamond), or a combination of ASO 1 and ds-siNA-0109 (G 27, triangle).

 DETAILED DESCRIPTION OF THE INVENTION

Disclosed herein are short interfering nucleic acid (siNA) molecules comprising modified nucleotides. The siNA molecules described herein may be double-stranded siNA (ds-siNA) molecules. The siNA molecules described herein may comprise modified nucleotides selected from 2′-O-methyl nucleotides and 2′-fluoro nucleotides. The siNA molecules described herein may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more phosphorothioate internucleoside linkages. The siNA molecules described herein may comprise a phosphorylation blocker. The siNA molecules described herein may comprise a 5′-stabilized end cap. The siNA molecules described herein may comprise a galactosamine. The siNA molecules described herein may comprise one or more blunt ends. The siNA molecules described herein may comprise one or more overhangs.

Further disclosed herein are short interfering nucleic acid (siNA) molecules comprising (a) a phosphorylation blocker; and (b) a short interfering nucleic acid (siNA). The siNA may comprise at least 5 nucleotides. The nucleotides may be modified nucleotides, non-modified nucleotides, or any combination thereof. The nucleotides may be ribonucleotides, deoxyribonucleotides, or any combination thereof. The siNA may be single-stranded. Alternatively, the siNA is double-stranded. The double-stranded siNA may comprise one or more blunt ends. The double-stranded siNA may comprise one or more overhangs. The double-stranded siNA may comprise a blunt end and an overhang.

Further disclosed herein are short interfering nucleic acid (siNA) molecules comprising (a) a conjugated moiety; and (b) a short interfering nucleic acid (siNA). The siNA may comprise at least 5 nucleotides. The nucleotides may be modified nucleotides, non-modified nucleotides, or any combination thereof. The nucleotides may be ribonucleotides, deoxyribonucleotides, or any combination thereof. The siNA may be single-stranded. Alternatively, the siNA is double-stranded. The double-stranded siNA may comprise one or more blunt ends. The double-stranded siNA may comprise one or more overhangs. The double-stranded siNA may comprise a blunt end and an overhang.

Further disclosed herein are short interfering nucleic acid (siNA) molecules comprising (a) a 5′-stabilized end cap; and (b) a short interfering nucleic acid (siNA). The siNA may comprise at least 5 nucleotides. The nucleotides may be modified nucleotides, non-modified nucleotides, or any combination thereof. The nucleotides may be ribonucleotides, deoxyribonucleotides, or any combination thereof. The siNA may be single-stranded. Alternatively, the siNA is double-stranded. The double-stranded siNA may comprise one or more blunt ends. The double-stranded siNA may comprise one or more overhangs. The double-stranded siNA may comprise a blunt end and an overhang.

Further disclosed herein are short interfering nucleic acid (siNA) molecules comprising (a) at least one phosphorylation blocker, conjugated moiety, or 5′-stabilized end cap; and (b) a short interfering nucleic acid (siNA). The siNA may comprise at least 5 nucleotides. The nucleotides may be modified nucleotides, non-modified nucleotides, or any combination thereof. The nucleotides may be ribonucleotides, deoxyribonucleotides, or any combination thereof. The siNA may be single-stranded. Alternatively, the siNA is double-stranded. The double-stranded siNA may comprise one or more blunt ends. The double-stranded siNA may comprise one or more overhangs. The double-stranded siNA may comprise a blunt end and an overhang.

An exemplary siNA molecule of the present disclosure is shown in FIG. 1. As shown in FIG. 1, an exemplary siNA molecule comprises a sense strand (101) and an antisense strand (102). The sense strand (101) may comprise a first oligonucleotide sequence (103). The first oligonucleotide sequence (103) may comprise one or more phosphorothioate internucleoside linkages (109). The phosphorothioate internucleoside linkage (109) may be between the nucleotides at the 5′ or 3′ terminal end of the first oligonucleotide sequence (103). The phosphorothioate internucleoside linkage (109) may be between the first three nucleotides from the 5′ end of the first oligonucleotide sequence (103). The first oligonucleotide sequence (103) may comprise one or more 2′-fluoro nucleotides (110). The first oligonucleotide sequence (103) may comprise one or more 2′-O-methyl nucleotides (111). The first oligonucleotide sequence (103) may comprise 15 or more modified nucleotides independently selected from 2′-fluoro nucleotides (110) and 2′-O-methyl nucleotides (111). The sense strand (101) may further comprise a phosphorylation blocker (105). The sense strand (101) may further comprise a galactosamine (106). The antisense strand (102) may comprise a second oligonucleotide sequence (104). The second oligonucleotide sequence (104) may comprise one or more phophorothioate internucleoside linkages (109). The phosphorothioate internucleoside linkage (109) may be between the nucleotides at the 5′ or 3′ terminal end of the second oligonucleotide sequence (104). The phosphorothioate internucleoside linkage (109) may be between the first three nucleotides from the 5′ end of the second oligonucleotide sequence (104). The phosphorothioate internucleoside linkage (109) may be between the first three nucleotides from the 3′ end of the second oligonucleotide sequence (104). The second oligonucleotide sequence (104) may comprise one or more 2′-fluoro nucleotides (110). The second oligonucleotide sequence (104) may comprise one or more 2′-O-methyl nucleotides (111). The second oligonucleotide sequence (104) may comprise 15 or more modified nucleotides independently selected from 2′-fluoro nucleotides (110) and 2′-O-methyl nucleotides (111). The antisense strand (102) may further comprise a 5′-stabilized end cap (107). The siNA may further comprise one or more blunt ends. Alternatively, or additionally, one end of the siNA may comprise an overhang (108). The overhang (108) may be part of the sense strand (101). The overhang (108) may be part of the antisense strand (102). The overhang (108) may be distinct from the first nucleotide sequence (103). The overhang (108) may be distinct from the second nucleotide sequence (104). The overhang (108) may be part of the first nucleotide sequence (103). The overhang (108) may be part of the second nucleotide sequence (104). The overhang (108) may comprise 1 or more nucleotides. The overhang (108) may comprise 1 or more deoxyribonucleotides. The overhang (108) may comprise 1 or more modified nucleotides. The overhang (108) may comprise 1 or more modified ribonucleotides. The sense strand (101) may be shorter than the antisense strand (102). The sense strand (101) may be the same length as the antisense strand (102). The sense strand (101) may be longer than the antisense strand (102).

An exemplary siNA molecule of the present disclosure is shown in FIG. 2. As shown in FIG. 2, an exemplary siNA molecule comprises a sense strand (201) and an antisense strand (202). The sense strand (201) may comprise a first oligonucleotide sequence (203). The first oligonucleotide sequence (203) may comprise one or more phophorothioate internucleoside linkages (209). The phosphorothioate internucleoside linkage (209) may be between the nucleotides at the 5′ or 3′ terminal end of the first oligonucleotide sequence (203). The phosphorothioate internucleoside linkage (209) may be between the first three nucleotides from the 5′ end of the first oligonucleotide sequence (203). The first oligonucleotide sequence (203) may comprise one or more 2′-fluoro nucleotides (210). The first oligonucleotide sequence (203) may comprise one or more 2′-O-methyl nucleotides (211). The first oligonucleotide sequence (203) may comprise 15 or more modified nucleotides independently selected from 2′-fluoro nucleotides (210) and 2′-O-methyl nucleotides (211). The sense strand (201) may further comprise a phosphorylation blocker (205). The sense strand (201) may further comprise a galactosamine (206). The antisense strand (202) may comprise a second oligonucleotide sequence (204). The second oligonucleotide sequence (204) may comprise one or more phophorothioate internucleoside linkages (209). The phosphorothioate internucleoside linkage (209) may be between the nucleotides at the 5′ or 3′ terminal end of the second oligonucleotide sequence (204). The phosphorothioate internucleoside linkage (209) may be between the first three nucleotides from the 5′ end of the second oligonucleotide sequence (204). The phosphorothioate internucleoside linkage (209) may be between the first three nucleotides from the 3′ end of the second oligonucleotide sequence (204). The second oligonucleotide sequence (204) may comprise one or more 2′-fluoro nucleotides (210). The second oligonucleotide sequence (204) may comprise one or more 2′-O-methyl nucleotides (211). The second oligonucleotide sequence (204) may comprise 15 or more modified nucleotides independently selected from 2′-fluoro nucleotides (210) and 2′-O-methyl nucleotides (211). The antisense strand (202) may further comprise a 5′-stabilized end cap (207). The siNA may further comprise one or more overhangs (208). The overhang (208) may be part of the sense strand (201). The overhang (208) may be part of the antisense strand. (202). The overhang (208) may be distinct from the first nucleotide sequence (203). The overhang (208) may be distinct from the second nucleotide sequence (204). The overhang (208) may be part of the first nucleotide sequence (203). The overhang (208) may be part of the second nucleotide sequence (204). The overhang (208) may be adjacent to the 3′ end of the first nucleotide sequence (203). The overhang (208) may be adjacent to the 5′ end of the first nucleotide sequence (203). The overhang (208) may be adjacent to the 3′ end of the second nucleotide sequence (204). The overhang (208) may be adjacent to the 5′ end of the second nucleotide sequence (204). The overhang (208) may comprise 1 or more nucleotides. The overhang (208) may comprise 1 or more deoxyribonucleotides. The overhang (208) may comprise a TT sequence. The overhang (208) may comprise 1 or more modified nucleotides. The overhang (208) may comprise 1 or more modified nucleotides disclosed herein (e.g., 2-fluoro nucleotide, 2′-O-methyl nucleotide, 2′-fluoro nucleotide mimic, 2′-O-methyl nucleotide mimic, or a nucleotide comprising a modified nucleobase). The overhang (208) may comprise 1 or more modified ribonucleotides. The sense strand (201) may be shorter than the antisense strand (202). The sense strand (201) may be the same length as the antisense strand (202). The sense strand (201) may be longer than the antisense strand (202).

FIGS. 3A-3G depict exemplary ds-siNA modification patterns. As shown in FIGS. 3A-3G, an exemplary ds-siNA molecule may have the following formula:

5′-An1Bn2An3Bn4An5Bn6An7Bn8An9-3′ 3′-Cq1Aq2Bq3Aq4Bq5Aq6Bq7Aq8Bq9Aq10Bq11Aq12-5′

wherein:
    • the top strand is a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence comprises 15 to 30 nucleotides;
    • the bottom strand is an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence comprises 15 to 30 nucleotides;
    • each A is independently a 2′-O-methyl nucleotide or a nucleotide comprising a 5′ stabilized end cap or phosphorylation blocker;
    • B is a 2′-fluoro nucleotide;
    • C represents overhanging nucleotides and is a 2′-O-methyl nucleotide;
    • n1=1-4 nucleotides in length;
    • each n2, n6, n8, q3, q5, q7, q9, q11, and q12 is independently 0-1 nucleotides in length;
    • each n3 and n4 is independently 1-3 nucleotides in length;
    • n5 is 1-10 nucleotides in length;
    • n7 is 0-4 nucleotides in length;
    • each n9, q1, and q2 is independently 0-2 nucleotides in length;
    • q4 is 0-3 nucleotides in length;
    • q6 is 0-5 nucleotides in length;
    • q8 is 2-7 nucleotides in length; and
    • q10 is 2-11 nucleotides in length.

The ds-siNA may further comprise a conjugated moiety. The conjugated moiety may comprise any of the galactosamines disclosed herein. The ds-siNA may further comprise (i) phosphorothioate internucleoside linkages between the nucleotides at positions 1 and 2 and positions 2 and 3 from the 5′ end of the sense strand; and (ii) phosphorothioate internucleoside linkages between the nucleotides at positions 1 and 2; positions 2 and 3; positions 19 and 20; and positions 20 and 21 from the 5′ end of the antisense strand. The ds-siNA may further comprise a 5′-stabilizing end cap. The 5′-stabilizing end cap may be a vinyl phosphonate. The 5′-stabilizing end cap may be attached to the 5′ end of the antisense strand. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the antisense strand is further modified to contain a phosphorylation blocker. An exemplary ds-siNA molecule may have the following formula:

5′-A2-4B1A1-3B2-3A2-10B0-1A0-4B0-1A0-2-3′ 3′-C2A0-2B0-1A0-3B0-1A0-5B0-1A2-7B1A2-11B1A1-5′

wherein:
    • the top strand is a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence comprises 15 to 30 nucleotides;
    • the bottom strand is an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence comprises 15 to 30 nucleotides;
    • each A is independently a 2′-O-methyl nucleotide or a nucleotide comprising a 5′ stabilized end cap or phosphorylation blocker;
    • B is a 2′-fluoro nucleotide;
    • C represents overhanging nucleotides and is a 2′-O-methyl nucleotide.
      The ds-siNA may further comprise a conjugated moiety. The conjugated moiety may comprise any of the galactosamines disclosed herein. The ds-siNA may further comprise (i) phosphorothioate internucleoside linkages between the nucleotides at positions 1 and 2 and positions 2 and 3 from the 5′ end of the sense strand; and (ii) phosphorothioate internucleoside linkages between the nucleotides at positions 1 and 2; positions 2 and 3; positions 19 and 20; and positions 20 and 21 from the 5′ end of the antisense strand. The ds-siNA may further comprise a 5′-stabilizing end cap. The 5′-stabilizing end cap may be a vinyl phosphonate. The vinyl phosphonate may be a deuterated vinyl phosphonate. The deuterated vinyl phosphonate may be a mono-deuterated vinyl phosphonate. The deuterated vinyl phosphonate may be a mono-di-deuterated vinyl phosphonate. The 5′-stabilizing end cap may be attached to the 5′ end of the antisense strand. The 5′-stabilizing end cap may be attached to the 3′ end of the antisense strand. The 5′-stabilizing end cap may be attached to the 5′ end of the sense strand. The 5′-stabilizing end cap may be attached to the 3′ end of the sense strand. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the antisense strand is further modified to contain a phosphorylation blocker.

The exemplary ds-siNA shown in FIGS. 3A-3G comprise (i) a sense strand comprising 19-21 nucleotides; and (ii) an antisense strand comprising 21-23 nucleotides. The ds-siNA may further comprise (iii) a conjugated moiety, wherein the conjugated moiety is attached to the 3′ end of the antisense strand. The ds-siNA may comprise a 2 nucleotide overhang consisting of nucleotides at positions 20 and 21 from the 5′ end of the antisense strand. The ds-siNA may comprise a 2 nucleotide overhang consisting of nucleotides at positions 22 and 23 from the 5′ end of the antisense strand. The ds-siNA may further comprise 1, 2, 3, 4, 5, 6 or more phosphorothioate (ps) internucleoside linkages. At least one phosphorothioate internucleoside linkage may be between the nucleotides at positions 1 and 2 or positions 2 and 3 from the 5′ end of the sense strand. At least one phosphorothioate internucleoside linkage may be between the nucleotides at positions 1 and 2 or positions 2 and 3 from the 5′ end of the antisense strand. At least one phosphorothioate internucleoside linkage may be between the nucleotides at positions 19 and 20, positions 20 and 21, positions 21 and 22, or positions 22 and 23 from the 5′ end of the antisense strand. As shown in FIGS. 3A-3G, 4-6 nucleotides in the sense strand may be 2′-fluoro nucleotides. As shown in FIGS. 3A-3G, 2-5 nucleotides in the antisense strand may be 2′-fluoro nucleotides. As shown in FIGS. 3A-3G, 13-15 nucleotides in the sense strand may be 2′-O-methyl nucleotides. As shown in FIGS. 3A-3G, 14-19 nucleotides in the antisense strand may be 2′-O-methyl nucleotides. As shown in FIGS. 3A-3G, the ds-siNA does not contain a base pair between 2′-fluoro nucleotides on the sense and antisense strands. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the antisense strand is further modified to contain a phosphorylation blocker.

As shown in FIG. 3A, a ds-siNA may comprise (a) a sense strand consisting of 19 nucleotides, wherein 2′-fluoro nucleotides are at positions 3, 7-9, 12, and 17 from the 5′ end of the sense strand, and wherein 2′-O-methyl nucleotides are at positions 1, 2, 4-6, 10, 11, 13-16, 18, and 19 from the 5′ end of the sense strand; (b) an antisense strand consisting of 21 nucleotides, wherein nucleotides at positions 2 and 14 from the 5′ end of the antisense strand are 2′-fluoro nucleotides; and wherein nucleotides at positions 1, 3-13, and 15-21 are 2′-O-methyl nucleotides. The ds-siNA may further comprise a conjugated moiety attached to the 3′ end of the sense strand. The ds-siNA may further comprise (i) phosphorothioate internucleoside linkages between the nucleotides at positions 1 and 2 and positions 2 and 3 from the 5′ end of the sense strand; and (ii) phosphorothioate internucleoside linkages between the nucleotides at positions 1 and 2; positions 2 and 3; positions 19 and 20; and positions 20 and 21 from the 5′ end of the antisense strand. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the antisense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the sense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the antisense strand is a d2vd3 nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the sense strand or antisense strand is a 2′-fluoro nucleotide mimic. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the sense strand or antisense strand is a f4P, f2P, or fX nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-O-methyl nucleotide on the sense or antisense strand is a 2′-O-methyl nucleotide mimic.

As shown in FIG. 3B, a ds-siNA may comprise (a) a sense strand consisting of 19 nucleotides, wherein 2′-fluoro nucleotides are at positions 3, 7, 8, and 17 from the 5′ end of the sense strand, and wherein 2′-O-methyl nucleotides are at positions 1, 2, 4-6, 9-16, 18, and 19 from the 5′ end of the sense strand; (b) an antisense strand consisting of 21 nucleotides, wherein nucleotides at positions 2 and 14 from the 5′ end of the antisense strand are 2′-fluoro nucleotides; and wherein nucleotides at positions 1, 3-13, and 15-21 are 2′-O-methyl nucleotides. The ds-siNA may further comprise a conjugated moiety attached to the 3′ end of the sense strand. The ds-siNA may further comprise (i) phosphorothioate internucleoside linkages between the nucleotides at positions 1 and 2 and positions 2 and 3 from the 5′ end of the sense strand; and (ii) phosphorothioate internucleoside linkages between the nucleotides at positions 1 and 2; positions 2 and 3; positions 19 and 20; and positions 20 and 21 from the 5′ end of the antisense strand. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the antisense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the sense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the antisense strand is a d2vd3 nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the sense strand or antisense strand is a 2′-fluoro nucleotide mimic. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the sense strand or antisense strand is a f4P, f2P, or fX nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-O-methyl nucleotide on the sense or antisense strand is a 2′-O-methyl nucleotide mimic.

As shown in FIG. 3C, a ds-siNA may comprise (a) a sense strand consisting of 19 nucleotides, wherein 2′-fluoro nucleotides are at positions 3, 7-9, 12 and 17 from the 5′ end of the sense strand, and wherein 2′-O-methyl nucleotides are at positions 1, 2, 4-6, 10, 11, 13-16, 18, and 19 from the 5′ end of the sense strand; (b) an antisense strand consisting of 21 nucleotides, wherein the nucleotides in the antisense strand comprise an alternating 1:3 modification pattern, and wherein 1 nucleotide is a 2′-fluoro nucleotide and 3 nucleotides are 2′-O-methyl nucleotides. The ds-siNA may further comprise a conjugated moiety attached to the 3′ end of the sense strand. The ds-siNA may further comprise (i) phosphorothioate internucleoside linkages between the nucleotides at positions 1 and 2 and positions 2 and 3 from the 5′ end of the sense strand; and (ii) phosphorothioate internucleoside linkages between the nucleotides at positions 1 and 2; positions 2 and 3; positions 19 and 20; and positions 20 and 21 from the 5′ end of the antisense strand. The ds-siNA may comprise 2-5 alternating 1:3 modification patterns on the antisense strand. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the antisense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the sense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the antisense strand is a d2vd3 nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the sense strand or antisense strand is a 2′-fluoro nucleotide mimic. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the sense strand is a f4P, f2P, or fX nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the antisense strand is a f4P, f2P, or fX nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-O-methyl nucleotide on the sense or antisense strand is a 2′-O-methyl nucleotide mimic.

As shown in FIG. 3D, a ds-siNA may comprise (a) a sense strand consisting of 19 nucleotides, wherein 2′-fluoro nucleotides are at positions 5 and 7-9 from the 5′ end of the sense strand, and wherein 2′-O-methyl nucleotides are at positions 1-4, 6, and 10-19 from the 5′ end of the sense strand; (b) an antisense strand consisting of 21 nucleotides, wherein the nucleotides in the antisense strand comprise an alternating 1:3 modification pattern, and wherein 1 nucleotide is a 2′-fluoro nucleotide and 3 nucleotides are 2′-O-methyl nucleotides. The ds-siNA may further comprise a conjugated moiety attached to the 3′ end of the sense strand. The ds-siNA may further comprise (i) phosphorothioate internucleoside linkages between the nucleotides at positions 1 and 2 and positions 2 and 3 from the 5′ end of the sense strand; and (ii) phosphorothioate internucleoside linkages between the nucleotides at positions 1 and 2; positions 2 and 3; positions 19 and 20; and positions 20 and 21 from the 5′ end of the antisense strand. The ds-siNA may comprise 2-5 alternating 1:3 modification patterns on the antisense strand. The alternating 1:3 modification pattern may start at the nucleotide at any of positions 2, 6, 10, 14, and/or 18 from the 5′ end of the antisense strand. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the antisense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the sense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the antisense strand is a d2vd3 nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the sense strand or antisense strand is a 2′-fluoro nucleotide mimic. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the sense strand is a f4P, f2P, or fX nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the antisense strand is a f4P, f2P, or fX nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-O-methyl nucleotide on the sense or antisense strand is a 2′-O-methyl nucleotide mimic.

As shown in FIG. 3E, a ds-siNA may comprise (a) a sense strand consisting of 19 nucleotides, wherein 2′-fluoro nucleotides are at positions 5 and 7-9 from the 5′ end of the sense strand, and wherein 2′-O-methyl nucleotides are at positions 1-4, 6, and 10-19 from the 5′ end of the sense strand; (b) an antisense strand consisting of 21 nucleotides, wherein the nucleotides in the antisense strand comprise an alternating 1:2 modification pattern, and wherein 1 nucleotide is a 2′-fluoro nucleotide and 2 nucleotides are 2′-O-methyl nucleotides. The ds-siNA may further comprise a conjugated moiety attached to the 3′ end of the sense strand. The ds-siNA may further comprise (i) phosphorothioate internucleoside linkages between the nucleotides at positions 1 and 2 and positions 2 and 3 from the 5′ end of the sense strand; and (ii) phosphorothioate internucleoside linkages between the nucleotides at positions 1 and 2; positions 2 and 3; positions 19 and 20; and positions 20 and 21 from the 5′ end of the antisense strand. The ds-siNA may comprise 2-5 alternating 1:2 modification patterns on the antisense strand. The alternating 1:2 modification pattern may start at the nucleotide at any of positions 2, 5, 8, 14, and/or 17 from the 5′ end of the antisense strand. In some embodiments, the ds-siNA comprises (a) a sense strand consisting of 19 nucleotides, wherein 2′-fluoro nucleotides are at positions 5 and 7-9 from the 5′ end of the sense strand, and wherein 2′-O-methyl nucleotides are at positions 1-4, 6, and 10-19 from the 5′ end of the sense strand; (b) an antisense strand consisting of 21 nucleotides, wherein 2′-fluoro nucleotides are at positions 2, 5, 8, 14, and 17 from the 5′ end of the antisense strand, and wherein 2′-O-methyl nucleotides are at positions 1, 3, 4, 6, 7, 9-13, 15, 16, and 18-21 from the 5′ end of the sense strand. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the antisense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the sense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the antisense strand is a d2vd3 nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the sense strand or antisense strand is a 2′-fluoro nucleotide mimic. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the sense strand is a f4P, f2P, or fX nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the antisense strand is a f4P, f2P, or fX nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-O-methyl nucleotide on the sense or antisense strand is a 2′-O-methyl nucleotide mimic.

As shown in FIG. 3F, a ds-siNA may comprise (a) a sense strand consisting of 19 nucleotides, wherein 2′-fluoro nucleotides are at positions 5 and 7-9 from the 5′ end of the sense strand, and wherein 2′-O-methyl nucleotides are at positions 1-4, 6, and 10-19 from the 5′ end of the sense strand; (b) an antisense strand consisting of 21 nucleotides, wherein 2′-fluoro nucleotides are at positions 2, 6, 14, and 16 from the 5′ end of the antisense strand, and wherein 2′-O-methyl nucleotides are at positions 1, 3-5, 7-13, 15, and 17-21 from the 5′ end of the antisense strand. The ds-siNA may further comprise a conjugated moiety attached to the 3′ end of the sense strand. The ds-siNA may further comprise (i) phosphorothioate internucleoside linkages between the nucleotides at positions 1 and 2 and positions 2 and 3 from the 5′ end of the sense strand; and (ii) phosphorothioate internucleoside linkages between the nucleotides at positions 1 and 2; positions 2 and 3; positions 19 and 20; and positions 20 and 21 from the 5′ end of the antisense strand. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the sense strand or antisense strand is a f4P, f2P, or fX nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the sense strand or antisense strand is a f4P nucleotide. In some embodiments, at least 1, 2, 3, or 4 of the 2′-fluoro-nucleotides at positions 2, 6, 14, and 16 from the 5′ end of the antisense strand is a f4P nucleotide. In some embodiments, at least one of the 2′-fluoro-nucleotides at positions 2, 6, 14, and 16 from the 5′ end of the antisense strand is a f4P nucleotide. In some embodiments, at least two of the 2′-fluoro-nucleotides at positions 2, 6, 14, and 16 from the 5′ end of the antisense strand is a f4P nucleotide. In some embodiments, less than or equal to 3 of the 2′-fluoro-nucleotides at positions 2, 6, 14, and 16 from the 5′ end of the antisense strand is a f4P nucleotide. In some embodiments, less than or equal to 2 of the 2′-fluoro-nucleotides at positions 2, 6, 14, and 16 from the 5′ end of the antisense strand is a f4P nucleotide. In some embodiments, the 2′-fluoro-nucleotide at position 2 from the 5′ end of the antisense strand is a f4P nucleotide. In some embodiments, the 2′-fluoro-nucleotide at position 6 from the 5′ end of the antisense strand is a f4P nucleotide. In some embodiments, the 2′-fluoro-nucleotide at position 14 from the 5′ end of the antisense strand is a f4P nucleotide. In some embodiments, the 2′-fluoro-nucleotide at position 16 from the 5′ end of the antisense strand is a f4P nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the sense strand or antisense strand is a f2P nucleotide. In some embodiments, at least 1, 2, 3, or 4 of the 2′-fluoro-nucleotides at positions 2, 6, 14, and 16 from the 5′ end of the antisense strand is a f2P nucleotide. In some embodiments, at least one of the 2′-fluoro-nucleotides at positions 2, 6, 14, and 16 from the 5′ end of the antisense strand is a f2P nucleotide. In some embodiments, at least two of the 2′-fluoro-nucleotides at positions 2, 6, 14, and 16 from the 5′ end of the antisense strand is a f2P nucleotide. In some embodiments, less than or equal to 3 of the 2′-fluoro-nucleotides at positions 2, 6, 14, and 16 from the 5′ end of the antisense strand is a f2P nucleotide. In some embodiments, less than or equal to 2 of the 2′-fluoro-nucleotides at positions 2, 6, 14, and 16 from the 5′ end of the antisense strand is a f2P nucleotide. In some embodiments, the 2′-fluoro-nucleotide at position 2 from the 5′ end of the antisense strand is a f2P nucleotide. In some embodiments, the 2′-fluoro-nucleotide at position 6 from the 5′ end of the antisense strand is a f2P nucleotide. In some embodiments, the 2′-fluoro-nucleotide at position 14 from the 5′ end of the antisense strand is a f2P nucleotide. In some embodiments, the 2′-fluoro-nucleotide at position 16 from the 5′ end of the antisense strand is a f2P nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the sense strand or antisense strand is a fX nucleotide. In some embodiments, at least 1, 2, 3, or 4 of the 2′-fluoro-nucleotides at positions 2, 6, 14, and 16 from the 5′ end of the antisense strand is a fX nucleotide. In some embodiments, at least one of the 2′-fluoro-nucleotides at positions 2, 6, 14, and 16 from the 5′ end of the antisense strand is a fX nucleotide. In some embodiments, at least two of the 2′-fluoro-nucleotides at positions 2, 6, 14, and 16 from the 5′ end of the antisense strand is a fX nucleotide. In some embodiments, less than or equal to 3 of the 2′-fluoro-nucleotides at positions 2, 6, 14, and 16 from the 5′ end of the antisense strand is a fX nucleotide. In some embodiments, less than or equal to 2 of the 2′-fluoro-nucleotides at positions 2, 6, 14, and 16 from the 5′ end of the antisense strand is a fX nucleotide. In some embodiments, the 2′-fluoro-nucleotide at position 2 from the 5′ end of the antisense strand is a fX nucleotide. In some embodiments, the 2′-fluoro-nucleotide at position 6 from the 5′ end of the antisense strand is a fX nucleotide. In some embodiments, the 2′-fluoro-nucleotide at position 14 from the 5′ end of the antisense strand is a fX nucleotide. In some embodiments, the 2′-fluoro-nucleotide at position 16 from the 5′ end of the antisense strand is a fX nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the antisense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the sense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the antisense strand is a d2vd3 nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the sense strand or antisense strand is a 2′-fluoro nucleotide mimic. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the sense strand is a f4P, f2P, or fX nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the antisense strand is a f4P, f2P, or fX nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-O-methyl nucleotide on the sense or antisense strand is a 2′-O-methyl nucleotide mimic.

As shown in FIG. 3G, a ds-siNA may comprise (a) a sense strand consisting of 21 nucleotides, wherein 2′-fluoro nucleotides are at positions 5, 9-11, 14, and 19 from the 5′ end of the sense strand, and wherein 2′-O-methyl nucleotides are at positions 1-4, 6-8, 12, 13, 15-18, 20, and 21 from the 5′ end of the sense strand; and (b) an antisense strand consisting of 23 nucleotides, wherein 2′-flouro nucleodies are at positions 2 and 14 from the 5′ end of the antisense strand, and wherein 2′-O-methyl nucleotides are at positions 1, 3-13, and 15-23 from the 5′ end of the antisense strand. The ds-siNA may further comprise a conjugated moiety attached to the 3′ end of the sense strand. The ds-siNA may further comprise (i) phosphorothioate internucleoside linkages between the nucleotides at positions 1 and 2 and positions 2 and 3 from the 5′ end of the sense strand; and (ii) phosphorothioate internucleoside linkages between the nucleotides at positions 1 and 2; positions 2 and 3; positions 19 and 20; and positions 20 and 21 from the 5′ end of the antisense strand. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a 5′ stabilizing end cap. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the sense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the antisense strand is further modified to contain a phosphorylation blocker. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the sense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 5′ end of the antisense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the sense strand is a d2vd3 nucleotide. In some embodiments, the 2′-O-methyl nucleotide at position 1 from the 3′ end of the antisense strand is a d2vd3 nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the sense strand or antisense strand is a 2′-fluoro nucleotide mimic. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the sense strand is a f4P, f2P, or fX nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-fluoro nucleotides on the antisense strand is a f4P, f2P, or fX nucleotide. In some embodiments, at least 1, 2, 3, 4 or more 2′-O-methyl nucleotide on the sense or antisense strand is a 2′-O-methyl nucleotide mimic.

Any of the siNAs disclosed herein may comprise a sense strand and an antisense strand. The sense strand may comprise a first nucleotide sequence that is 15 to 30 nucleotides in length. The antisense strand may comprise a second nucleotide sequence that is 15 to 30 nucleotides in length.

In some embodiments, the double-stranded short interfering nucleic acid (ds-siNA) molecule comprises: (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and the nucleotide at position 3, 5, 7, 8, 9, 10, 11, 12, 14, 17, and/or 19 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide; and (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide.

In some embodiments, the double-stranded short interfering nucleic acid (ds-siNA) molecule comprises: (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and the nucleotide at position 3, 5, 7, 8, 9, 10, 11, 12, 14, 17, and/or 19 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide; and (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide.

In some embodiments, the double-stranded short interfering nucleic acid (ds-siNA) molecule comprises: (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and the nucleotide at position 7 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide; and (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide.

In some embodiments, the double-stranded short interfering nucleic acid (ds-siNA) molecule comprises: (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and the nucleotide at position 7, 9, 10, and/or 11 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide; and (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide.

In some embodiments, the double-stranded short interfering nucleic acid (ds-siNA) molecule comprises: (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide; and (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and the nucleotide at position 2, 5, 6, 8, 10, 14, 16, 17, and/or 18 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide.

In some embodiments, the double-stranded short interfering nucleic acid (ds-siNA) molecule comprises: (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide; and (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and the nucleotide at position 2 of the second nucleotide sequence is a 2′-fluoro nucleotide.

In some embodiments, the double-stranded short interfering nucleic acid (ds-siNA) molecule comprises: (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence: (i) is 15 to 30 nucleotides in length; (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide; and (iii) comprises 1 or more phosphorothioate internucleoside linkage; and (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence: (i) is 15 to 30 nucleotides in length; (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide; and (iii) comprises 1 or more phosphorothioate internucleoside linkage.

In some embodiments, the double-stranded short interfering nucleic acid (ds-siNA) molecule comprises: (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide; and (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide, wherein the ds-siNA may further comprise a phosphorylation blocker, a galactosamine, or 5′-stabilized end cap.

In some embodiments, the double-stranded short interfering nucleic acid (ds-siNA) molecule comprises: (I) a sense strand comprising (A) a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide; and (B) a phosphorylation blocker or a galactosamine; and (II) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence: (a) is 15 to 30 nucleotides in length; and (b) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide.

In some embodiments, the double-stranded short interfering nucleic acid (ds-siNA) molecule comprises: (I) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence: (a) is 15 to 30 nucleotides in length; and (b) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide; and (II) an antisense strand comprising (A) a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide; and (B) a 5′-stabilized end cap.

In some embodiments, the double-stranded short interfering nucleic acid (ds-siNA) molecule comprises: (I) a sense strand comprising (A) a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide; and (B) a phosphorylation blocker or a galactosamine; and (II) an antisense strand comprising (A) a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence: (i) is 15 to 30 nucleotides in length; and (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide; and (B) a 5′-stabilized end cap.

In some embodiments, the double-stranded short interfering nucleic acid (ds-siNA) molecule comprises: (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence comprises a nucleotide sequence of any one SEQ ID NOs: 1-56, 103-158, and 205-260; and (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence comprises a nucleotide sequence of any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the double-stranded short interfering nucleic acid (ds-siNA) molecule comprises: (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence comprises a nucleotide sequence as shown in Tables 1-3; and (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence comprises a nucleotide sequence as shown in Tables 1-3.

In some embodiments, the double-stranded short interfering nucleic acid (ds-siNA) molecule comprises: (a) a sense strand comprising a nucleotide sequence of any one of SEQ ID NOs: 307-362 and 415-444; and (b) an antisense strand comprising a nucleotide sequence of any one of SEQ ID NOs: 363-409, 445-533, and 536-539. In some embodiments, the ds-siNA molecule comprises a double-stranded molecule as identified by the duplex ID (e.g., ds-siNA-001 to ds-siNA-0178) shown in Tables 6 and 10.

Further disclosed herein are compositions comprising two or more of the siNA molecules described herein.

Further disclosed herein are compositions comprising any of the siNA molecule described and a pharmaceutically acceptable carrier or diluent.

Further disclosed herein are compositions comprising two or more of the siNA molecules described herein for use as a medicament.

Further disclosed herein are compositions comprising any of the siNA molecule described and a pharmaceutically acceptable carrier or diluent for use as a medicament.

Further disclosed herein are methods of treating a disease in a subject in need thereof, the method comprising administering to the subject any of the siNA molecules described herein.

Further disclosed herein are uses of any of the siNA molecules described herein in the manufacture of a medicament for treating a disease.

Short Interfering Nucleic Acid (siNA) Molecules

As indicated above, the present disclosure provides siNA molecules comprising modified nucleotides. Any of the siNA molecules described herein may be double-stranded siNA (ds-siNA) molecules. The terms “siNA molecules” and “ds-siNA molecules” may be used interchangeably. In some embodiments, the ds-siNA molecules comprise a sense strand and an antisense strand.

Further disclosed herein are siNA molecules comprising (a) at least one phosphorylation blocker, conjugated moiety, or 5′-stabilized end cap; and (b) a short interfering nucleic acid (siNA). In some embodiments, the phosphorylation blocker is a phosphorylation blocker disclosed herein. In some embodiments, the conjugated moiety is a galactosamine disclosed herein. In some embodiments, the 5′-stabilized end cap is a 5′-stabilized end cap disclosed herein. The siNA may comprise any of the first nucleotide, second nucleotide, sense strand, or antisense strand sequences disclosed herein. The siNA may comprise 5 to 100, 5 to 90, 10 to 100, 10 to 90, 10 to 80, 10 to 70, 10 to 60, 10 to 50, 10 to 30, 10 to 25, 15 to 100, 15 to 90, 15 to 80, 15 to 70, 15 to 60, 15 to 50, 15 to 30, or 15 to 25 nucleotides. The siNA may comprise at least 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 nucleotides. The siNA may comprise less than or equal to 50, 45, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, or 19 nucleotides. The nucleotides may be modified nucleotides. The siNA may be single stranded. The siNA may be double stranded. The siNA may comprise (a) a sense strand comprising 15 to 30, 15 to 25, 15 to 24, 15 to 23, 15 to 22, 15 to 21, 17 to 30, 17 to 25, 17 to 24, 17 to 23, 17 to 22, 17 to 21, 18 to 30, 18 to 25, 18 to 24, 18 to 23, 18 to 22, 18 to 21, 19 to 30, 19 to 25, 19 to 24, 19 to 23, 19 to 22, 19 to 21, 20 to 25, 20 to 24, 20 to 23, 21 to 25, 21 to 24, or 21 to 23 nucleotides; and (b) an antisense strand comprising 15 to 30, 15 to 25, 15 to 24, 15 to 23, 15 to 22, 15 to 21, 17 to 30, 17 to 25, 17 to 24, 17 to 23, 17 to 22, 17 to 21, 18 to 30, 18 to 25, 18 to 24, 18 to 23, 18 to 22, 18 to 21, 19 to 30, 19 to 25, 19 to 24, 19 to 23, 19 to 22, 19 to 21, 20 to 25, 20 to 24, 20 to 23, 21 to 25, 21 to 24, or 21 to 23 nucleotides. The siNA may comprise (a) a sense strand comprising about 15, 16, 17, 18, 19, 20, 21, 22, or 23 nucleotides; and (b) an antisense strand comprising about 15, 16, 17, 18, 19, 20, 21, 22, or 23 nucleotides. The siNA may comprise (a) a sense strand comprising about 19 nucleotides; and (b) an antisense strand comprising about 21 nucleotides. The siNA may comprise (a) a sense strand comprising about 21 nucleotides; and (b) an antisense strand comprising about 23 nucleotides.

In some embodiments, any of the siNA molecules disclosed herein further comprise one or more linkers independently selected from a phosphodiester (PO) linker, phosphorothioate (PS) linker, phosphorodithioate linker, and PS-mimic linker. In some embodiments, the PS-mimic linker is a sulfur linker. In some embodiments, the linkers are internucleoside linkers. Alternatively, or additionally, the linkers connect a nucleotide of the siNA molecule to at least one phosphorylation blocker, conjugated moiety, or 5′-stabilized end cap. In some embodiments, the linkers connect a conjugated moiety to a phosphorylation blocker or 5′-stabilized end cap.

siNA Sense Strand

Any of the siNA molecules described herein may comprise a sense strand. The sense strand may comprise a first nucleotide sequence. The first nucleotide sequence may be 15 to 30, 15 to 25, 15 to 23, 17 to 23, 19 to 23, or 19 to 21 nucleotides in length. In some embodiments, the first nucleotide sequence is 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. In some embodiments, the first nucleotide sequence is at least 19 nucleotides in length. In some embodiments, the first nucleotide sequence is at least 21 nucleotides in length.

In some embodiments, the sense strand is the same length as the first nucleotide sequence. In some embodiments, the sense strand is longer than the first nucleotide sequence. In some embodiments, the sense strand may further comprise 1, 2, 3, 4, or 5 or more nucleotides than the first nucleotide sequence. In some embodiments, the sense strand may further comprise a deoxyribonucleic acid (DNA). In some embodiments, the DNA is thymine (T). In some embodiments, the sense strand may further comprise a TT sequence. In some embodiments, the sense strand may further comprise one or more modified nucleotides that are adjacent to the first nucleotide sequence. In some embodiments, the one or more modified nucleotides are independently selected from any of the modified nucleotides disclosed herein (e.g., 2′-fluoro nucleotide, 2′-O-methyl nucleotide, 2′-fluoro nucleotide mimic, 2′-O-methyl nucleotide mimic, or a nucleotide comprising a modified nucleobase).

In some embodiments, the first nucleotide sequence comprises 15, 16, 17, 18, 19, 20, 21, 22, 23, or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide. In some embodiments, 70%, 75%, 80%, 85%, 90%, 95% or 100% of the nucleotides in the first nucleotide sequence are modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide. In some embodiments, 100% of the nucleotides in the first nucleotide sequence are modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide. In some embodiments, the 2′-O-methyl nucleotide is a 2′-O-methyl nucleotide mimic. In some embodiments, the 2′-fluoro nucleotide is a 2′-fluoro nucleotide mimic.

In some embodiments, between about 15 to 30, 15 to 25, 15 to 24, 15 to 23, 15 to 22, 15 to 21, 17 to 30, 17 to 25, 17 to 24, 17 to 23, 17 to 22, 17 to 21, 18 to 30, 18 to 25, 18 to 24, 18 to 23, 18 to 22, 18 to 21, 19 to 30, 19 to 25, 19 to 24, 19 to 23, 19 to 22, 19 to 21, 20 to 25, 20 to 24, 20 to 23, 21 to 25, 21 to 24, or 21 to 23 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, between about 2 to 20 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, between about 5 to 25 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, between about 10 to 25 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, between about 12 to 25 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least about 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or 22 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least about 12 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least about 13 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least about 14 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least about 15 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least about 16 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least about 17 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least about 18 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least about 19 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, or 2 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 21 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 20 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 19 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 18 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 17 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 16 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 15 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 14 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 13 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least one modified nucleotide of the first nucleotide sequence is a 2′-O-methyl pyrimidine. In some embodiments, at least 5, 6, 7, 8, 9, or 10 modified nucleotides of the first nucleotide sequence are 2′-O-methyl pyrimidines. In some embodiments, at least one modified nucleotide of the first nucleotide sequence is a 2′-O-methyl purine. In some embodiments, at least 5, 6, 7, 8, 9, or 10 modified nucleotides of the first nucleotide sequence are 2′-O-methyl purines. In some embodiments, the 2′-O-methyl nucleotide is a 2′-O-methyl nucleotide mimic.

In some embodiments, between 2 to 15 modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, between 2 to 10 modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, between 2 to 6 modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, 1 to 6, 1 to 5, 1 to 4, or 1 to 3 modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least 1, 2, 3, 4, 5, or 6 modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least 1 modified nucleotide of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, at least 2 modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least 3 modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least 4 modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least 5 modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least 6 modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, 10, 9, 8, 7, 6, 5, 4, 3 or fewer modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, 10 or fewer modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, 7 or fewer modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, 6 or fewer modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, 5 or fewer modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, 4 or fewer modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, 3 or fewer modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, 2 or fewer modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least one modified nucleotide of the first nucleotide sequence is a 2′-fluoro pyrimidine. In some embodiments, 1, 2, 3, 4, 5, or 6 modified nucleotides of the first nucleotide sequence are 2′-fluoro pyrimidines. In some embodiments, at least one modified nucleotide of the first nucleotide sequence is a 2′-fluoro purine. In some embodiments, 1, 2, 3, 4, 5, or 6 modified nucleotides of the first nucleotide sequence are 2′-fluoro purines. In some embodiments, the 2′-fluoro nucleotide is a 2′-fluoro nucleotide mimic.

In some embodiments, the nucleotide at position 3, 5, 7, 8, 9, 10, 11, 12, 14, 17, and/or 19 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, at least two nucleotides at positions 3, 5, 7, 8, 9, 10, 11, 12, 14, 17, and/or 19 from the 5′ end of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least three nucleotides at positions 3, 5, 7, 8, 9, 10, 11, 12, 14, 17, and/or 19 from the 5′ end of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least four nucleotides at positions 3, 5, 7, 8, 9, 10, 11, 12, 14, 17, and/or 19 from the 5′ end of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least five nucleotides at positions 3, 5, 7, 8, 9, 10, 11, 12, 14, 17, and/or 19 from the 5′ end of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, the nucleotides at positions 3, 5, 7, 8, 9, 10, 11, 12, 14, 17, and/or 19 from the 5′ end of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, the nucleotide at position 3 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 7 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 8 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 9 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 12 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 17 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the 2′-fluoro nucleotide is a 2′-fluoro nucleotide mimic.

In some embodiments, at least 1, 2, 3, 4, 5, 6, or 7 nucleotides at position 3, 5, 7, 8, 9, 10, 11, 12, 14, 17, and/or 19 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at positions 3, 5, 7, 8, 9, 10, 11, 12, 14, 17, and/or 19 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, at least two nucleotides at positions 3, 5, 7, 8, 9, 10, 11, 12, 14, 17, and/or 19 from the 5′ end of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least three nucleotides at positions 3, 5, 7, 8, 9, 10, 11, 12, 14, 17, and/or 19 from the 5′ end of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, the nucleotides at positions 3, 5, 7, 8, 9, 10, 11, 12, 14, 17, and/or 19 from the 5′ end of the first nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, the nucleotide at position 3 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 5 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 7 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 8 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 9 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 10 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 11 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 12 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 14 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 17 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 19 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 3, 7, 8, 9, 12, and/or 17 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 3, 7, 8, and/or 17 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 3, 7, 8, 9, 12, and/or 17 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 5, 7, 8, and/or 9 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 5, 9, 10, 11, 12, and/or 19 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the 2′-fluoro nucleotide is a 2′-fluoro nucleotide mimic.

In some embodiments, the 2′-fluoro nucleotide or 2′-O-methyl nucleotide is a 2′-fluoro or 2′-O-methyl nucleotide mimic. In some embodiments, the 2′-fluoro or 2′-O—methyl nucleotide mimic is a nucleotide mimic of Formula (V):

wherein R1 is independently a nucleobase, aryl, heteroaryl, or H, Q1 and Q2 are independently S or O, R5 is independently —OCD3, —F, or —OCH3, and R6 and R7 are independently H, D, or CD3. In some embodiments, the nucleobase is selected from cytosine, guanine, adenine, uracil, aryl, heteroaryl, and an analogue or derivative thereof.

In some embodiments, the 2′-fluoro or 2′-O-methyl nucleotide mimic is a nucleotide mimic of Formula (16) -Formula (20):

wherein R1 is independently a nucleobase and R2 is F or —OCH3. In some embodiments, the nucleobase is selected from cytosine, guanine, adenine, uracil, aryl, heteroaryl, and an analogue or derivative thereof.

In some embodiments, the first nucleotide sequence comprises, consists of, or consists essentially of ribonucleic acids (RNAs). In some embodiments, the first nucleotide sequence comprises, consists of, or consists essentially of modified RNAs. In some embodiments, the modified RNAs are selected from a 2′-O-methyl RNA and 2′-fluoro RNA. In some embodiments, 15, 16, 17, 18, 19, 20, 21, 22, or 23 modified nucleotides of the first nucleotide sequence are independently selected from 2′-O-methyl RNA and 2′-fluoro RNA.

In some embodiments, the sense strand may further comprise one or more internucleoside linkages independently selected from a phosphodiester (PO) internucleoside linkage, phosphorothioate (PS) internucleoside linkage, phosphorodithioate internucleoside linkage, and PS-mimic internucleoside linkage. In some embodiments, the PS-mimic internucleoside linkage is a sulfo internucleoside linkage.

In some embodiments, the sense strand may further comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 or more phosphorothioate internucleoside linkages. In some embodiments, the sense strand comprises 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, or 3 or fewer phosphorothioate internucleoside linkages. In some embodiments, the sense strand comprises 2 to 10, 2 to 8, 2 to 6, 1 to 5, 1 to 4, 1 to 3, or 1 to 2 phosphorothioate internucleoside linkages. In some embodiments, the sense strand comprises 1 to 2 phosphorothioate internucleoside linkages. In some embodiments, the sense strand comprises 2 to 4 phosphorothioate internucleoside linkages. In some embodiments, at least one phosphorothioate internucleoside linkage is between the nucleotides at positions 1 and 2 from the 5′ end of the first nucleotide sequence. In some embodiments, at least one phosphorothioate internucleoside linkage is between the nucleotides at positions 2 and 3 from the 5′ end of the first nucleotide sequence. In some embodiments, the sense strand comprises two phosphorothioate internucleoside linkages between the nucleotides at positions 1 to 3 from the 5′ end of the first nucleotide sequence.

In some embodiments, any of the sense strands disclosed herein further comprise a monomer selected from Examples 21-32, 36, 37, 40-42, and 44-46 monomers. In some embodiments, any of the sense strands disclosed herein further comprise a 5′ end cap monomer. In some embodiments, the 5′ end cap monomer is selected from Examples 5-11, 33-35, 38, 39, 43, and 49-53 5′ end cap monomers.

In some embodiments, any of the first nucleotide sequences disclosed herein further comprise a monomer selected from Examples 21-32, 36, 37, 40-42, and 44-46 monomers. In some embodiments, any of the first nucleotide sequences disclosed herein further comprise a 5′ end cap monomer. In some embodiments, the 5′ end cap monomer is selected from Examples 5-11, 33-35, 38, 39, 43, and 49-53 5′ end cap monomers.

siNA Antisense Strand

Any of the siNA molecules described herein may comprise an antisense strand. The antisense strand may comprise a second nucleotide sequence. The second nucleotide sequence may be 15 to 30, 15 to 25, 15 to 23, 17 to 23, 19 to 23, or 19 to 21 nucleotides in length. In some embodiments, the second nucleotide sequence is 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. In some embodiments, the second nucleotide sequence is at least 19 nucleotides in length. In some embodiments, the second nucleotide sequence is at least 21 nucleotides in length.

In some embodiments, the antisense strand is the same length as the second nucleotide sequence. In some embodiments, the antisense strand is longer than the second nucleotide sequence. In some embodiments, the antisense strand may further comprise 1, 2, 3, 4, or 5 or more nucleotides than the second nucleotide sequence. In some embodiments, the antisense strand is the same length as the sense strand. In some embodiments, the antisense strand is longer than the sense strand. In some embodiments, the antisense strand may further comprise 1, 2, 3, 4, or 5 or more nucleotides than the sense strand. In some embodiments, the antisense strand may further comprise a deoxyribonucleic acid (DNA). In some embodiments, the DNA is thymine (T). In some embodiments, the antisense strand may further comprise a TT sequence. In some embodiments, the antisense strand may further comprise one or more modified nucleotides that are adjacent to the second nucleotide sequence. In some embodiments, the one or more modified nucleotides are independently selected from any of the modified nucleotides disclosed herein (e.g., 2′-fluoro nucleotide, 2′-O-methyl nucleotide, 2′-fluoro nucleotide mimic, 2′-O-methyl nucleotide mimic, or a nucleotide comprising a modified nucleobase).

In some embodiments, the second nucleotide sequence comprises 15, 16, 17, 18, 19, 20, 21, 22, 23, or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide. In some embodiments, 70%, 75%, 80%, 85%, 90%, 95% or 100% of the nucleotides in the second nucleotide sequence are modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide. In some embodiments, 100% of the nucleotides in the second nucleotide sequence are modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide.

In some embodiments, between about 15 to 30, 15 to 25, 15 to 24, 15 to 23, 15 to 22, 15 to 21, 17 to 30, 17 to 25, 17 to 24, 17 to 23, 17 to 22, 17 to 21, 18 to 30, 18 to 25, 18 to 24, 18 to 23, 18 to 22, 18 to 21, 19 to 30, 19 to 25, 19 to 24, 19 to 23, 19 to 22, 19 to 21, 20 to 25, 20 to 24, 20 to 23, 21 to 25, 21 to 24, or 21 to 23 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, between about 2 to 20 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, between about 5 to 25 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, between about 10 to 25 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, between about 12 to 25 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or 22 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least about 12 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least about 13 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least about 14 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least about 15 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least about 16 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least about 17 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least about 18 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least about 19 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, or 2 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 21 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 20 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 19 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 18 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 17 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 16 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 15 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 14 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, less than or equal to 13 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides. In some embodiments, at least one modified nucleotide of the second nucleotide sequence is a 2′-O-methyl pyrimidine. In some embodiments, at least 5, 6, 7, 8, 9, or 10 modified nucleotides of the second nucleotide sequence are 2′-O-methyl pyrimidines. In some embodiments, at least one modified nucleotide of the second nucleotide sequence is a 2′-O-methyl purine. In some embodiments, at least 5, 6, 7, 8, 9, or 10 modified nucleotides of the second nucleotide sequence are 2′-O-methyl purines. In some embodiments, the 2′-O-methyl nucleotide is a 2′-O-methyl nucleotide mimic.

In some embodiments, between 2 to 15 modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, between 2 to 10 modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, between 2 to 6 modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, 1 to 6, 1 to 5, 1 to 4, or 1 to 3 modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least 1, 2, 3, 4, 5, or 6 modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least 1 modified nucleotide of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, at least 2 modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least 3 modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least 4 modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least 5 modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, 10, 9, 8, 7, 6, 5, 4, 3 or fewer modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, 10 or fewer modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, 7 or fewer modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, 6 or fewer modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, 5 or fewer modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, 4 or fewer modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, 3 or fewer modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, 2 or fewer modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least one modified nucleotide of the second nucleotide sequence is a 2′-fluoro pyrimidine. In some embodiments, 1, 2, 3, 4, 5, or 6 modified nucleotides of the second nucleotide sequence are 2′-fluoro pyrimidines. In some embodiments, at least one modified nucleotide of the second nucleotide sequence is a 2′-fluoro purine. In some embodiments, 1, 2, 3, 4, 5, or 6 modified nucleotides of the second nucleotide sequence are 2′-fluoro purines. In some embodiments, the 2′-fluoro nucleotide is a 2′-fluoro nucleotide mimic.

In some embodiments, the 2′-fluoro nucleotide or 2′-O-methyl nucleotide is a 2′-fluoro or 2′-O-methyl nucleotide mimic. In some embodiments, the 2′-fluoro or 2′-O—methyl nucleotide mimic is a nucleotide mimic of Formula (V):

wherein R1 is independently a nucleobase, aryl, heteroaryl, or H, Q1 and Q2 are independently S or O, R5 is independently —OCD3, —F, or —OCH3, and R6 and R7 are independently H, D, or CD3. In some embodiments, the nucleobase is selected from cytosine, guanine, adenine, uracil, aryl, heteroaryl, and an analogue or derivative thereof.

In some embodiments, the 2′-fluoro or 2′-O-methyl nucleotide mimic is a nucleotide mimic of Formula (16) -Formula (20):

wherein R1 is a nucleobase and R2 is independently F or —OCH3. In some embodiments, the nucleobase is selected from cytosine, guanine, adenine, uracil, aryl, heteroaryl, and an analogue or derivative thereof.

In some embodiments, at least 1, 2, 3, 4, 5, 6, 7, 8, or 9 nucleotides at position 2, 5, 6, 8, 10, 14, 16, 17, and/or 18 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 2, 5, 6, 8, 10, 14, 16, 17, and/or 18 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, at least two nucleotides at positions 2, 5, 6, 8, 10, 14, 16, 17, and/or 18 from the 5′ end of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least three nucleotides at positions 2, 5, 6, 8, 10, 14, 16, 17, and/or 18 from the 5′ end of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least four nucleotides at positions 2, 5, 6, 8, 10, 14, 16, 17, and/or 18 from the 5′ end of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, at least five nucleotides at positions 2, 5, 6, 8, 10, 14, 16, 17, and/or 18 from the 5′ end of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, the nucleotides at positions 2 and/or 14 from the 5′ end of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, the nucleotides at positions 2, 6, and/or 16 from the 5′ end of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, the nucleotides at positions 2, 6, 14, and/or 16 from the 5′ end of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, the nucleotides at positions 2, 6, 10, 14, and/or 18 from the 5′ end of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, the nucleotides at positions 2, 5, 8, 14, and/or 17 from the 5′ end of the second nucleotide sequence are 2′-fluoro nucleotides. In some embodiments, the nucleotide at position 2 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 5 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 6 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 8 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 10 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 14 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 16 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 17 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the nucleotide at position 18 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide. In some embodiments, the 2′-fluoro nucleotide is a 2′-fluoro nucleotide mimic.

In some embodiments, the nucleotides in the second nucleotide sequence are arranged in an alternating 1:3 modification pattern, wherein 1 nucleotide is a 2′-fluoro nucleotide and 3 nucleotides are 2′-O-methyl nucleotides, and wherein the alternating 1:3 modification pattern occurs at least 2 times. In some embodiments, the alternating 1:3 modification pattern occurs 2-5 times. In some embodiments, at least two of the alternating 1:3 modification pattern occur consecutively. In some embodiments, at least two of the alternating 1:3 modification pattern occurs nonconsecutively. In some embodiments, at least 1, 2, 3, 4, or 5 alternating 1:3 modification pattern begins at nucleotide position 2, 6, 10, 14, and/or 18 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 2 from the 5′ end of the antisense strand. In some embodiments, wherein at least one alternating 1:3 modification pattern begins at nucleotide position 6 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 10 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 14 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:3 modification pattern begins at nucleotide position 18 from the 5′ end of the antisense strand. In some embodiments, the 2′-fluoro nucleotide is a 2′-fluoro nucleotide mimic.

In some embodiments, the nucleotides in the second nucleotide sequence are arranged in an alternating 1:2 modification pattern, wherein 1 nucleotide is a 2′-fluoro nucleotide and 2 nucleotides are 2′-O-methyl nucleotides, and wherein the alternating 1:2 modification pattern occurs at least 2 times. In some embodiments, the alternating 1:2 modification pattern occurs 2-5 times. In some embodiments, at least two of the alternating 1:2 modification pattern occurs consecutively. In some embodiments, at least two of the alternating 1:2 modification pattern occurs nonconsecutively. In some embodiments, at least 1, 2, 3, 4, or 5 alternating 1:2 modification pattern begins at nucleotide position 2, 5, 8, 14, and/or 17 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:2 modification pattern begins at nucleotide position 2 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:2 modification pattern begins at nucleotide position 5 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:2 modification pattern begins at nucleotide position 8 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:2 modification pattern begins at nucleotide position 14 from the 5′ end of the antisense strand. In some embodiments, at least one alternating 1:2 modification pattern begins at nucleotide position 17 from the 5′ end of the antisense strand. In some embodiments, the 2′-fluoro nucleotide is a 2′-fluoro nucleotide mimic.

In some embodiments, the second nucleotide sequence comprises, consists of, or consists essentially of ribonucleic acids (RNAs). In some embodiments, the second nucleotide sequence comprises, consists of, or consists essentially of modified RNAs. In some embodiments, the modified RNAs are selected from a 2′-O-methyl RNA and 2′-fluoro RNA. In some embodiments, 15, 16, 17, 18, 19, 20, 21, 22, or 23 modified nucleotides of the second nucleotide sequence are independently selected from 2′-O-methyl RNA and 2′-fluoro RNA. In some embodiments, the 2′-fluoro nucleotide is a 2′-fluoro nucleotide mimic.

In some embodiments, the sense strand may further comprise one or more internucleoside linkages independently selected from a phosphodiester (PO) internucleoside linkage, phosphorothioate (PS) internucleoside linkage, phosphorodithioate internucleoside linkage, and PS-mimic internucleoside linkage. In some embodiments, the PS-mimic internucleoside linkage is a sulfo internucleoside linkage.

In some embodiments, the antisense strand may further comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 or more phosphorothioate internucleoside linkages. In some embodiments, the antisense strand comprises 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, or 3 or fewer phosphorothioate internucleoside linkages. In some embodiments, the antisense strand comprises 2 to 10, 2 to 8, 2 to 6, 1 to 5, 1 to 4, 1 to 3, or 1 to 2 phosphorothioate internucleoside linkages. In some embodiments, the antisense strand comprises 2 to 10, 2 to 8, 2 to 6, 1 to 5, 1 to 4, 1 to 3, or 1 to 2 phosphorothioate internucleoside linkages. In some embodiments, the antisense strand comprises 2 to 8 phosphorothioate internucleoside linkages. In some embodiments, the antisense strand comprises 3 to 8 phosphorothioate internucleoside linkages. In some embodiments, the antisense strand comprises 4 to 8 phosphorothioate internucleoside linkages. In some embodiments, at least one phosphorothioate internucleoside linkage is between the nucleotides at positions 1 and 2 from the 5′ end of the second nucleotide sequence. In some embodiments, at least one phosphorothioate internucleoside linkage is between the nucleotides at positions 2 and 3 from the 5′ end of the second nucleotide sequence. In some embodiments, at least one phosphorothioate internucleoside linkage is between the nucleotides at positions 1 and 2 from the 3′ end of the second nucleotide sequence. In some embodiments, at least one phosphorothioate internucleoside linkage is between the nucleotides at positions 2 and 3 from the 3′ end of the second nucleotide sequence. In some embodiments, the antisense strand comprises two phosphorothioate internucleoside linkages between the nucleotides at positions 1 to 3 from the 5′ end of the first nucleotide sequence. In some embodiments, the antisense strand comprises two phosphorothioate internucleoside linkages between the nucleotides at positions 1 to 3 from the 3′ end of the first nucleotide sequence. In some embodiments, the antisense strand comprises (a) two phosphorothioate internucleoside linkages between the nucleotides at positions 1 to 3 from the 5′ end of the first nucleotide sequence; and (b) two phosphorothioate internucleoside linkages between the nucleotides at positions 1 to 3 from the 3′ end of the first nucleotide sequence.

In some embodiments, at least one end of the ds-siNA is a blunt end. In some embodiments, at least one end of the ds-siNA comprises an overhang, wherein the overhang comprises at least one nucleotide. In some embodiments, both ends of the ds-siNA comprise an overhang, wherein the overhang comprises at least one nucleotide. In some embodiments, the overhang comprises 1 to 5 nucleotides, 1 to 4 nucleotides, 1 to 3 nucleotides, or 1 to 2 nucleotides. In some embodiments, the overhang consists of 1 to 2 nucleotides.

In some embodiments, the first nucleotide sequence comprises a nucleotide sequence of any one SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the second nucleotide sequence comprises a nucleotide sequence of any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the sense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the antisense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 363-409, 445-533, and 536-539.

In some embodiments, any of the antisense strands disclosed herein further comprise a monomer selected from Examples 21-32, 36, 37, 40-42, and 44-46 monomers. In some embodiments, any of the antisense strands disclosed herein further comprise a 5′ end cap monomer. In some embodiments, the 5′ end cap monomer is selected from Examples 5-11, 33-35, 38, 39, 43, and 49-53 5′ end cap monomers.

In some embodiments, any of the secondnucleotide sequences disclosed herein further comprise a monomer selected from Examples 21-32, 36, 37, 40-42, and 44-46 monomers. In some embodiments, any of the second nucleotide sequences disclosed herein further comprise a 5′ end cap monomer. In some embodiments, the 5′ end cap monomer is selected from Examples 5-11, 33-35, 38, 39, 43, and 49-53 5′ end cap monomers.

Modified Nucleotides

Further disclosed herein are siNA molecules comprising one or more modified nucleotides. In some embodiments, any of the siNAs disclosed herein comprise one or more modified nucleotides. In some embodiments, any of the sense strands disclosed herein comprise one or more modified nucleotides. In some embodiments, any of the first nucleotide sequences disclosed herein comprise one or more modified nucleotides. In some embodiments, any of the antisense strands disclosed herein comprise one or more modified nucleotides. In some embodiments, any of the second nucleotide sequences disclosed herein comprise one or more modified nucleotides. In some embodiments, the one or more modified nucleotides is adjacent to the first nucleotide sequence. In some embodiments, at least one modified nucleotide is adjacent to the 5′ end of the first nucleotide sequence. In some embodiments, at least one modified nucleotide is adjacent to the 3′ end of the first nucleotide sequence. In some embodiments, at least one modified nucleotide is adjacent to the 5′ end of the first nucleotide sequence and at least one modified nucleotide is adjacent to the 3′ end of the first nucleotide sequence. In some embodiments, the one or more modified nucleotides is adjacent to the second nucleotide sequence. In some embodiments, at least one modified nucleotide is adjacent to the 5′ end of the second nucleotide sequence. In some embodiments, at least one modified nucleotide is adjacent to the 3′ end of the second nucleotide sequence. In some embodiments, at least one modified nucleotide is adjacent to the 5′ end of the second nucleotide sequence and at least one modified nucleotide is adjacent to the 3′ end of the second nucleotide sequence. In some embodiments, a 2′-O-methyl nucleotide in any of sense strands or first nucleotide sequences disclosed herein is replaced with a modified nucleotide. In some embodiments, a 2′-O-methyl nucleotide in any of antisense strands or second nucleotide sequences disclosed herein is replaced with a modified nucleotide.

In some embodiments, any of the siNA molecules, siNAs, sense strands, first nucleotide sequences, antisense strands, and second nucleotide sequences disclosed herein comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 or more modified nucleotides. In some embodiments, 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 70%, 75%, 80%, 85%, 86%, 87%, 88%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% of the nucleotides in the siNA molecule, siNA, sense strand, first nucleotide sequence, antisense strand, or second nucleotide sequence are modified nucleotides.

In some embodiments, a modified nucleotide is selected from the group consisting of 2′-fluoro nucleotide, 2′-O-methyl nucleotide, 2′-fluoro nucleotide mimic, 2′-O-methyl nucleotide mimic, a locked nucleic acid, and a nucleotide comprising a modified nucleobase.

In some embodiments, any of the siRNAs disclosed herein comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more 2′-fluoro or 2′-O-methyl nucleotide mimics. In some embodiments, any of the sense strands disclosed herein comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more 2′-fluoro or 2′-O-methyl nucleotide mimics. In some embodiments, any of the first nucleotide sequences disclosed herein comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more 2′-fluoro or 2′-O-methyl nucleotide mimics. In some embodiments, any of the antisense strand disclosed herein comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more 2′-fluoro or 2′-O-methyl nucleotide mimics. In some embodiments, any of the second nucleotide sequences disclosed herein comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more 2′-fluoro or 2′-O-methyl nucleotide mimics. In some embodiments, the 2′-fluoro or 2′-O-methyl nucleotide mimic is a nucleotide mimic of Formula (16) -Formula (20):

wherein R1 is a nucleobase and R2 is independently F or —OCH3. In some embodiments, the nucleobase is selected from cytosine, guanine, adenine, uracil, aryl, heteroaryl, and an analogue or derivative thereof. In some embodiments, the siNA molecules disclosed herein comprise at least one 2′-fluoro nucleotide, at least one 2′-O-methyl nucleotide, and at least one 2′-fluoro or 2′-O-methyl nucleotide mimic. In some embodiments, the at least one 2′-fluoro or 2′-O-methyl nucleotide mimic is adjacent to the first nucleotide sequence. In some embodiments, the at least one 2′-fluoro or 2′-O-methyl nucleotide mimic is adjacent to the 5′ end of first nucleotide sequence. In some embodiments, the at least one 2′-fluoro or 2′-O-methyl nucleotide mimic is adjacent to the 3′ end of first nucleotide sequence. In some embodiments, the at least one 2′-fluoro or 2′-O-methyl nucleotide mimic is adjacent to the second nucleotide sequence. In some embodiments, the at least one 2′-fluoro or 2′-O-methyl nucleotide mimic is adjacent to the 5′ end of second nucleotide sequence. In some embodiments, the at least one 2′-fluoro or 2′-O-methyl nucleotide mimic is adjacent to the 3′ end of second nucleotide sequence. In some embodiments, the first nucleotide sequence does not comprise a 2′-fluoro nucleotide mimic. In some embodiments, the first nucleotide sequence does not comprise a 2′-O-methyl nucleotide mimic. In some embodiments, the second nucleotide sequence does not comprise a 2′-fluoro nucleotide mimic. In some embodiments, the second nucleotide sequence does not comprise a 2′-O-methyl nucleotide mimic.

In some embodiments, any of the siRNAs disclosed herein comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more locked nucleic acids. In some embodiments, any of the sense strands disclosed herein comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more locked nucleic acids. In some embodiments, any of the first nucleotide sequences disclosed herein comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more locked nucleic acids. In some embodiments, any of the antisense strand disclosed herein comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more locked nucleic acids. In some embodiments, any of the second nucleotide sequences disclosed herein comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more locked nucleic acids. In some embodiments, the locked nucleic acid is selected from

where R is H or alkyl (or AmNA(N-Me)) when R is alkyl);

wherein B is a nucleobase. In some embodiments, any of the siRNAs, sense strands, first nucleotide sequences, antisense strands, or second nucleotide sequences disclosed herein comprise at least modified nucleotide that is

In some embodiments, any of the siRNAs, sense strands, first nucleotide sequences, antisense strands, or second nucleotide sequences disclosed herein comprise at least modified nucleotide that is

In some embodiments, any of the siRNAs, sense strands, first nucleotide sequences, antisense strands, or second nucleotide sequences disclosed herein comprise at least modified nucleotide that is

where R is H or alkyl (or AmNA(N-Me)) when R is alkyl). In some embodiments, any of the siRNAs, sense strands, first nucleotide sequences, antisense strands, or second nucleotide sequences disclosed herein comprise at least modified nucleotide that is

In some embodiments, any of the siRNAs, sense strands, first nucleotide sequences, antisense strands, or second nucleotide sequences disclosed herein comprise at least modified nucleotide that is

wherein B is a nucleobase.

Phosphorylation Blocker

Further disclosed herein are siNA molecules comprising a phosphorylation blocker. In some embodiments, a 2′-O-methyl nucleotide in any of sense strands or first nucleotide sequences disclosed herein is replaced with a nucleotide containing a phosphorylation blocker. In some embodiments, a 2′-O-methyl nucleotide in any of antisense strands or second nucleotide sequences disclosed herein is replaced with a nucleotide containing a phosphorylation blocker. In some embodiments, a 2′-O-methyl nucleotide in any of sense strands or first nucleotide sequences disclosed herein is further modified to contain a phosphorylation blocker. In some embodiments, a 2′-O-methyl nucleotide in any of antisense strands or second nucleotide sequences disclosed herein is further modified to contain a phosphorylation blocker.

In some embodiments, any of the siNA molecules disclosed herein comprise a phosphorylation blocker of Formula (IV):

wherein R1 is a nucleobase, R4 is —O—R30 or —NR31R32, R30 is C1-C8 substituted or unsubstituted alkyl; and R31 and R32 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring.

In some embodiments, any of the siNA molecules disclosed herein comprise a phosphorylation blocker of Formula (IV):

wherein R1 is a nucleobase, and R4 is —OCH3 or —N(CH2CH2)2O.

In some embodiments, a siNA molecule comprises (a) a phosphorylation blocker of Formula (IV):

wherein R1 is a nucleobase, R4 is —O—R30 or —NR31R32, R30 is C1-C8 substituted or unsubstituted alkyl; and R31 and R32 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring; and (b) a short interfering nucleic acid (siNA), wherein the phosphorylation blocker is conjugated to the siNA.

In some embodiments, a siNA molecule comprises (a) a phosphorylation blocker of Formula (IV):

wherein R1 is a nucleobase, and R4 is —OCH3 or —N(CH2CH2)2O; and (b) a short interfering nucleic acid (siNA), wherein the phosphorylation blocker is conjugated to the siNA.

In some embodiments, the phosphorylation blocker is attached to the 3′ end of the sense strand or first nucleotide sequence. In some embodiments, the phosphorylation blocker is attached to the 3′ end of the sense strand or first nucleotide sequence via 1, 2, 3, 4, or 5 or more linkers. In some embodiments, the phosphorylation blocker is attached to the 5′ end of the sense strand or first nucleotide sequence. In some embodiments, the phosphorylation blocker is attached to the 5′ end of the sense strand or first nucleotide sequence via 1, 2, 3, 4, or 5 or more linkers. In some embodiments, the phosphorylation blocker is attached to the 3′ end of the antisense strand or second nucleotide sequence. In some embodiments, the phosphorylation blocker is attached to the 3′ end of the antisense strand or second nucleotide sequence via 1, 2, 3, 4, or 5 or more linkers. In some embodiments, the phosphorylation blocker is attached to the 5′ end of the antisense strand or second nucleotide sequence. In some embodiments, the phosphorylation blocker is attached to the 5′ end of the antisense strand or second nucleotide sequence via 1, 2, 3, 4, or 5 or more linkers. In some embodiments, the one or more linkers are independently selected from the group consisting of a phosphodiester linker, phosphorothioate linker, and phosphorodithioate linker.

Conjugated Moiety

Further disclosed herein are siNA molecules comprising a conjugated moiety. In some embodiments, the conjugated moiety is selected from galactosamine, peptides, proteins, sterols, lipids, phospholipids, biotin, phenoxazines, active drug substance, cholesterols, phenanthridine, anthraquinone, acridine, fluoresceins, rhodamines, coumarins, and dyes. In some embodiments, the conjugated moiety is attached to the 3′ end of the sense strand or first nucleotide sequence. In some embodiments, the conjugated moiety is attached to the 3′ end of the sense strand or first nucleotide sequence via 1, 2, 3, 4, or 5 or more linkers. In some embodiments, the conjugated moiety is attached to the 5′ end of the sense strand or first nucleotide sequence. In some embodiments, the conjugated moiety is attached to the 5′ end of the sense strand or first nucleotide sequence via 1, 2, 3, 4, or 5 or more linkers. In some embodiments, the conjugated moiety is attached to the 3′ end of the antisense strand or second nucleotide sequence. In some embodiments, the conjugated moiety is attached to the 3′ end of the antisense strand or second nucleotide sequence via 1, 2, 3, 4, or 5 or more linkers. In some embodiments, the conjugated moiety is attached to the 5′ end of the antisense strand or second nucleotide sequence. In some embodiments, the conjugated moiety is attached to the 5′ end of the antisense strand or second nucleotide sequence via 1, 2, 3, 4, or 5 or more linkers. In some embodiments, the one or more linkers are independently selected from the group consisting of a phosphodiester linker, phosphorothioate linker, and phosphorodithioate linker.

In some embodiments, the conjugated moiety is galactosamine. In some embodiments, any of the siNAs disclosed herein are attached to a conjugated moiety that is galactosamine In some embodiments, the galactosamine is N-acetylgalactosamine (GalNAc). In some embodiments, any of the siNA molecules disclosed herein comprise GalNAc. In some embodiments, the GalNAc is of Formula (VI):

wherein m is 1, 2, 3, 4, or 5; each n is independently 1 or 2; p is 0 or 1; each R is independently H or a first protecting group; each Y is independently selected from —O—P(═O)(SH)—, —O—P(═O)(O)—, —O—P(═O)(OH)—, —O—P(S)S—, and —O—; Z is H or a second protecting group; either L is a linker or L and Y in combination are a linker; and A is H, OH, a third protecting group, an activated group, or an oligonucleotide. In some embodiments, the first protecting group is acetyl. In some embodiments, the second protecting group is trimethoxytrityl (TMT). In some embodiments, the activated group is a phosphoramidite group. In some embodiments, the phosphoramidite group is a cyanoethoxy N,N-diisopropylphosphoramidite group. In some embodiments, the linker is a C6—NH2 group. In some embodiments, A is a short interfering nucleic acid (siNA) or siNA molecule. In some embodiments, m is 3. In some embodiments, R is H, Z is H, and n is 1. In some embodiments, R is H, Z is H, and n is 2.

In some embodiments, the GalNAc is of Formula (VII):

wherein each n is independently 1 or 2.

In some embodiments, the galactosamine is attached to the 3′ end of the sense strand or first nucleotide sequence. In some embodiments, the galactosamine is attached to the 3′ end of the sense strand or first nucleotide sequence via 1, 2, 3, 4, or 5 or more linkers. In some embodiments, the galactosamine is attached to the 5′ end of the sense strand or first nucleotide sequence. In some embodiments, the galactosamine is attached to the 5′ end of the sense strand or first nucleotide sequence via 1, 2, 3, 4, or 5 or more linkers. In some embodiments, the galactosamine is attached to the 3′ end of the antisense strand or second nucleotide sequence. In some embodiments, the galactosamine is attached to the 3′ end of the antisense strand or second nucleotide sequence via 1, 2, 3, 4, or 5 or more linkers. In some embodiments, the galactosamine is attached to the 5′ end of the antisense strand or second nucleotide sequence. In some embodiments, the galactosamine is attached to the 5′ end of the antisense strand or second nucleotide sequence via 1, 2, 3, 4, or 5 or more linkers. In some embodiments, the one or more linkers are independently selected from the group consisting of a phosphodiester (p or po) linker, phosphorothioate (ps) linker, phosphoramidite (HEG) linker, triethylene glycol (TEG) linker, and/or phosphorodithioate linker. In some embodiments, the one or more linkers are independently selected from the group consisting of p-(PS)2, (PS)2-p-TEG-p, (PS)2-p-HEG-p, and (PS)2-p-(HEG-p)2.

In some embodiments, the conjugated moiety is a lipid moiety. In some embodiments, any of the siNAs disclosed herein are attached to a conjugated moiety that is a lipid moiety. Examples of lipid moieties include, but are not limited to, a cholesterol mnoiety, a thioether, e.g., hexyl-S-tritylthiol, a thiocholesterol, an aliphatic chain, e.g., dodecandiol or undecyl residues a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethylammonium 1-di-O-hexadecyl-rac-glycero-S-H-phosphonate, a polyamine or a polyethylene glycol chain, adamantane acetic acid, a palmityl moiety, or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety.

In some embodiments, the conjugated moiety is an active drug substance. In some embodiments, any of the siNAs disclosed herein are attached to a conjugated moiety that is an active drug substance. Examples of active drug substances include, but are not limited to, aspirin, warfarin, phenylbutazone, ibuprofen, suprofen, fenbufen, ketoprofen, (5)-(+)-pranoprofen, carprofen, dansylsarcosine, 2,3,5-triiodobenzoic acid, flufenamic acid, folinic acid, a benzothiadiazide, chlorothiazide, a diazepine, indomethicin, a barbiturate, a cephalosporin, a sulfa drug, an antidiabetic, an antibacterial or an antibiotic.

5′-Stabilized End Cap

Further disclosed herein are siNA molecules comprising a 5′-stabilized end cap. As used herein the terms “5′-stabilized end cap” and “5′ end cap” are used interchangeably. In some embodiments, a 2′-O-methyl nucleotide in any of sense strands or first nucleotide sequences disclosed herein is replaced with a nucleotide containing a 5′-stabilized end cap. In some embodiments, a 2′-O-methyl nucleotide in any of antisense strands or second nucleotide sequences disclosed herein is replaced with a nucleotide containing a 5′-stabilized end cap. In some embodiments, a 2′-O-methyl nucleotide in any of sense strands or first nucleotide sequences disclosed herein is further modified to contain a 5′-stabilized end cap. In some embodiments, a 2′-O-methyl nucleotide in any of antisense strands or second nucleotide sequences disclosed herein is further modified to contain a 5′-stabilized end cap.

In some embodiments, the 5′-stabilized end cap is a 5′ phosphate mimic. In some embodiments, the 5′-stabilized end cap is a modified 5′ phosphate mimic. In some embodiments, the modified 5′ phosphate is a chemically modified 5′ phosphate. In some embodiments, the 5′-stabilized end cap is a 5′-vinyl phosphonate. In some embodiments, the 5′-vinyl phosphonate is a 5′-(E)-vinyl phosphonate or 5′-(Z)-vinyl phosphonate. In some embodiments, the 5′-vinyl phosphonate is a deuterated vinyl phosphonate. In some embodiments, the deuterated vinyl phosphonate is a mono-deuterated vinyl phosphonate. In some embodiments, the deuterated vinyl phosphonate is a di-deuterated vinyl phosphonate. In some embodiments, the 5′-stabilized end cap is a phosphate mimic. Examples of phosphate mimics are disclosed in Parmar et al., 2018, J Med Chem, 61(3):734-744, International Publication Nos. WO2018/045317 and WO2018/044350, and U.S. Pat. No. 10,087,210, each of which is incorporated by reference in its entirety.

