Anti-PD-1 Antibodies and Fusion Proteins
Provided herein are recombinant antibodies, antigen-binding fragments, and fusion proteins thereof useful for binding to and inhibiting programmed death 1 (PD-1), nucleic acid molecules encoding the same and therapeutic compositions thereof, as well as methods of using such antibodies, including the methods for enhancing T cell and NK cell function to increase cell and cytokine mediated immunity and methods of treatment of various immune dysfunction related disorders including cancer and infectious diseases.
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This application is a national phase entry pursuant to 35 U.S.C. § 371 of International Application No. PCT/US2021/038740, filed Jun. 23, 2021, which claims the benefit of priority to U.S. Provisional Patent Application No. 63/043,114, filed Jun. 23, 2020, and to U.S. Provisional Patent Application No. 63/111,459, filed Nov. 9, 2020, which are incorporated by reference herein in their entireties.
SEQUENCE LISTINGThe present application contains a Sequence Listing which has been submitted in txt format. Said txt copy, created Jun. 28, 2023, is named “2023-06-28_01183-0208-00US-KAD_ST25_ST25” and is 435,942 bytes in size. The information in the electronic format of the sequence listing is incorporated herein by reference in its entirety.
FIELDThe present disclosure relates generally to the field of molecular biology and medicine. More particularly, the disclosure provides fusion proteins comprising an anti-PD-1 antibody or antigen-binding fragment thereof linked to an IL-15 polypeptide, which in turn is linked to an IL-15 receptor alpha (IL-15Rα) polypeptide comprising the IL-15Rα sushi domain. In addition, the disclosure provides antibodies, and antigen-binding fragments thereof, that specifically bind to PD-1 as well as fusion proteins comprising such anti-PD-1 antibodies and PD-1 binding fragments thereof. Also disclosed are therapeutic compositions comprising the antibody fusions or antibodies for treating disease.
BACKGROUNDPD-1 is a 55 KD type I transmembrane protein of 286 amino acids, which contains a membrane proximal immunoreceptor tyrosine inhibitory motif (ITIM) and a membrane distal tyrosine-based switch motif (ITSM). The PD-1 cytosolic domain contains two tyrosines, with the closest tyrosine (VAYEEL in mouse PD-1) located within the ITIM. The human PD-1 protein and the murine PD-1 protein share about 60% amino acid identity, with four potential N-glycosylation sites and residues that define the Ig-V domain are conserved. ITIM-like motifs surrounding the ITIM and C-terminal tyrosine in the cytoplasmic region are also conserved between human orthologue and murine orthologue. PD-1 is a member of CD-28 family of receptors, which is primarily expressed on mature T cells in peripheral tissues and the tumor microenvironment. PD-1 is also expressed on other non-T cell subsets including B cells, professional antigen presenting cells (APCs), and natural killer (NK) cells.
The ligands for PD-1 are the B7 family members PD-L1 (also known as B7-H1 and CD274) and PD-L2 (also known as B7-DC and CD273). PD-L1 is expressed primarily on both lymphoid and non-lymphoid tissues such as CD4 and CD8 T cells, macrophage lineage cells, peripheral tissues as well as on tumor cells, virally infected cells and autoimmune tissue cells. However, PD-L2 has a more restricted expression than PD-L1, being expressed only on macrophages and activated dendritic cells. PD-1 ligands are expressed in many human cancers, including melanoma, glioma, non-small cell lung cancer, squamous cell carcinoma of head and neck, leukemia, pancreatic cancer, renal cell carcinoma, and hepatocellular carcinoma, and may be inducible in nearly all cancer. Interaction between PD-1 and its ligands results in dephosphorylation and inactivation of the T cell kinase ZAP70, and the recruitment of SHP2. SHP2 directly dephosphorylates PI3K, which inhibits downstream activation of Aktin causing a decrease in tumor infiltrating lymphocytes, and a decrease in T cell receptor mediated proliferation, leading to immune evasion. Inhibiting interaction between PD-1 and PD-L1 reverses immune suppression and the effect may be additive when the interaction of PD-1 with PD-L2 is blocked as well.
Several commercial anti-PD-1 antibodies are currently used to treat diseases that involve PD-1-mediated immune suppression. However, only a subset of patients responds well to these therapies. Depending on the indication and other factors, the typical response rate of patients for each monotherapy ranges from 10% to 30%. One possible reason for this lack of response could be the absence of an inflammatory tumor microenvironment (TME), including activated anti-tumor CD8+ and CD4+ T cells as well as other effectors such as NK cells.
Combination therapies involving PD-1 antibodies with various cytokines such as IL-2, IL-15, IL-21, tumor necrosis factor (TNF), and granulocyte-macrophage colony-stimulating factor (GM-CSF) may have some efficacy in treating cancer and infection. However, these therapies are limited by the systemic toxicity that is associated both with the high blood concentrations of cytokines that is required to obtain efficacy and with the lack of specificity of the administered cytokine for affected cells and tissues.
IL-15 is a 12.5 KD glycoprotein with 114 amino acids and belongs to the four α-helix bundle family of cytokines that also includes IL-2, IL-4, IL-7, IL-9, granulocyte colony-stimulating factor (G-CSF), and GM-CSF. IL-15 is secreted by macrophages, dendritic cells, and monocytes. IL-15 can stimulate central memory CD8 cells to exert immunity without modulating effects on other T cells. Additionally, IL-15 can activate NK cells and effector and memory CD8 T cells and can rescue T cells from apoptosis induced by regulatory T cells (Tregs). Administration of IL-15 is also associated with a lower risk of inducing systemic toxicity at a higher dose compared to other cytokines. Human IL-15 can be soluble or membrane-bound. The membrane-bound I1-15, which is the major form of IL-15, is either formed by binding of IL-15 to cellular membrane directly or by presentation of IL-15 by the membrane-bound IL-15R receptor.
The I1-15 receptor is composed of three subunits: IL-15Rα, IL-15R, and IL-15Rγ. IL-15 typically forms a complex with IL-15 receptor α expressed on APCs prior to binding to functional IL-15Rβ and γ units on T cells and NK cells. IL-15 can bind to IL-15Rα receptor alone with affinity (Ka=1.1011 M−1). It can also bind to IL-15Rβγc signaling complex with lower affinity (Ka=1.109 M−1). The sushi domain (29.5 KD) of the IL-15Rα plays a critical role in complex formation of IL-15 and IL-15Rα.
One of the limitations with systemic IL-15 treatment is its very short half-life in vivo. Therefore, there is a need to generate a suitable immune-stimulatory form of IL-15/IL-15Rα that has a longer half-life in vivo while retaining its ability to medulate the immune response. Additionally, there is a need for effective IL-15 antagonists that can be selectively targeted to the disease site to avoid unwanted systemic toxicities and provide a more effective therapeutic benefit.
Compounds that modulate PD-1 activity have potential as therapeutic agents for the treatment of various diseases and disorders, including cancer, inflammation, and autoimmune diseases. There is a significant unmet need to develop new strategies to target various effector molecules to a disease site to provide therapeutic benefit without the side effects associated with non-specific immune activity.
SUMMARYProvided herein are fusion proteins, antibodies, and antigen-binding fragments thereof that bind to PD-1. In embodiments, the fusion proteins comprise an anti-PD-1 antibody, or antigen-binding fragment thereof. Also disclosed are anti-PD-1 antibodies and the antigen-binding fragments thereof that bind PD-1. Also provided are therapeutic compositions of such fusion proteins, antibodies, and antigen-binding fragments thereof, as well as methods of using these fusion proteins, antibodies and antigen-binding fragments thereof.
In one aspect, the disclosure provides a fusion protein comprising a PD-1 binding protein, an IL-15 receptor (IL-15R) binding protein (e.g., IL-15 or an IL-15R binding portion thereof), and an IL-15 binding protein (e.g., IL-15Rα or an IL-15 binding portion thereof comprising the IL-15Rα sushi domain). In one aspect, the PD-1 binding protein is an antibody or PD-1 binding fragment thereof. In one embodiment, the IL-15 receptor-binding portion is IL-15. In embodiments, IL-15 is joined, directly or indirectly, to the sushi domain of IL-15Rα.
In one embodiment, the fusion protein comprises an anti-PD-1 antibody and an IL-15 polypeptide, wherein the C-terminus of the IL-15 polypeptide is covalently linked, directly or via a polypeptide linker, to the N-terminus of the heavy chain variable region of one of the antibody heavy chains (i.e., the antibody heavy chains form a heterodimer wherein one of the heavy chains is linked to an IL-15 polypeptide. In one embodiment, the N-terminus of the IL-15 polypeptide is linked to the C-terminus of an IL-15Rα sushi domain polypeptide.
In one embodiment, the fusion protein comprises an anti PD-1 antibody and two IL-15 polypeptides, wherein each IL-15 polypeptide is covalently linked to the N-terminus of an antibody heavy chain.
In embodiments in which only one heavy chain is linked to IL-15/IL-15Rα sushi domain, the Fc domains of the antibody may comprise one or more amino acid substitutions promoting heterodimer formation (i.e., the association of a heavy chain fusion with a heavy chain lacking the fusion). In embodiments, an amino acid residue in the CH3 domain of one heavy chain (CH3-1) comprises an amino acid substitution replacing an amino acid with an amino acid residue having a larger side chain volume, thereby generating a “knob” within the CH3 domain, which is positionable in a “hole” present within the CH3 domain of the other heavy chain (CH3-2), generated by replacing an amino acid residue with an amino acid residue having a smaller side chain volume. In embodiments, the amino acid substitutions are selected from the following groups:
-
- (1) CH3 domain of first heavy chain: S354C, T366W; CH3 domain of second heavy chain: Y349C, T366S, L368A, Y407V
- (2) CH3 domain of first heavy chain: T350V, L351Y, F405A, Y407V; CH3 domain of second heavy chain: T350V, T366L, K392L, T394W
- (3) CH3 domain of first heavy chain: L351Y, F405A, Y407V; CH3 domain of second heavy chain: T366L, K392L, T394W.
Either the first or second heavy chain may be linked to the IL-15/IL-15Rα sushi domain.
In embodiments, the IL-15Rα polypeptide and the IL-15 polypeptide are joined by a first linker. In embodiments, the IL-15 polypeptide and the anti-PD-1 antibody, or antigen-binding portion thereof, are joined by a second linker. In embodiments, the length of the linker may independently be between 10 to 40 amino acids. In embodiments, the length of the linker is 25 to 35 amino acids. In embodiments, the linker sequences comprises near neutral amino acids selected from the group comprising Gly (G), Asn (N), Ser (S), Thr (T), Ala (A), Leu (L), and Gln (Q), most preferably in the group comprising Gly (G), Asn (N), and Ser (S). In certain embodiments, the linker sequences are glycine and serine rich, and in some embodiments, the linker contains only serine and glycine residues.
In certain embodiments, the IL-15 and/or the IL-15Rα sushi domain comprise one or more amino acid substitutions. In embodiments, the amino acid substitutions are located at position 1, 4, 8, 30, 45, 61, 64, 65, and/or 108 of IL-15. In some embodiments, the amino acid substitutions are located at positions 45, 65, and/or 108 of IL-15. In some embodiments the amino acid substitutions are one or more of N1D, N4D, D8N, D30N, D61N, E64Q, L45A, N65S/A/D/K, and/or Q108S/E substitutions in IL-15. In some embodiments, the amino acid substitutions are L45A, N65S/A/D/K, and/or Q108S substitutions in IL-15. In one embodiment, the amino acid substitution is an N65S substitution in IL-15.
In one embodiment, the amino acid substitution is an N60 substitution in the IL-15Rα sushi domain. In one embodiment, the amino acid substitution is an N60A substitution in the IL-15Rα sushi domain.
In embodiments, the fusion protein comprises an IL-15 polypeptide comprising one of the following amino acid substitutions: N65S, N65A, or N65D. In embodiments, the fusion protein comprises an IL-15 polypeptide comprising one or more of the following amino acid substitutions: (1) L45A, (2) N65S, N65A, or N65D, and (3) Q108S. In one embodiment, the fusion protein comprises an IL-15Rα sushi domain polypeptide comprisings an N60A amino acid substitution.
In one aspect, the disclosure relates to a fusion protein comprising:
-
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3;
- (ii) an IL-15 polypeptide or derivative thereof;
- (iii) an IL-15Rα sushi domain polypeptide or derivative thereof; and
- (iv) a linker polypeptide joining the IL-15Rα sushi domain polypeptide and the IL-15 polypeptide or derivative thereof.
In one aspect, the disclosure relates to a fusion protein comprising:
-
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3;
- (ii) an IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 212, or an amino acid sequence that is at least 90% or at least 95% identical to SEQ ID NO: 212;
- (iii) an IL-15Rα sushi domain polypeptide comprising the amino acid sequence of SEQ ID NO: 214, or an amino acid sequence that is at least 95% identical to SEQ ID NO: 214; and
- (iv) a first linker polypeptide joining the IL-15Rα sushi domain polypeptide and the IL-15 polypeptide.
The anti-PD-1 antibody, or antigen-binding fragment thereof, portion of the fusion protein can be any antibody, or antigen-binding fragment thereof, that specifically binds PD-1, including those comprising the corresponding heavy and light chain variable regions and/or CDRs provided in
-
- the sequence of CDR1 of the heavy chain variable region (CDR1H) comprises the sequence of SEQ ID NO: 21;
- the sequence of CDR2 of the heavy chain variable region (CDR2H) comprises the sequence of SEQ ID NO: 22;
- the sequence of CDR2 of the heavy chain variable region (CDR3H) comprises the sequence of SEQ ID NO: 23;
- the sequence of CDR1 of the light chain variable region (CDR1L) comprises the sequence RX13X14X15X16IX17X18WX19X20 (SEQ ID NO:135);
- wherein X13 is A or V;
- wherein X14 is S or G;
- wherein X15 is Q, E, or R;
- wherein X16 is G, S, D or N;
- wherein X17 is G, S, or N;
- wherein X18 is S, I, R, T, K, P, N, H, or V;
- wherein X19 is L or V; and
- wherein X20 is G or A; and
- the sequence of CDR2 of the light chain variable region (CDR2L) comprises the sequence X21AX22X23X24X23X26 (SEQ ID NO: 136); and
- wherein X21 is S, D, E, or A;
- wherein X22 is S or K;
- wherein X23 is S, N, T, R, or D;
- wherein X24 is L or V;
- wherein X25 is Q, E, or H; and
- wherein X26 is S, N, A, R, P, or T; and
- the sequence of CDR3 of the light chain variable region (CDR3L) comprises the sequence QQX27X28SFPX29X30 (SEQ ID NO: 137);
- wherein X27 is A or G;
- wherein X28 is N, D, or Y;
- wherein X29 is F or L; and
- wherein X30 is A or T.
In embodiments, the fusion protein comprises an anti-PD-1 antibody, or antigen-binding fragment thereof, wherein the CDRs of the heavy and light chain variable regions comprise the following sequences:
-
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 21;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 22;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 23
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 96;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 97; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 82.
In embodiments, the fusion protein comprises an anti-PD-1 antibody, or antigen-binding fragment thereof, wherein:
-
- the heavy chain variable region comprises SEQ ID NO: 24, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 24; and
- the light chain variable region comprises SEQ ID NO: 98, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 98.
In embodiments, the fusion protein comprises an anti-PD-1 antibody, or antigen-binding fragment thereof, wherein the CDRs of the heavy chain and light chain variable regions comprise the following sequences:
-
- the sequences of CDR1H, CDR2H and CDR3H comprise respectively SEQ ID NOS: 21, 22, and 23; and
- the sequences of CDR1L, CDR2L and CDR3L comprise respectively, SEQ ID NOS: 45, 46, and 47; SEQ ID NOS: 66, 67, and 68; SEQ ID NOS: 70, 67, and 71; SEQ ID NOS: 73, 74, and 75; SEQ ID NOS: 77, 78, and 47; SEQ ID NOS: 80, 81, and 82; SEQ ID NOS: 77, 78, and 84; SEQ ID NOS: 77, 86, and 47; SEQ ID NOS: 88, 89, and 47; SEQ ID NOS: 66, 67, and 47; SEQ ID NOS: 80, 92, and 75; SEQ ID NOS: 80, 94, and 71; SEQ ID NOS: 99, 100, and 47; SEQ ID NOS: 102, 103, and 104; SEQ ID NOS: 106, 103, and 47; SEQ ID NOS: 108, 103, and 47; SEQ ID NOS: 110, 111, and 75; SEQ ID NOS: 77, 103, and 113; SEQ ID NOS: 77, 111, and 47; SEQ ID NOS: 116, 67, and 47; SEQ ID NOS: 118, 119, and 47; SEQ ID NOS: 80, 78, and 47; SEQ ID NOS: 122, 103 and 47; SEQ ID NOS: 124, 125, and 75; SEQ ID NOS: 127, 38, and 68; SEQ ID NOS: 129, 130, and 47; or SEQ ID NOS: 132, 133, and 75.
In embodiments, the fusion protein comprises an anti-PD-1 antibody, or antigen-binding fragment thereof, wherein:
-
- the heavy chain variable region comprises SEQ ID NO: 24, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 24; and
- the light chain variable region comprises SEQ ID NO: 48, 69, 72, 76, 79, 83, 85, 87, 90, 91, 93, 95, 101, 105, 107, 109, 112, 114, 115, 117, 120, 121, 123, 126, 128, 131, or 134, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any of SEQ ID NO: 48, 69, 72, 76, 79, 83, 85, 87, 90, 91, 93, 95, 101, 105, 107, 109, 112, 114, 115, 117, 120, 121, 123, 126, 128, 131, or 134.
In embodiments, the fusion protein comprises an anti-PD-1 antibody, or antigen-binding fragment thereof, wherein the CDRs of the heavy and light chain variable regions comprise the following sequences:
-
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 17;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 18;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 19;
- the sequence of CDR1L comprises the sequence RSSX1SLLX2SNGX3X4YLD (SEQ ID NO:62),
- wherein X1 is Q or E;
- wherein X2 is H or Y;
- wherein X3 is Y or N; and
- wherein X4 is T or N;
- the sequence of CDR2L comprises the sequence X5X6SX7X8X9X10 (SEQ ID NO: 63),
- wherein X5 is L, Q or E;
- wherein X6 is S, A, or V;
- wherein X7 is H, N, T, or S;
- wherein X8 is R or L;
- wherein X9 is G, A, or H; and
- wherein X10 is S or T; and
- the sequence of CDR3L comprises the sequence MQGX11X12WPYT (SEQ ID NO: 64),
- wherein X11 is A, T, or S; and
- wherein X12 is H or R.
In embodiments, the fusion protein comprises an anti-PD-1 antibody, or antigen-binding fragment thereof, wherein the CDRs of the heavy chain and light chain variable regions comprise the following sequences:
-
- the sequence of CDR1H comprise the sequence of SEQ ID NO: 17;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 18;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 19;
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 41;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 49; and
- the sequence of CDR3 of the light chain variable region (CDR3L) comprises the sequence of SEQ ID NO: 50.
In embodiments, the fusion protein comprises an anti-PD-1 antibody, or antigen-binding fragment thereof, wherein:
-
- the heavy chain variable region comprises SEQ ID NO: 20, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 20; and
- the light chain variable region comprises SEQ ID NO: 51, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 51.
In embodiments, the fusion protein comprises an anti-PD-1 antibody, or antigen-binding fragment thereof, wherein the CDRs of the heavy chain and light chain variable regions comprise the following sequences:
-
- the sequence of CDR1H, CDR2H and CDR3H comprise SEQ ID NOS: 17, 18, and 19, respectively; and
- the sequence of CDR1L, CDR2L and CDR3L comprise respectively, SEQ ID NOS: 41, 42, and 43; SEQ ID NOS: 41, 52, and 53; SEQ ID NOS: 41, 55, and 56; or SEQ ID NOS: 58, 59, and 60.
In further embodiments the fusion protein comprises an anti-PD-1 antibody, or antigen-binding fragment thereof, wherein:
-
- the heavy chain variable region comprises SEQ ID NO: 20, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 20; and
- the light chain variable region comprises SEQ ID NO: 44, 54, 57, or 61, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of SEQ ID NO: 44, 54, 57, or 61.
In another aspect the disclosure provides an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof binds to PD-1, and wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3 and wherein the antibody heavy chains comprise a constant region comprising three constant domains CH1, CH2, and CH3.
In embodiments, the CDRs of the anti-PD-1 antibody, or antigen-binding fragment thereof, comprise the following sequences:
-
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 21;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 22;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 23;
- the sequence of CDR1L comprises the sequence RX13X14X15X16IX17X18WX19X20 (SEQ ID NO:135);
- wherein X13 is A or V;
- wherein X14 is S or G;
- wherein X15 is Q, E, or R;
- wherein X16 is G, S, D or N;
- wherein X17 is G, S, or N;
- wherein X18 is S, I, R, T, K, P, N, H, or V;
- wherein X19 is L or V;
- wherein X20 is G or A; and
- the sequence of CDR2L comprises the sequence X21AX22X23X24X23X26 (SEQ ID NO: 136); and
- wherein X21 is S, D, E, or A;
- wherein X22 is S or K;
- wherein X23 is S, N, T, R, or D;
- wherein X24 is L or V;
- wherein X25 is Q, E, or H; and
- wherein X26 is S, N, A, R, P, or T; and
- the sequence of CDR3L comprises the sequence QQX27X28SFPX29X30 (SEQ ID NO: 137);
- wherein X27 is A or G;
- wherein X28 is N, D, or Y;
- wherein X29 is F or L; and
- wherein X30 is A or T.
In embodiments, the CDRs of the anti-PD-1 antibody, or antigen-binding fragment thereof, comprise the following sequences:
-
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 21;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 22;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 23
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 96;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 97; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 82.
In embodiments, the anti-PD-1 antibody, or antigen-binding fragment thereof, comprises:
-
- a heavy chain variable region comprising SEQ ID NO: 24, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 24; and
- a light chain variable region comprising SEQ ID NO: 98, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 98.
In embodiments, the CDRs of the anti-PD-1 antibody, or antigen-binding fragment thereof, comprise the following sequences:
-
- the sequences of CDR1H, CDR2H and CDR3H comprise respectively SEQ ID NOS: 21, 22, and 23; and
- the sequences of CDR1L, CDR2L and CDR3L comprise respectively, SEQ ID NOS: 45, 46, and 47; SEQ ID NOS: 66, 67, and 68; SEQ ID NOS: 70, 67, and 71; SEQ ID NOS: 73, 74, and 75; SEQ ID NOS: 77, 78, and 47; SEQ ID NOS: 80, 81, and 82; SEQ ID NOS: 77, 78, and 84; SEQ ID NOS: 77, 86, and 47; SEQ ID NOS: 88, 89, and 47; SEQ ID NOS: 66, 67, and 47; SEQ ID NOS: 80, 92, and 75; SEQ ID NOS: 80, 94, and 71; SEQ ID NOS: 99, 100, and 47; SEQ ID NOS: 102, 103, and 104; SEQ ID NOS: 106, 103, and 47; SEQ ID NOS: 108, 103, and 47; SEQ ID NOS: 110, 111, and 75; SEQ ID NOS: 77, 103, and 113; SEQ ID NOS: 77, 111, and 47; SEQ ID NOS: 116, 67, and 47; SEQ ID NOS: 118, 119, and 47; SEQ ID NOS: 80, 78, and 47; SEQ ID NOS: 122, 103 and 47; SEQ ID NOS: 124, 125, and 75; SEQ ID NOS: 127, 38, and 68; SEQ ID NOS: 129, 130, and 47; or SEQ ID NOS: 132, 133, and 75.
In embodiments, the anti-PD-1 antibody, or antigen-binding fragment thereof, comprises:
-
- a heavy chain variable region comprising SEQ ID NO: 24, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 24; and
- a light chain variable region comprising SEQ ID NO: 48, 69, 72, 76, 79, 83, 85, 90, 91, 93, 101, 105, 107, 109, 112, 114, 115, 117, 120, 121, 123, 126, 128, 131, or 134, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of SEQ ID NO: 48, 69, 72, 76, 79, 83, 85, 90, 91, 93, 101, 105, 107, 109, 112, 114, 115, 117, 120, 121, 123, 126, 128, 131, or 134.
In embodiments, the CDRs of the anti-PD-1 antibody, or antigen-binding fragment thereof, comprise the following sequences:
-
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 17;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 18;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 19;
- the sequence of CDR1L comprises the sequence RSSX1SLLX2SNGX3X4YLD (SEQ ID NO:62),
- wherein X1 is Q or E;
- wherein X2 is H or Y;
- wherein X3 is Y or N; and
- wherein X4 is T or N;
- the sequence of CDR2L comprises the sequence X5X6SX7X8X9X10 (SEQ ID NO: 63),
- wherein X5 is L, Q or E;
- wherein X6 is S, A, or V;
- wherein X7 is H, N, T, or S;
- wherein X8 is R or L;
- wherein X9 is G, A, or H; and
- wherein X10 is S or T; and
- the sequence of CDR3L comprises the sequence MQGX11X12WPYT (SEQ ID NO: 64),
- wherein X11 is A, T, or S; and
- wherein X12 is H or R.
In embodiments, the CDRs of the anti-PD-1 antibody, or antigen-binding fragment thereof, comprise the following sequences:
-
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 17;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 18;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 19;
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 41;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 49; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 50.
In embodiments, the anti-PD-1 antibody, or antigen-binding fragment thereof, comprises:
-
- a heavy chain variable region comprising SEQ ID NO: 20, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 20; and
- a light chain variable region comprising SEQ ID NO: 51, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 51.
In embodiments, the CDRs of the anti-PD-1 antibody, or antigen-binding fragment thereof, comprise the following sequences:
-
- the sequence of CDR1H, CDR2H and CDR3H comprise SEQ ID NOS: 17, 18, and 19, respectively; and
- the sequence of CDR1L, CDR2L and CDR3L comprise respectively, SEQ ID NOS: 41, 42, and 43; SEQ ID NOS: 41, 52, and 53; SEQ ID NOS: 41, 55, and 56; or SEQ ID NOS: 58, 59, and 60.
