PEPTIDOMIMETIC MACROCYCLES AND USE THEREOF IN REGULATING HIF1ALPHA
The present invention provides peptidomimetic macrocycles capable of regulating HIF1α and methods of using such macrocycles for the treatment of diseases.
This application is a continuation of U.S. application Ser. No. 14/843,079, filed Sep. 2, 2015, which is a continuation of PCT/US14/21292, filed Mar. 6, 2014, which claims priority to U.S. Provisional Application No. 61/798,026, filed Mar. 15, 2013, U.S. Provisional Application No. 61/776,663, filed Mar. 11, 2013, and U.S. Provisional Application No. 61/773,769, filed Mar. 6, 2013, each of which applications are hereby incorporated by reference in their entirety.
SEQUENCE LISTINGThe instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on Jan. 29, 2019, is named 35224790302_SL.txt and is 392,988 bytes in size.
INCORPORATION BY REFERENCEAll publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.
BACKGROUND OF THE INVENTIONHypoxia-inducible factors (HIFs) are transcription factors that respond to changes in available oxygen in the cellular environment, in specific, to decreases in oxygen, or hypoxia. Most, if not all, oxygen-breathing species express the highly-conserved transcriptional complex HIF-1, which is a heterodimer composed of an alpha and a beta subunit, the latter being a constituitively-expressed aryl hydrocarbon receptor nuclear translocator (ARNT). HIF-1 belongs to the PER-ARNT-SIM (PAS) subfamily of the basic-helix-loop-helix (bHLH) family of transcription factors. The alpha subunit of HIF-1 is a target for prolyl hydroxylation by HIF prolyl-hydroxylase, which makes HIF1α a target for degradation by the E3 ubiquitin ligase complex, leading to quick degradation by the proteasome. This occurs only in normoxic conditions. In hypoxic conditions, HIF prolyl-hydroxylase is inhibited, since it utilizes oxygen as a cosubstrate.
HIFs facilitate both oxygen delivery and adaptation to oxygen deprivation by regulating the expression of genes that are involved in many cellular processes, including glucose uptake and metabolism, angiogenesis, erythropoiesis, cell proliferation, and apoptosis (Semenza G L. Curr Opin Cell Biol 2001; 13: 167-171). They are members of the PAS (PER-ARNT (arylhydrocarbon receptor nuclear translocator)-SIM) family of basic helix-loop-helix (bHLH) transcription factors that bind to DNA as heterodimers composed of an oxygen-sensitive a subunit and a constitutively expressed β subunit, also known as ARNT. To date, three HIFs (HIF-1, -2, and -3) have been identified that regulate transcriptional programs in response to low oxygen levels.
HIFs are transcription factors that mediate cellular adaptations to oxygen deprivation. Over 100 direct HIF target genes have been identified that regulate a number of cellular processes, including glucose metabolism, angiogenesis, erythropoiesis, proliferation, and invasion. HIF can also indirectly regulate cellular processes such as proliferation and differentiation through interactions with other signaling proteins such as C-Myc and Notch (Rankin E B and AJ Giaccia, Cell Death and Differtiation, 15, 2008).
Chronic hypoxia is a hallmark of many tumors and is associated with angiogenesis and more aggressive tumor phenotype. HIFs regulate multiple steps of tumorigenesis including tumor formation, progression, and response to therapy. There are multiple mechanisms by which HIF can become activated and promote tumor progression. Thus, it is apparent that downregulation of the HIF system is an attractive target for cancer therapy.
Cited2 is a cAMP-responsive element-binding protein (CBP)/p300 interacting transcriptional modulator, with Glu/Asp-rich carboxy-terminal domain, 2. Cited2 has been seen as a negative regulator of HIF1α-mediated signaling by competing with HIF1α for binding to CBP/p300 (Freedman et al., Nat Struct Biol. 2003 July; 10(7):504-12; Bhattacharya et al., Genes Dev. 13, 64-75, 1999).
SUMMARY OF THE INVENTIONThe present invention provides pharmaceutical formulations comprising an effective amount of peptidomimetic macrocycles or pharmaceutically acceptable salts thereof. The peptidomimetic macrocycles of the invention are cross-linked (e.g., stapled) and possess improved pharmaceutical properties relative to their corresponding uncross-linked peptidomimetic macrocycles. These improved properties include improved bioavailability, enhanced chemical and in vivo stability, increased potency, and reduced immunogenicity (i.e., fewer or less severe injection site reactions).