In some embodiments, any of the siNA molecules, sense strands, first nucleotide sequences, antisense strands, or second nucleotide sequences disclosed herein comprise a 5′-stabilized end cap of Formula (Ia):

wherein R1 is H, a nucleobase, aryl, or heteroaryl R2 is

—CH═CD-Z, —CD=CH-Z, —CD=CD-Z, —(CR21R22)n-Z, or —(C2-C6 alkenylene)-Z and R20 is H; or R2 and R20 together form a 3- to 7-membered carbocyclic ring substituted with —(CR21R22)n-Z or —(C2-C6 alkenylene)-Z; n is 1, 2, 3, or 4; Z is —ONR23R24, —OP(O)OH(CH2)mCO2R23, —OP(S)OH(CH2)mCO2R23, —P(O)(OH)2, —P(O)(OH)(OCH3), —P(O)(OH)(OCD3), —SO2(CH2)mP(O)(OH)2, —SO2NR23R25, —NR23R24, —NR23SO2R24; either R21 and R22 are independently hydrogen or C1-C6 alkyl, or R21 and R22 together form an oxo group; R23 is hydrogen or C1-C6 alkyl; R24 is —SO2R25 or —C(O)R25; or R23 and R24 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring; R25 is C1-C6 alkyl; and m is 1, 2, 3, or 4. In some embodiments, R1 is an aryl. In some embodiments, the aryl is a phenyl.

In some embodiments, any of the siNA molecules, sense strands, first nucleotide sequences, antisense strands, or second nucleotide sequences disclosed herein comprise a 5′-stabilized end cap of Formula (Ib):

wherein R1 is H, a nucleobase, aryl, or heteroaryl; R2 is

—CH═CD-Z, —CD=CH-Z, —CD=CD-Z, —(CR21R22)n-Z, or —(C2-C6 alkenylene)-Z and R20 is H; or R2 and R20 together form a 3- to 7-membered carbocyclic ring substituted with —(CR21R22)—Z or —(C2-C6 alkenylene)-Z; n is 1, 2, 3, or 4; Z is —ONR23R24, —OP(O)OH(CH2)mCO2R23, —OP(S)OH(CH2)mCO2R23, —P(O)(OH)2, —P(O)(OH)(OCH3), —P(O)(OH)(OCD3), —SO2(CH2)mP(O)(OH)2, —SO2NR23R25, —NR23R24, —NR23SO2R24; either R21 and R22 are independently hydrogen or C1-C6 alkyl, or R21 and R22 together form an oxo group; R23 is hydrogen or C1-C6 alkyl; R24 is —SO2R25 or —C(O)R25; or R23 and R24 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring; R25 is C1-C6 alkyl; and m is 1, 2, 3, or 4. In some embodiments, R1 is an aryl. In some embodiments, the aryl is a phenyl.

In some embodiments, any of the siNA molecules, sense strands, first nucleotide sequences, antisense strands, or second nucleotide sequences disclosed herein comprise a 5′-stabilized end cap of Formula (Ic):

wherein R1 is a nucleobase, aryl, heteroaryl, or H,

    • R2 is

—CH═CD-Z, —CD=CH-Z, —CD=CD-Z, —(CR21R22)—Z, or —(C2-C6 alkenylene)-Z and R20 is hydrogen; or R2 and R20 together form a 3- to 7-membered carbocyclic ring substituted with —(CR21R22)r-Z or —(C2-C6 alkenylene)-Z; n is 1, 2, 3, or 4; Z is —ONR23R24, —OP(O)OH(CH2)mCO2R23, —OP(S)OH(CH2)mCO2R23, —P(O)(OH)2, —P(O)(OH)(OCH3), —P(O)(OH)(OCD3), —SO2(CH2)mP(O)(OH)2, —SO2NR23R21, —NR23R24, or —NR23SO2R24; R21 and R22 either are independently hydrogen or C1-C6 alkyl, or R21 and R22 together form an oxo group; R23 is hydrogen or C1-C6 alkyl; R24 is —SO2R2S or —C(O)R25; or R23 and R24 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring; R25 is C1-C6 alkyl; and m is 1, 2, 3, or 4. In some embodiments, R1 is an aryl. In some embodiments, the aryl is a phenyl.

In some embodiments, any of the siNA molecules, sense strands, first nucleotide sequences, antisense strands, or second nucleotide sequences disclosed herein comprise a 5′-stabilized end cap of Formula (IIa):

wherein R1 is a nucleobase, aryl, heteroaryl, or H, R2 is

R9 is —SO2CH3 or —COCH3, is a double or single bond, R10═—CH2PO3H or —NHCH3, R11 is —CH2— or —CO—, and R12 is H and R13 is CH3 or R12 and R13 together form —CH2CH2CH2—. In some embodiments, R1 is an aryl. In some embodiments, the aryl is a phenyl.

In some embodiments, any of the siNA molecules, sense strands, first nucleotide sequences, antisense strands, or second nucleotide sequences disclosed herein comprise a 5′-stabilized end cap of Formula (IIb):

wherein R1 is a nucleobase, aryl, heteroaryl, or H, R2 is

R9 is —SO2CH3 or —COCH3, is a double or single bond, R10═—CH2PO3H or —NHCH3, R11 is —CH2— or —CO—, and R12 is H and R13 is CH3 or R12 and R13 together form —CH2CH2CH2—. In some embodiments, R1 is an aryl. In some embodiments, the aryl is a phenyl.

In some embodiments, any of the siNA molecules, sense strands, first nucleotide sequences, antisense strands, or second nucleotide sequences disclosed herein comprise a 5′-stabilized end cap of Formula (II):

wherein R1 is a nucleobase, aryl, heteroaryl, or H, L is —CH2—, —CH═CH—, —CO—, or —CH2CH2—, and A is —ONHCOCH3, —ONHSO2CH3, —PO3H, —OP(SOH)CH2CO2H, —SO2CH2PO3H, —SO2NHCH3, —NHSO2CH3, or —N(SO2CH2CH2CH2). In some embodiments, R1 is an aryl. In some embodiments, the aryl is a phenyl.

In some embodiments, any of the siNA molecules, sense strands, first nucleotide sequences, antisense strands, or second nucleotide sequences disclosed herein comprise a 5′-stabilized end cap selected from Examples 5-11, 33-35, 38, 39, 43, and 49-53 5′ end cap monomers.

Further disclosed herein are siNA molecules comprising (a) a 5′-stabilized end cap of Formula (Ia):

wherein R1 is a nucleobase, aryl, heteroaryl, or H; R2 is

—CH═CD-Z, —CD=CH-Z, —CD=CD-Z, —(CR21R22)n-Z, or —(C2-C6 alkenylene)-Z and R20 is H; or R2 and R20 together form a 3- to 7-membered carbocyclic ring substituted with —(CR21R22)-Z or —(C2-C6 alkenylene)-Z; n is 1, 2, 3, or 4; Z is —ONR23R24, —OP(O)OH(CH2)mCO2R23, —OP(S)OH(CH2)mCO2R23, —P(O)(OH)2, —P(O)(OH)(OCH3), —P(O)(OH)(OCD3), —SO2(CH2)mP(O)(OH)2, —SO2NR23R25, —NR23R24, —NR23SO2R24; either R21 and R22 are independently hydrogen or C1-C6 alkyl, or R21 and R22 together form an oxo group; R23 is hydrogen or C1-C6 alkyl; R24 is —SO2R21 or —C(O)R2S; or R23 and R24 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring; R21 is C1-C6 alkyl; and m is 1, 2, 3, or 4; and (b) a short interfering nucleic acid (siNA), wherein the 5′-stabilized end cap is conjugated to the siNA. In some embodiments, R1 is an aryl. In some embodiments, the aryl is a phenyl.

Further disclosed herein are siNA molecules comprising (a) a 5′-stabilized end cap of Formula (Ib):

wherein R1 is a nucleobase, aryl, heteroaryl, or H; R2 is

—CH═CD-Z, —CD=CH-Z, —CD=CD-Z, —(CR21R22)n-Z, or —(C2-C6 alkenylene)-Z and R20 is H; or R2 and R20 together form a 3- to 7-membered carbocyclic ring substituted with —(CR21R22)n-Z or —(C2-C6 alkenylene)-Z; n is 1, 2, 3, or 4; Z is —ONR23R24, —OP(O)OH(CH2)mCO2R23, —OP(S)OH(CH2)mCO2R23, —P(O)(OH)2, —P(O)(OH)(OCH3), —P(O)(OH)(OCD3), —SO2(CH2)mP(O)(OH)2, —SO2NR23R25, —NR23R24, —NR23SO2R24; either R21 and R22 are independently hydrogen or C1-C6 alkyl, or R21 and R22 together form an oxo group; R23 is hydrogen or C1-C6 alkyl; R24 is —SO2R25 or —C(O)R25; or R23 and R24 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring; R25 is C1-C6 alkyl; and m is 1, 2, 3, or 4; and (b) a short interfering nucleic acid (siNA), wherein the 5′-stabilized end cap is conjugated to the siNA. In some embodiments, R1 is an aryl. In some embodiments, the aryl is a phenyl.

Further disclosed herein are siNA molecules comprising (a) a 5′-stabilized end cap of Formula (Ic):

wherein R1 is a nucleobase, aryl, heteroaryl, or H, R2 is

—CH═CD-Z, —CD=CH-Z, —CD=CD-Z, —(CR21R22)—Z, or —(C2-C6 alkenylene)-Z and R20 is hydrogen; or R2 and R20 together form a 3- to 7-membered carbocyclic ring substituted with —(CR21R22)n-Z or —(C2-C6 alkenylene)-Z; n is 1, 2, 3, or 4; Z is —ONR21R24, —OP(O)OH(CH2)mCO2R23, —OP(S)OH(CH2)mCO2R23, —P(O)(OH)2, —P(O)(OH)(OCH3), —P(O)(OH)(OCD3), —SO2(CH2)mP(O)(OH)2, —SO2NR23R21, —NR23R24, or —NR23SO2R24; R21 and R22 either are independently hydrogen or C1-C6 alkyl, or R2 and R22 together form an oxo group; R23 is hydrogen or C1-C6 alkyl; R24 is —SO2R2S or —C(O)R25; or R23 and R24 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring; R25 is C1-C6 alkyl; and m is 1, 2, 3, or 4; and (b) a short interfering nucleic acid (siNA), wherein the 5′-stabilized end cap is conjugated to the siNA. In some embodiments, R1 is an aryl. In some embodiments, the aryl is a phenyl.

In some embodiments, a siNA molecule comprises (a) a 5′-stabilized end cap of

Formula (Ha):

wherein R1 is a nucleobase, aryl, heteroaryl, or H, R2 is

R9 is —SO2CH3 or —COCH3, wherein is a double or single bond, R10═—CH2PO3H or —NHCH3, R11 is —CH2— or —CO—, and R12 is H and R3 is CH3 or R2 and R13 together form —CH2CH2CH2—; and (b) a short interfering nucleic acid (siNA), wherein the 5′-stabilized end cap is conjugated to the siNA. In some embodiments, R1 is an aryl. In some embodiments, the aryl is a phenyl.

In some embodiments, a siNA molecule comprises (a) a 5′-stabilized end cap of Formula (IIb)

wherein R1 is a nucleobase, aryl, heteroaryl, or H, R2 is

R9 is —SO2CH3 or —COCH3, wherein is a double or single bond, R10═—CH2PO3H or —NHCH3, R11 is —CH2— or —CO—, and R12 is H and R13 is CH3 or R12 and R13 together form —CH2CH2CH2—; and (b) a short interfering nucleic acid (siNA), wherein the 5′-stabilized end cap is conjugated to the siNA. In some embodiments, R1 is an aryl. In some embodiments, the aryl is a phenyl.

In some embodiments, a siNA molecule comprises (a) a 5′-stabilized end cap of Formula (III):

wherein R1 is a nucleobase, aryl, heteroaryl, or H, L is ˜CH2—, —CH═CH—, —CO—, or —CH2CH2—, and A is —ONHCOCH3, —ONHSO2CH3, —PO3H, —OP(SOH)CH2CO2H, —SO2CH2PO3H, —SO2NHCH3, —NHSO2CH3, or —N(SO2CH2CH2CH2); and (b) a short interfering nucleic acid (siNA), wherein the 5′-stabilized end cap is conjugated to the siNA. In some embodiments, R1 is an aryl. In some embodiments, the aryl is phenyl.

In some embodiments, any of the siNA molecules disclosed herein comprise a 5′-stabilized end cap selected from the group consisting of Formula (1) to Formula (15), Formula (9X) to Formula (12X), and Formula (9Y) to Formula (12Y):

wherein R1 is a nucleobase, aryl, heteroaryl, or H. In some embodiments, R1 is an aryl. In some embodiments, the aryl is a phenyl.

In some embodiments, any of the siNA molecules disclosed herein comprise a 5′-stabilized end cap selected from the group consisting of Formulas (1A)-(15A), Formulas (9B)-(12B), Formulas (9AX)-(12AX), Formulas (9AY)-(12AY), Formulas (9BX)-(12BX), and Formulas (9BY)-(12BY):

In some embodiments, any of the siNA molecules disclosed herein comprise a 5′-stabilized end cap selected from the group consisting of Formula (21) to Formula (35):

wherein R1 is a nucleobase, aryl, heteroaryl, or H. In some embodiments, R1 is an aryl. In some embodiments, the aryl is a phenyl.

In some embodiments, any of the siNA molecules disclosed herein comprise a 5′-stabilized end cap selected from the group consisting of Formulas (21A)-(35A), Formulas (29B)-(32B), Formulas (29AX)-(32AX), Formulas (29AY)-(32AY), Formulas 29BX 32BX and Formulas 29BY 32BY):

In some embodiments, the 5′-stabilized end cap is attached to the 5′ end of the antisense strand. In some embodiments, the 5′-stabilized end cap is attached to the 5′ end of the antisense strand via 1, 2, 3, 4, or 5 or more linkers. In some embodiments, the one or more linkers are independently selected from the group consisting of a phosphodiester (p or po) linker, phosphorothioate (ps) linker (ps), phosphoramidite (HEG) linker, triethylene glycol (TEG) linker, and/or phosphorodithioate linker. In some embodiments, the one or more linkers are independently selected from the group consisting of p-(PS)2, (PS)2-p-TEG-p, (PS)2-p-HEG-p, and (PS)2-p-(HEG-p)2.

Linker

In some embodiments, any of the siRNAs, sense strands, first nucleotide sequences, antisense strands, and/or second nucleotide sequences disclosed herein comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23 or more internucleoside linkers. In some embodiments, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more internucleoside linkers are independently selected from the group consisting of a phosphodiester (p or po) linker, phosphorothioate (ps) linker, or phosphorodithioate linker.

In some embodiments, any of the siRNAs, sense strands, first nucleotide sequences, antisense strands, and/or second nucleotide sequences disclosed herein further comprise 1, 2, 3, 4 or more linkers that attach a conjugated moiety, phosphorylation blocker, and/or 5′ end cap to the siRNA, sense strand, first nucleotide sequence, antisense strand, and/or second nucleotide sequences. In some embodiments, the 1, 2, 3, 4 or more linkers are independently selected from the group consisting of a phosphodiester (p or po) linker, phosphorothioate (ps) linker, phosphoramidite (HEG) linker, triethylene glycol (TEG) linker, and/or phosphorodithioate linker. In some embodiments, the one or more linkers are independently selected from the group consisting of p-(PS)2, (PS)2-p-TEG-p, (PS)2-p-HEG-p, and (PS)2-p-(HEG-p)2.

Target Gene

Without wishing to be bound by theory, upon entry into a cell, any of the ds-siNA molecules disclosed herein may interact with proteins in the cell to form a RNA-Induced Silencing Complex (RISC). Once the ds-siNA is part of the RISC, the ds-siNA may be unwound to form a single-stranded siNA (ss-siNA). The ss-siNA may comprise the antisense strand of the ds-siNA. The antisense strand may bind to a complementary messenger RNA (mRNA), which results in silencing of the gene that encodes the mRNA.

The target gene may be any gene in a cell. In some embodiments, the target gene is a viral gene. In some embodiments, the viral gene is from a DNA virus. In some embodiments, the DNA virus is a double-stranded DNA (dsDNA) virus. In some embodiments, the dsDNA virus is a hepadnavirus. In some embodiments, the hepadnavirus is a hepatitis B virus (HBV). In some embodiments, the HBV is selected from HBV genotypes A-J.

In some embodiments, the target gene is selected from the S gene or X gene of the HBV. In some embodiments, the HBV has a genome sequence shown in the nucleotide sequence of SEQ ID NO: 410, which corresponds to the nucleotide sequence of GenBank Accession No. U95551.1, which is incorporated by reference in its entirety.

An exemplary HBV genome sequence is shown in SEQ ID NO: 596, corresponding to Genbank Accession No. KC315400.1, which is incorporated by reference in its entirety. Nucleotides 2307. . 3215, 1. . 1623 of SEQ ID NO: 596 correspond to the polymerase/RT gene sequence, which encodes for the polymerase protein. Nucleotides 2848. . 3215,1. . 835 of SEQ ID NO: 596 correspond to the PreS1/S2/S gene sequence, which encodes for the large S protein. Nucleotides 3205. . 3215,1. . 835 of SEQ ID NO: 596 correspond to the PreS2/S gene sequence, which encodes for the middle S protein. Nucleotides 155. . 835 of SEQ ID NO: 596 correspond to the S gene sequence, which encodes the small S protein. Nucleotides 1374. . 1838 of SEQ ID NO: 596 correspond to the X gene sequence, which encodes the X protein. Nucleotides 1814. . 2452 of SEQ ID NO: 596 correspond to the PreC/C gene sequence, which encodes the precore/core protein. Nucleotides 1901. . 2452 of SEQ ID NO: 596 correspond to the C gene sequence, which encodes the core protein. The HBV genome further comprises viral regulatory elements, such as viral promoters (preS2, preS1, Core, and X) and enhancer elements (ENH1 and ENH2). Nucleotides 1624. . 1771 of SEQ ID NO: 596 correspond to ENH2. Nucleotides 1742. . 1849 of SEQ ID NO: 596 correspond to the Core promoter. Nucleotides 1818 . . . 3215,1. . 1930 of SEQ ID NO: 596 correspond to the pregenomic RNA (pgRNA), which encodes the core and polymerase proteins.

In some embodiments, the ASO is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary or hybridizes to a viral target RNA sequence that begins in an X region of HBV or in an S region of HBV. The viral target may, e.g., begin at the 5′-end of target-site in acc. KC315400.1 (genotype B, “gt B”), or in any one of genotypes A, C, or D. The skilled person would understand the HBV position, e.g., as described in Wing-Kin Sung, et al., Nature Genetics 44:765 (2012). In some embodiments, the S region is defined as from the beginning of small S protein (in genotype B KC315400.1 isolate, position #155) to before beginning of X protein (in genotype B KC315400.1 isolate, position #1373). In some embodiments, the X region is defined as from the beginning X protein (in genotype B KC315400.1 isolate, position #1374) to end of DR2 site (in genotype B KC315400.1 isolate, position #1603).

In some embodiments, the second nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to 15 to 30, 15 to 25, 15 to 23, 15 to 22, 15 to 21, 17 to 25, 17 to 23, 17 to 22, 17 to 21, or 19 to 21 nucleotides within positions 200-720 or 1100-1700 of SEQ ID NO: 410. In some embodiments, the second nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to 15 to 30, 15 to 25, 15 to 23, 15 to 22, 15 to 21, 17 to 25, 17 to 23, 17 to 22, 17 to 21, or 19 to 21 nucleotides within positions 200-280, 300-445, 460-510, 650-720, 1170-1220, 1250-1300, or 1550-1630 of SEQ ID NO: 410. In some embodiments, the second nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to 15 to 30, 15 to 25, 15 to 23, 15 to 22, 15 to 21, 17 to 25, 17 to 23, 17 to 22, 17 to 21, or 19 to 21 nucleotides within positions 200-230, 250-280, 300-330, 370-400, 405-445, 460-500, 670-700, 1180-1210, 1260-1295, 1520-1550, or 1570-1610 of SEQ ID NO: 410. In some embodiments, the second nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to 15 to 30, 15 to 25, 15 to 23, 15 to 22, 15 to 21, 17 to 25, 17 to 23, 17 to 22, 17 to 21,or 19 to 21 nucleotides starting at position 203, 206, 254, 305, 375, 409, 412, 415, 416, 419, 462, 466, 467, 674, 676, 1182, 1262, 1263, 1268, 1526, 1577, 1578, 1580, 1581, 1583, or 1584 of SEQ ID NO: 410.

In some embodiments, the first nucleotide is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to a nucleotide region within SEQ ID NO: 410, with the exception that the thymines (Ts) in SEQ ID NO: 410 are replaced with uracil (U). In some embodiments, the first nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to 15 to 30, 15 to 25, 15 to 23, 15 to 22, 15 to 21, 17 to 25, 17 to 23, 17 to 22, 17 to 21, or 19 to 21 nucleotides within positions 200-720 or 1100-1700 of SEQ ID NO: 410. In some embodiments, the first nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to 15 to 30, 15 to 25, 15 to 23, 15 to 22, 15 to 21, 17 to 25, 17 to 23, 17 to 22, 17 to 21,or 19 to 21 nucleotides within positions 200-280, 300-445, 460-510, 650-720, 1170-1220, 1250-1300, or 1550-1630 of SEQ ID NO: 410. In some embodiments, the first nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to 15 to 30, 15 to 25, 15 to 23, 15 to 22, 15 to 21, 17 to 25, 17 to 23, 17 to 22, 17 to 21, or 19 to 21 nucleotides within positions 200-230, 250-280, 300-330, 370-400, 405-445, 460-500, 670-700, 1180-1210, 1260-1295, 1520-1550, or 1570-1610 of SEQ ID NO: 410. In some embodiments, the first nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to 15 to 30, 15 to 25, 15 to 23, 15 to 22, 15 to 21, 17 to 25, 17 to 23, 17 to 22, 17 to 21, or 19 to 21 nucleotides starting at position 203, 206, 254, 305, 375, 409, 412, 415, 416, 419, 462, 466, 467, 674, 676, 1182, 1262, 1263, 1268, 1526, 1577, 1578, 1580, 1581, 1583, or 1584 of SEQ ID NO: 410.

In some embodiments, the target gene is involved in liver metabolism. In some embodiments, the target gene is an inhibitor of the electron transport chain. In some embodiments, the target gene encodes the MCJ protein (MCJ/DnaJC15 or Methylation-Controlled J protein). In some embodiments, the MCJ protein is encoded by the mRNA sequence of SEQ ID NO: 411, which corresponds to the nucleotide sequence of GenBank Accession No. NM_013238.3, which is incorporated by reference in its entirety.

In some embodiments, the target gene is TAZ. In some embodiments, TAZ comprises the nucleotide sequence of SEQ ID NO: 412, which corresponds to the nucleotide sequence of GenBank Accession No. NM_000116.5, which is incorporated by reference in its entirety.

In some embodiments, the target gene is angiopoietin like 3 (ANGPTL3). In some embodiments, ANGPTL3 comprises the nucleotide sequence of SEQ ID NO: 413, which corresponds to the nucleotide sequence of GenBank Accession No. NM_014495.4, which is incorporated by reference in its entirety.

In some embodiments, the target gene is diacylglycerol acyltransferase 2 (DGAT2). In some embodiments, DGAT2 comprises the nucleotide sequence of SEQ ID NO: 414, which corresponds to the nucleotide sequence of GenBank Accession No. NM_001253891.1, which is incorporated by reference in its entirety.

Compositions

As indicated above, the present disclosure provides compositions comprising any of the siNA molecules, sense strands, antisense strands, first nucleotide sequences, or second nucleotide sequences described herein. The compositions may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or more siNA molecules described herein. The compositions may comprise a first nucleotide sequence comprising a nucleotide sequence of any one SEQ ID NOs: 1-56, 103-158, and 205-260. In some embodiments, the composition comprises a second nucleotide sequence comprising a nucleotide sequence of any one of SEQ ID NOs: 57-102, 159-204, and 261-306. In some embodiments, the composition comprises a sense strand comprising a nucleotide sequence of any one of SEQ ID NOs: 307-362 and 415-444. In some embodiments, the composition comprises an antisense strand comprising a nucleotide sequence of any one of SEQ ID NOs: 363-409, 445-533, and 536-539.

Alternatively, the compositions may comprise (a) a phosphorylation blocker; and (b) a short interfering nucleic acid (siNA). In some embodiments, the phosphorylation blocker is any of the phosphorylation blockers disclosed herein. In some embodiments, the siNA is any of the siNAs disclosed herein. In some embodiments, the siNA comprises any of the sense strands, antisense strands, first nucleotide sequences, or second nucleotide sequences described herein. In some embodiments, the siNA comprises any of the sense strands, antisense strands, first nucleotide sequences, or second nucleotide sequences described herein. In some embodiments, the siNA comprises one or more modified nucleotides. In some embodiments, the one or more modified nucleotides are independently selected from a 2′-fluoro nucleotide and a 2′-O-methyl nucleotide. In some embodiments, the 2′-fluoro nucleotide or the 2′-O-methyl nucleotide is independently selected from any of the 2′-fluoro or 2′-O-methyl nucleotide mimics disclosed herein. In some embodiments, the siNA comprises a nucleotide sequence comprising any of the modification patterns disclosed herein.

In some embodiments, the composition comprises (a) a conjugated moiety; and (b) a short interfering nucleic acid (siNA). In some embodiments, the conjugated moiety is any of the galactosamines disclosed herein. In some embodiments, the siNA is any of the siNAs disclosed herein. In some embodiments, the siNA comprises any of the sense strands, antisense strands, first nucleotide sequences, or second nucleotide sequences described herein. In some embodiments, the siNA comprises any of the sense strands, antisense strands, first nucleotide sequences, or second nucleotide sequences described herein. In some embodiments, the siNA comprises one or more modified nucleotides. In some embodiments, the one or more modified nucleotides are independently selected from a 2′-fluoro nucleotide and a 2′-O-methyl nucleotide. In some embodiments, the 2′-fluoro nucleotide or the 2′-O-methyl nucleotide is independently selected from any of the 2′-fluoro or 2′-O-methyl nucleotide mimics disclosed herein. In some embodiments, the siNA comprises a nucleotide sequence comprising any of the modification patterns disclosed herein.

In some embodiments, the composition comprises (a) a 5′-stabilized end cap; and (b) a short interfering nucleic acid (siNA). In some embodiments, the 5′-stabilized end cap is any of the 5-stabilized end caps disclosed herein. In some embodiments, the siNA is any of the siNAs disclosed herein. In some embodiments, the siNA comprises any of the sense strands, antisense strands, first nucleotide sequences, or second nucleotide sequences described herein. In some embodiments, the siNA comprises one or more modified nucleotides. In some embodiments, the one or more modified nucleotides are independently selected from a 2′-fluoro nucleotide and a 2′-O-methyl nucleotide. In some embodiments, the 2′-fluoro nucleotide or the 2′-O-methyl nucleotide is independently selected from any of the 2′-fluoro or 2′-O-methyl nucleotide mimics disclosed herein. In some embodiments, the siNA comprises a nucleotide sequence comprising any of the modification patterns disclosed herein.

In some embodiments, the composition comprises (a) at least one phosphorylation blocker, conjugated moiety, or 5′-stabilized end cap; and (b) a short interfering nucleic acid (siNA). In some embodiments, the phosphorylation blocker is any of the phosphorylation blockers disclosed herein. In some embodiments, the conjugated moiety is any of the galactosamines disclosed herein. In some embodiments, the 5′-stabilized end cap is any of the 5-stabilized end caps disclosed herein. In some embodiments, the siNA is any of the siNAs disclosed herein. In some embodiments, the siNA comprises any of the sense strands, antisense strands, first nucleotide sequences, or second nucleotide sequences described herein. In some embodiments, the siNA comprises one or more modified nucleotides. In some embodiments, the one or more modified nucleotides are independently selected from a 2′-fluoro nucleotide and a 2′-O-methyl nucleotide. In some embodiments, the 2′-fluoro nucleotide or the 2′-O-methyl nucleotide is independently selected from any of the 2′-fluoro or 2′-O-methyl nucleotide mimics disclosed herein. In some embodiments, the siNA comprises a nucleotide sequence comprising any of the modification patterns disclosed herein.

The composition may be a pharmaceutical composition. In some embodiments, the pharmaceutical composition comprises an amount of one or more of the siNA molecules described herein formulated with one or more pharmaceutically acceptable carriers (additives) and/or diluents. The pharmaceutical compositions may be specially formulated for administration in solid or liquid form, including those adapted for the following: (1) oral administration, for example, drenches (aqueous or non-aqueous solutions or suspensions), tablets, e.g., those targeted for buccal, sublingual, and systemic absorption, boluses, powders, granules, pastes for application to the tongue; (2) parenteral administration, for example, by subcutaneous, intramuscular, intravenous or epidural injection as, for example, a sterile solution or suspension, or sustained-release formulation; (3) topical application, for example, as a cream, ointment, or a controlled-release patch or spray applied to the skin; (4) intravaginally or intrarectally, for example, as a pessary, cream or foam; (5) sublingually; (6) ocularly; (7) transdermally; or (8) nasally.

The phrase “therapeutically-effective amount” as used herein means that amount of a compound, material, or composition comprising a siNA of the present disclosure which is effective for producing some desired therapeutic effect in at least a sub-population of cells in an animal at a reasonable benefit/risk ratio applicable to any medical treatment.

The phrase “pharmaceutically acceptable” is employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.

Wetting agents, emulsifiers and lubricants, such as sodium lauryl sulfate and magnesium stearate, as well as coloring agents, release agents, coating agents, sweetening, flavoring and perfuming agents, preservatives and antioxidants can also be present in the compositions.

Examples of pharmaceutically-acceptable antioxidants include: (1) water soluble antioxidants, such as ascorbic acid, cysteine hydrochloride, sodium bisulfate, sodium metabisulfite, sodium sulfite and the like; (2) oil-soluble antioxidants, such as ascorbyl palmitate, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), lecithin, propyl gallate, alpha-tocopherol, and the like; and (3) metal chelating agents, such as citric acid, ethylenediamine tetraacetic acid (EDTA), sorbitol, tartaric acid, phosphoric acid, and the like.

Formulations of the present disclosure include those suitable for oral, nasal, topical (including buccal and sublingual), rectal, vaginal and/or parenteral administration. The formulations may conveniently be presented in unit dosage form and may be prepared by any methods well known in the art of pharmacy. The amount of active ingredient which can be combined with a carrier material to produce a single dosage form will vary depending upon the host being treated, the particular mode of administration. The amount of active ingredient which can be combined with a carrier material to produce a single dosage form will generally be that amount of the compound (e.g., siNA molecule) which produces a therapeutic effect. Generally, out of one hundred percent, this amount will range from about 0.1 percent to about ninety-nine percent of active ingredient, preferably from about 5 percent to about 70 percent, most preferably from about 10 percent to about 30 percent.

In certain embodiments, a formulation of the present disclosure comprises an excipient selected from the group consisting of cyclodextrins, celluloses, liposomes, micelle forming agents, e.g., bile acids, and polymeric carriers, e.g., polyesters and polyanhydrides; and a compound (e.g., siNA molecule) of the present disclosure. In certain embodiments, an aforementioned formulation renders orally bioavailable a compound (e.g., siNA molecule) of the present disclosure.

Methods of preparing these formulations or compositions include the step of bringing into association a compound (e.g., siNA molecule) of the present disclosure with the carrier and, optionally, one or more accessory ingredients. In general, the formulations are prepared by uniformly and intimately bringing into association a compound (e.g., siNA molecule) of the present disclosure with liquid carriers, or finely divided solid carriers, or both, and then, if necessary, shaping the product.

Formulations of the disclosure suitable for oral administration may be in the form of capsules, cachets, pills, tablets, lozenges (using a flavored basis, usually sucrose and acacia or tragacanth), powders, granules, or as a solution or a suspension in an aqueous or non-aqueous liquid, or as an oil-in-water or water-in-oil liquid emulsion, or as an elixir or syrup, or as pastilles (using an inert base, such as gelatin and glycerin, or sucrose and acacia) and/or as mouth washes and the like, each containing a predetermined amount of a compound (e.g., siNA molecule) of the present disclosure as an active ingredient. A compound (e.g., siNA molecule) of the present disclosure may also be administered as a bolus, electuary or paste.

In solid dosage forms of the disclosure for oral administration (capsules, tablets, pills, dragées, powders, granules, trouches and the like), the active ingredient is mixed with one or more pharmaceutically-acceptable carriers, such as sodium citrate or dicalcium phosphate, and/or any of the following: (1) fillers or extenders, such as starches, lactose, sucrose, glucose, mannitol, and/or silicic acid; (2) binders, such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinyl pyrrolidone, sucrose and/or acacia; (3) humectants, such as glycerol; (4) disintegrating agents, such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate; (5) solution retarding agents, such as paraffin; (6) absorption accelerators, such as quaternary ammonium compounds and surfactants, such as poloxamer and sodium lauryl sulfate; (7) wetting agents, such as, for example, cetyl alcohol, glycerol monostearate, and non-ionic surfactants; (8) absorbents, such as kaolin and bentonite clay; (9) lubricants, such as talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, zinc stearate, sodium stearate, stearic acid, and mixtures thereof, (10) coloring agents; and (11) controlled release agents such as crospovidone or ethyl cellulose.

In the case of capsules, tablets and pills, the pharmaceutical compositions may also comprise buffering agents. Solid compositions of a similar type may also be employed as fillers in soft and hard-shelled gelatin capsules using such excipients as lactose or milk sugars, as well as high molecular weight polyethylene glycols and the like.

A tablet may be made by compression or molding, optionally with one or more accessory ingredients. Compressed tablets may be prepared using binder (for example, gelatin or hydroxypropylmethyl cellulose), lubricant, inert diluent, preservative, disintegrant (for example, sodium starch glycolate or cross-linked sodium carboxymethyl cellulose), surface-active or dispersing agent. Molded tablets may be made by molding in a suitable machine a mixture of the powdered compound moistened with an inert liquid diluent.

The tablets, and other solid dosage forms of the pharmaceutical compositions of the present disclosure, such as dragées, capsules, pills and granules, may optionally be scored or prepared with coatings and shells, such as enteric coatings and other coatings well known in the pharmaceutical-formulating art. They may also be formulated so as to provide slow or controlled release of the active ingredient therein using, for example, hydroxypropylmethyl cellulose in varying proportions to provide the desired release profile, other polymer matrices, liposomes and/or microspheres. They may be formulated for rapid release, e.g., freeze-dried.

They may be sterilized by, for example, filtration through a bacteria-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved in sterile water, or some other sterile injectable medium immediately before use. These compositions may also optionally contain opacifying agents and may be of a composition that they release the active ingredient(s) only, or preferentially, in a certain portion of the gastrointestinal tract, optionally, in a delayed manner. Examples of embedding compositions which can be used include polymeric substances and waxes. The active ingredient can also be in micro-encapsulated form, if appropriate, with one or more of the above-described excipients.

Liquid dosage forms for oral administration of the compounds (e.g., siNA molecules) of the disclosure include pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active ingredient, the liquid dosage forms may contain inert diluents commonly used in the art, such as, for example, water or other solvents, solubilizing agents and emulsifiers, such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, oils (I particular, cottonseed, groundnut, corn, germ, olive, castor and sesame oils), glycerol, tetrahydrofuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof.

Besides inert diluents, the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, coloring, perfuming and preservative agents.

Suspensions, in addition to the active compounds (e.g., siNA molecules), may contain suspending agents as, for example, ethoxylated isostearyl alcohols, polyoxyethylene sorbitol and sorbitan esters, microcrystalline cellulose, aluminum metahydroxide, bentonite, agar-agar and tragacanth, and mixtures thereof.

Formulations of the pharmaceutical compositions of the disclosure for rectal or vaginal administration may be presented as a suppository, which may be prepared by mixing one or more compounds (e.g., siNA molecules) of the disclosure with one or more suitable nonirritating excipients or carriers comprising, for example, cocoa butter, polyethylene glycol, a suppository wax or a salicylate, and which is solid at room temperature, but liquid at body temperature and, therefore, will melt in the rectum or vaginal cavity and release the active compound (e.g., siNA molecule).

Formulations of the present disclosure which are suitable for vaginal administration also include pessaries, tampons, creams, gels, pastes, foams or spray formulations containing such carriers as are known in the art to be appropriate.

Dosage forms for the topical or transdermal administration of a compound (e.g., siNA molecule) of this disclosure include powders, sprays, ointments, pastes, creams, lotions, gels, solutions, patches and inhalants. The active compound (e.g., siNA molecule) may be mixed under sterile conditions with a pharmaceutically acceptable carrier, and with any preservatives, buffers, or propellants which may be required.

The ointments, pastes, creams and gels may contain, in addition to an active compound (e.g., siNA molecule) of this disclosure, excipients, such as animal and vegetable fats, oils, waxes, paraffins, starch, tragacanth, cellulose derivatives, polyethylene glycols, silicones, bentonites, silicic acid, talc and zinc oxide, or mixtures thereof.

Powders and sprays can contain, in addition to a compound (e.g., siNA molecule) of this disclosure, excipients such as lactose, talc, silicic acid, aluminum hydroxide, calcium silicates and polyamide powder, or mixtures of these substances. Sprays can additionally contain customary propellants, such as chlorofluorohydrocarbons and volatile unsubstituted hydrocarbons, such as butane and propane.

Transdermal patches have the added advantage of providing controlled delivery of a compound (e.g., siNA molecule) of the present disclosure to the body. Such dosage forms can be made by dissolving or dispersing the compound (e.g., siNA molecule) in the proper medium. Absorption enhancers can also be used to increase the flux of the compound (e.g., siNA molecule) across the skin. The rate of such flux can be controlled by either providing a rate controlling membrane or dispersing the compound (e.g., siNA molecule) in a polymer matrix or gel.

Ophthalmic formulations, eye ointments, powders, solutions and the like, are also contemplated as being within the scope of this invention.

Pharmaceutical compositions of this disclosure suitable for parenteral administration comprise one or more compounds (e.g., siNA molecules) of the disclosure in combination with one or more pharmaceutically-acceptable sterile isotonic aqueous or nonaqueous solutions, dispersions, suspensions or emulsions, or sterile powders which may be reconstituted into sterile injectable solutions or dispersions just prior to use, which may contain sugars, alcohols, antioxidants, buffers, bacteriostats, solutes which render the formulation isotonic with the blood of the intended recipient or suspending or thickening agents.

Examples of suitable aqueous and nonaqueous carriers which may be employed in the pharmaceutical compositions of the disclosure include water, ethanol, polyols (such as glycerol, propylene glycol, polyethylene glycol, and the like), and suitable mixtures thereof, vegetable oils, such as olive oil, and injectable organic esters, such as ethyl oleate. Proper fluidity can be maintained, for example, by the use of coating materials, such as lecithin, by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants.

These compositions may also contain adjuvants such as preservatives, wetting agents, emulsifying agents and dispersing agents. Prevention of the action of microorganisms upon the subject compounds may be ensured by the inclusion of various antibacterial and antifungal agents, for example, paraben, chlorobutanol, phenol sorbic acid, and the like. It may also be desirable to include isotonic agents, such as sugars, sodium chloride, and the like into the compositions. In addition, prolonged absorption of the injectable pharmaceutical form may be brought about by the inclusion of agents which delay absorption such as aluminum monostearate and gelatin.

In some cases, in order to prolong the effect of a drug, it is desirable to slow the absorption of the drug from subcutaneous or intramuscular injection. This may be accomplished by the use of a liquid suspension of crystalline or amorphous material having poor water solubility. The rate of absorption of the drug then depends upon its rate of dissolution which, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally-administered drug form is accomplished by dissolving or suspending the drug in an oil vehicle.

Injectable depot forms are made by forming microencapsule matrices of the subject compounds (e.g., siNA molecules) in biodegradable polymers such as polylactide-polyglycolide. Depending on the ratio of drug to polymer, and the nature of the particular polymer employed, the rate of drug release can be controlled. Examples of other biodegradable polymers include poly(orthoesters) and poly(anhydrides). Depot injectable formulations are also prepared by entrapping the drug in liposomes or microemulsions which are compatible with body tissue.

When the compounds (e.g., siNA molecules) of the present disclosure are administered as pharmaceuticals, to humans and animals, they can be given per se or as a pharmaceutical composition containing, for example, 0.1 to 99% (more preferably, 10 to 30%) of active ingredient in combination with a pharmaceutically acceptable carrier.

Methods of Treatment and Administration

The siNA molecules of the present disclosure may be used to treat a disease in a subject in need thereof. In some embodiments, a method of treating a disease in a subject in need thereof comprises administering to the subject any of the siNA molecules disclosed herein. In some embodiments, a method of treating a disease in a subject in need thereof comprises administering to the subject any of the compositions disclosed herein.

The preparations (e.g., siNA molecules or compositions) of the present disclosure may be given orally, parenterally, topically, or rectally. They are of course given in forms suitable for each administration route. For example, they are administered in tablets or capsule form, administration by injection, infusion or inhalation; topical by lotion or ointment; and rectal by suppositories. Oral administrations are preferred.

The phrases “parenteral administration” and “administered parenterally” as used herein means modes of administration other than enteral and topical administration, usually by injection, and includes, without limitation, intravenous, intramuscular, intraarterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal and intrasternal injection and infusion.

The phrases “systemic administration,” “administered systemically,” “peripheral administration” and “administered peripherally” as used herein mean the administration of a compound, drug or other material other than directly into the central nervous system, such that it enters the patient's system and, thus, is subject to metabolism and other like processes, for example, subcutaneous administration.

These compounds may be administered to humans and other animals for therapy by any suitable route of administration, including orally, nasally, as by, for example, a spray, rectally, intravaginally, parenterally, intracisternally and topically, as by powders, ointments or drops, including buccally and sublingually.

Regardless of the route of administration selected, the compounds (e.g., siNA molecules) of the present disclosure, which may be used in a suitable hydrated form, and/or the pharmaceutical compositions of the present disclosure, are formulated into pharmaceutically-acceptable dosage forms by conventional methods known to those of skill in the art.

Actual dosage levels of the active ingredients in the pharmaceutical compositions of this disclosure may be varied so as to obtain an amount of the active ingredient which is effective to achieve the desired therapeutic response for a particular patient, composition, and mode of administration, without being toxic to the patient.

The selected dosage level will depend upon a variety of factors including the activity of the particular compound (e.g., siNA molecule) of the present disclosure employed, or the ester, salt or amide thereof, the route of administration, the time of administration, the rate of excretion or metabolism of the particular compound being employed, the rate and extent of absorption, the duration of the treatment, other drugs, compounds and/or materials used in combination with the particular compound employed, the age, sex, weight, condition, general health and prior medical history of the patient being treated, and like factors well known in the medical arts.

A physician or veterinarian having ordinary skill in the art can readily determine and prescribe the effective amount of the pharmaceutical composition required. For example, the physician or veterinarian could start doses of the compounds (e.g., siNA molecules) of the disclosure employed in the pharmaceutical composition at levels lower than that required in order to achieve the desired therapeutic effect and gradually increase the dosage until the desired effect is achieved.

In general, a suitable daily dose of a compound (e.g., siNA molecule) of the disclosure is the amount of the compound that is the lowest dose effective to produce a therapeutic effect. Such an effective dose generally depends upon the factors described above. Preferably, the compounds are administered at about 0.01 mg/kg to about 200 mg/kg, more preferably at about 0.1 mg/kg to about 100 mg/kg, even more preferably at about 0.5 mg/kg to about 50 mg/kg. In some embodiments, the compound is administered at a dose equal to or greater than 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.10, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23, 0.24, 0.25, 0.26, 0.27, 0.28, 0.29, 0.30, 0.35, 0.40, 0.45, 0.50, 0.55, 0.60, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, or 1 mg/kg. In some embodiments, the compound is administered at a dose equal to or less than 200, 190, 180, 170, 160, 150, 140, 130, 120, 110, 100, 95, 90, 85, 80, 75, 70, 65, 60, 55, 50, 45, 40, 35, 30, 25, 20, or 15 mg/kg. In some embodiments, the total daily dose of the compound is equal to or greater than 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, or 100 mg.

When the compounds (e.g., siNA molecules) described herein are co-administered with another, the effective amount may be less than when the compound is used alone.

If desired, the effective daily dose of the active compound (e.g., siNA molecule) may be administered as two, three, four, five, six or more sub-doses administered separately at appropriate intervals throughout the day, optionally, in unit dosage forms. Preferred dosing is one administration per day. In some embodiments, the compound is administered at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 times a week. In some embodiments, the compound is administered at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 times a month. In some embodiments, the compound is administered once every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 days. In some embodiments, the compound is administered once every 1, 2, 3, 4, 5, 6, 7, or 8 weeks.

Diseases

The siNA molecules and compositions described herein may be administered to a subject to treat a disease. Further disclosed herein are uses of any of the siNA molecules or compositions disclosed herein in the manufacture of a medicament for treating a disease.

In some embodiments, the disease is a viral disease. In some embodiments, the viral disease is caused by a DNA virus. In some embodiments, the DNA virus is a double stranded DNA (dsDNA virus). In some embodiments, the dsDNA virus is a hepadnavirus. In some embodiments, the hepadnavirus is a hepatitis B virus (HBV).

In some embodiments, the disease is a liver disease. In some embodiments, the liver disease is nonalcoholic fatty liver disease (NAFLD). In some embodiments, the NAFLD is nonalcoholic steatohepatitis (NASH). In some embodiments, the liver disease is hepatocellular carcinoma (HCC).

Administration of siNA

Administration of any of the siNAs disclosed herein may be conducted by methods known in the art. In some embodiments, the siNA is administered by subcutaneous (SC) or intravenous (IV) delivery. The preparations (e.g., siNAs or compositions) of the present disclosure may be given orally, parenterally, topically, or rectally. They are of course given in forms suitable for each administration route. For example, they are administered in tablets or capsule form, administration by injection, infusion or inhalation; topical by lotion or ointment; and rectal by suppositories. In some embodiments, subcutaneous administration is preferred.

The phrases “parenteral administration” and “administered parenterally” as used herein means modes of administration other than enteral and topical administration, usually by injection, and includes, without limitation, intravenous, intramuscular, intraarterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal and intrasternal injection and infusion.

The phrases “systemic administration,” “administered systemically,” “peripheral administration” and “administered peripherally” as used herein mean the administration of a compound, drug or other material other than directly into the central nervous system, such that it enters the patient's system and, thus, is subject to metabolism and other like processes, for example, subcutaneous administration.

These compounds may be administered to humans and other animals for therapy by any suitable route of administration, including orally, nasally, as by, for example, a spray, rectally, intravaginally, parenterally, intracisternally and topically, as by powders, ointments or drops, including buccally and sublingually.

Regardless of the route of administration selected, the compounds (e.g., siNAs) of the present disclosure, which may be used in a suitable hydrated form, and/or the pharmaceutical compositions of the present disclosure, are formulated into pharmaceutically-acceptable dosage forms by conventional methods known to those of skill in the art.

Actual dosage levels of the active ingredients in the pharmaceutical compositions of this disclosure may be varied so as to obtain an amount of the active ingredient which is effective to achieve the desired therapeutic response for a particular patient, composition, and mode of administration, without being toxic to the patient.

The selected dosage level will depend upon a variety of factors including the activity of the particular compound (e.g., siNA) of the present disclosure employed, or the ester, salt or amide thereof, the route of administration, the time of administration, the rate of excretion or metabolism of the particular compound being employed, the rate and extent of absorption, the duration of the treatment, other drugs, compounds and/or materials used in combination with the particular compound employed, the age, sex, weight, condition, general health and prior medical history of the patient being treated, and like factors well known in the medical arts.

A physician or veterinarian having ordinary skill in the art can readily determine and prescribe the effective amount of the pharmaceutical composition required. For example, the physician or veterinarian could start doses of the compounds (e.g., siNAs) of the disclosure employed in the pharmaceutical composition at levels lower than that required in order to achieve the desired therapeutic effect and gradually increase the dosage until the desired effect is achieved.

In general, a suitable daily dose of a compound (e.g., siNA) of the disclosure is the amount of the compound that is the lowest dose effective to produce a therapeutic effect. Such an effective dose generally depends upon the factors described above. Preferably, the compounds are administered at about 0.01 mg/kg to about 200 mg/kg, more preferably at about 0.1 mg/kg to about 100 mg/kg, even more preferably at about 0.5 mg/kg to about 50 mg/kg. In some embodiments, the compound is administered at about 1 mg/kg to about 40 mg/kg, about 1 mg/kg to about 30 mg/kg, about 1 mg/kg to about 20 mg/kg, about 1 mg/kg to about 15 mg/kg, or 1 mg/kg to about 10 mg/kg. In some embodiments, the compound is administered at a dose equal to or greater than 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.10, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23, 0.24, 0.25, 0.26, 0.27, 0.28, 0.29, 0.30, 0.35, 0.40, 0.45, 0.50, 0.55, 0.60, 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, or 1 mg/kg. In some embodiments, the compound is administered at a dose equal to or greater than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 mg/kg. In some embodiments, the compound is administered at a dose equal to or less than 200, 190, 180, 170, 160, 150, 140, 130, 120, 110, 100, 95, 90, 85, 80, 75, 70, 65, 60, 55, 50, 45, 40, 35, 30, 25, 20, or 15 mg/kg. In some embodiments, the total daily dose of the compound is equal to or greater than 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, or 100 mg.

If desired, the effective daily dose of the active compound (e.g., siNA) may be administered as two, three, four, five, six, seven, eight, nine, ten or more doses or sub-doses administered separately at appropriate intervals throughout the day, optionally, in unit dosage forms. In some embodiments, the compound is administered at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 times. Preferred dosing is one administration per day. In some embodiments, the compound is administered at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 times a week. In some embodiments, the compound is administered at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 times a month. In some embodiments, the compound is administered once every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 days. In some embodiments, the compound is administered every 3 days. In some embodiments, the compound is administered once every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 weeks. In some embodiments, the compound is administered every month. In some embodiments, the compound is administered once every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15 months. In some embodiments, the compound is administered at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, or 53 times over a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, or 70 days. In some embodiments, the compound is administered at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, or 53 times over a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, or 53 weeks. In some embodiments, the compound is administered at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, or 53 times over a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, or 53 months. In some embodiments, the compound is administered at least once a week for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, or 70 weeks. In some embodiments, the compound is administered at least once a week for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, or 70 months. In some embodiments, the compound is administered at least twice a week for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, or 70 weeks. In some embodiments, the compound is administered at least twice a week for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, or 70 months. In some embodiments, the compound is administered at least once every two weeks for a period of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, or 70 weeks. In some embodiments, the compound is administered at least once every two weeks for a period of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, or 70 months. In some embodiments, the compound is administered at least once every four weeks for a period of at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, or 70 weeks. In some embodiments, the compound is administered at least once every four weeks for a period of at least 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, or 70 months.

In some embodiments, any one of the siNAs or compositions disclosed herein is administered in a particle or viral vector. In some embodiments, the viral vector is a vector of adenovirus, adeno-associated virus (AAV), alphavirus, flavivirus, herpes simplex virus, lentivirus, measles virus, picornavirus, poxvirus, retrovirus, or rhabdovirus. In some embodiments, the viral vector is a recombinant viral vector. In some embodiments, the viral vector is selected from AAVrh.74, AAVrh.10, AAVrh.20, AAV-1, AAV-2, AAV-3, AAV-4, AAV-5, AAV-6, AAV-7, AAV-8, AAV-9, AAV-10, AAV-11, AAV-12 and AAV-13.

The subject of the described methods may be a mammal, and it includes humans and non-human mammals. In some embodiments, the subject is a human, such as an adult human.

Some embodiments include a method for treating an HBV virus in a subject infected with the virus comprising administering a therapeutically effective amount of one or more siNA of the present disclosure or a composition of the present disclosure to the subject in need thereof thereby reducing the viral load of the virus in the subject and/or reducing a level of a virus antigen in the subject. The siNA may be complementary or hybridize to a portion of the target RNA in the virus, e.g., an X region and/or an S region of HBV.

Combination Therapies

Any of the methods disclosed herein may further comprise administering to the subject an additional HBV treatment agent. Any of the compositions disclosed herein may further comprise an additional HBV treatment agent. In some embodiments, the additional HBV treatment agent is selected from a nucleotide analog, nucleoside analog, a capsid assembly modulator (CAM), a recombinant interferon, an entry inhibitor, a small molecule immunomodulator and oligonucleotide therapy. In some embodiments, the additional HBV treatment agent is selected from HBV STOPS™ ALG-010133, HBV CAM ALG-000184, ASO 1, recombinant interferon alpha 2b, IFN-α, PEG-IFN-α-2a, lamivudine, telbivudine, adefovir dipivoxil, clevudine, entecavir, tenofovir alafenamide, tenofovir disoproxil, NVR3-778, BAY41-4109, JNJ-632, JNJ-3989 (ARO-HBV), RG6004, GSK3228836, REP-2139, REP-2165, AB-729, VIR-2218, RG6346 (DCR-HBVS), JNJ-6379, GLS4, ABI-HO731, JNJ-440, NZ-4, RG7907, EDP-514, AB-423, AB-506, ABI-H03733 and ABI-H2158. In some embodiments, the oligonucleotide therapy is selected from Nucleic Acid Polymers or S-Antigen Transport-inhibiting Oligonucleotide Polymers (NAPs or STOPS), siRNA, and ASO. In some embodiments, the oligonucleotide therapy is an additional siNA. In some embodiments, the additional siNA is selected from any of ds-siNA-001 to ds-siNA-0178. In some embodiments, the oligonucleotide therapy is an antisense oligonucleotide (ASO). In some embodiments, the ASO is ASO 1. In some embodiments, any of the siNAs disclosed herein are co-administered with STOPS. Exemplary STOPS are described in International Publication No. WO2020/097342 and U.S. Publication No. 2020/0147124, both of which are incorporated by reference in their entirety. In some embodiments, the STOPS is ALG-010133. In some embodiments, any of the siNAs disclosed herein are co-administered with tenofovir. In some embodiments, any of the siNAs disclosed herein are co-administered with a CAM. Exemplary CAMs are described in Berke et al., Antimicrob Agents Chemother, 2017, 61(8):e00560-17, Klumpp, et al., Gastroenterology, 2018, 154(3):652-662.e8, International Application Nos. PCT/US2020/017974, PCT/US2020/026116, and PCT/US2020/028349 and U.S. application Ser. Nos. 16/789,298, 16/837,515, and 16/849,851, each which is incorporated by reference in its entirety. In some embodiments, the CAM is ALG-000184, ALG-001075, ALG-001024, JNJ-632, BAY41-4109, or NVR3-778. In some embodiments, the siNA and the HBV treatment agent are administered simultaneously. In some embodiments, the siNA and the HBV treatment agent are administered concurrently. In some embodiments, the siNA and the HBV treatment agent are administered sequentially. In some embodiments, the siNA is administered prior to administering the HBV treatment agent. In some embodiments, the siNA is administered after administering the HBV treatment agent. In some embodiments, the siNA and the HBV treatment agent are in separate containers. In some embodiments, the siNA and the HBV treatment agent are in the same container.

Any of the methods disclosed herein may further comprise administering to the subject a liver disease treatment agent. Any of the compositions disclosed herein may further comprise a liver disease treatment agent. In some embodiments, the liver disease treatment agent is selected from a peroxisome proliferator-activator receptor (PPAR) agonist, farnesoid X receptor (FXR) agonist, lipid-altering agent, and incretin-based therapy. In some embodiments, the PPAR agonist is selected from a PPARα agonist, dual PPARα/δ agonist, PPARγ agonist, and dual PPARα/γ agonist. In some embodiments, the dual PPARα agonist is a fibrate. In some embodiments, the PPARα/δ agonist is elafibranor. In some embodiments, the PPARγ agonist is a thiazolidinedione (TZD). In some embodiments, TZD is pioglitazone. In some embodiments, the dual PPARα/γ agonist is saroglitazar. In some embodiments, the FXR agonist is obeticholic acis (OCA). In some embodiments, the lipid-altering agent is aramchol. In some embodiments, the incretin-based therapy is a glucagon-like peptide 1 (GLP-1) receptor agonist or dipeptidyl peptidase 4 (DPP-4) inhibitor. In some embodiments, the GLP-1 receptor agonist is exenatide or liraglutide. In some embodiments, the DPP-4 inhibitor is sitagliptin or vildapliptin. In some embodiments, the siNA and the liver disease treatment agent are administered concurrently. In some embodiments, the siNA and the liver disease treatment agent are administered sequentially. In some embodiments, the siNA is administered prior to administering the liver disease treatment agent. In some embodiments, the siNA is administered after administering the liver disease treatment agent. In some embodiments, the siNA and the liver disease treatment agent are in separate containers. In some embodiments, the siNA and the liver disease treatment agent are in the same container.

Definitions

Unless defined otherwise, all technical and scientific terms used herein have the meaning commonly understood by a person skilled in the art to which this disclosure belongs. The following references provide one of skill with a general definition of many of the terms used in this invention: Singleton et al., Dictionary of Microbiology and Molecular Biology (2nd ed. 1994); The Cambridge Dictionary of Science and Technology (Walker ed., 1988); The Glossary of Genetics, 5th Ed., R. Rieger et al., (eds.), Springer Verlag (1991); and Hale & Marham, The Harper Collins Dictionary of Biology (1991). As used herein, the following terms have the meanings ascribed to them below, unless specified otherwise. The terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting of the disclosure.

The terms “a” and “an” as used herein mean “one or more” and include the plural unless the context is inappropriate.

As used herein, the terms “patient” and “subject” refer to organisms to be treated by the methods of the present disclosure. Such organisms are preferably mammals (e.g., marines, simians, equines, bovines, porcinis, canines, felines, and the like), and more preferably humans.

As used herein, the term “effective amount” refers to the amount of a compound (e.g., a siNA of the present disclosure) sufficient to effect beneficial or desired results. An effective amount can be administered in one or more administrations, applications, or dosages and is not intended to be limited to a particular formulation or administration route.

As used herein, the term “treating” includes any effect, e.g., lessening, reducing, modulating, ameliorating or eliminating, that results in the improvement of the condition, disease, disorder, and the like, or ameliorating a symptom thereof.

As used herein, the terms “alleviate” and “alleviating” refer to reducing the severity of the condition, such as reducing the severity by, for example, at least 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 95%.

As used herein, the term “pharmaceutical composition” refers to the combination of an active agent with a carrier, inert or active, making the composition especially suitable for diagnostic or therapeutic use in vivo or ex vivo.

As used herein, the term “pharmaceutically acceptable carrier” refers to any of the standard pharmaceutical carriers, such as a phosphate buffered saline solution, water, emulsions (e.g., such as an oil/water or water/oil emulsions), and various types of wetting agents. The compositions also can include stabilizers and preservatives. For examples of carriers, stabilizers and adjuvants, see, for example, Martin, Remington's Pharmaceutical Sciences, 15th Ed., Mack Publ. Co., Easton, PA [1975].

The term “about” as used herein when referring to a measurable value (e.g., weight, time, and dose) is meant to encompass variations, such as ±10%, ±5%, ±1%, or f0.1% of the specified value.

As used herein, the term “nucleobase” refers to a nitrogen-containing biological compound that forms a nucleoside. Examples of nucleobases include, but are not limited to, thymine, uracil, adenine, cytosine, guanine, aryl, heteroaryl, and an analogue or derivative thereof.

Throughout the description, where compositions are described as having, including, or comprising specific components, or where processes and methods are described as having, including, or comprising specific steps, it is contemplated that, additionally, there are compositions of the present disclosure that consist essentially of, or consist of, the recited components, and that there are processes and methods according to the present disclosure that consist essentially of, or consist of, the recited processing steps.

As a general matter, compositions specifying a percentage are by weight unless otherwise specified. Further, if a variable is not accompanied by a definition, then the previous definition of the variable controls.

All publications and patents cited in this specification are herein incorporated by reference as if each individual publication or patent were specifically and individually indicated to be incorporated by reference and are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited. The citation of any publication is for its disclosure prior to the filing date and should not be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates that may need to be independently confirmed.

EXAMPLES Example 1. siNA Synthesis

This example describes an exemplary method for synthesizing ds-siNAs, such as the siNAs disclosed in Table 6 (as identified by the ds-siNA ID).

The 2′-OMe phosphoramidite 5′-O-DMT-deoxy Adenosine (NH-Bz), 3′-O-(2-cyanoethyl-N,N-diisopropyl phosphoramidite, 5′-O-DMT-deoxy Guanosine (NH-ibu), 3′-0-(2-cyanoethyl-N,N-diisopropyl phosphoramidite, 5′-O-DMT-deoxy Cytosine (NH-Bz), 3′-O-(2-cyanoethyl-N,N-diisopropyl phosphoramidite, 5′-O-DMT-Uridine 3′-O-(2-cyanoethyl-N,N-diisopropyl phosphoramidite and solid supports were purchased from Chemgenes Corp. MA.

The 2′-F -5′-O-DMT-(NH-Bz) Adenosine-3′-O-(2-cyanoethyl-N,N-diisopropyl phosphoramidite, 2′-F -5′-O-DMT-(NH-ibu)-Guanosine, 3′-O-(2-cyanoethyl-N,N-diisopropyl phosphoramidite, 5′-O-DMT-(NH-Bz)-Cytosine, 2′-F-3′-O-(2-cyanoethyl-N,N-diisopropyl phosphoramidite, 5′-O-DMT-Uridine, 2′-F-3′-O-(2-cyanoethyl-N,N-diisopropyl phosphoramidite and solid supports were purchased from Thermo Fischer Milwaukee WI, USA.

All the monomers were dried in vacuum desiccator with desiccants (P2O5, RT 24 h). The solid supports (CPG) attached to the nucleosides and universal supports was obtained from LGC and Chemgenes. The chemicals and solvents for post synthesis workflow were purchased from commercially available sources like VWR/Sigma and used without any purification or treatment. Solvent (Acetonitrile) and solutions (amidite and activator) were stored over molecular sieves during synthesis.

The oligonucleotides were synthesized on a DNA/RNA Synthesizers (Expedite 8909 or ABI-394) using standard oligonucleotide phosphoramidite chemistry starting from the 3′ residue of the oligonucleotide preloaded on CPG support. An extended coupling of 0.1M solution of phosphoramidite in CH3CN in the presence of 5-(ethylthio)-1H-tetrazole activator to a solid bound oligonucleotide followed by standard capping, oxidation and deprotection afforded modified oligonucleotides. The 0.1 M I2, THF:Pyridine;Water-7:2:1 was used as oxidizing agent while DDTT ((dimethylamino-methylidene) amino)-3H-1,2,4-dithiazaoline-3-thione was used as the sulfur-transfer agent for the synthesis of oligoribonucleotide phosphorothioates. The stepwise coupling efficiency of all modified phosphoramidites was more than 98%.

Reagents Detailed Description Deblock Solution 3% Dichloroacetic acid (DCA) in Dichloromethane (DCM) Amidite Concentration 0.1M in Anhydrous Acetonitrile Activator 0.25M Ethyl-thio-Tetrazole (ETT) Cap-A solution Acetic anhydride in Pyridine/THF Cap-B Solution 16% 1-Methylimidazole in THF Oxidizing Solution 0.02M I2, THF: Pyridine; Water-7:2:1 Sulfurizing Solution 0.2M DDTT in Pyridine/Acetonitrile 1:1

Cleavage and Deprotection:

Deprotection and cleavage from the solid support was achieved with mixture of ammonia methylamine (1:1, AMA) for 15 min at 65° C., when the universal linker was used, the deprotection was left for 90 min at 65° C. or solid supports were heated with aqueous ammonia (28%) solution at 55° C. for 16 h to deprotect the base labile protecting groups.

Quantitation of Crude SiNA or Raw Analysis

Samples were dissolved in deionized water (1.0 mL) and quantitated as follows: Blanking was first performed with water alone (2 ul) on Nanodrop then Oligo sample reading obtained at 260 nm. The crude material is dried down and stored at −20° C.

Crude HPLC/LC-MS Analysis

The 0.1 OD of the crude samples were analyzed for crude HPLC and LC-MS analysis. After Confirming the crude LC-MS data then purification step was performed.

HPLC Purification

The unconjugated and GalNac modified oligonucleotides were purified by anion-exchange HPLC. The buffers were 20 mM sodium phosphate in 10% CH3CN, pH 8.5 (buffer A) and 20 mM sodium phosphate in 10% CH3CN, 1.0 M NaBr, pH 8.5 (buffer B). Fractions containing full-length oligonucleotides were pooled.

Desalting of Purified SiNA

The purified dry siNA was then desalted using Sephadex G-25 M (Amersham Biosciences). The cartridge was conditioned with 10 mL of deionized water thrice. Finally, the purified siNA dissolved thoroughly in 2.5 mL RNAse free water was applied to the cartridge with very slow drop wise elution. The salt free siNA was eluted with 3.5 ml deionized water directly into a screw cap vial.

IEX HPLC and Electrospray LC/MS Analysis

Approximately 0.10 OD of siNA is dissolved in water and then pipetted in special vials for IEX-HPLC and LC/MS analysis. Analytical HPLC and ES LC-MS established the integrity of the compounds.

Duplex Preparation:

Single strand oligonucleotides (Sense and Antisense strands) were annealed (1:1 by molar equivalents, heat 90° C. for 3 min followed by room temperature, 20 min) to give the duplex ds-siNA. The final compounds were analyzed on size exclusion chromatography (SEC).

Example 2. Ds-siNA Activity

This example investigates the activity of the ds-siNAs synthesized in Example 1.

Homo sapiens HepG2.2.15 cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) (ATCC 30-2002) supplemented to also contain 10% fetal calf serum (FCS). Cells were incubated at 37° C. in an atmosphere with 5% CO2 in a humidified incubator. For transfection of HepG2.2.15 cells with HBV targeting siRNAs, cells were seeded at a density of 15000 cells/well in 96-well regular tissue culture plates. Transfection of cells was carried out using RNAiMAX (Invitrogen/Life Technologies) according to the manufacturer's instructions. Dose-response experiments were done with oligo concentrations of 40, 20, 10, 5, 2.5, 1.25, 0.625, 0.3125, 0.15625 and 0.07813 nM. For each HBV targeting siRNA treatment (e.g., ds-siRNA, as identified by the ds-siNA ID in Table 6), four wells were transfected in parallel, and individual data points were collected from each well. After 24 h of incubation with siRNA, media was removed, and cells were lysed and analyzed with a QuantiGene2.0 branched DNA (bDNA) probe set specific for HBV genotype D (also called Hepatitis B virus subtype ayw, complete genome of 3182 base-pairs) as present in cell line HepG2.2.15.

For each well, the HBV on-target mRNA levels were normalized to the GAPDH mRNA level. As shown in Table 6, the activity of the HBV targeting ds-siRNAs was expressed as EC50, 50% reduction of normalized HBV RNA level from no drug control. As shown in Table 6, the cytotoxicity of the HBV targeting ds-siRNAs was expressed by CC50 of 50% reduction of GAPDH mRNA from no drug control.

Example 3. Use of Ds-siNAs to Treat Hepatitis B Virus Infection

In this example, the ds-siNAs synthesized in Example 1 are used to treat a hepatitis B virus infection in a subject. Generally, a composition comprising a ds-siNA from Table 6 (as identified by the ds-siNA ID) and a pharmaceutically acceptable carrier is administered to the subject suffering from hepatitis B virus. The ds-siNA from Table 6 is conjugated to N-acetylgalactosamine. The ds-siNA is administered at a dose of 0.3 to 5 mg/kg every three weeks by subcutaneous injection or intravenous infusion.

Example 4. Ds-siNA Hepatitis B Clinical Trial

In this example, the ds-siNAs from Tables 6A and 6B (as identified by the ds-siNA ID) will be evaluated for safety and efficacy in healthy volunteers and chronic hepatitis B patients.

ds-siNAs are being developed for the treatment of chronic hepatitis B (CHB) in adults. The study will be conducted in 3 parts, a single ascending-dose (SAD) phase in healthy volunteers (Group A), a single-dose (SD) phase in patients with CHB (Group B), and a multiple ascending-dose (MAD) phase in patients with CHB (Group C).

Study Design

Study Type: Interventional (Clinical Trial) Estimated 50 participants Enrollment: Allocation: Randomized Intervention Sequential Assignment Model: Intervention Progression from the SAD phase to the first cohort Model in the MAD phase is contingent upon the Safety Description: Review Committee (SRC) review of a minimum of 14 days post-dose safety and tolerability data from all HV in at least the first 2 SAD cohorts. The SRC will select one (or more) well-tolerated dose(s) from the SAD phase for administration in the SD and MAD phases. In all study phases, dosing will be staggered with the use of sentinel participants to allow time for the assessment of safety before additional subjects are exposed to study drug. Masking: Triple (Participant, Care Provider, Investigator) Masking This is a double-blind placebo-controlled study in Description: which the study site team, the Sponsor, and the participants will be blinded to treatment assignment. The unblinded pharmacist will cover each syringe, prior to transport to the bedside, to ensure blinding. Participants will be centrally assigned to randomized study intervention using an Interactive Voice/Web Response System (IVRS/IWRS). Primary Treatment Purpose:

Arm Intervention/treatment Experimental: Cohort A1 ds-siNA Drug: ds-siNA Single dose, Subcutaneous injection of ds-siNA is a synthetic ribonucleic acid 0.1 mg/kg of ds-siNA (HV) interference (RNAi) drug that consists of double- stranded oligonucleotides conjugated to an N- acetyl-D-galactosamine (GalNAc) ligand. ds- siNA, sterile solution of the ds-siNA at a concentration of 185 mg/mL in water for injection (WFI). Placebo Comparator: Cohort A1 Drug: Placebo for ds-siNA Placebo Sterile 9% saline for injection. Single dose, Subcutaneous injection of Other Name: Placebo 0.1 mg/kg of Placebo for ds-siNA (HV) Experimental: Cohort A2 ds-siNA Drug: ds-siNA Single dose, Subcutaneous injection of ds-siNA is a synthetic ribonucleic acid 1.5 mg/kg of ds-siNA (HV) interference (RNAi) drug that consists of double- stranded oligonucleotides conjugated to an N- acetyl-D-galactosamine (GalNAc) ligand. ds- siNA, sterile solution of the ds-siNA at a concentration of 185 mg/mL in water for injection (WFI). Placebo Comparator: Cohort A2 Drug: Placebo for ds-siNA Placebo Sterile 9% saline for injection. Single dose, Subcutaneous injection of Other Name: Placebo 1.5 mg/kg of Placebo for ds-siNA (HV) Experimental: Cohort A3 ds-siNA Drug: ds-siNA Single dose, Subcutaneous injection of ds-siNA is a synthetic ribonucleic acid 3 mg/kg of ds-siNA (HV) interference (RNAi) drug that consists of double- stranded oligonucleotides conjugated to an N- acetyl-D-galactosamine (GalNAc) ligand. ds- siNA, sterile solution of the ds-siNA at a concentration of 185 mg/mL in water for injection (WFI). Placebo Comparator: Cohort A3 Drug: Placebo for ds-siNA Placebo Sterile 9% saline for injection. Single dose, Subcutaneous injection of Other Name: Placebo 3 mg/kg of Placebo for ds-siNA (HV) Experimental: Cohort A4 ds-siNA Drug: ds-siNA Single dose, Subcutaneous injection of ds-siNA is a synthetic ribonucleic acid 6 mg/kg of ds-siNA (HV) interference (RNAi) drug that consists of double- stranded oligonucleotides conjugated to an N- acetyl-D-galactosamine (GalNAc) ligand. ds- siNA, sterile solution of the ds-siNA at a concentration of 185 mg/mL in water for injection (WFI). Placebo Comparator: Cohort A4 Drug: Placebo for ds-siNA Placebo Sterile 9% saline for injection. Single dose, Subcutaneous injection of Other Name: Placebo 6 mg/kg of Placebo for ds-siNA (HV) Experimental: Cohort A5 ds-siNA Drug: ds-siNA Single dose, Subcutaneous injection of ds-siNA is a synthetic ribonucleic acid 12 mg/kg of ds-siNA (HV) interference (RNAi) drug that consists of double- stranded oligonucleotides conjugated to an N- acetyl-D-galactosamine (GalNAc) ligand. ds- siNA, sterile solution of the ds-siNA at a concentration of 185 mg/mL in water for injection (WFI). Placebo Comparator: Cohort A5 Drug: Placebo for ds-siNA Placebo Sterile 9% saline for injection. Single dose, Subcutaneous injection of Other Name: Placebo 12 mg/kg of Placebo for ds-siNA (HV) Experimental: Cohort B ds-siNA Drug: ds-siNA Single dose, Subcutaneous injection of ds-siNA is a synthetic ribonucleic acid 3 mg/kg of for ds-siNA (NUC naïve, interference (RNAi) drug that consists of double- CHB) stranded oligonucleotides conjugated to an N- acetyl-D-galactosamine (GalNAc) ligand. ds- siNA, sterile solution of the ds-siNA at a concentration of 185 mg/mL in water for injection (WFI). Placebo Comparator: Cohort B Drug: Placebo for ds-siNA Placebo Sterile 9% saline for injection. Single dose, Subcutaneous injection of Other Name: Placebo 3 mg/kg of Placebo for ds-siNA (NUC naïve, CHB) Experimental: Cohort C1 ds-siNA Drug: ds-siNA 4 doses-Subcutaneous injection of ds-siNA is a synthetic ribonucleic acid 1.5 mg/kg of ds-siNA administered interference (RNAi) drug that consists of double- every 28 days (NUC experienced, stranded oligonucleotides conjugated to an N- CHB) acetyl-D-galactosamine (GalNAc) ligand. ds- siNA, sterile solution of the ds-siNA at a concentration of 185 mg/mL in water for injection (WFI). Placebo Comparator: Cohort C1 Drug: Placebo for ds-siNA Placebo Sterile 9% saline for injection. 4 doses-Subcutaneous injection of Other Name: Placebo 1.5 mg/kg of Placebo for ds-siNA administered every 28 days (NUC experienced, CHB) Experimental: Cohort C2 ds-siNA Drug: ds-siNA 4 doses-Subcutaneous injection of ds-siNA is a synthetic ribonucleic acid 3 mg/kg of ds-siNA administered every interference (RNAi) drug that consists of double- 28 days (NUC experienced, CHB) stranded oligonucleotides conjugated to an N- acetyl-D-galactosamine (GalNAc) ligand. ds- siNA, sterile solution of the ds-siNA at a concentration of 185 mg/mL in water for injection (WFI). Placebo Comparator: Cohort C2 Drug: Placebo for ds-siNA Placebo Sterile 9% saline for injection. 4 doses-Subcutaneous injection of Other Name: Placebo 3 mg/kg of Placebo for ds-siNA administered every 28 days (NUC experienced, CHB) Experimental: Cohort C3 ds-siNA Drug: ds-siNA 4 doses-Subcutaneous injection of ds-siNA is a synthetic ribonucleic acid 6 mg/kg of ds-siNA administered every interference (RNAi) drug that consists of double- 28 days (NUC experienced, CHB) stranded oligonucleotides conjugated to an N- acetyl-D-galactosamine (GalNAc) ligand. ds- siNA, sterile solution of the ds-siNA at a concentration of 185 mg/mL in water for injection (WFI). Placebo Comparator: Cohort C3 Drug: Placebo for ds-siNA Placebo Sterile 9% saline for injection. 4 doses-Subcutaneous injection of Other Name: Placebo 6 mg/kg of Placebo for ds-siNA administered every 28 days (NUC experienced, CHB)

Outcome Measures

Primary Outcome Measures:

Number of healthy volunteers with Adverse Events as assessed by CTCAE v5.0 [Time Frame: 4 weeks]

Number of participants with abnormalities in vital signs, electrocardiogram (ECG), and clinically significant laboratory findings

Number participants with non-cirrhotic chronic Hepatitis B with Adverse Events as assessed by CTCAE v5.0 [Time Frame: 16 weeks]

Number of participants with abnormalities in vital signs, electrocardiogram (ECG), and clinically significant laboratory findings.

Secondary Outcome Measures:

To characterize the pharmacokinetics of ds-siNA in healthy volunteers by monitoring plasma pharmacokinetics profiles of [Time Frame: 4 weeks] Measure the amount of ds-siNA excreted in urine

To characterize the pharmacokinetics of ds-siNA in healthy volunteers by monitoring through concentrations of [Time Frame: 4 weeks]

Measure the amount of ds-siNA renal clearance (CLR).

To characterize the pharmacokinetics of ds-siNA in participants with non-cirrhotic CHB by monitoring plasma pharmacokinetics profiles of ds-siNA. [Time Frame: 12 weeks]

Measure the amount of ds-siNA excreted in urine

To characterize the pharmacokinetics of ds-siNA in participants with non-cirrhotic CHB by monitoring through concentrations of ds-siNA. [Time Frame: 12 weeks]

Measure ds-siNA renal clearance (CLR).

Other Outcome Measures:

To evaluate the preliminary antiviral efficacy of ds-siNA in participants with CHB by monitoring changes in serum HBsAg levels (all Group B and C participants) during and after single dose and 12 weeks of treatment with DCR HBVS. [Time Frame: 12 weeks]

Proportion of participants achieving at least a 1-log reduction in HBsAg and achieving a HBsAg level <100 IU/mL at last scheduled visit Time to HBsAg loss (Kaplan-Mayer) Time to anti-HBs seroconversion

To evaluate the preliminary antiviral efficacy of ds-siNA in participants with CHB by monitoring HBeAg levels (HBeAg+participants only) during and after single dose and 12 weeks of treatment with DCR HBVS. [Time Frame: 12 weeks]

% of participants with HBeAg loss and anti HBe at last scheduled visit (if HBeAg positive at study entry)

To evaluate the preliminary antiviral efficacy of ds-siNA in participants with CHB by monitoring HBV DNA levels (all Group B and C participants) during and after single dose and 12 weeks of treatment with DCR HBVS. [Time Frame: 12 weeks]

Proportion of participants achieving HBV DNA <2000 IU/mL (if >2,000 IU/mL at Baseline); and proportion of participants achieving PCR-nondetectable HBV DNA (if HBV DNA was detectable at Baseline).

To characterize the pharmacodynamics (PD) of ds-siNA on plasma levels of HBsAg and HBV in blood. [Time Frame: 12 weeks]

Track post-treatment duration of any observed efficacy effects.

Eligibility Criteria

Ages Eligible for Study: 18 Years to 65 Years (Adult, Older Adult) Sexes Eligible for Study: All Accepts Healthy Volunteers: Yes

Inclusion Criteria:

Healthy at the time of screening as determined by medical evaluation.

Capable of giving informed consent.

12-lead ECG within normal limits or with no clinically significant abnormalities.

Negative screen for alcohol or drugs of abuse.

Non-smokers for at least 3 months with a negative urinary cotinine concentration at screening.

BMI within range 18.0-32.0 kg/m2 (inclusive).

Female participants not pregnant, not breastfeeding, and not of childbearing potential or willing to follow contraceptive guidance.

Chronic hepatitis B infection (Group B and C only).

Clinical history compatible with compensated liver disease with no evidence of cirrhosis (Group B and C only).

Continuously on nucleotides (NUC) therapy for at least 12 weeks prior to screening (Group C only).

Exclusion Criteria:

    • History of any medical condition that may interfere with the absorption, distribution, or elimination of study drug.

Poorly controlled or unstable hypertension.

History of diabetes mellitus treated with insulin or hypoglycemic agents.

History of asthma requiring hospital admission within the preceding 12 months.

Evidence of G-6-PD deficiency.

Currently poorly controlled endocrine conditions, excluding thyroid conditions.

History of multiple drug allergies or history of allergic reaction to an oligonucleotide or GalNAc.

Clinically relevant surgical history.

Use of prescription medications (excluding contraception for women) within 4 weeks prior to the administration of study intervention.

Use of clinically relevant over-the-counter medication or supplements (excluding routine vitamins) within 7 days of first dosing.

Has received an investigational agent within the 3 months prior to dosing or is in follow-up of another study.

Antiviral therapy (other than entecavir or tenofovir) within 3 months of screening or treatment with interferon in the last 3 years (Group B and C only).

Use within the last 6 months of anticoagulants or systemically administered corticosteroids, immunomodulators, or immunosuppressants (Group B and C only).

Example 5: Synthesis of 5′ End Cap Monomer

Example 5 Monomer Synthesis Scheme

Preparation of (2): To a solution of 1(15 g, 57.90 mmol) in DMF (150 mL) were added AcSK (11.24 g, 98.43 mmol) and TBAI (1.07 g, 2.89 mmol), and the mixture was stirred at 25° C. for 12 h. Upon completion as monitored by LCMS, the mixture was diluted with H2O (10 mL) and extracted with EA (200 mL * 3). The combined organic layers were washed with brine (200 mL * 3), dried over anhydrous Na2SO4, filtered and concentrated under reduced pressure to give 2 (14.5 g, 96.52% yield, 98% purity) as a colorless oil. ESI-LCMS: 254.28 [M+H]+; 1H NMR (400 MHz, CDCl3) δ=4.78-4.65 (m, 2H), 3.19 (d, J=14.1 Hz, 2H), 2.38 (s, 3H), 1.32 (t, J=6.7 Hz, 12H); 31P NMR (162 MHz, CDCl3) δ=20.59.