In embodiments, the anti-PD-1 antibody, or antigen-binding fragment thereof, comprises:
-
- a heavy chain variable region comprising SEQ ID NO: 20, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 20; and
- a light chain variable region comprising SEQ ID NO: 44, 54, 57, or 61, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of SEQ ID NO: 44, 54, 57, or 61.
In one aspect, the disclosure relates to a fusion protein comprising:
-
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 21;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 22;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 23;
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 96;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 97; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 82;
- (ii) an IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 212, or an amino acid sequence that is at least 90% or at least 95% identical to SEQ ID NO: 212;
- (iii) an IL-15Rα sushi domain polypeptide comprising the amino acid sequence of SEQ ID NO: 214, or an amino acid sequence that is at least 95% identical to SEQ ID NO: 214;
- (iv) a first linker polypeptide joining the IL-15Rα sushi domain polypeptide and the IL-15 polypeptide; and
- optionally wherein the anti-PD-1 antibody, or an antigen-binding fragment thereof, comprises two heavy chains, wherein:
- (a) the CH3 domain of first heavy chain comprises the amino acid substitutions S354C and T366W (Kabat EU index numbering); and
- (b) the CH3 domain of second heavy chain comprises the amino acid substitutions Y349C, T366S, L368A, and Y407V (Kabat EU index numbering).
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
In one aspect, the disclosure relates to a fusion protein comprising:
-
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 21;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 22;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 23;
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 96;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 97; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 82;
- (ii) an IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 212, or an amino acid sequence that is at least 90% or at least 95% identical to SEQ ID NO: 212;
- (iii) an IL-15Rα sushi domain polypeptide comprising the amino acid sequence of SEQ ID NO: 214, or an amino acid sequence that is at least 95% identical to SEQ ID NO: 214;
- (iv) a first linker polypeptide joining the IL-15Rα sushi domain polypeptide and the IL-15 polypeptide; and
- optionally wherein the anti-PD-1 antibody, or an antigen-binding fragment thereof, comprises two heavy chains, wherein:
- (a) the CH3 domain of first heavy chain comprises the amino acid substitutions T350V, L351Y, F405A, and Y407V (Kabat EU index numbering); and
- (b) the CH3 domain of second heavy chain comprises the amino acid substitutions T350V, T366L, K392L, and T394W (Kabat EU index numbering).
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
In one aspect, the disclosure relates to a fusion protein comprising:
-
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 21;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 22;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 23;
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 96;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 97; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 82;
- (ii) an IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 212, or an amino acid sequence that is at least 90% or at least 95% identical to SEQ ID NO: 212;
- (iii) an IL-15Rα sushi domain polypeptide comprising the amino acid sequence of SEQ ID NO: 214, or an amino acid sequence that is at least 95% identical to SEQ ID NO: 214;
- (iv) a first linker polypeptide joining the IL-15Rα sushi domain polypeptide and the IL-15 polypeptide; and
- optionally wherein the anti-PD-1 antibody, or an antigen-binding fragment thereof, comprises two heavy chains, wherein:
- (a) the CH3 domain of first heavy chain comprises the amino acid substitutions L351Y, F405A, and Y407V (Kabat EU index numbering); and
- (b) the CH3 domain of second heavy chain comprises the amino acid substitutions T366L, K392L, and T394W (Kabat EU index numbering).
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
In one aspect, the disclosure relates to a fusion protein comprising:
-
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 21;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 22;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 23;
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 96;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 97; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 82;
- (ii) an IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 212, optionally wherein amino acid N65 of SEQ ID NO: 212 is substituted with an S, D, or A;
- (iii) an IL-15Rα sushi domain polypeptide comprising the amino acid sequence of SEQ ID NO: 214, optionally wherein amino acid N28 of SEQ ID NO: 214 is substituted with an A;
- (iv) a first linker polypeptide joining the IL-15Rα sushi domain polypeptide and the IL-15 polypeptide; and
- optionally wherein the anti-PD-1 antibody, or an antigen-binding fragment thereof, comprises two heavy chains, wherein:
- (a) the CH3 domain of first heavy chain comprises the amino acid substitutions S354C and T366W (Kabat EU index numbering); and
- (b) the CH3 domain of second heavy chain comprises the amino acid substitutions Y349C, T366S, L368A, and Y407V (Kabat EU index numbering).
In one aspect, the disclosure relates to a fusion protein comprising:
-
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 21;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 22;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 23;
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 96;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 97; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 82;
- (ii) an IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 212, optionally wherein amino acid N65 of SEQ ID NO: 212 is substituted with an S, D, or A;
- (iii) an IL-15Rα sushi domain polypeptide comprising the amino acid sequence of SEQ ID NO: 214, optionally wherein amino acid N28 of SEQ ID NO: 214 is substituted with an A;
- (iv) a first linker polypeptide joining the IL-15Rα sushi domain polypeptide and the IL-15 polypeptide; and
- optionally wherein the anti-PD-1 antibody, or an antigen-binding fragment thereof, comprises two heavy chains, wherein:
- (a) the CH3 domain of first heavy chain comprises the amino acid substitutions T350V, L351Y, F405A, and Y407V (Kabat EU index numbering); and
- (b) the CH3 domain of second heavy chain comprises the amino acid substitutions T350V, T366L, K392L, and T394W (Kabat EU index numbering).
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
In one aspect, the disclosure relates to a fusion protein comprising:
-
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 21;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 22;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 23;
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 96;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 97; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 82;
- (ii) an IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 212, optionally wherein amino acid N65 of SEQ ID NO: 212 is substituted with an S, D, or A;
- (iii) an IL-15Rα sushi domain polypeptide comprising the amino acid sequence of SEQ ID NO: 214, optionally wherein amino acid N28 of SEQ ID NO: 214 is substituted with an A;
- (iv) a first linker polypeptide joining the IL-15Rα sushi domain polypeptide and the IL-15 polypeptide; and
- optionally wherein the anti-PD-1 antibody, or an antigen-binding fragment thereof, comprises two heavy chains, wherein:
- (a) the CH3 domain of first heavy chain comprises the amino acid substitutions L351Y, F405A, and Y407V (Kabat EU index numbering); and
- (b) the CH3 domain of second heavy chain comprises the amino acid substitutions T366L, K392L, and T394W (Kabat EU index numbering).
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
In one aspect, the disclosure relates to a fusion protein comprising:
-
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
- the sequence of CDR1H comprise the sequence of SEQ ID NO: 17;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 18;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 19;
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 41;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 49; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 50;
- (ii) an IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 212, or an amino acid sequence that is at least 90% or at least 95% identical to SEQ ID NO: 212;
- (iii) an IL-15Rα sushi domain polypeptide comprising the amino acid sequence of SEQ ID NO: 214, or an amino acid sequence that is at least 95% identical to SEQ ID NO: 214;
- (iv) a first linker polypeptide joining the IL-15Rα sushi domain polypeptide and the IL-15 polypeptide; and
- optionally wherein the anti-PD-1 antibody, or an antigen-binding fragment thereof, comprises two heavy chains, wherein:
- (a) the CH3 domain of first heavy chain comprises the amino acid substitutions S354C and T366W (Kabat EU index numbering); and
- (b) the CH3 domain of second heavy chain comprises the amino acid substitutions Y349C, T366S, L368A, and Y407V (Kabat EU index numbering).
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
In one aspect, the disclosure relates to a fusion protein comprising:
-
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
- the sequence of CDR1H comprise the sequence of SEQ ID NO: 17;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 18;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 19;
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 41;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 49; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 50;
- (ii) an IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 212, or an amino acid sequence that is at least 90% or at least 95% identical to SEQ ID NO: 212;
- (iii) an IL-15Rα sushi domain polypeptide comprising the amino acid sequence of SEQ ID NO: 214, or an amino acid sequence that is at least 95% identical to SEQ ID NO: 214;
- (iv) a first linker polypeptide joining the IL-15Rα sushi domain polypeptide and the IL-15 polypeptide; and
- optionally wherein the anti-PD-1 antibody, or an antigen-binding fragment thereof, comprises two heavy chains, wherein:
- (a) the CH3 domain of first heavy chain comprises the amino acid substitutions T350V, L351Y, F405A, and Y407V (Kabat EU index numbering); and
- (b) the CH3 domain of second heavy chain comprises the amino acid substitutions T350V, T366L, K392L, and T394W (Kabat EU index numbering).
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
In one aspect, the disclosure relates to a fusion protein comprising:
-
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
- the sequence of CDR1H comprise the sequence of SEQ ID NO: 17;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 18;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 19;
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 41;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 49; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 50;
- (ii) an IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 212, or an amino acid sequence that is at least 90% or at least 95% identical to SEQ ID NO: 212;
- (iii) an IL-15Rα sushi domain polypeptide comprising the amino acid sequence of SEQ ID NO: 214, or an amino acid sequence that is at least 95% identical to SEQ ID NO: 214;
- (iv) a first linker polypeptide joining the IL-15Rα sushi domain polypeptide and the IL-15 polypeptide; and
- optionally wherein the anti-PD-1 antibody, or an antigen-binding fragment thereof, comprises two heavy chains, wherein:
- (a) the CH3 domain of first heavy chain comprises the amino acid substitutions L351Y, F405A, and Y407V (Kabat EU index numbering); and
- (b) the CH3 domain of second heavy chain comprises the amino acid substitutions T366L, K392L, and T394W (Kabat EU index numbering).
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
In one aspect, the disclosure relates to a fusion protein comprising:
-
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
- the sequence of CDR1H comprise the sequence of SEQ ID NO: 17;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 18;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 19;
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 41;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 49; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 50;
- (ii) an IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 212, optionally wherein amino acid N65 of SEQ ID NO: 212 is substituted with an S, D, or A;
- (iii) an IL-15Rα sushi domain polypeptide comprising the amino acid sequence of SEQ ID NO: 214, optionally wherein amino acid N28 of SEQ ID NO: 214 is substituted with an A;
- (iv) a first linker polypeptide joining the IL-15Rα sushi domain polypeptide and the IL-15 polypeptide; and
- optionally wherein the anti-PD-1 antibody, or an antigen-binding fragment thereof, comprises two heavy chains, wherein:
- (a) the CH3 domain of first heavy chain comprises the amino acid substitutions S354C and T366W (Kabat EU index numbering); and
- (b) the CH3 domain of second heavy chain comprises the amino acid substitutions Y349C, T366S, L368A, and Y407V (Kabat EU index numbering).
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
In one aspect, the disclosure relates to a fusion protein comprising:
-
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
- the sequence of CDR1H comprise the sequence of SEQ ID NO: 17;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 18;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 19;
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 41;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 49; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 50;
- (ii) an IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 212, optionally wherein amino acid N65 of SEQ ID NO: 212 is substituted with an S, D, or A;
- (iii) an IL-15Rα sushi domain polypeptide comprising the amino acid sequence of SEQ ID NO: 214, optionally wherein amino acid N28 of SEQ ID NO: 214 is substituted with an A;
- (iv) a first linker polypeptide joining the IL-15Rα sushi domain polypeptide and the IL-15 polypeptide; and
- optionally wherein the anti-PD-1 antibody, or an antigen-binding fragment thereof, comprises two heavy chains, wherein:
- (a) the CH3 domain of first heavy chain comprises the amino acid substitutions T350V, L351Y, F405A, and Y407V (Kabat EU index numbering); and
- (b) the CH3 domain of second heavy chain comprises the amino acid substitutions T350V, T366L, K392L, and T394W (Kabat EU index numbering).
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
In one aspect, the disclosure relates to a fusion protein comprising:
-
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
- the sequence of CDR1H comprise the sequence of SEQ ID NO: 17;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 18;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 19;
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 41;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 49; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 50;
- (ii) an IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 212, optionally wherein amino acid N65 of SEQ ID NO: 212 is substituted with an S, D, or A;
- (iii) an IL-15Rα sushi domain polypeptide comprising the amino acid sequence of SEQ ID NO: 214, optionally wherein amino acid N28 of SEQ ID NO: 214 is substituted with an A;
- (iv) a first linker polypeptide joining the IL-15Rα sushi domain polypeptide and the IL-15 polypeptide; and
- optionally wherein the anti-PD-1 antibody, or an antigen-binding fragment thereof, comprises two heavy chains, wherein:
- (a) the CH3 domain of first heavy chain comprises the amino acid substitutions L351Y, F405A, and Y407V (Kabat EU index numbering); and
- (b) the CH3 domain of second heavy chain comprises the amino acid substitutions T366L, K392L, and T394W (Kabat EU index numbering).
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3; and wherein:
In one embodiment, the anti-PD-1 antibody or antigen-binding fragment thereof provided by the disclosure is a multispecific or a bispecific antibody or antigen-binding fragment thereof. In one embodiment, the antibody or antigen-binding fragment is a bispecific antibody comprising a complementary region that binds to PD-L1 or PD-L2. The disclosure also provides conjugates of the antibodies or the fusion molecules, for example, and without limitation, to fluorescent labels, imaging agents, therapeutic agents, or cytotoxic agents.
The disclosure further provides pharmaceutical compositions comprising one or more of an anti-PD-1 antibody or antigen-binding fragment thereof, or fusion protein comprising an anti-PD-1 antibody or antigen-binding fragment thereof, and a pharmaceutically acceptable carrier.
In embodiments, the disclosure provides nucleic acid molecules encoding the anti-PD-1 antibodies or antigen-binding fragments thereof disclosed herein and nucleic acid molecules encoding the fusion proteins disclosed herein, as well as vectors comprising such nucleic acid molecules. Also provided are cells comprising a vector encoding the anti-PD-1 antibodies or antigen-binding fragments thereof disclosed herein, or the fusion proteins disclosed herein.
In embodiments, the disclosure provides a method of inhibiting binding of PD-1 to a ligand of PD-1, the method comprising administering to a subject in need thereof an effective amount of an anti-PD-1 antibody, or antigen-binding fragment thereof, or a fusion protein disclosed herein.
In embodiments, the disclosure provides a method of treating a disease in a subject in need thereof, the method comprising administering to said subject a therapeutically effective amount of a composition comprising an anti-PD-1 antibody, or antigen-binding fragment thereof, or a fusion protein disclosed herein in a pharmaceutically acceptable form.
In embodiments, the disclosure provides a method for increasing T cell activation in a subject in need thereof, the method comprising administering an effective amount of an anti-PD-1 antibody, or antigen-binding fragment thereof, or a fusion protein disclosed herein. In one embodiment, the disclosure provides a method of stimulating the immune system in a subject in need thereof, the method comprising administering to said subject an effective amount of a composition comprising an anti-PD-1 antibody, or antigen-binding fragment thereof, or a fusion protein disclosed herein in a pharmaceutically acceptable form. In one embodiment, the disclosure provides a method of reducing replication of a virus in a subject in need thereof, the method comprising administering to the subject an effective amount of a composition comprising an anti-PD-1 antibody, or antigen-binding fragment thereof, or a fusion protein disclosed herein.
The disclosure also provides a method of inhibiting the interaction of PD-1 with PD-L1 and/or PD-L2 in a subject, the method comprising administering to a subject in need thereof an effective amount of an anti-PD-1 antibody, or antigen-binding fragment thereof, or a fusion protein disclosed herein. The disclosure further provides a method of inhibiting immunosuppression mediated by PD-1 in a subject in need thereof, the method comprising administering to the subject an effective amount of an anti-PD-1 antibody, or antigen-binding fragment thereof, or a fusion protein disclosed herein.
The disclosure further provides a method of stimulating an immune response against a cell or tissue that expresses PD-1 in a subject in need thereof, the method comprising administering to the subject an effective amount of an anti-PD-1 antibody, or antigen-binding fragment thereof, or a fusion protein disclosed herein. In certain embodiments, the cell or tissue expressing PD-1 is a cancerous cell or a cell infected with a pathogen, including, but not limited to, a virus or a bacterium.
In one aspect, the present disclosure provides a method of treating cancer, an immune disorder, or an infection in a patient in need thereof, the method comprising (a) treating a cell, in vitro, with an anti-PD-1 antibody, or antigen-binding fragment thereof, or a fusion protein disclosed herein; and (b) administering the treated cell to the patient. In some embodiments, the cell is a T cell.
In another aspect, the disclosure provides a method of increasing T cell activation in response to an antigen in a subject, the method comprising administering to the subject an effective amount of an anti-PD-1 antibody, or antigen-binding fragment thereof, or a fusion protein disclosed herein, or a pharmaceutical composition disclosed herein.
In another aspect, the disclosure provides a method of treating a condition in a subject that would benefit from an upregulation of the subject's immune response, the method comprising administering to the subject an effective amount of an anti-PD-1 antibody, or antigen-binding fragment thereof, or a fusion protein disclosed herein. In certain embodiments, the subject has upregulated expression of PD-L1, or the subject has been identified as positive for expression of PD-L1.
In one embodiment, the disclosure provides methods of using the anti-PD-1 antibodies, or antigen-binding fragments thereof, or fusion proteins disclosed herein for treating a subject that does not respond to therapy with a checkpoint inhibitor (primary resistance), and/or for treating a subject that initially responds to checkpoint inhibitor treatment, but later becomes resistant to checkpoint inhibitor blockade (secondary or acquired resistance). Such methods for treating comprise administering to said subject an anti-PD-1 antibody, or antigen-binding fragment thereof, or a fusion protein disclosed herein. In some embodiments, the subject has acquired resistance to therapy with one or more of a PD-1 inhibitor, a PD-L1 inhibitor, and a CTLA-4 inhibitor.
In one embodiment, the disclosure provides a method of administering an anti-PD-1 antibody, or antigen-binding fragment thereof, or a fusion protein disclosed herein to a subject in need thereof, the method further comprising administering an additional therapeutic agent or therapy to the subject, wherein the additional therapeutic agent or therapy is selected from the group consisting of a cancer vaccine, a checkpoint inhibitor, an antibody to a tumor-specific antigen, a Bacillus Calmette-Guerin (BCG) vaccine, a cytotoxin, an interleukin 6 receptor (IL-6R) inhibitor, an interleukin 4 receptor (IL-4R) inhibitor, an IL-10 inhibitor, IL-2, IL-7, IL-21, IL-15, an antibody-drug conjugate, an anti-inflammatory drug, and a dietary supplement. In embodiments, the disclosure provides a method of administering an anti-PD-1 antibody, or antigen-binding fragment thereof, or a fusion protein disclosed herein to a subject in need thereof, the method further comprising administering to the subject a checkpoint inhibitor selected from a CTLA-4, a PD-1, a PD-L1, and a PD-L2 inhibitor. In embodiments, the disclosure provides a method of administering an anti-PD-1 antibody, or antigen-binding fragment thereof, or a fusion protein disclosed herein to a subject in need thereof, the method further comprising administering to the subject one or more of an inhibitor of LAG3, TIGIT, LAP, Podoplanin, Protein C receptor, ICOS, GITR, CD226, and/or CD160. In embodiments, the disclosure provides a method of administering an anti-PD-1 antibody, or antigen-binding fragment thereof, or a fusion protein disclosed herein to a subject in need thereof, the method further comprising administering an additional therapeutic agent or therapy, wherein the additional therapeutic agent or therapy is administered concurrently or consecutively with the anti-PD-1 antibody, or antigen-binding fragment thereof, or fusion protein disclosed herein. In embodiments, the disclosure provides a method of administering an anti-PD-1 antibody, or antigen-binding fragment thereof, or a fusion protein disclosed herein to a subject in need thereof, the method further comprising administering to the subject an additional therapeutic agent or therapy, wherein the additional therapeutic agent or therapy is administered separately, or as a mixture with the anti-PD-1 antibody, or antigen-binding fragment thereof, or fusion protein disclosed herein. In one embodiment, the disclosure provides a method of administering an anti-PD-1 antibody, or antigen-binding fragment thereof, or a fusion protein disclosed herein in combination with chemotherapy, radiotherapy, or surgery.
The present disclosure provides fusion proteins comprising an anti-PD-1 antibody or antigen-binding fragment thereof linked to an IL-15 polypeptide, which in turn is linked to an IL-15 receptor alpha (IL-15Rα) polypeptide comprising the IL-15Rα sushi domain. In addition, provided herein are antibodies, and antigen-binding fragments thereof, that specifically bind to PD-1 and fusion proteins comprising such anti-PD-1 antibodies and PD-1 binding fragments thereof.
Fusion Proteins Comprising Anti-PD-1 Antibodies or Antigen-Fragments Thereof
In one aspect, the disclosure provides fusion proteins comprising an antibody, or antigen-binding fragment thereof that binds to PD-1. This portion of the fusion protein can be any antibody or antibody fragment that specifically binds PD-1, including those comprising the corresponding heavy and light chain variable regions or CDRs provided in
Disclosed herein are fusion proteins comprising a stimulatory domain. As used herein, a “stimulatory domain” is a domain that promotes an immune response. The stimulatory domain may stimulate an immune response mediated by, for example, inducing T cell or NK cell activity and/or proliferation. In embodiments, the stimulatory domain stimulates cells that respond to an interleukin or an interferon, such as, without limitation, IL-2, IL-7, IL-15, and IL-21. In one embodiment, the stimulatory domain binds to and stimulates a receptor that is responsive to an interleukin or an interferon, such as, without limitation, IL-2, IL-7, IL-13, IL-15, and IL-21. The stimulatory domain can also be a hybrid domain that is a hetero-complex of two or more ligands covalently linked to each other.
In embodiments, the stimulatory domain includes a sequence or domain that promotes IL-15 stimulation of the IL-15 receptor (IL-15R).
In one embodiment, the stimulatory domain that promotes IL-15R stimulation comprises IL-15 or an IL-15 derivative.
In one embodiment, the stimulatory domain that promotes IL-15R stimulation comprises an IL-15Rα polypeptide comprising the IL-15Rα sushi domain or a derivative thereof. In an embodiment, the stimulatory domain comprises the sushi domain of the IL-15Rα chain.
In an embodiment, the stimulatory domain comprises IL-15 or a derivative thereof, whose binding may be enhanced by the presence of an IL-15Rα polypeptide comprising the IL-15Rα sushi domain or a derivative thereof. In one embodiment, the stimulatory domain comprises a complex of IL-15 or a derivative thereof and an IL-15Rα polypeptide comprising the IL-15Rα sushi domain or a derivative thereof. In some embodiment, the stimulatory domain comprises an IL-15 or a derivative thereof and an IL-15Rα polypeptide comprising the IL-15Rα sushi domain or a derivative thereof, wherein the two polypeptides are covalently linked by a linker (including, but not limited to, a linker comprising SEQ ID NO: 215).
In one embodiment, the IL-15 or a derivative thereof is located N-terminally of the IL-15Rα polypeptide comprising the IL-15Rα sushi domain or derivative thereof. In one embodiment, the IL-15 or a derivative thereof is located C-terminally of the IL-15Rα polypeptide comprising the IL-15Rα sushi domain or derivative thereof. In one embodiment, the stimulatory domain comprises the sequence of the SD15 domain highlighted in any one of SEQ ID NOS:177-180.
As demonstrated herein, provided herein is a fusion protein which comprises (1) a PD-1 binding domain that blocks binding of PD-1 to PD-L1 and inhibits immunosuppression, and (2) a stimulatory domain that promotes an immune response, wherein the fusion proteins provides for increased immune cell activity, compared to two distinct molecules that provide the before mentioned functions separately. Specifically, the experiments disclosed herein demonstrate that fusion proteins containing both a PD-1 binding domain that blocks binding of PD-1 to PD-L1, and an stimulatory domain IL-15 or a derivative thereof and an IL-15Rα polypeptide comprising the IL-15Rα sushi domain or a derivative thereof, promoted increased proliferation, Th1 cytokine release, and killing activity-related molecules of NK and T cells, compared to providing the domains in separate molecules.
In certain embodiments, the fusion protein comprises a stimulatory domain disclosed herein that is covalently linked to an anti-PD-1 antibody or antigen-binding fragment thereof disclosed herein via a flexible linker. In some embodiments, provided herein is a fusion protein wherein the stimulatory domain disclosed herein is fused directly to an anti-PD-1 antibody or antigen-binding fragment disclosed herein.
As used herein, “covalently linked” or “fused” refers to the association of two or more polypeptides through a covalent bond. In some embodiments, two polypeptides that are covalently linked are fused to each other directly, i.e., without any additional polypeptide sequence between the first and the second peptide. Accordingly, in some embodiments, the N-terminus of the first polypeptide is fused directly to the C-terminus of the second polypeptide or vice versa. In other embodiments, the two polypeptides that are covalently linked are part of a continuous polypeptide chain, but are not directly fused to each other (i.e., the two polypeptides may be separated by one or more amino acids, a linker or another polypeptide). The term “covalently linked” does not imply a specific orientation of the two or more polypeptides that are fused to each other.
IL-15 is a 14-15 KD cytokine with structural similarity to IL-2. IL-15 is also known as MGC9721. A variety of cell types constitutively produce IL-15 mRNA, and these include monocytes, macrophages, DCs, keratinocytes, epidermal skin cells, fibroblasts, various epithelial cells, bone marrow stromal cells, and nerve cells. In addition, IL-15 mRNA is also produced in kidney, placenta, lung, heart, skeletal muscle, and brain tissues. However, only monocytes, DCs, epithelial cells, bone marrow stromal cells, fibroblasts, and very few other cells and tissues secrete detectable levels of IL-15. IL-15 and IL-2 are found to bind the same hematopoietin subunits and share many biological activities. IL-15 regulates T and NK cell activation and proliferation, and the number of CD8+ memory cells is affected by a balance between IL-15 and IL-2. In embodiments, the IL-15 or IL-15 derivative disclosed herein has at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90% of the activity of human IL-15. IL-15 may be a mammalian IL-15, preferably a primate IL-15, and more preferably a human IL-15. The human IL-15 (Accession number NP_000576) amino acids sequence is provided as SEQ ID NO:212.