Preparation of (3): To a solution of 2 (14.5 g, 57.02 mmol) in CH3CN (50 mL) and MeOH (25 mL) was added NaOH (3 M, 28.51 mL), and the mixture was stirred at 25° C. for 12 h under Ar. Upon completion as monitored by TLC, the reaction mixture was concentrated under reduced pressure to remove CH3CN and CH30H. The residue was diluted with water (50 mL) and adjust pH=7 by 6M HCl, and the mixture was extracted with EA (50 mL * 3). The combined organic layers were washed with brine (50 mL * 3), dried over anhydrous Na2SO4, filtered and concentrated under reduced pressure to give 3 (12.1 g, crude) as a colorless oil.

Preparation of (4): To a solution of 3 (12.1 g, 57.01 mmol) in CH3CN (25 mL) and MeOH (25 mL) was added A (14.77 g, 57.01 mmol) dropwise at 25° C., and the mixture was stirred at 25° C. under Ar for 12 h. Upon completion as monitored by LCMS, the reaction mixture was concentrated under reduced pressure to give 4 (19.5 g, 78.85% yield) as a colorless oil. 1H NMR (400 MHz, CDCl3) δ=4.80-4.66 (m, 4H), 2.93 (d, J=11.3 Hz, 4H), 1.31 (dd, J=3.9, 6.1 Hz, 24H); 31P NMR (162 MHz, CDCl3) δ=22.18.

Preparation of (5): To a solution of 4 (19.5 g, 49.95 mmol) in MeOH (100 mL) and H2O (100 mL) was added Oxone (61.41 g, 99.89 mmol) at 25° C. in portions, and the mixture was stirred at 25° C. for 12 h under Ar. Upon completion as monitored by LCMS, the reaction mixture was filtered, and the filtrate was concentrated under reduced pressure to remove MeOH. The residue was extracted with EA (50 mL *3). The combined organic layers were washed with brine (50 mL * 3), dried over anhydrous Na2SO4, filtered and concentrated under reduced pressure to give a residue. The crude product was triturated with i-Pr2O and n-Hexane (1:2, 100 mL) at 25° C. for 30 min to give 5 (15.6 g, 73.94% yield,) as a white solid. 1H NMR (400 MHz, CDCl3) δ=4.92-4.76 (m, 4H), 4.09 (d, J=16.1 Hz, 4H), 1.37 (dd, J=3.5, 6.3 Hz, 24H); 31P NMR (162 MHz, CDCl3) δ=10.17.

Preparation of (7): To a mixture of 5 (6.84 g, 16.20 mmol) in THF (20 mL) was added LiBr (937.67 mg, 10.80 mmol) until dissolved, followed by DIEA (1.40 g, 10.80 mmol, 1.88 mL) under argon at 15° C. The mixture was stirred at 15° C. for 15 min. 6 (4 g, 10.80 mmol) were added. The mixture was stirred at 15° C. for 3 h. Upon completion as monitored by LCMS, the reaction mixture was quenched by addition of H2O (40 mL) and extracted with EA (40 mL * 3). The combined organic layers were washed with brine (100 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash reverse-phase chromatography (120 g C-18 Column, Eluent of 0-60% ACN/H2O gradient @ 80 mL/min) to give 7 (5.7 g, 61.95% yield) as a colorless oil. ESI-LCMS: 611.2 [M+H]+; H NMR (400 MHz, CDCl3); δ=9.26 (s, 1H), 7.50 (d, J=8.1 Hz, 1H), 7.01 (s, 2H), 5.95 (d, J=2.7 Hz, 1H), 5.80 (dd, J=2.1, 8.2 Hz, 1H), 4.89-4.72 (m, 2H), 4.66 (d, J=7.2 Hz, 1H), 4.09-4.04 (m, 1H), 3.77 (dd, J=2.7, 4.9 Hz, 1H), 3.62 (d, J=3.1 Hz, 1H), 3.58 (d, J=3.1 Hz, 1H), 3.52 (s, 3H), 1.36 (td, J=1.7, 6.1 Hz, 12H), 0.92 (s, 9H), 0.12 (s, 6H); 31P NMR (162 MHz, CDCl3) δ=9.02

Preparation of (8): To a mixture of 7 (5.4 g, 8.84 mmol) in THF (80 mL) was added Pd/C (5.4 g, 10% purity) under N2. The suspension was degassed under vacuum and purged with H2 several times. The mixture was stirred under H2 (15 psi) at 20° C. for 1 hr. Upon completion as monitored by LCMS, the reaction mixture was filtered, and the filtrate was concentrated to give 8 (5.12 g, 94.5% yield) as a white solid. ESI-LCMS: 613.3 [M+H]+; H NMR (400 MHz, CD3CN) δ=9.31 (s, 1H), 7.37 (d, J=8.0 Hz, 1H), 5.80-5.69 (m, 2H), 4.87-4.75 (m, 2H), 4.11-4.00 (m, 1H), 3.93-3.85 (m, 1H), 3.80-3.74 (m, 1H), 3.66-3.60 (m, 1H), 3.57-3.52 (m, 1H), 3.49 (s, 3H), 3.46-3.38 (m, 1H), 2.35-2.24 (m, 1H), 2.16-2.03 (m, 1H), 1.89-1.80 (m, 1H), 1.37-1.34 (m, 12H), 0.90 (s, 9H), 0.09 (s, 6H); 31P NMR (162 MHz, CD3CN) δ=9.41.

Preparation of (9): To a solution of 8 (4.4 g, 7.18 mmol) in THF (7.2 mL) was added TBAF (1 M, 7.18 mL), and the mixture was stirred at 20° C. for 1 hr. Upon completion as monitored by LCMS, the reaction mixture was diluted with H2O (50 mL) and extracted with EA (50 mL*4). The combined organic layers were washed with brine (50 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 40 g SepaFlash@Silica Flash Column, Eluent of 0-5%, MeOH/DCM gradient @ 40 mL/min) to give 9 (3.2 g, 88.50% yield) as a white solid. ESI-LCMS: 499.2 [M+H]+1; 1H NMR (400 MHz, CD3CN) δ=9.21 (s, 1H), 7.36 (d, J=8.3 Hz, 1H), 5.81-5.72 (m, 2H), 4.88-4.74 (m, 2H), 3.99-3.87 (m, 2H), 3.84 (dd, J=1.9, 5.4 Hz, 1H), 3.66-3.47 (m, 7H), 2.98 (s, 1H), 2.44-2.15 (m, 2H), 1.36 (d, J=6.0 Hz, 12H); 31P NMR (162 MHz, CD3CN) δ=9.48.

Preparation of (Example 5 monomer): To a mixture of 9 (3.4 g, 6.82 mmol, 1 eq) and 4A MS (3.4 g) in MeCN (50 mL) was added P1(2.67 g, 8.87 mmol, 2.82 mL, 1.3 eq) at 0° C., followed by addition of 1H-imidazole-4,5-dicarbonitrile (886.05 mg, 7.50 mmol) at 0° C. The mixture was stirred at 20° C. for 2 h. Upon completion as monitored by LCMS, the reaction mixture was quenched by addition of saturated aq. NaHCO3(50 mL) and diluted with DCM (100 mL). The organic layer was washed with saturated aq. NaHCO3(50 mL * 2), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue was purified by prep-HPLC: column: YMC-Triart Prep C18 250*50 mm*10 um; mobile phase: [water (10 mM NH4HCO3)-ACN]; B %: 15% to give a impure product. The impure product was further purified by a flash silica gel column (0% to 5% i-PrOH in DCM with 0.5% TEA) to give Example 5 monomer (2.1 g, 43.18% yield) as a white solid. ESI-LCMS: 721.2 [M+Na]+; H NMR (400 MHz, CD3CN) δ=9.29 (s, 1H), 7.45 (d, J=8.1 Hz, 1H), 5.81 (d, J=4.2 Hz, 1H), 5.65 (d, J=8.1 Hz, 1H), 4.79-4.67 (m, 2H), 4.26-4.05 (m, 2H), 4.00-3.94 (m, 1H), 3.89-3.63 (m, 6H), 3.53-3.33 (m, 5H), 2.77-2.61 (m, 2H), 2.31-2.21 (m, 1H), 2.16-2.07 (m, 1H), 1.33-1.28 (m, 12H), 1.22-1.16 (m, 1H), 1.22-1.16 (m, 11H); 31P NMR (162 MHz, CD3CN) δ=149.89, 149.78, 10.07, 10.02.

Example 6. Synthesis of 5′ End Cap Monomer

Example 6 Monomer Synthesis Scheme

Preparation of (2): To a solution of 1(5 g, 13.42 mmol) in DMF (50 mL) were added PPh3 (4.58 g, 17.45 mmol) and 2-hydroxyisoindoline-1,3-dione (2.85 g, 17.45 mmol), followed by a solution of DIAD (4.07 g, 20. 13 mmol, 3.91 mL) in DMF (10 mL) dropwise at 15° C. The resulting solution was stirred at 15° C. for 18 hr. The reaction mixture was then diluted with DCM (50 mL), washed with H2O (60 mL*3) and brine (30 mL), dried over Na2SO4, filtered and evaporated to give a residue. The residue was then triturated with EtOH (55 mL) for 30 min, and the collected white powder was washed with EtOH (10 mL*2) and dried to give 2 (12.2 g, 85. 16% yield) as a white powder (the reaction was set up in two batches and combined) ESI-LCMS: 518.1 [M+H]+.

Preparation of (3): 2 (6 g, 11.59 mmol) was suspended in MeOH (50 mL), and then NH2NH2.H2O (3.48 g, 34. 74 mmol, 3.38 mL, 50% purity) was added dropwise at 20° C. The reaction mixture was stirred at 20° C. for 4 hr. Upon completion, the reaction mixture was diluted with EA (20 mL) and washed with NaHCO3(10 mL*2) and brine (10 mL). The combined organic layers were then dried over Na2SO4, filtered and evaporated to give 3 (8.3 g, 92.5% yield) as a white powder. (The reaction was set up in two batches and combined). ESI-LCMS: 388.0 [M+H]+; H NMR (400 MHz, DMSO-d6) δ=11.39 (br s, 1H), 7.72 (d, J=8.1 Hz, 1H), 6.24-6.09 (m, 2H), 5.80 (d, J=4.9 Hz, 1H), 5.67 (d, J=8.1 Hz, 1H), 4.26 (t, J=4.9 Hz, 1H), 4.03-3.89 (m, 1H), 3.87-3.66 (m, 3H), 3.33 (s, 3H), 0.88 (s, 9H), 0.09 (d, J=1.3 Hz, 6H)

Preparation of (4): To a solution of 3 (7 g, 18.06 mmol) and Py (1.43 g, 18.06 mmol, 1.46 mL) in DCM (130 mL) was added a solution of MsCl (2.48 g, 21.68 mmol, 1. 68 mL) in DCM (50 mL) dropwise at −78° C. under N2. The reaction mixture was allowed to warm to 15° C. in 30 min and stirred at 15° C. for 3 h. The reaction mixture was quenched by addition of ice-water (70 mL) at 0° C., and then extracted with DCM (50 mL * 3). The combined organic layers were washed with saturated aq. NaHCO3(50 mL) and brine (30 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 30 g SepaFlash@Silica Flash Column, Eluent of 0-20% i-PrOH/DCM gradient @ 30 mL/min to give 4 (6.9 g, 77.94% yield) as a white solid. ESI-LCMS: 466.1 [M+H]+; 1H NMR (400 MHz, DMSO-d) δ=11.41 (br s, 1H), 10. 15 (s, 1H), 7. 69 (d, J=8.1 Hz, 1H), 5.80 (d, J=4.4 Hz, 1H), 5.65 (d, J=8. 1 Hz, 1H), 4.24 (t, J=5.2 Hz, 1H), 4.16-3.98 (m, 3H), 3. 87 (t, J=4.8 Hz, 1H), 3.00 (s, 3H), 2.07 (s, 3H), 0.88 (s, 9H), 0. 10 (d, J=1.5 Hz, 6H)

Preparation of (5): To a solution of 4 (6.9 g, 14.82 mmol) in THF (70 mL) was added TBAF (1 M, 16.30 mL) at 15° C. The reaction mixture was stirred at 15° C. for 18 hr, and then evaporated to give a residue. The residue was purified by flash silica gel chromatography (ISCO@; 24 g SepaFlash@ Silica Flash Column, Eluent of 0˜9% MeOH/Ethyl acetate gradient @ 30 mL/min) to give 5 (1.8 g, 50.8% yield) as a white solid. ESI-LCMS: 352.0 [M+H]+; 1H NMR (400 MHz, DMSO-d6) δ=11.40 (s, 1H), 10.13 (s, 1H), 7.66 (d, J=8.1 Hz, 1H), 5.83 (d, J=4. 9 Hz, 1H), 5.65 (dd, J=1. 8, 8. 1 Hz, 1H), 5.36 (d, J=6. 2 Hz, 1H), 4.13-4.00 (m, 4H), 3. 82 (t, J=5.1 Hz, 1H), 3.36 (s, 3H), 3.00 (s, 3H)

Preparation of (Example 6 monomer): To a mixture of 5 (3 g, 8.54 mmol) and DIEA (2.21 g, 17.08 mmol, 2.97 mL) in ACN (90 mL) was added P2 (3.03 g, 12.81 mmol) dropwise at 15° C. The reaction mixture was stirred at 15° C. for 5 h. Upon completion, the reaction mixture was diluted with EA (40 mL) and quenched with 5% NaHCO3(20 mL). The organic layer was washed with brine (30 mL), dried over Na2SO4, filtered and evaporated to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 12 g SepaFlash@ Silica Flash Column, Eluent of 0-15% i-PrOH/(DCM with 2% TEA) gradient @ 20 mL/min) to Example 6 monomer (2.1 g, 43.93% yield) as a white solid. ESI-LCMS: 552.3 [M+H]+; 1H NMR (400 MHz, CD3CN) δ=8.78 (br s, 1H), 7.57 (dd, J=4.6, 8.2 Hz, 1H), 5.97-5.80 (m, 1H), 5.67 (d, J=8. 3 Hz, 1H), 4.46-4.11 (m, 4H), 3.95-3.58 (m, 5H), 3.44 (d, J=16. 3 Hz, 3H), 3.02 (d, J=7. 5 Hz, 3H), 2. 73-2.59 (m, 2H), 1.23-1.15 (m, 12H); 31P NMR (162 MHz, CD3CN) δ=150.30, 150.10

Example 7: Synthesis of 5′ End Cap Monomer

Example 7 Monomer Synthesis Scheme

Preparation of (2): To the solution of 1 (5 g, 12.90 mmol) and TEA (1.57 g, 15.48 mmol, 2.16 mL) in DCM (50 mL) was added P-4 (2.24 g, 15.48 mmol, 1.67 mL) in DCM (10 mL) dropwise at 15° C. under N2. The reaction mixture was stirred at 15° C. for 3 h. Upon completion as monitored by LCMS and TLC (PE: EtOAc=0:1), the reaction mixture was concentrated to dryness, diluted with H2O (20 mL), and extracted with EA (50 mL*3). The combined organic layers were washed with brine (30 mL*3), dried over anhydrous Na2SO4, filtered, and the filtrate was concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 40 g SepaFlash@ Silica Flash Column, Eluent of 0-95% Ethyl acetate/Petroleum ether gradient @ 60 mL/min) to give 2 (5.3 g, 71.3% yield) as a white solid. ESI-LCMS: 496.1 [M+H]+; H NMR (400 MHz, CDCl3) δ=0.10 (d, J=4.02 Hz, 6H) 0.91 (s, 9H) 3.42-3.54 (m, 3H) 3.65-3.70 (m, 1H) 3.76-3.89 (m, 6H) 4.00 (dd, J=10.92, 2.89 Hz, 1H) 4.08-4.13 (m, 1H) 4.15-4.23 (m, 2H) 5.73 (dd, J=8.28, 2.01 Hz, 1H) 5.84 (d, J=2.76 Hz, 1H) 6.86 (d, J=15.81 Hz, 1H) 7.72 (d, J=8.03 Hz, 1H) 9.10 (s, 1H); 31P NMR (162 MHz, CD3CN) 6=9.65

Preparation of (3): To a solution of 2 (8.3 g, 16.75 mmol) in THF (50 mL) were added TBAF (1 M, 16.75 mL) and CH3COOH (1.01 g, 16.75 mmol, 957.95 uL). The mixture was stirred at 20° C. for 12 hr. Upon completion as monitored by LCMS, the reaction mixture was concentrated under reduced pressure. The residue was purified by column chromatography (SiO2, PE: EA=0˜100%; MeOH/EA=0˜10%) to give 3 (5 g, 77.51% yield) as a white solid. ESI-LCMS: 382.1 [M+H]+; H NMR (400 MHz, CDCl3) δ=3.35 (s, 3H) 3.65 (br d, J=2.76 Hz, 3H) 3.68 (d, J=2.76 Hz, 3H) 3.77 (t, J=5.08 Hz, 1H) 3.84-4.10 (m, 4H) 5.33 (br d, J=5.52 Hz, 1H) 5.62 (d, J=7.77 Hz, 1H) 5.83 (d, J=4.94 Hz, 1H) 7.69 (d, J=7.71 Hz, 1H) 9.08 (d, J=16.81 Hz, 1H) 11.39 (br s, 1H); 31P NMR (162 MHz, CD3CN) 6=15.41

Preparation of (Example 7 monomer): To a solution of 3 (2 g, 5.25 mmol) and DIPEA (2.03 g, 15.74 mmol, 2.74 mL, 3 eq) in MeCN (21 mL) and pyridine (7 mL) was added P2 (1.86 g, 7.87 mmol) dropwise at 20° C., and the mixture was stirred at 20° C. for 3 hr. Upon completion as monitored by LCMS, the reaction mixture was diluted with water (20 mL) and extracted with EA (50 mL). The combined organic layers were washed with brine (30 mL), dried over anhydrous Na2SO4, filtered, and the filtrate was concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 25 g SepaFlash@ Silica Flash Column, Eluent of 0-45% (Ethyl acetate: EtOH=4:1)/Petroleum ether gradient) to give Example 7 monomer (1.2 g, 38.2% yield) as a white solid. ESI-LCMS: 604.1 [M+H]+; 1H NMR (400 MHz, CD3CN) & 1.12-1.24 (m, 12H) 2.61-2.77 (m, 2H) 3.43 (d, J=17.64 Hz, 3H) 3.59-3.69 (m, 2H) 3.71-3.78 (m, 6H) 3.79-4.14 (m, 5H) 4.16-4.28 (m, 1H) 4.29-4.42 (m, 1H) 5.59-5.72 (m, 1H) 5.89 (t, J=4.53 Hz, 1H) 7.48 (br d, J=12.76 Hz, 1H) 7.62-7.74 (m, 1H) 9.26 (br s, 1 H); 31P NMR (162 MHz, CD3CN) δ=150.57, 149.96, 9.87

Example 8: Synthesis of 5′ End Cap Monomer

Example 8 Monomer Synthesis Scheme

Preparation of (2): To a solution of 1 (30 g, 101.07 mmol, 87% purity) in CH3CN (1.2 L) and Py (60 mL) were added 12 (33.35 g, 131.40 mmol, 26.47 mL) and PPh3 (37.11 g, 141.50 mmol) in one portion at 10′° C. The reaction was stirred at 25° C. for 48 h. Upon completion, the mixture was diluted with saturated aq.Na2S2O3 (300 mL) and saturated aq.NaHCO3(300 mL), concentrated to remove CH3CN, and extracted with EtOAc (300 mL * 3). The combined organic layers were washed with brine (300 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 330 g SepaFlash@ Silica Flash Column, Eluent of 0.60%/Methanol/Dichloromethane gradient @ 100 mL/min) to give 2 (28.2 g, 72% yield) as a brown solid. ESI-LCMS: 369.1 [M+H]+; H NMR (400 MHz, DMSO-d6) δ=11.43 (s, 1H), 7.68 (d, J=8.1 Hz, 1H), 5.86 (d, J=5.5 Hz, 1H), 5.69 (d, J=8.1 Hz, 1H), 5.46 (d, J=6.0 Hz, 1H), 4.08-3.96 (m, 2H), 3.90-3.81 (m, 1H), 3.60-3.51 (m, 1H), 3.40 (dd, J=6.9, 10.6 Hz, 1H), 3.34 (s, 3H).

Preparation of (3): To the solution of 2 (12 g, 32.6 mmol) in DCM (150 mL) were added AgNO3 (11.07 g, 65.20 mmol), 2,4,6-trimethylpyridine (11.85 g, 97.79 mmol, 12.92 mL), and DMTC1 (22.09 g, 65.20 mmol) at 10° C., and the reaction mixture was stirred at 10° C. for 16 hr. Upon completion, the mixture was filtered and the filtrate was concentrated under reduced pressure. The residue was purified by flash silica gel chromatography (ISCO®; 120 g SepaFlash@ Silica Flash Column, Eluent of 0˜50% Ethyl acetate/Petroleum ethergradient @ 60 mL/min) to give 3 (17 g, 70.78% yield) as a yellow solid. ESI-LCMS: 693.1 [M+Na]+1; H NMR (400 MHz, DMSO-d6) δ=11.46 (s, 1H), 7.60 (d, J=8.4 Hz, 1H), 7.49 (d, J=7.2 Hz, 2H), 7.40-7.30 (m, 6H), 7.29-7.23 (m, 1H), 6.93 (d, J=8.8 Hz, 4H), 5.97 (d, J=6.0 Hz, 1H), 5.69 (d, J=8.0 Hz, 1H), 4.05-4.02 (m, 1H), 3.75 (d, J=1.2 Hz, 6H), 3.57 (t, J=5.6 Hz, 1H), 3.27 (s, 4H), 3.06 (t, J=10.4 Hz, 1H), 2.98-2.89 (m, 1H).

Preparation of (4): To a solution of 3 (17 g, 25.35 mmol) in DMF (200 mL) was added AcSK (11.58 g, 101.42 mmol) at 25° C., and the reaction was stirred at 60° C. for 2 hr. The mixture was diluted with H2O (600 mL) and extracted with EtOAc (300 mL * 4). The combined organic layers were washed with brine (300 mL), dried over Na2SO4, filtered, and concentrated under reduced pressure to give 4 (15.6 g, crude) as a brown solid, which was used directly without further purification. ESI-LCMS: 641.3 [M+H]+.

Preparation of (5): To a solution of 4 (15.6 g, 25.21 mmol) in CH3CN (200 mL) were added DTT (11.67 g, 75.64 mmol, 11.22 mL) and LiOH.H2O (1.06 g, 25.21 mmol) at 10° C. under Ar. The reaction was stirred at 10° C. for 1 hr. The mixture was concentrated under reduced pressure to remove CH3CN, and the residue was diluted with H2O (400 mL) and extracted with EtOAc (200 mL * 3). The combined organic layers were washed with brine (300 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 220 g SepaFlash@ Silica Flash Column, Eluent of 0˜60% Ethyl acetate/Petroleum ether gradient @ 100 mL/min) to give 5 (8.6 g, 56.78% yield) as a white solid. ESI-LCMS: 599.3 [M+Na]+; 1H NMR (400 MHz, DMSO-d6) δ=8.79 (s, 1H), 7.61 (d, .,8.0 Hz, 1H), 7.56-7.46 (m, 2H), 7.45-7.37 (m, 4H), 7.36-7.27 (m, 3H), 6.85 (dd, J=2.8, 8.8 Hz, 4H), 5.85 (d, J=1.3 Hz, 1H), 5.68 (dd, j=2.0, 8.2 Hz, 1H), 4.33-4.29 (m, 1H), 3.91 (dd, J=4.8, 8.2 Hz, 1H), 3.81 (d, J=1.6 Hz, 6H), 3.33 (s, 3H), 2.85-2.80 (m, 1H), 2.67-2.55 (m, 2H), 1.11 (t,.J=8.8 Hz, 1H).

Preparation of (Example 8 monomer): To a solution of 5 (6 g, 10.40 mmol) in DCM (120 mL) were added P1(4.08 g, 13.53 mmol, 4.30 mL) and DCI (1.35 g, 11.45 mmol) in one portion at 10° C. under Ar. The reaction was stirred at 10° C. for 2 hr. The reaction mixture was diluted with saturated aq.NaHCO3(50 mL) and extracted with DCM (20 mL * 3). The combined organic layers were washed with brine (30 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue was purified by prep-HPLC (column: YMC-Triart Prep C18 250*50 mm*10 um; mobile phase: [water(10 mM NH4HCO3)-ACN]; B %: 35%-81%,20 min) to give Example 8 monomer (3.54 g, 43.36% yield) as a yellow solid. ESI-LCMS: 776.4 [M+H]+; 1H NMR (400 MHz, DMSO-d6) δ=7.65-7.38 (m, 7H), 7.37-7.22 (m, 3H), 6.90 (d, J=8.4 Hz, 4H), 5.92 (s, 1H), 5.66 (t, J=8.2 Hz, 1H), 4.13 (d, J=4.0 Hz, 1H), 4.00-3.88 (m, 1H), 3.87-3.59 (m, 10H), 3.33 (d, J=5.8 Hz, 3H), 3.12-2.94 (m, 1H), 2.78-2.60 (m, 3H), 2.55-2.48 (m, 1H), 1.36-0.98 (m, 12H); 31P NMR (162 MHz, DMSO-d6) δ=162.69.

Example 9: Synthesis of 5′ End Cap Monomer

Example 9 Monomer Synthesis Scheme

Preparation of (2): To a solution of 1 (22.6 g, 45.23 mmol) in DCM (500 mL) and H2O (125 mL) were added TEMPO (6.40 g, 40.71 mmol) and DIB (29.14 g, 90.47 mmol) at 0° C. The mixture was stirred at 20° C. for 20 h. Upon completion as monitored by LCMS, saturated aq. NaHCO3 was added to the mixture to adjust pH>8. The mixture was diluted with H2O (200 mL) and washed with DCM (100 mL * 3). The aqueous layer was collected, adjusted to pH<5 by HCl (4M), and extracted with DCM (200 mL * 3). The combined organic layers were washed with brine (300 mL), dried over Na2SO4, filtered, and concentrated under reduced pressure to give 2 (17.5 g, 68.55% yield) as a yellow solid. ESI-LCMS: 514.2 [M+H]+; 1H NMR (400 MHz, DMSO-d6) δ=11.27 (s, 1H), 8.86 (s, 1H), 8.78 (s, 1H), 8.06 (d, J=7.5 Hz, 2H), 7.68-7.62 (m, 1H), 7.59-7.52 (m, 2H), 6.28 (d, J=6.8 Hz, 1H), 4.82-4.76 (m, 1H), 4.54 (dd, J=4.1, 6.7 Hz, 1H), 4.48 (d, J=1.8 Hz, 1H), 3.32 (s, 3H), 0.94 (s, 9H), 0.18 (d, J=4.8 Hz, 6H).

Preparation of (3): To a solution of 2 (9.3 g, 18.11 mmol) in MeOH (20 mL) was added SOCl2 (3.23 g, 27.16 mmol, 1.97 mL) dropwise at 0° C. The mixture was stirred at 20° C. for 0.5 hr. Upon completion as monitored by LCMS, the reaction mixture was quenched by addition of saturated aq. NaHCO3(80 mL) and concentrated under reduced pressure to remove MeOH. The aqueous layer was extracted with DCM (80 mL * 3). The combined organic layers were washed with brine (200 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 120 g SepaFlash@ Silica Flash Column, Eluent of 0-5%, MeOH/DCM gradient @ 85 mL/min) to give 3 (5.8 g, 60% yield) as a yellow solid. ESI-LCMS: 528.3 [M+H]+; 1H NMR (400 MHz, DMSO-d6) δ=11.28 (s, 1H), 8.79 (d, J=7.3 Hz, 2H), 8.06 (d, J=7.5 Hz, 2H), 7.68-7.62 (m, 1H), 7.60-7.53 (m, 2H), 6.28 (d, J=6.6 Hz, 1H), 4.87 (dd, J=2.4, 4.0 Hz, 1H), 4.61 (dd, J=4.3, 6.5 Hz, 1H), 4.57 (d, J=2.2 Hz, 1H), 3.75 (s, 3H), 3.32 (s, 3H), 0.94 (s, 9H), 0.17 (d, J=2.2 Hz, 6H).

Preparation of (4): To a mixture of 3 (5.7 g, 10.80 mmol) in CD30D (120 mL) was added NaBD4 (1.63 g, 43.21 mmol) in portions at 0° C., and the mixture was stirred at 20° C. for 1 hr. Upon completion as monitored by LCMS, the reaction mixture was neutralized by AcOH (−10 mL) and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 40 g SepaFlash@Silica Flash Column, Eluent of 0-5%, MeOH/DCM gradient @ 40 mL/min) to give 4 (4.15 g, 7.61 mmol, 70.45% yield) as a yellow solid. ESI-LCMS: 502.2 [M+H]+; 1H NMR (400 MHz, DMSO-d6) δ=11.23 (s, 1H), 8.76 (s, 2H), 8.04 (d, J=7.3 Hz, 2H), 7.69-7.62 (m, 1H), 7.60-7.52 (m, 2H), 6.14 (d, J=6.0 Hz, 1H), 5.18 (s, 1H), 4.60-4.51 (m, 2H), 3.98 (d, J=3.0 Hz, 1H), 3.32 (s, 3H), 0.92 (s, 9H), 0.13 (d, J=1.5 Hz, 6H).

Preparation of (5): To a solution of 4 (4.85 g, 9.67 mmol) in pyridine (50 mL) was added DMTrCl (5.90 g, 17.40 mmol) at 25° C. and the mixture was stirred for 2 hr. Upon completion as monitored by LCMS, the reaction mixture was concentrated under reduced pressure to remove pyridine. The residue was diluted with EtOAc (150 mL) and washed with H2O (50 mL * 3), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 80 g SepaFlash@ Silica Flash Column, Eluent of 0˜70%, EA/PE gradient @ 60 mL/min) to give 5 (6.6 g, 84.06% yield) as a yellow solid. ESI-LCMS: 804.3[M+H]+, 1H NMR (400 MHz, DMSO-d&) δ=11.22 (s, 1H), 8.68 (d, J=11.0 Hz, 2H), 8.03 (d, J=7.3 Hz, 2H), 7.68-7.60 (m, 1H), 7.58-7.49 (m, 2H), 7.37-7.30 (m, 2H), 7.27-7.16 (m, 7H), 6.88-6.79 (m, 4H), 6.17 (d, J=4.2 Hz, 1H), 4.72 (t, J=5.0 Hz, 1H), 4.60 (t, J=4.5 Hz, 1H), 4.03-3.98 (m, 1H), 3.71 (s, 6H), 0.83 (s, 9H), 0.12-0.03 (m, 6H).

Preparation of (6): To a solution of 5 (6.6 g, 8.21 mmol) in THF (16 mL) was added TBAF (1 M, 8.21 mL,), and the mixture was stirred at 20° C. for 2 hr. Upon completion as monitored by LCMS, the reaction mixture was diluted with EA (150 mL) and washed with H2O (50 mL*3). The organic layer was washed with brine (150 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 80 g SepaFlash@ Silica Flash Column, Eluent of 10-100%, EA/PE gradient @ 30 mL/min) to give 6 (5.4 g, 94.4% yield) as a yellow solid. ESI-LCMS: 690.3 [M+H]+; H NMR (400 MHz, DMSO-d6) δ=11.24 (s, 1H), 8.69 (s, 1H), 8.62 (s, 1H), 8.05 (d, J=7.3 Hz, 2H), 7.69-7.62 (m, 1H), 7.60-7.52 (m, 2H), 7.40-7.33 (m, 2H), 7.30-7.18 (m, 7H), 6.84 (dd, J=5.9, 8.9 Hz, 4H), 6.19 (d, J=4.8 Hz, 1H), 5.36 (d, J=6.0 Hz, 1H), 4.59-4.52 (m, 1H), 4.48 (q, J=5.1 Hz, 1H), 4.11 (d, J=4.8 Hz, 1H), 3.72 (d, J=1.0 Hz, 6H), 3.40 (s, 3H).

Preparation of (Example 9 monomer): To a solution of 6 (8.0 g, 11.60 mmol) in MeCN (150 mL) was added P-1 (4.54 g, 15.08 mmol, 4.79 mL) at 0° C., followed by DCI (1.51 g, 12.76 mmol) in one portion. The mixture was warmed to 20° C. and stirred for 2 h. Upon completion as monitored by LCMS, the reaction mixture was quenched by addition of saturated aq. NaHCO3(50 mL) and diluted with DCM (250 mL). The organic layer was washed with saturated aq.NaHCO3(50 mL * 2), dried over Na2SO4, filtered and concentrated under reduced pressure. The residue was purified by a flash silica gel column (0% to 60% EA in PE contain 0.5% TEA) to give Example 9 monomer (5.75 g, 55.37% yield, 99.4% purity) as a white solid. ESI-LCMS: 890.4 [M+H]+; 1H NMR (400 MHz, CD3CN) δ=9.55 (s, 1H), 8.63-8.51 (m, 1H), 8.34-8.24 (m, 1H), 7.98 (br d, J=7.5 Hz, 2H), 7.65-7.55 (m, 1H), 7.53-7.46 (m, 2H), 7.44-7.37 (m, 2H), 7.32-7.17 (m, 7H), 6.84-6.77 (m, 4H), 6.14 (d, J=4.3 Hz, 1H), 4.84-4.73 (m, 1H), 4.72-4.65 (m, 1H), 4.34-4.27 (m, 1H), 3.91-3.61 (m, 9H), 3.50-3.43 (m, 3H), 2.72-2.61 (m, 1H), 2.50 (t, J=6.0 Hz, 1H), 1.21-1.15 (m, 10H), 1.09 (d, J=6.8 Hz, 2H); 31P NMR (162 MHz, CD3CN) δ=150.01, 149.65

Example 10: Synthesis of 5′ End Cap Monomer

Example 10 Monomer Synthesis Scheme

Preparation of (2): To a solution of 1(10 g, 27.22 minol) in CH3CN (200 mL) and 1120 (50 mL) were added TEMPO (3.85 g, 24.50 minol) and DIB (17.54 g, 54.44 minol). The mixture was stirred at 25° C. for 12 h. Upon completion as monitored by LCMS, the reaction mixture was concentrated under reduced pressure to give a residue. The residue was triturated with EtOAc (600 mL) for 30 min. The resulting suspension was filtered and the collected solid was washed with EtOAc (300 mL*2) to give 2 (20.09 g, 91.5% yield) as a white solid. ESI-LCMS: 382.0 [M+H]+.

Preparation of (3): To a solution of 2 (6 g, 15.73 mmol) in MeOH (100 mL) was added SOCl2 (2.81 g, 23.60 mmol, 1.71 mL) dropwise at 0° C. The mixture was stirred at 25° C. for 12 h. Upon completion as monitored by LCMS, the reaction mixture was quenched by addition of NaHCO3(4 g) and stirred at 25° C. for 30 min. The reaction mixture was filtered and the filtrate was concentrated under reduced pressure to give 3 (18.8 g, 95.6% yield) as a white solid. The crude product was used for the next step without further purification. (The reaction was set up in parallel 3 batches and combined). ESI-LCMS: 396.1 [M+H]+;1H NMR (400 MHz, DMSO-d6) δ=12.26-11.57 (m, 2H), 8.42-8.06 (m, 1H), 6.14-5.68 (m, 2H), 4.56 (s, 2H), 4.33 (dd, J=4.0, 7.3 Hz, 1H), 3.77 (m, 3H),3.30 (s, 3H), 2.81-2.69 (m, 1H), 1.11 (s, 6H)

Preparation of (4 & 5): To a mixture of 3 (10.1 g, 25.55 mmol) in CD30D (120 mL) was added NaBD4 (3.29 g, 86.86 mmol, 3.4 eq) in portions at 0° C. The mixture was stirred at 25° C. for 1 h. Upon completion as monitored by LCMS, the reaction mixture was neutralized with AcOH (˜15 mL) and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 120 g SepaFlash@ Silica Flash Column, Eluent of 0-7.4%, MeOH/DCM gradient @ 80 mL/min) to give 4 (2.98 g, 6.88 mmol, 27% yield) as a yellow solid. ESI-LCMS: 370.1[M+H]+ and 5 (10.9 g, crude) as a yellow solid. ESI-LCMS: 300.1[M+H]+; 1H NMR (400 MHz, CD30D) δ=7.85 (s, 1H), 5.87 (d, J=6.0 Hz, 1H), 4.46-4.39 (m, 1H), 4.34 (t, J=5.4 Hz, 1H), 4.08 (d, J=3.1 Hz, 1H), 3.49-3.38 (m, 4H)

Preparation of 6: To a solution of 4 (1.9 g, 4.58 mmol, 85.7% purity) in pyridine (19 mL) was added DMTrCl (2.02 g, 5.96 mmol). The mixture was stirred at 25° C. for 2 h under N2. Upon completion as monitored by LCMS, the reaction mixture was quenched by MeOH (10 mL) and concentrated under reduce pressure to give a residue. The residue was diluted with H2O (10 mL*3) and extracted with EA (20 mL*3). The combined organic layers were washed with brine (20 mL), dried over anhydrous Na2SO4, filtered and concentrated under reduce pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 25 g SepaFlash@ Silica Flash Column, Eluent of 0-77%, PE: (EA with 10% EtOH): 1% TEA@ 35 mL/min) to give 6 (2.6 g, 81.71% yield, 96.71% purity) as a white foam. ESI-LCMS: 672.2 [M+H]+; 1H NMR (400 MHz, CDCl3) δ=12.02 (s, 1H), 7.96 (s, 1H), 7.83 (s, 1H), 7.51 (d, J=7.4 Hz, 2H), 7.37 (d, J=8.6 Hz, 4H), 7.25-7.17 (m, 2H), 6.80 (t, J=8.4 Hz, 4H), 5.88 (d, J=6.3 Hz, 1H), 4.69 (t, J=5.7 Hz, 1H), 4.64 (s, 1H), 4.54 (s, 1H), 4.19 (d, J=2.9 Hz, 1H), 3.77 (d, J=4.5 Hz, 6H), 3.60-3.38 (m, 3H), 2.81 (s, 1H), 1.81 (td, J=6.9, 13.7 Hz, 1H), 0.97 (d, J=6.8 Hz, 3H), 0.80 (d, J=6.9 Hz, 3H)

Preparation of Example 10 monomer: To a solution of 6 (8.4 g, 12.5 mmol) in MeCN (80 mL) was added P-1 (4.9 g, 16.26 mmol, 5.16 mL) at 0° C., followed by addition of DCI (1.624 g, 13.76 mmol) in one portion at 0° C. under Ar. The mixture was stirred at 25° C. for 2 h. Upon completion as monitored by LCMS, the reaction mixture was quenched with saturated aq.NaHCO3(20 mL) and extracted with DCM (50 mL*2). The combined organic layers were dried over anhydrous Na2SO4, filtered and concentrated under reduce pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 40 g SepaFlash@ Silica Flash Column, Eluent of 0-52% PE: EA (10% EtOH): 5% TEA, @ 80 mL/min) to give Example 10 monomer (3.4 g, 72.1% yield,) as a white foam. ESI-LCMS: 872.4 [M+H]+; 1H NMR (400 MHz, CD3CN) & 12.46-11.07 (m, 1H), 9.29 (s, 1H), 7.84 (d, J=14.6 Hz, 1H), 7.42 (t, J=6.9 Hz, 2H), 7.34-7.17 (m, 7H), 6.85-6.77 (m, 4H), 5.95-5.77 (m, 1H), 4.56-4.40 (m, 2H), 4.24 (dd, J=4.0, 13.3 Hz, 1H), 3.72 (d, J=2.0 Hz, 7H), 3.66-3.53 (m, 3H), 3.42 (d, J=11.8 Hz, 3H), 2.69-2.61 (m, 1H), 2.60-2.42 (m, 2H), 1.16-1.00 (m, 18H); 31P NMR (162 MHz, CD3CN) δ=149.975, 149.9

Example 11: Synthesis of 5′ End Cap Monomer

Example 11 Monomer Synthesis Scheme

Preparation of (2): To a solution of 1 (40 g, 58.16 mmol) in DMF (60 mL) were added imidazole (11.88 g, 174.48 mmol), NaI (13.08 g, 87.24 mmol), and TBSCI (17.52 g, 116.32 mmol) at 20° C. in one portion. The reaction mixture was stirred at 20° C. for 12 h. Upon completion, the mixture was diluted with EA (200 mL). The organic layer was washed with brine/water (80 mL/80 mL *4), dried over Na2SO4, filtered and evaporated to give 2 (50.8 g, crude) as yellow solid. ESI-LCMS: 802.3 [M+H]+

Preparation of (3): To a solution of 2 (8.4 g, 10.47 mmol) in DCM (120 mL) were added Et3SiH (3.06 g, 26.3 mmol, 4.2 mL) and TFA (1.29 g, 0.84 mL) dropwise at 0° C. The reaction mixture was stirred at 20° C. for 2 h. The reaction mixture was washed with saturated aq.NaHCO3(15 mL) and brine (80 mL). The organic layer was dried over Na2SO4, filtered and evaporated. The residue was purified by flash silica gel chromatography (ISCO@; 80 g SepaFlash@ Silica Flash Column, Eluent of 0˜83% EA/PE gradient @ 80 mL/min) to give 3 (2.92 g, 55.8% yield,) as a white solid. ESI-LCMS: 500.2 [M+H]+;1IH NMR (400 MHz, CDCl3) δ=8.79 (s, 1H), 8.14 (s, 1H), 8.02 (d, J=7.6 Hz, 2H), 7.64-7.58 (m, 1H), 7.56-7.49 (m, 2H), 5.98-5.93 (m, 1H), 4.63-4.56 (m, 2H), 4.23 (s, 1H), 3.98 (dd, J=1.5, 13.1 Hz, 1H), 3.75 (dd, J=1.5, 13.1 Hz, 1H), 3.28 (s, 3H), 2.06-1.99 (m, 1H), 1.00-0.90 (m, 9H), 0.15 (d, J=7.0 Hz, 6H).

Preparation of (4): 3 (6 g, 12.01 mmol) and tert-butyl N-methylsulfonylcarbamate (3.52 g, 18.01 mmol) were co-evaporated with toluene (50 mL), dissolved in dry THF (100 mL), and cooled to 0° C. PPh3 (9.45 g, 36.03 mmol,) was then added, followed by dropwise addition of DIAD (7.28 g, 36.03 mmol, 7.00 mL) in dry THF (30 mL). The reaction mixture was stirred at 20° C. for 18 h. Upon completion, the reaction mixture was then diluted with DCM (100 mL) and washed with water (70 mL) and brine (70 mL), dried over Na2SO4, filtered and evaporated to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 80 g SepaFlash@ Silica Flash Column, Eluent of 0˜100% Ethyl acetate/Petroleum ether gradient @ 60 mL/min) followed by reverse-phase HPLC (0.1% NH3.H2O condition, eluent at 74%) to give 4 (2.88 g, 25% yield) as a white solid. ESI-LCMS: 677.1 [M+H]+; 1H NMR (400 MHz, CDCl3) δ=9.24 (s, 1H), 8.84 (s, 1H), 8.36 (s, 1H), 8.05 (br d, J=7.3 Hz, 2H), 7.66-7.42 (m, 4H), 6.16 (d, J=5.0 Hz, 1H), 4.52 (br t, J=4.5 Hz, 1H), 4.25-4.10 (m, 1H), 3.97 (br dd, J=8.0, 14.8 Hz, 1H), 3.48 (s, 3H), 3.27 (s, 3H), 1.54 (s, 9H), 0.95 (s, 9H), 0.14 (d, J=0.8 Hz, 6H).

Preparation of (5): To a solution of 4 (2.8 g, 4.14 mmol) in THF (20 mL) was added TBAF (4 M, 1.03 mL) and the mixture was stirred at 20° C. for 12 h. The reaction mixture was then evaporated. The residue was purified by flash silica gel chromatography (ISCO®; 12 g SepaFlash@ Silica Flash Column, Eluent of 0-6% MeOH/ethyl acetate gradient @ 20 mL/min) to give 5 (2.1 g, 83.92% yield) as a white solid. ESI-LCMS: 563.1[M+H]+; 1H NMR (400 MHz, CDCl3) δ=8.85-8.77 (m, 1H), 8.38 (s, 1H), 8.11-7.99 (m, 2H), 7.64-7.50 (m, 4H), 6.19 (d, J=2.8 Hz, 1H), 4.36-4.33 (m, 1H), 4.29 (br d, J=4.3 Hz, 1H), 4.22-4.02 (m, 2H), 3.65-3.59 (m, 3H), 3.28 (s, 3H), 1.54 (s, 9H).

Preparation of (6): To a solution of 5 (2.1 g, 3.73 mmol) in DCM (20 mL) was added TFA (7.70 g, 67.53 mmol, 5 mL) at 0° C. The reaction mixture was stirred at 20° C. for 24 h. Upon completion, the reaction was quenched with saturated aq. NaHCO3 to reach pH 7. The organic layer was dried over Na2SO4, filtered, and evaporated at low pressure. The residue was purified by flash silica gel chromatography (ISCO®; 12 g SepaFlash@ Silica Flash Column, Eluent of 0-7% DCM/MeOH gradient @ 20 mL/min) to give 1.6 g (impure, 75% LCMS purity), followed by prep-HPLC [FA condition, column: Boston Uni C18 40*150*5 um; mobile phase: [water (0.225% FA)-ACN]; B %: 8%-38%,7.7 min.] to give 6 (1.04 g, 63.7% yield) as a white solid. ESI-LCMS: 485.0 [M+Na]+; 1H NMR (400 MHz, DMSO-d6) δ=11.27-11.21 (m, 1H), 8.77 (s, 1H), 8.74 (s, 1H), 8.05 (d, J=7.3 Hz, 2H), 7.68-7.62 (m, 1H), 7.59-7.53 (m, 2H), 7.39 (t, J=6.3 Hz, 1H), 6.16 (d, J=6.0 Hz, 1H), 5.48 (d, J=5.5 Hz, 1H), 4.55 (t, J=5.5 Hz, 1H), 4.43-4.37 (m, 1H), 4.08-4.02 (m, 1H), 3.41-3.36 (m, 1H), 3.35 (s, 3H), 3.31-3.22 (m, 1H), 2.91 (s, 3H).

Preparation of (Example 11 monomer): To a solution of 6 (1 g, 2.16 mmol) in DCM (30 mL) was added P1 (977.58 mg, 3.24 mmol, 1.03 mL), followed by DCI (306.43 mg, 2.59 mmol) at 0° C. in one portion under Ar atmosphere. The mixture was degassed and purged with Ar for 3 times, warmed to 20° C., and stirred for 2 hr under Ar atmosphere. Upon completion as monitored by LCMS and TLC (PE: EtOAc=4:1), the reaction mixture was diluted with sat.aq. NaHCO3(30 mL) and extracted with DCM (50 mL*2). The combined organic layers were dried over anhydrous Na2SO4, filtered, and the filtrate was concentrated under reduced pressure to give a residue. The crude product was purified by reversed-phase HPLC (40 g C18 column: neutral condition, Eluent of 0-57% of 0.3% NH4HCO3 in H2O/CH3CN ether gradient @ 35 mL/min) to give Example 11 monomer (0.49 g, 33.7% yield) as a white solid. ESI-LCMS: 663.1[M+H]+; 1H NMR (400 MHz, CD3CN) &=1.19-1.29 (m, 12H) 2.71 (q, J=5.77 Hz, 2H) 2.94 (d, J=6.27 Hz, 3H) 3.35 (d, J=15.56 Hz, 3H) 3.40-3.52 (m, 2H) 3.61-3.97 (m, 4H) 4.23-4.45 (m, 1H) 4.55-4.74 (m, 2H) 6.02 (dd, J=10.67, 6.40 Hz, 1H) 7.25 (br s, 1H) 7.47-7.57 (m, 2H) 7.59-7.68 (m, 1H) 8.01 (d, J=7.78 Hz, 2H) 8.28 (s, 1H) 8.66 (s, 1H) 9.69 (br s, 1H); 31P NMR (162 MHz, CD3CN) δ=150.92, 149.78.

Example 12. Synthesis of 5′-Stabilized End Cap Modified Oligonucleotides

This example provides an exemplary method for synthesizing the siNAs comprising a 5′-stabilized end caps disclosed herein. The 5′-stabilized end cap and/or deuterated phosphoramidites were dissolved in anhydrous acetonitrile and oligonucleotide synthesis was performed on a Expedite 8909 Synthesizer using standard phosphoramidite chemistry. An extended coupling (12 minutes) of 0.12 M solution of phosphoramidite in anhydrous CH3CN in the presence of Benzyl-thio-tetrazole (BTT) activator to a solid bound oligonucleotide followed by standard capping, oxidation and sulfurization produced modified oligonucleotides. The 0.02 M 12, THF: Pyridine; Water 7:2:1 was used as an oxidizing agent, while DDTT (dimethylamino-methylidene) amino)-3H-1,2,4-dithiazaoline-3-thione was used as the sulfur-transfer agent for the synthesis of oligoribonucleotide with a phosphorothioate backbone. The stepwise coupling efficiency of all modified phosphoramidites was achieved around 98%. After synthesis the solid support was heated with aqueous ammonia (28%) solution at 45° C. for 16 h or 0.05 M K2CO3 in methanol was used to deprotect the base labile protecting groups. The crude oligonucleotides were precipitated with isopropanol and centrifuged (Eppendorf 5810R, 3000 g, 4° C., 15 min) to obtain a pellet. The crude product was then purified using ion exchange chromatography (TSK gel column, 20 mM NaH2PO4, 10% CH3CN, 1 M NaBr, gradient 20-60% B over 20 column volumes) and fractions were analyzed by ion change chromatography on an HPLC. Pure fractions were pooled and desalted by Sephadex G-25 column and evaporated to dryness. The purity and molecular weight were determined by HPLC analysis and ESI-MS analysis. Single strand RNA oligonucleotides (sense and antisense strand) were annealed (1:1 by molar equivalents) at 90° C. for 3 min followed by RT 40 min) to produce the duplexes.

Example 13. siNA Activity Assays

This example provides exemplary methods for testing the activity of the siNAs disclosed herein.

In Vitro Assay:

Homo sapiens HepG2.2.15 cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) (ATCC 30-2002) supplemented to also contain 10% fetal calf serum (FCS). Cells were incubated at 37° C. in an atmosphere with 5% CO2 in a humidified incubator. For transfection of HepG2.2.15 cells with HBV targeting siRNAs, cells were seeded at a density of 15000 cells/well in 96-well regular tissue culture plates. Transfection of cells was carried out using RNAiMAX (Invitrogen/Life Technologies) according to the manufacturer's instructions. Dose-response experiments were done with oligo concentrations of 40, 20, 10, 5, 2.5, 1.25, 0.625, 0.3125, 0.15625 and 0.07813 nM. For each HBV targeting siRNA treatment (e.g., ds-siRNA, as identified by the ds-siNA ID in Table 6), four wells were transfected in parallel, and individual data points were collected from each well. After 24 h of incubation with siRNA, media was removed, and cells were lysed and analyzed with a QuantiGene2.0 branched DNA (bDNA) probe set specific for HBV genotype D (also called Hepatitis B virus subtype ayw, complete genome of 3182 base-pairs) as present in cell line HepG2.2.15.

For each well, the HBV on-target mRNA levels were normalized to the GAPDH mRNA level. As shown in Table 6, the activity of the HBV targeting ds-siRNAs was expressed as EC50, 50% reduction of normalized HBV RNA level from no drug control. As shown in Table 6, the cytotoxicity of the HBV targeting ds-siRNAs was expressed by CC50 of 50% reduction of GAPDH mRNA from no drug control.

Unconjugated siRNA 1) with or without a phosphorylation blocker; and 2) with or without end caps (e.g., 5′-stabilized end cap) are transfected into in vitro disease models or in vitro toxicity models. After transfection, target reduction and/or cell viability is measured and compared after a period of incubation. For HBV, exemplary disease cell models include, but are not limited to, HepG2.2.15, HepG2.117 or live HBV infected HepG2-NTCP or Primary Human Hepatocytes.

In Vivo Assay:

GalNAc conjugated siRNA 1) with or without phosphorylation blocker; and 2) with or without 5′-end caps are dosed subcutaneously or intravenously in animal disease models. The target knockdown magnitude and duration is measured from serum or liver samples and compared to each other and/or control animals (e.g., non-treated diseased animals). In some instances, the toxicity of the siRNAs is compared through routine Clinpath or Histopath assays. For HBV, exemplary animal efficacy models include, but are not limited to, AAV-HBV mouse model, HBV transgenic mouse model, PXB or FRG mouse models.

Example 14. Ds-siNA Testing in AAV-HBV Mouse Model

In this example, the efficacy of ds-siNAs in treating HBV in an adeno-associated virus (AAV)-HBV mouse model was evaluated. AAV-HBV mice were subcutaneously injected with a single dose of (a) 5 mL/kg of vehicle; or (b) 5 mg/kg a ds-siNA at day 0. The sequences of the ds-siNA tested in this example are shown in Table 7.

FIG. 4 shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0160 (G03), ds-siNA-0165 (G04), ds-siNA-0163 (G05), or ds-siNA-0166 (G06). These results demonstrate that the ds-siNAs containing various patterns of 2′-fluoro nucleotides and 2′-O-methyl nucleotides can effectively treated HBV.

TABLE 7  ds-siNA sequences tested in AAV-HBV mouse model Sense strand sequence Antisense strand sequence  ds-siNA ID  (5′-3′) (5′-3′) ds-siNA- mCpsmCpsfGmUmGmUfGfCfAmCmUf mUpsfGpsmAmAmGmCmGmAmAmGm 0160 UmCmGmCmUfUmCmA-p-(PS)2- UmGmCfAmCmAmCmGmGpsmUpsmC GalNAc4 (SEQ ID NO: 600) (SEQ ID NO: 272) ds-siNA- mGpsmUpsfGmGmUmGfGfAfCmUmU mApsfUpsmUmGmAmGmAmGmAmA 0165 fCmUmCmUmCfAmAmU-p-(PS)2- mGmUmCfCmAmCmCmAmCpsmGpsm GalNAc4 (SEQ ID NO: 601) A (SEQ ID NO: 292) ds-siNA- mGpsmCpsmUmGmCmUfAmUfGfCfC mApsfApsmGmAmAfGmAmUmGmAm 0163 mUmCmAmUmCmUmUmCmUmU-p- GmGmCfAmUfAmGmCmAmGmCpsmA (PS)2-GalNAc4 (SEQ ID NO: 602) psmG (SEQ ID NO: 287) ds-siNA- mUpsmGpsfUmGmCmAfCfUmUmCm mApsfGpsmGmUmGmAmAmGmCmGm 0166 GmCmUmUmCmAfCmCmU-p-(PS)2- AmAmGfUmGmCmAmCmApsmCpsmG GalNAc4 (SEQ ID NO: 603) (SEQ ID NO: 303)

Example 15. Ds-siNA Activity Assay and Testing in AAV-HBV Mouse

Model

This example investigates the in vitro and in vivo activity of ds-siNAs. The sequences of the ds-siNAs tested in this example are shown in Table 8. As shown in Table 8, the ds-siNAs comprise a sense and antisense strand comprising a mixture of 2′-fluoro and 2′-O-methyl nucleotides. The total number of 2′-fluoro nucleotides in the ds-siNAs are between 6-8. The 2′-fluoro nucleotides may be at specific positions, such as nucleotide position 3, 5, 7, 8, 9, 10, 11, 12, and/or 17 from the 5′ end of the sense strand or 2, 5, 6, 8, 10, 14, 16, 17, and/or 18. The 2′-fluoro nucleotides and 2′-O-methyl nucleotides might occur at specific patterns on the antisense strand, such as an alternating 1:2 or 1:3 pattern, wherein 1 nucleotide is a 2′-fluoro nucleotide and 2 or 3 nucleotides are 2-O-methyl nucleotides.

In Vitro Activity Assay

Homo sapiens HepG2.2.15 cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) (ATCC 30-2002) supplemented to also contain 10% fetal calf serum (FCS). Cells were incubated at 37° C. in an atmosphere with 5% CO2 in a humidified incubator. For transfection of HepG2.2.15 cells with HBV targeting siRNAs, cells were seeded at a density of 15000 cells/well in 96-well regular tissue culture plates. Transfection of cells was carried out using RNAiMAX (Invitrogen/Life Technologies) according to the manufacturer's instructions. Dose-response experiments were done with oligo concentrations of 40, 20, 10, 5, 2.5, 1.25, 0.625, 0.3125, 0.15625 and 0.07813 nM. For each HBV targeting siRNA treatment (e.g., ds-siRNA, as identified by the ds-siNA ID in Table 8), four wells were transfected in parallel, and individual data points were collected from each well. After 24 h of incubation with siRNA, media was removed, and cells were lysed and analyzed with a QuantiGene2.0 branched DNA (bDNA) probe set specific for HBV genotype D (also called Hepatitis B virus subtype ayw, complete genome of 3182 base-pairs) as present in cell line HepG2.2.15.

For each well, the HBV on-target mRNA levels were normalized to the GAPDH mRNA level. Table 8 shows the activity of the HBV targeting ds-siRNAs expressed as EC50, which is 50% reduction of normalized HBV RNA level from no drug control, where A=EC50<0.5 nM; B=0.5 nM<EC50<1; and C=EC50>1.

In vivo testing in AAV-HBV mouse model.

AAV/HBV is a recombinant AAV carrying replicable HBV genome. Taking advantage of the highly hepatotropic feature of genotype 8 AAV, the HBV genome can be efficiently delivered to the mouse liver cells. Infection of immune competent mouse with AAV/HBV can result in long term HBV viremia, which mimics chronic HBV infection in patients. The AAV/HBV model can be used to evaluate the in vivo activity of various types of anti-HBV agents. Mice were infected with AAV-HBV on day −28 of the study. The test articles or negative control (PBS) were dosed subcutaneously (unless specified otherwise) as single dose on days 0 at 5 mg/kg. Serial blood collections were usually taken every 5 days on day 0, 5, 10 and 15 etc. until the termination of studies. Serum HBV S antigen (HBsAg) was assayed through ELISA.

GalNAc conjugated ds-siNAs were further tested at a single dose of 5 mg/kg at day 0 in the adeno-associated virus (AAV)-HBV mouse model. The resulting nadir log10 reduction in serum HBsAg is presented in Table 8, where X≥1 log10 reduction in HBsAg, Y is 0.5-1 log10 reduction in HBsAg, and Z is <0.5 log10 reduction in HBsAg.

FIG. 5A shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01) or ds-siNA-0160 (G03). AAV-HBV mice were subcutaneously injected with a single dose of 5 mL/kg of vehicle or 5 mg/kg of ds-siNA-0160 on day 0.

FIG. 5B shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01) or ds-siNA-0160 (G15). AAV-HBV mice were subcutaneously injected with a single dose of 5 mL/kg of vehicle or 5 mg/kg of ds-siNA-0160 on day 0.

FIG. 5C shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01) or ds-siNA-0160 (G03). AAV-HBV mice were subcutaneously injected with a single dose of 5 mL/kg of vehicle or 5 mg/kg of each ds-siNA on day 0.

FIG. 5D shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0160 (G03), or ds-siNA-0109 (G09). AAV-HBV mice were subcutaneously injected with a single dose of 5 mL/kg of vehicle or 5 mg/kg of each ds-siNA on day 0.

FIGS. 5E-5F show a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01) or ds-siNA-0169 (G18). AAV-HBV mice were subcutaneously injected with a single dose of 5 mL/kg of vehicle or 5 mg/kg of ds-siNA-0169 on day 0.

FIG. 5G shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01) or ds-siNA-0169 (G04). AAV-HBV mice were subcutaneously injected with a single dose of 5 mL/kg of vehicle or 5 mg/kg of ds-siNA-0169 on day 0.

FIG. 5H shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01) or ds-siNA-0169 (G04). AAV-HBV mice were subcutaneously injected with a single dose of 5 mL/kg of vehicle or 5 mg/kg of each ds-siNA on day 0.

FIG. 5I shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0169 (G04) or ds-siNA-0147 (G08). AAV-HBV mice were subcutaneously injected with a single dose of 5 mL/kg of vehicle or 5 mg/kg of each ds-siNA on day 0.

FIG. 5J shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0166 (G06), or ds-siNA-0153 (G14). AAV-HBV mice were subcutaneously injected with a single dose of 5 mL/kg of vehicle or 5 mg/kg of each ds-siNA on day 0.

FIG. 5K shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0163 (G05), or ds-siNA-0119 (G13). AAV-HBV mice were subcutaneously injected with a single dose of 5 mL/kg of vehicle or 5 mg/kg of each ds-siNA on day 0.

These results demonstrate that ds-siNAs comprising combination of 2′-fluoro nucleotides and 2′-O-methyl nucleotides can be used to target HBV X and S gene sequences, which resulted in successful treatment of HBV.

As exemplified by ds-siNA-0160 and ds-siNA-0165, ds-siNAs comprising (a) a sense strand comprising 19 nucleotides, wherein 6 nucleotides are 2′-fluoro nucleotides and 13 nucleotides are 2′-O-methyl nucleotides; (b) an antisense strand comprising 21 nucleotides, wherein 2 nucleotides are 2′-fluoro nucleotides and 19 nucleotides are 2′-O-methyl nucleotides; and (c) a conjugated moiety, wherein the conjugated moiety is attached to the 3′ end of the sense strand, resulted in successful treatment of HBV as evidenced by HBsAg reduction in serum. See FIGS. 4 and 5A-5D, and Table 8. For ds-siNA-0160 and ds-siNA-0165, the 2′-fluoro nucleotides were located at positions 3, 7-9, 12, and 17 from the 5′ end of the sense strand and at positions 2 and 14 from the 5′ end of the antisense strand.

As exemplified by ds-siNA-0166, ds-siNAs comprising (a) a sense strand comprising 19 nucleotides, wherein 4 nucleotides are 2′-fluoro nucleotides and 15 nucleotides are 2′-O-methyl nucleotides; (b) an antisense strand comprising 21 nucleotides, wherein 2 nucleotides are 2′-fluoro nucleotides and 19 nucleotides are 2′-O-methyl nucleotides; and (c) a conjugated moiety, wherein the conjugated moiety is attached to the 3′ end of the sense strand, resulted in successful treatment of HBV as evidenced by HBsAg reduction in serum. See FIGS. 4 and 5J, and Table 8. For ds-siNA-0166, the 2′-fluoro nucleotides were located at positions 3, 7, 8, and 17 from the 5′ end of the sense strand and at positions 2 and 14 from the 5′ end of the antisense strand.

As exemplified by ds-siNA-0153, ds-siNAs comprising (a) a sense strand comprising 19 nucleotides; (b) an antisense strand comprising 21 nucleotides, wherein the nucleotides in the antisense strand comprise at least two alternating 1:3 modification pattern, and wherein approximate 1 nucleotide is a 2′-fluoro nucleotide and 3 nucleotides are 2′-O-methyl nucleotides in repeat pattern; and (c) a conjugated moiety, wherein the conjugated moiety is attached to the 3′ end of the sense strand, resulted in successful treatment of HBV as evidenced by HBsAg reduction in serum. See FIG. 5J. For ds-siNA-0153, the sense strand comprises 6 2′-fluoro nucleotides at positions 3, 7-9, 12, and 17 from the 5′ end of the sense strand. In addition, the antisense strand comprises 5 repeats of the 1:3 modification pattern starting at position 2 from the 5′ end of the antisense strand.

As exemplified by ds-siNA-0109, ds-siNAs comprising (a) a sense strand comprising 19 nucleotides wherein 4 nucleotides are 2′-fluoro nucleotides and 15 nucleotides are 2′-O-methyl nucleotides; (b) an antisense strand comprising 21 nucleotides, wherein 4 nucleotides are 2′-fluoro nucleotides and 17 nucleotides are 2′-O-methyl nucleotides; and (c) a conjugated moiety, wherein the conjugated moiety is attached to the 3′ end of the sense strand, resulted in successful treatment of HBV as evidenced by HBsAg reduction in serum. See FIG. 5D. For ds-siNA-0109 the sense strand comprises 4 2′-fluoro nucleotides at positions 5 and 7-9 from the 5′ end of the sense strand. In addition, the antisense strand comprises 5 repeats of the 1:2 modification pattern starting at positions 2, 5, 8, 14, and 17 from the 5′ end of the antisense strand.

As exemplified by ds-siNA-0147, ds-siNAs comprising (a) a sense strand comprising 19 nucleotides; (b) an antisense strand comprising 21 nucleotides, wherein the nucleotides in the antisense strand comprise at least two alternating 1:2 modification pattern, and wherein approximate 1 nucleotide is a 2′-fluoro nucleotide and 2 nucleotides are 2′-O-methyl nucleotides in repeat pattern; and (c) a conjugated moiety, wherein the conjugated moiety is attached to the 3′ end of the sense strand, resulted in successful treatment of HBV as evidenced by HBsAg reduction in serum. See FIG. 5I. For ds-siNA-0147, the 2′-fluoro nucleotides were located at positions 5 and 7-9 from the 5′ end of the sense strand and at positions 2, 6, 14, and 16 from the 5′ end of the antisense strand.

TABLE 8  ds-siNA tested in AAV-HBV Mouse Model ds- EC50 HBsAg siNA Sense strand  Antisense strand  HepG2. Nadir ID sequence (5′-3′) sequence (5′-3′) 2.15* (Log)** ds- mCpsmCpsmGmUfGmUfGfCf mUpsfGpsmAmAfGmCmGfA siNA- AmCmUmUmCmGmCmUmU mAmGmUmGmCfAmCmAfC 0109 mCmA-p-(PS)2-GalNac4 (SEQ mGmGpsmUpsmC (SEQ ID ID NO: 604) NO: 605) ds- mGpsmCpsmUmGfCmUmAm mApsfApsmGmAmAmGmA siNA- UfGfCfCmUmCfAmUmCmU mUmGmAmGmGmCfAmUm 0119 mUfCmUmU-p-(PS)2-GalNac4 AmGmCmAmGmCpsmApsm (SEQ ID NO: 606) G (SEQ ID NO: 495) ds- mGpsmUpsmGmGfUmGfGfAf mApsfUpsmUmGmAfGmAm siNA- CmUmUmCmUmCmUmCmA GmAmAmGmUmCfCmAfCm 0147 mAmU-p-(PS)2-GalNac4 (SEQ CmAmCpsmGpsmA (SEQ ID ID NO: 607) NO: 608) ds- mUpsmGpsfUmGmCmAfCfUf mApsfGpsmGmUmGfAmAm siNA- UmCmGfCmUmUmCmAfCm GmCfGmAmAmGfUmGmC 0153 CmU-p-(PS)2-GalNac4 (SEQ mAfCmApsmCpsmG (SEQ ID NO: 609) ID NO: 610) ds- mGpsmCpsfGmGmGmGfUfUf mUpsfCpsmAmAmCmAmAmGm A X siNA- UmUmUfCmUmUmGmUfUm AmAmAmAmAfCmCmCmCmGm 0167 GmA-p-(PS)2-GalNac4 (SEQ CpsmCpsmU ID NO: 611) (SEQ ID NO: 285) ds- mGpsmCpsfGmGmGmGfUfU mUpsfCpsmAmAmCmAmA C X siNA- mUmUmUmCmUmUmGmUf mGmAmAmAmAmAfCmCm 0162 UmGmA-p-(PS)2-GalNac4 CmCmGmCpsmCpsmU (SEQ (SEQ ID NO: 612) ID NO: 285) ds- mGpsmUpsfGmGmUmGfGfAf mApsfUpsmUmGmAmGmA A X siNA- CmUmUfCmUmCmUmCfAm mGmAmAmGmUmCfCmAm 0165 AmU-p-(PS)2-GalNac4 (SEQ CmCmAmCpsmGpsmA (SEQ ID NO: 601) ID NO: 292) ds- mUpsmCpsmGmUmGmGfUm mApsfUpsmUmGmAfGmAm A X siNA- GfGfAfCmUmUmCmUmCmU GmAmAmGmUmCfCmAfCm 0168 mCmAmAmU-p-(PS)2- CmAmCmGmApsmGpsmU GalNac4 (SEQ ID NO: 613) (SEQ ID NO: 298) ds- mGpsmCpsmUmGmCmUfAm mApsfApsmGmAmAfGmAm A Y siNA- UfGfCfCmUmCmAmUmCmU UmGmAmGmGmCfAmUfA 0163 mUmCmUmU-p-(PS)2- mGmCmAmGmCpsmApsmG GalNac4 (SEQ ID NO: 602) (SEQ ID NO: 287) ds- mCpsmUpsfGmCmUmAfUfGf mApsfGpsmAmAmGmAmU A Y siNA- CmCmUfCmAmUmCmUfUm mGmAmGmGmCmAfUmAm 0161 CmU-p-(PS)2-GalNac4 (SEQ GmCmAmGpsmCpsmA (SEQ ID NO: 614) ID NO: 277) ds- mCpsmCpsfGmUmGmUfGfCf mUpsfGpsmAmAmGmCmG A X siNA- AmCmUfUmCmGmCmUfUm mAmAmGmUmGmCfAmCm 0160 CmA-p-(PS)2-GalNac4 (SEQ AmCmGmGpsmUpsmC (SEQ ID NO: 600) ID NO: 272) ds- mCpsmCpsfGmUmGmUfGfCf mUpsfGpsmAmAmGmCmG A X siNA- AmCmUfUmCmGmCmUfUm mAmAmGmUmGmCfAmCm 0169 CmA-p-(PS)2-GalNac4 (SEQ AmCmGmGpsTpsT (SEQ ID ID NO: 600) NO: 375) ds- mUpsmGpsfUmGmCmAfCfUf mApsfGpsmGmUmGmAmAmGm A X siNA- UmCmGfCmUmUmCmAfCm CmGmAmAmGfUmGmCmAmCm 0170 CmU-p-(PS)2-GalNac4 (SEQ ApsmCpsmG ID NO: 609) (SEQ ID NO: 303) ds- mUpsmGpsfUmGmCmAfCfU mApsfGpsmGmUmGmAmA A X siNA- mUmCmGmCmUmUmCmAfC mGmCmGmAmAmGfUmGm 0166 mCmU-p-(PS)2-GalNAc4 CmAmCmApsmCpsmG (SEQ (SEQ ID NO: 615) ID NO: 303) ds- mUpsmGpsfUmGmCmAfCfU mApsfGpsmGmUmGmAmAmGm A X siNA- mUmCmGmCmUmUmCmAfC CmGmAmAmGfUmGmCmAmCm 0171 mCmU-p-(PS)2-GalNac4 ApsTpsT (SEQ ID NO: 615) (SEQ ID NO: 407) mX = 2′-O-methyl nucleotide; fX = 2′-fluoro nucleotide; ps = phosphorothioate linkage *For EC50, A = EC50 < 0.5 nM; B = 0.5 nM < EC50 < 1; and C = EC50 > 1. **For HBsAg Nadir, X ≥ 1 log10 reduction in HBsAg, Y is 0.5-1 log10 reduction in HBsAg, and Z is < 0.5 log10 reduction in HBsAg.

Example 16. Testing of Ds-siNAs Having a 5′-Stabilized End Cap in AAV-HBV Mouse Model

This example investigates the in vivo activity of ds-siNAs having a 5′-stabilized end cap. The sequences of the ds-siNAs tested in this example are shown in Table 9.

FIG. 6A shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0160 (G15) (ds-siNA without a 5′-stabilized end cap, e.g., vinyl phosphonate), or ds-siNA-080 (G14) (ds-siNA with a 5′-stabilized end cap, e.g., vinyl phosphonate). AAV-HBV mice were subcutaneously injected with a single dose of 5 mL/kg of vehicle or 5 mg/kg of each ds-siNA on day 0. The resulting nadir log10 reduction in serum HBsAg is presented in Table 9, where X≥1 log10 reduction in HBsAg, Y is 0.5-1 log10 reduction in HBsAg, and Z is <0.5 log10 reduction in HBsAg.

FIG. 6B shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0169 (G16) (ds-siNA without a 5′-stabilized end cap, e.g., vinyl phosphonate), or ds-siNA-081 (G13) (ds-siNA with a 5′-stabilized end cap, e.g., vinyl phosphonate). AAV-HBV mice were subcutaneously injected with a single dose of 5 mL/kg of vehicle or 5 mg/kg of each ds-siNA on day 0. The resulting nadir log10 reduction in serum HBsAg is presented in Table 9, where X≥1 log10 reduction in HBsAg, Y is 0.5-1 log10 reduction in HBsAg, and Z is <0.5 log10 reduction in HBsAg.

FIG. 7A shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0165 (G18) (ds-siNA without a 5′-stabilized end cap, e.g., vinyl phosphonate), or ds-siNA-0127 (G17) (ds-siNA with a 5′-stabilized end cap, e.g., vinyl phosphonate). AAV-HBV mice were subcutaneously injected with a single dose of 5 mL/kg of vehicle or 5 mg/kg of each ds-siNA on day 0. The resulting nadir log10 reduction in serum HBsAg is presented in Table 9, where X≥1 log10 reduction in HBsAg, Y is 0.5-1 log10 reduction in HBsAg, and Z is <0.5 log10 reduction in HBsAg.

FIG. 7B shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0168 (G20) (ds-siNA without a 5′-stabilized end cap, e.g., vinyl phosphonate), or ds-siNA-0150 (G19) (ds-siNA with a 5′-stabilized end cap, e.g., vinyl phosphonate). AAV-HBV mice were subcutaneously injected with a single dose of 5 mL/kg of vehicle or 5 mg/kg of each ds-siNA on day 0. The resulting nadir log10 reduction in serum HBsAg is presented in Table 9, where X≥1 log10 reduction in HBsAg, Y is 0.5-1 log10 reduction in HBsAg, and Z is <0.5 log10 reduction in HBsAg.

These results demonstrate that the addition of a 5′-stabilized end cap can improve the efficacy of ds-siNAs without a 5′-stabilized end cap.

TABLE 9  ds-siNA sequences and HBsAg Nadir HBsAg ds-siNA Sense strand  Antisense strand  Nadir ID sequence (5′-3′) sequence (5′-3′) (Log)* ds-siNA- mCpsmCpsfGmUmGmUfGfC mUpsfGpsmAmAmGmCmGmAmAm Y 0160 fAmCmUfUmCmGmCmUfU GmUmGmCfAmCmAmCmGmGpsm mCmA-(PS)2-p-GalNAc4 UpsmC (SEQ ID NO: 272) (SEQ ID NO: 616) ds-siNA- mCpsmCpsfGmUmGmUfGfC vmUpsfGpsmAmAmGmCmGmAmA X 080 fAmCmUfUmCmGmCmUfU mGmUmGmCfAmCmAmCmGmGps mCmA-(PS)2-p-GalNAc4 mUpsmC (SEQ ID NO: 462) (SEQ ID NO: 616) ds-siNA- mCpsmCpsfGmUmGmUfGfC mUpsfGpsmAmAmGmCmGmAmAm Y 0169 fAmCmUfUmCmGmCmUfU GmUmGmCfAmCmAmCmGmGpsTp mCmA-(PS)2-p-GalNAc4 sT (SEQ ID NO: 375) (SEQ ID NO: 616) ds-siNA- mCpsmCpsfGmUmGmUfGfC vmUpsfGpsmAmAmGmCmGmAmA X 081 fAmCmUfUmCmGmCmUfU mGmUmGmCfAmCmAmCmGmGpsT mCmA-(PS)2-p-GalNAc4 psT (SEQ ID NO: 463) (SEQ ID NO: 616) ds-siNA- mGpsmUpsfGmGmUmGfGfA mApsfUpsmUmGmAmGmAmGmAm X 0165 fCmUmUfCmUmCmUmCfA AmGmUmCfCmAmCmCmAmCpsmG mAmU-(PS)2-p-GalNAc4 psmA (SEQ ID NO: 292) (SEQ ID NO: 617) ds-siNA-  mGpsmUpsfGmGmUmGfGfA vmApsfUpsmUmGmAmGmAmGmA X 0127 fCmUmUfCmUmCmUmCfA mAmGmUmCfCmAmCmCmAmCpsm mAmU-(PS)2-p-GalNAc4 GpsmA (SEQ ID NO: 503) (SEQ ID NO: 617) ds-siNA-  mUpsmCpsmGmUmGmGfUm mApsfUpsmUmGmAfGmAmGmAmA Y 0168 GfGfAfCmUmUmCmUmCm mGmUmCfCmAfCmCmAmCmGmAp UmCmAmAmU-(PS)2-p- smGpsmU (SEQ ID NO: 298) GalNAc4 (SEQ ID NO: 618) ds-siNA-  mUpsmCpsmGmUmGmGfUm vmApsfUpsmUmGmAfGmAmGmAm X 0150 GfGfAfCmUmUmCmUmCm AmGmUmCfCmAfCmCmAmCmGm UmCmAmAmU-(PS)2-p- ApsmGpsmU (SEQ ID NO: 523) GalNAc4 (SEQ ID NO: 618) mX = 2′-O-methyl nucleotide; fX = 2′-fluoro nucleotide; ps = phosphorothioate linkage; VP = vinyl phosphonate *For HBsAg Nadir, X ≥ 1 log10 reduction in HBsAg, Y is 0.5-1 log10 reduction in HBsAg, and Z is < 0.5 log10 reduction in HBsAg.

Example 17. Efficacy of a Combination Therapy in AAV-HBV Mouse

Model

This example investigates the efficacy of a combination therapy comprising an antisense oligonucleotide (ASO 1, 5′ Ga1NAc4-ps-Ga1NAc4-ps-Ga1NAc4-po-mA-po-lnGpslnApslnTpslnApslnApsApsAps(50H)CpsGpsg5 m)Cpg(5 m)CpsGps(5 m)CpslnApslnG pslnApscp(5 m)C-3′(SEQ ID NO: 534)) and a ds-siNA-0160 for treating HBV in an AAV-HBV mouse model.

FIG. 8A shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0160 (G06), ASO 1 (G18), or a combination of ds-siNA-0160 and ASO 1 (G20). AAV-HBV mice were subcutaneously injected with (a) 5 mL/kg of vehicle, three times a week, from days 0-42 (G01); (b) a single dose of 3 mg/kg of ds-siNA-0160 on day 0 (G06); (c) 3 mg/kg of ASO 1 on a weekly basis, from days 0-21 (G18); or (d) a combination of ASO 1 and ds-siNA-0160, wherein ASO 1 was administered at a dose of 3 mg/kg on a weekly basis, from days 0-21; and ds-siNA-0160 was administered as a single dose of 3 mg/kg at day 0.

FIG. 8B shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G01), ds-siNA-0160 (G06), ASO 1 (G18), or a combination of ds-siNA-0160 and ASO 1 (G20). AAV-HBV mice were subcutaneously injected with (a) 5 mL/kg of vehicle, three times a week, from days 0-42 (G01); (b) a single dose of 10 mg/kg of ds-siNA-0160 on day 0 (G06); (c) 10 mg/kg of ASO 1 on a weekly basis, from days 0-21 (G18); or (d) a combination of ASO 1 and ds-siNA-0160, wherein ASO 1 was administered at a dose of 10 mg/kg on a weekly basis, from days 0-21; and ds-siNA-0160 was administered as a single dose of 3 mg/kg at day 0.

FIG. 8C shows a graph of a synergy analysis of an in vitro combination therapy with the ASO 2 and ds-siNA-0164. For the ds-siNA-0164 combination studies with ASO 2, 35,000 cells per well were reverse transfected in a collagen I-coated 96-well plate (Corning, Biocoat; Catalog 356698). Test articles ds-siNA-0164 and ASO 2 were diluted in Opti-MEM™ I Reduced Serum Medium (Thermo Fisher Scientific; Catalog 31985088) to 40x the desired final test concentration then serially diluted (1:3) up to 5 or 9 distinct concentrations, respectively. A 3.25 μL aliquot of each diluted compound was combined in a checkerboard fashion. This combination of compounds was mixed with 0.3 μL Lipofectamine® RNAiMAX Transfection Reagent (Thermo Fisher Scientific, Catalog 13778150) and 6.2 μL of Opti-MEM™ I Reduced Serum Medium. After incubating for 20 minutes, the mixture was added to the cells. Space was also allotted for titrations of each compound alone as reference controls. Cells were incubated with compounds for 3 days at 37° C. in a 5% CO2 atmosphere. After that, HBsAg in the supernatant of cell culture was assayed by ELISA and cell viability was measured with Cell Titer Glow, the same procedures as in HepG2.2.15 in vitro assay section. The HBsAg reduction synergy between two test articles were analyzed using MacSynergy Software.

These results demonstrate that a combination therapy with ASO 1 and ds-siNA-0160 resulted in a greater reduction in serum HBsAg as compared to treatment with ASO 1 or ds-siNA-0160 alone.

Example 18. siNA Activity Assays

This example evaluates the activity of the siNAs disclosed in Table 10 (as identified by the ds-siNA ID). siRNAs were synthesized as described in Example 1. A conjugated moiety (e.g., ligand monomer) was further conjugated to the 3′ end of the sense strand (note: for ds-siNA-067 and ds-siNA-083, the ligand monomer was conjugated to the 5′ end of the sense strand). A 5′-stabilized end cap was further attached to the 5′ end of the antisense strand of some siRNAs.

In Vitro Assay:

Homo sapiens HepG2.2.15 cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) (ATCC 30-2002) supplemented to also contain 10% fetal calf serum (FCS). Cells were incubated at 37° C. in an atmosphere with 5% CO2 in a humidified incubator. For transfection of HepG2.2.15 cells with HBV targeting siRNAs, cells were seeded at a density of 15000 cells/well in 96-well regular tissue culture plates. Transfection of cells was carried out using RNAiMAX (Invitrogen/Life Technologies) according to the manufacturer's instructions. Dose-response experiments were done with oligo concentrations of 40, 20, 10, 5, 2.5, 1.25, 0.625, 0.3125, 0.15625 and 0.07813 nM. For each HBV targeting siRNA treatment (e.g., ds-siRNA, as identified by the ds-siNA ID in Table 6), four wells were transfected in parallel, and individual data points were collected from each well. After 24 h of incubation with siRNA, media was removed, and cells were lysed and analyzed with a QuantiGene2.0 branched DNA (bDNA) probe set specific for HBV genotype D (also called Hepatitis B virus subtype ayw, complete genome of 3182 base-pairs) as present in cell line HepG2.2.15.

For each well, the HBV on-target mRNA levels were normalized to the GAPDH mRNA level. As shown in Table 10, the activity of the HBV targeting ds-siRNAs was expressed as EC50, 50% reduction of normalized HBV RNA level from no drug control, where A=EC50<5 nM; B=5 nM<EC50<10; C=EC50≥10. As shown in Table 10, the cytotoxicity of the HBV targeting ds-siRNAs was expressed by CC50 of 50% reduction of GAPDH mRNA from no drug control.

In Vivo Assay:

GalNAc conjugated siRNA with or without 5′-stabilized end caps were subcutaneously injected at a single dose of 5 mg/kg into AAV-HBV mice. The target knockdown magnitude was measured from serum. The resulting max HBsAg knockdown (log10) is presented in Table 10, where X≥1 log10 reduction in HBsAg, Y is 0.5-1 log10 reduction in HBsAg, and Z is <0.5 log10 reduction in HBsAg.

Example 19: Analysis of 5′-Stabilized End Cap on the Efficacy of siNAs

In this example, the role of a 5′-stabilized end cap on the efficacy of siNAs was investigated. Specifically, the first nucleotide on the 5′ end of the antisense strand was modified to contain a 5′-stabilized end cap. The ds-siNAs investigated in this example are shown in the table below:

ds-siNA Sense Strand  Antisense Strand Sequence ID Sequence (5′→3′) (5′→3′) ds-siNA- mUpsmGpsfUmGmCmAfCfUmUmCmG mApsfGpsmGmUmGmAmAmGmCm 0166 mCmUmUmCmAfCmCmU-p-(PS)2- GmAmAmGfUmGmCmAmCmApsm GalNAc4 (SEQ ID NO: 615) CpsmG (SEQ ID NO: 303) ds-siNA- mUpsmGpsfUmGmCmAfCfUmUmCmG vmApsfGpsmGmUmGmAmAmGmC 0155 mCmUmUmCmAfCmCmU-p-(PS)2- mGmAmAmGfUmGmCmAmCmAps GalNAc4 (SEQ ID NO: 615) mCpsmG (SEQ ID NO: 525) ds-siNA- mUpsmGpsfUmGmCmAfCfUmUmCmG d2vmApsfGpsmGmUmGmAmAmG 0157 mCmUmUmCmAfCmCmU-p-(PS)2- mCmGmAmAmGfUmGmCmAmCm GalNAc4 (SEQ ID NO: 615) ApsmCpsmG (SEQ ID NO: 529) mX = 2′-O-methyl nucleotide; fX = 2′-fluoro nucleotide; vmA = 5′-vinyl phosphonate 2′-O-methyl adenosine; d2vmA = deuterated 5′ vinyl phosphonate adenosine; ps = phosphorothioate linkage

AAV-HBV mice were subcutaneously injected with vehicle or ds-siNAs. ds-siNA-0166, ds-siNA-0155, or ds-siNA-0157 were subcutaneously injected at a single dose of 5 mg/kg into AAV-HBV mice. The target knockdown magnitude is measured from serum. As shown in FIG. 9, the presence of the 5′ stabilized end cap in the first nucleotide from the 5′ end of the antisense strand in ds-siNA-0155 (triangle) and ds-siNA-0157 (square) improved the efficacy of the siNA (squares and triangles) as compared to the siNA without the 5′ stabilized end cap (ds-siNA-0166, diamond). In addition, the presence of the deuterated 5′ vinyl phosphonate in ds-siNA-0157 resulted in a greater improvement in efficacy of a ds-siNA as compared to the presence of the 5′ vinylphosphanate in ds-siNA-0155. These results demonstrate that a 5′ stabilized end cap improves the efficacy of siNAs, with the greatest improvement seen in siNAs containing deuterated 5′ vinyl phosphonate.

Example 20: Analysis of HBV siRNA S and X Combination Therapy

In this example, combination therapy using an siNA targeting the S gene of HBV and an siNA targeting the X gene of HBV was examined. AAV-HBV mice were treated with vehicle, a single siNA therapy, or a combination siNA therapy targeting the S gene and X gene of HBV. AAV-HBV mice were subcutaneously injected with a single dose of ds-siNA-0160 or ds-siNA-0165 on day 0. For the combination siNA therapy, AAV-HBV mice were subcutaneously injected with a single dose of 1.5 mg/kg of ds-siNA-0165 (S trigger) and 1.5 mg/kg of ds-siNA-0160 (X trigger) on day 0. As shown in FIG. 10, the combination therapy with a siNA targeting the S gene and a siNA targeting the X gene was more potent than the single therapy with ds-siNA-0165 or ds-siNA-0160.

Example 21. Synthesis of Monomer

Preparation of (2a): To a solution of 1a (10.0 g, 29.5 mmol) in ACN (200.0 mL), KSAc (13.5 g, 118.6 mmol) was added at r.t., the mixture was stirred at r.t. for 15 h, TLC showed 1a was consumed completely. Mixture was filtered by silica gel and filter cake was washed with DCM (100.0 mL), the filtrate was concentrated to give crude 2a (11.1 g) as an oil. 1H-NMR (400 MHz, CDCl3): S 7.32-7.24 (m, 5H), 7.16 (d, J=8.9 Hz, 4H), 6.82 (d, J=8.9 Hz, 4H), 3.82 (s, 6H), 2.28 (s, 3H).

Preparation of (3a): To a solution of crude 2a (11.1 g, 29.2 mmol) in THF (290.0 mL), LiAlH4 (2.0 g, 52.6 mmol) was added at 0° C. and kept for 10 min, reaction was stirred at r.t. for 5 h under N2, TLC showed 2a was consumed completely. Mixture was put into aqueous NaHCO3 solution and extracted with EA (500.0 mL*2), organic phase was concentrated to give crude which was purified by column chromatography (SiO2, PE/EA=30:1 to 10:1) to give 3a (8.1 g, 95% purity) as a white solid. ESI-LCMS: m/z 335.3 [M−H]−; 1H-NMR (400 MHz, CDCl3): S 7.33-7.24 (m, 5H), 7.19 (d, J=8.8 Hz, 4H), 6.82 (d, J=8.8 Hz, 4H), 3.83 (s, 6H), 3.09 (s, 1H).

Preparation of (2): To a solution of 1(20.0 g, 81.3 mmol) in pyridine (400.0 mL), MsCl (10.23 g, 89.43 mmol) was added dropwise at −10° C., reaction was stirred at −10° C. for 1 h, LCMS showed 1 was consumed completely, 100.0 mL aqueous NaHCO3 solution was added and extracted with DCM (100.0 mL*2), organic phase was concentrated to give crude which was purified by column chromatography (SiO2, DCM/MeOH=30:1 to 10:1) to give 2 (9.5 g, 97% purity) as a white solid. ESI-LCMS: m/z 325.3 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.45 (s, 1H), 7.64-7.62 (d, J=8.0 Hz, 1H), 5.92-5.85 (m, 2H), 5.65-5.63 (d, J=8.0 Hz, 1H), 5.26-5.11 (m, 1H), 4.53-4.37 (m, 2H), 4.27-4.16 (m, 1H), 4.10-4.04 (m, 1H), 3.23 (s, 3H).

Preparation of (3): Intermediate 3 was prepared by prepared according to reaction condition described in reference Helvetica Chimica Acta, 2004, 87. 2812. To a solution of 2 (9.2 g, 28.3 mmol) in dry DMSO (130.0 mL). DMTrSH (14.31 g, 42.5 mmol) was added, followed by tetramethylguanidine (3.6 g, 31.2 mmol) was added under N2, reaction was stirred at r.t. for 3 h, LCMS showed 2 was consumed completely. 100.0 mL H2O was added and extracted with EA (100.0 mL*2), organic phase was concentrated to give crude which was purified by column chromatography (SiO2, PE/EA=5:1 to 1:1) to give 3 (12.0 g, 97% purity) as a white solid. ESI-LCMS: m/z 563.2 [M−H]−; 1H-NMR (400 MHz, DMSO-d6): δ 11.43-11.42 (d, J=4.0 Hz, 1H), 7.57-7.55 (d, J=8.0 Hz, 1H), 7.33-7.17 (m, 9H), 6.89-6.86 (m, 4H), 5.80-5.74 (m, 1H), 5.65-5.62 (m, 1H), 5.58-5.57 (d, J=4.0 Hz, 1H), 5.16-5.01 (m, 1H), 3.98-3.90 (m, 1H), 3.73 (s, 6H), 3.73-3.67 (m, 1H), 2.50-2.37 (m, 2H).

Preparation of Example 21 monomer: To a solution of 3 (10.0 g, 17.7 mmol) in dichloromethane (120.0 mL) with an inert atmosphere of nitrogen was added CEOP[N(iPr)2]2 (6.4 g, 21.2 mmol) and DCI (1.8 g, 15.9 mmol) in order at room temperature. The resulting solution was stirred for 1.0 h at room temperature and diluted with 50 mL dichloromethane and washed with 2×50 mL of saturated aqueous sodium bicarbonate and 1×50 mL of saturated aqueous sodium chloride respectively. The organic phase was dried over anhydrous sodium sulfate, filtered and concentrated till no residual solvent left under reduced pressure. The residue was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=6/1; Detector, UV 254 nm. This resulted in to give Example 21 monomer (12.8 g, 98% purity, 93% yield) as an oil. ESI-LCMS: m/z 765.2 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.44 (s, 1H), 7.70-7.66 (m, 1H), 7.32-7.18 (m, 9H), 6.89-6.85 (m, 4H), 5.80-5.64 (m, 2H), 5.38-5.22 (m, 1H), 4.38-4.15 (m, 1H), 3.81-3.70 (m, 8H), 3.61-3.43 (m, 3H), 2.76-2.73 (m, 1H), 2.66-2.63 (m, 1H), 2.50-2.41 (m, 2H), 1.12-1.05 (m, 9H), 0.97-0.95 (m, 3H); 31P-NMR (162 MHz, DMSO-d6): δ 149.01, 148.97, 148.74, 148.67; 19F-NMR (376 MHz, DMSO-d6): δ 149.01, 148.97, 148.74, 148.67.

Example 22. Synthesis of Monomer

Preparation of (2): To a stirred solution of 1 (2.0 g, 8.8 mmol) in pyridine (20 mL) were added DMTrCI (3.3 g, 9.7 mmol) at r.t. The reaction mixture was stirred at r.t. for 2.5 hrs. With ice-bath cooling, the reaction was quenched with water and the product was extracted with EA (100 mL). The organic phase was evaporated to dryness under reduced pressure to give a residue which was purified by silica gel column chromatography (eluent, DCM: MeOH=50:1˜20:1) to give 2 (3.7 g, 7.2 mmol, 80.1%) as a white solid. ESI-LCMS: m/z 527 [M−H]−.

Preparation of (3): To the solution of 2 (2.8 g, 5.3 mmol) in dry DMF (56 mL) was added (CD30)2Mg (2.9 g, 31.8 mmol) at r.t. under N2 atmosphere. The reaction mixture was stirred at 100° C. for 15 hrs. With ice-bath cooling, the reaction was quenched with saturated aq. NH4Cl and extracted with EA (300 mL). The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 3 (2.0 g, 3.6 mmol, 67.9%) as a white solid. ESI-LCMS: m/z 562 [M−H]−; 1H-NMR (400 MHz, DMSO-d6): δ 11.38 (s, 1H), 7.73 (d, J=8 Hz, 1H), 7.46-7.19 (m, 9H), 6.91 (d, J=7.4 Hz, 4H), 5.81-5.76 (AB, J=20 Hz, 1H), 5.30 (d, J=8 Hz, 1H), 5.22 (s, 1H), 4.25-4.15 (m, 1H), 3.99-3.92 (m, 1H), 3.85-3.79 (m, 1H), 3.74 (s, 6H), 3.34-3.18 (m, 31H).

Preparation of Example 22 monomer: To a suspension of 3 (2.0 g, 3.5 mmol) in DCM (20 mL) was added DCI (357 mg, 3.0 mmol) and CEP[N(iPr)2]2 (1.3 g, 4.3 mmol). The mixture was stirred at r.t. for 1 h. LC-MS showed 3 was consumed completely. The solution was washed with water twice and washed with brine and dried over Na2SO4. Then concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 22 monomer (2.1 g, 2.7 mmol, 77.1%) as a white solid. ESI-LCMS: m/z 764 [M+H]+; 1H-NMR (400 MHz, ACN-d3): δ 9.45-8.90 (m, 1H, exchanged with D20), 7.88-7.66 (m, 1H), 7.50-7.18 (m, 9H), 6.93-6.80 (m, 4H), 5.85 (d, J=8.2 Hz, 1H), 5.29-5.16 (m, 1H), 4.57-4.37 (m, 1H), 4.18-4.09 (m, 1H), 3.98-3.90 (m, 1H), 3.90-3.74 (m, 7H), 3.74-3.50 (m, 3H), 3.48-3.31 (m, 2H), 2.70-2.61 (m, 1H), 2.56-2.46 (m, 1H), 1.24-1.12 (m, 9H), 1.09-0.99 (m, 3H). 31P-NMR (162 MHz, ACN-d3): 6=149.87, 149.55.

Example 23. Synthesis of Monomer

Preparation of (2): To the solution of 1 (39.2 g, 151.9 mmol) in DMF (390.0 mL) was added imidazole (33.0 g, 485.3 mmol) and TBSCl (57.2 g, 379.6 mmol) at 0° C. The reaction mixture was stirred at room temperature for 15 hrs under N2 atmosphere. After addition of water, the resulting mixture was extracted with EA (500.0 mL). The combined organic layer was washed with water and brine, dried over Na2SO4, concentrated to give the crude 2 (85.6 g) as a white solid which was used directly for next step. ESI-LCMS: m/z 487.7 [M+H]+.

Preparation of (3): A solution of crude 2 (85.6 g) in a mixture solvent of TFA/H2O=1/1 (400.0 mL) and THF (400.0 mL) was stirred at 0° C. for 30 min. After completion of reaction, the resulting mixture was added con.NH3*H2O to pH=7, and then extracted with EA (500.0 mL). The organic layer was washed with brine, dried over sodium sulfate and removed to give the residue was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 3 (36.6 g, 98.4 mmol, 64.7% over two step) as a white solid. ESI-LCMS: m/z 372.5 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.36 (d, J=1 Hz, 1H), 7.92 (d, J=8 Hz, 1H), 5.83 (d, J=5 Hz, 1H), 5.67-5.65 (m, 1H), 5.19 (s, 1H), 4.30 (t, J=5 Hz, 1H), 3.85-3.83 (m, 2H), 3.68-3.52 (m, 2H), 0.88 (s, 9H), 0.09 (s, 6H).

Preparation of (4): To the solution of 3 (36.6 g, 98.4 mmol) in dry DCM (200.0 mL) and DMF (50.0 mL) was added PDC (73.9 g, 196.7 mmol), tert-butyl alcohol (188.0 mL) and Ac2O (93.0 mL) at r.t under N2 atmosphere, the reaction mixture was stirred at r.t for 2 hrs. The solvent was removed to give a residue which was purified by silica gel column chromatography (eluent, PE/EA=4:1-2:1) to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 4 (24.3 g, 54.9 mmol, 55.8%) as a white solid. ESI-LCMS: m/z 443.2 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.30 (d, J=1 Hz, 1H), 7.92 (d, J=8 Hz, 1H), 5.86 (d, J=6 Hz, 1H), 5.67-5.65 (m, 1H), 4.33-4.31 (m, 1H), 4.13 (d, J=3 Hz, 1H), 3.73-3.70 (m, 1H), 1.34 (s, 9H), 0.77 (s, 9H), 0.08 (s, 6H).

Preparation of (5): To the solution of 4 (18.0 g, 40.7 mmol) in dry THF/MeOD/D20=10/2/1 (145.0 mL) was added NaBD4 (5.1 g, 122.1 mmol) three times during an hour at 50° C., the reaction mixture was stirred at r.t. for 2 hrs. After completion of reaction, adjusted pH value to 7 with CH3COOD, after addition of water, the resulting mixture was extracted with EA (300.0 mL). The combined organic layer was washed with water and brine, dried over Na2SO4, concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 5 (10.4 g, 27.8 mmol, 68.3%) as a white solid. ESI-LCMS: m/z 375.2 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.36 (d, J=1 Hz, 1H), 7.92 (d, J=8 Hz, 1H), 5.83 (d, J=5 Hz, 1H), 5.67-5.65 (m, 1H), 5.19 (s, 1H), 4.30 (t, J=5 Hz, 1H), 3.85-3.83 (m, 2H), 0.88 (s, 9H), 0.09 (s, 6H).

Preparation of (6): To a stirred solution of 5 (10.4 g, 27.8 mmol) in pyridine (100.0 mL) was added DMTrC1 (12.2 g, 36.1 mmol) at r.t., The reaction mixture was stirred at r.t. for 2.5 hrs, the reaction was quenched with water and extracted with EA (200.0 mL). The organic phase was evaporated to dryness under reduced pressure to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 6 (13.5 g, 19.9 mmol, 71.6%) as a white solid. ESI-LCMS: m/z 677.8 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.39 (d, J=1 Hz, 1H), 7.86 (d, J=4 Hz, 1H), 7.35-7.21 (m, 9H), 6.90-6.88 (m, 4H), 5.78 (d, J=2 Hz, 1H), 5.30-5.27 (m, 1H), 4.33-4.30 (m, 1H), 3.91 (d, J=7 Hz, 1H), 3.85-3.83 (m, 1H), 3.73 (s, 6H), 3.38 (s, 3H), 0.77 (s, 9H), 0.03 (s, 3H), 0.01 (s, 3H).

Preparation of (7): To a solution of 6 (13.5 g, 19.9 mmol) in THF (130.0 mL) was added 1 M TBAF solution (19.0 mL). The reaction mixture was stirred at r.t. for 1.5 hrs. LC-MS showed 6 was consumed completely. Water (500.0 mL) was added and extracted with EA (300.0 mL), the organic layer was washed with brine and dried over Na2SO4. Then the organic layer was concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 7 (10.9 g, 19.4 mmol, 97.5%) as a white solid. ESI-LCMS: m/z 563.6 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.39 (s, 1H), 7.23 (d, J=8 Hz, 1H), 7.73 (d, J=8 Hz, 1H), 7.36-7.23 (m, 9H), 6.90 (d, J=8 Hz, 4H), 5.81 (d, J=3 Hz, 1H), 5.30-5.28 (m, 1H), 5.22 (d, J=7 Hz, 1H), 4.20 (q, J=7 Hz, 1H), 3.93 (d, J=7 Hz, 1H), 3.81 (t, J=5 Hz, 1H), 3.74 (s, 6H), 3.41 (s, 3H).

Preparation of Example 23 monomer: To a suspension of 7 (10.9 g, 19.4 mmol) in DCM (100.0 mL) was added DCI (1.8 g, 15.7 mmol) and CEP[N(iPr)2]2 (6.1 g, 20.4 mmol). The mixture was stirred at r.t. for 1 h. LC-MS showed 7 was consumed completely. The mixture was washed with water twice and brine, dried over Na2SO4. Then concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 23 monomer (12.5 g, 14.5 mmol, 74.7%) as a white solid. ESI-LCMS: m/z 863.6 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.39 (s, 1H), 7.81-7.55 (m, 1H), 7.40-7.22 (m, 9H), 6.92-6.87 (m, 4H), 5.83-5.80 (m, 1H), 5.32-5.25 (m, 1H), 4.46-4.34 (m, 1H), 4.10-3.98 (m, 2H), 3.84-3.73 (m, 7H), 3.60-3.50 (m, 3H), 3.42, 3.40 (s, 3H), 2.78 (t, J=6 Hz, 1H), 2.62-2.59 (m, 1H), 2.07 (s, 1H), 1.17-0.96 (m, 12H); 31P-NMR (162 MHz, DMSO-d6): δ 149.37, 149.06.

Example 24. Synthesis of Monomer

Preparation of (2): To the solution of 1 (13.0 g, 52.8 mmol) in DMF (100 mL) was added imidazole (12.6 g, 184.8 mmol) and TBSCl (19.8 g, 132.0 mmol) at 0° C., and the reaction mixture was stirred at room temperature for 15 h under N2 atmosphere. After addition of water, the resulting product was extracted with EA (500 mL). The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated to give the crude 2 (30.6 g) as a white solid which was used directly for next step. ESI-LCMS: m/z 475 [M+H]+. WO2017106710A1

Preparation of (3): A solution of crude 2 (30.6 g) in a mixture solvent of TFA/H2O=1/1 (100 mL) and THF (100 mL) was stirred at 0° C. for 30 min. After completion of reaction, the resulting mixture was added con.NH3*H2O to pH=7.5, and then the mixture was extracted with EA (500 mL), the organic layer was washed with brine, dried over Na2SO4 and removed to give the residue was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 3 (12.0 g, 33.3 mmol, 65.8% over two step) as a white solid. ESI-LCMS: m/z 361 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.39 (s, J=1 Hz, 1H, exchanged with D20), 7.88 (d, J=8 Hz, 1H), 5.91-5.86 (m, 1H), 5.66-5.62 (m, 1H), 5.21 (t, J=5.2 Hz, 1H, exchanged with D20), 5.18-5.03 (m, 1H), 4.37-4.29 (m, 1H), 3.87-3.83 (m, 1H), 3.78-3.73 (m, 1H), 3.56-3.51 (m, 1H), 0.87 (s, 9H), 0.09 (s, 6H). WO2017106710A1.

Preparation of (4): To the solution of 3 (11.0 g, 30.5 mmol) in dry DCM (60 mL) and DMF (15 mL) was added PDC (21. g, 61.0 mmol), tert-butyl alcohol (45 mL) and Ac2O (32 mL) at r.t under N2 atmosphere. And the reaction mixture was stirred at r.t for 2 h. The solvent was removed to give a residue which was purified by silica gel column chromatography (eluent, PE: EA=4:1-2:1) to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 4 (9.5 g, 22.0 mmol, 72.3%) as a white solid. ESI-LCMS: m/z 431 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.45 (s, J=1 Hz, 1H, exchanged with D20), 7.93 (d, J=8.5 Hz, 1H), 6.02-5.97 (m, 1H), 5.76-5.74 (m, 1H), 5.29-5.14 (m, 1H), 4.59-4.52 (m, 1H), 4.29-4.27 (m, 1H), 1.46 (s, 9H), 0.89 (s, 9H), 0.12 (s, 6H).

Preparation of (5): To the solution of 4 (8.5 g, 19.7 mmol) in dry THF/MeOD/D20=10/2/1 (80 mL) was added NaBD4 (2.5 g, 59.1 mmol) three times per an hour at 50° C. And the reaction mixture was stirred at r.t for 2 h. After completion of reaction, adjusted pH value to 7 with CH3COOD, after addition of water, the resulting mixture was extracted with EA (300 mL). The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 5 (3.5 g, 9.7 mmol, 50.3%) as a white solid. ESI-LCMS: m/z 363 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.41 (s, J=1 Hz, 1H, exchanged with D20), 7.88 (d, J=8 Hz, 1H), 5.91-5.86 (m, 1H), 5.66-5.62 (m, 1H), 5.19 (t, J=5.2 Hz, 1H, exchanged with D20), 5.18-5.03 (m, 1H), 4.37-4.29 (m, 1H), 3.87-3.83 (m, 1H), 0.88 (s, 9H), 0.10 (s, 6H).

Preparation of (6): To a stirred solution of 5 (3.4 g, 9.7 mmol) in pyridine (35 mL) were added DMTrCl (3.4 g, 10.1 mmol) at r.t. And the reaction mixture was stirred at r.t for 2.5 h. With ice-bath cooling, the reaction was quenched with water and the product was extracted with EA (200 mL). The organic phase was evaporated to dryness under reduced pressure to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 6 (PCT Int. Appl., 2019173602), (5.5 g, 8.3 mmol, 85.3%) as a white solid. ESI-LCMS: m/z 665 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.50 (d, J=1 Hz, 1H, exchanged with D20), 7.92 (d, J=4 Hz, 1H), 7.44-7.27 (m, 9H), 6.96-6.93 (m, 4H), 5.94 (d, J=20.5 Hz, 1H), 5.39-5.37 (m, 1H), 5.32-5.17 (m, 1H), 4.60-4.51 (m, 1H), 4.01 (d, J=8.8 Hz, 1H), 3.80 (s, 6H), 0.80 (s, 9H), 0.09 (s, 3H), −0.05 (s, 3H).

Preparation of (7): To a solution of 6 (5.5 g, 8.3 mmol) in THF (50 mL) was added 1 M TBAF solution (9 mL). The reaction mixture was stirred at r.t. for 1.5 h. LC-MS showed 6 was consumed completely. Water (500 mL) was added. The product was extracted with EA (300 mL) and the organic layer was washed with brine and dried over Na2SO4. Then the organic layer was concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 7 (4.1 g, 7.5 mmol, 90.0%) as a white solid. ESI-LCMS: m/z 551 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.42 (s, 1H, exchanged with D20), 7.76 (d, J=8.2 Hz, 1H), 7.39-7.22 (m, 9H), 6.90-6.88 (m, 4H), 5.83 (d, J=20.5 Hz, 1H), 5.65 (d, J=7.0 Hz, 1H, exchanged with D20), 5.29 (d, J=7.2 Hz, 1H), 5.18-5.03 (m, 1H), 4.40-4.28 (m, 1H), 4.01 (d, J=8.8 Hz, 1H), 3.74 (s, 6H).

Preparation of Example 24 monomer: To a suspension of 7 (4.1 g, 7.5 mmol) in DCM (40 mL) was added DCI (0.7 g, 6.4 mmol) and CEP[N(iPr)2]2 (2.9 g, 9.7 mmol). The mixture was stirred at r.t. for 1 h. LC-MS showed 7 was consumed completely. The solution was washed with water twice and washed with brine and dried over Na2SO4. Then concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 24 monomer (5.0 g, 6.6 mmol, 90.0%) as a white solid. ESI-LCMS: m/z 751 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.43 (s, 1H), 7.85-7.82 (m, 1H), 7.40-7.23 (m, 9H), 6.90-6.85 (m, 4H), 5.94-5.86 (m, 1H), 5.40-5.24 (m, 2H), 4.74-4.49 (m, 1H), 4.12-4.09 (m, 2H), 3.79-3.47 (m, 10H), 2.78-2.59 (m, 2H), 1.14-0.93 (m, 12H). 31P-NMR (162 MHz, DMSO-d6): δ 149.67, 149.61, 149.32, 149.27.

Example 25. Synthesis of Monomer

Preparation of (4): To the solution of 3 (14.3 g, 25.4 mmol, Scheme 2) in pyridine (150 mL) was added imidazole (4.5 g, 66.6 mmol) and TBSCI (6.0 g, 40.0 mmol) at 0° C., and the reaction mixture was stirred at room temperature for 15 h under N2 atmosphere. After addition of water, the resulting mixture was extracted with EA (500 mL). The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated to give the crude 4 (18.0 g) as a white solid which was used directly for next step. ESI-LCMS: m/z 676 [M−H]−.

Preparation of (5): To the solution of crude 4 (18.0 g) in the solution of DCA (6%) in DCM (200 mL) was added TES (50 mL) at r.t, and the reaction mixture was stirred at room temperature for 5-10 min. After completion of reaction, the resulting mixture was added pyridine to pH=7, and then the solvent was removed and the residue was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 5 (6.5 g, 17.2 mmol, 67.7% for two step) as a white solid. ESI-LCMS: m/z 376 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 7.92 (d, J=8 Hz, 1H), 5.82 (d, J=5.2 Hz, 1H), 5.68-5.63 (m, 1H), 5.20-5.15 (m, 1H), 4.32-4.25 (m, 1H), 3.87-3.80 (m, 2H), 3.69-3.61 (m, 1H), 3.57-3.49 (m, 1H), 0.88 (s, 9H), 0.09 (s, 6H).

Preparation of (6): To the solution of 5 (6.5 g, 17.2 mmol) in dry DCM (35 mL) and DMF (9 mL) was added PDC (12.9 g, 34.3 mmol), tert-butyl alcohol (34 mL) and Ac2O (17 mL) at r.t under N2 atmosphere. And the reaction mixture was stirred at r.t for 2 hrs. The solvent was removed to give a residue which was purified by silica gel column chromatography (eluent, PE: EA=4:1-2:1) to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 6 (5.5 g, 12.3 mmol, 70.1%) as a white solid. ESI-LCMS: m/z 446 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ=11.29 (s, 1H), 7.91 (d, J=8.4 Hz, 1H), 5.85 (d, J=6.4 Hz, 1H), 5.71-5.61 (m, 1H), 4.35-4.28 (m, 1H), 4.12 (d, J=3.2 Hz, 1H), 3.75-3.67 (m, 1H), 1.33 (s, 9H), 0.76 (s, 9H), 0.00 (d, J=1.6 Hz, 6H).

Preparation of (7): To the solution of 6 (5.4 g, 12.1 mmol) in THF/MeOD/D20=10/2/1 (44 mL) was added NaBD4 (1.5 g, 36.3 mmol) at r.t. and the reaction mixture was stirred at 50° C. for 2 hrs. After completion of reaction, adjusted pH value to 7 with CH3COOD. Water was added, the resulting mixture was extracted with EA (500 mL). The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 7 (2.6 g, 6.8 mmol, 56.1%) as a white solid. ESI-LCMS: m/z 378 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.35 (s, 1H), 7.91 (d, J=8.0 Hz, 1H), 5.82 (d, J=5.2 Hz, 1H), 5.69-5.60 (m, 1H), 5.14 (s, 1H), 4.34-4.20 (m, 1H), 3.88-3.76 (m, 2H), 0.87 (s, 9H), 0.08 (s, 6H).

Preparation of (8): To a stirred solution of 7 (2.6 g, 6.8 mmol) in pyridine (30 mL) were added DMTrCl (3.5 g, 10.3 mmol) at r.t. And the reaction mixture was stirred at r.t. for 2.5 hrs. With ice-bath cooling, the reaction was quenched with water and the product was extracted into EA (200 mL). The organic phase was evaporated to dryness under reduced pressure to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 8 (4.3 g, 6.3 mmol, 90.1%) as a white solid. ESI-LCMS: m/z 678 [M−H]−; 1H-NMR (400 MHz, DMSO-d6): δ 11.39 (s, 1H), 7.86 (d, J=8.0 Hz, 1H), 7.42-7.17 (m, 9H), 6.96-6.83 (m, 4H), 5.82-5.69 (m, 2H), 5.29 (d, J=8.4 Hz, 1H), 4.36-4.25 (m, 1H), 3.90 (d, J=7.2 Hz, 1H), 3.86-3.80 (m, 1H), 3.73 (s, 6H), 0.75 (s, 9H), 0.02 (s, 3H), −0.04 (s, 3H).

Preparation of (9): To a solution of 8 (4.3 g, 6.3 mmol) in THF (45 mL) was added 1 M TBAF solution (6 mL). The reaction mixture was stirred at r.t. for 1.5 hrs. LCMS showed 8 was consumed completely. Water (200 mL) was added. The product was extracted with EA (200 mL) and the organic layer was washed with brine and dried over Na2SO4. Then the organic layer was concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 8 (3.5 g, 6.1 mmol, 90.1%) as a white solid. ESI-LCMS: m/z 678 [M−H]−; 1H-NMR (400 MHz, DMSO-d6): δ 11.38 (d, J=2.0 Hz, 1H), 7.23 (d, J=8.0 Hz, 1H), 7.41-7.19 (m, 9H), 6.94-6.85 (m, 4H), 5.81 (d, J=4.0 Hz, 1H), 5.33-5.26 (m, 1H), 5.21 (d, J=7.2 Hz, 1H), 4.06-3.90 (m, 2H), 3.83-3.77 (m, 1H), 3.74 (s, 6H).

Preparation of Example 25 monomer: To a suspension of 9 (2.1 g, 3.7 mmol) in DCM (20 mL) was added DCI (373 mg, 3.1 mmol) and CEP[N(iPr)2]2 (1.3 g, 4.4 mmol). The mixture was stirred at r.t. for 1 h. LC-MS showed 9 was consumed completely. The solution was washed with water twice and washed with brine and dried over Na2SO4. Then concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 25 monomer (2.2 g, 3.5 mmol, 80%) as a white solid. ESI-LCMS: m/z 766 [M+H]+; 1H-NMR (400 MHz, ACN-d3): S 9.65-8.86 (m, 1H, exchanged with D20), 7.93-7. 68 (m, 1H), 7.52-7.19 (m, 9H), 6.94-6.78 (m, 4H), 5.95-5.77 (m, 1H), 5.31-5.17 (m, 1H), 4.61-4.37 (m, 1H), 4.20-4.07 (m, 1H), 4.01-3.51 (m, 10H), 2.74-2.59 (m, 1H), 2.57-2.43 (m, 1H), 1.27-1.10 (m, 9H), 1.09-0.95 (m, 3H). 31P-NMR (162 MHz, ACN-d3): δ=149.88, 149.55.

Example 26. Synthesis of Monomer

Preparation of (7): To a solution of 6 (17 g, 25.1 mmol, Scheme 3) in ACN (170 mL) was added DMAP (6.13 g, 50.3 mmol) and TEA (5.1 g, 50.3 mmol, 7.2 mL), Then added TPSCI (11.4 g, 37.7 mmol) at 0° C. under N2 atmosphere and the mixture was stirred at r.t. for 3 h under N2 atmosphere. Then con. NH3.H2O (27.3 g, 233.7 mmol) was added at r.t. and the mixture was stirred at r.t. for 16 h. The reaction was quenched with water and the product was extracted with EA (200 mL). The organic phase was concentrated to give the crude 7 (17.0 g) as a white solid which was used directly for next step.

Preparation of (8): To a stirred solution of 7 (17.0 g, 25.1 mmol) in pyridine (170 mL) were added BzCl (4.3 g, 30.1 mmol) 0° C. under N2 atmosphere. And the reaction mixture was stirred at r.t for 2.5 h. With ice-bath cooling, the reaction was quenched with water and the product was extracted with EA (200 mL). The organic phase was evaporated to dryness under reduced pressure to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 8 (19.0 g, 24.3 mmol, 95.6% over two step) as a white solid. ESI-LCMS: m/z 780 [M+H]+.

Preparation of (9): To a solution of 8 (19.0 g, 24.3 mmol) in THF (190 mL) was added 1 M TBAF solution (24 mL). The reaction mixture was stirred at r.t. for 1.0 h. LC-MS showed 8 was consumed completely. Water (500 mL) was added. The product was extracted with EA (300 mL) and the organic layer was washed with brine and dried over Na2SO4. Then the organic layer was concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 9 (15.2 g, 23.1 mmol, 95.5%) as a white solid. ESI-LCMS: m/z 666 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.28 (s, 1H), 8.41 (m, 1H), 8.00-7.99 (m, 2H), 7.63-7.15 (m, 13H), 6.93-6.89 (m, 4H), 5.87 (s, 1H), 5.20 (d, J=7.4 Hz, 1H), 4.30 (m, 1H), 4.02 (m, 1H), 3.75 (s, 7H), 3.53 (s, 3H).

Preparation of Example 26 monomer: To a suspension of 9 (10.0 g, 15.0 mmol) in DCM (100 mL) was added DCI (1.5 g, 12.7 mmol) and CEP[N(iPr)2]2 (5.4 g, 18.0 mmol). The mixture was stirred at r.t. for 1 h. LC-MS showed 9 was consumed completely. The solution was washed with water twice and washed with brine and dried over Na2SO4. Then concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 26 monomer (11.5 g, 13.5 mmol, 90.7%) as a white solid. ESI-LCMS: m/z 866 [M+H]+, 1H-NMR (400 MHz, DMSO-d6): δ=11.28 (s, 1H), 8.48-8.41 (m, 1H), 8.00-7.99 (m, 2H), 7.63-7.11 (m, 13H), 6.93-6.89 (m, 4H), 5.92 (m, 1H), 4.55-4.44 (m, 1H), 4.17 (m, 1H), 3.95 (m, 1H), 3.80-3.62 (m, 7H), 3.57-3.46 (m, 5H), 3.32 (s, 1H), 2.78 (m, 1H), 2.62-2.59 (m, 1H), 1.19-0.94 (m, 12H); 31P-NMR (162 MHz, DMSO-d6): δ=149.52, 148.82.

Example 27. Synthesis of Monomer

Preparation of (5): To the solution of 4 (18.8 g, Scheme 5) in dry ACN (200 mL) was added TPSCI (16.8 g, 65.2 mmol) and TEA (5.6 g, 65.2 mmol) and DMAP (6.8 g, 65.2 mmol), and the reaction mixture was stirred at room temperature for 3.5 hrs under N2 atmosphere. After addition of water, the resulting mixture was extracted with EA (300 mL). The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated to give the crude 5 (22.0 g) as a white solid which was used directly for next step. ESI-LCMS: m/z 677 [M−H]+.

Preparation of (6): To a solution of 5 (22.0 g) in pyridine (150 mL) was added BzCl (6.8 g, 48.9 mmol) under ice bath. The reaction mixture was stirred at r.t. for 2.5 hrs. LCMS showed 5 was consumed. The mixture was diluted with EA and water was added. The product was extracted with EA. The crude was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give the crude 6 (20.8 g, 26.7 mmol, 82% yield over two steps) as a white solid. ESI-LCMS: m/z 781 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.30 (s, 1H), 8.55 (d, J=8.0 Hz, 1H), 8.00-7.98 (m, 2H), 7.74-7.66 (m, 1H), 7.60-7.50 (m, 2H), 7.47-7.31 (m, 4H), 7.30-7.2(m, 5H), 7.20-7.1(m, 1H), 6.91 (d, J=7.4 Hz, 4H), 5.91-5.86 (AB, J=20.0 Hz, 1H), 4.30 (d, J=8.0 Hz, 1H), 3.87-3.78 (s, 1H), 3.78-3.70 (m, 6H), 3.62-3.51 (m, 1H), 3.28-3.2 (m, 1H), 2.15-2.05 (m, 3H), 0.73 (s, 9H), 0.00 (m, 6H).

Preparation of (7): To a solution of 6 (20.8 g, 26.7 mmol) in THF (210 mL) was added 1 M TBAF solution (32 mL). The reaction mixture was stirred at r.t. for 1.5 hrs. LCMS showed 6 was consumed completely. Water (600 mL) was added. The product was extracted with EA (400 mL) and the organic layer was washed with brine and dried over Na2SO4. Then the organic layer was concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 7 (12.4 g, 18.6 mmol, 70%) as a white solid. ESI-LCMS: m/z 667 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.03 (m, 1H), 8.51-8.48 (m, 1H), 8.08-7.95 (m, 2H), 7.63-7.54 (m, 1H), 7.52-7.19 (m, 9H), 7.16-7.07 (m, 1H), 6.94-6.89 (m, 3H), 5.95-5.87 (m, 1H), 5.31-5.17 (m, 1H), 4.61-4.37 (m, 1H), 4.20-4.07 (m, 1H), 3.82-3.47 (m, 7H), 2.57-2.42 (m, 2H).

Preparation of Example 27 monomer: To a suspension of 7 (12.4 g, 18.6 mmol) in DCM (120 mL) was added DCI (1.7 g, 15.8 mmol) and CEP[N(iPr)2]2 (7.3 g, 24.2 mmol). The mixture was stirred at r.t. for 2 hrs. LC-MS showed 7 was consumed completely. The solution was washed with water twice and washed with brine and dried over Na2SO4. Then concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 27 monomer (13.6 g, 15.7 mmol, 84.0%) as a white solid. ESI-LCMS: m/z 867 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.03 (m, 1H), 8.51-8.48 (m, 1H), 8.08-7.95 (m, 2H), 7.63-7.54 (m, 1H), 7.52-7.19 (m, 9H), 7.16-7.07 (m, 1H), 6.94-6.89 (m, 3H), 5.95-5.87 (m, 1H), 5.31-5.17 (m, 1H), 4.61-4.37 (m, 1H), 4.20-4.07 (m, 1H), 3.82-3.47 (m, 10H), 2.74-2.59 (m, 1H), 2.57-2.43 (m, 1H), 1.27-1.10 (m, 9H), 1.09-0.95 (m, 3H). 31P-NMR (162 MHz, DMSO-d6): δ 149.59, 148.85.

Example 28. Synthesis of Monomer

Preparation of (4): To a solution of 3 (13.1 g, 35.2 mmol, Scheme 3) in pyridine (130 mL) was added MsCl (4.8 g, 42.2 mmol) under −10 ˜0° C. The reaction mixture was stirred at r.t. for 2.5 h under N2 atmosphere. TLC (DCM/MeOH=15:1) showed the reaction was consumed. The mixture was diluted with EA and water was added. The product was extracted with EA. The organic layer was washed with brine and dried over Na2SO4 and concentrated to give the crude. This resulted in to give the product 4 (14.2 g) which was used directly for the next step. ESI-LCMS: m/z 451 [M+H]+; H-NMR (400 MHz, DMSO-d6) δ 11.43 (m, 1H), 7.67-7.65 (m, 1H), 5.90-5.80 (m, 1H), 5.75-5.64 (m, 1H), 4.52-4.21 (m, 3H), 4.12-3.90 (m, 2H), 3.48-3.21 (m, 6H), 0.95-0.78 (s, 9H), 0.13-0.03 (s, 6H).

Preparation of (5): To a solution of 4 (14.2 g) in DMSO (200 mL) was added DMTrSH (19.6 g, 63.2 mmol) and tetramethylguanidine (5.1 g, 47.4 mmol) at r.t. The reaction mixture was stirred at r.t. for 3.5 h under N2 atmosphere. LCMS showed 4 the reaction was consumed. The mixture was diluted with EA and water was added. The product was extracted with EA. The organic layer was washed with brine and dried over Na2SO4 and concentrated to give the crude. The crude was purified by silica gel column (SiO2, PE/EA=10:1-1:1) to give 5 (14.2 g, 20.6 mmol, 58.5% yield over two steps) as a white solid. ESI-LCMS: m/z 689 [M+H]; 1H-NMR (400 MHz, DMSO-d6) δ 11.39 (m, 1H), 7.63-7.61 (d, J=8.0 Hz, 1H), 7.45-7.1(m, 9H), 6.91-6.81 (m, 4H), 5.80-5.70 (m, 2H), 4.01-3.91 (m, 1H), 3.85-3.78 (m, 1H), 3.78-3.65 (m, 6H), 3.60-3.51 (m, 1H), 3.43-3.2(m, 3H), 2.50-2.32 (m, 2H), 0.95-0.77 (s, 9H), −0.00-0.02 (s, 6H).

Preparation of (6): To a solution of 5 (14.2 g, 20.6 mmol) in THF (140 mL) was added 1 M TBAF solution (20 mL). The reaction mixture was stirred at r.t. under N2 atmosphere for 2.5 h. LCMS showed 5 was consumed completely. Water was added. The product was extracted with EA and the organic layer was washed with brine and dried over Na2SO4. Then the organic layer was concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 6 (10.5 g, 18.2 mmol, 88.5%) as a white solid. ESI-LCMS: m/z 576 [M+H]+; H-NMR (400 MHz, DMSO-d6) δ 11.38 (m, 1H), 7.56-7.54 (d, J=8.0 Hz, 1H), 7.45-7.1(m, 9H), 6.91-6.81 (m, 4H), 5.80-5.70 (m, 2H), 4.05-4.00 (m, 1H), 3.81-3.79 (m, 1H), 3.74 (m, 2H), 3.78-3.65 (m, 6H), 3.60-3.51 (m, 1H), 3.43-3.2(m, 3H), 2.40-2.32 (m, 1H).

Preparation of Example 28 monomer: To a suspension of 9 (10.5 g, 18.2 mmol) in DCM (100 mL) was added DCI (1.7 g, 15.5 mmol) and CEP[N(iPr)2]2 (7.2 g, 23.7 mmol). The mixture was stirred at r.t. for 1 h. LC-MS showed 9 was consumed completely. The solution was washed with water twice and washed with brine and dried over Na2SO4. Then concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 28 monomer (12.5 g, 16.1 mmol, 88%) as a white solid. ESI-LCMS: m/z 776 [M+H]+ H-NMR (400 MHz, DMSO-d6) δ 11.41 (m, 1H), 7.64-7.59 (m, 1H), 7.40-7.25 (m, 4H), 7.25-7.10 (m, 5H), 6.89-6.86 (m, 4H), 5.72-5.67 (m, 2H), 4.02-4.00 (m, 2H), 3.76-3.74 (m, 8H), 3.74-3.73 (m, 3H), 3.51-3.49 (d, J=8 Hz, 1H), 3.33-3.29 (m, 1H), 2.77-2.73 (m, 1H), 2.63-2.60 (m, 1H), 2.50-2.47 (m, 1H), 1.12-0.99 (m, 12H). 31P-NMR (162 MHz, DMSO-d6): δ 148.92, 148.84.

Example 29. Synthesis of Monomer

Preparation of (7): To a solution of 6 (16 g, 24.1 mmol, Scheme 4) in ACN (160 mL) was added DMAP (5.9 g, 48.2 mmol) and TEA (4.8 g, 48.2 mmol), then added TPSCI (10.9 g, 36.1 mmol) at 0° C. under N2 atmosphere and the mixture was stirred at r.t. for 5 hrs under N2 atmosphere. Then con. NH3.H2O (30 mL) was added at r.t. and the mixture was stirred at r.t. for 16 h. The reaction was quenched with water and the product was extracted with EA (200 mL). The organic phase was concentrated to give the crude 7 (16.0 g) as a white solid which was used directly for next step.

Preparation of (8): To a stirred solution of 7 (16.0 g, 24.1 mmol) in pyridine (160 mL) were added BzCl (4.1 g, 28.9 mmol) 0° C. under N2 atmosphere. And the reaction mixture was stirred at r.t. for 2.5 h. With ice-bath cooling, the reaction was quenched with water and the product was extracted with EA (200 mL). The organic phase was evaporated to dryness under reduced pressure to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 8 (18.0 g, 23.4 mmol, 97.0%) as a white solid. ESI-LCMS: m/z 768 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.31 (s, 1H), 8.47 (d, J=7.2 Hz, 1H), 7.99 (d, J=7.6 Hz, 2H), 7.65-7.16 (m, 13H), 6.92 (d, J=8.8 Hz, 4H), 6.01 (d, J=18.4 Hz, 1H), 5.18-5.04 (dd, 1H), 4.58-4.52 (m, 1H), 4.07 (d, J=9.6 Hz, 1H), 3.75 (s, 6H), 0.73 (s, 9H), 0.05 (s, 3H), −0.06 (s, 3H).

Preparation of (9): To a solution of 8 (18.0 g, 23.4 mmol) in THF (180 mL) was added 1 M TBAF solution (23 mL). The reaction mixture was stirred at r.t. for 1.5 h. LC-MS showed 8 was consumed completely. Water (500 mL) was added. The product was extracted with EA (300 mL) and the organic layer was washed with brine and dried over Na2SO4. Then the organic layer was concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 7 (13.7 g, 21.1 mmol, 90.5%) as a white solid. ESI-LCMS: m/z 654.2 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.31 (s, 1H), 8.35 (d, J=7.4 Hz, 1H), 8.01 (m, 2H), 7.65-7.16 (m, 13H), 6.92 (d, J=8.8 Hz, 4H), 5.94 (d, J=18.0 Hz, 1H), 5.71 (d, J=7.0 Hz, 1H), 5.12-4.98 (dd, 1H), 4.51-4.36 (m, 1H), 4.09 (d, J=9.6 Hz, 1H), 3.75 (s, 6H).

Preparation of Example 29 monomer: To a suspension of 9 (10.6 g, 16.2 mmol) in DCM (100 mL) was added DCI (1.6 g, 13.7 mmol) and CEP[N(iPr)2]2 (5.8 g, 19.4 mmol). The mixture was stirred at r.t. for 1 h. LC-MS showed 9 was consumed completely. The solution was washed with water twice and washed with brine and dried over Na2SO4. Then concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 29 monomer (10.5 g, 14.5 mmol, 75.9%) as a white solid. ESI-LCMS: m/z 854.3 [M+H]−; 1H-NMR (400 MHz, DMSO-d6): δ 11.31 (s, 1H), 8.41-8.37 (m, 1H), 8.01 (d, J=7.7 Hz, 2H), 7.65-7.16 (m, 13H), 6.92-6.88 (m, 4H), 6.06-5.98 (m, 1H), 5.33-5.15 (m, 1H), 4.78-4.58 (m, 1H), 4.23-4.19 (m, 1H), 3.81-3.73 (m, 6H), 3.60-3.50 (m, 3H), 3.32 (s, 1H), 2.76 (t, J=6.0 Hz, 1H), 2.60 (t, J=5.8 Hz, 1H), 1.15-0.94 (m, 12H); 31P-NMR (162 MHz, DMSO-d6): δ 150.23, 150.18, 149.43, 149.38.

Example 30. Synthesis of Monomer

Preparation of (9): To a solution of 8 (18.8 g, 26.4 mmol, Scheme 5) in ACN (200 mL) was added TPSCI (16.8 g, 55.3 mmol) and DMAP (5.6 g, 55.3 mmol) and TEA (6.8 g, 55.3 mmol). The reaction mixture was stirred at r.t. for 3.5 hrs. LCMS showed the reaction was consumed. The mixture was diluted with con. NH4OH (28 mL). The mixture was diluted with water and EA. The product was extracted with EA. The organic layer was washed with brine and dried over Na2SO4 and concentrated to give the crude 9 (18.5 g) which was used directly for the next step.

Preparation of (10): To a solution of 9 (18.8 g, 27.69 mmol) in pyridine (200 mL) was added BzCl (5.8 g, 41.5 mmol) under ice bath. The reaction mixture was stirred at r.t. for 2.5 hrs. LCMS showed 9 was consumed. The mixture was diluted with EA and water was added. The product was extracted with EA. The crude was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 10 (19.8 g, 25.3 mmol, 91% yield) as a white solid. ESI-LCMS: m/z 783 [M−H]−; 1H-NMR (400 MHz, DMSO-d6): δ 11.29 (d, J=2.0 Hz, 1H), 8.42 (d, J=8.0 Hz, 1H), 8.02-8.00 (m, 2H), 7.64-7.62 (m, 1H), 7.60-7.41 (m, 2H), 7.47.41-7.19 (m, 9H), 6.94-6.85 (m, 4H), 5.81 (d, J=4.0 Hz, 1H), 5.33-5.26 (m, 1H), 5.21 (d, J=7.2 Hz, 1H), 4.06-3.90 (m, 2H), 3.83-3.77 (m, 1H), 3.74 (s, 6H).

Preparation of (11): To a solution of 10 (18.8 g, 26.4 mmol) in THF (190 mL) was added 1 M TBAF solution (28 mL). The reaction mixture was stirred at r.t. for 1.5 hrs. LCMS showed 10 was consumed completely. Water (200 mL) was added. The product was extracted with EA (200 mL) and the organic layer was washed with brine and dried over Na2SO4. Then the organic layer was concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 11 (17.1 g, 25.6 mmol, 96%) as a white solid. ESI-LCMS: m/z 669 [M−H]−; 1H-NMR (400 MHz, DMSO-d6): δ 11.29 (d, J=2.0 Hz, 1H), 8.42 (d, J=8.0 Hz, 1H), 8.02-8.00 (m, 2H), 7.64-7.62 (m, 1H), 7.60-7.41 (m, 2H), 7.47.41-7.19 (m, 9H), 6.94-6.85 (m, 4H), 5.81 (d, J=4.0 Hz, 1H), 5.33-5.26 (m, 1H), 5.21 (d, J=7.2 Hz, 1H), 4.06-3.90 (m, 2H), 3.83-3.77 (m, 1H), 3.74 (s, 6H).

Preparation of Example 30 monomer: To a suspension of 11(10.8 g, 16.2 mmol) in DCM (100 mL) was added DCI (1.5 g, 13.7 mmol) and CEP[N(iPr)2]2 (5.8 g, 19.3 mmol). The mixture was stirred at r.t. for 2 hrs. LC-MS showed 11 was consumed completely. The solution was washed with water twice and washed with brine and dried over Na2SO4. Then concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 30 monomer (11.3 g, 13 mmol, 80%) as a white solid. ESI-LCMS: m/z 868 [M+H]; 1H-NMR (400 MHz, DMSO-d6): δ 11.03 (m, 1H), 8.51-8.48 (m, 1H), 8.08-7.95 (m, 2H), 7.63-7.54 (m, 1H), 7.52-7.19 (m, 9H), 7.16-7.07 (m, 1H), 6.94-6.89 (m, 3H), 5.95-5.87 (m, 1H), 5.31-5.17 (m, 1H), 4.61-4.37 (m, 1H), 4.20-4.07 (m, 1H), 3.82-3.47 (m, 10H), 2.74-2.59 (m, 1H), 2.57-2.43 (m, 1H), 1.27-1.10 (m, 9H), 1.09-0.95 (m, 3H). 31P-NMR (162 MHz, DMSO-d6): δ 149.52, 148.81.

Example 31. Synthesis of Monomer

Preparation of (2): To a stirred solution of 1 (100.0 g, 406.5 mmol) in pyridine (1000 mL) were added DMTrCl (151.2 g, 447.1 mmol) at r.t. And the reaction mixture was stirred at r.t. for 2.5 hrs. With ice-bath cooling, the reaction was quenched with water and the product was extracted with EA (3000 mL). The organic phase was evaporated to dryness under reduced pressure to give a residue which was purified by silica gel column chromatography (SiO2, dichloromethane: methanol=100:1) to give 2 (210.0 g, 90%) as a white solid. ESI-LCMS: m/z 548.2 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.43 (d, J=1.8 Hz, 1H), 7.77 (d, J=8.0 Hz, 1H), 7.40-7.21 (m, 9H), 6.92-6.88 (m, 4H), 5.89 (d, J=20.0 Hz, 1H), 5.31-5.29 (m, 1H), 5.19-5.04 (dd, 1H), 4.38-4.31 (m, 1H), 4.02-3.98 (m, 1H), 3.74 (s, 6H), 3.30 (d, J=3.2 Hz, 2H); 19F-NMR (376 MHz, DMSO-d6): δ −199.51.

Preparation of (3): To a stirred solution of 2 (100.0 g, 182.8 mmol) in pyridine (1000 mL) were added MsCl (31.2 g, 274.2 mmol) at 0° C. under N2 atmosphere. And the reaction mixture was stirred at r.t for 2.5 h. With ice-bath cooling, the reaction was quenched with water and the product was extracted with EA (200 mL). The organic phase was evaporated to dryness under reduced pressure to give the crude (114.0 g) as a white solid which was used directly for next step. To the solution of the crude (114.0 g, 187.8 mmol) in DMF (2000 mL) was added K2CO3 (71.5 g, 548.4 mmol), and the reaction mixture was stirred at 90° C. for 15 h under N2 atmosphere. After addition of water, the resulting mixture was extracted with EA (500 mL). The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated to give a residue which was purified by silica gel column chromatography (SiO2, dichloromethane: methanol=30:1) to give 3 (100.0 g, 90%) as a white solid. ESI-LCMS: m/z 531.2 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 7.79 (d, J=8.0 Hz, 1H), 7.40-7.21 (m, 9H), 6.89-6.83 (m, 4H), 6.14 (d, J=5.4 Hz, 1H), 6.02-5.90 (dd, 1H), 5.87 (d, J=20.0 Hz, 1H), 5.45 (m, 1H), 4.61 (m, 1H), 3.73 (d, J=1.9 Hz, 6H), 3.30-3.15 (m, 2H), 1.24-1.16 (m, 1H); 19F-NMR (376 MHz, DMSO-d6): δ −204.23.

Preparation of (4): A solution of 3 (100 g, 187.8 mmol) in THF (1000 mL) was added 6N NaOH (34 mL, 206.5 mmol). The mixture was stirred at r.t. for 6 h. After completion of reaction, the resulting mixture was added H2O, and then the mixture was extracted with EA, the organic layer was washed with brine, dried over sodium sulfate and removed to give the residue was purified by silica gel column chromatography (SiO2, dichloromethane: methanol=30:1) to give 4 (90.4 g, 90%) as a white solid. ESI-LCMS: m/z 548.2 [M+H]+; 19F-NMR (376 MHz, DMSO-d6): δ −184.58.

Preparation of (5): To a stirred solution of 4 (90.4 g, 165.2 mmol) in pyridine (1000 mL) were added MsCl (61.5 g, 495.6 mmol) at 0° C. under N2 atmosphere. And the reaction mixture was stirred at r.t for 16 hrs. With ice-bath cooling, the reaction was quenched with water and the product was extracted with EA. the organic layer was washed with brine, dried over sodium sulfate and removed to give the residue was purified by silica gel column chromatography (SiO2, PE: EA=1:1) to give 5 (75.0 g, 90%) as a white solid. ESI-LCMS: m/z 626.2 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.51 (d, J=1.6 Hz, 1H), 7.43-7.23(m, 10H), 6.92-6.88 (m, 4H), 6.08 (d, J=20.0 Hz, 1H), 5.55-5.39 (m, 2H), 4.59 (m, 1H), 3.74 (s, 6H), 3.48-3.28 (m, 2H), 3.17 (s, 3H); 19F-NMR (376 MHz, DMSO-d6): δ −187.72.

Preparation of (6): To the solution of 5 (75.0 g, 120.4 mmol) in DMF (1500 mL) was added KSAc (71.5 g, 548.4 mmol) at 110° C. under N2 atmosphere, After the reaction mixture was stirred at 110° C. for 3 h were added KSAc (71.5 g, 548.4 mmol) under N2 atmosphere. And the reaction mixture was stirred at r.t for 16 h. After addition of water, the resulting mixture was extracted with EA. The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated to give a residue which was purified by silica gel column chromatography (SiO2, PE: EA=1:1) to give 6 (29.0 g, 90%) as a white solid. ESI-LCMS: m/z 605.2 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.45 (d, J=1.9 Hz, 1H), 7.95 (d, J=8.0 Hz, 1H), 7.38-7.21 (m, 9H), 6.92-6.87 (m, 4H), 5.93 (m, 1H), 5.50-5.36 (dd, 1H), 5.25-5.23 (dd, 1H), 4.54-4.42 (m, 1H), 4.17-4.12 (m, 1H), 3.74 (m, 7H), 3.35-3.22 (m, 2H), 2.39 (s, 1H); 19F-NMR (376 MHz, DMSO-d6): δ −181.97.

Preparation of (7): A solution of 6 (22 g, 36.3 mmol) in a mixture solvent of THF/MeOH (1:1, 200 mL) was added 1N NaOMe (70 mL, 72.6 mmol)was stirred at 20° C. for 4 h. After completion of reaction, the resulting mixture was added H2O, and then the mixture was extracted with EA, the organic layer was washed with brine, dried over sodium sulfate and removed to give the residue was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=4/3; Detector, UV 254 nm. This resulted in to give 7 (10.5 g, 14.5 mmol, 75.9%) as a white solid. ESI-LCMS: m/z 565.1 [M+H]+: 1H-NMR (400 MHz, DMSO-d6): δ 11.45 (s, 1H), 7.83 (d, J=8.0 Hz, 1H), 7.40-7.23 (m, 9H), 6.90 (d, J=8.8 Hz, 4H), 5.88 (m, 1H), 5.29-5.15 (m, 2H), 3.72 (m, 7H), 3.43 (m, 2H), 2.78 (d, J=10.6 Hz, 1H).

Preparation of Example 31 monomer: To a suspension of 7 (10.5 g, 18.6 mmol) in DCM (100 mL) was added DCI (1.8 g, 15.7 mmol) and CEP[N(iPr)2]2 (6.7 g, 22.3 mmol). The mixture was stirred at r.t. for 1 h. LC-MS showed 8 was consumed completely. The solution was washed with water twice and washed with brine and dried over Na2SO4. Then concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 31 monomer (10.5 g, 14.5 mmol, 75.9%) as a white solid. ESI-LCMS: m/z 765.3 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.40 (d, J=12.2 Hz, 1H), 7.90-7.86 (m, 1H), 7.41-7.24 (m, 9H), 6.91-6.89 (m, 4H), 5.97 (m, 1H), 5.33-5.10 (m, 2H), 4.18-4.16 (m, 1H), 3.91-3.39 (m, 17H), 2.81 (t, J=5.6 Hz, 1H), 2.66 (t, J=6.0 Hz, 1H), 1.33-0.97 (m, 12H); 31P-NMR (162 MHz, DMSO-d6): δ 164.57, 160.13.

Example 32. Synthesis of Monomer

Preparation of (2): To a stirred solution of 1 (100.0 g, 387.5 mmol) in pyridine (1000 mL) was added DMTrCl (151.2 g, 447.1 mmol) at r.t. And the reaction mixture was stirred at r.t. for 2.5 hrs. With ice-bath cooling, the reaction was quenched with water and the product was extracted with EA (3000 mL). The organic phase was evaporated to dryness under reduced pressure to give a residue which was purified by silica gel column chromatography (SiO2, dichloromethane: methanol=100:1) to give 2 (200.0 g, 90%) as a white solid. ESI-LCMS: m/z 561 [M+H]+.

Preparation of (3): To a stirred solution of 2 (73.0 g, 130.3 mmol) in pyridine (730 mL) were added MsCl (19.5 g, 169.2 mmol) at 0° C. under N2 atmosphere. And the reaction mixture was stirred at r.t for 2.5 h. With ice-bath cooling, the reaction was quenched with water and the product was extracted with EA (200 mL). The organic phase was evaporated to dryness under reduced pressure to give the crude (80.0 g) as a white solid which was used directly for next step. To the solution of the crude (80.0 g, 130.3 mmol) in DMF (1600 mL) was added K2CO3 (71.5 g, 390.9 mmol), and the reaction mixture was stirred at 90° C. for 15 h under N2 atmosphere. After addition of water, the resulting mixture was extracted with EA (500 mL). The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated to give a residue which was purified by silica gel column chromatography (SiO2, dichloromethane: methanol=30:1) to give 3 (55.0 g, 90%) as a white solid. ESI-LCMS: m/z 543. [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 7.68 (d, J=8.0 Hz, 1H), 7.40-7.21 (m, 9H), 6.89-6.83 (m, 4H), 5.96 (s, 1H), 5.83 (d, J=5.4 Hz, 1H), 5.26 (s, 1H), 4.59 (s, 1H), 4.46 (t, J=6.0 Hz, 1H), 3.72 (s, 6H), 3.44 (s, 3H), 3.18-3.12 (m, 2H).

Preparation of (4): A solution of 3 (55 g, 101.8 mmol) in THF (550 mL) was added 6N NaOH (34 mL, 206.5 mmol). The mixture was stirred at 20° C. for 6 hrs. After completion of reaction, the resulting mixture was added H2O, and then the mixture was extracted with EA, the organic layer was washed with brine, dried over sodium sulfate and removed to give the residue was purified by silica gel column chromatography (SiO2, dichloromethane: methanol=30:1) to give 4 (57.4 g, 87%) as a white solid. ESI-LCMS: m/z 561 [M+H]+.

Preparation of (5): To a stirred solution of 4 (57.4 g, 101.8 mmol) in pyridine (550 mL) were added MsCl (61.5 g, 495.6 mmol) at 0° C. under N2 atmosphere. And the reaction mixture was stirred at r.t for 16 h. With ice-bath cooling, the reaction was quenched with water and the product was extracted with EA. the organic layer was washed with brine, dried over sodium sulfate and removed to give the residue was purified by silica gel column chromatography (SiO2, PE: EA=1:1) to give 5 (57.0 g, 90%) as a white solid. ESI-LCMS: m/z 639 [M+H]+.

Preparation of (6): To the solution of 5 (57.0 g, 89.2 mmol) in DMF (600 mL) was added KSAc (71.5 g, 448.4 mmol) at 110° C. under N2 atmosphere, After the reaction mixture was stirred at 110° C. for 3 h were added KSAc (71.5 g, 448.4 mmol) under N2 atmosphere. And the reaction mixture was stirred at r.t for 16 h. After addition of water, the resulting mixture was extracted with EA. The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated to give a residue which was purified by silica gel column chromatography (SiO2, PE: EA=1:1) to give 6 (29.0 g, 47%) as a white solid. ESI-LCMS: m/z 619.2 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.41 (s, 1H), 8.06 (s, 1H), 7.40-7.23 (m, 9H), 6.90 (d, J=8.8 Hz, 4H), 5.82 (s, 1H), 5.10-5.08 (dd, 1H), 4.38-4.34 (m, 1H), 4.08-4.02 (m, 3H), 3.74 (s, 6H), 3.45 (s, 3H), 3.25 (m, 2H), 2.37 (s, 3H); ESI-LCMS: m/z 619 [M+H]+.

Preparation of (7): A solution of 6 (22 g, 35.3 mmol) in a mixture solvent of THF/MeOH (1:1, 200 mL) was added 1N NaOMe (70 mL, 72.6 mmol)was stirred at 20° C. for 4 h. After completion of reaction, the resulting mixture was added H2O, and then the mixture was extracted with EA, the organic layer was washed with brine, dried over sodium sulfate and removed to give the residue was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=4/3; Detector, UV 254 nm. This resulted in to give 7 (14.0 g, 70.9%) as a white solid. ESI-LCMS: m/z 576.1 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.38 (s, 1H), 7.90 (d, J=8.0 Hz, 1H), 7.40-7.23 (m, 9H), 6.90 (d, J=8.8 Hz, 4H), 5.80 (s, 1H), 5.15-5.13 (dd, 1H), 3.93 (m, 1H), 3.87 (d, J=5.0 Hz, 1H), 3.74 (s, 6H), 3.59 (m, 2H), 3.49 (s, 3H), 3.39 (d, J=2.2 Hz, 2H), 2.40 (d, J=10.2 Hz, 1H).

Preparation of Example 32 monomer: To a suspension of 7 (10.5 g, 18.6 mmol) in DCM (100 mL) was added DCI (1.8 g, 15.7 mmol) and CEP[N(iPr)2]2 (6.7 g, 22.3 mmol). The mixture was stirred at r.t. for 1 h. LC-MS showed 7 was consumed completely. The solution was washed with water twice and washed with brine and dried over Na2SO4. Then concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 32 monomer (10.5 g, 14.5 mmol, 75.9%) as a white solid. ESI-LCMS: m/z 776.3 [M+H], 1H-NMR (400 MHz, DMSO-d6): δ 11.40 (d, J=12.2 Hz, 1H), 8.04-7.96 (dd, 1H), 7.43-7.24 (m, 9H), 6.92-6.87 (m, 4H), 5.84 (m, 1H), 4.93 (m, 1H), 4.13 (m, 1H), 3.91-3.39 (m, 17H), 2.82 (t, J=5.6 Hz, 1H), 2.68 (t, J=6.0 Hz, 1H), 1.22-0.97 (m, 12H); 31P-NMR (162 MHz, DMSO-d6): δ 165.06, 157.59.

Example 33. Synthesis of 5′ End Cap Monomer

Preparation of (2): To a solution of 1(11.2 g, 24.7 mmol) in DCM (120 mL), imidazole (4.2 g, 61.9 mmol) and TBSCl (5.6 g, 37.1 mmol) were added at r.t., mixture was stirred at r.t. for 15 hrs, LCMS showed 1 was consumed completely. Mixture was added water (500 mL) and extracted with DCM (50 mL*2). The organic phase was dried over Na2SO4 and concentrated to give 2 (16.0 g) as an oil for the next step.

Preparation of (3): To a solution of 2 (16.0 g, 28.4 mmol) was added 6% DCA in DCM (160 mL) and triethylsilane (40 mL) at r.t. The reaction mixture was stirred at r.t. for 2 hrs. TLC showed 2 was consumed completely. Water (300 mL) was added, mixture was extracted with DCM (50 mL*4), organic phase was dried by Na2SO4, concentrated by reduce pressure to give crude which was purified by column chromatography (SiO2, PE/EA=10:1 to 1:1) to give 3 (4.9 g, 65.9% yield) as an oil. ESI-LCMS: m/z 263 [M+H]+;1H-NMR (400 MHz, DMSO-d6) δ 4.84-4.50 (m, 1H), 4.3-4.09 (m, 1H), 3.90-3.80 (m, 1H), 3.75-3.67 (m, 1H), 3.65-3.57 (m, 2H), 3.50-3.44 (m, 1H), 3.37-3.28 (m, 4H), 0.95-0.78 (s, 9H), 0.13-0.03 (s, 6H).

Preparation of (4): To a solution of 3 (3.3 g, 12.6 mmol) in DMSO (33 mL) was added EDCI (7.2 g, 37.7 mmol).The mixture was added pyridine (1.1 g, 13.8 mmol) and TFA (788.6 mg, 6.9 mmol). The reaction mixture was stirred at r.t. for 3 hrs. TLC (PE/EA=4:1) showed 3 was consumed. The mixture was diluted with EA and water was added. The product was extracted with EA. The organic layer was washed with brine and dried over Na2SO4 and concentrated to give the crude. This resulted in to give 4 (3.23 g) as an oil for the next step.

Preparation of (5): To a solution of 4 (3.3 g, 12.6 mmol) in toluene (30 mL) was added POM ester 4a (reference for 4a Journal of Medicinal Chemistry, 2018, 61 (3), 734-744) (7.9 g, 12.6 mmol) and KOH (1.3 g, 22.6 mmol) at r.t. The reaction mixture was stirred at 40° C. for 8 hrs. LCMS showed 4 was consumed. The mixture was diluted with water and EA was added. The product was extracted with EA. The organic layer was washed with brine and dried over Na2SO4 and concentrated to give the crude. The crude was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=91/9 Detector, UV 254 nm. This resulted in to give 5 (5.4 g, 9.5 mmol, 75.9% yield) as an oil. ESI-LCMS: m/z 567.2 [M+H]+; 1H-NMR (400 MHz, CDCl3) δ 6.89-6.77 (m, 1H), 6.07-5.96 (m, 1H), 5.86-5.55 (m, 4H), 4.85-4.73 (m, 1H), 4.36-4.27 (m, 1H), 4.05-3.96 (m, 1H), 3.95-3.85 (m, 1H), 3.73-3.65 (m, 1H), 3.44-3.35 (m, 3H), 1.30-1.25 (s, 18H), 0.94-0.84 (s, 9H), 0.14-0.05 (s, 6H). 31P-NMR (162 MHz, CDCl3) δ 18.30, 15.11.

Preparation of (6): To a solution of 5 (5.4 g, 9.5 mmol) in HCOOH (30 mL)/H2O (30 mL)=1:1 at r.t. The reaction mixture was stirred at r.t. for 15 hrs. LCMS showed the reaction was consumed. The mixture was diluted with con. NH4OH till pH=7.5. The product was extracted with EA. The organic layer was washed with brine and dried over Na2SO4 and concentrated to give the crude. The crude was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% HCOOH)=30/70 increasing to CH3CN/H2O (0.5% HCOOH)=70/30 within 45 min, the eluted product was collected at CH3CN/H2O (0.5% HCOOH)=59/41 Detector, UV 220 nm. This resulted in to give 6 (2.4 g, 5.7 mmol, 59.4% yield) as an oil. ESI-LCMS: m/z 453.2 [M+H]+; 1H-NMR (400 MHz, DMSO-d6) δ 6.84-6.68 (m, 1H), 6.07-5.90 (m, 1H), 5.64-5.55 (m, 4H), 5.32-5.24 (m, 1H), 4.23-4.15 (m, 1H), 4.00-3.90 (m, 1H), 3.89-3.80 (m, 1H), 3.78-3.69 (m, 2H), 3.37-3.30 (s, 3H), 1.30-1.10 (s, 18H). 31P-NMR (162 MHz, DMSO-d6) δ 18.14.

Preparation of Example 33 monomer: To a solution of 6 (2.1 g, 4.5 mmol) in DCM (21 mL) were added DCI (452.5 mg, 3.8 mmol) and CEP[N(iPr)2]2 (1.8 g, 5.9 mmol) at r.t. The reaction mixture was stirred at r.t. for 15 hrs under N2 atmosphere. LCMS showed 6 was consumed. The mixture was diluted with water. The product was extracted with DCM (30 mL). The organic layer was washed with brine and dried over Na2SO4 and concentrated to give the crude. The crude was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 28 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=80/20 Detector, UV 254 nm. This resulted in to give Example 33 monomer (2.8 g, 4.3 mmol, 95.2% yield) as an oil. ESI-LCMS: m/z 653.2 [M+H]+; 1H-NMR (400 MHz, DMSO-d6) δ 6.89-6.77 (m, 1H), 6.11-5.96 (m, 1H), 5.65-5.50 (m, 4H), 4.39-4.34 (d, J=20 Hz, 1H), 4.18-3.95 (m, 2H), 3.94-3.48 (s, 6H), 3.40-3.28 (m, 4H), 2.84-2.75 (m, 2H), 1.26-1.98 (s, 30H). 31P-NMR (162 MHz, DMSO-d6) δ 149.018, 148.736, 17.775, 17.508.

Example 34. Synthesis of 5′ End Cap Monomer

Preparation of (2): To a solution of 1 (ref for 1 Tetrahedron, 2013, 69, 600-606) (10.60 g, 47.32 mmol) in DMF (106 mL), imidazole (11.26 g, 165.59 mmol) and TBSCI (19.88 g, 132.53 mmol) were added. The mixture was stirred at r.t. for 3.5 hrs, LCMS showed 1 was consumed completely. Water was added and extracted with EA, dried over by Na2SO4. The filtrate was evaporated under reduced pressure to give 2 (20.80 g, 45.94 mmol, 97.19% yield) for the next step.

Preparation of (3): To a solution of 2 (20.80 g, 45.94 mmol) in THF (248 mL), was added TFA (124 mL) and H2O (124 mL) at 0° C., reaction mixture was stirred for 30 min. LCMS showed 2 was consumed completely. Then was extracted with EA, washed with sat. NaCl (aq.), dried over by Na2SO4. The filtrate was evaporated under reduced pressure to give the crude product which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 3 (10.00 g, 29.59 mmol, 64.31% yield). 1H-NMR (400 MHz, DMSO-d6): δ 7.33-7.18 (m, 5H), 4.83-4.80 (m, 1H), 4.61-4.59 (m, 1H), 4.21-4.19 (m, 1H), 3.75-3.74 (m, 1H), 3.23 (m, 3H), 3.13 (m, 3H), 2.41-2.40 (m, 1H), 0.81 (m, 9H), 0.00 (m, 6H).

Preparation of (4): To a solution of 3(3.70 g, 10.95 mmol) in DMSO (37 mL) was added EDCI (6.30 g, 32.84 mmol). Then pyridine (0.95 g, 12.05 mmol) and TFA (0.69 g, 6.02 mmol) was added in N2 atmosphere. The mixture was stirred for 3 hrs at r.t. LCMS showed 3 was consumed completely. Water was poured into and extracted with EA, washed with sat. NaCl (aq.), dried over by Na2SO4. The filtrate was evaporated under reduced pressure to give the crude product which was directly used for next step.

Preparation of (5): To a solution of 4 in toluene (100.00 mL), was added 4a (6.93 g, 10.97 mmol) and KOH (1.11 g, 19.78 mmol). It was stirred for 3.5 hrs at 40° C. in N2 atmosphere. TLC and LCMS showed 4 was consumed completely. Then was extracted with EA, washed with water and sat. NaCl (aq.), dried over by Na2SO4. The filtrate was evaporated under reduced pressure to give the crude product which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 5 (4.30 g, 6.70 mmol, 61.17% yield). 1H-NMR (400 MHz, CDCl3): δ 7.27-7.26 (m, 4H), 7.17 (m, 1H), 6.94-6.82 (m, 1H), 6.13-6.02 (m, 1H), 5.63-5.56 (m, 4H), 4.90-4.89 (m, 1H), 4.45-4.41 (m, 1H), 3.98-3.95 (m, 1H), 3.39-3.29 (m, 4H), 1.90 (m, 1H), 1.12-0.83 (m, 29H), 0.00 (m, 7H); 31P-NMR (162 MHz, CDCl3): δ 18.021, 14.472.

Preparation of (6): To a solution of 5 (4.30 g, 6.70 mmol) in THF (43.00 mL) was added HCOOH (100 mL) and H2O (100 mL). It was stirred overnight at r.t. LCMS showed 5 was consumed completely. NH4OH was poured into it and was extracted with EA, washed with sat. NaCl (aq.), dried over by Na2SO4. The filtrate was evaporated under reduced pressure to give the crude product which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 6 (2.10 g, 3.98 mmol, 59.32% yield). 1H-NMR (400 MHz, CDCl3): δ 7.40-7.28 (m, 5H), 7.11-7.00 (m, 1H), 6.19-6.14 (m, 1H), 5.71-5.68 (m, 4H), 4.95-4.94 (m, 1H), 4.48-4.47 (m, 1H), 4.05-4.03 (m, 1H), 3.62-3.61 (m, 1H), 3.46 (m, 3H), 3.00-2.99 (m, 1H), 1.22 (m, 18H); 31P-NMR (162 MHz, CDCl3): δ 18.134.

Preparation of Example 34 monomer: To a solution of 6 (2.10 g, 3.98 mmol) in DCM (21 mL) was added DCI (410 mg, 3.47 mmol). CEP (1.40 g, 4.65 mmol) was added in a N2 atmosphere. LCMS showed 6 was consumed completely. DCM and H2O was poured, the organic phase was washed with water and sat. NaCl (aq.), dried over by Na2SO4. The filtrate was evaporated under reduced pressure at 40° C. to give the crude product which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 34 monomer (2.10 g, 2.88 mmol). 1H-NMR (400 MHz, DMSO-d6): δ 7.39-7.32 (m, 6H), 6.21-6.11 (m, 1H), 5.64-5.61 (m, 4H), 4.91-4.85 (m, 1H), 4.59 (m, 1H), 4.28-4.25 (m, 1H), 3.84-3.60 (m, 5H), 3.36-3.36 (m, 2H), 2.83-2.79 (m, 2H), 1.18-1.14 (m, 29H); 31P-NMR (162 MHz, DMSO-d6): δ 149.588, 148.920, 17.355, 17.010.

Example 35. Synthesis of 5′ End Cap Monomer

Preparation of (2): To a solution of 1 (5.90 g, 21.50 mmol) in DMF (60.00 mL), imidazole (4.39 g, 64.51 mmol) and TBSCl (7.63 g, 49.56 mmol) were added. The mixture was stirred at r.t. for 3.5 hrs, LCMS showed 1 was consumed completely. Water was added and extracted with EA, dried over by Na2SO4. The filtrate was evaporated under reduced pressure to give 2 (11.00 g, 21.91 mmol, 98.19% yield) for the next step. ESI-LCMS: m/z 225.1 [M+H]+.

Preparation of (3): To a solution of 2 (11.00 g, 21.91 mmol) in THF (55.00 mL) was added TFA (110.00 mL) and H2O (55.00 mL) at 0° C., reaction mixture was stirred for 30 min. LCMS showed 2 was consumed completely. Then was extracted with EA, washed with sat. NaCl (aq.), dried over by Na2SO4. The filtrate was evaporated under reduced pressure to give the crude product which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 3 (6.20 g, 16.32 mmol, 72.94% yield). ESI-LCMS: m/z 411.2 [M+H]+.