The term “IL-15 derivative” refers to a polypeptide having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity with SEQ ID NO:212, the mature form of human I1-15. Techniques for making such derivatives are known in the art. In some embodiments, the IL-15 or IL-15 derivative sequence may comprise one or more amino acid substitutions. In some embodiments, the amino acid substitutions are located at positions 1, 4, 8, 30, 45, 61, 64, 65, and/or 108 of IL-15 (residue numbers are referring to the mature form of the IL-15 protein). In some embodiments, the amino acid substitutions are located at position 45, 65, and/or 108 of IL-15. In some embodiments the amino acid substitutions in IL-15 are N1D, N4D, D8N, D30N, D61N, E64Q, L45A, N65S/A/D/K, and/or Q108S/E. In some embodiments, the amino acid substitutions in IL-15 are L45A, N65S/A/D/K, and/or Q108S. In embodiments, a fusion protein disclosed herein comprises an IL-15 polypeptide comprising one of the following amino acid substitutions: N65S, N65A, or N65D. In embodiments, a fusion protein disclosed herein comprises an IL-15 polypeptide comprising one or more of the following amino acid substitutions: L45A, N65S, N65A, or N65D, and Q108S.
The amino acid sequence of human IL-15Rα isoform 1 precursor (Accession number NP_002180) is provided in SEQ ID NO:213. The IL-15 receptor, i.e., IL-15 receptor complex, specifically binds IL-15 with high affinity and consists of a unique interleukin 15 receptor αsubunit, IL-2/IL-15Rβ, and the common 7-chain/IL-2RT subunit. IL-15Rα is expressed by mitogen-activated macrophages, NK cells, and CD4+ and CD8+ T cells. The human IL-15Rα consists of seven exons, and alternative mRNA splicing may result in eight molecular IL-15Rα isoforms with different extra or intracellular domains. Full-length isoforms consist of an extracellular portion containing a conserved protein binding motif (sushi domain), a trans-membrane domain, and an intracellular tail.
As used herein, the term “sushi domain” of IL-15Rα refers to a domain beginning at the first cysteine residue (C1) after the signal peptide of IL-15Rα and ending at the fourth cysteine residue (C4) after said signal peptide. The sushi domain corresponding to a portion of the extracellular region of IL-15Rα is involved in binding to IL-15. The sushi domain in the present disclosure has at at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, or at least 90% of the activity of the sushi domain of the human IL-15Rα chain.
The amino acid sequence of human IL-15Rα isoform 1 precursor is provided in SEQ ID NO:213 (this sequence includes the signal sequence). The sushi domain amino acid sequence of human IL-15Rα is provided in SEQ ID NO: 214.
The term “IL-15Rα sushi domain derivative” or “IL-15Rα sushi domain variant” refers to a polypeptide having at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% sequence identity with the sequence of the human IL-15Rα sushi domain (SEQ ID NO:214). Techniques for making such derivatives or variants are known in the art. All such derivatives comprise the four cysteine residues of the sushi domain of IL-15Rα. In some such derivatives, naturally occurring amino acids may be replaced by chemically modified amino acids to alter the polypeptide half-life. In some embodiments, the IL-15Rα sushi domain or IL-15Rα sushi domain derivative sequence may comprise one or more amino acid substitutions. In some embodiments, the amino acid substitution is located at position 60 of IL-15Rα (numbering of the IL-15Rα residues include the signal peptide, see, e.g., SEQ ID NO:213). In some embodiments, the amino acid substitution in the IL-15Rα sushi domain is N60A (i.e., the asparagine (N) at amino acid 60 is substituted with alanine (A)).
IL-15 binds with high affinity to IL-15Rα, which then associates with an IL-15Rβ/γc complex expressed by the same target cell (cis-presentation). IL-15Rα is also known to trans-present IL-15 with high affinity to a different target cell expressing the IL-15Rβ/γ(c) complex (trans-presentation). IL-15 cis- and trans-presentation mechanisms lead to different dynamics of receptor activation and signal transduction, with cis-presentation inducing fast and transient responses, and trans-presentation inducing slower, more persistent ones.
In some embodiments, the fusion proteins disclosed herein comprise a stimulatory domain, which comprises a hybrid domain comprising the sushi domain of the IL-15Rα chain attached to IL-15 by a linker (including, but not limited to, the linker of SEQ ID NO: 215). In certain embodiments, the stimulatory domain disclosed herein is covalently linked to an anti-PD-1 antibody or antigen-binding fragment thereof disclosed herein via a second linker (including, but not limited to, the linker of SEQ ID NO: 216). In other embodiments, the stimulatory domain exemplified herein is directly fused to an anti PD-1 antibody or antigen-binding fragment disclosed herein.
In one embodiment, provided is an “N-terminal fusion protein,” wherein a stimulatory domain is linked directly or via a linker (e.g., via one or more peptides) to the N-terminus of an anti-PD1 binding portion of the fusion protein (e.g., the N-terminus of a heavy chain of an anti-PD-1 antibody disclosed herein).
N-terminal fusion proteins include but are not limited to the following (exemplary) fusion proteins (components recited from N- to C-terminus, “-” indicated direct covalent linkage or linkage via a linker (e.g., via one or more peptides):
-
- (1) (IL-15 or derivative thereof)—(heavy chain of anti-PD-1 antibody or antigen binding fragment thereof)
- (2) (IL-15 or derivative thereof)—(light chain of anti-PD-1 antibody or antigen binding fragment thereof)
- (3) (IL-15Rα polypeptide comprising the IL-15Rα sushi domain or a derivative thereof)—(IL-15 or derivative thereof)—(heavy chain of anti-PD-1 antibody or antigen binding fragment thereof)
- (4) (IL-15Rα polypeptide comprising the IL-15Rα sushi domain or a derivative thereof)—(IL-15 or derivative thereof)—(light chain of anti-PD-1 antibody or antigen binding fragment thereof)
- (5) (IL-15 or derivative thereof)—(IL-15Rα polypeptide comprising the IL-15Rα sushi domain or a derivative thereof)—(heavy chain of anti-PD-1 antibody or antigen binding fragment thereof)
- (6) (IL-15 or derivative thereof)—(IL-15Rα polypeptide comprising the IL-15Rα sushi domain or a derivative thereof)—(light chain of anti-PD-1 antibody or antigen binding fragment thereof)
N-terminal fusion proteins may comprise more than one stimulatory domain.
In one embodiment, provided is a fusion protein, wherein the stimulatory domain is covalently linked to the N-terminus of one (and only one) of the heavy chains of the anti-PD-1 antibody or antigen binding fragment thereof. An N-terminal fusion protein comprising a single stimulatory domain is referred to as a “i-N-terminal fusion protein.”
Provided herein is a fusion protein comprising (1) a stimulatory domain (2) a first heavy chain of an anti-PD-1 antibody or antigen binding fragment thereof, wherein the stimulatory domain is covalently linked to the N-terminus of the first heavy chain, and (3) a second heavy chain of an anti-PD-1 antibody or antigen binding fragment thereof, wherein the second heavy chain is not linked to a stimulatory domain. In some embodiments, the stimulatory domain comprises (i) IL-15 or a derivative thereof, or (ii) an IL-15Rα polypeptide comprising the IL-15Rα sushi domain or a derivative thereof, or (iii) both.
In one embodiment, provided is a fusion protein, wherein a stimulatory domain is covalently linked to the N-termini of both of the heavy chains of the anti-PD-1 antibody or antigen binding fragment thereof. An N-terminal fusion protein comprising two stimulatory domains, both linked to different antibody chains, is referred to as a “2-N-terminal fusion protein.”
In one embodiment, provided is an “C-terminal fusion protein,” wherein a stimulatory domain is linked directly or via a linker (e.g., via one or more peptides) to the C-terminus of an anti-PD1 binding portion of the fusion protein (e.g., the C-terminus of a heavy chain of an anti-PD-1 antibody disclosed herein).
C-terminal fusion proteins include but are not limited to the following (exemplary) fusion proteins (components recited from N- to C-terminus, “-” indicated direct covalent linkage or linkage via a linker (e.g., via one or more peptides):
-
- (1) (heavy chain of anti-PD-1 antibody or antigen binding fragment thereof)—(IL-15 or derivative thereof)
- (2) (light chain of anti-PD-1 antibody or antigen binding fragment thereof)—(IL-15 or derivative thereof)
- (3) (heavy chain of anti-PD-1 antibody or antigen binding fragment thereof)—(IL-15Rα polypeptide comprising the IL-15Rα sushi domain or a derivative thereof)—(IL-15 or derivative thereof)
- (4) (light chain of anti-PD-1 antibody or antigen binding fragment thereof)—(IL-15Rα polypeptide comprising the IL-15Rα sushi domain or a derivative thereof)—(IL-15 or derivative thereof)
- (5) (heavy chain of anti-PD-1 antibody or antigen binding fragment thereof)—(IL-15 or derivative thereof)—(an IL-15Rα polypeptide comprising the IL-15Rα sushi domain or a derivative thereof)
- (6) (light chain of anti-PD-1 antibody or antigen binding fragment thereof)—(IL-15 or derivative thereof)—(an IL-15Rα polypeptide comprising the IL-15Rα sushi domain or a derivative thereof)
C-terminal fusion proteins may comprise more than one stimulatory domain.
In one embodiment, provided is a fusion protein, wherein the stimulatory domain is covalently linked to the C-terminus one (and only one) of the heavy chains of the anti-PD-1 antibody or antigen binding fragment thereof. A C-terminal fusion protein comprising a single stimulatory domain is referred to as a “i-C-terminal fusion protein.”
Provided herein is a fusion protein comprising (1) a stimulatory domain, (2) a first heavy chain of an anti-PD-1 antibody or antigen binding fragment thereof, wherein the stimulatory domain is covalently linked to the C-terminus of the first heavy chain, and (3) a second heavy chain of an anti-PD-1 antibody or antigen binding fragment thereof, wherein the second heavy chain is not linked to a stimulatory domain. In some embodiments, the stimulatory domain comprises (i) IL-15 or a derivative thereof, or (ii) an IL-15Rα polypeptide comprising the IL-15Rα sushi domain or a derivative thereof, or (iii) both.
In one embodiment, provided is a fusion protein, wherein a stimulatory domain is covalently linked to the C-termini of both of the heavy chains of the anti-PD-1 antibody or antigen binding fragment thereof. A C-terminal fusion protein comprising two stimulatory domains, both linked to different antibody chains, is referred to as a “2-C-terminal fusion protein.”
Therapeutic levels of IL-2 are associated with high level of toxicity upon binding to the IL-2 receptor. Similarly, using therapeutic levels of IL-15 can also cause toxicity since IL-15 shares two receptor subunits with IL-2. The N-terminal fusion proteins, however, demonstrate reduced toxity compared to the C-terminal fusion proteins because when presented in cis position, the N-terminal IL-15 fusion proteins can selectively bind to tumor infiltrating lymphocyte (TIL) while showing a lower binding to peripheral T cells. When presented in cis position, N-terminal fusion proteins may bind to IL-15Rβγ and PD-1 simultaneously while reducing the IL-15Rβ/γ binding, allowing the N-terminal fusion proteins to selectively bind to TILs and promoting TIL proliferation. In contrast, C-terminal fusion proteins may bind to both peripheral T cells and TIL equally and may show higher toxicity than the N-terminal fusion proteins. (
In one aspect, the disclosure relates to a fusion protein comprising:
-
- (i) an anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein the anti-PD-1 antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3, and wherein the antibody heavy chain comprises a constant region comprising three constant domains CH1, CH2, and CH3;
- (ii) an interleukin 15 (IL-15) polypeptide comprising an amino acid sequence of SEQ ID NO: 212, or an amino acid sequence that is at least 90% or at least 95% identical to SEQ ID NO: 212;
- (iii) an IL-15Rα sushi domain polypeptide comprising an amino acid sequence of SEQ ID NO: 214, or an amino acid sequence that is at least 90% or at least 95% identical to SEQ ID NO: 214; and
- (iv) a first linker polypeptide joining the IL-15Rα sushi domain polypeptide and the IL-15 polypeptide.
The anti-PD-1 antibody, or antigen-binding fragment thereof, portion of the fusion protein can be any that specifically bind PD-1, including those comprising the corresponding variable regions or CDRs provided in
-
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 22;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 23;
- the sequence of CDR1L comprises the sequence RX13X14X15X16IX17X18WX19X20 (SEQ ID NO:135);
- wherein X13 is A or V;
- wherein X14 is S or G;
- wherein X15 is Q, E, or R;
- wherein X16 is G, S, D or N;
- wherein X17 is G, S, or N;
- wherein X18 is S, I, R, T, K, P, N, H, or V;
- wherein X19 is L or V; and
- wherein X20 is G or A; and
- the sequence of CDR2L comprises the sequence X21AX22X23X24X23X26 (SEQ ID NO: 136); and
- wherein X21 is S, D, E, or A;
- wherein X22 is S or K;
- wherein X23 is S, N, T, R, or D;
- wherein X24 is L or V;
- wherein X25 is Q, E, or H; and
- wherein X26 is S, N, A, R, P, or T; and
- the sequence of CDR3L comprises the sequence QQX27X28SFPX29X30 (SEQ ID NO: 137);
- wherein X27 is A or G;
- wherein X28 is N, D, or Y;
- wherein X29 is F or L; and
- wherein X30 is A or T.
In embodiments, the fusion protein comprises an anti-PD-1 antibody, or antigen-binding fragment thereof, wherein the CDRs of the heavy and light chain variable regions comprise the following sequences:
-
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 21;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 22;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 23
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 96;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 97; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 82.
In further embodiments, the fusion protein comprises an anti-PD-1 antibody, or antigen-binding fragment thereof, wherein:
-
- the heavy chain variable region comprises SEQ ID NO: 24, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 24; and
- the light chain variable region comprises SEQ ID NO: 98, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 98.
In embodiments, the fusion protein comprises an anti-PD-1 antibody, or antigen-binding fragment thereof, wherein the CDRs of the heavy chain and light chain variable regions comprise the following sequences:
-
- the sequences of CDR1H, CDR2H and CDR3H comprise respectively SEQ ID NOS: 21, 22, and 23; and
- the sequences of CDR1L, CDR2L and CDR3L comprise respectively, SEQ ID NOS: 45, 46, and 47; SEQ ID NOS: 66, 67, and 68; SEQ ID NOS: 70, 67, and 71; SEQ ID NOS: 73, 74, and 75; SEQ ID NOS: 77, 78, and 47; SEQ ID NOS: 80, 81, and 82; SEQ ID NOS: 77, 78, and 84; SEQ ID NOS: 77, 86, and 47; SEQ ID NOS: 88, 89, and 47; SEQ ID NOS: 66, 67, and 47; SEQ ID NOS: 80, 92, and 75; SEQ ID NOS: 80, 94, and 71; SEQ ID NOS: 99, 100, and 47; SEQ ID NOS: 102, 103, and 104; SEQ ID NOS: 106, 103, and 47; SEQ ID NOS: 108, 103, and 47; SEQ ID NOS: 110, 111, and 75; SEQ ID NOS: 77, 103, and 113; SEQ ID NOS: 77, 111, and 47; SEQ ID NOS: 116, 67, and 47; SEQ ID NOS: 118, 119, and 47; SEQ ID NOS: 80, 78, and 47; SEQ ID NOS: 122, 103 and 47; SEQ ID NOS: 124, 125, and 75; SEQ ID NOS: 127, 38, and 68; SEQ ID NOS: 129, 130, and 47; or SEQ ID NOS: 132, 133, and 75.
In further embodiments, the fusion protein comprises an anti-PD-1 antibody, or antigen-binding fragment thereof, wherein:
-
- the heavy chain variable region comprises SEQ ID NO: 24, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 24; and
- the light chain variable region comprises SEQ ID NO: 48, 69, 72, 76, 79, 83, 85, 90, 91, 93, 101, 105, 107, 109, 112, 114, 115, 117, 120, 121, 123, 126, 128, 131, or 134, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of SEQ ID NO: 48, 69, 72, 76, 79, 83, 85, 90, 91, 93, 101, 105, 107, 109, 112, 114, 115, 117, 120, 121, 123, 126, 128, 131, or 134.
In embodiments, the fusion protein comprises an anti-PD-1 antibody, or antigen-binding fragment thereof, wherein the CDRs of the heavy and light chain variable regions comprise the following sequences:
-
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 17;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 18;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 19;
- the sequence of CDR1L comprises the sequence RSSX1SLLX2SNGX3X4YLD (SEQ ID NO:62),
- wherein X1 is Q or E;
- wherein X2 is H or Y;
- wherein X3 is Y or N; and
- wherein X4 is T or N;
- the sequence of CDR2L comprises the sequence X5X6SX7X8X9X10 (SEQ ID NO: 63),
- wherein X5 is L, Q or E;
- wherein X6 is S, A, or V;
- wherein X7 is H, N, T, or S;
- wherein X8 is R or L;
- wherein X9 is G, A, or H; and
- wherein X10 is S or T; and
- the sequence of CDR3L comprises the sequence MQGX11X12WPYT (SEQ ID NO: 64),
- wherein X11 is A, T, or S; and
- wherein X12 is H or R.
In embodiments, the fusion protein comprises an anti-PD-1 antibody, or antigen-binding fragment thereof, wherein the CDRs of the heavy chain and light chain variable regions comprise the following sequences:
-
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 17;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 18;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 19;
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 41;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 49; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 50.
In further embodiments, the fusion protein comprises an anti-PD-1 antibody, or antigen-binding fragment thereof, wherein:
-
- the heavy chain variable region comprises SEQ ID NO: 20, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 20; and
- the light chain variable region comprises SEQ ID NO: 51, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 51.
In embodiments, the fusion protein comprises an anti-PD-1 antibody, or antigen-binding fragment thereof, wherein the CDRs of the heavy chain and light chain variable regions comprise the following sequences:
-
- the sequence of CDR1H, CDR2H and CDR3H comprise SEQ ID NOS: 17, 18, and 19, respectively; and
- the sequence of CDR1L, CDR2L and CDR3L comprise respectively, SEQ ID NOS: 41, 42, and 43; SEQ ID NOS: 41, 52, and 53; SEQ ID NOS: 41, 55, and 56; or SEQ ID NOS: 58, 59, and 60.
In further embodiments the fusion protein comprises an anti-PD-1 antibody, or antigen-binding fragment thereof, wherein:
-
- the heavy chain variable region comprises SEQ ID NO: 20, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 20; and
- the light chain variable region comprises SEQ ID NO: 44, 54, 57, or 61, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of SEQ ID NO: 44, 54, 57, or 61.
Provided herein is a fusion protein that comprises a sequence described in Tables 24-27.
Provided herein is a fusion protein that comprises a heavy chain comprising a sequence selected from the group consisting of SEQ ID NOS: 174-184, 187-190, 193-199, 206-211, 224-243. Provided herein is a fusion protein that comprises a light chain comprising a sequence selected from the group consisting of SEQ ID NOS: 170, 173, 186, 192, and 205.
Provided herein is a fusion protein that comprises a light chain and a heavy/heavy chain combination recited in Table 26.
Provided herein is a fusion protein that comprises a light chain and one or more heavy chains recited in Table 27.
In embodiments, provided is a fusion protein comprising a light chain sequence comprising SEQ ID NO:219 and/or SEQ ID NO:98 and:
-
- (1) a first heavy chain sequence comprising SEQ ID NO:220 and a second heavy chain sequence comprising SEQ ID NO:224;
- (2) a first heavy chain sequence comprising SEQ ID NO:221 and a second heavy chain sequence comprising SEQ ID NO:225;
- (3) a first heavy chain sequence comprising SEQ ID NO:222 and a second heavy chain sequence comprising SEQ ID NO:226;
- (4) a first heavy chain sequence comprising SEQ ID NO:223 and a second heavy chain sequence comprising SEQ ID NO:227.
In embodiments, provided is a fusion protein comprising a light chain sequence comprising SEQ ID NO:219 and/or SEQ ID NO:98 and:
-
- (1) a first heavy chain sequence comprising SEQ ID NO:220 and a second heavy chain sequence comprising SEQ ID NO:228;
- (2) a first heavy chain sequence comprising SEQ ID NO:221 and a second heavy chain sequence comprising SEQ ID NO:229;
- (3) a first heavy chain sequence comprising SEQ ID NO:222 and a second heavy chain sequence comprising SEQ ID NO:230;
- (4) a first heavy chain sequence comprising SEQ ID NO:223 and a second heavy chain sequence comprising SEQ ID NO:231;
- (5) a first heavy chain sequence comprising SEQ ID NO:220 and a second heavy chain sequence comprising SEQ ID NO:236;
- (6) a first heavy chain sequence comprising SEQ ID NO:221 and a second heavy chain sequence comprising SEQ ID NO:237;
- (7) a first heavy chain sequence comprising SEQ ID NO:222 and a second heavy chain sequence comprising SEQ ID NO:238;
- (8) a first heavy chain sequence comprising SEQ ID NO:223 and a second heavy chain sequence comprising SEQ ID NO:239;
- (9) a first heavy chain sequence comprising SEQ ID NO:240 and a second heavy chain sequence comprising SEQ ID NO:241; or
- (10) a first heavy chain sequence comprising SEQ ID NO:240 and a second heavy chain sequence comprising SEQ ID NO:242.
In embodiments, provided is a fusion protein comprising a light chain sequence comprising SEQ ID NO:219 and/or SEQ ID NO:98 and:
-
- (1) a first heavy chain sequence comprising SEQ ID NO:220 and a second heavy chain sequence comprising SEQ ID NO:232;
- (2) a first heavy chain sequence comprising SEQ ID NO:221 and a second heavy chain sequence comprising SEQ ID NO:233;
- (3) a first heavy chain sequence comprising SEQ ID NO:222 and a second heavy chain sequence comprising SEQ ID NO:234;
- (4) a first heavy chain sequence comprising SEQ ID NO:223 and a second heavy chain sequence comprising SEQ ID NO:235; or
- (5) a first heavy chain sequence comprising SEQ ID NO:240 and a second heavy chain sequence comprising SEQ ID NO:243.
In embodiments, provided is a fusion protein comprising a light chain sequence comprising SEQ ID NO:219 and/or SEQ ID NO:98 and:
-
- (1) a first heavy chain sequence comprising SEQ ID NO:220 and a second heavy chain sequence comprising SEQ ID NO:224; or a first heavy chain sequence comprising SEQ ID NO:221 and a second heavy chain sequence comprising SEQ ID NO:225; or
- (2) a first heavy chain sequence comprising SEQ ID NO:222 and a second heavy chain sequence comprising SEQ ID NO:226; or a first heavy chain sequence comprising SEQ ID NO:223 and a second heavy chain sequence comprising SEQ ID NO:227.
In embodiments, provided is a fusion protein comprising a light chain sequence comprising SEQ ID NO:219 and/or SEQ ID NO:98 and:
-
- (1) a first heavy chain sequence comprising SEQ ID NO:220 and a second heavy chain sequence comprising SEQ ID NO:228; or a first heavy chain sequence comprising SEQ ID NO:221 and a second heavy chain sequence comprising SEQ ID NO:229;
- (2) a first heavy chain sequence comprising SEQ ID NO:222 and a second heavy chain sequence comprising SEQ ID NO:230; or a first heavy chain sequence comprising SEQ ID NO:223 and a second heavy chain sequence comprising SEQ ID NO:231;
- (3) a first heavy chain sequence comprising SEQ ID NO:220 and a second heavy chain sequence comprising SEQ ID NO:236; or a first heavy chain sequence comprising SEQ ID NO:221 and a second heavy chain sequence comprising SEQ ID NO:237;
- (4) a first heavy chain sequence comprising SEQ ID NO:222 and a second heavy chain sequence comprising SEQ ID NO:238; or a first heavy chain sequence comprising SEQ ID NO:223 and a second heavy chain sequence comprising SEQ ID NO:239;
- (5) a first heavy chain sequence comprising SEQ ID NO:240 and a second heavy chain sequence comprising SEQ ID NO:241; or
- (6) a first heavy chain sequence comprising SEQ ID NO:240 and a second heavy chain sequence comprising SEQ ID NO:242.
In embodiments, provided is a fusion protein comprising a light chain sequence comprising SEQ ID NO:219 and/or SEQ ID NO:98 and:
-
- (1) a first heavy chain sequence comprising SEQ ID NO:220 and a second heavy chain sequence comprising SEQ ID NO:232; or a first heavy chain sequence comprising SEQ ID NO:221 and a second heavy chain sequence comprising SEQ ID NO:233;
- (2) a first heavy chain sequence comprising SEQ ID NO:222 and a second heavy chain sequence comprising SEQ ID NO:234; or a first heavy chain sequence comprising SEQ ID NO:223 and a second heavy chain sequence comprising SEQ ID NO:235; or
- (3) a first heavy chain sequence comprising SEQ ID NO:240 and a second heavy chain sequence comprising SEQ ID NO:243.
Antibodies and Antigen-Binding Fragments Thereof
The term antibody is used here in the broadest sense and includes monoclonal antibodies (including full length or intact monoclonal antibodies), polyclonal antibodies, bispecific antibodies, humanized antibodies, single chain antibodies, chimeric antibodies, synthetic antibodies, recombinant antibodies, hybrid antibodies, mutagenized antibodies and grafted antibodies (grafted antibodies), bispecific antibodies, a specific antibody portion (e.g., a domain antibody), as well as any antigen-binding portion thereof that competes with an intact antibody for specific binding, an antigen-binding portion thereof (e.g., paratopes, CDRs), and any other modified conformations of the immunoglobulin molecule comprising the antigen recognition site so long as they exhibit the desired biological activity and specificity. Accordingly, an antibody is an immunoglobulin molecule or fragment or derivative thereof including any polypeptide comprising an antigen-binding site, capable of specifically binding to a target through at least one antigen recognition site located in the variable region of the immunoglobulin molecule. The disclosed antibody can be murine, rat, human, or any other origin (including chimeric or humanized antibodies).
In certain embodiments, the framework regions of the antibody (or antigen-binding fragment thereof) may be identical to human germline sequences or may be naturally or artificially modified.
In one preferred embodiment, the disclosed antibody structures belong to the IgG class of immunoglobulin molecules. A standard IgG immunoglobulin molecule comprises two identical light chain polypeptides, and two identical heavy chain polypeptides. The molecular weight of the light chain polypeptide is around 23,000 Daltons and the molecular weight of the heavy chain polypeptide varies between 53,000-70,000 Daltons. The four chains are typically joined by disulfide bonds in a “Y” configuration.