Preparation of (4): To a solution of 3 (3.50 g, 9.02 mmol) in DMSO (35.00 mL) was added EDCI (5.19 g, 27.06 mmol). Then pyridine (0.78 g, 9.92 mmol) and TFA (0.57 g, 4.96 mmol) was added in N2 atmosphere. The mixture was stirred for 3 h at r.t. Water was poured into it and was extracted with EA, washed with sat. NaCl (aq.), dried over by Na2SO4. The filtrate was evaporated under reduced pressure to give the crude product which was directly used for next step. ESI-LCMS: m/z 406.2 [M+H]+.

Preparation of (5): To a solution of 4 in toluene (100.00 mL) was added 4a (5.73 g, 9.07 mmol) and KOH (916.3 g, 16.33 mmol). It was stirred for 3.5 h at 40° C. in N2 atmosphere. Then was extracted with EA, washed with water and sat. NaCl (aq.), dried over by Na2SO4. The filtrate was evaporated under reduced pressure to give the crude product which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 5 (5.02 g, 7.25 mmol, 80.44% yield). ESI-LCMS: m/z 693.2 [M+H]+; 31P-NMR (162 MHz, DMSO-d6): δ 17.811

Preparation of (6): To a solution of 5 (4.59 g, 6.63 mmol) in THF (46.00 mL) was added HCOOH (92.00 mL) and H2O (92.00 mL). It was stirred overnight at r.t. NH4OH was poured into it and extracted with EA, washed with sat. NaCl (aq.), dried over by Na2SO4. The filtrate was evaporated under reduced pressure to give the crude product which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 6 (2.52 g, 4.36 mmol, 65.80% yield).

Preparation of Example 35 monomer: To a solution of 6 (2.00 g, 3.46 mmol) in DCM (21.00 mL) was added DCI (370.00 mg, 3.11 mmol) and CEP (1.12 g, 4.15 mmol) was added in N2 atmosphere. DCM and H2O was poured, the organic phase was washed with water and sat. NaCl (aq.), dried over by Na2SO4. The filtrate was evaporated under reduced pressure at 38° C. to give the crude product which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 35 monomer (2.10 g, 2.70 mmol, 78.07% yield). 1H-NMR (400 MHz, DMSO-d6): δ 7.39-7.32 (m, 6H), 6.21-6.11 (m, 1H), 5.64-5.61 (m, 4H), 4.91-4.85 (m, 1H), 4.59 (m, 1H), 4.28-4.25 (m, 1H), 3.84-3.60 (m, 5H), 3.36-3.36 (m, 2H), 2.83-2.79 (m, 2H), 1.18-1.14 (m, 29H). 31P-NMR (162 MHz, DMSO-d6): δ 149.588, 148.920, 17.355, 17.010.

Example 36. Synthesis of Monomer

Preparation of(2): To a solution of 1(35.0 g, 53.2 mmol) in DMF (350 mL) was added imidazole (9.0 g, 133.0 mmol) then added TBSCl (12.0 g, 79.8 mmol) at 0° C. The mixture was stirred at r.t. for 14 hrs. TLC showed 1 was consumed completely. Water was added to the reaction. The product was extracted with EA, The organic layer was washed with NaHCO3 and brine. Then the solution was concentrated under reduced pressure the crude 2 (41.6 g) as a white solid which was used directly for next step. ESI-LCMS: m/z 772 [M+H]+.

Preparation of (3): To a solution of 2(41.0 g, 53.1 mmol) in 3% DCA (53.1 mmol, 350 mL) and Et3SiH (53.1 mmol, 100 mL) at 0° C. The mixture was stirred at 0° C. for 0.5 h. TLC showed 2 was consumed completely. NaHCO3 was added to the reaction. The product was extracted with EA, The organic layer was washed with NaHCO3 and brine. Then the solution was concentrated under reduced pressure. The residue silica gel column chromatography (eluent, DCM/MeOH=100:1-20:1). This resulted in to give 3 (20.0 g, 41.7 mmol, 78.6% over two step) as a white solid. ESI-LCMS: m/z 470 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 12.12 (s, 1H), 11.67 (s, 1H), 8.28 (s, 1H), 6.12-6.07 (dd, J=15 Hz, 1H), 5.75 (d, J=5 Hz, 1H), 5.48-5.24 (m, 2H), 4.55-4.49 (m, 1H), 3.97 (s, 1H), 3.75-3.55 (m, 2H), 2.79-2.76 (m, 1H), 1.12 (d, J=6 Hz, 6H), 0.88 (s, 9H), 0.11 (d, J=6 Hz, 6H).

Preparation of (4): To the solution of 3 (20 g, 42.6 mmol) in dry DCM (100 mL) and DMF (60 mL) was added PDC (20. g, 85.1 mmol), tert-butyl alcohol (63.1 g, 851.8 mmol) and Ac2O (43.4 g, 425.9 mmol) at r.t. under N2 atmosphere. And the reaction mixture was stirred at r.t. for 2 h. The solvent was removed to give a residue which was purified by silica gel column chromatography (eluent, PE: EA=4:1-2:1) to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 4 (16.0 g, 29.0 mmol, 68.2% yield) as a white solid. ESI-LCMS: m/z 540 [M+H]+; H-NMR (400 MHz, DMSO-d6): δ 12.12 (s, 1H), 11.69 (s, 1H), 8.28 (s, 1H), 6.21-6.17 (dd, J=15 Hz, 1H), 5.63-5.55 (m, 1H), 4.75-4.72 (m, 1H), 4.41 (d, J=5 Hz, 1H), 2.79-2.76 (m, 1H), 1.46 (s, 9H), 1.13-1.11 (m, 6H), 0.90 (s, 9H), 0.14 (d, J=2 Hz, 6H).

Preparation of (5): To the solution of 4 (16.0 g, 29.6 mmol) in dry THF/MeOD/D20=10/2/1 (195 mL) was added NaBD4 (3.4 g, 88.9 mmol) at r.t. and the reaction mixture was stirred at 50° C. for 2 h. After completion of reaction, adjusted pH value to 7 with CH3COOD, after addition of water, the resulting mixture was extracted with EA (300 mL). The combined organic layer was washed with water and brine, dried over Na2SO4, Then the solution was concentrated under reduced pressure the crude 5 (11.8 g) as a white solid which was used directly for next step. ESI-LCMS: m/z 402 [M+H]+.

Preparation of (6): To a solution of 5 (5.0 g, 12.4 mmol) in pyridine (50 mL) was added iBuCl (2.6 g, 24.9 mmol) at 0° C. under N2 atmosphere. The mixture was stirred at r.t. for 14 h. TLC showed 5 was consumed completely. Then the solution diluted with EA. The organic layer was washed with NaHCO3 and brine. Then the solution was concentrated under reduced pressure to give the crude. To a solution of the crude in pyridine (50 mL) was added 2N NaOH (MeOH/H2O=4:1, 15 mL) at 0° C. The mixture was stirred at 0° C. for 10 min. Then the solution diluted with EA. The organic layer was washed with NH4Cl and brine. Then the solution was concentrated under reduced pressure the residue was purified by Flash-Prep-HPLC with the following conditions(IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=4/1 within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=3/2; Detector, UV 254 nm. This resulted in to give 6 (6 g, 10.86 mmol, 87.17% yield) as a white solid. ESI-LCMS: m/z 472.2 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 12.12 (s, 1H), 11.67 (s, 1H), 8.28 (s, 1H), 6.12-6.07 (dd, J=15 Hz, 1H), 5.48-5.24 (m, 2H), 5.22 (s, 1H), 4.55-4.49 (m, 1H), 3.97 (d, J=5 Hz, 1H), 2.79-2.76 (m, 1H), 1.12 (d, J=6 Hz, 6H), 0.88 (s, 9H), 0.11 (d, J=6 Hz, 6H).

Preparation of (7): To a solution of 6 (3.8 g, 8.1 mmol) in pyridine (40 mL) was added DMTrCl (4.1 g, 12.1 mmol) at 20° C. The mixture was stirred at 20° C. for 1 h. TLC showed 7 was consumed completely. Water was added to the reaction. The product was extracted with EA, The organic layer was washed with NaHCO3 and brine. Then the solution was concentrated under reduced pressure to give the crude product of 7 (6 g, 7.6 mmol, 94.3% yield) as a yellow solid. ESI-LCMS: m/z 775 [M+H]+.

Preparation of (8): To a solution of 7 (6.0 g, 7.75 mmol) in THF (60 mL) was added TBAF (2.4 g, 9.3 mmol). The mixture was stirred at r.t. for 1 h. TLC showed 7 was consumed completely. Water was added to the reaction. The product was extracted with EA, The organic layer was washed with NaHCO3 and brine. Then the solution was concentrated under reduced pressure, the residue was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=4/1; Detector, UV 254 nm. This resulted in to give 8 (4.0 g, 5.9 mmol, 76.6% yield) as a white solid. ESI-LCMS: m/z 660 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 12.12 (s, 1H), 11.67 (s, 1H), 8.12 (s, 1H), 7.34-7.17 (m, 9H), 6.83-6.78 (m, 4H), 6.23-6.18 (m, 1H), 5.66 (d, J=7 Hz, 1H), 5.48-5.35 (m, 1H), 4.65-4.54 (m, 1H), 3.72 (d, J=2 Hz, 6H), 2.79-2.73 (m, 1H), 1.19-1.06 (m, 6H).

Preparation of Example 36 monomer: To a solution of 9 (4.0 g, 6.1 mmol) in DCM (40 mL) was added DCI (608 mg, 5.1 mmol) and CEP (2.2 g, 7.3 mmol) under N2 pro. The mixture was stirred at 20° C. for 0.5 h. TLC showed 9 was consumed completely. The product was extracted with DCM, The organic layer was washed with H2O and brine. Then the solution was concentrated under reduced pressure and the residue was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 36 monomer (5.1 g, 5.81 mmol, 95.8% yield) as a white solid. ESI-LCMS: m/z 860 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 12.12 (s, 1H), 11.67 (s, 1H), 8.12 (s, 1H), 7.34-7.17 (m, 9H), 6.83-6.78 (m, 4H), 6.23-6.18 (m, 1H), 5.67-5.54 (m, 1H), 4.70-4.67 (m, 1H), 4.23-4.20 (m, 1H), 3.72 (m, 6H), 3.60-3.48 (m, 3H), 2.79-2.58 (m, 3H), 1.13-0.94 (m, 18H); 31P-NMR (162 MHz, DMSO-d6): δ 150.31, 150.26, 140.62, 149.57.

Example 37: Synthesis of Monomer

Preparation of (2): To a solution of 1(35 g, 130.2 mmol) in DMF (350 mL) was added imidazole (26.5 g, 390.0 mmol) then added TBSCl (48.7 g, 325.8 mmol) at 0° C. The mixture was stirred at r.t. for 14 h. TLC showed 1 was consumed completely. Water was added to the reaction. The product was extracted with EA, The organic layer was washed with NaHCO3 and brine. Then the solution was concentrated under reduced pressure the crude 2 (64.6 g) as a white solid which was used directly for next step. ESI-LCMS: m/z 498 [M+H]+.

Preparation of (3): To a solution of 2 (64.6 g, 130.2 mmol) in THF (300 mL) and added TFA/H2O (1:1, 300 mL) at 0° C. The mixture was stirred at 0° C. for 2 h. TLC showed 2 was consumed completely. NaHCO3 was added to the reaction. The product was extracted with EA, The organic layer was washed with NaHCO3 and brine. Then the solution was concentrated under reduced pressure. The residue was purified by silica gel column chromatography (eluent, DCM: MEOH=100:1-20:1). This resulted in to give 3 (31.3 g, 81.7 mmol, 62.6% over two step) as a white solid. ESI-LCMS: m/z 384 [M+H]+.

Preparation of (4): To a solution of 3 (31.3 g, 81.7 mmol) in ACN/H2O (1:1, 350 mL) was added DAIB (78.0 g, 244.0 mmol) and Tempo (3.8 g, 24.4 mmol). The mixture was stirred at 40° C. for 2 h. TLC showed 3 was consumed completely. Then filtered to give 4 (22.5 g, 55.5 mmol, 70.9%) as a white solid. ESI-LCMS: m/z 398 [M+H]+.

Preparation of (5): To a solution of 4 (22.5 g, 55.5 mmol) in MeOH (225 mL) held at −15° C. with an ice/MeOH bath was added SOCl2 (7.6 mL, 94.5 mmol), dropwise at such a rate that the reaction temp did not exceed 7° C. After the addition was complete, cooling was removed, the reaction was allowed to stir at room temp. The mixture was stirred at r.t. for 14 h. TLC showed 4 was consumed completely. Then the solution was concentrated under reduced pressure to get crude 5 (23.0 g) as a white solid which was used directly for next step. ESI-LCMS: m/z 298 [M+H]+.

Preparation of (6): To a solution of 5 (23 g, 55.5 mmol) in DMF (220 mL) was added imidazole (11.6 g, 165.0 mmol) then added TBSCI (12.3 g, 82.3 mmol) at 0° C. The mixture was stirred at 20° C. for 14 h. TLC showed 1 was consumed completely. Water was added to the reaction. The product was extracted with EA, The organic layer was washed with NaHCO3 and brine. Then the solution was concentrated under reduced pressure. The residue was purified by silica gel column chromatography (eluent, DCM: MEOH=100:1-20:1). This resulted in to give 6 (21.3 g, 51.1 mmol, 90% over two step) as a white solid. ESI-LCMS: m/z 412 [M+H]+.

Preparation of (7): To the solution of 6 (21.0 g, 51.0 mmol) in dry THF/MeOD/D20=10/2/1 (260.5 mL) was added NaBD4 (6.4 g, 153.1 mmol) at r.t. and the reaction mixture was stirred at 50° C. for 2 h. After completion of reaction, the resulting mixture was added CH3COOD to pH=7, after addition of water, the resulting mixture was extracted with EA (300 mL). The combined organic layer was washed with water and brine, dried over Na2SO4. Then the solution was concentrated under reduced pressure and the residue was used for next step without further purification. ESI-LCMS: m/z 386 [M+H]+.

Preparation of (8): To a stirred solution of 7 (14.0 g, 35 mmol) in pyridine (50 mL) were added BzCl (17.2 g, 122.5 mmol) at 0° C. under N2 atmosphere. The mixture was stirred at r.t. for 14 h. TLC showed 7 was consumed completely. Then the solution diluted with EA. The organic layer was washed with NaHCO3 and brine. Then the solution was concentrated under reduced pressure and the residue was used for next step without further purification. To a solution of the crude in pyridine (300 mL) then added 2M NaOH (MeOH: H2O=4:1, 60 mL) at 0° C. The mixture was stirred at 0° C. for 10 min. Then the solution diluted with EA. The organic layer was washed with NH4Cl and brine. Then the solution was concentrated under reduced pressure and the residue was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=4/1 within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=3/2; Detector, UV 254 nm. This resulted in to give 8 (14 g, 28.02 mmol, 69.21% yield) as a white solid. ESI-LCMS: m/z 490 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.24 (s, 1H), 8.76 (s, 1H), 8.71 (m, 1H), 8.04 (d, J=7 Hz, 2H), 7.66-7.10 (m, 5H), 6.40-6.35 (dd, 1H), 5.71-5.56 (m, 1H), 5.16 (s, 1H), 4.79-4.72 (m, 1H), 4.01 (m, 1H), 0.91 (s, 9H), 0.14 (m, 6H).

Preparation of (9): To a solution of 8 (5.1 g, 10.4 mmol) in pyridine (50 mL) was added DMTrC1 (5.3 g, 15.6 mmol). The mixture was stirred at r.t. for 1 h. TLC showed 8 was consumed completely. Water was added to the reaction. The product was extracted with EA, The organic layer was washed with NaHCO3 and brine. Then the solution was concentrated under reduced pressure and the residue was used for next step without further purification. ESI-LCMS: m/z 792 [M+H]+.

Preparation of (10): To a solution of 9 (7.9 g, 10.0 mmol) in THF (80 mL) was added 1M TBAF in THF (12 mL). The mixture was stirred at r.t. for 1 h. TLC showed 9 was consumed completely. Water was added to the reaction. The product was extracted with EA, The organic layer was washed with NaHCO3 and brine. Then the solution was concentrated under reduced pressure the residue was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=4/1; Detector, UV 254 nm. This resulted in to give 10 as a white solid. ESI-LCMS: m/z 678 [M+H]; 1H-NMR (400 MHz, DMSO-d6): δ 11.25 (s, 1H), 8.74 (s, 1H), 8.62 (s, 1H), 8.04 (d, J=7 Hz, 2H), 7.66-7.53 (m, 3H), 7.33-7.15 (m, 9H), 6.82-6.78 (m, 4H), 6.43 (d, J=20 Hz, 1H), 5.76-5.60 (m, 1H), 4.88-4.80 (m, 1H), 4.13 (d, J=8 Hz, 1H), 3.71 (m, 6H).

Preparation of Example 37 monomer: To a solution of 10 (6.2 g, 9.1 mmol) in DCM (60 mL) was added DCI (1.1 g, 9.4 mmol) and CEP (3.3 g, 10.9 mmol) under N2 pro. The mixture was stirred at 20° C. for 0.5 h. TLC showed 10 was consumed completely. The product was extracted with DCM, The organic layer was washed with H2O and brine. Then the solution was concentrated under reduced pressure and the residue was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 37 monomer (7.5 g, 8.3 mmol, 90.7%) as a white solid. ESI-LCMS: m/z 878 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.25 (s, 1H), 8.68-8.65 (dd, 2H), 8.04 (m, 2H), 7.66-7.53 (m, 3H), 7.33-7.15 (m, 9H), 6.82-6.78 (m, 4H), 6.53-6.43 (m, 1H), 5.96-5.81 (m, 1H), 5.36-5.15 (m, 1H), 4.21 (m, 1H), 3.86-3.52 (m, 10H), 2.79-2.61 (m, 2H), 1.21-0.99 (m, 12H); 31P-NMR (162 MHz, DMSO-d6): δ 149.60, 149.56, 149.48.

Example 38. Synthesis of End Cap Monomer

Preparation of (2): To a solution of 1(20.0 g, 71.2 mmol) in dry pyridine (200.0 mL) was added TBSCl (26.8 g, 177.9 mmol) and imidazole (15.6 g, 227.8 mmol). The mixture was stirred at r.t. for 15 h. TLC showed 1 was consumed completely. The reaction mixture was concentrated to give residue. The residue was quenched with DCM (300.0 mL). The DCM layer was washed with H2O (100.0 mL*2) and brine. The DCM layer concentrated to give crude 2 (45.8 g) as a yellow oil. The crude used to next step directly. ESI-LCMS m/z 510.5 [M+H]+.

Preparation of (3): To a mixture solution of 2 (45.8 g) in THF (300.0 mL) was added mixture of H2O (100.0 mL) and TFA (100.0 mL) at 0° C. over 30 min. Then the reaction mixture was stirred at 0° C. for 4 h. TLC showed the 2 was consumed completely. The reaction mixture pH was adjusted to 7-8 with NH3.H2O (100 mL). Then the mixture was extracted with EA (500.0 mL*2). The combined EA layer was washed with brine and concentrated to give crude which was purified by c.c. (PE:EA=5:1-1:0) to give compound 3 (21.0 g, 53.2 mmol, 74.7% yield over 2 steps) as a white solid. ESI-LCMS m/z 396.2 [M+H]+.

Preparation of (4): To a solution of 3 (21.0 g, 53.2 mmol) in ACN (100.0 mL) and water (100.0 mL) were added (diacetoxyiodo)benzene (51.0 g, 159.5 mmol) and TEMPO (2.5 g, 15.9 mmol), The reaction mixture was stirred at 40° C. for 1 h. TLC showed the 3 was consumed completely. The reaction mixture was cooled down to r.t. and filtered, the filtrate was concentrated to give crude which was purified by crystallization (ACN) to give 4 (14.5 g, 35.4 mmol, 66.2% yield). ESI-LCMS m/z 410.1[M+H]+.

Preparation of (5): To a solution of 4 (14.5 g, 35.4 mmol) in toluene (90.0 mL) and MeOH (60.0 mL) was added trimethylsilyldiazomethane (62.5 mL, 2.0 M, 141.8 mmol) at 0° C., then stirred at r.t. for 2 h. TLC showed the 4 was consumed completely. The solvent was removed under reduce pressure, the residue was purified by crystallization (ACN) to give 5 (10.0 g, 23.6 mmol, 66.6% yield). ESI-LCMS m/z 424.2 [M+H]+

Preparation of (6): To the solution of 5 (10.0 g, 23.6 mmol) in dry THF/MeOD/D20=10/2/1 (100.0 mL) was added NaBD4 (2.98 g, 70.9 mmol) three times during an hour at 40° C., the reaction mixture was stirred at r.t. for 2.0 h. The resulting mixture was added CH3COOD change pH=7.5, after addition of water, the resulting mixture was extracted with EA (50.0 mL*3). The combined organic layer was washed with water and brine, dried over Na2SO4, concentrated to give a residue which was purified by c.c. (PE/EA=1:1-1:0). This resulted in to give 6 (6.1 g, 15.4 mmol, 65.3% yield) as a white solid. ESI-LCMS m/z 398.1 [M+H]+; 1H-NMR (400 MHz, DMSO-d6) δ 8.28 (s, 1H), 8.02 (s, 1H), 7.23 (s, 2H), 5.86 (d, J=6.4 Hz, 1H), 5.26 (s, 1H), 4.42-4.41 (m, 1H), 4.35-4.32 (m, 1H), 3.82 (d, J=2.6 Hz, 1H), 3.14 (s, 3H), 0.78 (s, 9H), 0.00 (d, J=0.9 Hz, 6H).

Preparation of (7): To a solution of 6 (6.1 g, 15.4 mmol) in pyridine (60.0 mL) was added the benzoyl chloride (6.5 g, 46.2 mmol) drop wise at 5° C. The reaction mixture was stirred at r.t. for 2 h. TLC showed the 6 was consumed completely. The reaction mixture was cooled down to 10° C. and quenched with H2O (20.0 mL), extracted with EA (200.0 mL*2), combined the EA layer. The organic phase was washed with brine and dried over Na2SO4, concentrated to give the crude (12.0 g) which was dissolved in pyridine (60.0 mL), cooled to 0° C., 20.0 mL NaOH (2 M in methanol: H2O=4: 1) was added and stirred for 10 min. The reaction was quenched by saturated solution of ammonium chloride, the aqueous layer was extracted with EA (200.0 mL*2), combined the EA layer, washed with brine and dried over Na2SO4, concentrated. The residue was purified by c.c. (PE/EA=10:1˜ 1:1) to give 7 (7.0 g, 13.9 mmol, 90.2% yield). ESI-LCMS m/z 502.2 [M+H]+; 1H-NMR (400 MHz, DMSO-d6) δ 11.24 (s, 1H, exchanged with D20) 8.77 (s, 2H), 8.04-8.06 (m, 2H), 7.64-7.66 (m, 2H), 7.54-7.58 (m, 2H), 6.14-6.16 (d, J=5.9 Hz, 1H), 5.20-5.23 (m, 1H), 4.58-4.60 (m, 1H), 4.52-4.55 (m, 1H), 3.99-4.01 (m, 1H), 3.34 (s, 4H), 0.93 (s, 9H), 0.14-0.15 (d, J=1.44 Hz, 6H).

Preparation of (8): To a stirred solution of 7 (5.5 g, 10.9 mmol) in DMSO (55.0 mL) was added EDCI (6.3 g, 32.9 mmol), pyridine (0.9 g, 10.9 mmol) and TFA(0.6 g,5.5 mmol), the reaction mixture was stirred at r.t. for 15 h. The reaction was quenched with water and extracted with EA (100.0 mL). The organic phase was washed by brine, dried over Na2SO4, The organic phase was evaporated to dryness under reduced pressure to give a residue 8 (4.8 g) which was used directly to next step. ESI-LCMS: m/z 517.1 [M+H2O]+.

Preparation of (9b): A solution of 9a (35.0 g, 150.8 mmol) and NaI (90.5 g, 603.4 mmol) in dry ACN (180.0 mL) was added chloromethyl pivalate (113.6 g, 754.3 mmol) at r.t., the reaction was stirred at 80° C. for 4 h. The reaction was cooled to r.t. and quenched by water, then the mixture was extracted with EA (500.0 mL *3), combined the organic layer was washed with saturated solution of ammonium chloride, followed by with brine and dried over Na2SO4. Then the organic layer was concentrated to give a residue which was purified by c.c., this resulted in to give 9b (38.0 g, 60.1 mmol, 39.8% yield) as a white solid. ESI-LCMS m/z 655.2 [M+Na]+; 1H-NMR (400 MHz, CDCl3): S 5.74-5.67 (m, 8H), 2.67 (t, J=21.6 Hz, 2H), 1.23 (s, 36H).

Preparation of (9): 3.8 g 10% Pd/C was washed with dry THF (30.0 mL) three times. Then transferred into a round-bottom flask charged with 9b (38.0 g, 60.1 mmol) and solvent (dry THF:D2O=5:1, 400.0 mL), the mixture was stirred at 80° C. under 1 L H2 balloon for 15 h. The reaction was cooled to r.t. and extracted with EA (500.0 mL *3), combined the organic layer was washed with brine and dried over Na2SO4. The residue 9 (3.0 g, 3.7 mmol, 38.8% yield) as a white solid was used directly to next step without further purification. ESI-LCMS m/z 657.2 [M+Na]+; 1H-NMR (400 MHz, CDCl3): δ 5.74-5.67 (m, 8H), 1.23 (s, 36H).

Preparation of (10): A solution of 8 (4.8 g, 9.6 mmol), 9 (7.3 g, 11.5 mmol) and K2CO3(4.0 g, 38.8 mmol) in dry THF (60.0 mL) and D20 (20.0 mL) was stirred at r.t. 18 h. LC-MS showed 8 was consumed completely. The product was extracted with EA (300.0 mL) and the organic layer was washed with brine and dried over Na2SO4. Then the organic layer was concentrated to give a residue which was purified by c.c. (PE/EA=5:1-1:1) and MPLC. This resulted in to give 10 (3.0 g, 3.7 mmol, 38.8% yield) as a white solid. ESI-LCMS m/z 806.4[M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.25 (s, 1H, exchanged with D20) 8.75 (s, 2H), 8.07-8.05 (d, J=8.0 Hz, 2H), 7.67-7.54 (m, 3H), 6.05 (d, J=5.1 Hz, 1H), 5.65-5.58 (m, 4H), 4.80-4.70 (m, 2H), 4.59-4.57 (m, 1H), 3.36 (s, 3H), 1.11 (s, 9H), 1.10 (s, 9H), 0.94 (s, 9H), 0.17-0.16 (m, 6H); 31P NMR (162 MHz, DMSO-d6) δ 17.02.

Preparation of (11): To a round-bottom flask was added 10 (3.0 g, 3.7 mmol) in a mixture of H2O (30.0 mL), HCOOH (30.0 mL). The reaction mixture was stirred at 40° C. for 15 hrs. LC-MS showed the 10 was consumed completely. The reaction mixture was adjusted the pH=6-7 with con. NH3.H2O (100.0 mL). Then the mixture was extracted with DCM (100.0 mL*3). The combined DCM layer was dried over Na2SO4. Filtered and filtrate was concentrated to give crude which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/2 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=3/2; Detector, UV 254 nm. To give product 11 (1.8 g, 2.6 mmol, 70.3% yield). ESI-LCMS m/z=692.2[M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.11 (s, 1H, exchanged with D20) 8.71-8.75 (d, J=14.4, 2H), 8.04-8.06 (m, 2H), 7.64-7.65 (m, 1H), 7.54-7.58 (m, 2H), 6.20-6.22 (d, J=5.4, 2H), 5.74-5.75 (d, J=5.72, 2H), 5.56-5.64 (m, 4H), 4.64-4.67 (m, 1H), 4.58-4.59 (m, 1H), 4.49-4.52 (m, 1H), 3.37 (s, 3H), 1.09-1.10 (d, J=1.96, 18H); 31P NMR (162 MHz, DMSO-d6) δ 17.46.

Preparation of Example 38 monomer: To a solution of 11 (1.8 g, 2.6 mmol) in DCM (18.0 mL) was added the DCI (276.0 mg, 2.3 mmol), then CEP[N(ipr)2]2 (939.5 mg, 3.1 mmol) was added. The mixture was stirred at r.t. for 1 h. TLC showed 11 consumed completely. The reaction mixture was washed with H2O (50.0 mL*2) and brine (50.0 mL*2), dried over Na2SO4 and concentrated to give crude which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=9/1; Detector, UV 254 nm. The product was concentrated to give Example 38 monomer (2.0 g, 2.2 mmol, 86.2% yield) as a white solid. ESI-LCMS m/z 892.3[M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.27 (s, 1H, exchanged with D20) 8.72-8.75 (m, 2H), 8.04-8.06 (m, 2H), 7.54-7.68 (m, 3H), 6.20-6.26 (m, 1H), 5.57-5.64 (m, 4H), 4.70-4.87 (m, 3H), 3.66-3.88 (m, 4H), 3.37-3.41 (m, 3H), 2.82-2.86 (m, 2H), 1.20-1.21 (m, 12H), 1.08-1.09 (m, 18H); 31P-NMR (162 MHz, DMSO-d6): δ 150.03, 149.19, 17.05, 16.81.

Example 39. Synthesis of 5′ End Cap Monomer

Preparation of (6): To a stirred solution of 5 (8.08 g, 21.3 mmol, Scheme 3) in DMSO (80.0 mL) were added EDCI(12.2 g, 63.9 mmol), pyridine(1.7 g,21.3 mmol),TFA(1.2 g,10.6 mmol) at r.t. And the reaction mixture was stirred at r.t. for 1.5 h. The reaction was quenched with water and extracted with EA (200.0 mL). The organic phase was washed by brine, dried over Na2SO4, The organic phase was evaporated to dryness under reduced pressure to give a residue 6 which was used directly to next step. ESI-LCMS: m/z 372.3 [M+H]+.

Preparation of (8): To a solution of K2CO3 (5.5 g, 8.3 mmol) in dry THF (60.0 mL) and D20 (20.0 mL) was added a solution of 6 (8.0 g, 21.5 mmol) in dry THF(10.0 mL). The reaction mixture was stirred at r.t. overnight. LC-MS showed 6 was consumed completely. The product was extracted with EA (300.0 mL) and the organic layer was washed with brine and dried over Na2SO4. Then the organic layer was concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 8 (5.0 g, 7.3 mmol, 40.0%) as a white solid. ESI-LCMS: m/z 679.3 [M+H]+; 1H-NMR (400 MHz, Chloroform-d): δ 9.91 (s, 1H), 7.29 (d, J=8.1 Hz, 1H), 5.82 (d, J=2.7 Hz, 1H), 5.72 (d, J=8.1 Hz, 1H), 5.65-5.54 (m, 4H), 4.43 (dd, J=7.2, 3.2 Hz, 1H), 3.92 (dd, J=7.2, 5.0 Hz, 1H), 3.65 (dd, J=5.1, 2.7 Hz, 1H), 3.44 (s, 3H), 1.13 (s, 18H), 0.82 (s, 9H), 0.01 (d, J=4.8 Hz, 6H); 31P NMR (162 MHz, Chloroform-d): δ 16.40.

Preparation of (9): To a solution of HCOOH (50.0 mL) and H2O (50.0 mL) was added 8 (5.0 g,7.3 mmol). The reaction mixture was stirred at 40° C. overnight. LC-MS showed 8 was consumed completely. A solution of NaHCO3(500.0 mL) was added. The product was extracted with EA (300.0 mL) and the organic layer was washed with brine and dried over Na2SO4. Then the organic layer was concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=3/2 within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 9 (3.0 g, 5.4 mmol, 73.2%) as a white solid. ESI-LCMS: m/z 565.2 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.43 (s, 1H), 7.64 (d, J=8.1 Hz, 1H), 5.83 (d, J=4.3 Hz, 1H), 5.69-5.56 (m, 5H), 5.54 (d, J=6.7 Hz, 1H), 4.37 (dd, J=6.1, 2.9 Hz, 1H), 4.12 (q, J=6.1 Hz, 1H), 3.96 (dd, J=5.4, 4.3 Hz, 1H), 3.39 (s, 3H), 1.16 (s, 18H); 31P NMR (162 MHz, DMSO-d6): δ 17.16.

Preparation of Example 39 monomer: To a suspension of 9 (2.6 g, 4.6 mmol) in DCM (40.0 mL) was added DCI (0.5 g, 5.6 mmol) and CEP[N(iPr)2]2 (1.7 g, 5.6 mmol). The mixture was stirred at r.t. for 1.0 h. LC-MS showed 9 was consumed completely. The solution was washed with water twice and washed with brine and dried over Na2SO4. Then concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 39 monomer (3.0 g, 3.9 mmol, 85.2%) as a white solid. . ESI-LCMS: m/z 765.3 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.44 (s, 1H), 7.71 (dd, J=8.1, 3.8 Hz, 1H), 5.81 (dd, J=4.4, 2.5 Hz, 1H), 5.74-5.53 (m, 5H), 4.59-4.33 (m, 2H), 4.20-4.14 (m, 1H), 3.88-3.53 (m, 4H), 3.39 (d, J=16.2 Hz, 3H), 2.80 (td, J=5.9, 2.9 Hz,2 H), 1.16 (d, J=1.9 Hz, 30H); 31P-NMR (162 MHz, DMSO-d6): δ 147.68, 149.16, 16.84, 16.55.

Example 40. Synthesis of Monomer

Preparation of (2): To a solution of 1(26.7 g*2, 0.1 mol) in DMF (400 mL) was added sodium hydride (4.8 g, 0.1 mol) for 30 min, then was added CD3I (16 g, 0.1 mol) at 0° C. for 2.5 hr (ref. for selective 2′-O-alkylation reaction conditions, J. Org. Chem. 1991, 56, 5846-5859). The mixture was stirring at r.t. for another 1 h. LCMS showed the reaction was consumed. The mixture was filtered and the clear solution was evaporated to dryness and was evaporated with CH30H. The crude was purified by silica gel column (SiO2, DCM/MeOH=50:1-15:1). This resulted in to give the product 2 (35.5 g, 124.6 mmol, 62% yield) as a solid. ESI-LCMS: m/z 285 [M+H]+.

Preparation of (3): To a solution of 2 (35.5 g, 124.6 mmol) in pyridine (360 mL) was added imidazole (29.7 g, 436.1 mmol) and TBSCI (46.9 g, 311.5 mmol). The mixture was stirred at r.t. over night. LCMS showed 2 was consumed completely. The reaction was quenched with water (500 mL). The product was extracted into ethyl acetate (1 L). The organic layer was washed with brine and dried over anhydrous Na2SO4. The crude was purified by silica gel column (SiO2, PE/EA=4:1-1:1). This resulted in to give the product 3 (20.3 g, 39.6 mmol, 31.8% yield) as a solid. ESI-LCMS: m/z 513 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 8.32 (m, 1H), 8.13 (m, 1H), 7.31 (m, 2H), 6.02-6.01 (d, J=4.0 Hz, 1H), 4.60-4.58 (m, 1H), 4.49-4.47 (m, 1H), 3.96-3.86 (m, 2H), 3.72-3.68 (m, 1H), 0.91-0.85 (m, 18H), 0.13-0.01 (m, 12H).

Preparation of (4): To a solution of 3 (20.3 g, 39.6 mmol) in THF (80 mL) was added TFA (20 mL) and water (20 mL) at 0° C. The reaction mixture was stirred at 0° C. for 5 h. LC-MS showed 3 was consumed completely. Con. NH4OH was added to the mixture at 0° C. to quench the reaction until the pH=7.5. The product was extracted into ethyl acetate (200 mL). The organic layer was washed with brine and dried over anhydrous Na2SO4. The solution was then concentrated under reduced pressure and the residue was washed by PE/EA=5:1. This resulted in to give 4 (10.5 g, 26.4 mmol, 66.6% yield) as a white solid. ESI-LCMS: m/z 399 [M+H]−; 1H-NMR (400 MHz, DMSO-d6): δ 8.41 (m, 1H), 8.14 (m, 1H), 7.37 (m, 2H), 5.99-5.97 (d, J=8.0 Hz, 1H), 5.43 (m, 1H), 4.54-4.44 (m, 2H), 3.97-3.94 (m, 1H), 3.70-3.53 (m, 2H), 0.91 (m, 9H), 0.13-0.12 (m, 6H).

Preparation of (5): To a solution of 4 (10.5 g, 26.4 mmol) in ACN/H2O=1:1 (100 mL) was added DAIB (25.4 g, 79.2 mmol) and TEMPO (1.7 g, 7.9 mmol). The reaction mixture was stirred at 40° C. for 2 h. LCMS showed 4 was consumed. The mixture was diluted with EA and water was added. The product was extracted with EA. The organic layer was washed with brine and dried over anhydrous Na2SO4. The solution was then concentrated under reduced pressure and the residue was washed by ACN. This resulted in to give 5 (6.3 g, 15.3 mmol, 57.9% yield) as a white solid. ESI-LCMS: m/z 413 [M+H]−; 1H-NMR (400 MHz, DMSO-d6): δ=8.48 (m, 1H), 8.16 (m, 1H), 7.41 (m, 2H), 6.12-6.10 (d, J=8.0 Hz, 1H), 4.75-4.73 (m, 1H), 4.42-4.36 (m, 2H), 3.17 (m, 6H), 2.07 (m, 2H), 0.93 (m, 9H), 0.17-0.15 (m, 6H).

Preparation of (6): To a solution of 5 (6.3 g, 15.3 mmol) in toluene (36 mL) and methanol (24 mL) was added (trimethylsilyl)diazomethane (7.0 g, 61.2 mmol) till the yellow color not disappear at r.t. for 2 min. LCMS showed the reaction was consumed. The solvent was removed to give the cured 6 (6.0 g) as a solid witch used for the next step. ESI-LCMS: m/z 427 [M+H]+;1H-NMR (400 MHz, DMSO-d6): δ 8.45 (m, 1H), 8.15 (m, 1H), 7.35 (m, 2H), 6.12-6.10 (d, J=8.0 Hz, 1H), 4.83-4.81 (m, 1H), 4.50-4.46 (m, 1H), 3.73 (m, 3H), 3.31 (m, 1H), 0.93 (m, 9H), 0.15-0.14 (m, 6H).

Preparation of (7): To the solution of 6 (6 g) in dry THF/MeOD/D20=10/2/1 (78 mL) was added NaBD4 (2.3 g, 54.8 mmol) at r.t. And the reaction mixture was stirred at r.t for 2.5 hr. After completion of reaction, adjusted pH value to 7 with CH3COOD, after addition of water, the resulting mixture was extracted with EA (100 mL). The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated to give 7 (5.7 g) which was used for the next step. ESI-LCMS: m/z 401 [M+H]+.

Preparation of (8): To a solution of 7 (5.7 g) in pyridine (60 mL) was added BzCl (10.0 g, 71.3 mmol) under ice bath. The reaction mixture was stirred at r.t. for 2.5 hrs. LCMS showed 7 was consumed. The mixture was diluted with EA and water was added. The product was extracted with EA. The crude was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=7/3; Detector, UV 254 nm. This resulted in to give the crude 8 (6.2 g, 8.7 mmol, 57% yield, over two steps) as a white solid. ESI-LCMS: m/z 713 [M+H]+.

Preparation of (9): To a solution of 8 (6.2 g, 8.7 mmol) in pyridine (70 mL) and was added 1M NaOH (MeOH/H2O=4/1) (24 mL). LCMS showed 8 was consumed. The mixture was added saturated NH4Cl till pH=7.5. The mixture was diluted with water and EA. The organic layer was washed with brine and dried over Na2SO4 and concentrated to give the crude. The crude was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=67/33 Detector, UV 254 nm. This resulted in to give the product 10 (4.3 g, 8.5 mmol, 98% yield) as a white solid. ESI-LCMS: m/z 505 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.23 (m, 1H), 8.77 (m, 2H), 8.06-8.04 (m, 2H), 7.66-7.63 (m, 2H), 7.57-7.53 (m, 3H), 6.16-6.14 (d, J=8.0 Hz, 1H), 5.17 (m, 1H), 4.60-4.52 (m, 2H), 3.34 (m, 1H), 0.93 (m, 9H), 0.14 (m, 6H).

Preparation of (10): To a stirred solution of 9 (4.3 g, 8.5 mmol) in pyridine (45 mL) were added DMTrCl (3.3 g, 9.8 mmol) at r.t. And the reaction mixture was stirred at r.t for 2.5 hr. With ice-bath cooling, the reaction was quenched with water and the product was extracted into EA. The organic layer was washed with brine and dried over Na2SO4 and concentrated to give the crude. The crude was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=97/3 Detector, UV 254 nm. This resulted in to give the product 10 (6.5 g, 8.1 mmol, 95% yield) as a white solid. ESI-LCMS: m/z 807 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 11.23 (m, 1H), 8.70-8.68 (m, 2H), 8.04-8.02 (m, 2H), 7.66-7.62 (m, 1H), 7.56-7.52 (m, 2H), 7.35-7.26 (m, 2H), 7.25-7.17 (m, 7H), 6.85-6.82 (m, 4H), 6.18-6.16 (d, J=8.0 Hz, 1H), 4.73-4.70 (m, 1H), 4.61-4.58 (m, 1H), 3.71 (m, 6H), 3.32 (m, 1H), 0.83 (m, 9H), 0.09-0.03 (m, 6H).

Preparation of (11): To a solution of 10 (3.5 g, 4.3 mmol) in THF (35 mL) was added 1 M TBAF solution (5 mL). The reaction mixture was stirred at r.t. for 1.5 h. LCMS showed 10 was consumed completely. Water (100 mL) was added. The product was extracted with EA (100 mL) and the organic layer was washed with brine and dried over Na2SO4. Then the organic layer was concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=62/38; Detector, UV 254 nm. This resulted in to give 11 (2.7 g, 3.9 mmol, 90.7%) as a white solid. ESI-LCMS: m/z 693 [M+H]+.

Preparation of Example 40 monomer: To a suspension of 11(2.7 g, 3.9 mmol) in DCM (30 mL) was added DCI (0.39 g, 3.3 mmol) and CEP[N(iPr)2]2 (1.4 g, 4.7 mmol). The mixture was stirred at r.t. for 2 h. LC-MS showed 11 was consumed completely. The solution was washed with water twice and washed with brine and dried over Na2SO4. Then concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=73/27; Detector, UV 254 nm. This resulted in to give Example 40 monomer (3.3 g, 3.7 mmol, 94.9%) as a white solid. ESI-LCMS: m/z 893 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ=11.24 (m, 1H), 8.66-8.64 (m, 2H), 8.06-8.03 (m, 2H), 7.65-7.53 (m, 3H), 7.42-7.38 (m, 2H), 7.37-7.34 (m, 2H), 7.25-7.19 (m, 7H), 6.86-6.80 (m, 4H), 6.20-6.19 (d, J=4.0 Hz, 1H), 4.78 (m, 2H), 4.22-4.21 (m, 1H), 3.92-3.83 (m, 1H), 3.72 (m, 6H), 3.62-3.57 (m, 3H), 2.81-2.78 (m, 1H), 2.64-2.61 (m, 1H), 1.17-1.04 (m, 12H); 31P-NMR (162 MHz, DMSO-d6): δ 149.51, 149.30.

Example 41. Synthesis of Monomer

Preparation of (3): To the solution of 1 (70 g, 138.9 mmol) in dry acetonitrile (700 mL) was added 2 (27.0 g, 166.7 mmol), BSA (112.8 g, 555.5 mmol). The mixture was stirred at 50° C. for 1 h. Then the mixture was cooled to −5° C. and TMSOTf (46.2 g, 208.3 mmol) slowly added to the mixture. Then the reaction mixture was stirred at r.t for 48 h. Then the solution was cooled to 0° C. and saturated aq. NaHCO3 was added and the resulting mixture was extracted with EA. The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated under reduced pressure to give a residue which was purified by silica gel column chromatography (eluent, PE: EA=3:1-1:1) to give 3 (70 g, 115.3 mmol, 81.6%) as a white solid. ESI-LCMS: m/z 605 [M−H]+.

Preparation of (4): To the solution of 3 (70.0 g, 115.3 mmol) in methylammonium solution (1 M, 700 mL), and the reaction mixture was stirred at 40° C. for 15 h. After completion of reaction, the resulting mixture was concentrated. The residue was crystallized from EA. Solid was isolated by filtration, washed with PE and dried overnight at 45° C. in vacuum to give 4 (31.0 g, 105.4 mmol, 91.1%) as a white solid. ESI-LCMS: m/z 295 [M+H]+; 1H-NMR (400 MHz, DMSO): δ 11.63 (s, 1H), 8.07-7.99 (m, 1H),7.81 (d, J=8.4 Hz, 1H), 7.72-7.63 (m, 1H), 7.34-7.26 (m, 1H), 6.18 (d, J=6.4 Hz, 1H), 5.24 (s, 1H), 5.00 (s, 2H), 4.58-4.47 (m, 1H), 4.19-4.10 (m, 1H), 3.85-3.77 (m, 1H), 3.75-3.66 (m, 1H), 3.66-3.57 (m, 1H).

Preparation of (5): To the solution of 4 (20.0 g, 68.0 mmol) in dry DMF (200 mL) was added DPC (18.9 g, 88.0 mmol) and NaHCO3(343 mg, 4 mmol) at r.t, and the reaction mixture was stirred at 150° C. for 35 min. After completion of reaction, the resulting mixture was poured into tert-Butyl methyl ether (4 L). Solid was isolated by filtration, washed with PE and dried in vacuum to give crude 5 (21.0 g) as a brown solid which was used directly for next step (ref for 5, Journal of Organic Chemistry, 1989, vol. 33, p. 1219-1225). ESI-LCMS: m/z 275 [M−H]−.

Preparation of (6): To the solution of 5 (crude, 21.0 g) in Pyridine (200 mL) was added AgNO3 (31.0 g, 180.0 mmol) and collidine (88.0 g, 720 mmol) and TrtCl (41.5 g, 181 mmol) at r.t, and the reaction mixture was stirred at r.t for 15 h. After addition of water, the resulting mixture was extracted with EA. The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated to give the crude. The crude was by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 6 (10.0 g, 13.1 mmol, 20% yield over 3 steps) as a white solid. ESI-LCMS: m/z 761 [M+H]+.

Preparation of (7): To the solution of 6 (10.0 g, 13.1 mmol) in THF (100 mL) was added 6 N NaOH (30 mL) at r.t, and the reaction mixture was stirred at r.t for 1 hr. After addition of NH4Cl, the resulting mixture was extracted with EA. The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated under reduced pressure and the residue was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=9/1; Detector, UV 254 nm. This resulted in to give 7 (9.3 g, 11.9 mmol, 90%) as a white solid. ESI-LCMS: m/z 777 [M−H]−;1H-NMR (400 MHz, DMSO-d6): δ 11.57 (s, 1H), 8.02 (d, J=8.7 Hz, 1H), 7.88-7.81 (m, 1H), 7.39-7.18 (m, 30H), 7.09-6.99 (m, 30H), 6.92-6.84 (m, 30H), 6.44 (d, J=4.0 Hz, 1H), 4.87 (d, J=4.0 Hz, 1H), 4.37-4.29 (m, 1H), 4.00-3.96 (m, 1H), 3.76-3.70 (m, 1H), 3.22-3.13 (m, 1H), 3.13-3.04 (m, 1H).

Preparation of (8): To the solution of 7 (8.3 g, 10.7 mmol) in dry DCM (80 mL) was added Pyridine (5.0 g, 64.2 mmol) and DAST (6.9 g, 42.8 mmol) at 0° C., and the reaction mixture was stirred at r.t for 15 hr. After addition of NH4Cl, the resulting mixture was extracted with DCM. The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated under reduced pressure and the residue was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 8 (6.8 g, 8.7 mmol, 81.2%) as a white solid. ESI-LCMS: m/z 779 [M−H]+; 19F-NMR (376 MHz, DMSO-d6): δ −183.05.

Preparation of (9): To the solution of 8 (5.8 g, 7.5 mmol) in dry ACN (60 mL) was added TEA (1.5 g, 15.1 mmol), DMAP (1.84 g, 15.1 mmol) and TPSCI (4.1 g, 13.6 mmol) at r.t, and the reaction mixture was stirred at room temperature for 3 h under N2 atmosphere. After completion of reaction, the mixture was added NH3.H2O (12 mL). After addition of water, the resulting mixture was extracted with EA. The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated under reduced pressure and the residue was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 9 (5.5 g, 7 mmol, 90.2%) as a white solid. ESI-LCMS: m/z 780 [M+H]+.

Preparation of (10): To a solution of 9 (5.5 g, 7 mmol) in DCM (50 mL) with an inert atmosphere of nitrogen was added pyridine (5.6 g, 70.0 mmol) and BzCl (1.2 g, 8.5 mmol) in order at 0° C. The reaction solution was stirred for 30 minutes at room temperature. The solution was diluted with DCM (100 mL) and the combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated under reduced pressure to give a residue which was purified by silica gel column chromatography (eluent, PE: EA=5:1-2:1) to give 10 (5.4 g, 6.1 mmol, 90.6%) as a white solid. ESI-LCMS: m/z 884 [M+H]+; 19F-NMR (376 MHz, DMSO-d6): δ −183.64.

Preparation of (11): To the solution of 10 (5.4 g, 6.1 mmol) in the solution of DCA (6%) in DCM (60 mL) was added TES (15 mL) at r.t, and the reaction mixture was stirred at room temperature for 5-10 min. After completion of reaction, the resulting mixture was added NaHCO3, the resulting mixture was extracted with DCM. The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated under reduced pressure and the residue was crystallized from EA. Solid was isolated by filtration, washed with PE and dried overnight at 450 in vacuum to give 11(2.0 g, 5.0 mmol, 83.2%) as a white solid. ESI-LCMS: m/z 400 [M+H]+.

Preparation of (12): To a solution of 11 (2.0 g, 5.0 mmol) in dry Pyridine (20 mL) was added DMTrCl (2.0 g, 6.0 mmol). The reaction mixture was stirred at r.t. for 2.5 h. LCMS showed 11 was consumed and water (200 mL) was added. The product was extracted with EA (200 mL) and the organic layer was washed with brine and dried over Na2SO4 and concentrated to give the crude. The crude was purified by c.c. (PE: EA=4:1-1:1) to give crude 12. The crude was further purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give 12 (2.1 g, 3 mmol, 60%) as a white solid. ESI-LCMS: m/z 702 [M+H]+:H-NMR (400 MHz, DMSO-d6): δ 12.63 (s, 1H), 8.54 (d, J=7.8 Hz, 1H), 8.25 (d, J=7.2 Hz, 2H), 7.82 (d, J=3.6 Hz, 2H), 7.67-7.58 (m, 1H), 7.57-7.49 (m, 2H), 7.49-7.39 (m, 1H), 7.39-7.31 (m, 2H), 7.27-7.09 (m, 7H), 6.82-6.69 (m, 4H), 6.23 (d, J=26.1 Hz, 1H), 5.59-5.49 (m, 1H), 4.83-4.61 (m, 1H), 4.15-4.01 (m, 1H), 3.74-3.59 (m, 6H), 3.33-3.28 (m, 1H), 3.16-3.05 (m, 1H). 19F-NMR (376 MHz, DMSO-d6): δ −191.66.

Preparation of Example 41 monomer: To a suspension of 12 (2.1 g, 3.0 mmol) in DCM (20 mL) was added DCI (310 mg, 2.6 mmol) and CEP[N(iPr)2]2 (1.1 g, 3.7 mmol). The mixture was stirred at r.t. for 1 h. LC-MS showed 12 was consumed completely. The solution was washed with water twice and washed with brine and dried over Na2SO4. Then concentrated to give the crude. The crude was by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 41 monomer (2.1 g, 2.3 mmol, 80.0%) as a white solid. ESI-LCMS: m/z 902 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 12.64 (s, 1H), 8.54 (d, J=7.6 Hz, 1H), 8.24 (d, J=7.7 Hz, 2H), 7.93-7.88 (m, 2H), 7.67-7.58 (m, 1H), 7.56-7.42 (m, 3H), 7.41-7.29 (m, 2H), 7.27-7.08 (m, 7H), 6.82-6.64 (m, 4H), 6.37-6.18 (m, 1H), 6.03-5.72 (m, 1H), 5.26-4.83 (m, 1H), 4.28-4.12 (m, 1H), 3.88-3.72 (m, 1H), 3.71-3.37 (m, 9H), 3.15-3.00 (m, 1H), 2.83-2.75 (m, 1H), 2.66-2.57 (m, 1H), 1.21-0.88 (m, 12H). 19F-NMR (376 MHz, DMSO-d6): δ −189.71. 31P-NMR (162 MHz, DMSO-d6): δ 149.48, 149.50, 148.95, 148.88.

Example 42. Synthesis of Monomer

Preparation of (3): To a solution of 1(40.0 g, 79.3 mmol), 1a (7.6 g, 80.1 mmol) in ACN (100 mL). Then added BSA (35.2 g, 174.4 mmol) under N2 atmosphere. The mixture was stirred at 50° C. for 1 h until the solution was clear. Then cool down to 0° C. and dropped TMSOTf (18.5 g, 83.2 mmol).The mixture was stirred at 75° C. for 1 h, TLC showed 1 was consumed completely. Then the solution was diluted with EA, washed with H2O twice. The solvent was concentrated under reduced pressure and the residue was used for next step. ESI-LCMS: m/z 540 [M+H]+.

Preparation of (3): To a solution of 2 (37.1 g, 68.7 mmol) in 30%CH2NH2/MeOH solution (200 mL). The mixture was stirred at 25° C. for 2 h. TLC showed 2 was consumed completely. The solvent was concentrated under reduced pressure and the residue was washed with EA twice to give 3 (12.5 g, 55.2 mmol) ( ref. for intermediate 3 Bioorganic & Medicinal Chemistry Letters, 1996, Vol. 6, No. 4, pp. 373-378,) which was used directly for the next step. ESI-LCMS: m/z 228 [M+H]+.

Preparation of (4): To a solution of 3 (12.5 g, 55.2 mmol) in pyridine (125 mL) and added DMAP (1.3 g, 11.0 mmol), TrtCl (30.7 g, 110.5 mmol). The mixture was stirred at r.t. for 24 h. TLC showed 3 was consumed completely. H2O was added to the mixture. Then filtered and the solution diluted with EA. The organic layer was washed with NaHCO3 and brine. The solvent was concentrated under reduced pressure and then added ACN, filtered to give 4a (17.0 g, 35.4 mmol, 64% yield) as a white solid.

To a solution of 4a (17.0 g, 35.4 mmol) in DMF (200 mL), collidine (5.2 g, 43.5 mmol), TrCl (13.1 g, 47.1 mmol) were added after 2 h and then again after 3 h TrCl (13.1 g, 47.1 mmol), AgNO3 (8.0 g, 47.1 mmol). The mixture was stirred at 25° C. for 24 h. TLC showed 4a was consumed completely. Then filtered and the solution diluted with EA. The organic layer was washed with NaHCO3 and brine. The solvent was concentrated under reduced pressure and then added ACN, filtered to get 4 (14.2 g, 19.5 mmol, 54% yield) as a white solid. ESI-LCMS: m/z 712 [M+H]+;H-NMR (400 MHz, DMSO-d6): δ 7.83 (d, J=8 Hz, 2H), 7.42-7.20 (m, 30H), 6.18 (d, J=7 Hz, 1H), 6.09 (d, J=8 Hz, 2H), 5.60 (d, J=7 Hz, 1H), 4.22 (m, 1H), 3.90 (d, J=5 Hz, 1H), 2.85 (d, J=10 Hz, 1H), 2.76 (s, 1H), 2.55-2.50 (dd, 1H).

Preparation of (5): To a solution of 4 (14.2 g, 19.9 mmol) in DCM (150 mL), DMAP (2.4 g, 19.9 mmol), TEA (4.0 g, 39.9 mmol, 5.6 mL) were added. Then cool down to 0° C., TfCl (6.7 g, 39.9 mmol) dissolved in DCM (150 mL) were dropped. The mixture was stirred at 25° C. for 1 h. TLC showed 4 was consumed completely. Then filtered and the solution diluted with EA. The organic layer was washed with NaHCO3 and brine. The solvent was concentrated under reduced pressure to get 5 (16.8 g, 19.9 mmol) as a brown solid. ESI-LCMS: m/z 844 [M+H]+.

Preparation of (6): To a solution of 5 (16.8 g, 19.9 mmol) in DMF (200 mL), KOAc (9.7 g, 99.6 mmol) were added, The mixture was stirred at 25° C. for 14 h and 50° C. for 3 h, TLC showed 5 was consumed completely. Then filtered and the solution diluted with EA. The organic layer was washed with H2O and brine. The solvent was concentrated under reduced pressure to get 6a (15.0 g, 18.9 mmol, 90% yield) as a brown solid. To a solution of 6a (15.0 g, 19.9 mmol) in 30% CH3NH2/MeOH solution (100 mL) were added. The mixture was stirred at 25° C. for 2 h, TLC showed 6a was consumed completely. Then the solvent was concentrated under reduced pressure and the residue was purified by cc (0-5% MeOH in DCM) to give 6 (11.6 g, 16.3 mmol, 82% yield) as a yellow solid. ESI-LCMS: m/z 712 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 7.59 (d, J=8 Hz, 2H), 7.37-7.22 (m, 30H), 6.01 (d, J=8 Hz, 2H), 5.84 (d, J=3 Hz, 1H), 5.42 (d, J=4 Hz, 1H), 3.78-3.70 (m, 3H), 3.10 (t, J=9 Hz, 1H), 2.53 (d, J=4 Hz, 6H), 1.77 (s, 6H).

Preparation of (7): To a solution of 6 (11.6 g, 16.32 mmol) in DCM (200 mL), DAST (7.9 g, 48.9 mmol)were added at 0° C., The mixture was stirred at 25° C. for 16 h, TLC showed 6 was consumed completely. Then the solution was diluted with EA, washed with NaHCO3 twice, The solvent was concentrated under reduced pressure the residue purified by Flash-Prep-HPLC with the following conditions(IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=4/1; Detector, UV 254 nm. This resulted in to give 7 (11.6 g, 13.8 mmol, 84% yield) as a white solid. ESI-LCMS: m/z 714 [M+H]+.

Preparation of (8): To a solution of 7 (11.6 g, 16.2 mmol) in DCM (100 mL) was added TFA (10 mL). The mixture was stirred at 20° C. for 1 h. TLC showed 7 was consumed completely. Then the solution was concentrated under reduced pressure the residue was purified by silica gel column (0˜20% MeOH in DCM) and Flash-Prep-HPLC with the following conditions(IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=0/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=1/3 within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=0/1; Detector, UV 254 nm. This resulted in to give 9 (1.7 g, 7.2 mmol, 45% yield) as a white solid. ESI-LCMS: m/z 229.9 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 7.91 (d, J=8 Hz, 2H), 6.14 (d, J=8 Hz, 2H), 5.81-5.76 (m, 2H), 5.28 (t, J=5 Hz, 1H), 5.13-4.97 (t, J=4 Hz, 1H), 4.23 (m, 1H), 3.97 (m, 1H), 3.74-3.58 (m, 2H); 19F-NMR (376 MHz, DMSO-d6): δ −206.09.

Preparation of (9): To a solution of 8 (1.4 g, 6.1 mmol) in pyridine (14 mL) was added DMTrC1 (2.5 g, 7.3 mmol) at 20° C. The mixture was stirred at 20° C. for 1 h. TLC showed 8 was consumed completely. Water was added to the reaction. The product was extracted with EA, The organic layer was washed with NaHCO3 and brine. Then the solution was concentrated under reduced pressure and the residue was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=4/1 within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 9 (2.5 g, 4.6 mmol, 76 yield) as a white solid. ESI-LCMS: m/z 532.2 [M+H]:H-NMR (400 MHz, DMSO-d6): δ 7.87-7.84 (m, 2H), 7.40-7.22 (m, 9H), 6.91-6.87 (m, 4H), 5.98-5.95 (m, 2H), 5.88-5.77 (m, 2H), 5.16-5.02 (m, 1H), 4.42 (m, 1H), 4.05 (m, 1H), 3.74 (s, 6H), 3.35 (m, 2H); 19F-NMR (376 MHz, DMSO-d6): δ −202.32.

Preparation of Example 42 monomer: To a solution of 9 (2.2 g, 4.1 mmol) in DCM (20 mL) was added DCI (415 mg, 3.5 mmol) and CEP (1.5 g, 4.9 mmol) under N2 pro. The mixture was stirred at 20° C. for 0.5 h. TLC showed 9 was consumed completely. The product was extracted with DCM, The organic layer was washed with H2O and brine. Then the solution was concentrated under reduced pressure and the residue was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 42 monomer (2.6 g, 3.5 mmol, 85% yield) as a white solid. ESI-LCMS: m/z 732.2 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 7.87-7.84 (m, 2H), 7.40-7.22 (m, 9H), 6.91-6.87 (m, 4H), 5.98-5.95 (m, 2H), 5.90-5.88 (m, 1H), 5.30-5.17 (m, 1H), 4.62 (m, 1H), 4.19 (m, 1H), 3.78-3.73 (m, 7H), 3.62-3.35 (m, 5H), 2.78 (t, J=5 Hz, 1H), 2.63 (t, J=6 Hz, 1H), 1.14-0.96 (m, 12H); 19F-NMR (376 MHz, DMSO-d6): δ −200.77, 200.80, 201.62, 201.64. 31P-NMR (162 MHz, DMSO-d6): δ 150.31, 150.24, 149.66, 149.60.

Example 43. Synthesis of End Cap Monomer

Preparation of (8): To a stirred solution of 7 (13.4 g, 35.5 mmol, Scheme 5) in DMSO (135 mL) were added EDCI (6.3 g, 32.9 mmol) and pyridine (0.9 g, 10.9 mmol), TFA (0.6 g, 5.5 mmol) at r.t. And the reaction mixture was stirred at r.t for 2 h. LCMS showed 7 consumed completely. The reaction was quenched with water and the product was extracted with EA (1800 mL). The organic phase was washed by brine, dried over Na2SO4, The organic phase was evaporated to dryness under reduced pressure to give a residue 8 (13.2 g, 35.3 mmol, 99.3% yield). Which was used directly to next step. ESI-LCMS: m/z=375 [M+H2O]+

Preparation of (10): A solution of 8 (13.2 g, 35.3 mmol), 9 (26.8 g, 42.3 mmol, Scheme 18) and K2CO3 (19.5 g, 141.0 mmol) in dry THF (160 mL) and D20 (53 mL) was stirred at r.t. 17 h. LCMS showed most of 8 was consumed. The product was extracted with EA (2500 mL) and the organic layer was washed with brine and dried over Na2SO4. Then the organic layer was concentrated to give a residue which was purified by c.c. (PE: EA=10:1-1:2) to give product 10 (8.1 g, 11.8 mmol, 33.4% yield) as a white solid. ESI-LCMS m/z=682 [M+H]+, 1H-NMR (400 MHz, DMSO-d6): δ 11.42 (s, 1H), 7.69-7.71 (d, J=8.1 Hz, 1H), 5.78-5.79 (d, J=3.7 Hz, 1H), 5.65-5.67 (m, 1H), 5.59-5.63 (m, 4H), 4.29-4.35 (m, 2H), 3.97-3.99 (m, 1H), 1.15 (s, 18H), 0.87 (s, 9H), 0.07-0.08 (d,.J=5.1 Hz, 6H). 31P-NMR (162 MHz, DMS 046) S 16.62.

Preparation of (11): To a round-bottom flask was added 10 (7.7 g, 11.1 mmol) in a mixture of HCOOH (80 mL) and H2O (80 mL). The reaction mixture was stirred at 40° C. for 3 h. LCMS showed the 10 was consumed completely. The reaction mixture was adjusted the pH=7.0 with con.NH3.H2O (100 mL). Then the mixture was extracted with DCM (100 mL*3). The combined DCM layer was dried over Na2SO4. Filtered and filtrate was concentrated to give crude which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/2 increasing to CH3CN/H2O (0.5% NH4HCO3)=1/1 within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. To give product 11 (5.5 g, 9.6 mmol, 86.1% yield) as a white solid. ESI-LCMS m/z=568 [M+H]+, 1H-NMR (400 MHz, DMSO-d6): δ 11.42 (s, 1H, exchanged with D20), 7.62-7.64 (d, J=8.1, 1H), 5.81-5.82 (d, J=4.3, 1H), 5.58-5.66 (m, 5H), 5.52-5.53 (d, J=6.6, 1H), 4.34-4.37 (m, 1H), 4.09-4.13 (m, 1H), 3.94-3.96 (t, J=9.7, 1H), 1.15 (s, 18H), 0 (s, 1H). 31P NMR (162 MHz, DMSO-d6) δ 17.16.

Preparation of Example 43 monomer: To a solution of 11 (5.3 g, 9.3 mmol) in DCM (40 mL) was added the DCI (1.1 g, 7.9 mmol), then CEP[N(ipr)2]2 (3.4 g, 11.2 mmol) was added. The mixture was stirred at r.t. for 1 h. LCMS showed 11 consumed completely. The reaction mixture was washed with H2O (50 mL*2) and brine (50 mL*1). Dried over Na2SO4 and concentrated to give crude which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. The product was concentrated to give Example 43 monomer (6.2 g, 8.0 mmol, 85.6% yield) as a white solid. ESI-LCMS m/z=768 [M+H]+;H-NMR (400 MHz, DMSO-d6): δ 11.43 (s, 1H), 7.68-7.71 (m, 1H), 5.79-5.81 (m, 1H), 5.58-5.67 (m, 5H), 4.34-4.56 (m, 2H), 4.14-4.17 (m, 1H), 3.54-3.85 (m, 4H), 2.78-2.81 (m, 2H), 1.13-1.17 (m, 30H). 31P-NMR (162 MHz, DMSO-d6): δ 149.66, 149.16, 16.84, 16.56.

Example 44. Synthesis of Monomer

Preparation of (2): To a solution of 1(20.0 g, 66.4 mmol) in dry DMF (400 mL) was added sodium hydride (1.9 g, 79.7 mmol) for 30 min, then was added CD3I (9.1 g, 79.7 mmol) in dry DCM (40 mL) at −20° C. for 5.5 hr. LCMS showed the reaction was consumed. The mixture was filtered and the clear solution was evaporated to dryness and was evaporated with CH30H. The crude was purified by silica gel column (SiO2, DCM/MeOH=50:1-10:1). This resulted in to give the product 2 (7.5 g, 23.5 mmol, 35.5% yield) as a solid. ESI-LCMS: m/z 319 [M+H]+; H-NMR (400 MHz, DMSO-d3): δ=8.38 (m, 1H), 6.97 (m, 2H), 5.93-5.81 (m, 1H), 5.27-5.26 (d, J=4 Hz, 1H), 5.13-5.11 (m, 1H), 4.39-4.31 (m, 1H), 4.31-4.25 (m, 1H), 3.96-3.94 (m, 1H), 3.66-3.63 (m, 1H), 3.63-3.56 (m, 1H).

Preparation of (3): To a solution of 2 (7.5 g, 23.5 mmol) in dry DMF (75 mL) was added Imidazole (5.6 g, 82.3 mmol) and TBSCl (8.9 g, 58.8 mmol). The mixture was stirred at r.t. over night. LCMS showed 2 was consumed completely. The reaction was quenched with water (300 mL). The product was extracted into ethyl acetate (100 mL). The organic layer was washed with brine and dried over anhydrous Na2SO4. The solvent was removed to give the cured 3 (9.8 g) as a solid witch used for the next step. ESI-LCMS: m/z 547 [M+H]+.

Preparation of (4): To a solution of 3 (9.8 g) in THF (40 mL) was added TFA (10 mL) and water (10 mL) at 0° C. The reaction mixture was stirred at 0° C. for 5 h. LC-MS showed 3 was consumed completely. Con. NH4OH was added to the mixture at 0° C. to quench the reaction until the pH=7.5. The product was extracted into ethyl acetate (200 mL). The organic layer was washed with brine and dried over anhydrous Na2SO4. The solvent was removed to give the cured 4 (8.4 g) as a solid witch used for the next step. ESI-LCMS: m/z 433 [M+H]+.

Preparation of (5): To a solution of 4 (8.4 g) in DCM/H2O=2:1 (84 mL) was added DAIB (18.8 g, 58.4 mmol) and TEMPO (0.87 g, 5.8 mmol). The reaction mixture was stirred at 40° C. for 2 h. LCMS showed 4 was consumed. The mixture was diluted with DCM and water was added. The product was extracted with DCM. The organic layer was washed with brine and dried over anhydrous Na2SO4. The solution was then concentrated under reduced pressure. This resulted in to give 5 (14.4 g) as a white solid. ESI-LCMS: m/z 447 [M+H]+.

Preparation of (6): To a solution of 5 (14.4 g) in toluene (90 mL) and methanol (60 mL) was added 2M TMSCHN2 (8.9 g, 78.1 mmol) till the yellow color not disappear at r.t. for 10 min. LCMS showed 5 was consumed. The crude was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=65/35 Detector, UV 254 nm. This resulted in to give the product 6 (3.5 g, 7.6 mmol, 32.3% yield over three steps, 70% purity) as a white solid. ESI-LCMS: m/z 461 [M+H]+.

Preparation of (7): To the solution of 6 (3.5 g, 7.6 mmol) in dry THF/MeOD/D20=10/2/1 (45 mL) was added NaBD4 (0.96 g, 22.8 mmol). And the reaction mixture was stirred at r.t for 2.5 hr. After completion of reaction, the resulting mixture was added CH3COOD to pH=7, after addition of water, the resulting mixture was extracted with EA (100 mL). The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated to give 7 (3.3 g) which was used for the next step. ESI-LCMS: m/z 435 [M+H]+.

Preparation of (8): To a solution of 7 (3.3 g) in dry DCM (30 mL) was added pyridine (5.9 g, 74.5 mmol) and iBuCl (2.4 g, 22.4 mmol) in DCM (6 mL) under ice bath. The reaction mixture was stirred at 0° C. for 2.5 hr. LCMS showed 7 was consumed. The mixture was diluted with EA and water was added. The product was extracted with EA. The crude was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=87/13; Detector, UV 254 nm. This resulted in to give the crude 8 (1.6 g, 2.8 mmol, 36.8% yield over two steps) as a white solid. ESI-LCMS: m/z 575 [M+H]+.

Preparation of (9): To a solution of 8 (1.6 g, 2.8 mmol,) in H2O/dioxane=1:1 (30 ml) was added K2CO3 (772.8 mg, 5.6 mmol) and DABCO (739.2 mg, 2.9 mmol). The reaction mixture was stirred at 50° C. for 3 hr. LCMS showed 8 was consumed. The mixture was diluted with EA and water was added. The product was extracted with EA. The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated to give 9 (1.8 g) which was used for the next step. ESI-LCMS: m/z 557 [M+H]+.

Preparation of (10): To a solution of 9 (1.8 g) in pyridine (20 mL) and was added 2M NaOH (MeOH/H2O=4/1) (5 mL) at 0° C. for 1 h. LCMS showed 9 was consumed. The mixture was added saturated NH4Cl till pH=7.5. The mixture was diluted with water and EA. The organic layer was washed with brine and dried over Na2SO4 and concentrated to give the crude. This resulted in to give the product 10 (1.5 g) as a white solid which was used for the next step. ESI-LCMS: m/z 487 [M+H]+.

Preparation of (11): To a stirred solution of 10 (1.5 g) in pyridine (20 mL) were added DMTrCl (1.1 g, 3 mmol) at r.t. And the reaction mixture was stirred at r.t for 2.5 hr. With ice-bath cooling, the reaction was quenched with water and the product was extracted into EA. The organic layer was washed with brine and dried over Na2SO4 and concentrated to give the crude. The crude was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=7/3 Detector, UV 254 nm. This resulted in to give the product 11(1.9 g, 2.4 mmol, 85.7% yield over two steps) as a white solid. ESI-LCMS: m/z 789.3 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 12.10 (m, 1H), 11.63 (m, 1H), 8.20 (m, 1H), 7.35-7.33 (m, 2H), 7.29-7.19 (m, 7H), 6.86-6.83 (m, 4H), 5.89-5.88 (d, J=4 Hz, 1H), 4.40-4.28 (m, 2H), 3.72 (m, 6H), 2.81-2.76 (m, 1H), 1.13-1.11 (m, 6H), 0.80 (m, 9H), 0.05-0.01 (m, 7H).

Preparation of (12): To a solution of 11 (1.9 g, 2.4 mmol) in THF (20 mL) was added 1 M TBAF solution (3 mL). The reaction mixture was stirred at r.t. for 1.5 h. LCMS showed 11 was consumed completely. Water (100 mL) was added. The product was extracted with EA (50 mL) and the organic layer was washed with brine and dried over Na2SO4. Then the organic layer was concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=58/42; Detector, UV 254 nm. This resulted in to give 12 (1.5 g, 2.2 mmol, 91.6% yield) as a white solid. ESI-LCMS: m/z 675.3 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): S 12.09 (m, 1H), 11.60 (m, 1H), 8.14 (m, 1H), 7.35-7.27 (m, 2H), 7.25-7.20 (m, 7H), 6.85-6.80 (m, 4H), 5.96-5.94 (d, J=8 Hz, 1H), 5.26-5.24 (m, 1H), 4.35-4.28 (m, 2H), 3.72 (m, 6H), 3.32 (m, 1H), 2.79-2.72 (m, 1H), 1.13-1.11 (m, 6H).

Preparation of Example 44 monomer: To a suspension of 11(1.5 g, 2.2 mmol) in DCM (15 mL) was added DCI (220.8 mg, 1.9 mmol) and CEP[N(iPr)2]2 (795.7 mg, 2.6 mmol) under N2 pro. The mixture was stirred at r.t. for 2 h. LCMS showed 11 was consumed completely. The solution was washed with water twice and washed with brine and dried over Na2SO4. Then concentrated to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=4/1; Detector, UV 254 nm. This resulted in to give Example 44 monomer (1.6 g, 1.8 mmol, 83% yield) as a white solid. ESI-LCMS: m/z 875 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 12.12 (m, 1H), 11.60 (m, 1H), 8.15 (m, 1H), 7.37-7.29 (m, 2H), 7.27-7.20 (m, 7H), 6.86-6.81 (m, 4H), 5.94-5.88 (m, 1H), 4.54-4.51 (m, 2H), 4.21-4.20 (m, 1H), 3.73-3.54 (m, 10H), 2.80-2.75 (m, 1H), 2.61-2.58 (m, 1H), 1.19-1.11 (m, 19H). 31P-NMR (162 MHz, DMSO-d6): δ=149.77, 149.71.

Example 45. Synthesis of Monomer

Preparation of (2): To a solution of 1(50.0 g, 99.2 mmol) and 1a (11.3 g, 119.0 mmol) in ACN (500.0 mL). Then added BSA (53.2 g, 218.0 mmol) under N2 Pro. The mixture was stirred at 50° C. for 1 h until the solution was clear. Then cool down to 0° C. and dropped TMSOTf (26.4 g, 119.0 mmol).The mixture was stirred at 75° C. for 1 h, TLC showed 1 was consumed completely. The reaction was quenched by sodium bicarbonate solution at 0° C., then the solution was diluted with EA, washed with H2O twice. The solvent was concentrated under reduced pressure and the crude 2 (60.1 g) was used for next step. ESI-LCMS: m/z 540.2 [M+H]+.

Preparation of (3): To a solution of 2 (60.1 g) in CH3NH2/ethanol (500.0 mL). The mixture was stirred at 25° C. for 2 h. TLC showed 2 was consumed completely. The solvent was concentrated under reduced pressure and the residue was purified by c.c. (MeOH:DCM=50:1-10:1) to give 3 (22.0 g, 96.9 mmol, 97.3% yield over two steps). ESI-LCMS: m/z 228.0 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 8.01-7.98 (m, 1H), 7.43-7.38 (m, 1H), 6.37-6.35 (m, 1H), 6.27-6.23 (m, 1H), 6.03 (d, J=3.5 Hz, 1H), 5.39 (d, J=4.2 Hz, 1H), 5.11 (t, J=5.1 Hz, 1H), 5.03 (d, J=5.1 Hz, 1H), 3.98-3.95 (m, 2H), 3.91-3.88 (m, 1H), 3.74-3.57 (m, 2H).

Preparation of (4): To a solution of 3 (22.0 g, 96.9 mmol) in pyridine (250.0 mL), TrtCl (30.7 g, 110.5 mmol) was added. The mixture was stirred at 25° C. for 24 h. TLC showed 3 was consumed completely, H2O was added to the mixture. Then filtered and the filtrate diluted with EA, the organic layer was washed with NaHCO3 and brine. The solvent was concentrated under reduced pressure and then purified by c.c. (PE/EA=5:1-0:1) to give 4 (38.8 g, 82.5 mmol, 85.1% yield) as a white solid. ESI-LCMS: m/z 470.1 [M+H]+.

Preparation of (5): To a solution of 4 (38.8 g, 82.5 mmol) in DMF (500.0 mL), collidine (10.0 g, 107.3 mmol), TrtCl (27.6 g, 99.1 mmol) were added followed by AgNO3 (18.0 g, 105.1 mmol). The mixture was stirred at 25° C. for 4 h. TLC showed 4 was consumed completely. Then filtered and the filtrate diluted with EA. The organic layer was washed with NaHCO3 and brine. The solvent was concentrated under reduced pressure and then purified by c.c. (PE/EA=5:1-1:1) to give a mixture of 5 (52.3 g, 73.5 mmol, 86.3% yield) as white solid. ESI-LCMS: m/z 711.1 [M+H]+.

Preparation of (6): To a solution of 5 (52.3 g, 73.5 mmol) in DCM (500.0 mL), DMAP (8.9 g, 73.5 mmol), TEA (14.9 g, 147.3 mmol, 20.6 mL) were added, cool down to 0° C., TfCl (16.1 g, 95.6 mmol) dissolved in DCM (100.0 mL) were dropped. The mixture was stirred at 25° C. for 1 h. TLC showed 5 was consumed completely. Then filtered and the solution diluted with EA. The organic layer was washed with NaHCO3 and brine. The solvent was concentrated under reduced pressure to get crude 6 (60.2 g) as a brown solid. ESI-LCMS: m/z 844.2 [M+H]+.

Preparation of (7): To a solution of 6 (60.2 g) in DMF (500.0 mL), KOAc (36.1 g, 367.8 mmol) were added, The mixture was stirred at 25° C. for 14 h and 50° C. for 3 h, TLC showed 6 was consumed completely. Then filtered and the solution diluted with EA. The organic layer was washed with H2O and brine. The solvent was concentrated under reduced pressure, residue was purified by c.c. (PE/EA=5:1-1:1) to give 7 (28.0 g, 39.3 mmol, 53.5% yield) as yellow solid. ESI-LCMS: m/z 710.2 [M−H]−; H-NMR (400 MHz, DMSO-d6): δ 7.37-7.25 (m, 33H), 6.34-6.31 (m, 2H), 6.13-6.10 (m, 1H), 5.08 (d, J=4.2 Hz, 1H), 3.99 (d, J=7.6 Hz, 1H), 3.74 (s, 1H), 3.12 (t, J=9.2 Hz, 1H), 2.72-2.69 (m, 1H).

Preparation of (8): To a solution of 7 (28.0 g, 39.3 mmol) in DCM (300.0 mL), DAST (31.6 g, 196.6 mmol) was added at 0° C., the mixture was stirred at 25° C. for 16 h, TLC showed 7 was consumed completely. Then the solution was diluted with EA, washed with NaHCO3 twice, the solvent was removed under reduced pressure, residue was purified by c.c. (PE/EA=5:1-3:1) to give 8 (5.0 g, 7.0 mmol, 17.8% yield) as a white solid. ESI-LCMS: m/z 748.2 [M+2NH4]+; 1H-NMR (400 MHz, DMSO-d6): δ 7.57-7.18 (m, 35H), 6.30 (d, J=8.8 Hz, 1H), 6.00 (d, J=19.5 Hz, 1H), 5.92-5.88 (m, 1H), 4.22-4.17 (m, 2H), 3.94 (s, 0.5H), 3.80 (s, 0.5H), 3.35-3.31 (m, 1H), 3.14-3.10 (m, 1H); 19F-NMR (376 MHz, DMSO-d6): δ −193.54.