Two heavy chains (HC) and two light chains (LC) of an immunoglobulin molecule are covalently bonded to each other, and the end portions of the two heavy chains are bonded to each other by covalent disulfide linkages or non-covalent linkages when the immunoglobulins are generated by either hybridomas, B cells, or genetically engineered host cells. The light and heavy chains both contain regions of structural and functional homology. The term “variable” and “constant” are used functionally. Each heavy chain is comprised of a heavy chain variable region (“HCVR” or “VH”) and a heavy chain constant region (comprised of domains CH1, CH2, and CH3). Each light chain is comprised of a light chain variable region (“LCVR or “VL”) and a light chain constant region (CL). The VH and VL regions can be further subdivided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR). Each VH and VL is composed of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4.
The variable region allows the antibody to recognize and specifically bind epitopes located on antigens. The variable domains of both the light (VL) and heavy (VH) chain portions determine antigen recognition and specificity. The antigen-binding site of an antibody is comprised of the VL domain and VH domain, or a subset of the CDRs. More specifically, the antigen-binding site is defined by one, two, or three CDRs on each of the VH and VL chains (i.e. CDR-H1, CDR-H2, CDR-H3, CDR-L1, CDR-L2, and CDR-L3). Conversely, the constant domains of the light chain (CL) and the heavy chain (CH1, CH2, or CH3) confer biological properties such as secretion, transplacental mobility, Fc receptor binding, complement binding, and the like. By convention, the numbering of the constant region domains increases as they become more distal from the antigen-binding site or amino-terminus of the antibody.
As used herein, the term “Complementarity Determining Regions” (CDRs) refers to portions of an antibody variable domain that are (typically) involved in antigen binding. Each variable region has three non-consecutive CDRs, known as CDR1, CDR2, and CDR3. The CDRs are separated by structurally conserved regions called framework regions (FR-1, -2, -3, and -4) that form a “core” β-sheet structure displaying these loops on the surface of the variable domain. The six CDRs present in each antigen-binding domain are short, non-contiguous sequences of amino acids that are specifically positioned to form the antigen-binding domain as the antibody assumes its three dimensional configuration in an aqueous environment. The length and composition of the CDR sequences are highly variable, especially in the CDR3. The remainder of the amino acids located in the antigen-binding domains or the “framework” regions, show less inter-molecular variability. The antigen-binding domain formed by the positioned CDRs defines a surface complementary to the epitope on the immunoreactive antigen. This complementary surface promotes the non-covalent binding of the antibody to its cognate epitope. Each CDR can comprise amino acid residues from a CDR as defined by e.g. Kabat (i.e., about residues 24-34 (L1), 50-56 (L2) and 89-97 (L3) in the light chain variable domain and 31-35 (H1), 50-65 (H2) and 95-102 (H3) in the heavy chain variable domain (Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1987, 1991)). Each CDR can also comprise amino acid residues from a “hypervariable loop” (i.e., about residues 26-32 (L1), 50-52 (L2) and 91-96 (L3) in the light chain variable domain and 26-32 (H1), 53-55 (H2) and 96-101 (H3) in the heavy chain variable domain (Chothia & Lesk 196 J. Mol. Biol. 901 (1987)). In some instances, a CDR can include amino acids from both a CDR region defined according to Kabat and a hypervariable loop. The Kabat numbering may not always correspond to the linear numbering on the amino acid residues due to a shortening of, or insertion into, a structural component, whether framework or CDR, of the basic variable domain structure. The correct Kabat numbering of residues may be determined for a given antibody or antigen-binding fragment thereof by alignment of residues of homology in the sequence of the antibody or antigen-binding fragment thereof with a “standard” Kabat numbered sequence or be defined according to ImMunoGeneTics (IMGT) system (Lefranc, M.-P. et al., Dev. Comp. Immunol., 27, 55-77 (2003)).
As used herein, the term “antigen-binding portion” or “antigen-binding fragment” may be a fragment comprising a Fab, Fab′, F(ab′)2, Fd, Fv, domain antibodies (dAbs such as shark and camel antibodies), ScFv, a maxibody, a minibody, a nanobody, an intrabody, a diabody, a triabody, a tetrabody, a v-NAR and a bis-scFv, or a polypeptide that contain at least certain portions of an immunoglobulin sufficient to confer specific antigen-binding to the polypeptide.
The antibody may be any class of antibody, such as IgG, IgA, or IgM (or a subclass thereof), and the antibody need not be of any particular class, and any of the immunoglobulin molecules comprising the antigen recognition site of the required specificity, other modified configurations (including glycosylation variants of antibodies, amino acid sequence variants of antibodies, and covalently modified antibodies) can be encompassed. Modified versions of each of these classes and isotypes are known to a person skilled in the art, accordingly, are within the scope of the instant disclosure.
In some embodiments of the aspects described herein, the anti-PD-1 antibody fragment is a Fab fragment, which comprises or consist essentially of a variable (VL) and constant (CL) domain of the light chain and a variable domain (VH) and the first constant domain (CH1) of the heavy chain.
In some embodiments of the aspects described herein, the anti-PD-1 antibody fragment is a Fab′ fragment, which refers to a Fab fragment having one or more cysteine residues at the C-terminus of the CH1 domain.
In some embodiments of the aspects described herein, the anti-PD-1 antibody fragment is an Fd fragment comprising or consisting essentially of VH and CH1 domains.
In some embodiments of the aspects described herein, the anti-PD-1 antibody fragment is an Fd′ fragment comprising VH and CH1 domains and one or more cysteine residues at the C-terminus of the CH1 domain.
Single-chain Fv or scFv antibody fragments comprise or consist essentially of the VH and VL domains of an antibody, such that these domains are present in a single polypeptide chain. Generally, an Fv polypeptide further comprises a polypeptide linker between the VH and VL domains, which allows the scFv to form the desired structure for antigen-binding. Accordingly, in some embodiments of the aspects described herein, the anti-PD-1 antibody fragment is a Fv fragment comprising or consisting essentially of the VL and VH domains of a single arm of an antibody.
In some embodiments of the aspects described herein, the anti-PD-1 antibody fragment is a diabody comprising two antigen-binding sites, comprising a heavy chain variable domain (VH) connected to a light chain variable domain (VL) in the same polypeptide chain.
In some embodiments of the aspects described herein, the anti-PD-1 antibody fragment is a dAb fragment comprising or consisting essentially of a VH domain.
In some embodiments of the aspects described herein, the anti-PD-1 antibody fragment is a F(ab′)2 fragment, which comprises a bivalent fragment comprising two Fab′ fragments linked by a disulfide bridge at the hinge region.
In some embodiments of the aspects described herein, the anti-PD-1 antibody fragment is a linear antibody comprising a pair of tandem Fd segments (VH-CH1-VH-CH1) which, together with complementary light chain polypeptides, form a pair of antigen-binding regions.
A person skilled in the arts can use various techniques that have been developed and are available for the production of antibody fragments. Traditionally, these fragments were derived via proteolytic digestion of intact antibodies. However, F(ab′)2 fragments can be isolated directly from recombinant host cell culture. Other techniques for the production of antibody fragments will be apparent to the skilled practitioner. In other embodiments, the antibody fragment of choice is a single chain Fv fragment (scFv). See, for example, WO 93/16185. Alternatively, these fragments can also be produced directly by recombinant host cells. For example, antibody fragments can be isolated from the antibody phage libraries discussed herein. In another approach, Fab′-SH fragments can be directly recovered from E. coli and chemically coupled to form F(ab′)2 fragments (Carter et al., 1992).
In one embodiment, the antibody is a bispecific antibody comprising a complementary region that binds PD-1.
Contemplated antibodies or antigen-binding fragments may have all types of constant regions, including IgM, IgG, IgD, and IgE, and any isotype, including IgG1, IgG2, IgG3, and IgG4. In one embodiment, the isotype is human IgG1. In another embodiment, the human isotype IgG4 is used. Light chain constant regions can be X or u. The antibody or antigen-binding fragment thereof may comprise sequences from more than one class or isotype.
Anti-PD-1 Antibodies and PD-1 Binding Fragments Thereof
The disclosure describes antibodies that bind to PD-1, and antigen-binding fragments thereof that bind to PD-1, as well as fusion proteins comprising such anti-PD-1 antibodies or antigen-binding fragments thereof. The term “PD-1” refers to programmed death-1 protein (also known as CD279), a T cell co-inhibitor. The term PD-1 encompasses recombinant PD-1 and/or a fragment thereof. The term also includes PD-1 or a fragment thereof coupled to, for example, mouse or human Fc, histidine tag, and/or a signal sequence. The term may further encompass a fusion protein comprising PD-1. The amino acid sequence of full-length PD-1 is provided in GenBank as accession number NP_005009.2. The ligands for PD-1 include PD-L1 and PD-L2. The amino acid sequence of full-length PD-L1 is provided in GenBank as accession number NP_054862.1. The amino acid sequence of full-length PD-L2 is provided in GenBank as accession number NP_079515.2.
In embodiments, the anti-PD-1 antibody or antigen binding fragment thereof specifically binds to PD-1 and antagonizes PD-1 mediated immune suppression. The anti-PD-1 antibodies and antigen-binding fragments thereof disclosed herein may interrupt, inhibit, or reduce PD-1 biological activity including downstream events mediated by PD-1. The anti-PD-1 antibodies and antigen-binding fragments thereof disclosed herein may exhibit any one or more of the following features: (a) binding to PD-1 and blocking of downstream signaling events; (b) blocking PD-L1-binding to PD-1; (c) increasing T cell proliferation; (d) upregulating the T cell-mediated immune response; (e) stimulating TNF secretion; (f) reducing inhibitory signal transduction through PD-1; and/or (g) stimulating IFNγ secretion. The anti-PD-1 antibodies and antigen-binding fragments thereof disclosed herein exhibit potent binding and inhibitory activities and are useful for therapeutic and diagnostics uses.
In one aspect, the disclosure provides antibodies and antigen-binding fragments thereof that bind to PD-1. In certain embodiments, the disclosure provides bispecific antibodies and binding proteins that bind specifically to PD-1 and at least one other molecule.
In another aspect the disclosure provides an antibody, or an antigen-binding fragment thereof, wherein the antibody or antigen-binding fragment thereof binds to PD-1, and wherein the antibody or antigen-binding fragment thereof comprises a heavy chain variable region and a light chain variable region wherein each of the heavy chain and the light chain variable regions comprise a CDR1, CDR2, and CDR3 and wherein the antibody heavy chain comprises a constant region comprising three constant domains CH1, CH2, and CH3.
In embodiments, the CDRs of the anti-PD-1 antibody, or antigen-binding fragment thereof, comprise the following sequences:
-
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 21;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 22;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 23;
- the sequence of CDR1L comprises the sequence RX13X14X15X16IX17X15WX19X20 (SEQ ID NO:135);
- wherein X13 is A or V;
- wherein X14 is S or G;
- wherein X15 is Q, E, or R;
- wherein X16 is G, S, D or N;
- wherein X17 is G, S, or N;
- wherein X18 is S, I, R, T, K, P, N, H, or V;
- wherein X19 is L or V; and
- wherein X20 is G or A; and
- the sequence of CDR2L comprises the sequence X21AX22X23X24X23X26 (SEQ ID NO: 136); and
- wherein X21 is S, D, E, or A;
- wherein X22 is S or K;
- wherein X23 is S, N, T, R, or D;
- wherein X24 is L or V;
- wherein X25 is Q, E, or H; and
- wherein X26 is S, N, A, R, P, or T; and
- the sequence of CDR3L comprises the sequence QQX27X28SFPX29X30 (SEQ ID NO: 137);
- wherein X27 is A or G;
- wherein X28 is N, D, or Y;
- wherein X29 is F or L; and
- wherein X30 is A or T.
In embodiments, the CDRs of the anti-PD-1 antibody, or antigen-binding fragment thereof, comprise the following sequences:
-
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 21;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 22;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 23
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 96;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 97; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 82.
In embodiments, the antibody, or antigen-binding fragment thereof, comprises:
-
- a heavy chain variable region comprising SEQ ID NO: 24, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 24; and
- a light chain variable region comprising SEQ ID NO: 98, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 98.
In embodiments, the CDRs of the anti-PD-1 antibody, or antigen-binding fragment thereof, comprise the following sequences:
-
- the sequences of CDR1H, CDR2H and CDR3H comprise respectively SEQ ID NOS: 21, 22, and 23; and
- the sequences of CDR1L, CDR2L and CDR3L comprise respectively, SEQ ID NOS: 45, 46, and 47; SEQ ID NOS: 66, 67, and 68; SEQ ID NOS: 70, 67, and 71; SEQ ID NOS: 73, 74, and 75; SEQ ID NOS: 77, 78, and 47; SEQ ID NOS: 80, 81, and 82; SEQ ID NOS: 77, 78, and 84; SEQ ID NOS: 77, 86, and 47; SEQ ID NOS: 88, 89, and 47; SEQ ID NOS: 66, 67, and 47; SEQ ID NOS: 80, 92, and 75; SEQ ID NOS: 80, 94, and 71; SEQ ID NOS: 99, 100, and 47; SEQ ID NOS: 102, 103, and 104; SEQ ID NOS: 106, 103, and 47; SEQ ID NOS: 108, 103, and 47; SEQ ID NOS: 110, 111, and 75; SEQ ID NOS: 77, 103, and 113; SEQ ID NOS: 77, 111, and 47; SEQ ID NOS: 116, 67, and 47; SEQ ID NOS: 118, 119, and 47; SEQ ID NOS: 80, 78, and 47; SEQ ID NOS: 122, 103 and 47; SEQ ID NOS: 124, 125, and 75; SEQ ID NOS: 127, 38, and 68; SEQ ID NOS: 129, 130, and 47; or SEQ ID NOS: 132, 133, and 75.
In embodiments, the anti-PD-1 antibody, or antigen-binding fragment thereof, comprises:
-
- a heavy chain variable region comprising SEQ ID NO: 24, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 24; and
- a light chain variable region comprising SEQ ID NO: 48, 69, 72, 76, 79, 83, 85, 90, 91, 93, 101, 105, 107, 109, 112, 114, 115, 117, 120, 121, 123, 126, 128, 131, or 134, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of SEQ ID NO: 48, 69, 72, 76, 79, 83, 85, 90, 91, 93, 101, 105, 107, 109, 112, 114, 115, 117, 120, 121, 123, 126, 128, 131, or 134.
In embodiments, the CDRs of the anti-PD-1 antibody, or antigen-binding fragment thereof, comprise the following sequences:
-
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 17;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 18;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 19;
- the sequence of CDR1L comprises the sequence RSSX1SLLX2SNGX3X4YLD (SEQ ID NO:62),
- wherein X1 is Q or E;
- wherein X2 is H or Y;
- wherein X3 is Y or N; and
- wherein X4 is T or N;
- the sequence of CDR2L comprises the sequence X5X6SX7X8X9X10 (SEQ ID NO: 63),
- wherein X5 is L, Q or E;
- wherein X6 is S, A, or V;
- wherein X7 is H, N, T, or S;
- wherein X8 is R or L;
- wherein X9 is G, A, or H; and
- wherein X10 is S or T; and
- the sequence of CDR3L comprises the sequence MQGX11X12WPYT (SEQ ID NO: 64),
- wherein X11 is A, T, or S; and
- wherein X12 is H or R.
In embodiments, the CDRs of the anti-PD-1 antibody, or antigen-binding fragment thereof, comprise the following sequences:
-
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 17;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 18;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 19;
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 41;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 49; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 50.
In embodiments, the anti-PD-1 antibody, or antigen-binding fragment thereof, comprises:
-
- a heavy chain variable region comprising SEQ ID NO: 20, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 20; and
- a light chain variable region comprising SEQ ID NO: 51, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 51.
In embodiments, the CDRs of the anti-PD-1 antibody, or antigen-binding fragment thereof, comprise the following sequences:
-
- the sequence of CDR1H, CDR2H and CDR3H comprise SEQ ID NOS: 17, 18, and 19, respectively; and
- the sequence of CDR1L, CDR2L and CDR3L comprise respectively, SEQ ID NOS: 41, 42, and 43; SEQ ID NOS: 41, 52, and 53; SEQ ID NOS: 41, 55, and 56; or SEQ ID NOS: 58, 59, and 60.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 8, 12, 16, 20, and 24, and wherein the sequence of the light chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a light chain variable region amino acid sequence selected from the group consisting of SEQ ID NOs: 28, 32, 36, 40, 44, 48, 51, 54, 57, 61, 65, 69, 72, 76, 79, 83, 85, 88, 90, 91, 93, 95, 98, 101, 105, 107, 109, 112, 114, 115, 117, 120, 121, 123, 126, 128, 131, 134, and 138.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 20, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 65.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence SEQ ID NO: 20; and wherein the sequence of the light chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a light chain variable region amino acid sequence selected from the group consisting of SEQ ID NOs: 44, 51, 54, 57, and 61.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 20, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 51.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 20, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 54.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 20, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 57.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 20, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 61.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 138.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence SEQ ID NO: 20; and wherein the sequence of the light chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a light chain variable region amino acid sequence selected from the group consisting of SEQ ID NOs: 69, 72, 76, 79, 83, 85, 87, 90, 91, 93, 95, 98, 101, 105, 107, 109, 112, 114, 115, 117, 120, 121, 123, 126, 128, 131, 134, and 138.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 98.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 69.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 72.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 76.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 79.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 83.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 85.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 87.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 90.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 91.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 93.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 95.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 101.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 105.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 107.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 109.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 112.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 114.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 115.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 117.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 120.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 121.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 123.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 126.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 128.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 131.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 24, and wherein the sequence of the light chain variable region comprises the sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the light chain variable region amino acid sequence of SEQ ID NO: 134.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein the sequence of the heavy chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the heavy chain variable region amino acid sequence of SEQ ID NO: 142, and wherein the sequence of the light chain variable region comprises a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to a light chain variable region amino acid sequence selected from the group consisting of SEQ ID NOs: 146, 150, 153, 156, 160, 164, and 167.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprises a CDR1, CDR2, and CDR3, and wherein:
-
- the sequence of CDR1H comprises the sequence, SEQ ID NO: 139;
- the sequence of CDR2H comprises the sequence, SEQ ID NO: 140;
- the sequence of CDR3H comprises the sequence, SEQ ID NO: 141;
- the sequence of CDR1L comprises the sequence, SEQ ID NO: 143;
- the sequence of CDR2L comprises the sequence, SEQ ID NO: 144; and
- the sequence of CDR3L comprises the sequence, SEQ ID NO: 145.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprises a CDR1, CDR2, and CDR3, and wherein:
-
- the sequence of CDR1H comprises the sequence, SEQ ID NO: 139;
- the sequence of CDR2H comprises the sequence, SEQ ID NO: 140;
- the sequence of CDR3H comprises the sequence, SEQ ID NO: 141;
- the sequence of CDR1L comprises the sequence, SEQ ID NO: 147;
- the sequence of CDR2L comprises the sequence, SEQ ID NO: 148; and
- the sequence of CDR3L comprises the sequence, SEQ ID NO: 149.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprises a CDR1, CDR2, and CDR3, and wherein:
-
- the sequence of CDR1H comprises the sequence, SEQ ID NO: 139;
- the sequence of CDR2H comprises the sequence, SEQ ID NO: 140;
- the sequence of CDR3H comprises the sequence, SEQ ID NO: 141;
- the sequence of CDR1L comprises the sequence, SEQ ID NO: 151;
- the sequence of CDR2L comprises the sequence, SEQ ID NO: 148; and
- the sequence of CDR3L comprises the sequence, SEQ ID NO: 152.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprises a CDR1, CDR2, and CDR3, and wherein:
-
- the sequence of CDR1H comprises the sequence, SEQ ID NO: 139;
- the sequence of CDR2H comprises the sequence, SEQ ID NO: 140;
- the sequence of CDR3H comprises the sequence, SEQ ID NO: 141;
- the sequence of CDR1L comprises the sequence, SEQ ID NO: 154;
- the sequence of CDR2L comprises the sequence, SEQ ID NO: 148; and
- the sequence of CDR3L comprises the sequence, SEQ ID NO: 155.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprises a CDR1, CDR2, and CDR3, and wherein:
-
- the sequence of CDR1H comprises the sequence, SEQ ID NO: 139;
- the sequence of CDR2H comprises the sequence, SEQ ID NO: 140;
- the sequence of CDR3H comprises the sequence, SEQ ID NO: 141;
- the sequence of CDR1L comprises the sequence, SEQ ID NO: 157;
- the sequence of CDR2L comprises the sequence, SEQ ID NO: 158; and
- the sequence of CDR3L comprises the sequence, SEQ ID NO: 159.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprises a CDR1, CDR2, and CDR3, and wherein:
-
- the sequence of CDR1H comprises the sequence, SEQ ID NO: 139;
- the sequence of CDR2H comprises the sequence, SEQ ID NO: 140;
- the sequence of CDR3H comprises the sequence, SEQ ID NO: 141;
- the sequence of CDR1L comprises the sequence, SEQ ID NO: 161;
- the sequence of CDR2L comprises the sequence, SEQ ID NO: 162; and
- the sequence of CDR3L comprises the sequence, SEQ ID NO: 163.
In one embodiment, the disclosure provides an antibody or antigen-binding fragment thereof, which binds to PD-1, wherein the antibody or antigen-binding fragment comprises a heavy chain variable region and a light chain variable region, wherein each of the heavy chain and the light chain variable regions comprises a CDR1, CDR2, and CDR3, and wherein:
-
- the sequence of CDR1H comprises the sequence, SEQ ID NO: 139;
- the sequence of CDR2H comprises the sequence, SEQ ID NO: 140;
- the sequence of CDR3H comprises the sequence, SEQ ID NO: 141;
- the sequence of CDR1L comprises the sequence, SEQ ID NO: 157;
- the sequence of CDR2L comprises the sequence, SEQ ID NO: 165; and
- the sequence of CDR3L comprises the sequence, SEQ ID NO: 166.
In addition to the above description,
The anti-PD-1 antibodies and antigen-binding fragments thereof disclosed herein and the fusion proteins disclosed herein can have one or more amino acid substitutions, deletions, insertions, and/or additions. In some embodiments, one or more CDR residues of the anti-PD-1 antibodies or antigen-binding fragments (or the fusion proteins comprising the anti-PD-1 antibodies or antigen-binding fragments) disclosed herein have been changed by amino acid substitution, deletion, insertion, and/or addition. Amino acid substitutions can be conservative or non-conservative substitutions. The present disclosure also includes anti-PD-1 antibodies, and antigen-binding fragments thereof (and the fusion proteins comprising the anti-PD-1 antibodies or antigen-binding fragments), which are derived from the amino acid sequences disclosed herein, wherein one or more amino acids within one or more framework and/or CDR regions are mutated to the corresponding residue(s) of the germline sequence from which the antibody was derived, or to the corresponding residue(s) of another human germline sequence, or to a conservative amino acid substitution of the corresponding germline residue(s) (such sequence changes are referred to herein collectively as “germline mutations”). In certain embodiments, the anti-PD-1 antibodies or binding fragments thereof (or the fusion proteins comprising the anti-PD-1 antibodies or antigen-binding fragments) comprise one or more CDRs, or one or more variable domains with an amino acid sequence at least 85% at least 90%, at least 95%, at least 97%, at least 98%, or at least 99%, identical to the CDR and/or variable domain sequences set forth in
Also provided herein variable heavy chain and variable light chain sequences as well as pairing thereof that are similar, but not identical to the variable heavy chain and variable light chains disclosed in Table 25 and pairings thereof. It will be evident that any of the frameworks described herein can be utilized in combination with any of the CDRs and CDR motifs described herein. In some embodiments, the anti-PD-1 antibody or antigen-binding fragment thereof utilizes a framework described in Table 25.
Also provided herein is a chimeric antigen receptor (CAR) comprising one, two, three, four, five, or six CDRs of the anti-PD1 antibodies and antigen binding fragments disclosed herein. Also provided herein is CAR comprising the six CDRs of any one of the anti-PD1 antibodies and antigen binding fragments disclosed herein.
Disclosed is an immune cell expressing a CAR comprising one, two, three, four, five, or six CDRs of the anti-PD1 antibodies and antigen binding fragments disclosed herein. Disclosed is an immune cell expressing a CAR comprising the six CDRs of any one of the anti-PD1 antibodies and antigen binding fragments disclosed herein. In some embodiments, the immune cell is a T cell.
“Identity” refers to the number or percentage of identical positions shared by two amino acid or nucleic acid sequences in optimally aligned sequences after considering number of gaps and the length of each gap that were needed for the optimal alignment. “Substantially identical” means an amino acid sequence, which differs from the original sequence only by conservative amino acid substitutions, which do not destroy the function of the protein.
Also disclosed herein are anti-PD-1 antibodies or antigen-binding fragments thereof or fusion proteins comprising an amino acid sequence that is at least 80%, or at least 85%, or at least 90%, or at least 95%, or at least 98%, or at least 99% identical to an amino acid sequence disclosed herein. Methods and computer programs for determining sequence similarity are publically available, including, but not limited to, the GCG program package (Devereux et al., Nucleic Acids Research 12: 387, 1984), BLASTP, BLASTN, FASTA (Altschul et al., J. Mol. Biol. 215:403 (1990), and the ALIGN program (version 2.0). The Smith Waterman algorithm may also be used to determine similarity. The BLAST program is publicly available from NCBI and other sources (BLAST Manual, Altschul, et al., NCBI NLM NIH, Bethesda, Md. 20894; BLAST 2.0 at http://www.ncbi.nlm.nih.gov/blast/). In comparing sequences, these methods account for various substitutions, deletions, and other modifications.
In some embodiments of the aspects described herein, amino acid sequence modification(s) of the antibodies or antigen-binding fragments thereof that bind to PD-1 or the fusion proteins that bind to PD-1 described herein are contemplated. Amino acid sequence variants of the anti-PD-1 antibody or antigen-binding fragment thereof or the fusion proteins are prepared by introducing appropriate nucleotide changes into the nucleic acid encoding the anti-PD-1 antibody or antigen-binding fragment thereof or the fusion protein, or by peptide synthesis. Such modifications include, for example, deletions from, and/or insertions into and/or substitutions of, residues within the amino acid sequences of the antibody or antigen-binding fragment thereof. Any combination of deletion, insertion, and substitution is made to arrive at the final construct, if the final construct possesses the desired characteristics, e.g., binding specificity, inhibition of biological activity.
Amino acid substitutions can be made, in some cases, by selecting substitutions that do not differ significantly in their effect on maintaining (a) the structure of the peptide backbone in the area of the substitution, (b) the charge or hydrophobicity of the molecule at the target sit; or (c) the bulk of the side chain (conservative amino acid substitution variant. These variants have at least one amino acid residue in the antibody or antigen-binding fragment thereof or fusion protein replaced by a different residue that has similar side chain properties. Amino acids can be grouped according to similarities in the properties of their side chains (see Lehninger, BIOCHEMISTRY (2nd ed., Worth Publishers, New York, 1975):
-
- (1) non-polar: Ala (A), Val (V), Leu (L), Ile (I), Pro (P), Phe (F), Trp (W), Met (M);
- (2) uncharged polar: Gly (G), Ser (S), Thr (T), Cys (C), Tyr (Y), Asn (N), Gln (Q);
- (3) acidic: Asp (D), Glu (E);
- (4) basic: Lys (K), Arg (R), His (H).
As such, a non-limiting example for a conservative amino acid substitution is one that replaces a non-polar amino acid with another non-polar amino acid.
Alternatively, naturally occurring residues can be divided into groups based on common side-chain properties:
-
- (1) hydrophobic: Ala (A), Val (V), Leu (L), Ile (I), Met (M);
- (2) neutral hydrophilic: Ser (S), Thr (T), Cys (C), Asn (N), Gln (Q);
- (3) acidic: Asp (D), Glu (E);
- (4) basic: Lys (K), Arg (R), His (H);
- (5) residues that influence chain orientation: Gly (G), Pro (P);
- (6) aromatic: Phe (F), Trp (W), Tyr (Y).
Substitutions made within these groups can be considered conservative substitutions. Examples of non-limiting substitutions include, substitution of valine for alanine, lysine for arginine, glutamine for asparagine, glutamic acid for aspartic acid, serine for cysteine, asparagine for glutamine, aspartic acid for glutamic acid, proline for glycine, arginine for histidine, leucine for isoleucine, isoleucine for leucine, arginine for lysine, leucine for methionine, leucine for phenylalanine, glycine for proline, threonine for serine, serine for threonine, tyrosine for tryptophan, phenylalanine for tyrosine, and/or leucine for valine.
Further contemplated are amino acid sequence insertions, which can include amino- and/or carboxyl-terminal fusions ranging in length from one residue to polypeptides containing a hundred or more residues, as well as intrasequence insertions of single or multiple amino acid residues. Examples of terminal fusions include an antibody or antigen-binding fragment thereof with an N-terminal methionyl residue or an antibody or antigen-binding fragment thereof fused to a cytotoxic polypeptide (or fusion proteins comprising such antibody or antigen-binding fragment thereof). Other examples of terminal fusions of the antibody or antigen-binding fragment thereof include the fusion to the N- or C-terminus of the antibody or antigen-binding fragment thereof to an enzyme or a polypeptide which increases the serum half-life of the antibody or antigen-binding fragment thereof, such as, for example, biotin (or fusion proteins comprising such antibody or antigen-binding fragment thereof).
Any cysteine residue not involved in maintaining the proper conformation of the antibodies or antigen-binding fragments thereof that bind to PD-1 also can be substituted, for example with a serine or an alanine, to improve the oxidative stability of the molecule and prevent aberrant crosslinking.
Conversely, cysteine bond(s) can be added to the anti-PD-1 antibody or antigen-binding fragment thereof to improve its stability (particularly where the anti-PD-1 antibody or antigen-binding fragment thereof is an antibody fragment such as an Fv fragment).
In some embodiments, the anti-PD-1 antibodies or antigen-binding fragments thereof or the fusion protein comprising antibodies or antigen-binding fragments thereof describes have amino acid alterations that alter the original glycosylation pattern of the anti-PD-1 antibody or antigen-binding fragment thereof. By “altering the original glycosylation pattern” is meant deleting one or more carbohydrate moieties found in the antibody or antigen-binding fragment thereof, and/or adding one or more glycosylation sites that are not present in the antibody or antigen-binding fragment thereof. Glycosylation of antibodies is typically either N-linked or O-linked. N-linked refers to the attachment of the carbohydrate moiety to the side chain of an asparagine residue. The tripeptide sequences asparagine-X-serine and asparagine-X-threonine, wherein X is any amino acid except proline, are the recognition sequences for enzymatic attachment of the carbohydrate moiety to the asparagine side chain. Thus, the presence of either of these tripeptide sequences in a polypeptide creates a potential glycosylation site. O-linked glycosylation refers to the attachment of one of the sugars N-aceylgalactosamine, galactose, or xylose to a hydroxyamino acid, most commonly serine or threonine, although 5-hydroxyproline or 5-hydroxylysine can also be used. The alteration can also be made by the addition of, or substitution by, one or more serine or threonine residues to the sequence of the original antibody or antigen-binding fragment thereof (for O-linked glycosylation sites).
In some embodiments, the anti-PD-1 antibody or antigen-binding fragment thereof may include a modification, including, but not limited to glycosylation, acetylation, pegylation, phosphorylation, phosphorylation, amidation, derivatization by known protecting/blocking groups, proteolytic cleavage, linkage to a cellular ligand or other protein, etc. The process of chemical modifications are known in the art, which may include, but are not limited to, specific chemical cleavage, acetylation, formylation, metabolic synthesis of tunicamycin, etc. Additionally, the molecules may contain one or more non-classical amino acids.
The anti-PD-1 antibodies and antigen-binding fragments thereof disclosed herein may include anti-PD-1 antibodies and antigen-binding fragments thereof whose binding characteristics have been altered by direct mutation, affinity maturation, phage display, or chain shuffling. The affinity and specificity may be altered by mutating CDRs and screening for CDRs with desired characteristics. Methods of mutagenesis are known to one of skill in the art.
Antibody Binding
Also provided herein are anti-PD-1 antibodies and antigen-binding fragments thereof, and fusion proteins comprising anti-PD-1 antibodies or antigen-binding fragments thereof, that bind to the same epitope on PD-1 as one of the anti-PD-1 antibodies or antigen-binding fragments thereof disclosed herein.
In some embodiments, the anti-PD-1 antibodies and antigen-binding fragments thereof provided herein bind selectively to PD-1 over one or more PD family members. In one embodiment, the anti-PD-1 antibody or antigen-binding fragment thereof does not exhibit significant binding to other PD family members, including to CTLA-4 and/or CD28. The human PD-1 gene produces four alternatively spliced PD-1 mRNA transcripts. One of these variants produces a soluble form of PD-1. In one aspect, the disclosure provides anti-PD-1 antibodies or antigen-binding fragments thereof that bind to all isoforms of PD-1. In some embodiments, the provided anti-PD-1 antibodies and antigen-binding fragments thereof bind to mammalian PD-1.
As used herein, “binding” of an antibody or antigen-binding fragment thereof, or fusion protein comprising an antibody or antigen-binding fragment thereof, to PD-1, an epitope on PD-1, or, in certain embodiments described below, particular residues on PD-1, includes the selective interaction of the antibody or antigen-binding fragment thereof with PD-1. Binding therefore includes, e.g., primary and secondary interactions including hydrogen bonds, ionic interactions, salt bridges, as well as hydrophilic and hydrophobic interactions.
In certain embodiments, the anti-PD-1 antibodies or antigen-binding fragments thereof described herein bind to PD-1 with an equilibrium constant for the dissociation (KD) of 10−2 to 10−10 mol/l, 10−3 to 10−10 mol/l, 10−4 to 10−10 mol/l, 10−5 to 10−10 mol/l, 10−6 to 10−10 mol/l, 10−7 to 10−10 mol/l, 10−8 to 10−10 mol/l or 10−9 to 10−10 mol/l. In other embodiments, the anti-PD-1 antibodies or antigen-binding fragments thereof described herein bind to PD-1 with a KD of 10−2 to 10−9 mol/l, 10−3 to 10−9 mol/l, 10−4 to 10−9 mol/l, 10−5 to 10−9 mol/l, 10−6 to 10−9 mol/l, 10−7 to 10−9 mol/l, 10−8 to 10−9 mol/l, or 10−9 10−10 mol/l.
As used herein, “affinity,” represented by the KD of an antigen with an antigen-binding protein, is a measure of the binding strength between an antigenic determinant and an antigen-binding site on the antigen-binding protein, such as an antibody or antibody fragment thereof. The value of KD is inversely proportional to the binding strength between an antigenic determinant and the antigen-binding molecule. Alternatively, the affinity can also be expressed as the association constant (KA), which is 1/KD). Affinity can be determined in a manner known per se, depending on the specific antigen of interest by a person skilled in the art.
The term “specificity” herein refers to the ability of an antibody or antigen-binding fragment thereof, such as an anti-PD-1 antibody or antigen-binding fragment thereof, to recognize an epitope within PD-1, while only having little or no detectable reactivity with other portions of PD-1. Specificity can be relatively determined by competition assays or by epitope identification/characterization techniques described herein or their equivalents known in the art.
The term “epitope” herein refers to the specific target to which an antibody binds. Epitopes can be formed both by a contiguous stretch of amino acids (continuous epitopes) and by three-dimensional arrangement of amino acid residues that exists only when the target protein is folded in a particular conformation (discontinuous epitopes.) In general, an epitope comprises at least 3 amino acids, at least 4, at least 5, or about 7-10 amino acids.
Disclosed herein are anti-PD-1 antibodies and antigen-binding fragments thereof as well as fusion proteins comprising an anti-PD1 antibody or antigen-binding fragment thereof that specifically bind to the same epitope as anti-PD-1 antibody 38B2. Also disclosed herein are anti-PD-1 antibodies and antigen-binding fragments thereof as well as fusion proteins comprising an anti-PD1 antibody or antigen-binding fragment thereof that bind to the same epitope as anti-PD-1 antibody 31B1.
As used herein, a “blocking” antibody or an antibody “antagonist” is one that inhibits or reduces the biological activity of the antigen to which it binds. For example, in some embodiments, an anti-PD-1 antagonist antibody or antigen-binding fragment thereof binds PD-1 and inhibits activity of PD-1 and/or binding of PD-1 to binding partners such as PD-L1 or PD-L2. Inhibition of activity and inhibition of binding includes partial inhibition. Methods for the identification of PD-1 antibodies that block PD-1 interactions are described herein and are known to the ones skilled in the art. For instance, competing, cross-blocking, and cross-blocked antibodies can be identified using any suitable method known in the art, including competition ELISAs or BIACORE® assays where binding of the competing or cross-blocking antibody to human PD-1 prevents the binding of an antibody disclosed herein or vice versa.
In certain embodiments, not all CDRs are directly involved in binding to the antigen. In one embodiment, four out of six CDRs of the anti-PD-1 antibody or antigen-binding fragment thereof make contact with the antigen. In one embodiment, five out of six CDRs of the anti-PD-1 antibody or antigen-binding fragment thereof make contact with the antigen. In one embodiment, six out of six CDRs of the anti-PD-1 antibody or antigen-binding fragment thereof make contact with the antigen.
The terms “selective” and “selectivity” herein refer to the preferential binding of an antibody or antigen-binding fragment thereof (i.e., a PD-1 antibody or antigen-binding fragment thereof), for a particular region, target, or peptide; typically a region or epitope in PD-1, as opposed to one or more other biological molecules, including other PD-1 family members.
In one aspect, provided are anti-PD-1 antibodies and antigen-binding fragments thereof that specifically bind to at least part of the binding site on PD-1, thereby blocking PD-1 interactions with the one or more PD-1 ligands. These PD-1 ligands include, but are not limited to, PD-L1 and PD-L2.
In certain embodiments, the anti-PD-1 antibody or antigen-binding fragments according to the disclosure comprises an Fc domain, composed of a first and a second subunit. The Fc domain of an antibody consists of a pair of polypeptide chains comprising heavy chain domains of an immunoglobulin molecule. The two subunits of the Fc domain form a stable association. In embodiments, the two subunits of the Fc domain are identical. In alternative embodiments, the two subunits of the Fc domain are non-identical. In embodiments, one subunit of the Fc domain may be fused with an immunoconjugate molecule. In embodiments, the Fc domain of the antibody may be an IgG Fc domain, an IgG1 Fc domain, an IgG2Fc domain, an IgG3 Fc domain, an IgG4 Fc domain. In a further particular embodiment, the Fc domain is a human Fc domain.
Fc Domain Modifications Promoting Heterodimerization
Further contemplated are modifications in the Fc domain of the disclosed anti-PD-1 antibodies or antigen-binding fragments thereof promoting dimerization. In embodiments, the Fc domain of the anti-PD-1 antibody or antigen-binding fragment thereof comprises a modification promoting the association of the first and the second subunit of the Fc domain. In one embodiment, said modification is in the CH3 domain of the Fc domain. In a specific embodiment, said modification promoting the association of the first and the second subunit of the Fc domain is a so-called “knob-into-hole” modification, comprising a “knob” modification in one of the two subunits of the Fc domain and a “hole” modification in the other one of the two subunits of the Fc domain.
Knob-into-hole modifications are a “protuberance-into-cavity” strategy, which serves to engineer an interface between a first and second polypeptide for hetero-oligomerization. “Protuberances” (i.e., the knobs) are constructed by replacing small amino acid side chains from the interface of the first polypeptide with larger side chains. Compensatory “cavities” (i.e., holes) of identical or similar size to the protuberances are optionally created on the interface of the second polypeptide by replacing large amino acid side chains with smaller ones. In particular embodiment, an amino acid residue in the CH3 domain of the first Fc subunit is replaced with an amino acid residue having a larger side chain volume, thereby generating a knob within the CH3 domain of the first Fc subunit which is positionable in a hole present within the CH3 domain of the second Fc subunit, generated by replacing one amino acid residue with an amino acid residue having a smaller side chain volume in the CH3 domain of the second Fc subunit. Preferably said amino acid residue having a larger side chain volume is selected from the group consisting of cysteine (C), valine (V), alanine (A), phenylalanine (F), tyrosine (Y), leucine (L), lysine (K), Proline (P), glutamic acid (E), and tryptophan (W). Preferably said amino acid residue having a smaller side chain volume is selected from the group consisting of alanine (A), serine (S), threonine (T), arginine (R), tryptophan (W), cysteine (C), lysine (L), glutamic acid (E), aspartic acid (D), and valine (V).
The mutations corresponding to the knob and the hole can be made by altering the nucleic acid encoding the polypeptides, e.g. by site-specific mutagenesis, or by peptide synthesis.
In fusion protein embodiments, which only one heavy chain is linked to IL-15/IL-15Rα sushi, the Fc domains of the anti-PD-1 antibody or antigen-binding fragment thereof may comprise one or more amino acid substitutions promoting heterodimer formation (i.e., the association the heavy chain fusion with a heavy chain lacking the fusion). In embodiments, an amino acid residue in the CH3 domain of one heavy chain (CH3-1) comprises an amino acid substitution replacing an amino acid with an amino acid residue having a larger side chain volume, thereby generating a “knob” within the CH3 domain, which is positionable in a “hole” present within the CH3 domain of the other heavy chain (CH3-2), generated by replacing an amino acid residue with an amino acid residue having a smaller side chain volume. In embodiments, the CH3 domain of the first subunit of the Fc domain (the “knobs” subunit) may comprise one or more substitution from the following; T350V, L351Y, S354C, S364H, T366Y, T366W, F405A, Y407V. In specific embodiments, the CH3 domain of the second subunit of the Fc domain (the “holes” subunit) may comprise one or more substitutions from the following; Y349C, T350V, T366L, T366S, L368A, K392L, T394W, Y407V, Y407T.
In some embodiments, the amino acid substitutions are selected from:
-
- (1) CH3 domain of first heavy chain: S354C, T366W; CH3 domain of second heavy chain: Y349C, T366S, L368A, Y407V;
- (2) CH3 domain of first heavy chain: T350V, L351Y, F405A, Y407V; CH3 domain of second heavy chain: T350V, T366L, K392L, T394W;
- (3) CH3 domain of first heavy chain: L351Y, F405A, Y407V; CH3 domain of second heavy chain: T366L, K392L, T394W;
- (4) CH3 domain of first heavy chain: T366W; CH3 domain of second heavy chain: Y407T;
- (5) CH3 domain of first heavy chain: T366Y; CH3 domain of second heavy chain: Y407T;
- (6) CH3 domain of first heavy chain: T366W; CH3 domain of second heavy chain: Y407A;
- (7) CH3 domain of first heavy chain: F405A; CH3 domain of second heavy chain: T394W;
- (8) CH3 domain of first heavy chain: F405W; CH3 domain of second heavy chain: T394S;
- (9) CH3 domain of first heavy chain: T366Y and F405A; CH3 domain of second heavy chain: T394W and Y407T;
- (10) CH3 domain of first heavy chain: T366W and F405W; CH3 domain of second heavy chain: T394S: and 407A;
- (11) CH3 domain of first heavy chain: F405W and Y407A; CH3 domain of second heavy chain: T366W and T394S.
- (12)
Provided herein is an antibody or antigen-binding fragment thereof, which binds to PD-1 (or a fusion protein comprising such an antibody or antigen-binding fragment thereof), wherein the antibody comprises a heavy chain comprising a sequence selected from the group consisting of SEQ ID NOS: 168-169, 171-172, 185, 191, and 201-203.
Provided herein is an antibody or antigen-binding fragment thereof (or a fusion protein comprising such an antibody or antigen-binding fragment thereof), which binds to PD-1, wherein the antibody comprises a light chain comprising a sequence selected from the group consisting of SEQ ID NOS: 170, 173, 186, 192, and 205.
In specific embodiments, the Fc domain according to the disclosure exhibits reduced binding affinity to an Fc receptor and/or reduced effector function, as compared to a native IgG1 Fc domain. In certain embodiments, the Fc domain is engineered to have reduced binding affinity to an Fc receptor and/or reduced effector function, as compared to a non-engineered Fc domain.
Linkers
In embodiments, the fusion proteins provided herein may comprise one or more linkers joining components of the fusion proteins disclosed herein. A linker may be located (i) between the IL-15 polypeptide and the IL15Rα polypeptide comprising the sushi domain; (ii) between a heavy chain of the anti-PD-1 antibody or antigen-binding fragment thereof and the IL-15 polypeptide or the IL15Rα polypeptide comprising the sushi domain; or (iii) both. In embodiments of the disclosure, the IL-15 polypeptide and the IL15Rα polypeptide comprising the sushi domain are joined or linked by a first linker amino acid sequence. In embodiments, the IL-15 polypeptide (or the IL15Rα polypeptide) is linked to an antibody, or antigen binding fragment thereof, described herein by a second linker amino acid sequence. In embodiments, the second linker joins the N terminus of the heavy chain variable region to the C terminus of the IL-15 polypeptide. The first and second linkers may have the same or different amino acid sequences.
The linker amino acids sequences described herein may be of a length sufficient to ensure that the fusion protein forms proper secondary and tertiary structures. The length of the linker amino may be between 5 to 40 amino acids, preferably 10 to 40 amino acids, more preferably 15 to 40 amino acids, still more preferably 20 to 40 amino acids, most preferably 25 to 35 amino acids.
Preferably, the linker sequences comprise near neutral amino acids selected in the group comprising Gly (G), Asn (N), Ser (S), Thr (T), Ala (A), Leu (L), and Gln (Q), most preferably in amino acids selected from the group comprising Gly (G), Asn (N), and Ser (S). Preferably, the linker sequences are glycine- and serine-rich, and in some embodiments, the linker contains only serine and glycine residues.
In some embodiments, the linker comprises a portion of the IL15Rα polypeptide outside of the sushi domain, including, but not limited to the sequence bolded in the linker of SEQ ID NO:215 (below).
Some non-limiting linker examples of amino acid sequences include
In embodiments, the linker joining the IL-15 polypeptide and the IL-15Rα sushi comprises IRDPALVHQRPAPPSGGSGGGGSGGGSGGGGSLQ (SEQ ID NO: 215), IRDPSGGGGSGGGGSGGGGSGGGGSGGGGSGGGG (SEQ ID NO: 217), or IRDPGGGGSGGGGSGGGGSGGGGSGGGGSGGGGS (SEQ ID NO:218).
In embodiments, the linker joining the IL-15 polypeptide to the anti-PD-1 antibody heavy chain comprises GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS (SEQ ID NO: 216) or GGGGSGGGGSGGGGSGGGGS (SEQ ID NO:244).
In embodiments, the heavy and light chains of the anti-PD-1 antibody or antigen-binding fragment thereof disclosed herein may be connected into a single polypeptide chain (a “single-chain Fv” or “scFv”) using a third linker that allows the VR and VL domains to associate to form an antigen-binding site. The amino acid sequence of the linkers may be the same or different.
In one embodiment, an IL-15 polypeptide or an IL-15 derivative is covalently linked to an IL-15Rα sushi polypeptide or an IL-15Rα sushi derivative by a linker.
In one embodiment, the IL-15 polypeptide or IL-15 derivative is covalently linked to an anti-PD-1 antibody or antigen-binding fragment thereof by a linker. In one embodiment, the C-terminus of the IL-15 polypeptide or IL-15 derivative is covalently linked to the N-terminus of the anti-PD-1 antibody or antigen-binding fragment thereof by a linker. In one embodiment, the N-terminus of the IL-15 polypeptide or IL-15 derivative is covalently linked to the C-terminus of the anti-PD-1 antibody or antigen-binding fragment thereof by a linker. In one embodiment, the N-terminus of the IL-15 polypeptide or IL-15 derivative is covalently linked to the CH3 region of the anti-PD-1 antibody or antigen-binding fragment thereof by a linker.
In one embodiment, the IL-15Rα sushi or an IL-15Rα sushi derivative is covalently linked to an anti-PD-1 antibody or antigen-binding fragment thereof by a linker. In one embodiment, the C-terminus of the IL-15Rα sushi polypeptide or IL-15Rα sushi derivative is covalently linked to the N-terminus of the anti-PD-1 antibody or antigen-binding fragment thereof by a linker. In one embodiment, the N-terminus of the IL-15Rα sushi polypeptide or IL-15Rα sushi derivative is covalently linked to the C-terminus of the anti-PD-1 antibody or antigen-binding fragment thereof by a linker. In one embodiment, the N-terminus of the IL-15Rα sushi polypeptide or IL-15Rα sushi derivative is covalently linked to the CH3 region of the anti-PD-1 antibody or antigen-binding fragment thereof by a linker.
In some embodiments, an IL-15 polypeptide or an IL-15 derivative is covalently linked to an IL-15Rα sushi polypeptide or a IL-15Rα sushi derivative by a first linker and either the IL-15 polypeptide or IL-15 derivative or the IL-15Rα sushi polypeptide or IL-15Rα sushi derivative is covalently linked to an anti-PD-1 antibody or antigen-binding fragment thereof by a second linker. In some embodiments, the amino acid sequences of the first and the second linker are identical. In other embodiments, the amino acid sequences of the first and the second linker are different.
Conjugates
The anti-PD-1 antibodies, antigen-binding fragments thereof, and the fusion proteins disclosed herein may further comprise one or more functional moieties. Examples of useful functional moieties include, but are not limited to, a blocking moiety, a detectable moiety, a diagnostic moiety, a targeting, and a therapeutic moiety.
A blocking moiety may include moieties of sufficient steric bulk and/or charge such that reduced glycosylation occurs, for example, by blocking the ability of a glycosidase to glycosylate the antibody or antigen-binding fragment thereof. Preferred blocking moieties include cysteine adducts such as cysteine, mixed disulfide adducts, or disulfide linkages and PEG moieties such as polyethylene glycol (“PEG”), polypropylene glycol (“PPG”), polyoxyethylated glycerol (“POG”) and other polyoxyethylated polyols, polyvinyl alcohol (“PVA”) and other polyalkylene oxides, polyoxyethylated sorbitol, or polyoxyethylated glucose. PEG is a preferred moiety in biological applications for several reasons. PEGylating can improve pharmacokinetic performance of a molecule by increasing the molecule's apparent molecular weight. The increased apparent molecular weight reduces the rate of clearance from the body following subcutaneous or systemic administration. In many cases, pegylation can decrease antigenicity and immunogenicity. PEGylating can also increase the solubility of a biologically active molecule. Additionally, PEG typically is clear, colorless, odorless, soluble in water, stable to heat, inert to many chemical agents, does not hydrolyze, and is nontoxic, making it a preferable choice for biological applications.
The examples of detectable moieties that can be conjugated with the anti-PD-1 antibody or the antigen-binding fragments or fusions disclosed herein may include fluorescent moieties or labels, imaging agents, radioisotopic moieties, radiopaque moieties, and the like, e.g. detectable labels such as biotin, fluorophores, chromophores, spin resonance probes, or radiolabels. Examples of fluorophores include fluorescent dyes (e.g. fluorescein, rhodamine, and the like) and other luminescent molecules (e.g. luminal). A fluorophore may be environmentally-sensitive such that its fluorescence changes if it is located close to one or more residues in the modified protein that undergo structural changes upon binding a substrate (e.g. dansyl probes). Exemplary radiolabels include small molecules containing atoms with one or more low sensitivity nuclei (13C, 15N, 2H, 125I, 123I, 99Tc, 43K, 52Fe, 67Ga, 68Ga, 111In and the like).
Diagnostic moieties include detectable moieties suitable for revealing the presence of a disease or disorder. Typically, a diagnostic moiety allows for determining the presence, absence, or levels of a molecule, for example, a target peptide, protein, or proteins, that are associated with a disease or disorder. Such diagnostics are also suitable for prognosing and/or diagnosing a disease or disorder and its progression.
Examples of therapeutic moieties include anti-inflammatory agents, anti-cancer agents, anti-neurodegenerative agents, anti-infective agents, or generally a therapeutic. The functional moiety may also have one or more of the above-mentioned functions. Exemplary therapeutic moieties may include an antibiotic, a second anti-PD-1 antibody, or an antibody to another antigen such a tumor-specific antigen, an autoimmune tissue antigen, a virally-infected cell antigen, a Fc receptor, a T cell receptor, or a T cell co-inhibitor, or an immunotoxin, or any other therapeutic moiety useful for treating a disease or condition including cancer, autoimmune disease or chronic viral infection. Exemplary therapeutic moieties may also cytotoxin, radioactive agent, cytokine, interferon, target or reporter moiety, enzyme, toxin, peptide or therapeutic agent at any location along the molecule so long as it is able to bind its target. Examples of immunoconjugates include antibody drug conjugates and antibody-toxin fusion proteins. In certain embodiments, the antibody may be conjugated to an agent specific for a tumor cell or a virally infected cell.