Preparation of (9): To a solution of 8 (5.0 g, 7.0 mmol) in DCM (60.0 mL) was added DCA (3.6 mL) and TES (15.0 mL). The mixture was stirred at 20° C. for 1 h, TLC showed 8 was consumed completely. Then the solution was concentrated under reduced pressure, the residue was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=0/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=1/3 within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=0/1; Detector, UV 254 nm. This resulted in to give 9 (1.6 g, 6.9 mmol, 98.5% yield) as a white solid. ESI-LCMS: m/z 229.9 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 8.06-8.04 (m, 1H), 7.48-7.43 (m, 1H), 6.39 (d, J=9.0 Hz, 1H), 6.31-6.27 (m, 1H), 6.16-6.11 (m, 1H), 5.63 (s, 1H), 5.26 (s, 1H), 4.95-4.81 (m, 1H), 4.20-411 (m, 1H), 3.95 (d, J=8.2 Hz, 1H), 3.84 (d, J=12.4 Hz, 1H), 3.64 (d, J=12.1 Hz, 1H); 19F-NMR (376 MHz, DMSO-d6): δ −201.00.

Preparation of (10): To a solution of 9 (1.6 g, 6.9 mmol) in pyridine (20.0 mL) was added DMTrCl (3.5 g, 10.5 mmol) at 20° C. and stirred for 1 h. TLC showed 9 was consumed completely. Water was added and extracted with EA, the organic layer was washed with NaHCO3 and brine. Then the solution was concentrated under reduced pressure and the residue was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=4/1 within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=1/1; Detector, UV 254 nm. This resulted in to give 10 (2.2 g, 4.2 mmol, 60.8% yield) as a white solid. ESI-LCMS: m/z 530.1 [M−H]−; 1H-NMR (400 MHz, DMSO-d6): δ 7.93-7.91 (m, 1H), 7.47-7.23 (m, 10H), 6.91-6.89 (m, 4H), 6.41 (d, J=8.8 Hz, 1H), 6.13 (d, J=18.8 Hz, 1H), 6.00-5.96 (m, 1H), 5.68 (d, J=6.6 Hz, 1H), 5.01 (d, J=4.2 Hz, 0.5H), 4.88 (d, J=4.2 Hz, 0.5H), 4.42-4.31 (m, 1H), 4.10-4.08 (m, 1H), 3.74 (s, 6H), 3.40-3.34 (m, 2H); 19F-NMR (376 MHz, DMSO-d6): δ −199.49.

Preparation of Example 45 monomer: To a solution of 10 (2.2 g, 4.2 mmol) in DCM (20.0 mL) was added DCI (415 mg, 3.5 mmol) and CEP (1.5 g, 4.9 mmol) under N2 pro. The mixture was stirred at 20° C. for 0.5 h. TLC showed 10 was consumed completely. The product was extracted with DCM, the organic layer was washed with H2O and brine. Then the solution was concentrated under reduced pressure and the residue was purified by cc (PE/EA=5:1-1:1) and Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 45 monomer (2.1 g, 3.0 mmol, 73.1% yield) as a white solid. ESI-ESI-LCMS: m/z 732.2 [M+H]+; 1H-NMR (400 MHz, DMSO-d6): δ 7.98-7.92 (m, 1H), 7.42-7.24 (m, 10H), 6.91-6.85 (m, 4H), 6.43-6.39 (m, 1H), 6.18-6.11 (m, 1H), 6.01-5.97 (m, 1H), 5.22-5.19 (m, 0.5H), 5.09-5.06 (m, 0.5H), 4.73-4.52 (m, 1H), 4.21-4.19 (m, 1H), 3.79-3.62 (m, 7H), 3.57-3.47 (m, 4H), 3.32-3.28 (m, 1H), 2.75-2.58 (m, 1H), 1.13-0.92 (m, 12H); 19F-NMR (376 MHz, DMSO-d6): δ −196.82 , −196.84 , −197.86 , −197.88; 31P-NMR (162 MHz, DMSO-d6): δ 149.88, 149.83, 149.39, 149.35.

Example 46. Synthesis of Monomer

Preparation of (2): To the solution of Bromobenzene (2.1 g, 13.6 mmol) in dry THF (15 mL) was added 1.6 M n-BuLi (7 mL, 11.8 mmol) drop wise at −78° C. The mixture was stirred at −78° C. for 0.5 h. Then the 1 (3.0 g, 9.1 mmol, Wang, Guangyi et al, Journal of Medicinal Chemistry, 2016, 59(10), 4611-4624) was dissolved in THF (15 mL) and added to the mixture drop wise with keeping at −78° C. Then the reaction mixture was stirred at −78° C. for 1 hr. LC-MS showed 1 was consumed completely. Then the solution was added to saturated aq. NH4Cl and the resulting mixture was extracted with EA. The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated under reduced pressure to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=4/1 within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=3/2; Detector, UV 254 nm. This resulted in to give 2 (3.0 g, 7.3 mmol, 80.0%) as a white solid. ESI-LCMS: m/z 391 [M-OH]−.

Preparation of (3): To the solution of 2 (4.0 g, 9.8 mmol) in DCM (40 mL) was added TES (1.9 g, 11.7 mmol) at −78° C., and the mixture was added BF3.OEt2 (2.1 g, 14.7 mmol) drop wise at −78° C. The mixture was stirred at −40° C. for 1 hr. LC-MS showed 2 was consumed completely. Then the solution was added to saturated aq. NaHCO3 and the resulting mixture was extracted with DCM. The combined organic layer was washed with water and brine, dried over Na2SO4, and concentrated under reduced pressure to give a residue which was purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=2/3 increasing to CH3CN/H2O (0.5% NH4HCO3)=4/1 within 25 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=7/3; Detector, UV 254 nm. This resulted in to give 3 (3.1 g, 5.3 mmol, 54.0%) as a water clear oil. ESI-LCMS: m/z 410 [M+H2O]+; 1H-NMR (400 MHz, CDCl3: S 7.48-7.25 (m, 15H), 5.24-5.13 (m, 1H), 4.93-4.74 (m, 1H), 4.74-4.46 (m, 4H), 4.37-4.25 (m, 1H), 4.19-4.05 (m, 1H), 4.00-3.80 (m, 1H), 3.77-3.63 (m, 1H). 19F-NMR (376 MHz, CDCl3): δ −196.84.

Preparation of (4): To the solution of 3 (2.1 g, 5.3 mmol) in dry DCM (20 mL) was added 1 M BCl3 (25 mL, 25.5 mmol) drop wise at −78° C., and the reaction mixture was stirred at −78° C. for 0.5 hr. LC-MS showed 3 was consumed completely. After completion of reaction, the resulting mixture was poured into water (50 mL). The solution was extracted with DCM and the combined organic layer was concentrated under reduced pressure to give a crude. The crude in MeOH (4 mL) was added 1 M NaOH (15 mL), and the mixture was stirred at r.t for 5-10 min. The mixture was extracted with EA. The combined organic layer was washed with brine, dried over Na2SO4, and concentrated under reduced pressure to give a residue which was purified by silica gel column chromatography (eluent, DCM: MeOH=40:1˜15:1) to give 4 (1.0 g, 4.7 mmol, 88.6%) as a water clear oil. ESI-LCMS: m/z 211 [M−H]−; 1H-NMR (400 MHz, DMSO-d6): δ 7.58-7.19 (m, 5H), 5.41 (d, J=6.1 Hz, 1H), 5.09-5.95 (m, 1H), 5.95-4.84 (m, 1H), 4.82-4.59 (m, 1H), 4.14-3.94 (m, 1H), 3.89-3.80 (m, 1H), 3.78-3.67 (m, 1H), 3.65-3.53 (m, 1H). 19F-NMR (376 MHz, DMSO-d6): δ −196.46.

Preparation of (5): To a solution of 4 (1.0 g, 4.7 mmol) in Pyridine (10 mL) was added DMTrCl (2.0 g, 5.7 mmol). The reaction mixture was stirred at r.t. for 2 hr. LCMS showed 4 was consumed and water (100 mL) was added. The product was extracted with EA (100 mL) and the organic layer was washed with brine and dried over Na2SO4 and concentrated to give the crude. The crude was further purified by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=9/1; Detector, UV 254 nm. This resulted in to give 5 (2.1 g, 4.1 mmol, 87.0%) as a red oil. ESI-LCMS: m/z 513 [M−H]−; 1H-NMR (400 MHz, DMSO-d6): δ 7.56-7.16 (m, 14H), 6.94-9.80 (m, 4H), 5.45 (d, J=6.3 Hz, 1H), 5.21-5.09 (m, 1H), 4.89-4.68 (m, 1H), 4.18-4.03 (m, 2H), 3.74 (s, 6H), 3.33-3.29 (m, 1H), 3.26-3.17 (m, 1H). 19F-NMR (376 MHz, DMSO-d6): δ −194.08.

Preparation of Example 46 monomer: To a suspension of 5 (2.1 g, 4.1 mmol) in DCM (20 mL) was added DCI (410 mg, 3.4 mmol) and CEP[N(iPr)2]2 (1.5 g, 4.9 mmol). The mixture was stirred at r.t. for 1 h. LC-MS showed 5 was consumed completely. The solution was washed with water twice and washed with brine and dried over Na2SO4. Then concentrated to give the crude. The crude was purification by Flash-Prep-HPLC with the following conditions (IntelFlash-1): Column, C18 silica gel; mobile phase, CH3CN/H2O (0.5% NH4HCO3)=1/1 increasing to CH3CN/H2O (0.5% NH4HCO3)=I/O within 20 min, the eluted product was collected at CH3CN/H2O (0.5% NH4HCO3)=I/O; Detector, UV 254 nm. This resulted in to give Example 46 monomer (2.1 g, 2.9 mmol, 70.0%) as a white solid. ESI-LCMS: m/z 715 [M+H]+; H-NMR (400 MHz, DMSO-d6): δ 7.59-7.16 (m, 14H), 6.94-9.80 (m, 4H), 5.26-5.12 (m, 1H), 5.06-4.77 (m, 1H), 4.50-4.20 (m, 1H), 4.20-4.10 (m, 1H), 3.83-3.63 (m, 7H), 3.59-3.37 (m, 4H), 3.25-3.13 (m, 1H), 2.80-2.66 (m, 1H), 2.63-2.53 (m, 1H), 1.18-0.78 (m, 12H). 19F-NMR (376 MHz, DMSO-d6): δ −194.40 , −194.42 , −194.50,-194.53. 31P-NMR (162 MHz, DMSO-d6): δ 149.38, 149.30, 149.02, 148.98.

Example 47. Deuterated Vinyl Phosphonate Improves Potency of siNA

This example investigates whether a deuterated vinyl phosphonate improves potency of siNA in an AAV-HBV mouse. AAV-HBV mice were subcutaneously injected with vehicle, ds-siNA-0165 (e.g., siNA without a deuterated vinyl phosphonate), or ds-siNA-0144 (e.g., siNA with a deuterated vinyl phosphonate). For siNA-treated AAV-HBV mice, AAV-HBV mice were subcutaneously injected with a single dose of 5 mg/kg of siNA. As shown in FIG. 11, siNA molecules having 2′-fluoro nucleotides at positions 3, 7-9, 12, and 17 from the 5′ end of the sense strand and 2′-fluoro nucleotides at positions 2 and 14 from the 5′ end of the antisense strand resulted in at least a 0.5-log reduction in HBsAg, with the greatest reduction in HBsAg found in mice treated with the deuterated vinylphopshonate siNA (ds-siNA-0165). Thus, FIG. 11 demonstrates that the presence of a deuterated vinyl phosphonate improves potency of the siNA.

Example 48. Deuterated Vinyl Phosphonate Results in a Greater Reduction in Serum HBsAg

AAV-HBV mice were subcutaneously injected with vehicle, ds-siNA-0163 (e.g., siNA without a vinyl phosphonate), ds-siNA-0122 (e.g., siNA with a vinyl phosphonate), or ds-siNA-0123 (e.g., siNA with a deuterated vinyl phosphonate). For siNA-treated AAV-HBV mice, AAV-HBV mice were subcutaneously injected with a single dose of 5 mg/kg of siNA. As shown in FIG. 12, siNA molecules having 2′-fluoro nucleotides at positions 7, 9-11 from the 5′ end of the sense strand and 2′-fluoro nucleotides at positions 2 and 14 from the 5′ end of the antisense strand resulted in at least a 0.5-log reduction in HBsAg, with the greatest reduction in HBsAg found in mice treated with the deuterated vinylphopshonate siNA (ds-siNA-0165). Thus, FIG. 12 demonstrates that the presence of a deuterated vinyl phosphonate improves potency of the siNA, as compared to the siNA without a vinyl phosphonate and the siNA with the vinyl phosphonate.

Example 49: Synthesis of 5′ End Cap Monomer

Example 49 Monomer Synthesis Scheme

Preparation of(2): 1(15 g, 58.09 mmol) and tert-butyl N-methylsulfonylcarbamate (17.01 g, 87.13 mmol) were dissolved in THF (250 mL), and PPh3 (30.47 g, 116.18 mmol) was added followed by dropwise addition of DIAD (23.49 g, 116.18 mmol, 22.59 mL) at 0° C. The reaction mixture was stirred at 15° C. for 12 h. Upon completion as monitored by TLC(DCM/MeOH=10/1), the reaction mixture was evaporated to give a residue. The residue was purified by flash silica gel chromatography (ISCO@; 120 g SepaFlash@ Silica Flash Column, Eluent of 0˜20%/MeOH/DCM gradient @ 60 mL/min) to give 2 (6.9 g, 24.28% yield) as a white solid. ESI-LCMS: m/z 457.9 [M+Na]+; 1H NMR (400 MHz, CDCl3) δ=8.64 (br s, 1H), 7.64 (d, J=8.2 Hz, 1H), 5.88 (d, J=1.9 Hz, 1H), 5.80 (dd, J=2.2, 8.2 Hz, 1H), 4.19-4.01 (m, 3H), 3.90 (dt, J=5.5, 8.2 Hz, 1H), 3.82-3.78 (m, 1H), 3.64 (s, 3H), 3.32 (s, 3H), 2.75 (d, J=8.9 Hz, 1H), 1.56 (s, 9H).

Preparation of (3): 2 (6.9 g, 15.85 mmol) was dissolved in MeOH (40 mL), and a solution of HCl/MeOH (4 M, 7.92 mL) was added dropwise. The reaction mixture was stirred at 15° C. for 12 h, and then evaporated to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 40 g SepaFlash@ Silica Flash Column, Eluent of 0˜10% MeOH/DCM gradient @ 40 mL/min) to give 3 (2.7 g, 50.30% yield) as a white solid. ESI-LCMS: m/z 336.0 [M+H]+; 1H NMR (400 MHz, CD3CN) δ=9.20 (br s, 1H), 7.52 (d, J=8.1 Hz, 1H), 5.75 (d, J=3.8 Hz, 1H), 5.64 (dd, J=2.0, 8.1 Hz, 1H), 5.60-5.52 (m, 1H), 4.15-3.99 (m, 1H), 3.96-3.81 (m, 2H), 3.46 (s, 3H), 3.44-3.35 (m, 1H), 3.34-3.26 (m, 1H), 2.92 (s, 3H).

Preparation of (Example 49 monomer): To a solution of 3 (2.14 g, 6.38 mmol) in DCM (20 mL) was added dropwise 3-bis(diisopropylamino)phosphanyloxypropanenitrile (2.50 g, 8.30 mmol, 2.63 mL) at 0° C., followed by 1H-imidazole-4, 5-dicarbonitrile (829 mg, 7.02 mmol), and the mixture was purged under Ar for 3 times. The reaction mixture was stirred at 15° C. for 2 h. Upon completion, the mixture was quenched with 5% NaHCO3(20 mL), extracted with DCM (20 mL*2), washed with brine (15 mL), dried over Na2SO4, filtered, and evaporated to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 40 g SepaFlash@ Silica Flash Column, Eluent of 0˜10% (Phase B: i-PrOH/DCM=1/2)/Phase A: DCM with 5% TEA gradient @ 40 mL/min) to give Example 49 monomer (1.73 g, 48.59% yield) as a white solid. ESI-LCMS: m/z 536.3 [M+H]+; 1H NMR (400 MHz, CD3CN) δ=7.58-7.48 (m, 1H), 5.83-5.78 (m, 1H), 5.71-5.64 (m, 1H), 4.40-4.29 (m, 1H), 4.19-4.07 (m, 1H), 3.98 (td, J=5.3, 13.3 Hz, 1H), 3.90-3.78 (m, 2H), 3.73-3.59 (m, 3H), 3.41 (d, J=14.8 Hz, 4H), 2.92 (br d, J=7.0 Hz, 3H), 2.73-2.63 (m, 2H), 1.23-1.11 (m, 12H); 31P NMR (162 MHz, CD3CN) δ=149.81, 150.37.

Example 50: Synthesis of 5′ End Cap Monomer

Example 50 Monomer Synthesis Scheme

Preparation of (2): To a solution of 1(10 g, 27.16 mmol) in DMF (23 mL) were added imidazole (3.70 g, 54.33 mmol) and ThSCI (8.19 g, 54.33 mmol) at 25 C. The mixture was stirred at 25° C. for 2 hr. Upon completion, the reaction mixture was diluted with H2O (20 mL) and extracted with EA (30 mL * 2). The combined organic layers were washed with brine (20 mL * 2), dried over Na2SO4, filtered and concentrated under reduced pressure to give 2 (13 g 99.2% yield) as a white solid. ESI-LCMS: m/z 482.9 [M+H]1.

Preparation of (3): To a solution of 2 (35.00 g, 72.56 mmol) in DMF (200 mL) was added NaN3 (14.15 g, 217.67 mmol). The mixture was stirred at 60° C. for 17 h. Upon completion, the reaction mixture was diluted with H2O (200 mL) and extracted with EA (200 mL*2). The combined organic layers were washed with brine (100 mL * 2), dried over Na2SO4, filtered and concentrated under reduced pressure to give 3 (31.8 g, crude) as a yellow solid. ESI-LCMS: m/z 398.1 [M+H]+; 1H NMR (400 MHz, DMSO-d6) δ=11.21 (d, J=1.3 Hz, 1H), 7.50 (d, J=8.1 Hz, 1H), 5.57 (d, J=4.5 Hz, 1H), 5.46 (dd, J=2.1, 8.0 Hz, 1H), 4.06 (t, J=5.2 Hz, 1H), 3.81-3.64 (m, 2H), 3.44-3.30 (m, 2H), 2.31-2.25 (m, 3H), 0.65 (s, 9H), −0.13 (s, 6H).

Preparation of (4): To a solution of 3 (7 g, 17.61 mmol) in THF (60 mL) was added Pd/C (2 g) at 25° C. The reaction mixture was stirred at 25° C. for 3 h under H2 atmosphere (15 PSI). The reaction mixture was filtered, and the filtrate was concentrated to give 4 (5.4 g, 75.11% yield) as a gray solid. ESI-LCMS: m/z 372.1 [M+H]+; 1H NMR (400 MHz, DMSO-d6) δ=7.93 (d, J=8.0 Hz, 1H), 5.81 (d, J=5.5 Hz, 1H), 5.65 (d, J=8.3 Hz, 1H), 4.28 (t, J=4.6 Hz, 1H), 3.88 (t, J=5.3 Hz, 1H), 3.74 (q, J=4.6 Hz,1 H), 3.31 (s, 3H), 2.83-2.66 (m, 2H), 0.88 (s, 9H), 0.09 (s, 6H).

Preparation of (5): To a solution of 4 (3 g, 8.08 mmol) in DCM (30 mL) was added TEA (2.45 g, 24.23 mmol, 3.37 mL) followed by dropwise addition of 3-chloropropane-1-sulfonyl chloride (1.50 g, 8.48 mmol, 1.03 mL) at 25° C. The reaction mixture was stirred at 25° C. for 18 h under N2 atmosphere. Upon completion, the reaction mixture was diluted with H2O (50 mL) and extracted with DCM (50 mL * 2). The combined organic layers were washed with brine (50 mL*2), dried over Na2SO4, filtered and concentrated under reduced pressure. The residue was purified by flash silica gel chromatography (ISCO@; 24 g SepaFlash@ Silica Flash Column, Eluent of 0˜30% MeOH/DCM @ 50 mL/min) to give 5 (3.6 g, 84.44% yield) as a white solid. ESI-LCMS: m/z 512.1 [M+H]+; 1H NMR (400 MHz, DMSO-d6) δ=11.42 (s, 1H), 7.75 (d, J=8.1 Hz, 1H), 7.49 (t, J=6.2 Hz, 1H), 5.83 (d, J=5.8 Hz, 1H), 5.70-5.61 (m, 1H), 4.33-4.23 (m, 1H), 3.95 (t, J=5.5 Hz, 1H), 3.90-3.78 (m, 1H), 3.73 (t, J=6.5 Hz, 2H), 3.30 (s, 3H), 3.26-3.12 (m, 4H), 2.14-2.02 (m, 2H), 0.88 (s, 9H), 0.11 (d, J=3.3 Hz, 6H).

Preparation of (6): To a solution of 5 (5 g, 9.76 mmol) in DMF (45 mL) was added DBU (7.43 g, 48.82 mmol, 7.36 mL). The mixture was stirred at 25° C. for 16 h. The reaction mixture was concentrated to give a residue. diluted with H2O (50 mL) and extracted with EA (50 mL * 2). The combined organic layers were washed with brine (50 mL * 2), dried over Na2SO4, filtered and concentrated under reduced pressure. The residue was purified by flash silica gel chromatography (ISCO®; 24 g SepaFlash@ Silica Flash Column, Eluent of 0˜80% EA/PE @ 40 mL/min) to give 6 (4.4 g, 89.06% yield) as a white solid. ESI-LCMS: m/z 476.1 [M+H]+; H NMR (400 MHz, DMSO-d6) δ=11.43 (d, 1=1.7 Hz, 1H), 7.72 (d, J=8.1 Hz, 1H), 5.82 (d, J=4.8 Hz, 1H), 5.67 (dd, J=2.1, 8.1 Hz, 1H), 4.22 (t, J=5.1 Hz, 1H), 3.99-3.87 (m, 2H), 3.33-3.27 (m, 6H), 3.09 (dd, J=6.6, 14.7 Hz, 1H), 2.26-2.16 (m, 2H), 0.88 (s, 9H), 0.10 (d, J=3.8 Hz, 6H).

Preparation of (7): To a solution of 6 (200 mg, 420.49 umol) in MeOH (2 mL) was added NH4F (311.48 mg, 8.41 mmol, 20 eq), and the mixture was stirred at 80° C. for 2 h. The mixture was filtered and concentrated to give a residue, which was purified by flash silica gel chromatography (ISCO®; 4 g SepaFlash@ Silica Flash Column, Eluent of 0˜50% MeOH/DCM @ 20 mL/min) to give 7 (120 mg, 76.60% yield) as a white solid. ESI-LCMS: m/z 362.1 [M+H]+; 1H NMR (400 MHz, DMSO-d6) δ=11.37 (br s, 1H), 7.68 (d, J=8.1 Hz, 1H), 5.81 (d, J=4.6 Hz, 1H), 5.65 (d, J=8.0 Hz, 1H), 4.02 (q, J=5.6 Hz,1 H), 3.95-3.83 (m, 2H), 3.34 (s, 9H), 3.09 (dd, J=6.9, 14.6 Hz, 1H), 2.26-2.14 (m, 2H).

Preparation of (Example 50 monomer): To a solution of 7 (1.5 g, 4.15 mmol) in CH3CN (12 mL) were added 3-bis(diisopropylamino)phosphanyloxypropanenitrile (1.63 g, 5.40 mmol, 1.71 mL) and 1H-imidazole-4,5-dicarbonitrile (539.22 mg, 4.57 mmol) in one portion at 0° C. The reaction mixture was gradually warmed to 25° C. The reaction mixture was stirred at 25° C. for 2 h under N2 atmosphere. Upon completion, the reaction mixture was diluted with NaHCO3(20 mL) and extracted with DCM (20 mL * 2). The combined organic layers were washed with brine (20 mL * 2), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue, which was purified by flash silica gel chromatography (ISCO®; 12 g SepaFlash@ Silica Flash Column, Eluent of 0-85% EA/PE with 0.5% TEA @ 30 mL/min to give Example 50 monomer (800 mg, 33.6% yield,) as a white solid. ESI-LCMS: m/z 562.3 [M+H]+; 1H NMR (400 MHz, CD3CN) δ=9.28 (br s, 1H), 7.55 (br dd, J=8.3, 12.8 Hz,1 H), 5.86 (br d, J=3.9 Hz, 1H), 5.65 (br d, J=8.0 Hz, 1H), 4.33-4.06 (m, 2H), 4.00-3.89 (m, 1H), 4.08-3.86 (m, 1H), 3.89-3.72 (m, 4H), 3.43 (br d, J=15.1 Hz, 6H), 3.23-3.05 (m, 3H), 2.69 (br s, 2H), 2.36-2.24 (m, 2H), 1.26-1.10 (m, 12H); 31P NMR (162 MHz, CD3CN) δ=149.94, 149.88.

Example 51: Synthesis of 5′ End Cap Monomer

Example 51 Monomer Synthesis Scheme

Preparation of (2): To a solution of 1(30 g, 101.07 mmol, 87% purity) in CH3CN (1.2 L) and Py (60 mL) were added I2 (33.35 g, 131.40 mmol, 26.47 mL) and PPh3 (37.11 g, 141.50 mmol) in one portion at 10° C. The reaction was stirred at 25° C. for another 48 h. The mixture was diluted with aq.Na2S203 (300 mL) and aq.NaHCO3(300 mL), concentrated to remove CH3CN, and then extracted with EtOAc (300 mL * 3). The combined organic layers were washed with brine (300 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 330 g SepaFlash@ Silica Flash Column, Eluent of 0.60%/Methanol/Dichloromethane gradient @ 100 mL/min) to give 2 (28.2 g, 72.00% yield, 95% purity) as a brown solid. ESI-LCMS: m/z 369.1 [M+H]+; 1H NMR (400 MHz, DMSO-d6) δ=11.43 (s, 1H), 7.68 (d, J=8.1 Hz, 1H), 5.86 (d, J=5.5 Hz, 1H), 5.69 (d, J=8.1 Hz, 1H), 5.46 (d, J=6.0 Hz, 1H), 4.08-3.96 (m, 2H), 3.90-3.81 (m, 1H), 3.60-3.51 (m, 1H), 3.40 (dd, J=6.9, 10.6 Hz, 1H), 3.34 (s, 3H).

Preparation of (3): To a solution of 2 in DMF (90 mL) were added imidazole (4.25 g, 62.48 mmol) and TBSCI (6.96 g, 46.18 mmol) in one portion at 15° C. The mixture was stirred at 15° C. for 6 h. The reaction mixture was quenched by addition of H2O (300 mL) and extracted with EtOAc (300 mL * 2). The combined organic layers were washed with brine (300 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give 3 (13.10 g, crude) as a white solid. ESI-LCMS: m/z 483.0 [M+H]+.

Preparation of (4): To a solution of 3 (10 g, 20.73 mmol) in MeOH (20 mL), H2O (80 mL), and dioxane (20 mL) was added Na2SO3 (15.68 g, 124.38 mmol), and the mixture was stirred at 80° C. for 24 h. The reaction mixture was concentrated under reduced pressure to remove MeOH. The aqueous layer was extracted with EtOAc (80 mL * 2) and concentrated under reduced pressure to give a residue. The residue was triturated with MeOH (100*3 mL) to give 4 (9.5 g, 94.48% yield, 90% purity) as a white solid. ESI-LCMS: m/z 437.0 [M+H]+.

Preparation of (5): To a solution of 4 (11 g, 21.42 mmol, 85% purity) in DCM (120 mL) was added DMF (469.65 mg, 6.43 mmol, 494.37 uL) at 0° C., followed by dropwise addition of oxalyl dichloride (13.59 g, 107.10 mmol, 9.37 mL). The mixture was stirred at 20° C. for 2 h. The reaction mixture was quenched by addition of water (60 mL) and the organic layer 5 (0.1125 M, 240 mL DCM) was used directly for next step. (This reaction was set up for two batches and combined) ESI-LCMS: m/z 455.0 [M+H]+.

Preparation of (6): 5 (186.4 mL, 0.1125 M in DCM) was diluted with DCM (60 mL) and treated with methylamine (3.26 g, 41.93 mmol, 40% purity). The mixture was stirred at 20° C. for 2 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 40 g SepaFlash@ Silica Flash Column, Eluent of 0˜10%, MeOH/DCM gradient @ 40 mL/min) to give AGS-9-3-008 (1.82 g, 18.53% yield, 96% purity) as a yellow solid. ESI-LCMS: m/z 472.0 [M+Na]+; 1H NMR (400 MHz, CDCl3) δ=9.08 (s, 1H), 7.31 (d, J=8.1 Hz, 1H), 5.78 (d, J=8.1 Hz, 1H), 5.57 (d, J=3.8 Hz, 1H), 4.61-4.48 (m, 1H), 4.41-4.27 (m, 2H), 4.13-4.03 (m, 1H), 3.46 (s, 3H), 3.43-3.33 (m, 2H), 2.78 (d, J=5.2 Hz, 3H), 0.92 (s, 9H), 0.13 (s, 6H).

Preparation of (7): To a solution of 6 (2.3 g, 5.12 mmol) in MeOH (12 mL) was added HCl/MeOH (4 M, 6.39 mL). The mixture was stirred at 20° C. for 2 h. The reaction mixture was concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 24 g SepaFlash@ Silica Flash Column, Eluent of 0-15%, MeOH/DCM gradient @ 30 mL/min) to give 7 (1.4 g, 79.98% yield) as a pink solid. ESI-LCMS: m/z 336.1 [M+H]+; 1H NMR (400 MHz, CDCl3) δ=9.12 (s, 1H), 7.39 (d, J=8.0 Hz, 1H), 5.79 (d, J=3.3 Hz, 1H), 5.66 (dd, J=2.1, 8.2 Hz, 1H), 5.13 (s, 1H), 4.13 (t, J=4.0, 7.4 Hz, 1H), 4.07-4.02 (m, 1H), 3.87 (dd, J=3.3, 5.5 Hz, 1H), 3.47 (s, 3H), 3.43-3.37 (m, 2H), 2.65 (d, J=4.5 Hz, 3H).

Preparation of (Example 51 monomer): To a mixture of 7 (1.7 g, 5.07 mmol) and 4A MS (1.4 g) in MeCN (18 mL) was added 3-bis(diisopropylamino)phosphanyloxypropanenitrile (1.99 g, 6.59 mmol, 2.09 mL) at 0° C., followed by addition of 1H-imidazole-4,5-dicarbonitrile (658.57 mg, 5.58 mmol) in one portion at 0° C. The mixture was stirred at 20° C. for 2 h. Upon completion, the reaction mixture was quenched by addition of sat. NaHCO3 solution (20 mL) and diluted with DCM (40 mL). The organic layer was washed with sat. NaHCO3(20 mL * 2), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue was purified by a flash silica gel column (0% to 5% i-PrOH in DCM with 5% TEA) to give Example 51 monomer (1.30 g, 46.68% yield) as a white solid. ESI-LCMS: m/z 536.2 [M+H]+; 1H NMR (400 MHz, CD3CN) δ=9.00 (s, 1H), 7.40 (d, J=8.0 Hz, 1H), 5.85-5.76 (m, 1H), 5.64 (d, J=8.0 Hz, 1H), 5.08 (d, J=5.0 Hz, 1H), 4.42-4.21 (m, 2H), 4.00 (td, J=4.6, 9.3 Hz, 1H), 3.89-3.61 (m, 4H), 3.47-3.40 (m, 4H), 3.37-3.22 (m, 1H), 2.71-2.60 (m, 5H), 1.21-1.16 (m, 11H), 1.21-1.16 (m, 1H); 31P NMR (162 MHz, CD3CN) δ=150.07, 149.97

Example 52: Synthesis of 5′ End Cap Monomer

Example 52 Monomer Synthesis Scheme

Preparation of (2): To a solution of 1(13.10 g, 27.16 mmol) in THF (100 mL) was added DBU (20.67 g, 135.78 mmol, 20.47 mL). The mixture was stirred at 60° C. for 6 h. Upon completion, the reaction mixture was quenched by addition of sat. NH4Cl solution (600 mL) and extracted with EA (600 mL * 2). The combined organic layers were washed with brine (100 ml), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO@; 120 g SepaFlash@ Silica Flash Column, Eluent of 0˜50% (Phase B: ethyl acetate: dichloromethane=1:1)/Phase A: petroleum ethergradient@ 45 mL/min) to give 2 (5.9 g, 60.1% yield,) as a white solid. ESI-LCMS: m/z 355.1 [M+H]+; 1H NMR (400 MHz, DMSO-d6) δ=11.61-11.30 (m, 1H), 7.76-7.51 (m, 1H), 6.04 (d, J=5.4 Hz, 1H), 5.75 (s, 1H), 5.73-5.67 (m, 1H), 4.78 (d, J=4.9 Hz, 1H), 4.41 (d, J=1.1 Hz, 1H), 4.30 (t, J=4.8 Hz, 1H), 4.22 (d, J=1.4 Hz, 1H), 4.13 (t, J=5.1 Hz, 1H), 4.06-3.97 (m, 1H), 3.94-3.89 (m, 1H), 3.82-3.75 (m, 1H), 3.33 (s, 3H), 3.30 (s, 2H), 1.17 (t, J=7.2 Hz, 1H), 0.89 (s, 9H), 0.16-0.09 (m, 6H).

Preparation of (3): To a solution of 2 (4 g, 11.28 mmol) in DCM (40 mL) was added Ru(II)-Pheox (214.12 mg, 338.53 umol) in one portion followed by addition of diazo(dimethoxyphosphoryl)methane (2.54 g, 16.93 mmol) dropwise at 0° C. under N2. The reaction was stirred at 20° C. for 16 h. Upon completion, the reaction mixture was filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 80 g SepaFlash@ Silica Flash Column, Eluent of 0-4% MeOH/DCM@ 60 mL/min) to give 3 (5 g, 86.47% yield) as a red liquid. ESI-LCMS: m/z 477.1 [M+H]+; 1H NMR (400 MHz, DMSO-d6) δ=11.46 (s, 1H), 7.49 (d, .,8.0 Hz, 1H), 6.01-5.87 (m, 1H), 5.75 (dd, J=2.0, 8.0 Hz, 1H), 4.58 (d, .,3.8 Hz, 1H), 4.23 (dd, J=3.8, 7.8 Hz, 1H), 3.80-3.68 (m, 6H), 3.30 (s, 3H), 1.65-1.46 (m, 2H), 1.28-1.16 (m, 1H), 0.91 (s, 9H), 0.10 (d, J=4.3 Hz, 6H); 31P NMR (162 MHz, DMSO-d6) δ=27.5

Preparation of (4): To a mixture of 3 (2.8 g, 5.88 mmol) and NaI (1.76 g, 11.75 mmol) in CH3CN (30 mL) was added chloromethyl 2,2-dimethylpropanoate (2.21 g, 14.69 mmol, 2.13 mL) at 25° C. The mixture was stirred at 80° C. for 40 h under Ar. The reaction mixture was filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 40 g SepaFlash@ Silica Flash Column, Eluent of 0˜50% Ethylacetate/Petroleum ether gradient @ 40 mL/min) to give 4 (2.1 g, 51.23% yield, 97% purity) as a yellow solid. ESI-LCMS: 677.3 [M+H]+.

Preparation of (5): A mixture of 4 (2.09 g, 3.09 mmol) in H2O (1.5 mL) and HCOOH (741.81 mg, 15.44 mmol, 6 mL) was stirred at 15° C. for 40 h. Upon completion, the reaction mixture was quenched by saturated aq.NaHCO3(300 mL) and extracted with EA (300 mL * 2). The combined organic layers were washed with brine (300 mL), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 20 g SepaFlash® Silica Flash Column, Eluent of 0-5% Methanol/Dichloromethane@ 45 mL/min) to give 5 (1.51 g, 85.19% yield) as a yellow solid. ESI-LCMS: 585.1 [M+Na]+; 1H NMR (400 MHz, DMSO-d6) δ=11.45 (d, J=1.8 Hz, 1H), 7.44 (d, J=8.2 Hz, 1H), 6.04 (d, J=7.5 Hz, 1H), 5.78-5.51 (m, 6H), 4.39 (t, J=4.4 Hz, 1H), 4.15 (dd, J=4.3, 7.4 Hz, 1H), 4.03 (q, J=7.1 Hz, 1H),1.99 (s, 1H), 1.66 (dd, J=8.6, 10.8 Hz, 1H), 1.55-1.29 (m, 2H), 1.18 (d, J=2.0 Hz, 18H).

Preparation of (Example 52 monomer): To a solution of 5 (2.5 g, 4.44 mmol) in MeCN (30 mL) was added 3-bis(diisopropylamino)phosphanyloxypropanenitrile (1.74 g, 5.78 mmol, 1.84 mL) at 0° C., followed by 1H-imidazole-4,5-dicarbonitrile (577.36 mg, 4.89 mmol) in one portion under Ar. The mixture was gradually warmed to 20° C. and stirred at 20° C. for 1 h. The reaction mixture was quenched by addition of sat. NaHCO3 solution (50 mL) and diluted with DCM (250 mL). The organic layer was washed with sat. NaHCO3 solution (50 mL * 2), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue was purified by a flash silica gel column (0% to 50% EA/PE with 0.5% TEA) to give Example 52 monomer (1.85 g, 54.1% yield) as a white solid. ESI-LCMS: 785.2 [M+Na]+;1H NMR (400 MHz, CD3CN) δ=9.18 (s, 1H), 7.31 (d, J=8.3 Hz, 1H), 6.06 (d, J=7.8 Hz, 1H), 5.72-5.60 (m, 5H), 4.85-4.76 (m, 1H), 4.27 (m, 1H), 3.93-3.64 (m, 4H), 3.41 (d, J=16.6 Hz, 3H), 2.80-2.62 (m, 2H), 1.76-1.49 (m, 3H), 1.23-1.19 (m, 30H); 31P NMR (162 MHz, CD3CN) δ=150.66 (s), 150.30, 24.77, 24.66.

Example 53: Synthesis of 5′ End Cap Monomer

Example 53 Monomer Synthesis Scheme

Preparation of (2): To a solution of 1 (15 g, 137.43 mmol) in DCM (75 mL) were added Boc2O (31.49 g, 144.30 mmol, 33.15 mL) and DMAP (839.47 mg, 6.87 mmol, 0.05 eq) at 0° C. The mixture was stirred at 20° C. for 16 hr, and concentrated under reduced pressure to give 2 (29.9 g, crude) as a yellow oil. 1H NMR (400 MHz, CDCl3) δ=3.23 (s, 3H), 3.16 (s, 3H), 1.51 (s, 9H).

Preparation of (3): To a solution of 2 (24.9 g, 118.99 mmol) in THF (250 mL) was added n-BuLi (2.5 M, 47.60 mL) dropwise at −78° C. under Ar and stirred at −78° C. for 1 hr. P-3 (17.19 g, 118.99 mmol, 12.83 mL) was added at 0° C. and stirred for 1 hr. The reaction mixture was quenched by saturated aq. NH4Cl (100 mL), and then extracted with EA (100 mL*2). The combined organic layers were washed with brine (100 mL*2), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 80 g SepaFlash® Silica Flash Column, Eluent of 0-50% Ethylacetate/Petroleum ethergradient @ 65 mL/min) to give 3 (7.1 g, 18.62% yield) as a yellow oil. ESI-LCMS: 339.9 [M+Na]+, NMR (400 MHz, CDCl3) δ=4.12 (s, 1H), 4.08 (s, 1H), 3.83 (s, 3H), 3.81 (s, 3H), 3.22 (s, 3H), 1.51 (s, 9H).

Preparation of (5): To a mixture of 4 (15 g, 40.27 mmol) and PPTS (10.12 g, 40.27 mmol) in DMSO (75 mL) was added EDCI (23.16 g, 120.81 mmol) at 20° C. The mixture was stirred at 20° C. for 4 hr. The reaction mixture was diluted with water (150 mL) and extracted with EA (150 mL*2). The combined organic layers were washed with brine (150 mL*2), dried over Na2SO4, filtered and concentrated under reduced pressure to give 5 (12 g, crude) as a white solid. ESI-LCMS: 371.2[M+H]+; 1H NMR (400 MHz, CDCl3) δ=9.77 (s, 1H), 7.62 (d, J=8.1 Hz, 1H), 5.83-5.76 (m, 2H), 4.53 (d, J=4.3 Hz, 1H), 4.43 (br t, J=4.4 Hz, 1H), 3.95 (br t, J=4.7 Hz, 1H), 3.47-3.35 (m, 5H), 0.92 (s, 9H), 0.13 (d, J=5.8 Hz, 6H).

Preparation of (6): To a solution of P4 (8.02 g, 25.27 mmol) in THF (40 mL) was added n-BuLi (2.5 M, 8.42 mL) dropwise under Ar at −78° C., and the mixture was stirred at −78° C. for 0.5 hr. A solution of 4 (7.8 g, 21.05 mmol) in THF (40 mL) was added dropwise. The mixture was allowed to warm to 0° C. and stirred for another 2 hr. The reaction mixture was quenched by saturated aq. NH4Cl solution (80 mL) and extracted with EA (80 mL). The combined organic layers were washed with brine (80 mL * 2), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 80 g SepaFlash@ Silica Flash Column, Eluent of 0-38% ethylacetate/petroleum ether gradient @ 60 mL/min) to give 7 (7.7 g, 13.43 mmol, 63.8% yield) as a white solid. ESI-LCMS: 506.2 [M-tBu]+; 1H NMR (400 MHz, CDCl3) δ=8.97 (s, 1H), 7.25 (d, J=8.3 Hz, 1H), 6.95-6.88 (m, 1H), 6.87-6.81 (m, 1H), 5.83-5.77 (m, 2H), 4.58 (dd, J=4.4, 6.7 Hz, 1H), 4.05 (dd, J=5.0, 7.5 Hz, 1H), 3.82-3.77 (m, 1H), 3.53 (s, 3H), 3.20 (s, 3H), 1.50 (s, 9H), 0.91 (s, 9H), 0.11 (d, J=2.5 Hz, 6H).

Preparation of (7): To a solution of 6 (7.7 g, 13.71 mmol) in MeOH (10 mL) was added HCl/MeOH (4 M, 51.40 mL) at 20° C. The mixture was stirred at 20° C. for 16 hr. Upon completion, the reaction mixture was concentrated under reduced pressure to remove MeOH. The residue was purified by flash silica gel chromatography (ISCO®; 80 g SepaFlash@ Silica Flash Column, Eluent of 0-4% MeOH/DCM @ 60 mL/min) to give 7 (4.1 g, 86.11% yield) as a white solid. ESI-LCMS: 369.9 [M+Na]+; 1H NMR (400 MHz, DMSO-d6) δ=11.44 (s, 1H), 7.66 (d, J=8.3 Hz, 1H), 7.11 (q, J=4.9 Hz, 1H), 6.69 (dd, J=6.0, 15.1 Hz, 1H), 6.56-6.47 (m, 1H), 5.82 (d, J=4.0 Hz, 1H), 5.67 (dd, J=2.0, 8.0 Hz, 1H), 5.56 (br s, 1H), 4.42 (t, J=6.1 Hz, 1H), 4.13 (t, J=5.8 Hz, 1H), 3.97 (t, J=4.8 Hz, 1H), 3.39 (s, 3H), 2.48 (d, J=5.3 Hz, 3H)

Preparation of (8): To a solution of 7 (2.5 g, 7.20 mmol) in THF (25 mL) was added Pd/C (2.5 g, 10% purity) under H2 atmosphere, and the suspension was degassed and purged with H2 for 3 times. The mixture was stirred under H2 (15 Psi) at 20° C. for 1 hr. Upon completion, the reaction mixture was filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 25 g SepaFlash@ Silica Flash Column, Eluent of 0-5% Ethylacetate/Petroleum ethergradient @ 50 mL/min) to give 8 (2.2 g, 87.49% yield,) as a white solid. ESI-LCMS: 372.1 [M+Na]+; 1H NMR (400 MHz, DMSO-d6) δ=11.40 (s, 1H), 7.62 (d, J=8.0 Hz, 1H), 6.93 (q, J=4.9 Hz, 1H), 5.76 (d, J=4.5 Hz, 1H), 5.66 (d, J=8.0 Hz, 1H), 5.26 (d, J=6.3 Hz, 1H), 3.97 (q, J=5.9 Hz, 1H), 3.91-3.79 (m, 2H), 3.36 (s, 3H), 3.14-3.00 (m, 2H), 2.56 (d, J=5.0 Hz, 3H), 2.07-1.87 (m, 2H).

Preparation of (Example 53 monomer): To a solution of 8 (2.2 g, 6.30 mmol, 1 eq) in CH3CN (25 mL) was added P-1 (2.47 g, 8.19 mmol, 2.60 mL, 1.3 eq) at 0° C., and then 1H-imidazole-4,5-dicarbonitrile (818.07 mg, 6.93 mmol, 1.1 eq) was added in one portion at 0° C. under Ar. The mixture was stirred at 20° C. for 2 hr. Upon completion, the reaction mixture was quenched by saturated aq. NaHCO3(25 mL), and extracted with DCM (25 mL * 2). The combined organic layers were washed with brine (25 mL * 2), dried over Na2SO4, filtered and concentrated under reduced pressure to give a residue. The residue was purified by flash silica gel chromatography (ISCO®; 40 g SepaFlash@ Silica Flash Column, Eluent of 40-85% ethylacetate/petroleum ether gradient @ 40 mL/min) to give Example 53 monomer (2.15 g, 61.32% yield) as a white solid. ESI-LCMS: 572.2 [M+Na]+;1H NMR (400 MHz, CD3CN) δ=9.32 (br s, 1H), 7.39 (d, J=8.1 Hz, 1H), 5.82-5.75 (m, 1H), 5.66 (dd, J=0.7, 8.1 Hz, 1H), 5.14 (qd, J=4.9, 9.4 Hz, 1H), 4.24-4.02 (m, 2H), 3.99-3.93 (m, 1H), 3.90-3.60 (m, 4H), 3.43 (d, J=17.5 Hz, 3H), 3.18-3.08 (m, 2H), 2.74-2.61 (m, 5H), 2.19-2.11 (m, 1H), 2.09-1.98 (m, 1H), 1.19 (ddd, J=2.4, 4.0, 6.6 Hz, 12H).31P NMR (162 MHz, CD3CN) δ=149.77 (s), 149.63 (br s).

Example 54. Long-Term Efficacy of siNA in an AAV-HBV Mouse Model

AAV/HBV is a recombinant AAV carrying replicable HBV genome. Taking advantage of the highly hepatotropic feature of genotype 8 AAV, the HBV genome can be efficiently delivered to the mouse liver cells. Infection of immune competent mouse with AAV/HBV can result in long term HBV viremia, which mimics chronic HBV infection in patients. The AAV/HBV model can be used to evaluate the in vivo activity of various types of anti-HBV agents. Mice were infected with AAV-HBV on day −28 of the study. AAV-HBV mice were subcutaneously injected with a single dose of 5 mL/kg of vehicle or 5 mg/kg of ds-siNA-0147 on day 0. Serial blood collections were usually taken every 5 days on day 0, 5, 10, and 15, etc. until the termination of the study. Serum HBV S antigen (HBsAg) was assayed through ELISA. FIG. 13 shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G 15) or ds-siNA-0147 (G 19). As shown in FIG. 13, ds-siNA-0147 was effective in reducing serum HBsAg levels and the reduction in serum HBsAg levels was observed for the duration of the study (i.e., 100 days). Thus, FIG. 13 demonstrates that ds-siNA-0147 is effective and durable after a single dose of 5 mg/kg.

ds-siNA SEQ ID Strand Sequence ID NO: ds-siNA- Sense 5′-mGpsmUpsmGmGfUmGfGfAfCm 438 0147 UmUmCmUmCmUmCmAmAmU-p-ps2- GalNAc4-3′ Antisense 3′-mApsmGpsmCmAmCfCmAfCmCm 501 UmGmAmAmGmAfGmAmGmUpsfUpsm A-5′

Example 55. Deuterated Vinyl Phosphonate Improves Potency of siNA

This example investigates whether a deuterated vinyl phosphonate improves potency of siNA in an AAV-HBV mouse. AAV-HBV mice were subcutaneously injected with vehicle, ds-siNA-0109 (e.g., siNA without a deuterated vinyl phosphonate), or ds-siNA-0172 (e.g., siNA with a deuterated vinyl phosphonate). AAV-HBV mice were subcutaneously injected with a single dose of 5 mL/kg of vehicle or 5 mg/kg of ds-siNA-0149 or ds-siNA-0172 at day 0. Serial blood collections were usually taken every 5 days on day 0, 5, 10, and 15, etc. until the termination of the study. Serum HBV S antigen (HBsAg) was assayed through ELISA.

As shown in FIG. 14, siNA molecules having 2′-fluoro nucleotides at positions 5 and 7-9 from the 5′ end of the sense strand and 2′-fluoro nucleotides at positions 2, 5, 8, 14, and 17 from the 5′ end of the antisense strand resulted in greater than a 0.5-log reduction in HBsAg, with the greatest reduction in HBsAg found in mice treated with the deuterated vinylphopshonate siNA (ds-siNA-0172). In addition, the duration of the reduction in serum HBsAg levels was significantly longer for the deuterated vinylphosphonate siNA (ds-siNA-0172). Thus, FIG. 14 demonstrates that the presence of a deuterated vinyl phosphonate improves potency and durability of the siNA.

ds-siNA SEQ ID ID Strand Sequence NO: ds-siNA- Sense 5′-mCpsmCpsmGmUfGmUfGfCfAmCmUmUmCmGmC 424 0109 mUmUmCmAp-ps2-GalNAc4 Antisense 3′-mCpsmUpsmGmGfCmAmCfAmCmGmUmGmAfAmG 485 mCfGmAmApsfGpsmU-5′ ds-siNA- Sense 5′-mCpsmCpsmGmUfGmUfGfCfAmCmUmUmCmGmC 424 0172 mUmUmCmA-p-ps2-GalNAc4-3′ Antisense 3′-mCpsmUpsmGmGfCmAmCfAmCmGmUmGmAfAmG 536 mCfGmAmApsfGpsd2vd3U-5′ d2vd3U =

Example 56. Comparison of siNAs

AAV/HBV is a recombinant AAV carrying replicable HBV genome. Taking advantage of the highly hepatotropic feature of genotype 8 AAV, the HBV genome can be efficiently delivered to the mouse liver cells. Infection of immune competent mouse with AAV/HBV can result in long term HBV viremia, which mimics chronic HBV infection in patients. The AAV/HBV model can be used to evaluate the in vivo activity of various types of anti-HBV agents. Mice were infected with AAV-HBV on day −28 of the study. AAV-HBV mice were subcutaneously injected with a single dose of 5 mL/kg of vehicle or 5 mg/kg of ds-siNA-0109, ds-siNA-0119, or ds-siNA-0153 on day 0. Serial blood collections were usually taken every 5 days on day 0, 5, 10, and 15, etc. until the termination of the study. Serum HBV S antigen (HBsAg) was assayed through ELISA. FIG. 15 shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G 01, circle), ds-siNA-0109 (G 07, square), ds-siNA-0119 (G11, triangle), or ds-siNA-0153 (G13, diamond). As shown in FIG. 14, all three ds-siNAs were effective in reducing serum HBsAg levels and the reduction in serum HBsAg levels was observed for the duration of the study (i.e., 100 days), with the best potency and durability observed for ds-siNA-0153. Thus, FIG. 15 demonstrates that ds-siNA-0109, ds-siNA-0119, and ds-siNA-0153 were effective and durable after a single dose of 5 mg/kg.

ds-siNA SEQ ID Strand Sequence ID NO: ds-siNA- Sense 5′-mCpsmCpsmGmUfGmUfGfCfAm 424 0109 CmUmUmCmGmCmUmUmCmAp-ps2- GalNAc4 Antisense 3′-mCpsmUpsmGmGfCmAmCfAmCm 485 GmUmGmAfAmGmCfGmAmApsfGpsm U-5′ ds-siNA- Sense 5′-mGpsmCpsmUmGfCmUmAmUfGf 430 0119 CfCmUmCfAmUmCmUmUfCmUmU- p-ps2-GalNAc4 Antisense 3′-mGpsmApsmCmGmAmCmGmAmUf 595 AmCmGmGmAmGmUmAmGmAmAmGpsf ApsmA-5′ ds-siNA- Sense 5′-mUpsmGpsfUmGmCmAfCfUfUm 441 0153 CmGfCmUmUmCmAfCmCmU-p-ps2- GalNAc4-3′ Antisense 3′-mGpsmCpsmAfCmAmCmGfUmGm 526 AmAfGmCmGmAfAmGmUmGpsfGpsm A-5

Example 57. Efficacy of a Combination Therapy in AAV-HBV Mouse Model

This example investigates the efficacy of a combination therapy comprising an antisense oligonucleotide (ASO 1, 5′ GalNAc4-ps-GalNAc4-ps-GalNAc4-po-mA-po-lnGpslnApslnTpslnApslnApsApsAps(50H)CpsGps(5 m)Cps(5 m)CpsGps(5 m)CpslnApslnG pslnApscp(5 m)C-3′(SEQ ID NO: 534)) and a ds-siNA-0147 for treating HBV in an AAV-HBV mouse model.

AAV-HBV mice were subcutaneously injected with (a) 5 mL/kg of vehicle, three times a week, on days 0, 7, and 14 (G 01); (b) 5 mg/kg of ASO 1 on a weekly basis, on days 0, 7, and 14 (G 20); (c) a single dose of 5 mg/kg of ds-siNA-0147 on day 0 (G 24); or (d) a combination of ASO 1 and ds-siNA-0147, wherein ASO 1 was administered at a dose of 5 mg/kg on a weekly basis, on days 0, 7, and 14; and ds-siNA-0160 was administered as a single dose of 5 mg/kg at day 0 (G25). Serial blood collections were usually taken every 5 days on day 0, 5, 10, and 15, etc. until the termination of the study. Serum HBV S antigen (HBsAg) was assayed through ELISA. FIG. 16 shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G 01, circle), ASO 1 (G 20, square), ds-siNA-0147 (G 24, diamond), or a combination of ds-siNA-0147 and ASO 1 (G 25, triangle). As shown in FIG. 16, treatment with ASO 1, ds-siNA-0147, or a combination of ASO 1 and ds-siNA-0147 resulted in a reduction in serum, with the greatest reduction observed in mice treated with the combination of ASO 1 and ds-siNA-0147.

ds-siNA SEQ ID Strand Sequence ID NO: ds-siNA- Sense 5′-mGpsmUpsmGmGfUmGfGfAf 438 0147 CmUmUmCmUmCmUmCmAmAmU-p- ps2-GalNAc4-3′ Anti- 3′-mApsmGpsmCmAmCfCmAfCm 501 sense CmUmGmAmAmGmAfGmAmGmUpsf UpsmA-5′

Example 58. Efficacy of a Combination Therapy in AAV-HBV Mouse Model

This example investigates the efficacy of a combination therapy comprising an antisense oligonucleotide (ASO 1, 5′ GalNAc4-ps-GalNAc4-ps-GalNAc4-po-mA-po-lnGpslnApslnTpslnApslnApsApsAps(50H)CpsGps(5 m)Cps(5 m)CpsGps(5 m)CpslnApslnG pslnApscp(5 m)C-3′(SEQ ID NO: 534)) and a ds-siNA-0109 for treating HBV in an AAV-HBV mouse model.

AAV-HBV mice were subcutaneously injected with (a) 5 mL/kg of vehicle, three times a week, on days 0, 7, and 14 (G 01); (b) 5 mg/kg of ASO 1 on a weekly basis, on days 0, 7, and 14 (G 20); (c) a single dose of 5 mg/kg of ds-siNA-0109 on day 0 (G 26); or (d) a combination of ASO 1 and ds-siNA-0109, wherein ASO 1 was administered at a dose of 5 mg/kg on a weekly basis, on days 0, 7, and 14; and ds-siNA-0160 was administered as a single dose of 5 mg/kg at day 0 (G27). Serial blood collections were usually taken every 5 days on day 0, 5, 10, and 15, etc. until the termination of the study. Serum HBV S antigen (HBsAg) was assayed through ELISA. FIG. 17 shows a graph of the change in serum HBsAg from AAV-HBV mice treated with vehicle (G 01, circle), ASO 1 (G 20, square), ds-siNA-0109 (G 26, diamond), or a combination of ds-siNA-0109 and ASO 1 (G 27, triangle). As shown in FIG. 17, treatment with ASO 1, ds-siNA-0109, or a combination of ASO 1 and ds-siNA-0109 resulted in a reduction in serum, with the greatest reduction observed in mice treated with the combination of ASO 1 and ds-siNA-0109.

ds-siNA SEQ ID Strand Sequence ID NO: ds-siNA- Sense 5′-mCpsmCpsmGmUfGmUfGfCf 424 0109 AmCmUmUmCmGmCmUmUmCmAp- ps2-GalNAc4 Antisense 3′-mCpsmUpsmGmGfCmAmCfAm 485 CmGmUmGmAfAmGmCfGmAmApsf GpsmU-5′

Example 59. Role of 2′-Fluoro Mimics on siNA Activity

This example investigates the role of 2′-fluoro mimics, f4P and f2P monomers, on siNA activity. The f4P monomer was produced as described in Example 42. The f2P monomer was produced as described in Example 45.

The activity of ds-siNA-0173, ds-siNA-0174, and ds-siNA-0175 was assayed using an in vitro HBsAg secretion assay with HepG2.2.15 cells. Generally, HepG2.2.15 cells were maintained in DMEM medium with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin, 1% Glutamine, 1% non-essential amino acids, 1% Sodium Pyruvate and 250 ug/ml G418. Cells were maintained at 37° C. in a 5% CO2 atmosphere. For HBsAg release assay, an assay medium was made that DMEM with 5% FBS, 1% penicillin/streptomycin, 1% Glutamine and 1% DMSO. The day before the assay, HepG2.2.15 cells were trypsinized and washed with Assay Medium once, then spun at 250 g×5 min, resuspended with Assay Medium. The resuspenced cells were seeded at 50,000/well in assay medium in collagen coated 96 well plates. On the next day, siRNA was diluted with Opti-MEM, 9-pt, 3-fold dilution and dilute Lipofectamine RNAiMAX (Invitrogen) according manufacturer's manual. siRNA dilution and RNAiMAX dilution were mixed and incubated at room temperature for 5 minutes. 15 μl of the siRNA/RNAiMax mixture was added each well of the collagen coated 96 well plate. The plates were placed in a 37° C., 5% CO2 incubator for 4 days. After incubation, the supernatant was harvested and measured for HBsAg with ELISA kit (Diasino). The cell viability was measured with CellTiter-Glo (Promega). The EC50, the concentration of the drug required for reducing HBsAg secretion by 50% in relation to the untreated cell control, was calculated using the Prism Graphpad. The CC50, the concentration of the drug required for reducing cell viability by 50% in relation to the untreated cell control, was calculated with the same software. The EC50 and CC50 values are shown in Table 11.

TABLE 11 siNA Activity ds-siNA SEQ ID EC50 CC50 ID Strand Sequence NO: (nM)* (nM) ds-siNA- Sense 5′-mGpsmUpsmGmGfUmGfGfAfC 438 C >1 0173 mUmUmCmUmCmUmCmAmAmU Antisense 3′-mApsmGpsmCmAmCfCmA 537 fCmCmUmGmAmAmGmAfGmAmG mUpsf4PpsmA-5′ ds-siNA- Sense 5′-mGpsmUpsmGmGfUmGfGfAfC 438 A >1 0174 mUmUmCmUmCmUmCmAmAmU Antisense 3′-mApsmGpsmCmAmCfCmAf2P 538 mCmUmGmAmAmGmAfGmAmGm UpsfUpsmA-5′ ds-siNA- Sense 5′-mGpsmUpsmGmGfUmGfGfAfC 438 B >1 0175 mUmUmCmUmCmUmCmAmAmU (control) Antisense 5′-mApsfUpsmUmGmAfGmAmG 501 mAmAmGmUmCfCmAfCmCmAmC psmGpsmA-3′ *A = EC50 < 0.2 nM; B = 0.2 nM < EC50 < 0.1 nm; C = EC50 > 0.1 nm f4P = f2P =

Example 60. Role of 2′-Fluoro Mimics on siNA Activity

This example investigates the role of 2′-fluoro mimics, f4P, f2P, and fx monomers, on siNA activity of Ga1NAc4 conjugated siNAs. The f4P monomer was produced as described in Example 42. The f2P monomer was produced as described in Example 45. The fx monomer was produced as described in Example 41.

ds-siNA SEQ ID ID Strand Sequence NO: ds-siNA- Sense 5′-mGpsmUpsmGmGfUmGfGfAfCmUmUmCmUmCmU 438 0176 mCmAmAmU-p-(PS)2-GalNAc4 Antisense 3′-mApsmGpsmCmAmCfCmAfCmCmUmGmAmAmGmA 537 fGmAmGmUpsf4PpsmA-5′ ds-siNA- Sense 5′-mGpsmUpsmGmGfUmGfGfAfCmUmUmCmUmCmU 438 0177 mCmAmAmU-p-(PS)2-GalNAc4 Antisense 3′-mApsmGpsmCmAmCfCmAf2PmCmUmGmAmAmGm 538 AfGmAmGmUpsfUpsmA-5′ ds-siNA- Sense 5′-mGpsmUpsmGmGfUmGfGfAfCmUmUmCmUmCmU 438 0178 mCmAmAmU-p-(PS)2-GalNAc4 Antisense 3′-mApsmGpsmCmAmCfCmAfXmCmUmGmAmAmG 539 mAfGmAmGmUpsfUpsmA-5′ ds-siNA- Sense 5′-mGpsmUpsmGmGfUmGfGfAfCmUmUmCmUmCmU 438 0147 mCmAmAmU-p-ps2-GalNAc4 Antisense 3′-mApsmGpsmCmAmCfCmAfCmCmUmGmAmAmG 501 mAfGmAmGmUpsfUpsmA-5′ f4P = f2P = fX =

The activity of ds-siNA-017, ds-siNA-017, ds-siNA-017, and ds-siNA-0147 can be assayed using in vitro or in vivo methods. An exemplary in vitro assay can be performed as follows:

Homo sapiens HepG2.2.15 cells are cultured in Dulbecco's Modified Eagle's Medium (DMEM) (ATCC 30-2002) supplemented to also contain 10% fetal calf serum (FCS). Cells were incubated at 37° C. in an atmosphere with 5% CO2 in a humidified incubator. For transfection of HepG2.2.15 cells with HBV targeting siRNAs, cells are seeded at a density of 15000 cells/well in 96-well regular tissue culture plates. Transfection of cells is carried out using RNAiMAX (Invitrogen/Life Technologies) according to the manufacturer's instructions. Dose-response experiments are done with oligo concentrations of 40, 20, 10, 5, 2.5, 1.25, 0.625, 0.3125, 0.15625 and 0.07813 nM. For each HBV targeting siRNA treatment (e.g., ds-siNA-0176, ds-siNA-0177, ds-siNA-0178, or ds-siNA-0147), four wells are transfected in parallel, and individual data points were collected from each well. After 24 h of incubation with siRNA, media is removed, and cells are lysed and analyzed with a QuantiGene2.0 branched DNA (bDNA) probe set specific for HBV genotype D (also called Hepatitis B virus subtype ayw, complete genome of 3182 base-pairs) as present in cell line HepG2.2.15.

For each well, the HBV on-target mRNA levels is normalized to the GAPDH mRNA level. The activity of the HBV targeting ds-siNAs can be expressed as EC50, 50% reduction of normalized HBV RNA level from no drug control. The cytotoxicity of the HBV targeting ds-siRNAs can be expressed by CC50 of 50% reduction of GAPDH mRNA from no drug control.

The AAV/HBV model can be used to evaluate the in vivo activity of the siRNA treatment (e.g., ds-siNA-0173, ds-siNA-0174, ds-siNA-0175, and ds-siNA-0147). Mice are infected with AAV-HBV on day −28 of the study. AAV-HBV mice are subcutaneously injected with a single dose of 5 mL/kg of vehicle or 5 mg/kg of ds-siNA-0173, ds-siNA-0174, ds-siNA-0175, or ds-siNA-0147 on day 0. Serial blood collections can be taken every 5 days on day 0, 5, 10, and 15, etc. until the termination of the study. Serum HBV S antigen (HBsAg) can be assayed through ELISA.

Exemplary Embodiments

Exemplary Embodiments are Provided Below:

1. A short interfering nucleic acid (siNA) molecule comprising:

    • (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence:
      • (i) is 15 to 30 nucleotides in length; and
      • (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and the nucleotide at position 3, 5, 7, 8, 9, 10, 11, 12, 14, 17, and/or 19 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide; and
    • (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence:
      • (i) is 15 to 30 nucleotides in length; and
      • (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide.

2. A short interfering nucleic acid (siNA) molecule comprising:

    • (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence:
      • (i) is 15 to 30 nucleotides in length; and
      • (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide; and
    • (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence:
      • (i) is 15 to 30 nucleotides in length; and
      • (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and the nucleotide at position 2, 5, 6, 8, 10, 14, 16, 17, and/or 18 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide.

3. The siNA of embodiment 1 or 2, wherein the first nucleotide sequence comprises 16, 17, 18, 19, 20, 21, 22, 23, or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide.

4. The siNA of embodiment 1 or 2, wherein 70%, 75%, 80%, 85%, 90%, 95% or 100% of the nucleotides in the first nucleotide sequence are modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide.

5. The siNA of any one of embodiments 1-4, wherein at least 2, 3, 4, 5, or 6 modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides.

6. The siNA of any one of embodiments 1-5, wherein no more than 10, 9, 8, 7, 6, 5, 4, 3, or 2 modified nucleotides of the first nucleotide sequence are 2′-fluoro nucleotides.

7. The siNA of any one of embodiments 1-6, wherein at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or 22 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides.

8. The siNA of any one of embodiments 1-7, wherein no more than 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, or 2 modified nucleotides of the first nucleotide sequence are 2′-O-methyl nucleotides.

9. The siRNA of any one of embodiments 1-8, wherein the second nucleotide sequence comprises 16, 17, 18, 19, 20, 21, 22, 23, or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide.

10. The siNA of any one of embodiments 1-9, wherein 70%, 75%, 80%, 85%, 90%, 95% or 100% of the nucleotides in the second nucleotide sequence are modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide.

11. The siNA of any one of embodiments 1-10, wherein at least 2, 3, 4, 5, or 6 modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides.

12. The siNA of any one of embodiments 1-11, wherein less than or equal to 10, 9, 8, 7, 6, 5, 4, 3, or 2 modified nucleotides of the second nucleotide sequence are 2′-fluoro nucleotides.

13. The siNA of any one of embodiments 1-12, wherein at least 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, or 22 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides.

14. The siNA of any one of embodiments 1-12, wherein less than or equal to 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, or 2 modified nucleotides of the second nucleotide sequence are 2′-O-methyl nucleotides.

15. A short interfering nucleic acid (siNA) molecule comprising:

    • (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence:
      • (i) is 15 to 30 nucleotides in length;
      • (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide; and
      • (iii) comprises 1 or more phosphorothioate internucleoside linkage; and
    • (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence:
      • (i) is 15 to 30 nucleotides in length;
      • (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide; and
      • (iii) comprises 1 or more phosphorothioate internucleoside linkage.

16. A short interfering nucleic acid (siNA) molecule comprising:

    • (a) a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence:
      • (i) is 15 to 30 nucleotides in length; and
      • (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide; and
    • (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence:
      • (i) is 15 to 30 nucleotides in length; and
      • (ii) comprises 15 or more modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, wherein at least one modified nucleotide is a 2′-O-methyl nucleotide and at least one modified nucleotide is a 2′-fluoro nucleotide,

wherein the siNA further comprises a phosphorylation blocker, a galactosamine, or 5′-stabilized end cap.

17. The siNA according to any preceding embodiment, wherein at least 1, 2, 3, 4, 5, 6, or 7 nucleotides at position 3, 5, 7, 8, 9, 10, 11, 12, and/or 17 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide.

18. The siNA according to any preceding embodiment, wherein the nucleotide at position 3 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide.

19. The siNA according to any preceding embodiment, wherein the nucleotide at position 5 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide.

20. The siNA according to any preceding embodiment, wherein the nucleotide at position 7 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide.

21. The siNA according to any preceding embodiment, wherein the nucleotide at position 8 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide.

22. The siNA according to any preceding embodiment, wherein the nucleotide at position 9 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide.

23. The siNA according to any preceding embodiment, wherein the nucleotide at position 12 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide.

24. The siNA according to any preceding embodiment, wherein the nucleotide at position 17 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide.

25. The siNA according to any preceding embodiment, wherein the nucleotide at position 10 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide.

26. The siNA according to any preceding embodiment, wherein the nucleotide at position 11 from the 5′ end of the first nucleotide sequence is a 2′-fluoro nucleotide.

27. The siNA according to any preceding embodiment, wherein at least 1, 2, 3, 4, 5, 6, 7, 8, or 9 nucleotides at position 2, 5, 6, 8, 10, 14, 16, 17, and/or 18 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide.

28. The siNA according to any preceding embodiment, wherein the nucleotide at position 2 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide.

29. The siNA according to any preceding embodiment, wherein the nucleotide at position 5 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide.

30. The siNA according to any preceding embodiment, wherein the nucleotide at position 6 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide.

31. The siNA according to any preceding embodiment, wherein the nucleotide at position 8 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide.

32. The siNA according to any preceding embodiment, wherein the nucleotide at position 10 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide.

33. The siNA according to any preceding embodiment, wherein the nucleotide at position 14 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide.

34. The siNA according to any preceding embodiment, wherein the nucleotides at position 16 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide.

35. The siNA according to any preceding embodiment, wherein the nucleotide at position 17 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide.

36. The siNA according to any preceding embodiment, wherein the nucleotide at position 18 from the 5′ end of the second nucleotide sequence is a 2′-fluoro nucleotide.

37. The siNA according to any preceding embodiment, wherein the nucleotides in the second nucleotide sequence are arranged in an alternating 1:3 modification pattern, and wherein 1 nucleotide is a 2′-fluoro nucleotide and 3 nucleotides are 2′-O-methyl nucleotides.

38. The siNA of embodiment 37, wherein the alternating 1:3 modification pattern occurs 2-5 times.

39. The siNA according to embodiment 37 or 38, wherein at least two of the alternating 1:3 modification pattern occur consecutively.

40. The siNA according to any of embodiments 37-39, wherein at least two of the alternating 1:3 modification pattern occurs nonconsecutively.

41. The siNA according to any of clams 37-40, wherein at least 1, 2, 3, 4, or 5 alternating 1:3 modification pattern begins at nucleotide position 2, 6, 10, 14, and/or 18 from the 5′ end of the antisense strand.

42. The siNA according to any of clams 37-41, wherein at least one alternating 1:3 modification pattern begins at nucleotide position 2 from the 5′ end of the antisense strand.

43. The siNA according to any of clams 37-42, wherein at least one alternating 1:3 modification pattern begins at nucleotide position 6 from the 5′ end of the antisense strand.

44. The siNA according to any of clams 37-43, wherein at least one alternating 1:3 modification pattern begins at nucleotide position 10 from the 5′ end of the antisense strand.

45. The siNA according to any of clams 37-44, wherein at least one alternating 1:3 modification pattern begins at nucleotide position 14 from the 5′ end of the antisense strand.

46. The siNA according to any of clams 37-45, wherein at least one alternating 1:3 modification pattern begins at nucleotide position 18 from the 5′ end of the antisense strand.

47. The siNA according to any one of embodiments 1-37, wherein the nucleotides in the second nucleotide sequence are arranged in an alternating 1:2 modification pattern, and wherein 1 nucleotide is a 2′-fluoro nucleotide and 2 nucleotides are 2′-O-methyl nucleotides.

48. The siNA of embodiment 47, wherein the alternating 1:2 modification pattern occurs 2-5 times.

49. The siNA according to embodiment 47 or 48, wherein at least two of the alternating 1:2 modification pattern occurs consecutively.

50. The siNA according to any of embodiments 47-49, wherein at least two of the alternating 1:2 modification pattern occurs nonconsecutively.

51. The siNA according to any of clams 47-50, wherein at least 1, 2, 3, 4, or 5 alternating 1:2 modification pattern begins at nucleotide position 2, 5, 8, 14, and/or 17 from the 5′ end of the antisense strand.

52. The siNA according to any of clams 47-51, wherein at least one alternating 1:2 modification pattern begins at nucleotide position 2 from the 5′ end of the antisense strand.

53. The siNA according to any of clams 47-52, wherein at least one alternating 1:2 modification pattern begins at nucleotide position 5 from the 5′ end of the antisense strand.

54. The siNA according to any of clams 47-53, wherein at least one alternating 1:2 modification pattern begins at nucleotide position 8 from the 5′ end of the antisense strand.

55. The siNA according to any of clams 47-54, wherein at least one alternating 1:2 modification pattern begins at nucleotide position 14 from the 5′ end of the antisense strand.

56. The siNA according to any of clams 47-55, wherein at least one alternating 1:2 modification pattern begins at nucleotide position 17 from the 5′ end of the antisense strand.

57. A short interfering nucleic acid (siNA) molecule represented by Formula (VIII): 5′-An1Bn2An3Bn4An5Bn6An7Bn8An9-3′ 3′-Cq1Aq2Bq3Aq4Bq5Aq6Bq7Aq8Bq9Aq10Bq11Aq12-5′ wherein:

    • the top strand is a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence comprises 15 to 30 nucleotides;
    • the bottom strand is an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence comprises 15 to 30 nucleotides;
    • each A is independently a 2′-O-methyl nucleotide or a nucleotide comprising a 5′-stabilized end cap or a phosphorylation blocker;
    • B is a 2′-fluoro nucleotide;
    • C represents overhanging nucleotides and is a 2′-O-methyl nucleotide;
    • n1=1-4 nucleotides in length;
    • each n2, n6, n8, q3, q5, q7, q9, q11, and q12 is independently 0-1 nucleotides in length;
    • each n3 and n4 is independently 1-3 nucleotides in length;
    • n5 is 1-10 nucleotides in length;
    • n7 is 0-4 nucleotides in length;
    • each n9, q1, and q2 is independently 0-2 nucleotides in length;
    • q4 is 0-3 nucleotides in length;
    • q6 is 0-5 nucleotides in length;
    • q8 is 2-7 nucleotides in length; and
    • q10 is 2-11 nucleotides in length.

58. A short interfering nucleic acid (siNA) molecule represented by Formula (IX):

5′-A2-4B1A1-3B2-3 A2-10B0-1A0-4B0-1A0-2-3′
3′-C2A0-2B0-1A0-3B0-1A0-5B0-1A2-7B1A2-11B1A1-5′ wherein:

    • the top strand is a sense strand comprising a first nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence comprises 15 to 30 nucleotides;
    • the bottom strand is an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence comprises 15 to 30 nucleotides;
    • each A is independently a 2′-O-methyl nucleotide or a nucleotide comprising a 5′-stabilized end cap or a phosphorylation blocker;
    • B is a 2′-fluoro nucleotide;
    • C represents overhanging nucleotides and is a 2′-O-methyl nucleotide.

59. A short interfering nucleic acid (siNA) molecule comprising

    • (a) a sense strand comprising a first nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 3, 7-9, 12, and 17 from the 5′ end of the first nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1, 2, 4-6, 10, 11, and 13-16 from the 5′ end of the first nucleotide sequence; and
    • (b) an antisense strand comprising a second nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 2 and 14 from the 5′ end of the second nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1, 3-13, and 15-17 from the 5′ end of the second nucleotide sequence.

60. The siNA molecule of embodiment 59, wherein the first nucleotide sequence consists of 19 nucleotides.

61. The siNA molecule of embodiment 60, wherein 2′-O-methyl nucleotides are at positions 18 and 19 from the 5′ end of the first nucleotide sequence.

62. The siNA molecule according to any one of embodiments 59-61, wherein the second nucleotide sequence consists of 21 nucleotides.

63. The siNA molecule of embodiment 62, wherein 2′-O-methyl nucleotides are at positions 18-21 from the 5′ end of the second nucleotide sequence.

64. A short interfering nucleic acid (siNA) molecule comprising

    • (a) a sense strand comprising a first nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 3, 7, 8, and 17 from the 5′ end of the first nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1, 2, 4-6, and 9-16 from the 5′ end of the first nucleotide sequence; and
    • (b) an antisense strand comprising a second nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 2 and 14 from the 5′ end of the first nucleotide sequence; and wherein 2′-O-methyl nucleotides are at positions 1, 3-13, and 15-17 from the 5′ end of the first nucleotide sequence.

65. The siNA molecule of embodiment 64, wherein the first nucleotide sequence consists of 19 nucleotides.

66. The siNA molecule of embodiment 65, wherein 2′-O-methyl nucleotides are at positions 18 and 19 from the 5′ end of the first nucleotide sequence.

67. The siNA molecule according to any one of embodiments 64-66, wherein the second nucleotide sequence consists of 21 nucleotides.

68. The siNA molecule of embodiment 67, wherein 2′-O-methyl nucleotides are at positions 18-21 from the 5′ end of the second nucleotide sequence.

69. A short interfering nucleic acid (siNA) molecule comprising

    • (a) a sense strand comprising a first nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 3, 7-9, 12 and 17 from the 5′ end of the first nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1, 2, 4-6, 10, 11, and 13-16 from the 5′ end of the first nucleotide sequence; and
    • (b) an antisense strand comprising a second nucleotide sequence consisting of 17 to 23 nucleotides, wherein the nucleotides in the second nucleotide sequence are arranged in an alternating 1:3 modification pattern, and wherein 1 nucleotide is a 2′-fluoro nucleotide and 3 nucleotides are 2′-O-methyl nucleotides.

70. The siNA molecule of embodiment 69, wherein the first nucleotide sequence consists of 19 nucleotides.

71. The siNA molecule of embodiment 70, wherein 2′-O-methyl nucleotides are at positions 18 and 19 from the 5′ end of the first nucleotide sequence.

72. The siNA molecule according to any one of embodiments 69-71, wherein the second nucleotide sequence consists of 21 nucleotides.

73. The siNA molecule of embodiment 72, wherein 2′-O-methyl nucleotides are at positions 19-21 from the 5′ end of the second nucleotide sequence.

74. The siRNA molecule according to any one of embodiments 69-73, wherein the alternating 1:3 modification pattern occurs 2-5 times.

75. The siRNA molecule according to any one of embodiments 69-74, wherein at least two of the alternating 1:3 modification pattern occur consecutively.

76. The siRNA molecule according to any one of embodiments 69-75, wherein at least two of the alternating 1:3 modification pattern occurs nonconsecutively.

77. The siNA according to any one of embodiments 69-76, wherein at least 1, 2, 3, 4, or 5 alternating 1:3 modification pattern begins at nucleotide position 2, 6, 10, 14, and/or 18 from the 5′ end of the antisense strand.

78. The siNA according to any one of embodiments 69-77, wherein at least one alternating 1:3 modification pattern begins at nucleotide position 2 from the 5′ end of the antisense strand.

79. The siNA according to any one of embodiments 69-78, wherein at least one alternating 1:3 modification pattern begins at nucleotide position 6 from the 5′ end of the antisense strand.

80. The siNA according to any one of embodiments 69-79, wherein at least one alternating 1:3 modification pattern begins at nucleotide position 10 from the 5′ end of the antisense strand.

81. The siNA according to any one of embodiments 69-80, wherein at least one alternating 1:3 modification pattern begins at nucleotide position 14 from the 5′ end of the antisense strand.

82. The siNA according to any one of embodiments 69-81, wherein at least one alternating 1:3 modification pattern begins at nucleotide position 18 from the 5′ end of the antisense strand.

83. A short interfering nucleic acid (siNA) molecule comprising

    • (a) a sense strand comprising a first nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 5 and 7-9 from the 5′ end of the first nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1-4, 6, and 10-17 from the 5′ end of the first nucleotide sequence; and
    • (b) an antisense strand comprising a second nucleotide sequence consisting of 17 to 23 nucleotides, wherein the nucleotides in the second nucleotide sequence are arranged in an alternating 1:3 modification pattern, and wherein 1 nucleotide is a 2′-fluoro nucleotide and 3 nucleotides are 2′-O-methyl nucleotides.

84. The siNA molecule of embodiment 83, wherein the first nucleotide sequence consists of 19 nucleotides.

85. The siNA molecule of embodiment 84, wherein 2′-O-methyl nucleotides are at positions 18 and 19 from the 5′ end of the first nucleotide sequence.

86. The siNA molecule according to any one of embodiments 83-85, wherein the second nucleotide sequence consists of 21 nucleotides.

87. The siNA molecule of embodiment 86, wherein 2′-O-methyl nucleotides are at positions 19-21 from the 5′ end of the second nucleotide sequence.