A salvage receptor binding epitope as described, e.g., in U.S. Pat. No. 5,739,277 may also be attached to the antibody or antigen-binding fragment thereof (especially an antibody fragment) to increase the half-life of the antibodies or the antigen-binding fragments described herein. The term “salvage receptor binding epitope” may refer to an epitope of the Fc region of an IgG molecule (e.g., IgG1, IgG2, IgG3, or IgG4) that is responsible for increasing the in vivo serum half-life of the IgG molecule (e.g., Ghetie et al., 18 Ann. Rev. Immunol. 739 (2000).
Nucleic Acids
Also provided herein are nucleic acids encoding anti-PD-1 antibodies, antigen-binding fragments thereof and fusion proteins disclosed herein, as well as vectors, host cells, and expression systems. The term “nucleic acid” as used herein refers to a polymeric form of nucleotides of any length, either ribonucleotides or desoxyribonucleotides and includes but is not limited to, single-, double- or multi-stranded DNA or RNA, genomic DNA, cDNA, DNA-RNA hybrids, or a polymer comprising purine and pyrimidine bases, or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases. The nucleic acids encoding anti-PD-1 antibodies and antigen-binding fragments thereof and fusion proteins disclosed herein may be, e.g., DNA, cDNA, RNA, synthetically produced DNA or RNA, or a recombinantly produced chimeric nucleic acid molecule comprising any of those polynucleotides either alone or in combination.
The term “vector” refers to vehicle comprising a nucleic acid molecule that is capable of transporting the nucleic acid molecule into a cell. A “vector” includes, but is not limited to, a viral vector, a plasmid, a RNA vector or a linear or circular DNA or RNA molecule, which may consists of a chromosomal, non-chromosomal, semi-synthetic or synthetic nucleic acids. In some embodiments, the employed vectors are those capable of autonomous replication (episomal vector) and/or expression of nucleic acids to which they are linked (expression vectors). A number of suitable vectors are known to those of skill in the art and are commercially available.
Antibody and Fusion Protein Preparation and Expression Systems
The anti-PD-1 antibodies, antigen-binding fragments or the fusion proteins disclosed herein are typically produced by recombinant expression. Nucleic acids encoding light and heavy chain variable regions, optionally linked to constant regions, may be inserted into the same expression vectors. Alternatively, the nucleic acids encoding light and heavy chain variable regions, optionally linked to constant regions, are inserted into different expression vectors. The expression vector may further comprise one or more expression control sequences, which include, but are not limited to, promoters (e.g., homologous or heterologous promoters), signal sequences, enhancer elements, and transcription termination sequences. Preferably, the expression control sequences are eukaryotic promoter systems in vectors capable of transforming or transfecting eukaryotic host cells. Typically, the host is maintained under conditions suitable for high-level expression of the nucleotide sequences, and the collection and purification of the cross-reacting antibodies after the vector is incorporated into the appropriate host.
Commonly, expression vectors contain selection markers (e.g., ampicillin-resistance, hygromycin-resistance, tetracycline resistance or neomycin resistance) to permit detection of those cells transformed with the desired DNA sequences.
The host used to express the anti-PD-1 antibodies, antigen-binding fragments thereof or the fusion proteins disclosed herein can be a prokaryotic or eukaryotic host. Examples of suitable hosts include bacterial or eukaryotic hosts, including yeast, insects, fungi, bird and mammalian cells either in vivo, or in situ, or host cells of mammalian, insect, bird, or yeast origin. The mammalian cell or tissue can be of human, primate, hamster, rabbit, rodent, cow, pig, sheep, horse, goat, dog, or cat origin, but any other mammalian cell may be used.
Examples of bacterial hosts that can be used to express the antibodies, antigen-binding fragments or the fusion protein disclosed herein can be E. coli, bacilli, such as Bacillus subtilus, and other enterobacteriaceae, such as Salmonella, Serratia, and various Pseudomonas species.
Yeasts may also be used as hosts for expressing the express the antibodies, antigen-binding fragments or the fusion protein disclosed herein. Saccharomyces and Pichia are exemplary yeast hosts, with suitable vectors having expression control sequences (e.g., promoters), an origin of replication, termination sequences, and the like as desired. Typical promoters include 3-phosphoglycerate kinase and other glycolytic enzymes. Inducible yeast promoters include, among others, promoters from alcohol dehydrogenase, isocytochrome C, and enzymes responsible for methanol, maltose, and galactose utilization.
Mammalian cells in culture may also be used as host cells for expressing the antibodies, antigen-binding fragments or the fusion proteins disclosed herein. Examples of suitable host cell lines capable of secreting heterologous proteins (e.g., intact immunoglobulins) which are well known in the art, include CHO cell lines, various COS cell lines, HeLa cells, 293 cells, myeloma cell lines, transformed B-cells, and hybridomas. Expression vectors for these cells can include expression control sequences, such as an origin of replication, a promoter, an enhancer and necessary processing information sites such as ribosome binding site, RNA splice site and/or transcriptional terminator sequences. Examples of expression control sequences include SV40, adenovirus, bovine papilloma virus, cytomegalovirus and the like.
The anti-PD-1 antibodies, antigen-binding fragments thereof, and the fusion proteins disclosed herein can be expressed using a single expression construct or vector or multiple expression constructs or vectors (e.g., two or three expression constructs). When the antibody heavy and light chains are cloned on separate expression vectors, the vectors are co-transfected to obtain expression and assembly of intact immunoglobulins. Once expressed, the whole antibodies, their dimers, individual light and heavy chains, or other immunoglobulin forms disclosed herein can be purified according to standard procedures of the art, including ammonium sulfate precipitation, affinity columns, column chromatography, HPLC purification, gel electrophoresis, and the like (see generally Scopes, Protein Purification (Springer-Verlag, N.Y., (1982)). Substantially pure immunoglobulins of at least about 90 to 95% homogeneity are preferred, and 98 to 99% or more homogeneity most preferred, for pharmaceutical uses.
The disclosed anti-PD-1 antibodies, antigen-binding fragments, and the fusion proteins can be made by any method known in the art. General techniques for generating human or mouse antibodies or fusion molecules are known in the art.
Methods for Modulating PD-1 Activity
In one aspect, the disclosure provides methods of using the anti-PD-1 antibodies, antigen-binding fragments thereof, and fusion proteins described herein for decreasing the interaction between PD-1 and PD-ligands, including, but not limited to, PD-L1 and PD-L2. In some embodiments, the anti-PD-1 antibody, antigen-binding fragment thereof, or fusion protein disrupts the interaction between PD-1 monomers.
The anti-PD-1 antibodies, antigen-binding fragments thereof, and fusion proteins disclosed herein are useful for reducing immunosuppression, e.g., T cell tolerance. By “reducing” is meant the ability to cause an overall decrease of about 20% or greater, 30% or greater, 40% or greater, 45% or greater, 50% or greater, of 55% or greater, of 60% or greater, of 65% or greater, of 70% or greater, or 75% or greater, 80% or greater, 85% or greater, 90% or greater, or 95% or greater, as compared to a control that is not treated. Immunosuppression can be mediated by immune inhibitory receptors expressed on the surface of an immune cell, and their interactions with their ligands. Methods of measuring T cell activity are known in the art. By way of non-limiting example, T cell tolerance can be induced by contacting T cells with recall antigen, anti-CD3 in the absence of co-stimulation, and/or ionomycin. Levels of, e.g., IL-27, LDH-A, RAB10, and/or ZAP70 (both intracellular or secreted) can be monitored, for example, to determine the extent of T cell tolerogenesis (with levels of IL-2, interferon-7 and TNF correlating with increased T cell tolerance).
The anti-PD-1 antibodies, antigen-binding fragments thereof, and fusion proteins disclosed herein are further useful for enhancing T cell expansion, activation, and proliferation.
Methods of Treatment
PD-1 μlays an important role in the immune system in regulating autoimmunity, tumor immunity, and infectious immunity. PD-1-mediated T cell inhibition is an important mechanism to prevent autoimmunity. In addition, cancer and chronic infectious diseases may usurp this regulation mechanism to drive immune suppression. Blocking PD-1 with antagonists, including monoclonal antibodies, has been studied in treatments of cancer and chronic viral infections. The ability of PD-1 to inhibit T cell activation is exploited by chronic viral infections and tumors to evade immune response. In chronic viral infections, PD-1 is highly expressed on virus-specific T cells and these T cells become “exhausted” with loss of effector functions and proliferative capacity.
PD-1 deficient animal models develop various autoimmune phenotypes including autoimmune cardiomayopathy, rheumatoid arthritis, and graft versus host disease. Specifically, they have elevated levels of IgG2b and IgA and develop mild lupus-like autoimmunity and dilated cardiomyopathy. Considering the role of PD-1 in modulating immune responses, the therapeutic agents disclosed herein that antagonize PD-1 signaling can be administered to treat diseases that involve PD-1-mediated immune suppression.
Immunomodulation is a useful therapeutic approach for treating various diseases and disorders. One approach to immunomodulation is to intervene at one or more immune checkpoints by regulators of immune activation that play a key role in maintaining immune homeostasis and preventing autoimmunity. Depending on the disease or disorder, it may be desirable to upregulate or downregulate the immune response. Tumor cells that display non-self-antigens, can evade immune attack by secreting cytokines or ligands that activate immune checkpoints. In cancer therapy, thus it is generally desirable to upregulate the immune response against tumor cells. In contrast, in treatment of autoimmune diseases, it is generally desirable to downregulate the immune response in certain tissues.
In one aspect, the disclosure provides anti-PD-1 antibodies, antigen-binding fragments thereof, and fusion proteins that are useful for treatments of subjects in need thereof.
In the methods described herein, a therapeutically effective amount of an anti-PD-1 antibody, antigen-binding fragment thereof or fusion protein disclosed herein is administered to a mammal in need thereof. The term “mammal” as used herein includes, but is not limited to, humans, laboratory animals, domestic pets, and farm animals. Preferably, the mammal is a human. “Therapeutically effective amount” as described herein refers to an amount of an anti-PD-1 antibody, antigen-binding fragment thereof or fusion protein which, when administered to a mammal, is effective in producing the desired therapeutic effect.
By “subject” is meant a mammal, including, but not limited to, a human or non-human mammal, such as a bovine, equine, canine, ovine, or feline, etc. Individuals and patients are also subjects herein.
The terms “treat,” “treated,” “treating,” or “treatment” as used herein refer to therapeutic treatment, wherein the object is to slow down (lessen) an undesired physiological condition, disorder, or disease, or to obtain beneficial or desired clinical results. For the purposes of this disclosure, beneficial or desired clinical results include, but are not limited to, alleviation of symptoms; diminishment of the extent of the condition, disorder or disease; stabilization (i.e., not worsening) of the state of the condition, disorder or disease; delay in onset or slowing of the progression of the condition, disorder or disease; amelioration of one or more symptoms of the condition, disorder or disease state; and remission (whether partial or total). Treatment includes eliciting a clinically significant response without excessive levels of side effects. Treatment also includes prolonging survival as compared to expected survival if not receiving treatment. The terms “prevent,” “prevention,” and the like refer to acting prior to overt disease or disorder onset, to prevent the disease or disorder from developing or to minimize the extent of the disease or disorder or slow its course of development.
In one aspect, the anti-PD-1 antibodies, antigen-binding fragments thereof and fusion proteins disclosed herein may be used to treat subjects suffering from an autoimmune disease, including but not limited to, alopecia areata, autoimmune hepatitis, celiac disease, Graves' disease, Guillain-Barre syndrome, Hashimoto's disease, hemolytic anemia, inflammatory bowel disease, inflammatory myopathies, multiple sclerosis, primary biliary cirrhosis, psoriasis, rheumatoid arthritis, scleroderma, Sjogren's syndrome, systemic lupus, erthyematosus, vitiligo, autoimmune pancreatitis, autoimmune urticaria, autoimmune thrombocytopenic purpura, Crohn's disease, diabetes type I, eosinophilic fasciitis, eosinophilic enterogastritis, Goodpasture's syndrome, myasthenia gravis, psoriatic arthritis, rheumatic fever, ulcerative colitis, vasculitis and Wegener's granulomatosis. In certain embodiments, an activating antibody disclosed herein may be used to treat a subject suffering from autoimmune disease.
In one aspect, the anti-PD-1 antibodies, antigen-binding fragments thereof and fusion proteins disclosed herein may be used to treat subjects suffering from a chronic viral infection. In a specific embodiment, the anti-PD-1 antibodies, antigen-binding fragments thereof and fusion proteins disclosed herein can be used to rescue exhausted T cells and/or decrease viral titers in a subject in need thereof. In certain embodiments, the anti-PD-1 antibodies, antigen-binding fragments thereof and fusion proteins disclosed herein may be used to treat chronic viral infection by administering a therapeutically effective dose to a subject in need thereof. In some embodiments, the subject is suffering from a viral infection caused by lymphocytic choriomeningitis virus (LCMV), human immunodeficiency virus (HIV) or human papilloma virus (HPV) or hepatitis B/C virus (HBV/HCV) or simian immunodeficiency virus (SIV).
In another aspect, the anti-PD-1 antibodies, antigen-binding fragments thereof and fusion proteins disclosed herein can be used to treat subjects suffering from primary or recurrent cancer, including, but not limited to, renal cell carcinoma, colorectal cancer, non-small-cell lung cancer, brain cancer (e.g., glioblastoma multiforme), squamous cell carcinoma of head and neck, gastric cancer, prostate cancer, ovarian cancer, kidney cancer, breast cancer, multiple myeloma, and melanoma.
In certain embodiments, anti-PD-1 antibodies, antigen-binding fragments thereof and fusion proteins disclosed herein may be administered in a therapeutically effective amount to a subject suffering from a cancer or a viral infection.
One or more anti-PD-1 antibodies, antigen-binding fragments thereof or fusion proteins disclosed herein may be administered to relieve or prevent or decrease the severity of one or more of the symptoms or conditions of the disease or disorder. In a certain embodiment, the anti-PD-1 antibodies, antigen-binding fragments thereof and fusion proteins disclosed herein may be administered prophylactically to a subject in need therefore to reduce the risk of developing a chronic viral infection or an autoimmune disease. The anti-PD-1 antibodies, antigen-binding fragments thereof and fusion proteins disclosed herein may be used as an adjunct therapy with any other agent or any other therapy known to those skilled in the art useful for treating cancer, autoimmune disease, or viral infection.
Combination Therapy
The anti-PD-1 antibodies, antigen-binding fragments thereof and fusion proteins disclosed herein may be advantageously combined with an additional therapeutic agent. Such additional agents include, but are not limited to, cytotoxic agents, chemotherapeutic agents, growth inhibitory agents, anti-inflammatory agents, anti-cancer agents, anti-neurodegenerative agents, immunosuppressive agents, and anti-infective agents. The administration of the anti-PD-1 antibody or antigen-binding fragment thereof or the fusion protein and the additional therapeutic agent may be concurrently, consecutively or intermittently. The administration of the anti-PD-1 antibody or antigen-binding fragment thereof or the fusion protein and the additional therapeutic agent may be separately or as a mixture. Further, the methods of treatment provided herein can relate to a treatment in combination with one or more therapies including but not limited to the group of antibody therapy, chemotherapy, cytokine therapy, dendritic cell therapy, gene therapy, hormone therapy, laser light therapy, and radiation therapy.
The anti-PD-1 antibodies, antigen-binding fragments thereof, and the fusion proteins of the present disclosure may be combined synergistically with one or more anti-cancer drugs or therapy used to treat cancer, including, but not limited to, renal cell carcinoma, colorectal cancer, glioblastoma multiforme, squamous cell carcinoma of head and neck, non-small-cell lung cancer, colon cancer, ovarian cancer, adenocarcinoma, prostate cancer, glioma, and melanoma. Examples of such agents include but are not limited to with an antibody to PD-L1, a second antibody to PD-1 (e.g., nivolumab), a LAG-3 inhibitor, a CTLA-4 inhibitor (e.g., ipilimumab), a TIM3 inhibitor, a BTLA inhibitor, a T IGIT inhibitor, a CD47 inhibitor, an antagonist of another T cell co-inhibitor or ligand (e.g., an antibody to CD-28, 2B4, LY108, LAI R 1, ICOS, CD1 60 or VISTA), an indoleamine-2,3-dioxygenase (IDO) inhibitor, a vascular endothelial growth factor (VEGF) antagonist [e.g., a “VEGF-Trap”such as aflibercept or other VEGF-inhibiting fusion protein as set forth in U.S. Pat. No. 7,087,411, or an anti-VEGF antibody or antigen-binding fragment thereof (e.g., bevacizumab, or ranibizumab) or a small molecule kinase inhibitor of VEGF receptor (e.g., sunitinib, sorafenib, or pazopanib)], an Ang2 inhibitor (e.g., nesvacumab), a transforming growth factor β (TGF3) inhibitor, an epidermal growth factor receptor (EGFR) inhibitor (e.g., erlotinib, cetuximab), an agonist to a costimulatory receptor (e.g., an agonist to glucocorticoid-induced TNFR-related protein), an antibody to a tumor-specific antigen (e.g., CA9, CA1 25, melanoma-associated antigen 3 (MAGE3), carcinoembryonic antigen (CEA), anti-viral drugs (e.g., zidovudine, lamivudine, abacavir, ribavirin, lopinavir, efavirenz, cobicistat, tenofovir, rilpivirine and corticosteroids), vimentin, tumor-M2-PK, prostate-specific antigen (PSA), mucin-1, MART-1, and CA1 9-9), a vaccine (e.g., Bacillus Calmette-Guerin, a cancer vaccine), an adjuvant to increase antigen presentation (e.g., granulocyte-macrophage colony stimulating factor), a bispecific antibody (e.g., CD3×CD20 bispecific antibody, PSMA×CD3 bispecific antibody), cancer vaccines (e.g., MAGE3, MUC1, EGFRv3, ALVAC-CEA), a cytotoxin, a chemotherapeutic agent (e.g., dacarbazine, temozolomide, cyclophosphamide, docetaxel, doxorubicin, daunorubicin, cisplatin, carboplatin, gemcitabine, methotrexate, mitoxantrone, oxaliplatin, paclitaxel, and vincristine), cyclophosphamide, radiotherapy, an IL-6R inhibitor (e.g., sarilumab), an IL-4R inhibitor (e.g., dupilumab), an IL-1 0 inhibitor, a cytokine such as IL-2, IL-7, IL-21, and IL-15, an antibody-drug conjugate (ADC) (e.g., anti-CD1 9-DM4 ADC, and anti-DS6-DM4 ADC), an anti-inflammatory drug (e.g., corticosteroids, and non-steroidal anti-inflammatory drugs), a dietary supplement such as anti-oxidants or any palliative care to treat cancer, radiation therapy, and/or an antibody to a Fc receptor on immune cells for the treatment of an autoimmune disease.
Methods of Administration
The therapeutic compositions comprising any of the anti-PD-1 antibodies, antigen-binding fragments thereof or fusion proteins described herein may be administered to a subject in need thereof in any convenient manner including but not limited to by injection, transfusion, implantation or transplantation. The compositions described herein may be administered to a subject in need thereof subcutaneously, intradermally, intratumorally, intranodally, intramedullary, intramuscularly, intracranially, by intravenous or intralymphatic injection, or intraperitoneally. In one embodiment, the cell compositions of the present disclosure are preferably administered by intravenous injection.
In certain embodiments, the anti-PD-1 antibody, antigen-binding fragment thereof or the fusion protein is administered to the mammal by intravenous infusion, i.e., introduction of the anti-PD-1 antibody, antigen-binding fragment thereof or the fusion protein into the vein of a mammal over a certain period. In certain embodiments, the period is about 5 min, about 10 min, about 30 min, about 1 h, about 2 h, about 4 h, or about 8 h.
Administrative Regimens
The methods according to this aspect of the disclosure comprise sequentially administering to a subject multiple doses of an anti-PD-1 antibody, antigen-binding fragment thereof, or a fusion protein of the disclosure. As used herein, “sequentially administering,” means that each dose of an anti-PD-1 antibody, antigen-binding fragment thereof, or a fusion protein of the disclosure is administered to the subject at a different point in time, e.g., on different days separated by a predetermined interval (e.g., hours, days, weeks or months). The present disclosure includes methods, which comprise sequentially administering to the patient a single initial dose of an anti-PD-1 antibody, antigen-binding fragment thereof, or a fusion protein of the disclosure, followed by one or more secondary doses of an anti-PD-1 antibody, antigen-binding fragment thereof, or a fusion protein of the disclosure, and optionally followed by one or more tertiary doses of an anti-PD-1 antibody, antigen-binding fragment thereof, or a fusion protein of the disclosure. An anti-PD-1 antibody, antigen-binding fragment thereof, or a fusion protein of the disclosure may be administered at a dose between 0.01 mg/kg to 100 mg/kg.
In certain embodiments, a dose of a compound or a composition is administered to a subject every day, every other day, every couple of days, every third day, once a week, twice a week, three times a week, once every two weeks, or once a month. In other embodiments, two, three or four doses of a compound or a composition is administered to a subject every day, every couple of days, every third day, once a week, once every two weeks or once a month. In some embodiments, a dose(s) of a compound or a composition is administered for 2 days, 3 days, 5 days, 7 days, 14 days, 21 days, or 28 days. In certain embodiments, a dose of a compound or a composition is administered for 1 month, 1.5 months, 2 months, 2.5 months, 3 months, 4 months, 5 months, 6 months or more.
Pharmaceutical Compositions
In another aspect, provided are pharmaceutically acceptable compositions that comprise a therapeutically effective amount of an anti-PD-1 antibody, antigen-binding fragment thereof, or a fusion protein of the disclosure formulated together with one or more pharmaceutically acceptable excipients.
The dosage of active agent(s) may vary, depending on the reason for use, the individual subject, and the mode of administration. The dosage may be adjusted based on the subject's weight, the age, and health of the subject, and tolerance for the compound(s) or composition.
The active agent and excipient(s) may be formulated into compositions and dosage forms according to methods known in the art. The pharmaceutical compositions provided herein may be specially formulated in solid or liquid form, including those adapted for parenteral administration, for example, by subcutaneous, intratumoral, intramuscular or intravenous injection as, for example, a sterile solution, or suspension.
Therapeutic compositions comprising anti-PD-1 antibodies or antigen-binding fragments thereof, or fusion proteins thereof may formulated with one or more pharmaceutically-acceptable excipients, which can be a pharmaceutically-acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, carrier, manufacturing aid (e.g., lubricant, talc magnesium, calcium or zinc stearate, or steric acid), solvent or encapsulating material, involved in carrying or transporting the therapeutic compound for administration to the subject, bulking agent, salt, surfactant and/or a preservative. Some examples of materials which can serve as pharmaceutically-acceptable excipients include: sugars, such as lactose, glucose and sucrose; starches, such as corn starch and potato starch; cellulose and its derivatives, such as sodium carboxymethyl cellulose, ethyl cellulose and cellulose acetate; gelatin; talc; waxes; oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; glycols, such as ethylene glycol and propylene glycol; polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol; esters, such as ethyl oleate and ethyl laurate; agar; buffering agents; water; isotonic saline; pH buffered solutions; and other non-toxic compatible substances employed in pharmaceutical formulations.
A bulking agent as referred herein may be described as a compound added to increase the mass of a pharmaceutical composition and to contribute to the physical structure of the formulation in the lyophilized form. Examples of bulking agent may include but is not limited to Suitable mannitol, glycine, polyethylene glycol, and sorbitol.
The therapeutic composition may optionally include a surfactant. The use of a surfactant can reduce aggregation of the reconstituted protein and/or reduce the formation of particulates in the reconstituted formulation. Examples of suitable surfactants that might be used according to the present disclosure includes but is not limited to polysorbates (e.g. polysorbates 20 or 80); poloxamers (e.g. poloxamer 188); Triton; sodium dodecyl sulfate (SDS); sodium laurel sulfate; sodium octyl glycoside; lauryl-, myristyl-, linoleyl-, or stearyl-sulfobetaine; lauryl-, myristyl-, linoleyl- or stearyl-sarcosine; linoleyl-, myristyl-, or cetyl-betaine; lauroamidopropyl-, cocamidopropyl-, linoleamidopropyl-, myristamidopropyl-, palmidopropyl-, or isostearamidopropyl-betaine (e.g. lauroamidopropyl); myristamidopropyl-, palmidopropyl-, or isostearamidopropyl-dimethylamine; sodium methyl cocoyl-, or disodium methyl oleyl-taurate; and polyethyl glycol, polypropyl glycol, and copolymers of ethylene and propylene glycol (e.g. Pluronics, PF68, etc.).
A preservative may optionally be used in the therapeutic composition described herein. Suitable preservatives for use in the formulation provided herein include octadecyldimethylbenzyl ammonium chloride, hexamethonium chloride, benzalkonium chloride (a mixture of alkylbenzyl-dimethylammonium chlorides in which the alkyl groups are long-chain compounds), and benzethonium chloride. Other types of preservatives include aromatic alcohols such as phenol, butyl, and benzyl alcohol, alkyl parabens such as methyl or propyl paraben, catechol, resorcinol, cyclohexanol, 3-pentanol, and m-cresol.
The therapeutic composition described herein may have a varying concentration of the anti-PD-1 antibody, antigen-binding fragment thereof, or fusion protein. For example, the compositions may comprise an anti-PD-1 antibody, antigen-binding fragment thereof or fusion protein at 10 mg/ml to 200 mg/ml, 25 mg/ml to 130 mg/ml, 50 mg/ml to 125 mg/ml, 75 mg/ml to 110 mg/ml, or 80 mg/ml to 100 mg/ml. The compositions also may comprise an anti-PD-1 antibody, antigen-binding fragment thereof or fusion protein at about 10 mg/ml, 20 mg/ml, 30 mg/ml, 40 mg/ml, 50 mg/ml, 60 mg/ml, 70 mg/ml, 80 mg/ml, 90 mg/ml, 100 mg/ml, 110 mg/ml, 120 mg/ml, 130 mg/ml, 140 mg/ml, or 150 mg/ml. In some embodiments, the therapeutic composition may be lyophilized and provided in a composition for reconstitution prior to administration.
Diagnostic Uses
The anti-PD-1 antibodies, antigen-binding fragments thereof or the fusion proteins of the present disclosure may be used to detect and/or measure PD-1 in a sample, e.g., for diagnostic purposes. The anti-PD-1 antibodies, antigen-binding fragments thereof or the fusion proteins disclosed herein may be used in an assay to detect a disease or disorder such as cancer, autoimmune disease, or chronic viral infection. Exemplary diagnostic assays for PD-1 may comprise, e.g., contacting a sample, obtained from a patient, with an anti-PD-1 antibody, antigen-binding fragment thereof, or a fusion protein of the disclosure, wherein the anti-PD-1 antibody, antigen-binding fragment thereof, or the fusion protein is labeled with a detectable label or reporter molecule or used as a capture ligand to selectively isolate PD-1 from patient samples or alternatively used in combination with a secondary antibody which is itself detectably labeled. The detectable label or reporter molecule can be a radioisotope, such as 3H, C, 32P, 35S, or 25 1; a fluorescent or chemiluminescent moiety such as fluorescein isothiocyanate, or rhodamine; or an enzyme such as alkaline phosphatase, β-galactosidase, horseradish peroxidase, or luciferase. Specific exemplary assays that can be used to detect or measure PD-1 in a sample include enzyme linked immunosorbent assay (ELISA), radioimmunoassay (RIA), and fluorescence-activated cell sorting (FACS).
Kits of the present disclosure can include any combination of agents, compositions, components, reagents, administration devices, or mechanisms, or other entities provided herein. For instance, a kit of the present disclosure may include one or more anti-PD-1 antibodies or antigen-binding fragments thereof or fusion proteins disclosed herein and one or more of a carrier composition, an administration device, and a combination therapy agent. Kits may further include a device to facilitate delivery such as syringe for injection or a tool that facilitates the delivery of therapeutic compositions to the subject in need thereof. Any of the kits provided herein can be included in a container, pack, or dispenser together with instructions for administration.
All other referenced patents and applications are incorporated herein by reference in their entirety. Furthermore, where a definition or use of a term in a reference, which is incorporated by reference herein, is inconsistent or contrary to the definition of that term provided herein, the definition of that term provided herein applies and the definition of that term in the reference does not apply.
It is to be understood that this disclosure is not limited to the particular molecules, compositions, methodologies, or protocols described, as these may vary. Any methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the present disclosure. It is further to be understood that the current disclosure in this specification includes all possible combinations of such particular features. For example, where a particular feature is disclosed in the context of a particular aspect or embodiment of the disclosure herein, or a particular claim, that feature can also be used, to the extent possible, in combination with and/or in the context of other particular aspects and embodiments of the disclosure, and in the disclosure generally.
Where reference is made herein to a method comprising two or more defined steps, the defined steps can be carried out in the order as listed, or in any order or simultaneously (except where the context excludes that possibility), and the method can include one or more other steps which are carried out before any of the defined steps, between two of the defined steps, or after all the defined steps (except where the context excludes those possibilities).
To facilitate a better understanding of the present disclosure, the following examples of specific embodiments are given. The following examples should not be read to limit or define the entire scope of the disclosure.
EXAMPLES Example 1: Identification of Anti-PD-1 Antibodies from a Distributed Bio SuperHuman 2.0 Inc. LibraryhPD-1-Fc (human IgV domain fused to the N-terminal of human IgG1Fc; present as dimer in solution) or hPD-1-his (human IgV domain of PD-1 connected to the N-terminal of a six histidine peptide; present as monomer in solution) was immobilized on immuno-tubes, which were coated with an anti-his antibody or an anti-hFc antibody. Biotin-labeled hPD-1-his was captured by strepavidin-conjugated magnetic beads. The phage library was blocked with 3% PBS milk, added to the antigen-coated tubes or mixed with antigen-coated beads, and incubated at room temperature for 0.5-1 h to allow the phages to bind to the immobilized antigens. Unbound phages were washed out, while bound phages were eluted with triethlamine (pH>11). The neutralized phages were used to infect log phase E. coli, which were grown at 30° C. overnight. The harvested bacteria were used to amplify the phage for the next round panning.
The heavy and light chain variable domains of selected scFv antibodies isolated from the phage library were amplified by PCR and inserted into a mammalian expression vector containing modified human IgG 1 constant domains, from which the effector functions have been removed. The full length IgG antibodies were expressed in HEK293 cells and purified by Protein A. Purified antibodies 19B6, 19B10, 23A8, 23H9, 24H9, and 23A11 (see SEQ ID NOs: 1-48, Table 25) were characterized by binding (soluble and cell expressed PD-1) and blocking assays, Biacore kinetics analysis and cytokine secretion in SEB stimulated human PBMC.
To identify higher affinity antibodies, two light chain-shuffling libraries were constructed by combining the heavy chain of lead antibody 23H9 or 24H9, respectively, with the light chain mixture from R1 panning. Higher-affinity and/or more stable variants were identified by panning in conditions that were more restricted. These matured antibodies were converted to IgG, expressed, purified, and characterized again. The higher affinity clones were expressed in CHO cells, purified by protein A and SE-HPLC to obtain higher quality to run further studies. Antibodies 31B1, 33C4, 33G8, 34C1 (see SEQ ID NOs: 49-65, Table 25) were obtained by light chain shuffling using the heavy chain of 23H9. Antibodies 32A11, 32D11, 32D2, 32G6, 38A10, 38A11, 38A4, 38A6, 38A8, 38B1, 38B10, 38B2, 38C11, 38C6, 38G11, 38G9, 38H3, 39A3, 39B11, 39B3, 39B6, 39F11, 39G5, 39G8, 39H11, 39H2, and 39H7 (see SEQ ID NOs: 66-138, Table 25) were obtained by light chain shuffling using the heavy chain of 24H9.
The ability of anti-hPD1 antibodies 19B6, 19B10, 23A8, 23H9, 24H9, 23A11 (isolated from HEK293 cells) to bind to hPD1 was evaluated using a dose response binding ELISA using the indicated antibodies as primary antibodies. For this, high-binding (Immulon 2HB) plates were directly coated with human PD-1-Fc (R&D, cat #1086-PD-050). Biotin labeled hPD-1-his (Sino Biologicals, cat #10377-H08H) were captured by strepavidin (Jackson 016-000-114) or anti-his antibody (R&D, cat #MAB050-100) which were coated on the plate one day before. Serial dilutions of antibodies 19B6, 19B10, 23A8, 23H9, 24H9, and 23A11 were added to antigen-coated plates and incubated at room temperature for 1-2 hs. After washing the plates with PBST (0.05%) for three times, 1/5000-1/10,000 diluted anti-hFab-HRP antibody (Jackson 109-036-097) was added to the plates, which were incubated at room temperature for about 1 h. Color was developed by adding 1:1 dilution of substrate A and B from TMB (Fisher, cat #5120-0050) followed by neutralizing with 1N H2SO4. OD450 was read using a TECAN plate reader (Table 1). The means±S.D. of the OD450 reading was plotted against the log antibody concentration using GraphPad Prism8. The EC50 value was calculated by plotting log (agonist) vs. response (three parameters) or log(agonist) vs. response-variable slope (four parameters) (
Example 3: Antibodies isolated from phage display library block hPD-1/hPD-L1 interactions To examine the ability of anti-hPD1 antibodies 19B6, 19B10, 23A8, 23H9, 24H9, 23A11 (isolated from HEK293 cells) to block hPD-1/hPD-L1 interactions, high-binding (Immulon 2HB) plates were coated with human PD-L1-Fc (R&D, cat #156-B7-100) or PD-L2-Fc (R&D, cat #1224_PL), respectively, and blocked with 3% PBS milk. Serial dilutions of antibodies 19B6, 19B10, 23A8, 23H9, 24H9, and 23A11 were mixed with 0.5 μg/ml (final concentration) of biotin labeled hPD-1-Fc and incubated at room temperature for 1 h. The mixture was transferred to the PD-L1-Fc or PD-L2-Fc coated plate and incubated at RT for additional 1-2 h. After washing plate with PBST (0.05%) three times, 1/5000-1/10,000 diluted Strepavidin-HRP (Thermofisher, cat #21140) was added to the plates, which were incubated at room temperature for about 1 h. Color was developed by adding 1:1 dilution of substrate A and B from TMB, followed by neutralizing with 1N H2SO4. OD450 was read using a TECAN plate reader (Table 2). The means±S.D. of OD reading was plotted against the log antibody concentration using GraphPad Prism8. The EC50 value was calculated by analyzing log (agonist) vs. response (three parameters) or log(agonist) vs.—response variable slope (four parameters). The data points are the means±S.D. of duplicate determinations (
Binding of anti-PD-1 antibodies to HEK293 and Jurkat cells over-expressing human PD-1: Cells were cultured in IMDM medium with glutamine, supplemented with 10% heat-inactive fetal bovine serum (FBS). Cells were first incubated with the indicated anti-PD-1 antibodies, followed by incubation with an PE-anti human IgG1-Fc (R-phycoerythrin-conjugated goat anti-human IgG: Jackson ImmunoResearch cat #109-116-098). Antibody binding to hPD-1 was determined using a flow cytometry Guava EasyCyte™ HT Sampling Flow Cytometer (EMD Millipore). The data points in
Binding of anti-PD-1 antibodies to SEB-activated human PBMCs: PBMCs were isolated from LeukoPak (an enriched leukapheresis containing highly concentrated blood cells including monocytes, lymphocytes, platelets, plasma, as well as red cells) using Histopaque-1077 (Sigma) using the manufacturer's instructions. PBMCs were cultured at 2×106/mL in a 12-well plate containing IMDM (Gibco, Life Technologies) supplemented with 10% FBS (GE Healthcare HyClone) and activated by 1 ug/mL SEB (Staphylococcal enterotoxin B, Sigma) for 3 to 4 days. Activated PBMCs were first incubated with indicated anti-PD-1 antibodies, followed by incubation with a combination of PE-anti human IgG1-Fc (R-phycoerythrin-conjugated goat anti-human IgG: Jackson ImmunoResearch cat #109-116-098) and either anti human CD4-APC (eBioscience clone RPA-T4 cat #17-0049-42) or anti human CD8-APC (eBioscience clone RPA-T8 cat #17-0088-42). Antibody binding to PD-1 expressed on cells was evaluated using a Guava EasyCyte™ HT Sampling Flow Cytometer (EMD Millipore). Data points were generated by calculating the means±S.D. of duplicate determinations (Table 3 and
To assess the ability of selected anti-PD-1 antibodies to disrupt the binding of PD-1 expressing cells to PD-L1 expressing cells, the Promega PD-1/PD-L1 Blockade Bioassay was used. This assay consists of two genetically engineered cell lines, PD-1 effector cells and PD-L1 aAPC/CHO-K1 cells. When co-cultured, the PD-1/PD-L1 interaction inhibits TCR-mediated luminescence. When the PD-1/PD-L1 interaction is disrupted, TCR activation induces luminescence (via activation of the NFAT pathway) that can be detected by addition of Bio-Glo™ Reagent and quantitation with a luminometer.
The experiment was performed according to the manufacturer's instructions. Briefly, PD-L1 aAPC/CHO-K1 cells were plated and incubated for 16-20 h prior to the addition of increasing concentrations of anti-PD-1 antibodies and PD-1 effector cells. After 6 h of incubation at 37° C., Bio-Glo™ Reagent was added and luminescence (recorded as relative light unites, RLU) was measured by using a TECAN plate reader. Fold induction was calculated by RLU (induced-background)/RLU (no antibody control-background). Data points are represented as means±S.D. of duplicate determinations (
Antibodies 23H9 and 24H9 were selected for light chain shuffling, wherein the heavy chains of 23H9 or 24H9, respectively, were paired with a library of light chains. Antibodies 31B1, 33C4, 33G8, 34C1 (see SEQ ID NOs: 49-65, Table 25) were obtained by light chain shuffling using the heavy chain of 23H9. Antibodies 32A11, 32D11, 32D2, 32G6, 38A10, 38A1i, 38A4, 38A6, 38A8, 38B1, 38B10, 38B2, 38C11, 38C6, 38G11, 38G9, 38H3, 39A3, 39B11, 39B3, 39B6, 39F11, 39G5, 39G8, 39H11, 39H2, and 39H7 (see SEQ ID NOs: 66-138, Table 25 were obtained by light chain shuffling using the heavy chain of 24H9.
Example 6: Anti-hPD-1 Antibody 23H9 and its Derivatives Bind to hPD-1 and Block hPD-1/hPD-L1 InteractionsThe ability of anti-hPD1 antibody 23H9 and its derivatives 31B1, 33C4, 33G8, and 34C1 to bind to hPD1 and to block hPD-1/hPD-L1 interactions was determined using the protocols described in Examples 2 and 3, respectively. The parental antibody 23H9 and its derivatives showed no significant difference in binding to hPD-1-Fc and biotin-hPD-1-his captured by strepavidin (Table 5 and
The ability of anti-hPD1 antibody 24H9 and its derivatives 32A11, 32D2, 32D11, 38A6, 38A10, 38A11, 38B2, 38C11, 39B3, 39B11, 39G8 and 38H11 to bind to hPD1 and to block hPD-1/hPD-L1 interactions was determined using the protocols described in Examples 2 and 3, respectively. The parental antibody 24H9 and its derivatives showed no significant difference in binding to hPD-1-Fc and hPD-A-his captured by strepavidin (
Two clones (38A6 and 38D2) were picked for further characterization (Table 6).
Dose response binding assay using 23H9, 31B1, 33C4, 24H9, 38A6, and 38B2 were performed according to the protocol disclosed in Example 4. The results are shown in
A PD-1 blockade bioassay was performed using antibodies 23H9, 31B1, 33C4, 24H9, 38A6, and 38B2 according to the protocol outlined in Example 5. All derivatives were found to be more potent than their parental antibody 23H9 and 24H9 in blocking hPD-1-hPD-L1 interactions (
The effect of anti-PD-1 antibodies on cytokine production using 38A6, 38B2, 31B1, and 33C4 in SEB activated PBMC from donor FA was assessed by measuring the amount of cytokines released by PBMCs in the culture medium. PBMCs were isolated from LeukoPak (an enriched leukapheresis containing highly concentrated blood cells including monocytes, lymphocytes, platelets, plasma, as well as red cells) using Histopaque-1077 (Sigma) per manufacture instruction. PBMCs were cultured at 1×105 per well in 96 well plate containing IMDM (Gibco, Life Technologies) supplemented with 10% FBS (GE Healthcare HyClone). The cells were activated by 0.01 ug/mL SEB (Staphylococcal enterotoxin B, Sigma) for 2 days. Supernatants were collected for the measurement of IL-2 using Duoset ELISA Kit (R&D Systems) per the manufacturer's instructions (
The experiment was repeated to obtain EC50 values for antibodies 23H9, 31B1, 24H9, and 38B2 using PBMCs from donor EA (
IL-2 concentration increased in the presence of all antibodies in a dose-dependent manner (
The binding kinetics of the antibodies to either hPD-1-Fc or hPD-1-his was measured by surface plasmon resonance (SPR) using the Biacore T200. Human PD-1-Fc or PD-1-his protein was immobilized at pH5 onto a Series S CM5 sensor chip using standard amine coupling chemistry. Antibodies 23H9 and 23H9 derivatives 31B1, 33C4 as well as 24H9 and 24H9 derivatives 38A6, 38B2, 32D11, 39G8, 38A10, and 38A11 were injected at 30 μl/min at concentrations ranging from 1.5 to 100 nM over the immobilized surface using 1×HBSEP as the running buffer. The contact time (association phase) was 3 mins. The dissociation time was 6-10 mins. Regeneration was performed after each binding cycle with an injection of 20 mM HCl for 30 sat 30 μl/min flow rate. Sensorgrams were obtained at each concentration and the derived curves were fit to a 1:1 Langmuir binding model using Biaevaluation software. Derivative 31B1 and 33C4 were found to be more potent than the parental 23H9 in their binding to hPD-1-Fc (Table 10). All derivatives of 24H9 were found to be more potent than the parental antibody 24H9 in their binding to hPD-1-his and hPD-1-Fc.
Selected 23H9 and 24H9 derivatives, 31B1, 33C4, 38A6, and 38B2 were cloned and expressed by WuXi Biologics by using WuXi's mammalian expression vector and CHO knockout cell line. All antibodies were purified using protein A and SEC-HPLC. More than 2.5 mg of purified antibody was obtained from 20 ml culture after Protein A and SEC-HPLC purification. The monomer percentage of all antibodies was over 96% with endotoxin levels lower than 1.0 EU/mg. Differential scanning calorimetry (DSC) was used to determine the stability of the four antibodies. The DSC analysis was performed using a Malven DSC system. The protein sample was first diluted to 1 mg/mL with formulation buffer before analysis. 400 μl respective formulation buffer was added to a 96-well plate as reference and 400 μL protein sample was added. The samples were heated from 10° C. to 100° C. at a heating rate of 90° C./h in the capillary DSC system. The DSC results (Tm onset and Tm values) were analyzed using the vendor's software. The lowest thermal transition midpoint (Tm1) of 31B1, 33C4, 38A6, and 38B2 were 70.5, 74.0, 71.0, and 71.9° C. respectively (
Binding and Blocking ELISA were performed using antibodies 31B1, 33C4, 38A6, 38B2 isolated from transient CHOk cells using the protocols outlined in Examples 2 and 3, respectively. Comparison of the antibodies using binding ELISA showed no significant differences among the derivatives in binding to hPD-1-Fc, strepavidin-captured biotin-labeled hPD-1his and anti-his antibody captured hPD-1-his directly bound to the plates (
Comparison of the antibodies using blocking ELISAs showed no significant differences among the derivatives in blocking hPD-1/hPD-1 and hPD-1/hPD-L2 interactions (
Dose response binding assays were performed using antibodies 33B1, 33C4 (both 23H9 derivatives), 38A6 and 38B2 (both 24H9 derivatives) using the protocols outlined in Example 4.
Dose-response binding assays showed no difference between the two derivatives from the same parental antibody in binding of the antibodies to hPD-1 transfected HEK-293 and Jurkat cells, and SEB-activated PBMCs (Table 14 and
Binding of selected antibodies to hPD-1 his and hPD-1Fc was determined by SPR. Biacore analysis of 31B1, 33C4, 38A6, and 38B2 was performed using the protocol described in Example 11. All four antibodies were found to have high affinity to both hPD-1-Fc and hPD-1-his (Table 15 and
To assess the ability of 31B1 and 38B2 to disrupt the binding of PD-1 expressing cells to PD-L1 expressing cells, Promega PD-1/PD-L1 Blockade Bioassays were performed using the protocol described in Example 5. No significant difference was observed in EC50 and fold induction between 31B1 and 38B2 (
The effect of 31B1 and 38B2 on cytokine production in SEB-activated PBMCs was determined using the protocol outlined in Example 4. 38B2 was found to be more potent than 31B1 and the two control antibodies tested (Table 17 and
PD-1 antibodies that bind to both murine and human PD-1 were isolated using mPD-1-Fc (mouse IgV domain to fuse to the N-terminus of human IgG1Fc; present as dimer in solution) or mPD-1-his (mouse IgV domain of PD-1 connected to N-terminus of six histidine; present as monomer in solution) using the protocol outlined in Example 1.
Derivatives of anti-mPD-1 antibody R3A9 (SEQ ID NOs:139-146) by light pair shuffling using the VH chain of R3A9. R3A9 and its derivatives (see, e.g., SEQ ID NOs: 147-167) were select to develop further. The antibodies were cloned and expressed by WuXi Biologics using Wuxi's mammalian expression vector and CHO knockout cell line. The antibodies were purified by protein A and SEC-HPLC. More than 2.5 mg purified antibodies are obtained from 20 ml culture after Protein A purification. Antibodies further purified by SEC-HPLC.
The biological properties of selected antibodies generated in accordance with the methods of this Example are described in detail in the Examples set forth below.
Dose Response Binding and Blocking ELISA were performed using R3A9 and its derivatives using the protocols as outlined in Examples 2 and 3. Binding of antibodies to mPD-1 expressing cells was performed as described in Example 4. Blockage of intercellular PD-1/PD-L1 interactions was examined using the Promega Bioassay described in Example 5. The results are illustrated in
The R3A9 derivative m3A7 was found to be more potent than the parental R3A9 antibody in both binding to the soluble cell expressed mPD-1 and blocking mPD-1/mPD-L1 interactions (Table 18).
Dose response Binding and Blocking ELISAs for antibodies were performed using the protocols outlined in Examples 2 and 3, respectively. The experiments showed all R3A9 derivatives bound strongly to both hPD-1 and mPD-1 (
Binding of R3A9 and its R3A9 derivatives m2A1, m2C1, m4D1, m3A7 to PBMCs cells were tested using the protocol outlined in Example 4. Further, Biacore analysis was performed on all the antibodies disclosed in this Example using the protocol provided in Example 11.
Only three derivatives, m4d1, m2AM, and m3CM, were found to bind to both human and mouse PD-1 expressed on cells (Table 21 and
Promega blockade bioassays were performed to compare the potency of m4D1, m3A7 and 38B2 to disrupt intercellular PD-1/PD-L1 interactions using the protocol outlined in Example 4. The results are depicted in
m4D1 was found to block both hPD-1/PD-L1 and mPD-1/mPD-L1 interactions. Further, m4D1 was found to be as potent as m3A7 in mPD-1/mPD-L1 blockade assay and 3 folds less potent than 38B2 (
Anti-mPD-1 fusion antibodies comprising antibody m3A7 (referred to as m3A7/IL-15) were engineered by appending the sushi-domain of IL-15Rα and an IL-15 polypeptide to either the C-terminus or N-terminus of the antibody. The fusion of the IL-15Rα sushi domain along with a portion of the hinge region, linker 1, and IL-15 is called “SD15.” See, for an example of an SD15 domain, SEQ ID NO:174 in Table 25, SD15 domain highlighted in bold.
In the first version of the fusion protein, the SD15 domain was fused to the C-terminus of only one of the IgG1 CH1-CH2-CH3 domain (designated “1C-m3A7/IL-15”).
In a second version, the SD15 domain was fused to the C-termini of both IgG1 CH1-CH2-CH3 domains (designated “2C-m3A7/IL-15”).
In a third version of the fusion protein, the SD15 domain was linked to the N-terminus of only one of the VH domains via a second linker (designated “1N-m3A7/IL-15”).
In a fourth version of the fusion protein, the SD15 domain was linked to the N-terminus of both of the VH domains via a second linker (designated “2N-m3A7/IL-15).
In the four constructs above, the light chains were that of a conventional antibody. Amino acid substitutions, L234A, L235A, P329G (LALA-PG) were introduced in both the CH2 domains for eliminating complement binding and fixation as well as Fc-7 dependent antibody-dependent cell-mediated cytotoxity (ADCC).
Further, for heterodimeric fusions, mutations were introduced into constant regions of the heavy chains, wherein the amino acid substitutions were selected from one of the following groups: (1) CH3-1:T366Y (“knob”); CH3-2: Y407T (“hole”), (2) CH3-1: S354C, T366W (“knob”); CH3-2: Y349C, T366S, L368A, Y407V (“hole”) and (3) CH3-1: T350V, L351Y, F405A, Y407V (“knob”); CH3-2: T350V, T366L, K392L, T394W (“hole”).
The fusion antibodies were expressed transiently in CHOk cells. At least 95% purity of the monomer was obtained after purification with Protein A and SEC-HPLC. Four corresponding versions of anti hPD-1/IL-15 fusion antibodies comprising antibody 38B2 (described herein as 38B2-hSD15 or 38B2/IL-15)—1C-38B2-hSD15, 2C-38B2-hSD15, 1N-38B2-hSD15, 2N_-38B2-hSD15—were created following the same procedure. Three corresponding versions of 1N_38B2-SD15 bearing an amino acid substitution in position 65 of the IL-15 sequence, 65A_1N_38B2-hSD15, 65D_1N_38B2-hSd15, and 65S_1N_38B2-hSD15 were created using the same procedure.
Four corresponding versions of control fusion antibodies (DP47/IL-15) 1C-DP47/IL-15, 2C-DP47/IL-15, 1N-DP47/IL-15, 2N-DP47/IL-15 were created following the same procedure. DP47 was used as a non-targeting control antibody. Schematic diagram showing the antibody orientations are shown in
The ability of fusion proteins 1N-m3A7/IL-15, 1C-m3A7/IL-15, 2N-m3A7/IL-15, and 2C-m3A7/IL-15 to bind to mPD-1 and to block interactions between mPD-1 and mPD-L1 was assessed by ELISA, following the protocols described in Example 2 and 3, respectively.
No significant differences in binding and blocking capacity were observed among the four different molecules (Table 22 and
CTLL2 Culture and Proliferation Assay: The murine T lymphocyte cell line CTLL2 was cultured in IMDM medium supplemented with 10% heat-inactivated FBS and 10% IL-2 supplement (T cell culture supplement with ConA, Corning). The following fusion proteins were tested in this example: 1N-m3A7/IL-15, 2N-m3A7/IL-15, 1C-m3A7/IL-15 and 2C-m3A7/IL-15. 1N-DP47/IL-15, 2N-DP47/IL-15, 1C-DP47/IL-15, 2C-DP47/IL-15 and m3A7 were used as controls.
Serial dilutions of antibodies or fusion proteins were added in a 96-well plate, and then cells were seeded at 2.5×104 per well in IMDM medium supplemented with 10% heat-inactivated FBS. The cells were incubated at 37° C. for 3-5 days and cell proliferation was detected using CellTiter-Glo® luminescent cell viability assay kit (Promega).