88. The siRNA molecule according to any one of embodiments 83-87, wherein the alternating 1:3 modification pattern occurs 2-5 times.

89. The siRNA molecule according to any one of embodiments 83-88, wherein at least two of the alternating 1:3 modification pattern occur consecutively.

90. The siRNA molecule according to any one of embodiments 83-89, wherein at least two of the alternating 1:3 modification pattern occurs nonconsecutively.

91. The siNA according to any one of embodiments 83-90, wherein at least 1, 2, 3, 4, or 5 alternating 1:3 modification pattern begins at nucleotide position 2, 6, 10, 14, and/or 18 from the 5′ end of the antisense strand.

92. The siNA according to any one of embodiments 83-91, wherein at least one alternating 1:3 modification pattern begins at nucleotide position 2 from the 5′ end of the antisense strand.

93. The siNA according to any one of embodiments 83-92, wherein at least one alternating 1:3 modification pattern begins at nucleotide position 6 from the 5′ end of the antisense strand.

94. The siNA according to any one of embodiments 83-93, wherein at least one alternating 1:3 modification pattern begins at nucleotide position 10 from the 5′ end of the antisense strand.

95. The siNA according to any one of embodiments 83-94, wherein at least one alternating 1:3 modification pattern begins at nucleotide position 14 from the 5′ end of the antisense strand.

96. The siNA according to any one of embodiments 83-95, wherein at least one alternating 1:3 modification pattern begins at nucleotide position 18 from the 5′ end of the antisense strand.

97. A short interfering nucleic acid (siNA) molecule comprising

    • (a) a sense strand comprising a first nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 5 and 7-9 from the 5′ end of the first nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1-4, 6, and 10-17 from the 5′ end of the first nucleotide sequence; and
    • (b) an antisense strand comprising a second nucleotide sequence consisting of 17 to 23 nucleotides, wherein the nucleotides in the second nucleotide sequence are arranged in an alternating 1:2 modification pattern, and wherein 1 nucleotide is a 2′-fluoro nucleotide and 2 nucleotides are 2′-O-methyl nucleotides.

98. The siNA molecule of embodiment 97, wherein the first nucleotide sequence consists of 19 nucleotides.

99. The siNA molecule of embodiment 98, wherein 2′-O-methyl nucleotides are at positions 18 and 19 from the 5′ end of the first nucleotide sequence.

100. The siNA molecule according to any one of embodiments 97-99, wherein the second nucleotide sequence consists of 21 nucleotides.

101. The siNA molecule of embodiment 100, wherein 2′-O-methyl nucleotides are at positions 18-21 from the 5′ end of the second nucleotide sequence.

102. The siRNA molecule according to any one of embodiments 97-101, wherein the alternating 1:2 modification pattern occurs 2-5 times.

103. The siRNA molecule according to any one of embodiments 97-102, wherein at least two of the alternating 1:2 modification pattern occur consecutively.

104. The siRNA molecule according to any one of embodiments 97-103, wherein at least two of the alternating 1:2 modification pattern occurs nonconsecutively.

105. The siNA according to any one of embodiments 97-104, wherein at least 1, 2, 3, 4, or 5 alternating 1:2 modification pattern begins at nucleotide position 2, 5, 8, 14, and/or 17 from the 5′ end of the antisense strand.

106. The siNA according to any one of embodiments 97-105, wherein at least one alternating 1:2 modification pattern begins at nucleotide position 2 from the 5′ end of the antisense strand.

107. The siNA according to any one of embodiments 97-106, wherein at least one alternating 1:2 modification pattern begins at nucleotide position 5 from the 5′ end of the antisense strand.

108. The siNA according to any one of embodiments 97-107, wherein at least one alternating 1:2 modification pattern begins at nucleotide position 8 from the 5′ end of the antisense strand.

109. The siNA according to any one of embodiments 74-85, wherein at least one alternating 1:2 modification pattern begins at nucleotide position 14 from the 5′ end of the antisense strand.

110. The siNA according to any one of embodiments 97-109, wherein at least one alternating 1:2 modification pattern begins at nucleotide position 17 from the 5′ end of the antisense strand.

111. A short interfering nucleic acid (siNA) molecule comprising

    • (a) a sense strand comprising a first nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 5 and 7-9 from the 5′ end of the first nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1-4, 6, and 10-17 from the 5′ end of the first nucleotide sequence; and
    • (b) an antisense strand comprising a second nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 2, 6, 14, and 16 from the 5′ end of the second nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1, 3-5, 7-13, 15, and 17 from the 5′ end the second nucleotide sequence.

112. The siNA molecule of embodiment 111, wherein the first nucleotide sequence consists of 19 nucleotides.

113. The siNA molecule of embodiment 112, wherein 2′-O-methyl nucleotides are at positions 18 and 19 from the 5′ end of the first nucleotide sequence.

114. The siNA molecule according to any one of embodiments 111-113, wherein the second nucleotide sequence consists of 21 nucleotides.

115. The siNA molecule of embodiment 114, wherein 2′-O-methyl nucleotides are at positions 18-21 from the 5′ end of the second nucleotide sequence.

116. A short interfering nucleic acid (siNA) molecule comprising:

    • (a) a sense strand comprising a first nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 5, 9-11, and 14 from the 5′ end of the first nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1-4, 6-8, and 12-17 from the 5′ end of the first nucleotide sequence; and
    • (b) an antisense strand comprising a second nucleotide sequence consisting of 17 to 23 nucleotides, wherein 2′-fluoro nucleotides are at positions 2 and 14 from the 5′ end of the second nucleotide sequence, and wherein 2′-O-methyl nucleotides are at positions 1, 3-13, and 15-17 from the 5′ end the second nucleotide sequence.

117. The siNA molecule of embodiment 116, wherein the first nucleotide sequence consists of 21 nucleotides.

118. The siNA molecule of embodiment 117, wherein 2′-O-methyl nucleotides are at positions 18-21 from the 5′ end of the first nucleotide sequence.

119. The siNA molecule according to any one of embodiments 116-118, wherein the second nucleotide sequence consists of 23 nucleotides.

120. The siNA molecule of embodiment 119, wherein 2′-O-methyl nucleotides are at positions 18-23 from the 5′ end of the second nucleotide sequence.

121. The siNA according to any preceding embodiment, wherein the sense strand further comprises TT sequence adjacent to the first nucleotide sequence.

122. The siNA according to any preceding embodiment, wherein the sense strand further comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more phosphorothioate internucleoside linkages.

123. The siNA of embodiment 122, wherein at least one phosphorothioate internucleoside linkage is between the nucleotides at positions 1 and 2 from the 5′ end of the first nucleotide sequence.

124. The siNA of embodiment 122 or 123, wherein at least one phosphorothioate internucleoside linkage is between the nucleotides at positions 2 and 3 from the 5′ end of the first nucleotide sequence.

125. The siNA according to any preceding embodiment, wherein the antisense strand further comprises TT sequence adjacent to the second nucleotide sequence.

126. The siNA according to any preceding embodiment, wherein the antisense strand further comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more phosphorothioate internucleoside linkages.

127. The siNA of embodiment 126, wherein at least one phosphorothioate internucleoside linkage is between the nucleotides at positions 1 and 2 from the 5′ end of the second nucleotide sequence.

128. The siNA of embodiment 126 or 127, wherein at least one phosphorothioate internucleoside linkage is between the nucleotides at positions 2 and 3 from the 5′ end of the second nucleotide sequence.

129. The siNA of any one of embodiments 126-128, wherein at least one phosphorothioate internucleoside linkage is between the nucleotides at positions 1 and 2 from the 3′ end of the second nucleotide sequence.

130. The siNA of any one of embodiments 126-129, wherein at least one phosphorothioate internucleoside linkage is between the nucleotides at positions 2 and 3 from the 3′ end of the second nucleotide sequence.

131. The siNA according to any preceding embodiment, wherein the first nucleotide from the 5′ end of the first nucleotide sequence comprises a 5′ stabilizing end cap.

132. The siNA according to any preceding embodiment, wherein the first nucleotide from the 5′ end of the second nucleotide sequence comprises a 5′ stabilizing end cap.

133. The siNA according to any preceding embodiment, wherein the first nucleotide from the 5′ end of the first nucleotide sequence comprises a phosphorylation blocker.

134. The siNA according to any preceding embodiment, wherein the first nucleotide from the 5′ end of the second nucleotide sequence comprises a phosphorylation blocker.

135. The siNA according to any preceding embodiment, wherein the first nucleotide sequence or second nucleotide sequence comprises at least one modified nucleotide selected from

where R is H or alkyl (or AmNA(N-Me)) when R is alkyl);

wherein B is a nucleobase.

136. A short-interfering nucleic acid (siNA) molecule comprising:

    • (a) a phosphorylation blocker of Formula (IV):

wherein

    • R1 is a nucleobase,
    • R4 is —θ-R30 or —NR31R32,
    • R30 is C1-C8 substituted or unsubstituted alkyl; and
    • R31 and R32 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring; and
    • (b) a short interfering nucleic acid (siNA).

137. A short-interfering nucleic acid (siNA) molecule comprising:

    • (a) a 5′-stabilized end cap of Formula (Ia):

wherein

    • R1 is a nucleobase, aryl, heteroaryl, or H,
    • R2 is

—CH═CD-Z, —CD=CH-Z, —CD=CD-Z, —(CR21R22)n-Z, or —(C2-C6 alkenylene)-Z and R20 is hydrogen; or

    • R2 and R20 together form a 3- to 7-membered carbocyclic ring substituted with —(CR21R22)n-Z or —(C2-C6 alkenylene)-Z;
    • n is 1, 2, 3, or 4;
    • Z is —ONR23R24, —OP(O)OH(CH2)mCO2R23, —OP(S)OH(CH2)mCO2R21, —P(O)(OH)2, —P(O)(OH)(OCH3), —P(O)(OH)(OCD3), —SO2(CH2)mP(O)(OH)2, —SO2NR23R25, —NR23R24,
    • R21 and R22 are independently hydrogen or C1-C6 alkyl; R21 and R22 together form an oxo group;
    • R23 is hydrogen or C1-C6 alkyl;
    • R24 is —SO2R25 or —C(O)R25; or
    • R23 and R24 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring;
    • R25 is C1-C6 alkyl; and
    • m is 1, 2, 3, or 4; and
    • (b) a short interfering nucleic acid (siNA).

138. A short-interfering nucleic acid (siNA) molecule comprising:

    • (a) a 5′-stabilized end cap of Formula (Ib):

wherein

    • R1 is a nucleobase, aryl, heteroaryl, or H,
    • R2 is

  • —CH═CD-Z, —CD=CH-Z, —CD=CD-Z, —(CR21R22)n-Z, or —(C2-C6 alkenylene)-Z and R20 is hydrogen; or
    • R2 and R20 together form a 3- to 7-membered carbocyclic ring substituted with —(CR21R22)n-Z or —(C2-C6 alkenylene)-Z;
    • n is 1, 2, 3, or 4;
    • Z is —ONR23R24, —OP(O)OH(CH2)mCO2R23, —OP(S)OH(CH2)mCO2R21, —P(O)(OH)2, —P(O)(OH)(OCH3), —P(O)(OH)(OCD3), —SO2(CH2)mP(O)(OH)2, —SO2NR23R25, —NR23R24,
    • R21 and R22 are independently hydrogen or C1-C6 alkyl; R21 and R22 together form an oxo group;
    • R23 is hydrogen or C1-C6 alkyl;
    • R24 is —SO2R25 or —C(O)R25; or
    • R23 and R24 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring;
    • R25 is C1-C6 alkyl; and
    • m is 1, 2, 3, or 4; and
    • (b) a short interfering nucleic acid (siNA).

139. A short-interfering nucleic acid (siNA) molecule comprising:

    • (a) a 5′-stabilized end cap selected from the group consisting of Formula (1) to Formula (15), Formula (9X) to Formula (12X), and Formula (9Y) to Formula (12Y):

wherein R1 is a nucleobase, aryl, heteroaryl, or H; and

    • (b) a short interfering nucleic acid (siNA).

140. A short-interfering nucleic acid (siNA) molecule comprising:

    • (a) a 5′-stabilized end cap selected from the group consisting of Formulas (1A)-(15A), Formulas (9B)-(12B), Formulas (9AX)-(12AX), Formulas (9AY)-(12AY), Formulas (9BX)-(12BX), and Formulas (9BY)-(12BY):

and

    • (b) a short interfering nucleic acid (siNA).

141. The siNA molecule according to any one of embodiments 136-140, wherein the siNA comprises the sense strand of any one of embodiments 1-135.

142. The siNA molecule according to any one of embodiments 136-141, wherein the siNA comprises the antisense strand of any one of embodiments 1-135.

143. A short interfering nucleic acid (siNA) molecule comprising:

    • (a) a sense strand comprising a first nucleotide sequence that is at least about 60%/, 65%, 70%/, 75%, 80%/, 85%, 90%/, 95%, or 100%/identical to an RNA corresponding to a target gene, wherein the first nucleotide sequence comprises a nucleotide sequence of any one SEQ ID NOs: 1-56, 103-158, and 205-260; and
    • (b) an antisense strand comprising a second nucleotide sequence that is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to the RNA corresponding to the target gene, wherein the second nucleotide sequence comprises a nucleotide sequence of any one of SEQ ID NOs: 57-102, 159-204, and 261-306.

144. A interfering nucleic acid (siNA) molecule comprising:

    • (a) a sense strand comprising a nucleotide sequence of any one of SEQ ID NOs: 307-362 and 415-444; and
    • (b) an antisense strand comprising a nucleotide sequence of any one of SEQ ID NOs: 363-409, 445-533, and 536-539.

145. The siNA according to any one of embodiments 1-132, 135, and 137-144, wherein the siNA further comprises a phosphorylation blocker.

146. The siNA according to any one of embodiments 16, 133, 134, and 145, wherein the phosphorylation blocker has the structure of Formula (IV):

wherein

    • R1 is a nucleobase,
    • R4 is —O—R0 or —NR31R32, R30 is C1-C8 substituted or unsubstituted alkyl; and
    • R31 and R32 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring.

147. The siNA of embodiment 136 or 146, wherein R4 is —OCH3 or —N(CH2CH2)2O.

148. The siNA according to any one of embodiments 16, 133, 134, 136, and 145-147, wherein the phosphorylation blocker is attached to the 5′ end of the sense strand.

149. The siNA of embodiment 148, wherein the phosphorylation blocker is attached to the 5′ end of the sense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, and phosphorodithioate linker.

150. The siNA according to any one of embodiments 16, 133, 134, 136, and 145-147, wherein the phosphorylation blocker is attached to the 3′ end of the sense strand.

151. The siNA of embodiment 150, wherein the phosphorylation blocker is attached to the 3′ end of the sense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, and phosphorodithioate linker.

152. The siNA according to any one of embodiments 16, 133, 134, 136, and 145-147, wherein the phosphorylation blocker is attached to the 5′ end of the antisense strand.

153. The siNA of embodiment 152, wherein the phosphorylation blocker is attached to the 5′ end of the antisense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, and phosphorodithioate linker.

154. The siNA according to any one of embodiments 16, 133, 134, 136, and 144-147, wherein the phosphorylation blocker is attached to the 3′ end of the antisense strand.

155. The siNA of embodiment 154, wherein the phosphorylation blocker is attached to the 3′ end of the antisense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, and phosphorodithioate linker.

156. The siNA according to any preceding embodiment, wherein the siNA further comprises a galactosamine.

157. The siNA of embodiment 16 or 156, wherein the galactosamine is N-acetylgalactosamine (GalNAc) of Formula (VII):

wherein each n is independently 1 or 2.

158. The siNA of embodiment 16 or 156, wherein the galactosamine is N-acetylgalactosamine (GalNAc) of Formula (VI):

wherein

    • m is 1, 2, 3, 4, or 5;
    • each n is independently 1 or 2;
    • p is 0 or 1;
    • each R is independently H;
    • each Y is independently selected from —O—P(═O)(SH)—, —O—P(═O)(O)—, —O—P(═O)(OH)—, and —O—P(S)S—;
    • Z is H or a second protecting group;
    • either L is a linker or L and Y in combination are a linker; and
    • A is H, OH, a third protecting group, an activated group, or an oligonucleotide.

159. The siNA of embodiment 158, wherein A is an oligonucleotide.

160. The siNA of embodiment 158, wherein A is 1-2 oligonucleotides.

161. The siNA of any one of embodiments 158-160, wherein the oligonucleotide is dTdT.

162. The siNA according to any one of embodiments 16 and 156-161, wherein the galactosamine is attached to the 3′ end of the sense strand.

163. The siNA of embodiment 162, wherein the galactosamine is attached to the 3′ end of the sense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, or phosphorodithioate linker.

164. The siNA according to any one of embodiments 16 and 156-161, wherein the galactosamine is attached to the 5′ end of the sense strand.

165. The siNA of embodiment 164, wherein the galactosamine is attached to the 5′ end of the sense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, or phosphorodithioate linker.

166. The siNA according to any one of embodiments 16 and 156-161, wherein the galactosamine is attached to the 3′ end of the antisense strand.

167. The siNA of embodiment 166, wherein the galactosamine is attached to the 3′ end of the atnisense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, or phosphorodithioate linker.

168. The siNA according to any one of embodiments 16 and 156-161, wherein the galactosamine is attached to the 5′ end of the antisense strand.

169. The siNA of embodiment 168, wherein the galactosamine is attached to the 5′ end of the atnisense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, or phosphorodithioate linker.

170. The siNA according to any one of embodiments 1-130, 133-136, and 139-169, wherein the siNA further comprises a 5′-stabilized end cap.

171. The siNA according to any one of embodiments 16, 131, 132, and 170, wherein the 5′-stabilized end cap is a 5′ vinyl phosphonate or deuterated 5′ vinyl phosphonate.

172. The siNA according to any one of embodiments 16, 131, 132, and 170, wherein the

    • 5′-stabilized end cap has the structure of Formula (Ia):

wherein

    • R1 is a nucleobase, aryl, heteroaryl, or H,
    • R2 is

—CH═CD-Z, —CD=CH-Z, —CD=CD-Z, —(CR21R22)n-Z, or —(C2-C6 alkenylene)-Z and R20 is hydrogen; or

    • R2 and R20 together form a 3- to 7-membered carbocyclic ring substituted with —(CR21R22)n—
    • Z or —(C2-C6 alkenylene)-Z;
    • n is 1, 2, 3, or 4;
    • Z is —ONR23R24, —OP(O)OH(CH2)mCO2R23, —OP(S)OH(CH2)mCO2R23, —P(O)(OH)2, —P(O)(OH)(OCH3), —P(O)(OH)(OCD3), —SO2(CH2)mP(O)(OH)2, —SO2NR23R21, —NR23R24, or —NR23SO2R24;
    • R21 and R22 either are independently hydrogen or C1-C6 alkyl, or R21 and R22 together form an oxo group;
    • R23 is hydrogen or C1-C6 alkyl;
    • R24 is —SO2R2′ or —C(O)R25; or
    • R23 and R24 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring;
    • R2S is C1-C6 alkyl; and
    • m is 1, 2, 3, or 4.

173. The siNA according to any one of embodiments 131, 132, and 170, wherein the 5′-stabilized end cap has the structure of Formula (Ib):

wherein

    • R1 is a nucleobase, aryl, heteroaryl, or H,

R2 is

—CH═CD-Z, —CD=CH-Z, —CD=CD-Z, —(CR21R22)n-Z, or —(C2-C6 alkenylene)-Z and R20 is hydrogen; or

    • R2 and R20 together form a 3- to 7-membered carbocyclic ring substituted with —(CR21R22)n—
    • Z or —(C2-C6 alkenylene)-Z;
    • n is 1, 2, 3, or 4;
    • Z is —ONR23R24, —OP(O)OH(CH2)mCO2R23, —OP(S)OH(CH2)mCO2R23, —P(O)(OH)2, —P(O)(OH)(OCH3), —P(O)(OH)(OCD3), —SO2(CH2)mP(O)(OH)2, —SO2NR23R21, —NR23R24, or —NR23SO2R24;
    • R2′ and R22 either are independently hydrogen or C1-C6 alkyl, or R21 and R22 together form an oxo group;
    • R23 is hydrogen or C1-C6 alkyl;
    • R24 is —SO2R25 or —C(O)R25; or
    • R23 and R24 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring;
    • R25 is C1-C6 alkyl; and
    • m is 1, 2, 3, or 4.

174. The siNA of embodiment 172 or 173, wherein R1 is an aryl.

175. The siNA of embodiment 174, wherein the aryl is a phenyl.

176. The siNA according to any one of embodiments 16, 131, 132, and 170, wherein the 5′-stabilized end cap is selected from the group consisting of Formula (1) to Formula (15), Formula (9X) to Formula (12X), and Formula (9Y) to Formula (12Y):

wherein R1 is a nucleobase, aryl, heteroaryl, or H.

177. The siNA according to any one of embodiments 16, 131, 132, and 170, wherein the 5′-stabilized end cap is selected from the group consisting of Formulas (1A)-(15A), Formulas (9B)-(12B), Formulas (9AX)-(12AX), Formulas (9AY)-(12AY), Formulas (9BX)-(12BX), and Formulas (9BY)-(12BY):

178. The siNA according to any one of embodiments 131, 132, and 170, wherein the 5′-stabilized end cap has the structure of Formula (Ic):

wherein

    • R1 is a nucleobase, aryl, heteroaryl, or H,
    • R2 is

—CH═CD-Z, —CD=CH-Z, —CD=CD-Z, —(CR2R2)n-Z, or —(C2-C6 alkenylene)-Z and Ra is hydrogen; or

    • R2 and R20 together form a 3- to 7-membered carbocyclic ring substituted with —(CR21R22)n—
    • Z or —(C2-C6 alkenylene)-Z;
    • n is 1, 2, 3, or 4;
    • Z is —ONR23R24, —OP(O)OH(CH2)mCO2R23, —OP(S)OH(CH2)mCO2R23, —P(O)(OH)2, —P(O)(OH)(OCH3), —P(O)(OH)(OCD3), —SO2(CH2)mP(O)(OH)2, —SO2NR23R21, —NR23R24, or —NR23SO2R24;
    • R21 and R22 either are independently hydrogen or C1-C6 alkyl, or R21 and R22 together form an oxo group;
    • R23 is hydrogen or C1-C6 alkyl;
    • R24 is —SO2R25 or —C(O)R25; or
    • R23 and R24 together with the nitrogen to which they are attached form a substituted or unsubstituted heterocyclic ring;
    • R2S is C1-C6 alkyl; and
    • m is 1, 2, 3, or 4.

179. The siNA of embodiment 178, wherein R1 is an aryl.

180. The siNA of embodiment 179, wherein the aryl is a phenyl.

181. The siNA according to any one of embodiments 16, 131, 132, and 170, wherein the 5′-stabilized end cap is selected from the group consisting of Formula (21) to Formula (35):

wherein R1 is a nucleobase, aryl, heteroaryl, or H.

182. The siNA according to any one of embodiments 16, 131, 132, and 170, wherein the 5′-stabilized end cap is selected from the group consisting of Formulas (21A)-(35A), Formulas (29B)-(32B), Formulas (29AX)-(32AX), Formulas (29AY)-(32AY), Formulas (29BX)-(32BX), and Formulas (29BY)-(32BY):

183. The siNA according to any one of embodiments 1-182, wherein the antisense strand comprises at least one thermally destabilizing nucleotide selected from:

184. The siNA according to any one of embodiments 1-182, wherein the sense strand comprises at least one thermally destabilizing nucleotide selected from:

185. The siNA according to any one of embodiments 1-182, wherein the first nucleotide sequence comprises at least one thermally destabilizing nucleotide selected from:

186. The siNA according to any one of embodiments 1-182, wherein the second nucleotide sequence comprises at least one thermally destabilizing nucleotide selected from:

187. The siNA according to any one of embodiments 16, 131, 132, and 170-186, wherein the 5′-stabilized end cap is attached to the 5′ end of the antisense strand.

188. The siNA of embodiment 187, wherein the 5′-stabilized end cap is attached to the 5′ end of the antisense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, or phosphorodithioate linker.

189. The siNA according to any one of embodiments 16, 131, 132, and 170-186, wherein the 5′-stabilized end cap is attached to the 5′ end of the sense strand.

190. The siNA of embodiment 189, wherein the 5′-stabilized end cap is attached to the 5′ end of the sense strand via one or more linkers independently selected from a phosphodiester linker, phosphorothioate linker, or phosphorodithioate linker.

191. The siNA according to any preceding embodiment, wherein the target gene is a viral gene.

192. The siNA of embodiment 191, wherein the viral gene is from a DNA virus.

193. The siNA of embodiment 192, wherein the DNA virus is a double-stranded DNA (dsDNA) virus.

194. The siNA of embodiment 193, wherein the dsDNA virus is a hepadnavirus.

195. The siNA of embodiment 194, wherein the hepadnavirus is a hepatitis B virus (HBV).

196. The siNA of embodiment 195, wherein the HBV is selected from HBV genotypes A-J.

197. The siNA of embodiment 195 or 196, wherein the target gene is selected from the S gene or X gene of the HBV.

198. The siNA according to any one of embodiments 1-197, wherein the second nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to 15 to 30 nucleotides within positions 200-720 or 1100-1700 of SEQ ID NO: 410.

199. The siNA according to any one of embodiments 1-197, wherein the second nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to 15 to 30 nucleotides within positions 200-280, 300-445, 460-510, 650-720, 1170-1220, 1250-1300, or 1550-1630 of SEQ ID NO: 410.

200. The siNA according to any one of embodiments 1-197, wherein the second nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to 15 to 30 nucleotides within positions 200-230, 250-280, 300-330, 370-400, 405-445, 460-500, 670-700, 1180-1210, 1260-1295, 1520-1550, or 1570-1610 of SEQ ID NO: 410.

201. The siNA according to any one of embodiments 1-197, wherein the second nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% complementary to 15 to 30 nucleotides starting at position 203, 206, 254, 305, 375, 409, 412, 415, 416, 419, 462, 466, 467, 674, 676, 1182, 1262, 1263, 1268, 1526, 1577, 1578, 1580, 1581, 1583, or 1584 of SEQ ID NO: 410.

202. The siNA according to any one of embodiments 1-201, wherein the first nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to 15 to 30 nucleotides within positions 200-720 or 1100-1700 of SEQ ID NO: 410.

203. The siNA according to any one of embodiments 1-201, wherein the first nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to 15 to 30 nucleotides within positions 200-280, 300-445, 460-510, 650-720, 1170-1220, 1250-1300, or 1550-1630 of SEQ ID NO: 410.

204. The siNA according to any one of embodiments 1-201, wherein the first nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to 15 to 30 nucleotides within positions 200-230, 250-280, 300-330, 370-400, 405-445, 460-500, 670-700, 1180-1210, 1260-1295, 1520-1550, or 1570-1610 of SEQ ID NO: 410.

205. The siNA according to any one of embodiments 1-201, wherein the first nucleotide sequence is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100% identical to 15 to 30 nucleotides starting at position 203, 206, 254, 305, 375, 409, 412, 415, 416, 419, 462, 466, 467, 674, 676, 1182, 1262, 1263, 1268, 1526, 1577, 1578, 1580, 1581, 1583, or 1584 of SEQ ID NO: 410.

206. The siNA according to any preceding embodiment, wherein the first nucleotide sequence comprises a nucleotide sequence of any one SEQ ID NOs: 1-56, 103-158, and 205-260.

207. The siNA according to any preceding embodiment, wherein the second nucleotide sequence comprises a nucleotide sequence of any one of SEQ ID NOs: 57-102, 159-204, and 261-306.

208. The siNA according to any preceding embodiment, wherein the sense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 307-362 and 415-444.

209. The siNA according to any preceding embodiment, wherein the antisense strand comprises a nucleotide sequence of any one of SEQ ID NOs: 363-409, 445-533, and 536-539.

210. The siNA according to any preceding embodiment, wherein at least one end of the siNA is a blunt end.

211. The siNA according to any preceding embodiment, wherein at least one end of the siNA comprises an overhang, wherein the overhang comprises at least one nucleotide.

212. The siNA according to any one of embodiments 1-209, wherein both ends of the siNA comprise an overhang, wherein the overhang comprises at least one nucleotide.

213. The siNA according to any preceding embodiment, wherein the siNA is selected from ds-siNA-001 to ds-siNA-0178.

214. The siNA according to any preceding embodiment, wherein at least one 2′-fluoro nucleotide or 2′-O-methyl nucleotide is a 2′-fluoro or 2-O-methyl nucleotide mimic of Formula (V):

wherein

    • R1 is independently a nucleobase, aryl, heteroaryl, or H, Q1 and Q2 are independently S or O,
    • R5 is independently —OCD3, —F, or —OCH3, and
    • R6 and R7 are independently H, D, or CD3.

215. The siNA of embodiment 214, wherein the 2′-fluoro or 2′-O-methyl nucleotide mimic is a nucleotide mimic of Formula (16) -Formula (20):

wherein R1 is a nucleobase and R2 is independently F or —OCH3.

216. The siNA according to any preceding embodiment, wherein at least one 2′-fluoro nucleotide is a 2′-fluoro nucleotide mimic.

217. The siNA according to embodiment 216, wherein at least one 2′-fluoro nucleotide on the antisense strand or the second nucleotide sequence is a 2′-fluoro nucleotide mimic.

218. The siNA according to embodiment 216 or 217, wherein the nucleotide at position 2 from the 5′ end of the antisense strand or the second nucleotide sequence is a 2′-fluoro nucleotide mimic.

219. The siNA according to any one of embodiments 216-218, wherein the nucleotide at position 5 from the 5′ end of the antisense strand or the second nucleotide sequence is a 2′-fluoro nucleotide mimic.

220. The siNA according to any one of embodiments 216-219, wherein the nucleotide at position 6 from the 5′ end of the antisense strand or the second nucleotide sequence is a 2′-fluoro nucleotide mimic.

221. The siNA according any one of embodiments 216-220, wherein the nucleotide at position 8 from the 5′ end of the antisense strand or the second nucleotide sequence is a 2′-fluoro nucleotide mimic.

222. The siNA according to any one of embodiments 216-221, wherein the nucleotide at position 10 from the 5′ end of the antisense strand or the second nucleotide sequence is a 2′-fluoro nucleotide mimic.

223. The siNA according to any one of embodiments 216-222, wherein the nucleotide at position 14 from the 5′ end of the antisense strand or the second nucleotide sequence is a 2′-fluoro nucleotide mimic.

224. The siNA according to any one of embodiments 216-223, wherein the nucleotide at position 16 from the 5′ end of the antisense strand or the second nucleotide sequence is a 2′-fluoro nucleotide mimic.

225. The siNA according to any one of embodiments 216-224, wherein the nucleotide at position 17 from the 5′ end of the antisense strand or the second nucleotide sequence is a 2′-fluoro nucleotide mimic.

226. The siNA according to any one of embodiments 216-225, wherein at least one 2′-fluoro nucleotide on the sense strand or the first nucleotide sequence is a 2′-fluoro nucleotide mimic.

227. The siNA according to any one of embodiments 216-226, wherein the nucleotide at position 3 from the 5′ end of the sense strand or the first nucleotide sequence is a 2′-fluoro nucleotide mimic.

228. The siNA according to any one of embodiments 216-227, wherein the nucleotide at position 5 from the 5′ end of the sense strand or the first nucleotide sequence is a 2′-fluoro nucleotide mimic.

229. The siNA according to any one of embodiments 216-228, wherein the nucleotide at position 7 from the 5′ end of the sense strand or the first nucleotide sequence is a 2′-fluoro nucleotide mimic.

230. The siNA according to any one of embodiments 216-229, wherein the nucleotide at position 8 from the 5′ end of the sense strand or the first nucleotide sequence is a 2′-fluoro nucleotide mimic.

231. The siNA according to any one of embodiments 216-230, wherein the nucleotide at position 9 from the 5′ end of the sense strand or the first nucleotide sequence is a 2′-fluoro nucleotide mimic.

232. The siNA according to any one of embodiments 216-231, wherein the nucleotide at position 10 from the 5′ end of the sense strand or the first nucleotide sequence is a 2′-fluoro nucleotide mimic.

233. The siNA according to any one of embodiments 216-232, wherein the nucleotide at position 11 from the 5′ end of the sense strand or the first nucleotide sequence is a 2′-fluoro nucleotide mimic.

234. The siNA according to any one of embodiments 216-233, wherein the nucleotide at position 12 from the 5′ end of the sense strand or the first nucleotide sequence is a 2′-fluoro nucleotide mimic.

235. The siNA according to any one of embodiments 216-234, wherein the nucleotide at position 14 from the 5′ end of the sense strand or the first nucleotide sequence is a 2′-fluoro nucleotide mimic.

236. The siNA according to any one of embodiments 216-235, wherein the nucleotide at position 17 from the 5′ end of the sense strand or the first nucleotide sequence is a 2′-fluoro nucleotide mimic.

237. The siNA according to any one of embodiments 216-236, wherein at least 1, 2, 3, 4, 5, 6, or more 2′-fluoro nucleotide mimics is a f4P nucleotid

238. The siNA according to any one of embodiments 216-237, wherein less than or equal to 10, 9, 8, 7, 6, 5, 4, 3, or 2 2′-fluoro nucleotide mimics is a f4P nucleotide

239. The siNA according to any one of embodiments 216-238, wherein 1, 2, 3, 4, 5, 6, or more 2′-fluoro nucleotide mimics is a f2P nucleotide

240. The siNA according to any one of embodiments 216-239, wherein less than or equal to 10, 9, 8, 7, 6, 5, 4, 3, or 2 2′-fluoro nucleotide mimics is a f2P nucleotide

241. The siNA according to any one of embodiments 216-240, wherein 1, 2, 3, 4, 5, 6, or more 2′-fluoro nucleotide mimics is a fX nucleotide

242. The siNA according to any one of embodiments 216-241, wherein less than or equal to 10, 9, 8, 7, 6, 5, 4, 3, or 2 2′-fluoro nucleotide mimics is a fX nucleotide

243. The siNA according to any preceding embodiment, wherein the first nucleotide from the 5′ end of the sense strand or first nucleotide sequence is a d2vd3 nucleotide

244. The siNA according to any preceding embodiment, wherein the first nucleotide from the 3′ end of the sense strand or first nucleotide sequence is a d2vd3 nucleotide

245. The siNA according to any preceding embodiment, wherein the first nucleotide from the 5′ end of the antisense strand or second nucleotide sequence is a d2vd3 nucleotide

246. The siNA according to any preceding embodiment, wherein the first nucleotide from the 3′ end of the antisense strand or second nucleotide sequence is a d2vd3 nucleotide

247. A composition comprising the siNA according to any one of embodiments 1-246.

248. A composition comprising 2, 3, 4, 5, 6, 7, 8, 9, 10 or more siNAs according to any one of embodiments 1-246.

249. The composition of embodiment 248, wherein at least 1, 2, 3, 4, 5, or more siNAs target an S gene of HBV.

250. The composition of embodiment 248 or 249, wherein at least 1, 2, 3, 4, 5, or more siNAs target an X gene of HBV.

251. The composition according to any one of embodiments 247-250, further comprising an additional HBV treatment agent.

252. The composition of embodiment 251, wherein the additional HBV treatment agent is selected from a nucleotide analog, nucleoside analog, a capsid assembly modulator (CAM), a recombinant interferon, an entry inhibitor, a small molecule immunomodulator and oligonucleotide therapy.

253. The composition of embodiment 252, wherein the oligonucleotide therapy is an additional siNA.

254. The composition of embodiment 253, wherein the additional siNA is selected from any of ds-siNA-001 to ds-siNA-0178.

255. The composition of embodiment 252, wherein the oligonucleotide therapy is an antisense oligonucleotide (ASO), NAPs, or STOPS™

256. The composition of embodiment 255, wherein the ASO is ASO 1 or ASO 2.

257. The composition of embodiment 251 or 252, wherein the additional HBV treatment agent is selected from HBV STOPS™ ALG-010133, HBV CAM ALG-000184, ASO 1, recombinant interferon alpha 2b, IFN-α, PEG-IFN-α-2a, lamivudine, telbivudine, adefovir dipivoxil, clevudine, entecavir, tenofovir alafenamide, tenofovir disoproxil, NVR3-778, BAY41-4109, JNJ-632, JNJ-3989 (ARO-HBV), RG6004, GSK3228836, REP-2139, REP-2165, AB-729, VIR-2218, RG6346 (DCR-HBVS), JNJ-6379, GLS4, ABI-HO731, JNJ-440, NZ-4, RG7907, EDP-514, AB-423, AB-506, ABI-H03733 and ABI-H2158.

258. A method of treating a disease in a subject in need thereof, comprising administering to the subject the siNA according to any one of embodiments 1-246.

259. A method of treating a disease in a subject in need thereof, comprising administering to the subject the composition according to any one of embodiments 247-257.

260. The method of embodiment 258 or 259, wherein the disease is a viral disease.

261. The method of embodiment 260, wherein the viral disease is caused by a DNA virus.

262. The method of embodiment 261, wherein the DNA virus is a double stranded DNA (dsDNA) virus.

263. The method of embodiment 262, wherein the dsDNA virus is a hepadnavirus.

264. The method of embodiment 263, wherein the hepadnavirus is a hepatitis B virus (HBV).

265. The method of embodiment 264, wherein the HBV is selected from HBV genotypes A-J.

266. The method of any of embodiments 258-265, further comprising administering an additional HBV treatment agent.

267. The method of embodiment 266, wherein the siNA or the composition and the additional HBV treatment agent are administered concurrently.

268. The method of embodiment 266, wherein the siNA or the composition and the additional HBV treatment agent are administered sequentially.

269. The method of embodiment 266, wherein the siNA or the composition is administered prior to administering the additional HBV treatment agent.

270. The method of embodiment 266, wherein the siNA or the composition is administered after administering the additional HBV treatment agent.

271. The method of any one of embodiments 266-270, wherein the additional HBV treatment agent is selected from a nucleotide analog, nucleoside analog, a capsid assembly modulator (CAM), a recombinant interferon, an entry inhibitor, a small molecule immunomodulator and oligonucleotide therapy.

272. The method of embodiment 271, wherein the oligonucleotide therapy is an additional siNA.

273. The method of embodiment 272, wherein the additional siNA is selected from any of ds-siNA-001 to ds-siNA-0178.

274. The method of embodiment 271, wherein the oligonucleotide therapy is an antisense oligonucleotide (ASO), NAPs, or STOPs.

275. The method of embodiment 274, wherein the ASO is ASO 1 or ASO 2.

276. The method of embodiment 270 or 271, wherein the additional HBV treatment agent is selected from HBV STOPS™ ALG-010133, HBV CAM ALG-000184, ASO 1, recombinant interferon alpha 2b, IFN-α, PEG-IFN-α-2a, lamivudine, telbivudine, adefovir dipivoxil, clevudine, entecavir, tenofovir alafenamide, tenofovir disoproxil, NVR3-778, BAY41-4109, JNJ-632, JNJ-3989 (ARO-HBV), RG6004, GSK3228836, REP-2139, REP-2165, AB-729, VIR-2218, RG6346 (DCR-HBVS), JNJ-6379, GLS4, ABI-HO731, JNJ-440, NZ-4, RG7907, EDP-514, AB-423, AB-506, ABI-H03733 and ABI-H2158.

277. The method of embodiment 258 or 259, wherein the disease is a liver disease.

278. The method of embodiment 277, wherein the liver disease is a nonalcoholic fatty liver disease (NAFLD) or hepatocellular carcinoma (HCC).

279. The method of embodiment 278, wherein the NAFLD is nonalcoholic steatohepatitis (NASH).

280. The method of any of embodiments 277-279 further comprising administering to the subject a liver disease treatment agent.

281. The method of embodiment 280, wherein the liver disease treatment agent is selected from a peroxisome proliferator-activator receptor (PPAR) agonist, farnesoid X receptor (FXR) agonist, lipid-altering agent, and incretin-based therapy.

282. The method of embodiment 281, wherein the PPAR agonist is selected from a PPARα agonist, dual PPARα/δ agonist, PPARγ agonist, and dual PPARα/γ agonist.

283. The method of embodiment 282, wherein the dual PPARα agonist is a fibrate.

284. The method of embodiment 282, wherein the PPARα/δ agonist is elafibranor.

285. The method of embodiment 282, wherein the PPARγ agonist is a thiazolidinedione (TZD).

286. The method of embodiment 282, wherein TZD is pioglitazone.

287. The method of embodiment 282, wherein the dual PPARα/γ agonist is saroglitazar.

288. The method of embodiment 281, wherein the FXR agonist is obeticholic acis (OCA).

289. The method of embodiment 281, wherein the lipid-altering agent is aramchol.

290. The method of embodiment 281, wherein the incretin-based therapy is a glucagon-like peptide 1 (GLP-1) receptor agonist or dipeptidyl peptidase 4 (DPP-4) inhibitor.

291. The method of embodiment 290, wherein the GLP-1 receptor agonist is exenatide or liraglutide.

292. The method of embodiment 290, wherein the DPP-4 inhibitor is sitagliptin or vildapliptin.

293. The method of any one of embodiments 280-292, wherein the siNA or composition and the liver disease treatment agent are administered concurrently.

294. The method of any one of embodiments 280-292, wherein the siNA or composition and the liver disease treatment agent are administered sequentially.

295. The method of any one of embodiments 280-292, wherein the siNA or composition is administered prior to administering the liver disease treatment agent.

296. The method of any one of embodiments 280-292, wherein the siNA or composition is administered after administering the liver disease treatment agent.

297. The method of any of one embodiments 258-296, wherein the siNA or the composition is administered at a dose of at least 1 mg/kg, 2 mg/kg, 3 mg/kg, 4 mg/kg, 5 mg/kg, 6 mg/kg, 7 mg/kg, 8 mg/kg, 9 mg/kg, 10 mg/kg, 11 mg/kg, 12 mg/kg, 13 mg/kg 14 mg/kg, or 15 mg/kg.

298. The method of any of one embodiments 258-296, wherein the siNA or the composition is administered at a dose of between 0.5 mg/kg to 50 mg/kg, 0.5 mg/kg to 40 mg/kg 0.5 mg/kg to 30 mg/kg, 1 mg/kg to 50 mg/kg, 1 mg/kg to 40 mg/kg, 1 mg/kg to 30 mg/kg, 1 mg/kg to 20 mg/kg, 3 mg/kg to 50 mg/kg, 3 mg/kg to 40 mg/kg, 3 mg/kg to 30 mg/kg, 3 mg/kg to 20 mg/kg, 3 mg/kg to 15 mg/kg, 3 mg/kg to 10 mg/kg, 4 mg/kg to 50 mg/kg, 4 mg/kg to 40 mg/kg, 4 mg/kg to 30 mg/kg, 4 mg/kg to 20 mg/kg, 4 mg/kg to 15 mg/kg, 4 mg/kg to 10 mg/kg, 5 mg/kg to 50 mg/kg, 5 mg/kg to 40 mg/kg, 5 mg/kg to 30 mg/kg, 5 mg/kg to 20 mg/kg, 5 mg/kg to 15 mg/kg, or 5 mg/kg to 10 mg/kg.

299. The method of any of one embodiments 258-298, wherein the siNA or the composition is administered at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times.

300. The method of any of one embodiments 258-298, wherein the siNA or the composition is administered at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times a day, at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times a week, or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 times a month.

301. The method of any of one embodiments 258-300, wherein the siNA or the composition are administered at least once every 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 days.

302. The method of any of one embodiments 258-301, wherein the siNA or the composition is administered for a period of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or 21 days, or at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 51, 52, 53, 54, or 55 weeks.

303. The method of any of one embodiments 258-302, wherein the siNA or the composition is administered at a single dose of 5 mg/kg.

304. The method of any of one embodiments 258-302, wherein the siNA or the composition is administered at a single dose of 10 mg/kg.

305. The method of any of one embodiments 258-302, wherein the siNA or the composition is administered at three doses of 10 mg/kg once a week.

306. The method of any of one embodiments 258-302, wherein the siNA or the composition is administered at three doses of 10 mg/kg once every three days.

307. The method of any of one embodiments 258-302, wherein the siNA or the composition is administered at five doses of 10 mg/kg once every three days.

308. The method of any of one embodiments 258-302, wherein the siNA or the composition is administered at six doses of ranging from 1 mg/kg to 15 mg/kg, 1 mg/kg to 10 mg/kg, 2 mg/kg to 15 mg/kg, 2 mg/kg to 10 mg/kg, 3 mg/kg to 15 mg/kg, or 3 mg/kg to 10 mg/kg.

309. The method of embodiment 308, wherein the first dose and second dose are administered at least 3 days apart.

310. The method of embodiment 308 or 309, wherein the second dose and third dose are administered at least 4 days apart.

311. The method of any one of embodiments 308-310, wherein the third dose and fourth dose, fourth dose and fifth dose, or fifth dose and sixth dose are administered at least 7 days apart.

312. The method of any one of embodiments 258-311, wherein the siNA or the composition are administered in a particle or viral vector.

313. The method of embodiment 312, wherein the viral vector is a vector of adenovirus, adeno-associated virus (AAV), alphavirus, flavivirus, herpes simplex virus, lentivirus, measles virus, picornavirus, poxvirus, retrovirus, or rhabdovirus.

314. The method of embodiment 312, wherein the viral vector is a recombinant viral vector.

315. The method according to any one of embodiments 312-314, wherein the viral vector is selected from AAVrh.74, AAVrh.10, AAVrh.20, AAV-1, AAV-2, AAV-3, AAV-4, AAV-5, AAV-6, AAV-7, AAV-8, AAV-9, AAV-10, AAV-11, AAV-12 and AAV-13.

316. The method according to any one of embodiments 258-315, wherein the siNA or the composition is administered systemically.

317. The method according to any one of embodiments 258-315, wherein the siNA or the composition is administered locally.

318. The method according to any one of embodiments 258-317, wherein the siNA or the composition is administered intravenously, subcutaneously, or intramuscularly.

319. Use of the siNA according to any one of embodiments 1-246 or the composition according to any one of embodiments 247-257 in the manufacture of a medicament for treating a disease.

320. The use of embodiment 319, wherein the disease is a viral disease.

321. The use of embodiment 320, wherein the viral disease is caused by a DNA virus.

322. The use of embodiment 321, wherein the DNA virus is a double stranded DNA (dsDNA virus).

323. The use of embodiment 321, wherein the dsDNA virus is a hepadnavirus.

324. The use of embodiment 323, wherein the hepadnavirus is a hepatitis B virus (HBV).

325. The use of embodiment 324, wherein the HBV is selected from HBV genotypes A-J.

326. The use of any of one of embodiments 319-325, further comprising an additional HBV treatment agent in the manufacture of the medicament.

327. The use of embodiment 326, wherein the additional HBV treatment agent is selected from a nucleotide analog, nucleoside analog, a capsid assembly modulator (CAM), a recombinant interferon, an entry inhibitor, a small molecule immunomodulator and oligonucleotide therapy.

328. The use of embodiment 327, wherein the oligonucleotide therapy is an additional siNA.

329. The use of embodiment 328, wherein the additional siNA is selected from any of ds-siNA-001 to ds-siNA-0178.

330. The use of embodiment 327, wherein the oligonucleotide therapy is an antisense oligonucleotide (ASO), NAPs, or STOPs.

331. The use of embodiment 330, wherein the ASO is ASO 1 or ASO2.

332. The use of embodiment 326 or 327, wherein the additional HBV treatment agent is selected from HBV STOPS™ ALG-010133, HBV CAM ALG-000184, ASO 1, recombinant interferon alpha 2b, IFN-α, PEG-IFN-α-2a, lamivudine, telbivudine, adefovir dipivoxil, clevudine, entecavir, tenofovir alafenamide, tenofovir disoproxil, NVR3-778, BAY41-4109, JNJ-632, JNJ-3989 (ARO-HBV), RG6004, GSK3228836, REP-2139, REP-2165, AB-729, VIR-2218, RG6346 (DCR-HBVS), JNJ-6379, GLS4, ABI-HO731, JNJ-440, NZ-4, RG7907, EDP-514, AB-423, AB-506, ABI-H03733 and ABI-H2158.

333. The use of embodiment 319, wherein the disease is a liver disease.

334. The use of embodiment 333, wherein the liver disease is a nonalcoholic fatty liver disease (NAFLD) or hepatocellular carcinoma (HCC).

335. The use of embodiment 334, wherein the NAFLD is nonalcoholic steatohepatitis (NASH).

336. The use of any of embodiments 333-335, further comprising a liver disease treatment agent in the manufacture of the medicament.

337. The use of embodiment 336, wherein the liver disease treatment agent is selected from a peroxisome proliferator-activator receptor (PPAR) agonist, farnesoid X receptor (FXR) agonist, lipid-altering agent, and incretin-based therapy.

338. The use of embodiment 337, wherein the PPAR agonist is selected from a PPARα agonist, dual PPARα/δ agonist, PPARγ agonist, and dual PPARα/γ agonist.

339. The use of embodiment 338, wherein the dual PPARα agonist is a fibrate.

340. The use of embodiment 338, wherein the PPARα/δ agonist is elafibranor.

341. The use of embodiment 338, wherein the PPARγ agonist is a thiazolidinedione (TZD).

342. The use of embodiment 341, wherein TZD is pioglitazone.

343. The use of embodiment 338, wherein the dual PPARα/γ agonist is saroglitazar.

344. The use of embodiment 337, wherein the FXR agonist is obeticholic acis (OCA).

345. The use of embodiment 337, wherein the lipid-altering agent is aramchol.

346. The use of embodiment 337, wherein the incretin-based therapy is a glucagon-like peptide 1 (GLP-1) receptor agonist or dipeptidyl peptidase 4 (DPP-4) inhibitor.

347. The use of embodiment 346, wherein the GLP-1 receptor agonist is exenatide or liraglutide.

348. The use of embodiment 346, wherein the DPP-4 inhibitor is sitagliptin or vildapliptin.

349. The siNA according to any one of embodiments 1-246 for use as a medicament.

350. The composition according to any one of embodiments 247-257 for use as a medicament.

351. The siNA according to any one of embodiments 1-246 for use in the treatment of a disease.

352. The siNA of embodiment 351, wherein the disease is a viral disease.

353. The siNA of embodiment 352, wherein the viral disease is caused by a DNA virus.

354. The siNA of embodiment 353, wherein the DNA virus is a double stranded DNA (dsDNA virus).

355. The siNA of embodiment 354, wherein the dsDNA virus is a hepadnavirus.

356. The siNA of embodiment 355, wherein the hepadnavirus is a hepatitis B virus (HBV).

357. The siNA of embodiment 356, wherein the HBV is selected from HBV genotypes A-J.

358. The siNA of embodiment 351, wherein the disease is a liver disease.

359. The siNA of embodiment 358, wherein the liver disease is a nonalcoholic fatty liver disease (NAFLD) or hepatocellular carcinoma (HCC).

360. The siNA of embodiment 359, wherein the NAFLD is nonalcoholic steatohepatitis (NASH).

361. The composition according to any one of embodiments 247-257, for use in the treatment of a disease.

362. The composition of embodiment 361, wherein the disease is a viral disease.

363. The composition of embodiment 362, wherein the viral disease is caused by a DNA virus.

364. The composition of embodiment 363, wherein the DNA virus is a double stranded DNA (dsDNA virus).

365. The composition of embodiment 364, wherein the dsDNA virus is a hepadnavirus.

366. The composition of embodiment 365, wherein the hepadnavirus is a hepatitis B virus (HBV).

367. The composition of embodiment 366, wherein the disease is a liver disease.

368. The composition of embodiment 367, wherein the liver disease is a nonalcoholic fatty liver disease (NAFLD) or hepatocellular carcinoma (HCC).

369. The composition of embodiment 368, wherein the NAFLD is nonalcoholic steatohepatitis (NASH).

TABLE 1 Non-modified Nucleotide Sequences First Nucleotide Second Nucleotide SEQ ID NO. Sequence (5′-3′) SEQ ID NO. Sequence (5′-3′  1 ACCGUGUGCACUUCGCUUC  57 GAAGCGAAGUGCACACGGUCC  2 ACCGUGUGCACUUCGCUUC  58 GAAGCGAAGUGCACACGGU  3 ACUUCGCUUCACCUCUGCA  59 UGCAGAGGUGAAGCGAAGUGC  4 AGUGUUUGCUGACGCAACC  60 GGUUGCGUCAGCAAACACUUG  5 CAGGCGGGGUUUUUCUUGU  61 ACAAGAAAAACCCCGCCUGUA  6 CAGGCGGGGUUUUUCUUGU  62 ACAAGAAAAAACCCCGCCUG  7 CAGUUUACUAGUGCCAUUU  63 AAAUGGCACUAGUAAACUGAG  8 CAGUUUACUAGUGCCAUUU  64 AAAUGGCACUAGUAAACUG  9 CAUCCUGCUGCUAUGCCUC  65 GAGGCAUAGCAGCAGGAUGAA 10 CAUCCUGCUGCUAUGCCUCAU  66 AUGAGGCAUAGCAGCAGGAUGAA 11 CAUCCUGCUGCUAUGCCUC  67 GAGGCAUAGCAGCAGGAUG 12 CCGUGUGCACUUCGCUUCA  68 UGAAGCGAAGUGCACACGGUC 13 CCGUGUGCACUUCGCUUCA  69 UGAAGCGAAGUGCACACGG 14 CCUGCUGCUAUGCCUCAUCUU  70 AAGAUGAGGCAUAGCAGCAGGAU 15 CUCAGUUUACUAGUGCCAU  71 AUGGCACUAGUAAACUGAGCC 16 CUCAGUUUACUAGUGCCAU  71 AUGGCACUAGUAAACUGAGCC 17 CUCAGUUUACUAGUGCCAU  71 AUGGCACUAGUAAACUGAGCC 18 CUCAGUUUACUAGUGCCAU  72 AUGGCACUAGUAAACUGAG 19 CUCAGUUUACUAGUGCCAU  72 AUGGCACUAGUAAACUGAG 20 CUGCUAUGCCUCAUCUUCU  73 AGAAGAUGAGGCAUAGCAGCA 21 CUGCUAUGCCUCAUCUUCU  73 AGAAGAUGAGGCAUAGCAGCA 22 CUGCUAUGCCUCAUCUUCU  74 AGAAGAUGAGGCAUAGCAG 23 CUGCUAUGCCUCAUCUUCU  74 AGAAGAUGAGGCAUAGCAG 24 CUGCUGCUAUGCCUCAUCU  75 AGAUGAGGCAUAGCAGCAGGA 25 CUGCUGCUAUGCCUCAUCU  76 AGAUGAGGCAUAGCAGCAG 26 CUGCUGCUAUGCCUCAUCU  76 AGAUGAGGCAUAGCAGCAG 27 CUUCGCUUCACCUCUGCACGU  77 ACGUGCAGAGGUGAAGCGAAGUG 28 GCACUUCGCUUCACCUCUGCA  78 UGCAGAGGUGAAGCGAAGUGCAC 29 GCCGAUCCAUACUGCGGAA  79 UUCCGCAGUAUGGAUCGGCAG 30 GCCGGGUUUUUCUUGUUGA  80 UUCCGCAGUAUGGAUCGGC 31 GCGGGGUUUUUCUUGUUGA  81 UCAACAAGAAAAACCCCGCCU 32 GCGGGGUUUUUCUUGUUGA  81 UCAACAAGAAAAACCCCGCCU 33 GCGGGGUUUUUCUUGUUGA  82 UCAACAAGAAAAACCCCGC 34 GCGGGGUUUUUCUUGUUGA  82 UCAACAAGAAAAACCCCGC 35 GCUGCUAUGCCUCAUCUUCUU  83 AAGAAGAUGAGGCAUAGCAGCAG 36 GGAUGUGUCUGCGGCGUUUUA  84 UAAAACGCCGCAGACACAUCCAG 37 GGCCAAAAUUCGCAGUCCC  85 GGGACUGCGAAUUUUGGCCAA 38 GGCGCACCUCUCUUUACGC  86 GCGUAAAGAGAGGUGCGCCCC 39 GUAUGUUGCCCGUUUGUCC  87 GGACAAACGGGCAACAUACCU 40 GUGGUGGACUUCUCUCAAU  88 AUUGAGAGAAGUCCACCACGA 41 GUGUGCACUUCGCUUCACC  89 GGUGAAGCGAAGUGCACACGG 42 GUUGCCCGUUUGUCCUCUA  90 UAGAGGACAAACGGGCAACAU 43 GUUGCCCGUUUGUCCUCUA  91 UAGAGGACAAACGGGCAAC 44 UCCAUACUGCGGAACUCCU  92 AGGAGUUCCGCAGUAUGGAUC 45 UCCAUACUGCGGAACUCCU  93 AGGAGUUCCGCAGUAUGGA 46 UCGUGGUGGACUUCUCUCAAU  94 AUUGAGAGAAGUCCACCACGAGU 47 UGCACUUCGCUUCACCUCU  95 AGAGGUGAAGCGAAGUGCACA 48 UGCCGAUCCAUACUGCGGA  96 UCCGCAGUAUGGAUCGGCAGA 49 UGCCGAUCCAUACUGCGGA  97 UCCGCAGUAUGGAUCGGCA 50 UGCUAUGCCUCAUCUUCUU  98 AAGAAGAUGAGGCAUAGCAGC 51 UGUGCACUUCGCUUCACCU  99 AGGUGAAGCGAAGUGCACACG 52 UGUGCACUUCGCUUCACCU  99 AGGUGAAGCGAAGUGCACACG 53 UGUGCACUUCGCUUCACCU 100 AGGUGAAGCGAAGUGCACA 54 UGUGCACUUCGCUUCACCU 100 AGGUGAAGCGAAGUGCACA 55 UUGCCCGUUUGUCCUCUAA 101 UUAGAGGACAAACGGGCAACA 56 UUGCCCGUUUGUCCUCUAA 102 UUAGAGGACAAACGGGCAA

TABLE 2 2′-OMe and 2′-F Modified Nucleotide Sequences First Nucleotide Second Nucleotide SEQ ID NO. Sequence (5′-3′) SEQ ID NO. Sequence (5′-3′) 103 mAmCfCmGmUmGfUfGfCmAm 159 mGfAmAmGmCmGmAmAmGmUmGm CfUmUmCmGmCfUmUmC CmAfCmAmCmGmGmUmCmC 104 mAmCfCmGmUmGfUfGfCmAm 160 mGfAmAmGmCmGmAmAmGmUmGm CfUmUmCmGmCfUmUmC CmAfCmAmCmGmGmU 105 mAmCfUmUmCmGfCfUfUmCm 161 mUfGmCmAmGmAmGmGmUmGmAm AfCmCmUmCmUfGmCmA AmGfCmGmAmAmGmUmGmC 106 mAmGfUmGmUmUfUfGfCmUm 162 mGfGmUmUmGmCmGmUmCmAmGm GfAmCmGmCmAfAmCmC CmAfAmAmCmAmCmUmUmG 107 mCmAfGmGmCmGfGfGfGmUm 163 mAfCmAmAmGmAmAmAmAmAmCm UfUmUmUmCmUfUmGmU CmCfCmGmCmCmUmGmUmA 108 mCmAfGmGmCmGfGfGfGmUm 164 mAfCmAmAmGmAmAmAmAmAmAm UfUmUmUmCmUfUmGmU CmCmCfCmGmCmCmUmG 109 mCmAfGmUmUmUfAfCfUmAm 165 mAfAmAmUmGmGmCmAmCmUmAm GfUmGmCmCmAfUmUmU GmUfAmAmAmCmUmGmAmG 110 mCmAfGmUmUmUfAfCfUmAm 166 mAfAmAmUmGmGmCmAmCmUmAm GfUmGmCmCmAfUmUmU GmUfAmAmAmCmUmG 111 mCmAfUmCmCmUfGfCfUmGm 167 mGfAmGmGmCmAmUmAmGmCmAm CfUmAmUmGmCfCmUmC GmCfAmGmGmAmUmGmAmA 112 mCmAmUmCmCmUfGmCfUfGf 168 mAfUmGmAmGfGmCmAmUmAmGm CmUmAmUmGmCmCmUmCmAmU CmAfGmCfAmGmGmAmUmGmAmA 113 mCmAfUmCmCmUfGfCfUmGm 169 mGfAmGmGmCmAmUmAmGmCmAm CfUmAmUmGmCfCmUmC GmCfAmGmGmAmUmG 114 mCmCfGmUmGmUfGfCfAmC 170 mUfGmAmAmGmCmGmAmAmGmUm mUfUmCmGmCmUfUmCmA GmCfAmCmAmCmGmGmUmC 115 mCmCfGmUmGmUfGfCfAmCm 171 mUfGmAmAmGmCmGmAmAmGmUm UfUmCmGmCmUfUmCmA GmCfAmCmAmCmGmG 116 mCmCmUmGmCmUfGmCfUfAf 172 mAfAmGmAmUfGmAmGmGmCmAm UmGmCmCmUmCmAmUmCmUmU UmAfGmCfAmGmCmAmGmGmAmU 117 mCmUfCmAmGmUfUfUfAmCm 173 mAfUmGmGmCmAmCmUmAmGmUm UfAmGmUmGmCfCmAmU AmAfAmCmUmGmAmGmCmC 118 mCmUmCmAmGmUfUmUmAmCm 173 mAfUmGmGmCmAmCmUmAmGmUm UmAmGmUmGmCmCmAmU AmAfAmCmUmGmAmGmCmC 119 mCmUfCmAmGmUfUfUmAmCm 173 mAfUmGmGmCmAmCmUmAmGmUm UmAmGmUmGmCfCmAmU AmAfAmCmUmGmAmGmCmC 120 mCmUfCmAmGmUfUfUfAmCm 174 mAfUmGmGmCmAmCmUmAmGmUm UfAmGmUmGmCfCmAmU AmAfAmCmUmGmAmG 121 mCmUfCmAmGmUfUfUmAmCm 174 mAfUmGmGmCmAmCmUmAmGmUm UmAmGmUmGmCfCmAmU AmAfAmCmUmGmAmG 122 mCmUfGmCmUmAfUfGfCmCm 175 mAfGmAmAmGmAmUmGmAmGmGm UfCmAmUmCmUfUmCmU CmAfUmAmGmCmAmGmCmA 123 mCmUfGmCmUmAfUfGmCmCm 175 mAfGmAmAmGmAmUmGmAmGmGm UmCmAmUmCmUfUmCmU CmAfUmAmGmCmAmGmCmA 124 mCmUfGmCmUmAfUfGfCmCm 176 mAfGmAmAmGmAmUmGmAmGmGm UfCmAmUmCmUfUmCmU CmAfUmAmGmCmAmG 125 mCmUfGmCmUmAfUfGmCmCm 176 mAfGmAmAmGmAmUmGmAmGmGm UmCmAmUmCmUfUmCmU CmAfUmAmGmCmAmG 126 mCmUfGmCmUmGfCfUfAmUm 177 mAfGmAmUmGmAmGmGmCmAmUm GfCmCmUmCmAfUmCmU AmGfCmAmGmCmAmGmGmA 127 mCmUfGmCmUmGfCfUfAmUm 178 mAfGmAmUmGmAmGmGmCmAmUm GfCmCmUmCmAfUmCmU AmGfCmAmGmCmAmG 128 mCmUfGmCmUmGfCfUmAmUm 178 mAfGmAmUmGmAmGmGmCmAmUm GmCmCmUmCmAfUmCmU AmGfCmAmGmCmAmG 129 mCmUmUmCmGmCfUmUfCfAf 179 mAfCmGmUmGfCmAmGmAmGmGm CmCmUmCmUmGmCmAmCmGmU UmGfAmAfGmCmGmAmAmGmUmG 130 mGmCmAmCmUmUfCmGfCfUf 180 mUfGmCmAmGfAmGmGmUmGmAm UmCmAmCmCmUmCmUmGmCmA AmGfCmGfAmAmGmUmGmCmAmC 131 mGmCfCmGmAmUfCfCfAmU 181 mUfUmCmCmGmCmAmGmUmAmUm mAfCmUmGmCmGfGmAmA GmGfAmUmCmGmGmCmAmG 132 mGmCfCmGmGmGfUfUfUmUm 182 mUfUmCmCmGmCmAmGmUmAmUm UfCmUmUmGmUfUmGmA GmGfAmUmCmGmGmC 133 mGmCfGmGmGmGfUfUfUmUm 183 mUfCmAmAmCmAmAmGmAmAmAm UfCmUmUmGmUfUmGmA AmAfCmCmCmCmGmCmCmU 134 mGmCfGmGmGmGfUfUmUmUm 183 mUfCmAmAmCmAmAmGmAmAmAm UmCmUmUmGmUfUmGmA AmAfCmCmCmCmGmCmCmU 135 mGmCfGmGmGmGfUfUfUmUm 184 mUfCmAmAmCmAmAmGmAmAmAm UfCmUmUmGmUfUmGmA AmAfCmCmCmCmGmC 136 mGmCfGmGmGmGfUfUmUmUm 184 mUfCmAmAmCmAmAmGmAmAmAm UmCmUmUmGmUfUmGmA AmAfCmCmCmCmGmC 137 mGmCmUmGmCmUfAmUfGfCf 185 mAfAmGmAmAfGmAmUmGmAmGm CmUmCmAmUmCmUmUmCmUmU GmCfAmUfAmGmCmAmGmCmAmG 138 mGmGmAmUmGmUfGmUfCfUf 186 mUfAmAmAmAfCmGmCmCmGmCm GmCmGmGmCmGmUmUmUmUmA AmGfAmCfAmCmAmUmCmCmAmG 139 mGmGfCmCmAmAfAfAfUmUm 187 mGfGmGmAmCmUmGmCmGmAmAm CfGmCmAmGmUfCmCmC UmUfUmUmGmGmCmCmAmA 140 mGmGfCmGmCmAfCfCfUmCm 188 mGfCmGmUmAmAmAmGmAmGmAm UfCmUmUmUmAfCmGmC GmGfUmGmCmGmCmCmCmC 141 mGmUfAmUmGmUfUfGfCmCm 189 mGfGmAmCmAmAmAmCmGmGmGm CfGmUmUmUmGfUmCmC CmAfAmCmAmUmAmCmCmU 142 mGmUfGmGmUmGfGfAfCmUm 190 mAfUmUmGmAmGmAmGmAmAmGm UfCmUmCmUmCfAmAmU UmCfCmAmCmCmAmCmGmA 143 mGmUfGmUmGmCfAfCfUmU 191 mGfGmUmGmAmAmGmCmGmAmAm mCfGmCmUmUmCfAmCmC GmUfGmCmAmCmAmCmGmG 144 mGmUfUmGmCmCfCfGfUmU 192 mUfAmGmAmGmGmAmCmAmAmAm mUfGmUmCmCmUfCmUmA CmGfGmGmCmAmAmCmAmU 145 mGmUfUmGmCmCfCfGfUmUm 193 mUfAmGmAmGmGmAmCmAmAmAm UfGmUmCmCmUfCmUmA CmGfGmGmCmAmAmC 146 mUmCfCmAmUmAfCfUfGmCm 194 mAfGmGmAmGmUmUmCmCmGmCm GfGmAmAmCmUfCmCmU AmGfUmAmUmGmGmAmUmC 147 mUmCfCmAmUmAfCfUfGmCm 195 mAfGmGmAmGmUmUmCmCmGmCm GfGmAmAmCmUfCmCmU AmGfUmAmUmGmGmA 148 mUmCmGmUmGmGfUmGfGfAf 196 mAfUmUmGmAfGmAmGmAmAmGm CmUmUmCmUmCmUmCmAmAmU UmCfCmAfCmCmAmCmGmAmGmU 149 mUmGfCmAmCmUfUfCfGmCm 197 mAfGmAmGmGmUmGmAmAmGmCm UfUmCmAmCmCfUmCmU GmAfAmGmUmGmCmAmCmA 150 mUmGfCmCmGmAfUfCfCmAm 198 mUfCmCmGmCmAmGmUmAmUmGm UfAmCmUmGmCfGmGmA GmAfUmCmGmGmCmAmGmA 151 mUmGfCmCmGmAfUfCfCmAm 199 mUfCmCmGmCmAmGmUmAmUmGm UfAmCmUmGmCfGmGmA GmAfUmCmGmGmCmA 152 mUmGfCmUmAmUfGfCfCmUm 200 mAfAmGmAmAmGmAmUmGmAmGm CfAmUmCmUmUfCmUmU GmCfAmUmAmGmCmAmGmC 153 mUmGfUmGmCmAfCfUfUmCm 201 mAfGmGmUmGmAmAmGmCmGmAm GfCmUmUmCmAfCmCmU AmGfUmGmCmAmCmAmCmG 154 mUmGfUmGmCmAfCfUmUmCm 201 mAfGmGmUmGmAmAmGmCmGmAm GmCmUmUmCmAfCmCmU AmGfUmGmCmAmCmAmCmG 155 mUmGfUmGmCmAfCfUfUmCm 202 mAfGmGmUmGmAmAmGmCmGmAm GfCmUmUmCmAfCmCmU AmGfUmGmCmAmCmA 156 mUmGfUmGmCmAfCfUmUmCm 202 mAfGmGmUmGmAmAmGmCmGmAm GmCmUmUmCmAfCmCmU AmGfUmGmCmAmCmA 157 mUmUfGmCmCmCfGfUmUmUm 203 mUfUmAmGmAmGmGmAmCmAmAm GmUmCmCmUmCfUmAmA AmCfGmGmGmCmAmAmCmA 158 mUmUfGmCmCmCfGfUfUmUm 204 mUfUmAmGmAmGmGmAmCmAmAm GfUmCmCmUmCfUmAmA AmCfGmGmGmCmAmA mX = 2′-O-methyl nucleotide; fX = 2′-fluoro nucleotide

TABLE 3 2′-O-methyl and 2′-fluoro Modified Nucleotide Sequences with Phosphorothioate Linkages First Nucleotide Second Nucleotide SEQ ID NO. Sequence (5′-3′) SEQ ID NO. Sequence (5′-3′ 205 mApsmCpsfCmGmUmGfUfGfC 261 mGpsfApsmAmGmCmGmAmAmGm mAmCfUmUmCmGmCfUmUmC UmGmCmAfCmAmCmGmGmUpsmC psmC 206 mApsmCpsfCmGmUmGfUfGfC 262 mGpsfApsmAmGmCmGmAmAmGm mAmCfUmUmCmGmCfUmUmC UmGmCmAfCmAmCmGmGmU 207 mApsmCpsfUmUmCmGfCfUfU 263 mUpsfGpsmCmAmGmAmGmGmUm mCmAfCmCmUmCmUfGmCmA GmAmAmGfCmGmAmAmGmUpsmG psmC 208 mApsmGpsfUmGmUmUfUfGfC 264 mGpsfGpsmUmUmGmCmGmUmCm mUmGfAmCmGmCmAfAmCmC AmGmCmAfAmAmCmAmCmUpsmU psmG 209 mCpsmApsfGmGmCmGfGfGfG 265 mApsfCpsmAmAmGmAmAmAmAm mUmUfUmUmUmCmUfUmGmU AmCmCmCfCmGmCmCmUmGpsmU psmA 210 mCpsmApsfGmGmCmGfGfGfG 266 mApsfCpsmAmAmGmAmAmAmAm mUmUfUmUmUmCmUfUmGmU AmAmCmCmCfCmGmCmCmUmG 211 mCpsmApsfGmUmUmUfAfCfU 267 mApsfApsmAmUmGmGmCmAmCm mAmGfUmGmCmCmAfUmUmU UmAmGmUfAmAmAmCmUmGpsmA psmG 212 mCpsmApsfGmUmUmUfAfCfU 268 mApsfApsmAmUmGmGmCmAmCm mAmGfUmGmCmCmAfUmUmU UmAmGmUfAmAmAmCmUmG 213 mCpsmApsfUmCmCmUfGfCfU 269 mGpsfApsmGmGmCmAmUmAmGm mGmCfUmAmUmGmCfCmUmC CmAmGmCfAmGmGmAmUmGpsmA psmA 214 mCpsmApsmUmCmCmUfGmCf 270 mApsfUpsmGmAmGfGmCmAmUm UfGfCmUmAmUmGmCmCmUmCm AmGmCmAfGmCfAmGmGmAmUmG AmU psmApsmA 215 mCpsmApsfUmCmCmUfGfCfU 271 mGpsfApsmGmGmCmAmUmAmGm mGmCfUmAmUmGmCfCmUmC CmAmGmCfAmGmGmAmUmG 216 mCpsmCpsfGmUmGmUfGfCfA 272 mUpsfGpsmAmAmGmCmGmAmAm mCmUfUmCmGmCmUfUmCmA GmUmGmCfAmCmAmCmGmGpsmU psmC 217 mCpsmCpsfGmUmGmUfGfCfA 273 mUpsfGpsmAmAmGmCmGmAmAm mCmUfUmCmGmCmUfUmCmA GmUmGmCfAmCmAmCmGmG 218 mCpsmCpsmUmGmCmUfGmCf 274 mApsfApsmGmAmUfGmAmGmGm UfAfUmGmCmCmUmCmAmUmCm CmAmUmAfGmCfAmGmCmAmGmG UmU psmApsmU 219 mCpsmUpsfCmAmGmUfUfUfA 275 mApsfUpsmGmGmCmAmCmUmAm mCmUfAmGmUmGmCfCmAmU GmUmAmAfAmCmUmGmAmGpsmC psmC 220 mCpsmUpsmCmAmGmUfUmU 275 mApsfUpsmGmGmCmAmCmUmAm mAmCmUmAmGmUmGmCmCmAmU GmUmAmAfAmCmUmGmAmGpsmC psmC 221 mCpsmUpsfCmAmGmUfUfUmA 275 mApsfUpsmGmGmCmAmCmUmAm mCmUmAmGmUmGmCfCmAmU GmUmAmAfAmCmUmGmAmGpsmC psmC 222 mCpsmUpsfCmAmGmUfUfUfA 276 mApsfUpsmGmGmCmAmCmUmAm mCmUfAmGmUmGmCfCmAmU GmUmAmAfAmCmUmGmAmG 223 mCpsmUpsfCmAmGmUfUfUmA 276 mApsfUpsmGmGmCmAmCmUmAm mCmUmAmGmUmGmCfCmAmU GmUmAmAfAmCmUmGmAmG 224 mCpsmUpsfGmCmUmAfUfGfC 277 mApsfGpsmAmAmGmAmUmGmAm mCmUfCmAmUmCmUfUmCmU GmGmCmAfUmAmGmCmAmGpsmC psmA 225 mCpsmUpsfGmCmUmAfUfGmC 277 mApsfGpsmAmAmGmAmUmGmAm mCmUmCmAmUmCmUfUmCmU GmGmCmAfUmAmGmCmAmGpsmC psmA 226 mCpsmUpsfGmCmUmAfUfGfC 278 mApsfGpsmAmAmGmAmUmGmAm mCmUfCmAmUmCmUfUmCmU GmGmCmAfUmAmGmCmAmG 227 mCpsmUpsfGmCmUmAfUfGmC 278 mApsfGpsmAmAmGmAmUmGmAm mCmUmCmAmUmCmUfUmCmU GmGmCmAfUmAmGmCmAmG 228 mCpsmUpsfGmCmUmGfCfUfA 279 mApsfGpsmAmUmGmAmGmGmCm mUmGfCmCmUmCmAfUmCmU AmUmAmGfCmAmGmCmAmGpsmG psmA 229 mCpsmUpsfGmCmUmGfCfUfA 280 mApsfGpsmAmUmGmAmGmGmCm mUmGfCmCmUmCmAfUmCmU AmUmAmGfCmAmGmCmAmG 230 mCpsmUpsfGmCmUmGfCfUmA 280 mApsfGpsmAmUmGmAmGmGmCm mUmGmCmCmUmCmAfUmCmU AmUmAmGfCmAmGmCmAmG 231 mCpsmUpsmUmCmGmCfUmUf 281 mApsfCpsmGmUmGfCmAmGmAm CfAfCmCmUmCmUmGmCmAmCm GmGmUmGfAmAfGmCmGmAmAmG GmU psmUpsmG 232 mGpsmCpsmAmCmUmUfCmGf 282 mUpsfGpsmCmAmGfAmGmGmUm CfUfUmCmAmCmCmUmCmUmGm GmAmAmGfCmGfAmAmGmUmGmC CmA psmApsmC 233 mGpsmCpsfCmGmAmUfCfCfA 283 mUpsfUpsmCmCmGmCmAmGmUm mUmAfCmUmGmCmGfGmAmA AmUmGmGfAmUmCmGmGmCpsmA psmG 234 mGpsmCpsfCmGmGmGfUfUfU 284 mUpsfUpsmCmCmGmCmAmGmUm mUmUfCmUmUmGmUfUmGmA AmUmGmGfAmUmCmGmGmC 235 mGpsmCpsfGmGmGmGfUfUfU 285 mUpsfCpsmAmAmCmAmAmGmAm mUmUfCmUmUmGmUfUmGmA AmAmAmAfCmCmCmCmGmCpsmC psmU 236 mGpsmCpsfGmGmGmGfUfUmU 285 mUpsfCpsmAmAmCmAmAmGmAm mUmUmCmUmUmGmUfUmGmA AmAmAmAfCmCmCmCmGmCpsmC psmU 237 mGpsmCpsfGmGmGmGfUfUfU 286 mUpsfCpsmAmAmCmAmAmGmAm mUmUfCmUmUmGmUfUmGmA AmAmAmAfCmCmCmCmGmC 238 mGpsmCpsfGmGmGmGfUfUmU 286 mUpsfCmAmAmCmAmAmGmAmA mUmUmCmUmUmGmUfUmGmA mAmAmAfCmCmCmCmGmC 239 mGpsmCpsmUmGmCmUfAmUf 287 mApsfApsmGmAmAfGmAmUmGm GfCfCmUmCmAmUmCmUmUmCm AmGmGmCfAmUfAmGmCmAmGmC UmU psmApsmG 240 mGpsmGpsmAmUmGmUfGmUf 288 mUpsfApsmAmAmAfCmGmCmCm CfUfGmCmGmGmCmGmUmUmUm GmCmAmGfAmCfAmCmAmUmCmC UmA psmApsmG 241 mGpsmGpsfCmCmAmAfAfAfU 289 mGpsfGpsmGmAmCmUmGmCmGm mUmCfGmCmAmGmUfCmCmC AmAmUmUfUmUmGmGmCmCpsmA psmA 242 mGpsmGpsfCmGmCmAfCfCfU 290 mGpsfCpsmGmUmAmAmAmGmAm mCmUfCmUmUmUmAfCmGmC GmAmGmGfUmGmCmGmCmCpsmC psmC 243 mGpsmUpsfAmUmGmUfUfGfC 291 mGpsfGpsmAmCmAmAmAmCmGm mCmCfGmUmUmUmGfUmCmC GmGmCmAfAmCmAmUmAmCpsmC psmU 244 mGpsmUpsfGmGmUmGfGfAfC 292 mApsfUpsmUmGmAmGmAmGmAm mUmUfCmUmCmUmCfAmAmU AmGmUmCfCmAmCmCmAmCpsmG psmA 245 mGpsmUpsfGmUmGmCfAfCfU 293 mGpsfGpsmUmGmAmAmGmCmGm mUmCfGmCmUmUmCfAmCmC AmAmGmUfGmCmAmCmAmCpsmG psmG 246 mGpsmUpsfUmGmCmCfCfGfU 294 mUpsfApsmGmAmGmGmAmCmAm mUmUfGmUmCmCmUfCmUmA AmAmCmGfGmGmCmAmAmCpsmA psmU 247 mGpsmUpsfUmGmCmCfCfGfU 295 mUpsfApsmGmAmGmGmAmCmAm mUmUfGmUmCmCmUfCmUmA AmAmCmGfGmGmCmAmAmC 248 mUpsmCpsfCmAmUmAfCfUfG 296 mApsfGpsmGmAmGmUmUmCmCm mCmGfGmAmAmCmUfCmCmU GmCmAmGfUmAmUmGmGmApsmU psmC 249 mUpsmCpsfCmAmUmAfCfUfG 297 mApsfGpsmGmAmGmUmUmCmCm mCmGfGmAmAmCmUfCmCmU GmCmAmGfUmAmUmGmGmA 250 mUpsmCpsmGmUmGmGfUmGf 298 mApsfUpsmUmGmAfGmAmGmAm GfAfCmUmUmCmUmCmUmCmAm AmGmUmCfCmAfCmCmAmCmGmA AmU psmGpsmU 251 mUpsmGpsfCmAmCmUfUfCfG 299 mApsfGpsmAmGmGmUmGmAmAm mCmUfUmCmAmCmCfUmCmU GmCmGmAfAmGmUmGmCmApsmC psmA 252 mUpsmGpsfCmCmGmAfUfCfC 300 mUpsfCpsmCmGmCmAmGmUmAm mAmUfAmCmUmGmCfGmGmA UmGmGmAfUmCmGmGmCmApsmG psmA 253 mUpsmGpsfCmCmGmAfUfCfC 301 mUpsfCpsmCmGmCmAmGmUmAm mAmUfAmCmUmGmCfGmGmA UmGmGmAfUmCmGmGmCmA 254 mUpsmGpsfCmUmAmUfGfCfC 302 mApsfApsmGmAmAmGmAmUmGm mUmCfAmUmCmUmUfCmUmU AmGmGmCfAmUmAmGmCmApsmG psmC 255 mUpsmGpsfUmGmCmAfCfUfU 303 mApsfGpsmGmUmGmAmAmGmCm mCmGfCmUmUmCmAfCmCmU GmAmAmGfUmGmCmAmCmApsmC psmG 256 mUpsmGpsfUmGmCmAfCfUmU 303 mApsfGpsmGmUmGmAmAmGmCm mCmGmCmUmUmCmAfCmCmU GmAmAmGfUmGmCmAmCmApsmC psmG 257 mUpsmGpsfUmGmCmAfCfUfU 304 mApsfGpsmGmUmGmAmAmGmCm mCmGfCmUmUmCmAfCmCmU GmAmAmGfUmGmCmAmCmA 258 mUpsmGpsfUmGmCmAfCfUmU 304 mApsfGpsmGmUmGmAmAmGmCm mCmGmCmUmUmCmAfCmCmU GmAmAmGfUmGmCmAmCmA 259 mUpsmUpsfGmCmCmCfGfUmU 305 mUpsfUpsmAmGmAmGmGmAmCm mUmGmUmCmCmUmCfUmAmA AmAmAmCfGmGmGmCmAmApsmC psmA 260 mUpsmUpsfGmCmCmCfGfUfU 306 mUpsfUpsmAmGmAmGmGmAmCm mUmGfUmCmCmUmCfUmAmA AmAmAmCfGmGmGmCmAmA mX = 2′-O-methyl nucleotide; fX = 2′-fluoro nucleotide; ps = phosphorothioate linkage

TABLE 4 siNA Sequences SEQ ID SEQ NO. Sense Sequence (5′-3′) ID NO. Antisense Sequence (5′-3′) 307 mApsmCpsfCmGmUmGfUfGfC 363 mGpsfApsmAmGmCmGmAmAmGmU mAmCfUmUmCmGmCfUmUmC mGmCmAfCmAmCmGmGmUpsmCps mC 308 mApsmCpsfCmGmUmGfUfGfC 364 mGpsfApsmAmGmCmGmAmAmGmU mAmCfUmUmCmGmCfUmUmC mGmCmAfCmAmCmGmGmUpsTpsT TT 309 mApsmCpsfUmUmCmGfCfUfU 365 mUpsfGpsmCmAmGmAmGmGmUmG mCmAfCmCmUmCmUfGmCmA mAmAmGfCmGmAmAmGmUpsmGps mC 310 mApsmGpsfUmGmUmUfUfGfC 366 mGpsfGpsmUmUmGmCmGmUmCmA mUmGfAmCmGmCmAfAmCmC mGmCmAfAmAmCmAmCmUpsmUps mG 311 mCpsmApsfGmGmCmGfGfGfG 367 mApsfCpsmAmAmGmAmAmAmAmA mUmUfUmUmUmCmUfUmGm mCmCmCfCmGmCmCmUmGpsmUps U mA 312 mCpsmApsfGmGmCmGfGfGfG 368 mApsfCpsmAmAmGmAmAmAmAmA mUmUfUmUmUmCmUfUmGm mAmCmCmCfCmGmCmCmUmGpsTp UTT sT 313 mCpsmApsfGmUmUmUfAfCfU 369 mApsfApsmAmUmGmGmCmAmCmU mAmGfUmGmCmCmAfUmUm mAmGmUfAmAmAmCmUmGpsmAps U mG 314 mCpsmApsfGmUmUmUfAfCfU 370 mApsfApsmAmUmGmGmCmAmCmU mAmGfUmGmCmCmAfUmUm mAmGmUfAmAmAmCmUmGpsTpsT UTT 315 mCpsmApsfUmCmCmUfGfCfU 371 mGpsfApsmGmGmCmAmUmAmGmC mGmCfUmAmUmGmCfCmUmC mAmGmCfAmGmGmAmUmGpsmAps mA 316 mCpsmApsmUmCmCmUfGmCf 372 mApsfUpsmGmAmGfGmCmAmUmA UfGfCmUmAmUmGmCmCmUm mGmCmAfGmCfAmGmGmAmUmGps CmAmU mApsmA 317 mCpsmApsfUmCmCmUfGfCfU 373 mGpsfApsmGmGmCmAmUmAmGmC mGmCfUmAmUmGmCfCmUmC mAmGmCfAmGmGmAmUmGpsTpsT TT 318 mCpsmCpsfGmUmGmUfGfCfA 374 mUpsfGpsmAmAmGmCmGmAmAmG mCmUfUmCmGmCmUfUmCmA mUmGmCfAmCmAmCmGmGpsmUps mC 319 mCpsmCpsfGmUmGmUfGfCfA 375 mUpsfGpsmAmAmGmCmGmAmAmG mCmUfUmCmGmCmUfUmCmA mUmGmCfAmCmAmCmGmGpsTpsT TT 320 mCpsmCpsmUmGmCmUfGmCf 376 mApsfApsmGmAmUfGmAmGmGmC UfAfUmGmCmCmUmCmAmUm mAmUmAfGmCfAmGmCmAmGmGps CmUmU mApsmU 321 mCpsmUpsfCmAmGmUfUfUfA 377 mApsfUpsmGmGmCmAmCmUmAmG mCmUfAmGmUmGmCfCmAmU mUmAmAfAmCmUmGmAmGpsmCps mC 322 mCpsmUpsmCmAmGmUfUmU 377 mApsfUpsmGmGmCmAmCmUmAmG mAmCmUmAmGmUmGmCmC mUmAmAfAmCmUmGmAmGpsmCps mAmU mC 323 mCpsmUpsfCmAmGmUfUfUmA 377 mApsfUpsmGmGmCmAmCmUmAmG mCmUmAmGmUmGmCfCmAm mUmAmAfAmCmUmGmAmGpsmCps U mC 324 mCpsmUpsfCmAmGmUfUfUfA 378 mApsfUpsmGmGmCmAmCmUmAmG mCmUfAmGmUmGmCfCmAmU mUmAmAfAmCmUmGmAmGpsTpsT TT 325 mCpsmUpsfCmAmGmUfUfUmA 378 mApsfUpsmGmGmCmAmCmUmAmG mCmUmAmGmUmGmCfCmAm mUmAmAfAmCmUmGmAmGpsTpsT UTT 326 mCpsmUpsfGmCmUmAfUfGfC 379 mApsfGpsmAmAmGmAmUmGmAmG mCmUfCmAmUmCmUfUmCmU mGmCmAfUmAmGmCmAmGpsmCps mA 327 mCpsmUpsfGmCmUmAfUfGmC 379 mApsfGpsmAmAmGmAmUmGmAmG mCmUmCmAmUmCmUfUmCm mGmCmAfUmAmGmCmAmGpsmCps U mA 328 mCpsmUpsfGmCmUmAfUfGfC 380 mApsfGpsmAmAmGmAmUmGmAmG mCmUfCmAmUmCmUfUmCmU mGmCmAfUmAmGmCmAmGpsTpsT TT 329 mCpsmUpsfGmCmUmAfUfGmC 380 mApsfGpsmAmAmGmAmUmGmAmG mCmUmCmAmUmCmUfUmCm mGmCmAfUmAmGmCmAmGpsTpsT UTT 330 mCpsmUpsfGmCmUmGfCfUfA 381 mApsfGpsmAmUmGmAmGmGmCmA mUmGfCmCmUmCmAfUmCmU mUmAmGfCmAmGmCmAmGpsmGps mA 331 mCpsmUpsfGmCmUmGfCfUfA 382 mApsfGpsmAmUmGmAmGmGmCmA mUmGfCmCmUmCmAfUmCmU mUmAmGfCmAmGmCmAmGpsTpsT TT 332 mCpsmUpsfGmCmUmGfCfUmA 383 mApsfGpsmAmUmGmAmGmGmCmA mUmGmCmCmUmCmAfUmCm mUmAmGfCmAmGmCmAmGpsTpsT UTT 333 mCpsmUpsmUmCmGmCfUmUf 384 mApsfCpsmGmUmGfCmAmGmAmG CfAfCmCmUmCmUmGmCmAm mGmUmGfAmAfGmCmGmAmAmGp CmGmU smUpsmG 334 mGpsmCpsmAmCmUmUfCmGf 385 mUpsfGpsmCmAmGfAmGmGmUmG CfUfUmCmAmCmCmUmCmUm mAmAmGfCmGfAmAmGmUmGmCps GmCmA mApsmC 335 mGpsmCpsfCmGmAmUfCfCfA 386 mUpsfUpsmCmCmGmCmAmGmUmA mUmAfCmUmGmCmGfGmAm mUmGmGfAmUmCmGmGmCpsmAps A mG 336 mGpsmCpsfCmGmGmGfUfUfU 387 mUpsfUpsmCmCmGmCmAmGmUmA mUmUfC mUmUmGmUfUmGm mUmGmGfAmUmCmGmGmCpsTpsT ATT 337 mGpsmCpsfGmGmGmGfUfUfU 388 mUpsfCpsmAmAmCmAmAmGmAmA mUmUfC mUmUmGmUfUmGm mAmAmAfCmCmCmCmGmCpsmCps A mU 338 mGpsmCpsfGmGmGmGfUfUmU 388 mUpsfCpsmAmAmCmAmAmGmAmA mUmUmCmUmUmGmUfUmGm mAmAmAfCmCmCmCmGmCpsmCps A mU 339 mGpsmCpsfGmGmGmGfUfUfU 389 mUpsfCpsmAmAmCmAmAmGmAmA mUmUfCmUmUmGmUfUmGm mAmAmAfCmCmCmCmGmCpsTpsT ATT 340 mGpsmCpsfGmGmGmGfUfUmU 389 mUpsfCmAmAmCmAmAmGmAmAm mUmUmCmUmUmGmUfUmGm AmAmAfCmCmCmCmGmCpsTpsT ATT 341 mGpsmCpsmUmGmCmUfAmUf 390 mApsfApsmGmAmAfGmAmUmGmA GfCfCmUmCmAmUmCmUmUm mGmGmCfAmUfAmGmCmAmGmCps CmUmU mApsmG 342 mGpsmGpsmAmUmGmUfGmUf 391 mUpsfApsmAmAmAfCmGmCmCmG CfUfGmCmGmGmCmGmUmUm mCmAmGfAmCfAmCmAmUmCmCps UmUmA mApsmG 343 mGpsmGpsfCmCmAmAfAfAfU 392 mGpsfGpsmGmAmCmUmGmCmGmA mUmCfGmCmAmGmUfCmCmC mAmUmUfUmUmGmGmCmCpsmAps mA 344 mGpsmGpsfCmGmCmAfCfCfU 393 mGpsfCpsmGmUmAmAmAmGmAmG mCmUfCmUmUmUmAfCmGmC mAmGmGfUmGmCmGmCmCpsmCps mC 345 mGpsmUpsfAmUmGmUfUfGfC 394 mGpsfGpsmAmCmAmAmAmCmGmG mCmCfGmUmUmUmGfUmCmC mGmCmAfAmCmAmUmAmCpsmCps mU 346 mGpsmUpsfGmGmUmGfGfAfC 395 mApsfUpsmUmGmAmGmAmGmAmA mUmUfCmUmCmUmCfAmAmU mGmUmCfCmAmCmCmAmCpsmGps mA 347 mGpsmUpsfGmUmGmCfAfCfU 396 mGpsfGpsmUmGmAmAmGmCmGmA mUmCfGmCmUmUmCfAmCmC mAmGmUfGmCmAmCmAmCpsmGps mG 348 mGpsmUpsfUmGmCmCfCfGfU 397 mUpsfApsmGmAmGmGmAmCmAmA mUmUfGmUmCmCmUfCmUmA mAmCmGfGmGmCmAmAmCpsmAps mU 349 mGpsmUpsfUmGmCmCfCfGfU 398 mUpsfApsmGmAmGmGmAmCmAmA mUmUfGmUmCmCmUfCmUmA mAmCmGfGmGmCmAmAmCpsTpsT TT 350 mUpsmCpsfCmAmUmAfCfUfG 399 mApsfGpsmGmAmGmUmUmCmCmG mCmGfGmAmAmCmUfCmCmU mCmAmGfUmAmUmGmGmApsmUps mC 351 mUpsmCpsfCmAmUmAfCfUfG 400 mApsfGpsmGmAmGmUmUmCmCmG mCmGfGmAmAmCmUfCmCmU mCmAmGfUmAmUmGmGmApsTpsT TT 352 mUpsmCpsmGmUmGmGfUmGf 401 mApsfUpsmUmGmAfGmAmGmAmA GfAfCmUmUmCmUmCmUmCm mGmUmCfCmAfCmCmAmCmGmAps AmAmU mGpsmU 353 mUpsmGpsfCmAmCmUfUfCfG 402 mApsfGpsmAmGmGmUmGmAmAmG mCmUfUmCmAmCmCfUmCmU mCmGmAfAmGmUmGmCmApsmCps mA 354 mUpsmGpsfCmCmGmAfUfCfC 403 mUpsfCpsmCmGmCmAmGmUmAmU mAmUfAmCmUmGmCfGmGm mGmGmAfUmCmGmGmCmApsmGps A mA 355 mUpsmGpsfCmCmGmAfUfCfC 404 mUpsfCpsmCmGmCmAmGmUmAmU mAmUfAmCmUmGmCfGmGm mGmGmAfUmCmGmGmCmApsTpsT ATT 356 mUpsmGpsfCmUmAmUfGfCfC 405 mApsfApsmGmAmAmGmAmUmGmA mUmCfAmUmCmUmUfCmUmU mGmGmCfAmUmAmGmCmApsmGps mC 357 mUpsmGpsfUmGmCmAfCfUfU 406 mApsfGpsmGmUmGmAmAmGmCmG mCmGfCmUmUmCmAfCmCmU mAmAmGfUmGmCmAmCmApsmCps mG 358 mUpsmGpsfUmGmCmAfCfUmU 406 mApsfGpsmGmUmGmAmAmGmCmG mCmGmCmUmUmCmAfCmCm mAmAmGfUmGmCmAmCmApsmCps U mG 359 mUpsmGpsfUmGmCmAfCfUfU 407 mApsfGpsmGmUmGmAmAmGmCmG mCmGfCmUmUmCmAfCmCmU mAmAmGfUmGmCmAmCmApsTpsT TT 360 mUpsmGpsfUmGmCmAfCfUmU 407 mApsfGpsmGmUmGmAmAmGmCmG mCmGmCmUmUmCmAfCmCm mAmAmGfUmGmCmAmCmApsTpsT UTT 361 mUpsmUpsfGmCmCmCfGfUmU 408 mUpsfUpsmAmGmAmGmGmAmCmA mUmGmUmCmCmUmCfUmAm mAmAmCfGmGmGmCmAmApsmCps A mA 362 mUpsmUpsfGmCmCmCfGfUfU 409 mUpsfUpsmAmGmAmGmGmAmCmA mUmGfUmCmCmUmCfUmAmA mAmAmCfGmGmGmCmAmApsTpsT TT 415 5dcd3Cps5dcd3CpsfG5dcd3UmG 445 5dcd3UpsfGpsmAmAmG5dcd3CmGm 5dcd3UfG5dfCfA5dcd3C5dcd3U AmAmG5dcd3UmG5dcd3CfA5dcd3C 5dfU5dcd3CmG5dcd3C5dcd3U5d mA5dcd3CmGmGps5dcd3Ups5dcd3U fU5dcd3CmA 415 5dcd3Cps5dcd3CpsfG5dcd3UmG 446 5dcd3UpsfGpsmAmAmGmCmGmAm 5dcd3UfG5dfCfA5dcd3C5dcd3U AmGmUmGmCfAmCmAmCmGmGps 5dfU5dcd3CmG5dcd3C5dcd3U5d 5dcd3Ups5dcd3U fU5dcd3CmA 415 5dcd3Cps5dcd3CpsfG5dcd3UmG 447 mUpsfGpsmAmAmGmCmGmAmAmG 5dcd3UfG5dfCfA5dcd3C5dcd3U mUmGmCfAmCmAmCmGmGpsmUps 5dfU5dcd3CmG5dcd3C5dcd3U5d mU fU5dcd3CmA 416 fCpsmCpsfGmUfGmUfGfCfAmC 448 mUpsfGpsmAfAmGfCmGfAmAfGmU fUmUfCmGfCmUfUmCfA mGmCfAmCfAmCfGmGpsmUpsmC 416 fCpsmCpsfGmUfGmUfGfCfAmC 449 vmUpsfGpsmAfAmGfCmGfAmAfGm fUmUfCmGfCmUfUmCfA UmGmCfAmCfAmCfGmGpsmUpsmC 416 fCpsmCpsfGmUfGmUfGmCfAm 450 mUpsfGpsmAfAmGfCmGfAmAfGmUf CfUmUfCmGfCmUfUmCfA GmCfAmCfAmCfGmGpsmUpsmC 416 fCpsmCpsfGmUfGmUfGmCfAm 451 vmUpsfGpsmAfAmGfCmGfAmAfGm CfUmUfCmGfCmUfUmCfA UfGmCfAmCfAmCfGmGpsmUpsmC 417 fCpsmUpsfGmCfUmAfUmGfCm 452 mApsfGpsmAfAmGfAmUfGmAfGmGf CfUmCfAmUfCmUfUmCfU CmAfUmAfGmCfAmGpsmUpsmU 417 fCpsmUpsfGmCfUmAfUmGfCm 452 mApsfGpsmAfAmGfAmUfGmAfGmGf CfUmCfAmUfCmUfUmCfU CmAfUmAfGmCfAmGpsmUpsmU 417 fCpsmUpsfGmCfUmAfUmGfCm 452 mApsfGpsmAfAmGfAmUfGmAfGmGf CfUmCfAmUfCmUfUmCfU CmAfUmAfGmCfAmGpsmUpsmU 417 fCpsmUpsfGmCfUmAfUmGfCm 452 mApsfGpsmAfAmGfAmUfGmAfGmGf CfUmCfAmUfCmUfUmCfU CmAfUmAfGmCfAmGpsmUpsmU 418 fGpsmUpsfGmGfUmGfGfAfCm 453 mApsfUpsmUfGmAfGmAfGmAfAmG UfUmCfUmCfUmCfAmAfU mUmCfCmAfCmCfAmCpsmGpsmA 418 fGpsmUpsfGmGfUmGfGfAfCm 454 vmApsfUpsmUfGmAfGmAfGmAfAm UfUmCfUmCfUmCfAmAfU GmUmCfCmAfCmCfAmCpsmGpsmA 419 fGpsmUpsfGmGfUmGfGmAfCm 455 mApsfUpsmUfGmAfGmAfGmAfAmGf UfUmCfUmCfUmCfAmAfU UmCfCmAfCmCfAmCpsmGpsmA 419 fGpsmUpsfGmGfUmGfGmAfCm 456 vmApsfUpsmUfGmAfGmAfGmAfAm UfUmCfUmCfUmCfAmAfU GfUmCfCmAfCmCfAmCpsmGpsmA 420 mCpsmCpsfGmUfGmUfGfCfAm 457 mUpsfGpsmAmAmGfCmGmAmAmG CmUmUmCmGmCmUmUmCm mUmGmCfAmCfAmCmGmGpsmUps A mC 421 mCpsmCpsfGmUmGmUfGfCfA 458 mUpsfGpsmAmAmGmCmGmAmAmG mAmUfUmCmGmCmUfUmCmA mUmGmCfAmCmAmCmGmGpsmUps mC 422 mCpsmCpsfGmUmGmUfGfCfA 459 mUpsfGpsmAmAmGmCmGmAmAmG mCmUfUmCmGmCmUfUmCmA mUmGmCfAmCmAmCmGmGpsmU3s mU 423 mCpsmCpsfGmUmGmUfGfCfA 460 mUpsfGpsmAmAmGmCmGmAmAmG mCmUfUmCmGmCmUfUmCmA mUmGmCfAmCmAmCmGmG5smU5s mU 423 mCpsmCpsfGmUmGmUfGfCfA 461 mUpsfGpsmAmAmGmCmGmAmAmG mCmUfUmCmGmCmUfUmCmA mUmGmCfAmCmAmCmGmGpsmU5s mU 423 mCpsmCpsfGmUmGmUfGfCfA 458 mUpsfGpsmAmAmGmCmGmAmAmG mCmUfUmCmGmCmUfUmCmA mUmGmCfAmCmAmCmGmGpsmUps mC 423 mCpsmCpsfGmUmGmUfGfCfA 458 mUpsfGpsmAmAmGmCmGmAmAmG mCmUfUmCmGmCmUfUmCmA mUmGmCfAmCmAmCmGmGpsmUps mC 423 mCpsmCpsfGmUmGmUfGfCfA 458 mUpsfGpsmAmAmGmCmGmAmAmG mCmUfUmCmGmCmUfUmCmA mUmGmCfAmCmAmCmGmGpsmUps mC 423 mCpsmCpsfGmUmGmUfGfCfA 462 vmUpsfGpsmAmAmGmCmGmAmAm mCmUfUmCmGmCmUfUmCmA GmUmGmCfAmCmAmCmGmGpsmU psmC 423 mCpsmCpsfGmUmGmUfGfCfA 463 vmUpsfGpsmAmAmGmCmGmAmAm mCmUfUmCmGmCmUfUmCmA GmUmGmCfAmCmAmCmGmGpsTps T 423 mCpsmCpsfGmUmGmUfGfCfA 447 mUpsfGpsmAmAmGmCmGmAmAmG mCmUfUmCmGmCmUfUmCmA mUmGmCfAmCmAmCmGmGpsmUps mU 423 mCpsmCpsfGmUmGmUfGfCfA 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vinyl phosphonate, 2′-O-methylnucleotide; vmB = vmN = VmU = cmU = mesnmU = mesnomU = d2vmU = d2vmA = d2vd3U = f4P = f2P = fX = ps = phosphorothioate linkage

TABLE 5 SEQ ID NO: Description Sequence+ 410 Hepatitis B aattccacaacctttcaccaaactctgcaagatcccagagtgagaggcctgtatttccctgctggtgg virus ctccagttcaggagcagtaaaccctgttccgactactgcctctcccttatcgtcaatcttctcgaggatt (Genbank ggggaccctgcgctgaacatggagaacatcacatcaggattcctaggaccccttctcgtgttacagg Accession cggggtttttcttgttgacaagaatcctcacaataccgcagagtctagactcgtggtggacttctctca No. attttctagggggaactaccgtgtgtcttggccaaaattcgcagtccccaacctccaatcactcacca U95551.1) acctcctgtcctccaacttgtcctggttatcgctggatgtgtctgcggcgttttatcatcttcctcttcatc ctgctgctatgcctcatcttcttgttggttcttctggactatcaaggtatgttgcccgtttgtcctctaattc caggatcctcaaccaccagcacgggaccatgccgaacctgcatgactactgctcaaggaacctcta tgtatccctcctgttgctgtaccaaaccttcggacggaaattgcacctgtattcccatcccatcatcctg ggctttcggaaaattcctatgggagtgggcctcagcccgtttctcctggctcagtttactagtgccattt gttcagtggttcgtagggctttcccccactgtttggctttcagttatatggatgatgtggtattgggggc caagtctgtacagcatcttgagtccctttttaccgctgttaccaattttcttttgtctttgggtatacatttaa accctaacaaaacaaagagatggggttactctctgaattttatgggttatgtcattggaagttatgggtc cttgccacaagaacacatcatacaaaaaatcaaagaatgttttagaaaacttcctattaacaggcctat tgattggaaagtatgtcaacgaattgtgggtcttttgggttttgctgccccatttacacaatgtggttatc ctgcgttaatgcccttgtatgcatgtattcaatctaagcaggctttcactttctcgccaacttacaaggcc tttctgtgtaaacaatacctgaacctttaccccgttgcccggcaacggccaggtctgtgccaagtgttt gctgacgcaacccccactggctggggcttggtcatgggccatcagcgcgtgcgtggaaccttttcg gctcctctgccgatccatactgcggaactcctagccgcttgttttgctcgcagcaggtctggagcaaa cattatcgggactgataactctgttgtcctctcccgcaaatatacatcgtatccatggctgctaggctgt gctgccaactggatcctgcgcgggacgtcctttgtttacgtcccgtcggcgctgaatcctgcggacg accatcteggggtcgcttgggactctctcgtccccttctccgtctgccgttccgaccgaccacgggg cgcacctctattacgcggactccccgtctgtgccttctcatctgccggaccgtgtgcacttcgcttca cctctgcacgtcgcatggagaccaccgtgaacgcccaccgaatgttgcccaaggtcttacataaga ggactatggactctctgcaatgtcaacgaccgaccttgaggcatacttcaaagactgtttgtttaaag actgggaggagttgggggaggagattagattaaaggtetttgtactaggaggctgtaggcataaatt ggtctgcgcaccagcaccatgcaactttttcacctctgcctaatcatctcttgttcatgtcctactgttca agcctccaagctgtgccttgggtggctttggggcatggacatcgacccttataaagaatttggagcta ctgtggagttactctcgttfttgccttctgacttctttccttcagtacgagatcttctagataccgcctcag ctctgtatcgggaagccttagagtctcctgagcattgttcacctcaccatactgcactcaggcaagca attctttgctggggggaactaatgactctagctacctgggtgggtgttaatttggaagatccagcatct agagacctagtagtcagttatgtcaacactaatatgggcctaaagttcaggcaactcttgtggtttcac atttcttgtctcacttttggaagagaaaccgttatagagtatttggtgtctttcggagtgtggattcgcact cctccagatatagaccaccaaatgcccctatcctatcaacacttccggaaactactgttgttagacga cgaggcaggtcccctagaagaagaactccctcgcctcgcagacgaaggtctcaatcgccgcgtcg cagaagatctcaatctcgggaacctcaatgttagtattccttggactcataaggtggggaactttactg gtctttattcttctactgtacctgtctttaatcctcattggaaaacaccatcttttcctaatatacatttacacc aagacattatcaaaaaatgtgaacagtttgtaggcccacttacagttaatgagaaaagaagattgcaa ttgattatgcctgctaggttttatccaaaggttaccaaatatttaccattggataagggtattaaaccttat tatccagaacatctagttaatcattacttccaaactagacactatttacacactctatggaaggcgggta tattatataagagagaaacaacacatagcgcctcattttgtgggtcaccatattcttgggaacaagatc tacagcatggggcagaatctttccaccagcaatcctctgggattctttcccgaccaccagttggatcc agccttcagagcaaacacagcaaatccagattgggacttcaatcccaacaaggacacctggccag acgccaacaaggtaggagctggagcattcgggctgggtttcaccccaccgcacggaggccttttg gggtggagccctcaggctcagggcatactacaaactttgccagcaaatccgcctcctgcctccacc aatcgccagacaggaaggcagcctaccccgctgtctccacctttgagaaacactcatcctcaggcc atgcagtgg 411 MCJ mRNA agtcactgccgcggcgccttgagtctccgggccgccttgccatggctgcccgtggtgtcatcgctc (GenBank cagttggcgagagtttgcgctacgctgagtacttgcagccctcggccaaacggccagacgccgac Accession gtcgaccagcagagactggtaagaagtttgatagctgtaggactgggtgttgcagctcttgcatttgc No. aggtcgctacgcatttcggatctggaaacctctagaacaagttatcacagaaactgcaaagaagattt NM_013238.3) caactcctagcttttcatcctactataaaggaggatttgaacagaaaatgagtaggcgagaagctggt cttattttaggtgtaagcccatctgctggcaaggctaagattagaacagctcataggagagtcatgatt ttgaatcacccagataaaggtggatctccttacgtagcagccaaaataaatgaagcaaaagacttgct agaaacaaccaccaaacattgatgcttaaggaccacactgaaggaaaaaaaaagaggggacttcg aaaaaaaaaaaagccctgcaaaatattctaaaacatggtcttcttaattttctatatggattgaccacag tcttatcttccaccattaagctgtataacaataaaatgttaatagtcttgctttttattatcttttaaagatctc cttaaattctataactgatcttttttcttattttgtttgtgacattcatacatttttaagatttttgttatgttctgaa ttcccccctacacacacacacacacacacacacacacacacgtgcaaaaaatatgatcaagaatgc aattgggatttgtgagcaatgagtagacctcttattgtttatatttgtaccctcattgtcaatttttttttagg gaatttgggactctgcctatataaggtgttttaaatgtcttgagaacaagcactggctgatacctcttgg agatatgatctgaaatgtaatggaatttattaaatggtgtttagtaaagtaggggttaaggacttgttaaa gaaccccactatctctgagaccctatagccaaagcatgaggacttggagagctactaaaatgattca ggtttacaaaatgagccctgtgaggaaaggttgagagaagtctgaggagtttgtatttaattatagtctt ccagtactgtatattcattcattactcattctacaaatatttattgaccccttttgatgtgcaaggcactatc gtgcgtcccctgagagttgcaagtatgaagcagtcatggatcatgaaccaaaggaacttatatgtag aggaaggataaatcacaaatagtgaatactgttagatacagatgatatattttaaaagttcaaaggaag aaaagaatgtgttaaacactgcatgagaggaggaataagtggcatagagctaggctttagaaaaga aaaatattccgataccatatgattggtgaggtaagtgttattctgagatgagaattagcagaaatagat atatcaatcggagtgattagagtgcagggtttctggaaagcaaggtttggacagagtggtcatcaaa ggccagccctgtgacttacactgcattaaattaatttcttagaacatagtccctgatcattatcactttact attccaaaggtgagagaacagattcagatagagtgccagcattgtttcccagtattcctttacaaatctt gggttcattccaggtaaactgaactactgcattgtttctatcttaaaatactttttagatatcctagatgcat cttcaacttctaacattctgtagtttaggagttctcaaccttggcattattgacatgttaggccaaataatt ttttttgtgggaggtctcttgtgcgttttagatgattagcaataatccctgacctgttatctactaaagact agtcgtttctcatcagttgtgacaacaaaaatggttccagatattgccaaatgccctttagaggacagt aatcgcccccagttgagaaccatttcagtaaaactttaattactattttttcttttggtttataaaataatgat cctgaattaaattgatggaaccttgaagtcgataaaatatatttcttgctttaaagtccccatacgtgtcct actaattttctcatgctttagtgttttcacttttctcctgttatccttgtacctaagaatgccatcccaatccc cagatgtccacctgcccaaagtctaggcatagctgaaggccaagctaaaatgtatccctctttttctgg tacatgcagcaaaagtaatatgaattatcagctttctgagagcaggcattgtatctgtcttgtttggtgtt acattggcacccaataaatatttgttgagtgaatgaataaattcccatagcactttattcttcacatggta cataactataggggctatagcttggtaccttgtgaagcaactcttggtgtaacataccttatttctcatac taaaatgcaagaacctttagagcaaggatcttgccattcatctttgtaacctctttactctggagcacttg catttagcaggcatcataaagttttacgtaccaagaaaatgttgctgttttctgaatactatgcatcaaaa aatgttaccactaatttttaaagctctgctaaggaatattggggcaccctcagatgcaccttttaattgat gtcatattttcctaatccatactttattcatgagaatttgagtcaccccagcattagcttggaatttccttatt tcccatttgctttgcaggtgccttggagtcagatctggttttgaatactatcttcctgttatgtgatcttgg gcagttacttaattttctagtcaataacccgtatctataaaatagagaaaataatcctacacaccgggg cctgttgtggggcggggagaggggggagggatcgcatttggagatatactaatgtaaatgacaagt taattggtgcagcacaccaacatggctcatgtctacatatgtaacaaacctgcacgttgtgcacatgtg ccctagaacttaaagtataataaaaagaaattttaaaaaatcctgtcaaataaggttatagtagagaata aggatgtgtaaagcatttagtcacgtaaatgcttaaaaaaatgtaatttttacttctttcactgcctcattta attagttttatctttaataataccttggattcagggtaaagtttcagttatgtcccagtaatcatttattttacc ctcgaatctgcaatttggatagaacatggtggggacagctcgtctctattccttgcagcattaacagg ctggaggcaccacttctctggccagcaagttgggcctggttgttggctgagagcctcagttcctttct gcacaggttcctctttacataggcttctcaacagggctactagagcatcgtcaccatagcagctgtctt ataacagagagtggtcggtctgagagacaaaaaatggaagctgccaaattgttctgggtctggaaa ctgtcagggcatcacttgtgccatattcagttggcctaagaattacagagcctgcctcgattcaaagg gagaggatagagaggactgaaggaatcagtgctcatctttaatatgcagcaggacaggtttgggatt ttttttcccccttgagtctgtgaaggcattacttaagaacaaagtcaggcatgtataattgaactacagtt acttgaaatataagcccagaaagtttcagataataaatacaactatttttctgctgttacccttgtacctaa agatgccatcctaatccccagatctccacaactatacctacatagtagaaggttaaaatgtatccctctt tttctggtgcatccagcaaaagtaatatcatgaattatgagctctctgagagcaaggatcatatcagtct tgtttattgttgcagtgaacaagtacagttgcagatattcaggagtaattatctaaatggcagtaggctt ataaaactgaattttcaccagccacaccctccccccaactccttatctgtaaaaagcttatttgagtggt tacctgtcttcagtaaagattgcgcttgcatatttgctgtcattgcatattctgcttaattaagctctgttga tattgcagtttctgtgcatacttacatcttagatgcaatctgagggcctaggaaggccttttaaaaataa aacaattccgattgcagagaaagtgtaagtcaaggacagttaattcaaggggaacatagaaagctat ttagattttagttgatggtgccagtcttcagcgtaaagtcaaaagtggagggaagtttagtaaggaaa aaatgttgggcttggaatacattgtttagtcttcaaagcactttactttttatgaaatatattttagacattca gcaaatattgaatacttactatatcaggcagtaaagatataaattcattcttaaaatgtgcaacatgttca aactgaaaaaaatacattcttaaacaggaaactttttccttcatactttttaattaacaagacatataaga gttgcattaatgggcgtgcttatgattgatcacccagcagcatcattagaaataatatattttattcatgt gcagaaatcttttggttgtcctggggaaccttgaacacagaaaagagcttttattgataaggtaattga acacacttgacaattagcttaatatggtttaataccatttgtgggagaagatgaatcagccaggctcttt acgtcaagaatatgaagtttctcttgagtcaaccaacttaagatgagctacggagactgcagtgaaaa gttaaatatccaagtacaccagccaatttcacacagtggaaccatgctgtcctcgggcacctgcac ctcgcccaacagtcatcaactagatggaggctcctggctgcaaggaggatttgatgggaatgagta aatgtgtcagcatagtccgtcccttctaatggaaaagcaacccaaagagcaaatcctattaatggctg gatcagtatcatctacttgtcaaaaacattccatgaattatgagtcaaaattttatttatggtggcattaca cacattaagagatgaggacttctgttagcataatttattagctggaaaagttgagaaggttctctggact catttttataggtggaacctaagtgatctggataattgcccaccagcaaaattgctgggcatggtgga caaagaaaatgttccttctaatgattttttatgagctgagtagctattgttcccagctgagtgctcttttcct ctttttattgttgctgagcaaaagaatttataaaaagctctttcttttgtattaaaaaccctgctcaattgaa atgcaagttcattaagtaatcttcatttctcttcctgccataataaccctttccctctctgttcgattcaaca gtatctagcagcactgctccaaattttaagtctgaacagactatattacatagatgtagagaaatactca atcttcagcattaagagggagcttaatttcacacgggtggaatatgatcactcaggctagatgttggc cataaatttcaaattagtatctcaacttagcaggggggatcaacagtggcaaacttcaattatgacagg ataaaaatcacatagagatattggttcaatatggacatctaaactataatgctaaaagccaataattaga ataagttcattttaagaaaagcattaataatattagctaacgtttagtacctgtgccaaacattctacctat gttaccttgattttcatagccagcctaagaggtactattatgtatccccattttacaggttaagaaacagg ctcagaggagtttaggatcttttccaagattacatagccagtaagtggtggcactaggaaccaaattc agactctgaatcgcatgctgtttatattatattgcactcattctaaatatgtgggaatcagaatgaaggg gcttgtatgacttttggctcattttttgatgcatgtgacctgggattataaatgtgaaattaggtttacgaa aggatccagtgtcattgtgcatcatgggcaaggagtacctaatctctttaattcttccctggaagcttac gatgtccatccaagtgcacatagcaaaagttctgttgtaaagtttagcagagtgactttctttgactcag agtgatgacggaggaagctttgataagattttatctgaaatgttcatggacaagagctttcaaggaga acatccagagcaaggttctgaagacagctcatgaaggtgaagcagcagacctggcacaagaaatg aagagagagctcagtgtattaaagatgaaaacaagaaaaccgaatatattgaaaggagcagagag gcaatgaaaacaagacaactgaaatgaggtaacttgcagcaattgaaagggaatttcagtacttttat agaattcttaaaaattgtttcctgctgtttattttcaattttgaacagggttatttgtccatgccatacttttttt gccaaattccaaaattgtgtatagttctatagttgtctggtggagtcaatggaactttagttaccagtcta agaatgtgtctttgagattgtccagttaattctctatttccagtagctgtaataaatggtgaaaaggtttct gactcctggagaaagtttctaactccttatgactaatattcataacagacttgtgagttccttgaacatgg atacacctatatgcaagagtgtattccaaagctaactcagtgatctttccatttatctattcttggattagt ggtgcctttgctctttccttctgtaaatgtgaatagttaagagttgactgcagaagtgtttacactttggct tccatgcctctggaatgtttgtgctttggtggtgagatgtgagactatatttgtatagtctgcatctctcag gctgccccagaatgttgtacagtgcagtgctgaagaaagcagcaggtacacacagaaatgcagcc tttcctggttaaccctgcttggatctgagttacactttgtttcctgacttcttgggacttaggtaatcagttt gccttctactctatctcattttgtactcgcttacatactacattcttgtttgggctttcgtttcttcttgtaagc agagattttttaaaatccaatatgtgaaaatacggatgcactacaattaaataaataaaatgctgttgtgt ttgttttgctttaaaattgtaaaggataaacaataagatagttttatctatgtggttttcccgatgcagttaa aataaaacctaatctgctaaaattgaa 412 TAZ gctttccggcggttgcaccgggccggggtgccagcgcccgccttcccgtttcctcccgttccgcag (GenBank cgcgcccacggcctgtgaccccggcgaccgctccccagtgacgagagagcggggccgggcgc Accession tgctccggcctgacctgcgaagggacctcggtccagtcccctgttgcgccgcgcccccgtccgtcc No. gtgcgcgggccagtcaggggccagtgtctcgagcggtcgaggtcgcagacctagaggcgcccc NM_000116.5) acaggccggcccggggcgctgggagcgccggccgcgggccgggtggggatgcctctgcacgt gaagtggccgttccccgcggtgccgccgctcacctggaccctggccagcagcgtcgtcatgggct tggtgggcacctacagctgcttctggaccaagtacatgaaccacctgaccgtgcacaacagggag gtgctgtacgagctcatcgagaagcgaggcccggccacgcccctcatcaccgtgtccaatcacca gtcctgcatggacgaccctcatctctgggggatcctgaaactccgccacatctggaacctgaagttg atgcgttggacccctgcagctgcagacatctgcttcaccaaggagctacactcccacttcttcagctt gggcaagtgtgtgcctgtgtgccgaggagcagaatttttccaagcagagaatgaggggaaaggtg ttctagacacaggcaggcacatgccaggtgctggaaaaagaagagagaaaggagatggcgtcta ccagaaggggatggacttcattttggagaagctcaaccatggggactgggtgcatatcttcccagaa gggaaagtgaacatgagttccgaattcctgcgtttcaagtggggaatcgggcgcctgattgctgagt gtcatctcaaccccatcatcctgcccctgtggcatgtcggaatgaatgacgtccttcctaacagtccg ccctacttcccccgctttggacagaaaatcactgtgctgatcgggaagcccttcagtgccctgcctgt actcgagcggctccgggcggagaacaagtcggctgtggagatgcggaaagccctgacggacttc attcaagaggaattccagcatctgaagactcaggcagagcagctccacaaccacctccagcctgg gagataggccttgcttgctgccttctggattcttggcccgcacagagctggggctgagggatggact gatgcttttagctcaaacgtggcttttagacagatttgttcatagaccctctcaagtgccctctccgagc tggtaggcattccagctcctccgtgcttcctcagttacacaaaggacctcagctgcttctcccacttgg ccaagcagggaggaagaagcttaggcagggctctctttccttcttgccttcagatgttctctcccagg ggctggcttcaggagggagcatagaaggcaggtgagcaaccagttggctaggggagcaggggg cccaccagagctgtggagaggggaccctaagactcctcggcctggctcctacccaccgcccttgc cgaaccaggagctgctcactacctcctcagggatggccgttggccacgtcttccttctgcctgagctt cccccccaccacaggccctttcctcaggcaaggtctggcctcaggtgggccgcaggcgggaaaa gcagcccttggccagaagtcaagcccagccacgtggagcctagagtgagggcctgaggtctggc tgcttgcccccatgctggcgccaacaacttctccatcctttctgcctctcaacatcacttgaatcctagg gcctgggttttcatgtttttgaaacagaaccataaagcatatgtgttggcttgttgtaaaa 413 ANGPTL3 agaagaaaacagttccacgttgcttgaaattgaaaatcaagataaaaatgttcacaattaagctccttc (GenBank tttttattgttcctctagttatttcctccagaattgatcaagacaattcatcatttgattctctatctccagag Accession ccaaaatcaagatttgctatgttagacgatgtaaaaattttagccaatggcctccttcagttgggacatg No. gtcttaaagactttgtccataagacgaagggccaaattaatgacatatttcaaaaactcaacatatttga NM_014495.4) tcagtctttttatgatctatcgctgcaaaccagtgaaatcaaagaagaagaaaaggaactgagaaga actacatataaactacaagtcaaaaatgaagaggtaaagaatatgtcacttgaactcaactcaaaactt gaaagcctcctagaagaaaaaattctacttcaacaaaaagtgaaatatttagaagagcaactaactaa cttaattcaaaatcaacctgaaactccagaacacccagaagtaacttcacttaaaacttttgtagaaaa acaagataatagcatcaaagaccttctccagaccgtggaagaccaatataaacaattaaaccaacag catagtcaaataaaagaaatagaaaatcagctcagaaggactagtattcaagaacccacagaaattt ctctatcttccaagccaagagcaccaagaactactccctttcttcagttgaatgaaataagaaatgtaa aacatgatggcattcctgctgaatgtaccaccatttataacagaggtgaacatacaagtggcatgtat gccatcagacccagcaactctcaagtttttcatgtctactgtgatgttatatcaggtagtccatggacatt aattcaacatcgaatagatggatcacaaaacttcaatgaaacgtgggagaactacaaatatggttttg ggaggcttgatggagaattttggttgggcctagagaagatatactccatagtgaagcaatctaattat gttttacgaattgagttggaagactggaaagacaacaaacattatattgaatattctttttacttgggaaa tcacgaaaccaactatacgctacatctagttgcgattactggcaatgtccccaatgcaatcccggaaa acaaagatttggtgttttctacttgggatcacaaagcaaaaggacacttcaactgtccagagggttatt caggaggctggtggtggcatgatgagtgtggagaaaacaacctaaatggtaaatataacaaaccaa gagcaaaatctaagccagagaggagaagaggattatcttggaagtctcaaaatggaaggttatactc tataaaatcaaccaaaatgttgatccatccaacagattcagaaagctttgaatgaactgaggcaaattt aaaaggcaataatttaaacattaacctcattccaagttaatgtggtctaataatctggtattaaatccttaa gagaaagcttgagaaatagattttttttatcttaaagtcactgtctatttaagattaaacatacaatcacat aaccttaaagaataccgtttacatttctcaatcaaaattcttataatactatttgttttaaattttgtgatgtg ggaatcaattttagatggtcacaatctagattataatcaataggtgaacttattaaataacttttctaaata aaaaatttagagacttttattttaaaaggcatcatatgagctaatatcacaactttcccagtttaaaaaact agtactcttgttaaaactctaaacttgactaaatacagaggactggtaattgtacagttcttaaatgttgt agtattaatttcaaaactaaaaatcgtcagcacagagtatgtgtaaaaatctgtaatacaaatttttaaac tgatgcttcattttgctacaaaataatttggagtaaatgtttgatatgatttatttatgaaacctaatgaagc agaattaaatactgtattaaaataagttcgctgtctttaaacaaatggagatgactactaagtcacattg actttaacatgaggtatcactataccttatttgttaaaatatatactgtatacattttatatattttaacactta atactatgaaaacaaataattgtaaaggaatcttgtcagattacagtaagaatgaacatatttgtggcat cgagttaaagtttatatttcccctaaatatgctgtgattctaatacattcgtgtaggttttcaagtagaaat aaacctcgtaacaagttactgaacgtttaaacagcctgacaagcatgtatatatgtttaaaattcaataa acaaagacccagtccctaaattatagaaatttaaattattcttgcatgtttatcgacatcacaacagatcc ctaaatccctaaatccctaaagattagatacaaattttttaccacagtatcacttgtcagaatttatttttaa atatgattttttaaaactgccagtaagaaattttaaattaaacccatttgttaaaggatatagtgcccaagt tatatggtgacctacctttgtcaatacttagcattatgtatttcaaattatccaatatacatgtcatatatattt ttatatgtcacatatataaaagatatgtatgatctatgtgaatcctaagtaaatattttgttccagaaaagt acaaaataataaaggtaaaaataatctataattttcaggaccacagactaagctgtcgaaattaacgct gatttttttagggccagaataccaaaatggctcctctcttcccccaaaattggacaatttcaaatgcaaa ataattcattatttaatatatgagttgcttcctctatttggtttcc 414 DGAT2 tgccccgttgtgaggtgataaagtgttgcgctccgggacgccagcgccgcggctgccgcctctgct (GenBank ggggtctaggctgtttctctcgcgccaccactggccgccggccgcagctccaggtgtcctagccgc Accession ccagcctcgacgccgtcccgggacccctgtgctctgcgcgaagccctggccccgggggccggg No. gcatgggccaggggcgcggggtgaagcggcttcccgcggggccgtgactgggcgggcttcagc NM_001253891.1) catgaagaccctcatagccgcctactccggggtcctgcgcggcgagcgtcaggccgaggctgac cggagccagcgctctcacggaggacctgcgctgtcgcgcgaggggtctgggagatggggagtg gcctgcagtgccatcctcatgtacatattctgcactgattgctggctcatcgctgtgctctacttcacttg gctggtgtttgactggaacacacccaagaaaggtggcaggaggtcacagtgggtccgaaactggg ctgtgtggcgctactttcgagactactttcccatccagctggtgaagacacacaacctgctgaccacc aggaactatatctttggataccacccccatggtatcatgggcctgggtgccttctgcaacttcagcac agaggccacagaagtgagcaagaagttcccaggcatacggccttacctggctacactggcaggca acttccgaatgcctgtgttgagggagtacctgatgtctggaggtatctgccctgtcagccgggacac catagactatttgctttcaaagaatgggagtggcaatgctatcatcatcgtggtcgggggtgcggctg agtctctgagctccatgcctggcaagaatgcagtcaccctgcggaaccgcaagggctttgtgaaact ggccctgcgtcatggagctgacctggttcccatctactcctttggagagaatgaagtgtacaagcag gtgatcttcgaggagggctcctggggccgatgggtccagaagaagttccagaaatacattggtttcg ccccatgcatcttccatggtcgaggcctcttctcctccgacacctgggggctggtgccctactccaag cccatcaccactgttgtgggagagcccatcaccatccccaagctggagcacccaacccagcaaga catcgacctgtaccacaccatgtacatggaggccctggtgaagctcttcgacaagcacaagaccaa gttcggcctcccggagactgaggtcctggaggtgaactgagccagccttcggggccaattccctg gaggaaccagctgcaaatcacttttttgctctgtaaatttggaagtgtcatgggtgtctgtgggttattta aaagaaattataacaattttgctaaaccattacaatgttaggtcttttttaagaaggaaaaagtcagtattt caagttctttcacttccagcttgccctgttctaggtggtggctaaatctgggcctaatctgggtggctca gctaacctctcttcttcccttcctgaagtgacaaaggaaactcagtcttcttggggaagaaggattgcc attagtgacttggaccagttagatgattcactttttgcccctagggatgagaggcgaaagccacttctc atacaagcccctttattgccactaccccacgctcgtctagtcctgaaactgcaggaccagtttctctgc caaggggaggagttggagagcacagttgccccgttgtgtgagggcagtagtaggcatctggaatg ctccagtttgatctcccttctgccacccctacctcacccctagtcactcatatcggagcctggactggc ctccaggatgaggatgggggtggcaatgacaccctgcaggggaaaggactgccccccatgcacc attgcagggaggatgccgccaccatgagctaggtggagtaactggtttttcttgggtggctgatgac atggatgcagcacagactcagccttggcctggagcacatgcttactggtggcctcagtttaccttccc cagatcctagattctggatgtgaggaagagatccctcttcagaaggggcctggccttctgagcagca gattagttccaaagcaggtggcccccgaacccaagcctcacttttctgtgccttcctgagggggttg ggccggggaggaaacccaaccctctcctgtgtgttctgttatctcttgatgagatcattgcaccatgtc agacttttgtatatgccttgaaaataaatgaaagtgagaatcctctaaaaaaaaaaaa 596 HBV ctccaccactttccaccaaactcttcaagatcccagagtcagggccctgtactttcctgctggtggctc Genbank aagttccggaacagtaaaccctgctccgactactgcctctcccatatcgtcaatcttctcgaggactg Accession gggaccctgtaccgaatatggagagcaccacatcaggattcctaggacccctgctcgtgttacagg No. cggggtttttcttgttgacaagaatcctcacaataccacagagtctagactcgtggtggacttctctca KC315400.1 attttctagggggagcacccacgtgtcctggccaaaatttgcagtccccaacctccaatcactcacca acctcttgtcctccaatttgtcctggttatcgctggatgtgtctgcggcgttttatcatcttcctcttcatcc tgctgctatgcctcatcttcttgttggttcttctggactaccaaggtatgttgcccgtttgtcctctacttcc aggaacatcaactaccagcaccggaccatgcaaaacctgcacaactactgctcaagggacctctat gtttccctcatgttgctgtacaaaacctacggacggaaactgcacctgtattcccatcccatcatcttgg gctttcgcaaaatacctatgggagtgggcctcagtccgtttctcttggctcagtttactagtgccatttgt tcagtggttcgtagggattcccccactgtctggctttcagttatatggatgatgtggttttgggggcca agtctgtacaacatcttgagtccctttataccgctgttaccaattttcttttatctttgggtatacatttaaac cctcacaaaacaaaaagatggggatattcccttaacttcatgggatatgtaattgggagttggggcac tttgcctcaggaacatattgtacaaaaaatcaagcaatgttttaggaaacttcctgtaaacaggcctatt gattggaaagtatgtcaacraattgtgggtcttttggggtttgccgcccctttcacgcaatgtggatatc ctgctttaatgcctttatatgcatgtatacaagctaagcaggcttttactttctcgccaacttacaaggcct ttctgtgtaaacaatatctgaacctttaccccgttgctcggcaacggtcaggtctttgccaagtgtttgct gacgcaacccccactggttggggcttggccataggccatcagcgcatgcgtggaacctttgtggct cctctgccgatccatactgcggaactcctagcagcttgttttgctcgcagccggtctggagcaaaact tatcggcaccgacaactctgttgtcctctctcggaaatacacctcctttccatggctgctaggatgtgct gccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctgaatcccgcggacgac ccatctcggggccgtttgggactctaccgtccccttctgcgtctgccgttccgcccgaccacggggc gcacctctctttacgcggtctccccgtctgtgccttctcatctgccggaccgtgtgcacttcgcttcacc tctgcacgtcgcatggagaccaccgtgaacgcccacgggaacctgcccaaggtcttgcataagag gactcttggactttcagcaatgtcaacgaccgaccttgaggcatacttcaaagactgtgtgtttactga gtgggaggagttgggggaggaggttaggttaaaggtctttgtactaggaggctgtaggcataaattg gtgtgttcaccagcaccatgcaactttttcacctctgcctaatcatctcatgttcatgtcctactgttcaag cctccaagctgtgccttgggtggctttggggcatggacattgacccgtataaagaatttggagcttct gtggagttactctattttttgccttctgacttctttccttctattcgagatctcctcgacaccgcctctgctct gtatcgggaggccttagagtctccggaacattgttcacctcaccatacggcactcaggcaagcaatt ctgtgttggggtgagttaatgaatctagccacctgggtgggaagtaatttggaagatccagcatcca gggaattagtagtcagctatgtcaacgttaatatgggcctaaaaatcagacaactattgtggtttcaca tttcctgtcttacttttgggagagaaactgttcttgaatatttggtgtcttttggagtgtggattcgcactcc tcctgcatatagaccacaaaatgcccctatcttatcaacacttccggaaactactgttgttagacgaag aggcaggtcccctagaagaagaactccctcgcctcgcagacgaaggtctcaatcgccgcgtcgca gaagatctcaatctcgggaatctcaatgttagtattccttggacacataaggtgggaaactttacggg gctttattcttctacggtaccttgctttaatcctaaatggcaaactccttcttttcctgacattcatttgcag gaggacattgttgatagatgtaagcaatttgtggggccccttacagtaaatgaaaacaggagacttaa attaattatgcctgctaggttttatcccaatgttactaaatatttgcccttagataaagggatcaaaccgta ttatccagagtatgtagttaatcattacttccagacgcgacattatttacacactctttggaaggcgggg atcttatataaaagagagtccacacgtagcgcctcattttgcgggtcaccatattcttgggaacaagat ctacagcatgggaggttggtcttccaaacctcgaaaaggcatggggacaaatctttctgtccccaatc ccctgggattcttccccgatcatcagttggaccctgcattcaaagccaactcagaaaatccagattgg gacctcaacccacacaaggacaactggccggacgccaacaaggtgggagtgggagcattcggg ccagggttcacccctcctcatgggggactgttggggtggagccctcaggctcagggcatattcaca acagtgccagcagctcctcctcctgcctccaccaatcggcagtcaggaaggcagcctactcccttct ctccacctctaagagacactcatcctcaggccatgcagtggaa 534 ASO 1 GalNAc4-ps-GalNAc4-ps-GalNAc4-po-mA-po- lnGpslnApslnTpslnApslnApsApsAps(5OH)CpsGps(5m)Cps(5m)Cps Gps(5m)CpslnApslnGpslnApscp(5m)C 535 ASO 2 mA-po- lnGpslnApslnTpslnApslnApsApsAps(5OH)CpsGps(5m)Cps(5m)Cps Gps(5m)CpslnApslnGpslnApscp(5m)C +ln = Locked nucleic acid (LNA) = lnA = Locked nucleic acid (LNA) A; ln(5m)C = ln(5m)C = Locked nucleic acid (LNA)-5 methyl C; lnG = Locked nucleic acid (LNA) G; lnT = Locked nucleic acid (LNA) T; (5m)C = 5 methyl C; cp = scp = cyclopropyl; cpC = scpC = cyclopropyl C; scp(5m)C = cyclopropyl-5 methyl C; (5OH)C = po = phosphodiester linkage; ps = phosphorothioate linkage

TABLE 6 siNA Activity HepG2.2.15 HepG2.2.15 Sense Strand Antisense Strand in vitro in vitro ds-siNA ID SEQ ID NO. SEQ ID NO. EC50* CC50 (nM) ds-siNA-001 307 363 A >40 ds-siNA-002 308 364 A >40 ds-siNA-003 309 365 B >40 ds-siNA-004 310 366 B >40 ds-siNA-005 311 367 B >40 ds-siNA-006 312 368 C >40 ds-siNA-007 313 369 A >40 ds-siNA-008 314 370 A >40 ds-siNA-009 315 371 B >40 ds-siNA-010 316 372 A >40 ds-siNA-011 317 373 B >40 ds-siNA-012 318 374 A >40 ds-siNA-013 319 375 A >40 ds-siNA-014 320 376 B >40 ds-siNA-015 321 377 A >40 ds-siNA-016 322 377 C >40 ds-siNA-017 323 377 A >40 ds-siNA-018 324 378 A >40 ds-siNA-019 325 378 A >40 ds-siNA-020 326 379 A >40 ds-siNA-021 327 379 B >40 ds-siNA-022 328 380 A >40 ds-siNA-023 329 380 B >40 ds-siNA-024 330 381 A >40 ds-siNA-025 331 382 A >40 ds-siNA-026 332 383 C >40 ds-siNA-027 333 384 A >40 ds-siNA-028 334 385 B >40 ds-siNA-029 335 386 A >40 ds-siNA-030 336 387 C >40 ds-siNA-031 337 388 A >40 ds-siNA-032 338 388 C >40 ds-siNA-033 339 389 B >40 ds-siNA-034 340 389 C >40 ds-siNA-035 341 390 A >40 ds-siNA-036 342 391 A >40 ds-siNA-037 343 392 B >40 ds-siNA-038 344 393 A >40 ds-siNA-039 345 394 A >40 ds-siNA-040 346 395 A >40 ds-siNA-041 347 396 C >40 ds-siNA-042 348 397 A >40 ds-siNA-043 349 398 B >40 ds-siNA-044 350 399 A >40 ds-siNA-045 351 400 A >40 ds-siNA-046 352 401 A >40 ds-siNA-047 353 402 A >40 ds-siNA-048 354 403 A >40 ds-siNA-049 355 404 B >40 ds-siNA-050 356 405 A >40 ds-siNA-051 357 406 A >40 ds-siNA-052 358 406 A >40 ds-siNA-053 359 407 A >40 ds-siNA-054 360 407 A >40 ds-siNA-055 361 408 A >40 ds-siNA-056 362 409 A >40 ds-siNA-0164 423 482 *A = EC50 < 0.5 nM; B = 0.5 nM < EC50 < 1; C = EC50 > 1 nm

TABLE 10 siNA Activity Sense Antisense Strand Strand Max HBsAg SEQ 3′ Ligand SEQ HepG2.2.15 HepG2.2.15 Knock Down ds-siNA ID ID NO Monomer+ ID NO EC50* CC50 (nM) (Log10)** ds-siNA-057 415 p-(PS)2-GalNac4 445 ND ND X ds-siNA-058 415 p-(PS)2-GalNac4 446 ND ND X ds-siNA-059 415 p-(PS)2-GalNac4 447 ND ND Y ds-siNA-060 416 p-(PS)2-GalNac4 448 ND ND Y ds-siNA-061 416 p-(PS)2-GalNac4 449 ND ND Y ds-siNA-062 416 p-(PS)2-GalNac4 450 ND ND Y ds-siNA-063 416 p-(PS)2-GalNac4 451 ND ND X ds-siNA-064 417 5′-GalNAc4- 452 ND ND Y (PS)2-p-TEG-p ds-siNA-065 417 5′-GalNAc4- 452 ND ND Y (PS)2-p-HEG-p ds-siNA-066 417 5′-GalNAc4- 452 ND ND Y (PS)2-p-(HEG-p)2 ds-siNA-067 417 5′-GalNAc4- 452 ND ND Z (PS)2-p-(HEG-p)2 ds-siNA-068 418 p-(PS)2-GalNac4 453 ND ND Y ds-siNA-069 418 p-(PS)2-GalNac4 454 ND ND Y ds-siNA-070 419 p-(PS)2-GalNac4 455 ND ND Y ds-siNA-071 419 p-(PS)2-GalNac4 456 ND ND Y ds-siNA-072 420 p-(PS)2-GalNac4 457 ND ND X ds-siNA-073 421 p-(PS)2-GalNac4 458 ND ND X ds-siNA-074 422 p-(PS)2-GalNac4 459 ND ND Y ds-siNA-075 423 p-(PS)2-GalNac4 460 ND ND Y ds-siNA-076 423 p-(PS)2-GalNac4 461 ND ND Y ds-siNA-077 423 5′-GalNAc4- 458 ND ND Y (PS)2-p-TEG-p ds-siNA-078 423 5′-GalNAc4- 458 ND ND X (PS)2-p-HEG-p ds-siNA-079 423 5′-GalNAc4- 458 ND ND Y (PS)2-p-(HEG-p)2 ds-siNA-080 423 p-(PS)2-GalNac4 462 ND ND X ds-siNA-081 423 p-(PS)2-GalNac4 463 ND ND X ds-siNA-082 423 p-(PS)2-GalNac4 447 ND ND X ds-siNA-083 423 5′-GalNAc4- 458 ND ND Z (PS)2-p-(HEG-p)2 ds-siNA-084 423 p-(PS)2-GalNac4 457 ND ND X ds-siNA-085 423 p-(PS)2-GalNac4 464 ND ND X ds-siNA-086 423 p-(PS)2-GalNac4 465 ND ND X ds-siNA-087 423 p-(PS)2-GalNac4 466 ND ND Y ds-siNA-088 423 p-(PS)2-GalNac4 467 ND ND Z ds-siNA-089 423 p-(PS)2-GalNac4 468 ND ND Z ds-siNA-090 423 p-(PS)2-GalNac4 469 B >1000 X ds-siNA-091 423 p-(PS)2-GalNac4 470 C >1000 ND ds-siNA-092 423 p-(PS)2-GalNac4 471 B >1000 ND ds-siNA-093 423 p-(PS)2-GalNac4 472 B >1000 ND ds-siNA-094 423 p-(PS)2-GalNac4 473 B >1000 ND ds-siNA-095 423 p-(PS)2-GalNac4 474 C >1000 ND ds-siNA-096 423 p-(PS)2-GalNac4 475 B >1000 ND ds-siNA-097 423 p-(PS)2-GalNac4 476 B >1000 ND ds-siNA-098 423 p-(PS)2-GalNac4 477 A >1000 ND ds-siNA-099 423 p-(PS)2-GalNac4 478 B >1000 ND ds-siNA-0100 423 p-(PS)2-GalNac4 479 B >1000 ND ds-siNA-0101 423 p-(PS)2-GalNac4 480 B >1000 ND ds-siNA-0102 423 p-(PS)2-GalNac4 481 A >1000 ND ds-siNA-0103 423 p-(PS)2-GalNac4 482 ND ND ND ds-siNA-0104 423 p-(PS)2-GalNac4 483 ND ND ND ds-siNA-0105 423 p-(PS)2-GalNac4 458 ND ND Z ds-siNA-0106 423 p-(PS)2-GalNac4 458 ND ND Y ds-siNA-0107 424 p-(PS)2-GalNac4 457 ND ND X ds-siNA-0108 424 p-(PS)2-GalNac4 484 ND ND X ds-siNA-0109 424 p-(PS)2-GalNac4 485 ND ND X ds-siNA-0110 425 p-(PS)2-GalNac4 486 ND ND ND ds-siNA-0111 425 p-(PS)2-GalNac4 487 ND ND ND ds-siNA-0112 425 p-(PS)2-GalNac4 488 ND ND ND ds-siNA-0113 426 p-(PS)2-GalNac4 489 ND ND ND ds-siNA-0114 427 p-(PS)2-GalNac4 490 ND ND X ds-siNA-0115 428 p-(PS)2-GalNac4 491 ND ND Y ds-siNA-0116 429 p-(PS)2-GalNac4 492 ND ND ND ds-siNA-0117 429 p-(PS)2-GalNac4 493 ND ND ND ds-siNA-0118 429 p-(PS)2-GalNac4 494 ND ND ND ds-siNA-0119 430 p-(PS)2-GalNac4 495 ND ND X ds-siNA-0120 430 p-(PS)2-GalNac4 496 ND ND ND ds-siNA-0121 431 p-(PS)2-GalNac4 497 ND ND Y ds-siNA-0122 432 p-(PS)2-GalNac4 498 ND ND ND ds-siNA-0123 432 p-(PS)2-GalNac4 500 ND ND ND ds-siNA-0124 433 p-(PS)2-GalNac4 501 ND ND ND ds-siNA-0125 434 p-(PS)2-GalNac4 502 ND ND Y ds-siNA-0126 435 p-(PS)2-GalNac4 502 ND ND Y ds-siNA-0127 435 p-(PS)2-GalNac4 503 ND ND X ds-siNA-0128 435 p-(PS)2-GalNac4 501 ND ND X ds-siNA-0129 435 p-(PS)2-GalNac4 504 ND ND Y ds-siNA-0130 435 p-(PS)2-GalNac4 505 ND ND Z ds-siNA-0131 435 p-(PS)2-GalNac4 506 ND ND Y ds-siNA-0132 435 p-(PS)2-GalNac4 507 ND ND Z ds-siNA-0133 435 p-(PS)2-GalNac4 508 ND ND Z ds-siNA-0134 435 p-(PS)2-GalNac4 509 ND ND Z ds-siNA-0135 435 p-(PS)2-GalNac4 510 ND ND Y ds-siNA-0136 435 p-(PS)2-GalNac4 511 B >1000 ND ds-siNA-0137 435 p-(PS)2-GalNac4 512 B >1000 ND ds-siNA-0138 435 p-(PS)2-GalNac4 513 A >1000 ND ds-siNA-0139 435 p-(PS)2-GalNac4 514 B >1000 ND ds-siNA-0140 435 p-(PS)2-GalNac4 515 C >1000 ND ds-siNA-0141 435 p-(PS)2-GalNac4 516 A >1000 ND ds-siNA-0142 435 p-(PS)2-GalNac4 517 C >1000 ND ds-siNA-0143 435 p-(PS)2-GalNac4 518 C >1000 ND ds-siNA-0144 435 p-(PS)2-GalNac4 519 ND ND ND ds-siNA-0145 436 p-(PS)2-GalNac4 520 ND ND ND ds-siNA-0146 437 p-(PS)2-GalNac4 502 ND ND Y ds-siNA-0147 438 p-(PS)2-GalNac4 501 ND ND X ds-siNA-0148 438 p-(PS)2-GalNac4 521 ND ND X ds-siNA-0149 438 p-(PS)2-GalNac4 522 ND ND X ds-siNA-0150 439 p-(PS)2-GalNac4 523 ND ND X ds-siNA-0151 440 p-(PS)2-GalNac4 524 ND ND Y ds-siNA-0152 441 p-(PS)2-GalNac4 525 ND ND Y ds-siNA-0153 441 p-(PS)2-GalNac4 526 ND ND X ds-siNA-0154 441 p-(PS)2-GalNac4 527 ND ND ND ds-siNA-0155 442 p-(PS)2-GalNac4 525 ND ND X ds-siNA-0156 442 p-(PS)2-GalNac4 528 ND ND Y ds-siNA-0157 442 p-(PS)2-GalNac4 529 ND ND ND ds-siNA-0158 443 p-(PS)2-GalNac4 458 ND ND Y ds-siNA-0159 444 p-(PS)2-GalNac4 502 ND ND Y ds-siNA-0160 423 p-(PS)2-GalNac4 458 ND ND ND ds-siNA-0161 533 p-(PS)2-GalNac4 489 ND ND ND ds-siNA-0162 534 p-(PS)2-GalNac4 491 ND ND ND ds-siNA-0163 432 p-(PS)2-GalNac4 496 ND ND ND ds-siNA-0165 435 p-(PS)2-GalNac4 502 ND ND ND ds-siNA-0166 442 p-(PS)2-GalNac4 530 ND ND ND ds-siNA-0167 427 p-(PS)2-GalNAc4 491 ND ND ND ds-siNA-0168 439 p-(PS)2-GalNac4 531 ND ND ND ds-siNA-0169 423 p-(PS)2-GalNac4 532 ND ND ND ds-siNA-0170 441 p-(PS)2-GalNAc4 530 ND ND ND ds-siNA-0171 442 p-(PS)2-GalNac4 533 ND ND ND ds-siNA-0172 424 p-(PS)2-GalNac4 536 A   >1 ND ds-siNA-0173 438 None 537 ds-siNA-0174 438 None 538 ds-siNA-0175 438 None 501 ds-siNA-0176 438 p-(PS)2-GalNAc4 537 ds-siNA-0177 438 p-(PS)2-GalNAc4 538 ds-siNA-0178 438 p-(PS)2-GalNAc4 539 +Ligand monomers are attached to the 3′ end of the sense strand, unless the ligand monomer is annotated with 5′, in which the ligand monomer is attached to the 5′ end of the sense strand. Linkers are represented as p-(PS)2, (PS)2-p-TEG-p, (PS)2-p-HEG-p, or (PS)2-p-(HEG-p)2. *For EC50, A = EC50 ≤ 5 nM; B = 5 nM < EC50 < 10; C = EC50 ≥ 10. **For Max HBsAg knock down, X ≥1 log10 reduction in HBsAg, Y is 0.5-1 log10 reduction in HBsAg, and Z is <0.5 log10 reduction in HBsAg.

Claims

1. A method of treating hepatitis B virus (HBV) comprising administering to a subject with HBV a double stranded short interfering nucleic acid (siNA) comprising:

(a) a sense strand comprising 19-21 nucleotides in a nucleic acid sequence that is at least 80% identical to SEQ ID NO: 40, wherein 15 or more of the nucleotides are modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, and wherein at least 11 of the modified nucleotides are a 2′-O-methyl nucleotide and at least 4 of the modified nucleotides are a 2′-fluoro nucleotide; and
(b) an antisense strand comprising 19-21 nucleotides in a nucleic acid sequence that is at least 80% complementary to SEQ ID NO: 40, wherein 15 or more of the nucleotides are modified nucleotides independently selected from a 2′-O-methyl nucleotide and a 2′-fluoro nucleotide, and wherein at least 11 of the modified nucleotides are a 2′-O-methyl nucleotide and 4 to 6 of the modified nucleotides are a 2′-fluoro nucleotide.

2. The method of claim 1, wherein:

(a) the nucleotide(s) at position 3, 5, 7, 8, 9, 10, 11, 12, 14, 17, or 19 from the 5′ end of the sense strand is a 2′-fluoro nucleotide; and
(b) the nucleotide(s) at position 2, 5, 6, 8, 10, 14, 16, 17, or 18 from the 5′ end of the antisense strand is a 2′-fluoro nucleotide.

3. The method of claim 1, wherein the sense strand comprises SEQ ID NO: 438 or SEQ ID NO: 435, and the antisense strand comprises any one of SEQ ID NOs: 501-519, SEQ ID NO: 537, SEQ ID NO: 538, or SEQ ID NO: 539.

4. The method of claim 1, further comprising a N-acetylgalactosamine (GalNAc) attached to the 3′ of the sense strand.

5. A method of treating hepatitis B virus (HBV) comprising administering to a subject with HBV a double stranded short interfering nucleic acid (siNA) comprising:

(a) a sense strand comprising 19 nucleotides, wherein 2′-fluoro nucleotides are at positions 5 and 7-9 from the 5′ end of the sense strand, and wherein 2′-O-methyl nucleotides are at positions 1-4, 6, and 10-19 from the 5′ end of the sense strand; and
(b) an antisense strand comprising 21 nucleotides, wherein 2′-fluoro nucleotides are at positions 2, 6, 14, and 16 from the 5′ end of the antisense strand, and wherein 2′-O-methyl nucleotides are at positions 1, 3-5, 7-13, 15, and 17-21 from the 5′ end of the antisense strand.

6. The method of claim 5 further comprising (i) the nucleotides at positions 1 and 2 and positions 2 and 3 from the 5′ end of the sense strand are connected by phosphorothioate internucleoside linkages; and (ii) the nucleotides at positions 1 and 2; positions 2 and 3; positions 19 and 20; and positions 20 and 21 from the 5′ end of the antisense strand are connected by phosphorothioate internucleoside linkages.

7. The method of claim 5 further comprising a galactosamine attached to the sense strand.

8. The method of claim 7, wherein the conjugated moiety is N-acetylgalactosamine (GalNAc).

9. The method of claim 5, wherein the sense strand comprises SEQ ID NO: 438, and the antisense strand comprises any one of SEQ ID NO: 501, SEQ ID NO: 537, SEQ ID NO: 538, or SEQ ID NO: 539.

10. The method of claim 9, wherein the senses strand comprises SEQ ID NO: 438 and the antisense comprises SEQ ID NO: 501.

11. The method of claim 10, wherein the conjugated moiety is N-acetylgalactosamine (GalNAc).

12. The method of claim 11, wherein the GalNAc comprises a structure of Formula (VII): wherein n is 1, and R is OH.

13. The method of claim 5, wherein the sense strand is at least 80% identical to SEQ ID NO: 40 and the antisense strand is at least 80% complementary to SEQ ID NO: 40.

14. The method of claim 5, wherein the sense strand, the antisense strand, or both comprises at least one overhang consisting of 1 or 2 nucleotides.

15. A method of treating hepatitis B virus (HBV) comprising administering to a subject with HBV a double stranded short interfering nucleic acid (siNA) comprising: wherein GalNAc comprises a structure of Formula (VII): wherein n is 1, and R is OH.

(a) a sense strand of 5′-mGpsmUpsmGmGfUmGfGfAfCmUmUmCmUmCmUmCmAmAmU-p-ps2-GalNAc-3′ (SEQ ID NO: 438) and an anti sense strand of 5′-mApsfUJpsmUmGmAfGmAmGmAmAmGmUmCfCmAfCmCmAmCpsmG psmA-3′ (SEQ ID NO: 501);
(b) a sense strand of 5′-mGpsmUpsmGmGfUmGfGfAfCmUmUmCmUmCmUmCmAmAmU-p-ps2-GalNAc-3′ (SEQ ID NO: 438) and an anti sense strand of 5′-mApsfUpsmUmGmAfGmAfGfAmAmGmUmCf CmAfCmCmAmCpsmGps mA-3′ (SEQ ID NO: 521);
(c) a sense strand of 5′-mGpsmUpsmGmGfUmGfGfAfCmUmUmCmUmCmUmCmAmAmU-p-ps2-GaaNAc-3′ (SEQ ID NO: 438) and an antitsense strand of 5′-mApsfUpsmUmGfAmGmAfGmAmAmGmUmCfCmAmCfCmAmCpsmGp smA-3′ (SEQ ID NO: 522);
(d) a sense strand of 5′-mGpsmUpsmGmGfUmGfGfAfCmUmUmCmUmCmUmCmAmAmU-p-ps2-GalNAc-3′ (SEQ ID NO: 438) and an antisense strand of 5′-mApsf4PpsmUmGmAfGmAmGmAmAmGmUmCfCmAfCmCmAmCpsmG psmA-3′ (SEQ ID NO: 537);
(e) a sense strand of 5′-mGpsmUpsmGmGfUmGfGfAfCmUmUmCmUmCmUmCmAmAmU-p-ps2-GalNAc-3′ (SEQ ID NO: 438) and an antisense strand of 5′-mApsfUpsmUmGmAfGmAmGmAmAmGmUmCf2PmAfCmCmAmCpsmG psmA-3′ (SEQ ID NO: 538); or
(f) a sense strand of 5′-mGpsmUpsmGmGfUmGfGfAfCmUmUmCmUmCmUmCmAmAmU-p-ps2-GalNAc-3′ (SEQ ID NO: 438) and an antisense strand of 5′-mApsfJpsmUmGmAfGmAmGmAmAmGmUmCfCmAfXmCmAmCpsmG psmA-3′ (SEQ ID NO: 539), wherein fX is

16. The method of claim 15, comprising a sense strand of 5′-mGpsmUpsmGmGfUmGfGfAfCmUmUmCmUmCmUmCmAmAmU-p-ps2-GalNAc-3′ (SEQ ID NO: 438) and an antisense strand of 5′-mApsfUpsmUmGmAfGmAmGmAmAmGmUmCfCmAfCmCmAmCpsmGpsmA-3′ (SEQ ID NO: 501).

17. The method of claim 15, comprising a sense strand of 5′-mGpsmUpsmGmGfUmGfGfAfCmUmUmCmUmCmUmCmAmAmU-p-ps2-GalNAc-3′ (SEQ ID NO: 438) and an antisense strand of 5′-mApsfUpsmUmGmAfGmAfGfAmAmGmUmCfCmAfCmCmAmCpsmGpsmA-3′ (SEQ ID NO: 521).

18. The method of claim 15, comprising a sense strand of 5′-mGpsmUpsmGmGfUmGfGfAfCmUmUmCmUmCmUmCmAmAmU-p-ps2-GalNAc-3′ (SEQ ID NO: 438) and an antisense strand of 5′-mApsfUpsmUmGfAmGmAfGmAmAmGmUmCfCmAmCfCmAmCpsmGpsmA-3′ (SEQ ID NO: 522).

19. The method of claim 15, comprising a sense strand of 5′-mGpsmUpsmGmGfUmGfGfAfCmUmUmCmUmCmUmCmAmAmU-p-ps2-GalNAc-3′ (SEQ ID NO: 438) and an antisense strand of 5′-mApsf4PpsmUmGmAfGmAmGmAmAmGmUmCfCmAfCmCmAmCpsmGpsmA-3′ (SEQ ID NO: 537).

20. The method of claim 15, comprising a sense strand of 5′-mGpsmUpsmGmGfUmGfGfAfCmUmUmCmUmCmUmCmAmAmU-p-ps2-GalNAc-3′ (SEQ ID NO: 438) and an antisense strand of 5′-mApsfUpsmUmGmAfGmAmGmAmAmGmUmCf2PmAfCmCmAmCpsmGpsmA-3′ (SEQ ID NO: 538).

21. The method of claim 15, comprising a sense strand of 5′-mGpsmUpsmGmGfUmGfGfAfCmUmUmCmUmCmUmCmAmAmU-p-ps2-GalNAc-3′ (SEQ ID NO: 438) and an antisense strand of 5′-mApsfUpsmUmGmAfGmAmGmAmAmGmUmCfCmAfXmCmAmCpsmGpsmA-3′ (SEQ ID NO: 539), wherein fX is

22. A method of treating hepatitis B virus (HBV) comprising administering to a subject with HBV a short interfering nucleic acid (siNA) molecule comprising:

(a) a sense strand comprising a nucleic acid sequence consisting of SEQ ID NO: 438 or SEQ ID NO: 435, and
(b) an antisense strand comprising a nucleic acid sequence consisting of any one of SEQ ID NO: 501, SEQ ID NO: 505, SEQ ID NO: 506, SEQ ID NO: 537, SEQ ID NO: 538, and SEQ ID NO: 539.

23. The method of claim 22 further comprising a N-acetylgalactosamine (GalNAc) attached to the 3′ of the sense strand.

24. The method of claim 22, wherein the GalNAc comprises a structure of Formula (VII): wherein n is 1, and R is OH.

25. The method of claim 22, wherein the senses strand comprises a nucleic acid sequence consisting of SEQ ID NO: 438 and the antisense comprises a nucleic acid sequence consisting of SEQ ID NO: 501.

26. The method of claim 25 further comprising a N-acetylgalactosamine (GalNAc) attached to the 3′ of the sense strand.

27. The method of claim 26, wherein the GalNAc comprises a structure of Formula (VII): wherein n is 1, and R is OH.

28. The method of claim 25, wherein:

(a) the nucleotide(s) at position 3, 5, 7, 8, 9, 10, 11, 12, 14, 17, or 19 from the 5′ end of the sense strand is a 2′-fluoro nucleotide;
(b) the nucleotide(s) at position 2, 5, 6, 8, 10, 14, 16, 17, or 18 from the 5′ end of the antisense strand is a 2′-fluoro nucleotide;
(c) the nucleotides at positions 1 and 2 and positions 2 and 3 from the 5′ end of the sense strand are connected by phosphorothioate internucleoside linkages; and
(d) the nucleotides at positions 1 and 2; positions 2 and 3; positions 19 and 20; and positions 20 and 21 from the 5′ end of the antisense strand are connected by phosphorothioate internucleoside linkages.

29. The method of claim 28 further comprising a N-acetylgalactosamine (GalNAc) attached to the 3′ of the sense strand.

30. The method of claim 29, wherein the GalNAc comprises a structure of Formula (VII): wherein n is 1, and R is OH.

Patent History
Publication number: 20230332153
Type: Application
Filed: Nov 29, 2022
Publication Date: Oct 19, 2023
Applicant: Aligos Therapeutics, Inc. (South San Francisco, CA)
Inventors: Leonid Beigelman (San Mateo, CA), Vivek Kumar Rajwanshi (Cupertino, CA), Markus Hossbach (Kulmbach), Rajendra K. Pandey (Foster City, CA), Jin Hong (Pacifica, CA), Laxman Eltepu (San Ramon, CA), Saul Martinez Montero (San Bruno, CA), N. Tilani S. De Costa (South San Francisco, CA)
Application Number: 18/059,561
Classifications
International Classification: C12N 15/113 (20100101); A61K 31/713 (20060101); A61K 45/06 (20060101); A61P 31/20 (20060101);