Mouse Spleen Cell Isolation and Proliferation Assay: C57BL/6 mouse spleens were homogenized in IMDM medium through the 70 μm cell strainer. 1×RBC lysis buffer (eBioscience) was added to spleen cells and left for 3 min with occasional shaking, and then diluted with 5-fold volume of PBS buffer. After washing with PBS buffer, the splenocyte cell suspension was prepared in complete IMDM medium supplemented with 10% heat-inactivated FBS for proliferation assay immediately. The following fusion proteins were tested in this example: 1N-m3A7/IL-15, 2N-m3A7/IL-15, 1C-m3A7/IL-15 and 2C-m3A7/IL-15. 1N-DP47/IL-15, 2N-DP47/IL-15, 1C-DP47/IL-15, and 2C-DP47/IL-15 were used as controls.
Serial dilutions of the fusion proteins and controls were added in a 96-well plate and then cells were seeded at 1×105 per well. The cells were cultured for 5-7 days at 37° C. and collected for flow-cytometry analysis. The cells were washed and stained with fixable viability dye Fluor780 (eBioscience) for 30 min at 4° C. The cells were fixed after washing and were permeabilized with Foxp3 transcription factor staining buffer set (eBioscience), followed by staining with CD3(145-2C11)-PE, CD4(RM4-5)-APC, CD8α-(53-6.7)-PECy7 and Ki67(SolA15)-FITC from eBioscience. Proliferative CD4 (CD4+Ki67+) or CD8 (CD8+Ki67+) T cell population were analyzed and defined using Guava Flow Cytometry EasyCyte system.
All mPD-1/IL-15 fusion constructs stimulated both IL-2 dependent mouse lymphocyte CTLL2 (
To determine if the orientation or the number of IL-15/IL-15Rα sushi domains in a fusion protein have any effect on the ability of the fusion molecules to reduce tumor growth, an in vivo efficacy study in an LL/2 Murine Lung Cancer Syngeneic Model was conducted by Crown Bioscience (Taicang) using the m3A7/IL-15/IL-15Rα sushi fusion proteins Inc. Constructs 1N-m3A7/IL-15 and 1C-m3A7/IL-15 were tested in this Example, while 1N-DP47/IL-15 and 1C-DP47/IL-15 were used as controls.
C57BL6 strain mice, age from 8 to 10 weeks and weight from 16.5 to 20.7 g, were purchased from Shanghai Lingchang Biotechnology Co., Ltd (Shanghai, China). The LL/2 tumor cells were maintained in vitro with DMEM medium supplemented with 10% fetal bovine serum at 37° C. in presence of 5% CO2. The cells were harvested in exponential growth phase and counted before tumor inoculation. The fusion proteins used in this example were produced by WuXi Biologics and exhibited at least 95% purities and contained more than 95% monomer.
Each mouse was inoculated subcutaneously at the right rear-flank region with LL/2 tumor cells (3×105) in 0.1 ml of PBS for tumor development. The date of randomization and the first dosing day was denoted as day 0. When the mean tumor size reached approximately 100 mm3 the randomization process was started. Mice were randomly allocated to different study groups. Randomization was performed based on a “matched distribution” method using the multi-task method (StudyDirector™ software, version 3.1.399.19) randomized block design.
The fusion proteins were diluted according to the indicated dose and 10 μl/kg of fusion proteins was injected intravenously to the mice once every week for three weeks. The mice were weighed twice per week after randomization. Tumor volumes were measured twice per week in two dimensions using a caliper, and the volume was expressed in mm3 using the formula: “V=(L×W×W)/2, where V denoted tumor volume, L denoted tumor length (the longest tumor dimension) and W denoted tumor width (the longest tumor dimension perpendicular to L). Dosing as well as tumor and body weight measurements were conducted in a Laminar Flow Cabinet. The body weights and tumor volumes were measured by using StudyDirectorm software (version 3.1.399.19).
To determine antitumor activity of the fusion proteins, tumor growth inhibition (TGI) percentages were measured and recorded daily using the following formula TGI (%)=100×(1−T/C), where T and C denoted mean tumor volume (or weight) of the treated and control groups respectively for each of the fusion proteins and controls.
Of the fusion proteins tested, 1N-m3A7/IL-15 showed the most inhibitory effect on tumor growth (Table 23 and
Taken together, the data obtained from Examples 25 and 26 suggests that compared to the C-terminal fusion antibodies, the N-terminal fusion antibodies reduce the toxicity further because of the lower stimulation for the peripheral T cells. The data further shows that the N-terminal fusion molecules are particularly effective in stimulating tumor infiltrating lymphocytes (TIL) as compared on peripheral T cells due to the cis-presentation; the reduction of IL-2Rβγ binding in N-terminal fusion molecules allows the PD-1/IL-15 to selectively bind to TIL, therefore reducing its toxicity. Finally, the data shows that 1N-fusion molecules are superior to the 2N-fusion molecules.
Promega Blockade Bioassay was performed as described in Example 5 using fusion proteins 1C-38B2-hSD15, 2C-38B2-hSD15, 1N-38B2-hSD15, 2N-38B2-hSD15, 1N-65D-hSD15-38B2, and 1N-65S-hSD15-38B2. All fusion molecules retained PD-1/PD-L1 inhibitory functions as compared to 38B2 (
ExaM07e Culture and Proliferation Assay: To determine the ability of the fusion proteins to stimulate IL-15 in vitro, the human acute megakaryoblastic leukemia M07e cell line was cultured in INDM medium supplemented with 15% heat-inactivated FBS and 20% conditioned medium of cell line 5637.
Serial dilutions of antibodies or fusion proteins were added to a 96-well plate, and then cells were seeded at 2.5×104 per well in INDM medium supplemented with 10% heat-inactivated FBS. The cells were incubated at 37° C. for 3-5 days and cell proliferation was detected using CellTiter-Glo® luminescent cell viability assay kit (Promega).
While all tested fusion protein constructs stimulated IL-15 activity, IN fusions showed a decreased ability to stimulate as compared to 1C, 2C, or 2N constructs (
To determine if the orientation or the number of IL-15/IL-15Rα sushi domains have any effect on the ability of the fusion molecules to inhibit tumor growth, an in vivo efficacy study was performed in a CT26 syngeneic model using 1N-SD15-D7A8, 2N-SD15-D7A8, 1C-SD15-D7A8, and 2C-SD15-D7A8. CT26 syngeneic model mice were treated with the fusion proteins and observed for tumor development/reduction. CT26 is a murine colon carcinoma line.
Tumor volumes were measured twice per week in two dimensions using a caliper, and the volume was expressed in mm3 using the formula: “V=(L×W×W)/2, where V denoted tumor volume, L denoted tumor length (the longest tumor dimension) and W denoted tumor width (the longest tumor dimension perpendicular to L). Dosing as well as tumor and body weight measurements were conducted in a Laminar Flow Cabinet. The body weights and tumor volumes were measured by using StudyDirectorm software (version 3.1.399.19).
Results of the efficacy study with PD-L1/IL-15 molecules are shown in
Promega Blockade Bioassays (
Similarly, no significant differences were observed in the strong binding of 1N-fusion proteins comprising wild-type IL-15 or IL-15 N65S, respectively, to soluble PD-1 or cells expressing PD-1 (
The ability of 1N-fusion proteins to stimulate IL-15 activity in human and in mouse cells was examined. In the presence of N65S-1N-IL-15/38B2, human acute megakaryoblastic leukemia cells (M07e,
Further, both 1N-IL-15/38B2 and mut-1N-IL-15/38B2 induced a better dose response in proliferating CD8+ T cells than CD4+ T cells in both mouse spleen (
In vivo efficacy of 1N-fusion proteins comprising wild-type IL-15, IL-15 N65S, or IL-15 N65D, respectively, was evaluated in hPD-1/hPD-L1 transgenic BALB/c mice bearing Keytruda (an anti-PD-1 antibody) resistant hPD-L1-CT26 tumors. The fusion antibodies (once per week) and controls (twice per week) were injected (intraperitoneal) when the tumor size reached approximately 100 mms.
Both 1N-38B2/IL-15 and N65S-1N-38B2/IL-15 exhibited strong antitumor activity (
1N-fusion proteins comprising IL-15 N65S showed improved efficacy as compared to 1N-fusion proteins comprising IL-15 N65D (
In sum, fusion proteins comprising mutated IL-15 lowered IL-15-associated potency and stimulation, resulting in lower toxicity and an increased therapeutic treatment window.
Example 33: 1N-Fusion Proteins Comprising an IL-15 Amino Acid Substitution Exhibited Strong Anti-Tumor Activity In Vivo in Mice that were Rechangelled with Tumor CellsIn vivo efficacy of 1N-fusion proteins comprising IL-15 N65S or IL-15 N65D, respectively, was evaluated in hPD-1/hPD-L1 transgenic mice.
0.5×106 of hPDL1/CT26 was subcutaneously inoculated to the right lower flank of the mice. When the tumor size reached to about 100 mm3, the mice were intraperitoneally injected with 12 mg/kg of N65S-1N-38B2/IL-15 or N65D-1N-38B2/IL-15 once every week and twice every week for three weeks respectively. The tumors in 5 mice (of 6) completely disappeared in about 25 days for N65S-1N-38B2/IL-15 treatment and 40 days for N65D-1N-38B2/IL-15 treatment.
At day 88, 0.5×106 of hPDL1/CT26 cells and 0.1×106 of CT26 cells were subcutaneously inoculated to the left lower flank and left upper flank respectively. No tumor growth was observed for both cell lines up to day 135 days, showing that the fusion protein protect mice against rechallenges with tumor cells (
0.5×106 of hPDL1/CT26 cells were subcutaneously inoculated to the right lower flank of the mice. When the tumor size reached to about 100 mm3, the mice were intraperitoneally injected with 10 mg/kg of 38B2, 12 mg/kg of N65S-1N-38B2/IL-15, and combination of 10 mg/kg of 38B2 with 12 mg/kg of N65S-1N-DP47/IL-15 once every week for three weeks respectively. For the combination treatment, two test articles were injected sequentially with one hour.
The ability to suppress tumor growth was compared for the following constructs: (1) N65S-1N-38B2/IL-15 fusion protein; (2) a non-targeted fusion N65S-1N-DP47/IL-15; (3) a combination of anti-PD-1 antibody 38B2 and the non-targeted fusion (i.e., N65S-1N-DP47/IL-15); and (4) anti-PD-1 antibody 38B2 only.
Tumors grew significantly slower in the N65S-1N-38B2/IL-15 group as compared to the combination group (
This data illustrates the robust anti-tumor activity of N65S-1N-38B2/IL-15 fusion proteins and highlights its bi-functionality and its ability to bind to both PD1 and IL2Rβγ, which are co-expressed on TILs.
Example 35: Additional Administration of an Anti-PD-1 Antibody does not Lead to a Further Increase in Anti-Tumor Activity of 1N-Fusion Proteins0.5×106 of hPDL1/CT26 cells were subcutaneously inoculated to the right lower flank of the mice. When the tumor size reached to about 100 mm3, the mice were intraperitoneally injected with 10 mg/kg of 38B2, 12 mg/kg of N65S-1N-38B2/IL-15, and combination of 10 mg/kg of 38B2 with 12 mg/kg of N65S-1N-38B2/IL-15 once every week for three weeks respectively. For the combination treatment, two test articles were mixed first, then injected to the mice.
The ability to suppress tumor growth was compared for the following constructs: (1) N65S-1N-38B2/IL-15 fusion protein; (2) a combination of anti-PD-1 antibody 38B2 and N65S-1N-38B2/IL-15 fusion protein; and (3) anti-PD-1 antibody 38B2 only.
Tumor grew significantly more slowly in the N65S-1N-38B2/IL-15 group as compared to the combination group (
This data shows that 1N-fusion proteins are more effective in reducing tumor growth than combinations of 1N-fusion proteins and anti-PD-1 antibodies.
Example 36: N65S-1N-38B2/IL-15 Fusion Protein Showed a Long Serum Half-Life in hPD1/PDL1 Transgenic Mice Bearing hPDL1-CT 26 TumorshPD1/PDL1 transgenic Balb/c mice were inoculated subcutaneously at the right lower flank with hPDL1/CT26 tumor cells (0.5×106) in 0.1 mL of PBS. The animals were randomized and treatments were started when the average tumor volume reaches approximately 83 mms. The 5.1 mg/kg (0.35 μmol/kg) of 38B2, or 1 or 6 mg/kg (0.06 or 35 μmol/kg) of N65S-1N-38B2/IL-15 were administrated to the mice either intraperitoneally (IP) or intravenously (IV). After dosing, blood was collected at 0.2 h, 5 h, 2 h, 4 h, 12 h, 24 h, 48 h, 72 h, 120 h and 168 h post injection and the purified serum were used to measure the antibody concentration by the traditional ELISA, in which human PD1 was used as the captured protein and biotin-IL15 and anti-human Fab was used separately to detect the KD050 and 38B2 binding.
N65S-1N-38B2/IL-15 exhibited a similar serum half-life profile as antibody 38B2 in both IV (
0.5×106 of hPDL1/CT26 cells were subcutaneously inoculated to the right lower flank of the hPD1/PDL1 transgenic BALB/c mice. When the tumor size reached to about 17 5 mms, the mice were intravenously injected with 0.06 or 0.35 μmol/kg each of (1) N65S-1N-38B2/IL-1, (2) N65S-1N-DP47/IL-15 (non-targeted control), (3) antibody 38B2 and (4) the combination of antibody 38B2 and N65S-1N-38B2/IL-15. The tumor size was measured twice per week and mice were terminated at day 7 after dosing (
It was shown that N65S-1N-38B2/IL-15 bound to PD1 and IL2Rβγ expressing TIL and differently proliferated CD8+ T cells. Specifically, when analyzing the CD8/CD4 ratio in tumors, the blood, and draining lymph nodes (treated with antibody (1) 38B2, (2) PD1 targeted fusion protein N65S-1N-38B2/IL-15, (3) non-targeted fusion protein N65S-1N-DP47/IL-15, or (4) a combination of 38B2 and N65S-1N-38B2/IL-15), it was found that N65S-1N-38B2/IL-15 promoted CD8+ T cells growth in tumor, but not in the blood and draining lymph nodes. The CD8/CD4 ratio did not change as result of the other treatments ( )1) 38B2, (2) non-targeted fusion protein N65S-1N-DP47/IL-15, or (3) a combination of 38B2 and N65S-1N-38B2/IL-15)) (
Next, CD8 and CD4 subtypes in tumors (treated with antibody (1) 38B2, (2) PD1 targeted fusion protein N65S-1N-38B2/IL-15, (3) non-targeted fusion protein N65S-1N-DP47/IL-15, or (4) a combination of 38B2 and N65S-1N-38B2/IL-15) were analyzed. It was found that effector memory CD8 T cells were significantly increased in the tumor for N65S-1N-38B2/IL-15 reated samples and slightly increased for the 38B2 treated samples (
The indicated amount of tumor cells (Table 24) in 0.1 mL of PBS was subcutaneously inoculated to the right flank of the mice. The animals were randomized and treatments were started when the average tumor volume reaches approximately 100 mms (between 75-125 mm3). Tumor volumes were measured 2 times per week in two dimensions using a caliper, and the volume was expressed in mm3 using the formula: V=(L×W×W)/2, where V is tumor volume, L is tumor length (the longest tumor dimension) and W is tumor width (the longest tumor dimension perpendicular to L).
Significant anti-tumor efficacies were observed in all 12 models (TGI>50%) in single dose treatment (Table 24). Completed response (tumor free) were found for CT26, EMT6, MC38, H22, A20 and Pan02 (Table 24). Data for EMT6 as shown as an illustrative example (
Claims
1-76. (canceled)
77. An anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein:
- a. the sequences of CDR1H, CDR2H and CDR3H comprise SEQ ID NOS: 21, 22, and 23; and
- b. the sequences of CDR1L, CDR2L and CDR3L comprise: i. SEQ ID NOS: 96, 97 and 82 ii. SEQ ID NOS: 45, 46, and 47; iii. SEQ ID NOS: 66, 67, and 68; iv. SEQ ID NOS: 70, 67, and 71; v. SEQ ID NOS: 73, 74, and 75; vi. SEQ ID NOS: 77, 78, and 47; vii. SEQ ID NOS: 80, 81, and 82; viii. SEQ ID NOS: 77, 78, and 84; ix. SEQ ID NOS: 77, 86, and 47; x. SEQ ID NOS: 88, 89, and 47; xi. SEQ ID NOS: 66, 67, and 47; xii. SEQ ID NOS: 80, 92, and 75; xiii. SEQ ID NOS: 80, 94, and 71; xiv. SEQ ID NOS: 99, 100, and 47; xv. SEQ ID NOS: 102, 103, and 104; xvi. SEQ ID NOS: 106, 103, and 47; xvii. SEQ ID NOS: 108, 103, and 47; xviii. SEQ ID NOS: 110, 111, and 75; xix. SEQ ID NOS: 77, 103, and 113; xx. SEQ ID NOS: 77, 111, and 47; xxi. SEQ ID NOS: 116, 67, and 47; xxii. SEQ ID NOS: 118, 119, and 47; xxiii. SEQ ID NOS: 80, 78, and 47; xxiv. SEQ ID NOS: 122, 103 and 47; xxv. SEQ ID NOS: 124, 125, and 75; xxvi. SEQ ID NOS: 127, 38, and 68; xxvii. SEQ ID NOS: 129, 130, and 47; or xxviii. SEQ ID NOS: 132, 133, and 75.
78. The anti-PD-1 antibody, or an antigen-binding fragment thereof, of claim 77, wherein:
- a. the heavy chain variable region comprises: i. SEQ ID NO: 24, or ii. a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 24; and
- b. the light chain variable region comprises: i. SEQ ID NO: 48, 69, 72, 76, 79, 83, 85, 87, 90, 91, 93, 95, 98, 101, 105, 107, 109, 112, 114, 115, 117, 120, 121, 123, 126, 128, 131, or 134, or ii. a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any of SEQ ID NO: 48, 69, 72, 76, 79, 83, 85, 87, 90, 91, 93, 95, 98, 101, 105, 107, 109, 112, 114, 115, 117, 120, 121, 123, 126, 128, 131, or 134.
79. The anti-PD-1 antibody, or an antigen-binding fragment thereof, of claim 77, wherein:
- the sequence of CDR1H comprises the sequence of SEQ ID NO: 21;
- the sequence of CDR2H comprises the sequence of SEQ ID NO: 22;
- the sequence of CDR3H comprises the sequence of SEQ ID NO: 23
- the sequence of CDR1L comprises the sequence of SEQ ID NO: 96;
- the sequence of CDR2L comprises the sequence of SEQ ID NO: 97; and
- the sequence of CDR3L comprises the sequence of SEQ ID NO: 82.
80. The anti-PD-1 antibody, or an antigen-binding fragment thereof, of claim 79, wherein:
- a. the heavy chain variable region comprises SEQ ID NO: 24, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 24; and
- b. the light chain variable region comprises SEQ ID NO: 98, or a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 98.
81. An anti-PD-1 antibody, or an antigen-binding fragment thereof, wherein:
- a. the sequences of CDR1H, CDR2H and CDR3H comprise SEQ ID NOS: 17, 18, and 19; and
- b. the sequences of CDR1L, CDR2L and CDR3L comprise: i. SEQ ID NOS: 41, 49, and 50; ii. SEQ ID NOS: 41, 42, and 43; iii. SEQ ID NOS: 41, 52, and 53; iv. SEQ ID NOS: 41, 55, and 56; or v. SEQ ID NOS: 58, 59, and 60.
82. The anti-PD-1 antibody, or an antigen-binding fragment thereof, of claim 81, wherein:
- a. the heavy chain variable region comprises: i. SEQ ID NO: 20, or ii. a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to SEQ ID NO: 20; and
- b. the light chain variable region comprises: i. SEQ ID NO: 44, 51, 54, 57, or 61, or ii. a sequence that is at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to any one of SEQ ID NO: 44, 51, 54, 57, or 61.
83. The anti-PD-1 antibody, or an antigen-binding fragment thereof, of claim 77, wherein the antibody or antigen-binding fragment is a multispecific or a bispecific antibody or antigen-binding fragment thereof.
84. The anti-PD-1 antibody, or an antigen-binding fragment thereof, of claim 77, wherein the antibody or antigen-binding fragment is an scFv, Fv, Fab′, Fab, F(ab′)2, or diabody.
85. The anti-PD-1 antibody, or an antigen-binding fragment thereof, of claim 77, wherein the antibody is an IgG class immunoglobulin, optionally having isotype IgG1 or IgG4.
86. The anti-PD-1 antibody, or an antigen-binding fragment thereof, of claim 77, wherein the antibody or antigen-binding fragment comprises a first and a second heavy chain constant region, and wherein the antibody or antigen-binding fragment thereof comprises at least one modification in the CH3 domains of the first and the second heavy chain causing heterodimerization.
87. The anti-PD-1 antibody, or an antigen-binding fragment thereof, of claim 86, wherein:
- a. the CH3 domain of the first heavy chain comprises one or more of amino acid substitutions S354C and T366W; and the CH3 domain of the second heavy chain comprises one or more of amino acid substitutions Y349C, T366S, L368A, and Y407V;
- b. the CH3 domain of the first heavy chain comprises one or more of amino acid substitutions T350V, L351Y, F405A, and Y407V; and the CH3 domain of the second heavy chain comprises one or more of amino acid substitutions T350V, T366L, K392L, and T394W; or
- c. the CH3 domain of the first heavy chain comprises one or more of amino acid substitutions L351Y, F405A, and Y407V; and the CH3 domain of the second heavy chain comprises one or more of amino acid substitutions T366L, K392L, and T394W (Kabat EU index numbering).
88. The anti-PD-1 antibody, or an antigen-binding fragment thereof, of claim 86, wherein the Fc domain, if present, comprises one or more amino acid substitution that reduces binding to an Fc receptor or reduces effector function, wherein the one or more amino acid substitution is selected from L234A, L235A, and P329G (Kabat EU index numbering).
89. A fusion protein comprising:
- a. the anti-PD-1 antibody, or an antigen-binding fragment thereof, of claim 77;
- b. an IL-15Rα sushi domain polypeptide comprising the amino acid sequence of SEQ ID NO: 214, or an amino acid sequence that is at least 95% identical to SEQ ID NO:
- 214;
- c. an IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 212, or an amino acid sequence that is at least 90% or at least 95% identical to SEQ ID NO: 212; and
- d. a first linker polypeptide joining the IL-15Rα sushi domain polypeptide and the IL-15 polypeptide, optionally wherein the IL-15Rα sushi domain polypeptide is fused to the N-terminus of the IL-15 polypeptide.
90. The fusion protein of claim 89, wherein (i) the IL-15Rα sushi domain polypeptide and the IL-15 polypeptide are fused to (ii) the N-terminus of the heavy chain variable region, optionally by a second linker.
91. The fusion protein of claim 90, wherein the first linker (i) is between 5 and 40 amino acids long, optionally, consists predominantly of Gly (G), Asn (N), Ser (S), Thr (T), Ala (A), Leu (L), and Gln (Q); and/or (ii) comprises a sequence selected from the group consisting of SEQ ID NOS: 215-218 and 244.
92. The fusion protein of claim 91, wherein the second linker (i) is between 5 and 40 amino acids long, optionally, consists predominantly of Gly (G), Asn (N), Ser (S), Thr (T), Ala (A), Leu (L), and Gln (Q), and/or (ii) comprises a sequence selected from the group consisting of SEQ ID NOS: 215-218 and 244.
93. The fusion protein of claim 92, wherein the fusion protein comprises not more than one IL-15Rα sushi domain polypeptide and not more than one IL-15 polypeptide.
94. The fusion protein of claim 92, wherein the IL-15 polypeptide is a mutant IL-15 polypeptide comprising one or more amino acid substitutions at positions 45, 65, or 108 as numbered according to the mature human IL-15 sequence of SEQ ID NO: 212, wherein the one or more amino acid substitutions in the IL-15 polypeptide are selected from L45A, N65A, N65D, N65S, N65K, and Q108S as numbered according to the mature human IL-15 sequence of SEQ ID NO: 212.
95. A fusion protein comprising a light chain sequence comprising SEQ ID NO: 219 or SEQ ID NO: 98 and a first heavy chain sequence comprising SEQ ID NO: 240 and a second heavy chain sequence comprising SEQ ID NO: 241.
96. A nucleic acid sequence encoding the anti-PD-1 antibody, or an antigen-binding fragment thereof of claim 77.
97. A cell comprising the nucleic acid of claim 96.
98. A vector comprising nucleic acids encoding the light and heavy chains encoding the anti-PD-1 antibody, or an antigen-binding fragment thereof, of claim 77.
99. A pharmaceutical composition comprising (i) the anti-PD-1 antibody, or an antigen-binding fragment thereof, of claim 77; and (ii) a pharmaceutically acceptable carrier.
100. A method of inhibiting binding of PD-1 to a ligand of PD-1, optionally PD-L1 or PD-L2, in a subject in need thereof, the method comprising administering to the subject an effective amount of the anti-PD-1 antibody, or an antigen-binding fragment thereof, of claim 77.
101. A method for increasing T cell activation or stimulating the immune system in a subject in need thereof, the method comprising administering to the subject an effective amount of the anti-PD-1 antibody, or an antigen-binding fragment thereof, of claim 77.
102. A method of treating cancer or reducing tumor growth or tumor metastasis in a subject in need thereof, the method comprising administering to the subject an effective amount of the anti-PD-1 antibody, or an antigen-binding fragment thereof, of claim 77.
103. A method of inhibiting binding of PD-1 to a ligand of PD-1, optionally PD-L1 or PD-L2, in a subject in need thereof, the method comprising administering to the subject an effective amount of the fusion protein of claim 89.
104. A method for increasing T cell activation or stimulating the immune system in a subject in need thereof, the method comprising administering to the subject an effective amount of the fusion protein of claim 89.
105. A method of treating cancer or reducing tumor growth or tumor metastasis in a subject in need thereof, the method comprising administering to the subject an effective amount of fusion protein of claim 89.
Type: Application
Filed: Jun 23, 2021
Publication Date: Dec 28, 2023
Applicant: Kadmon Corporation, LLC (New York, NY)
Inventors: Dan Lu (Montvale, NJ), Zhanna Polonskaya (Mountainside, NJ), Tzu-Pei Chang (New York, NY), Stella Aviaty Martomo (Edgewater, NJ), Jeegar P. Patel (Hillsborough, NJ), Faical Miyara (Bronxville, NY)
Application Number: 18/011,878