In some embodiments, the present invention provides a peptidomimetic macrocycle comprising an amino acid sequence which is at least about 60% identical to an amino acid sequence selected from the group consisting of the amino acid sequences in Tables 1a, 1b and 1c, further comprising at least one macrocycle-forming linker, wherein the macrocycle-forming linker connects a first amino acid to a second amino acid. In some embodiments, the peptidomimetic macrocycle comprises an amino acid sequence which is at least about 65%, 70%, 75%, 80%, 85%, 90% or 95% an amino acid sequence identical to selected from the group consisting of the amino acid sequences in Tables 1a, 1b and 1c. In some embodiments, the peptidomimetic macrocycle comprises an amino acid sequence selected from the group consisting of the amino acid sequences in Tables 1a, 1b and 1c. In some embodiments, a macrocycle-forming linker of the peptidomimetic macrocycle of the invention connects one of the following pairs of amino acids: 9 and 13, 9 and 16, 10 and 14, 10 and 17, 11 and 15, 11 and 18, 12 and 16, 12 and 19, 13 and 17, 13 and 20, 14 and 18, and 15 and 19. In some embodiments, the macrocycle-forming linker connects amino acids 10 and 14. In some embodiments, the macrocycle-forming linker connects amino acids 14 and 18.
In some embodiments, the present invention provides a peptidomimetic macrocycle comprising an amino acid sequence which is at least about 60% identical to an amino acid sequence selected from the group consisting of the amino acid sequences in Table 2, further comprising at least one macrocycle-forming linker, wherein the macrocycle-forming linker connects a first amino acid to a second amino acid. In some embodiments, the peptidomimetic macrocycle comprises an amino acid sequence which is at least about 65%, 70%, 75%, 80%, 85%, 90% or 95% identical to an amino acid sequence selected from the group consisting of the amino acid sequences in Table 2. In some embodiments, the peptidomimetic macrocycle comprises an amino acid sequence selected from the group consisting of the amino acid sequences in Table 2. In some embodiments, one or more macrocycle-forming linkers of the peptidomimetic macrocycle of the invention connect one or more of the following pairs of amino acids: 4 and 8, 4 and 11, 5 and 9, 5 and 12, 6 and 10, 6 and 13, 7 and 11, 8 and 12, 9 and 13, 19 and 23, 19 and 26, 20 and 27, 21 and 25, 21 and 28, 23 and 27, and 41 and 45. In some embodiments, the peptidomimetic macrocycle comprise two macrocycle-forming linkers. In some embodiments, the macrocycle-forming linkers connect amino acids 6 and 13 and amino acids 23 and 27. In some embodiments, the macrocycle-forming linkers connect amino acids 8 and 12 and amino acids 19 and 26. In some embodiments, the macrocycle-forming linkers connect amino acids 8 and 12 and amino acids 23 and 27. In some embodiments, the macrocycle-forming linkers connect amino acids 23 and 27 and amino acids 41 and 45.
In some embodiments, a peptidomimetic macrocycle of the invention comprises a helix, for example an α-helix. In some embodiments, a peptidomimetic macrocycle of the invention comprises an α,α-disubstituted amino acid. In some embodiments, each amino acid connected by the macrocycle-forming linker is an α,α-disubstituted amino acid.
In some embodiments, the present invention provides a peptidomimetic macrocycle having Formula (I):
wherein:
each A, C, D, and E is independently an amino acid,
B is an amino acid,
[—NH-L3-CO—], [—NH-L3-SO2—], or [—NH-L3-],
wherein A, B, C, D, and E, taken together with the cross-linked amino acids connected by the macrocycle-forming linker L, form the amino acid sequence of the peptidomimetic macrocycle;
L is a macrocycle-forming linker of the formula -L1-L2- or the formula
R1 and R2 are independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, cycloalkylalkyl, heteroalkyl, or heterocycloalkyl, each of which except for —H is optionally substituted with halo;
R3 is —H, alkyl, alkenyl, alkynyl, arylalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, cycloalkylalkyl, cycloaryl, or heterocycloaryl, each of which except for —H is optionally substituted with R5;
L1, L2, and L3 are independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, cycloarylene, heterocycloarylene, or [—R4—K—R4-]n, each being optionally substituted with R5;
each R4 is alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, arylene, or heteroarylene;
each K is O, S, SO, SO2, CO, CO2, or CONR3;
each R5 is independently halogen, alkyl, —OR6, —N(R6)2, —SR6, —SOR6, —SO2R6, —CO2R6, a fluorescent moiety, a radioisotope, or a therapeutic agent;
each R6 is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heterocycloalkyl, a fluorescent moiety, a radioisotope, or a therapeutic agent;
R7 is —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, cycloaryl, or heterocycloaryl, each of which except for —H is optionally substituted with R5, or part of a cyclic structure with a D residue;
R8 is —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, cycloaryl, or heterocycloaryl, each of which except for —H is optionally substituted with R5, or part of a cyclic structure with an E residue;
R9 is alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, heteroaryl, or heterocyclyl group, unsubstituted or optionally substituted with Ra and/or Rb;
Ra and Rb are independently alkyl, OCH3, CF3, NH2, CH2NH2, F, Br, I,
v and w are independently integers from 1-100;
u is an integer from 1 to 3;
x, y and z are independently integers from 0-10; and
n is an integer from 1-5.
In some embodiments, u is 1.
In some embodiments, the sum of x+y+z is 2, 3 or 6, for example 3.
In some embodiments, each of v and w is independently an integer from 1 to 10, 1 to 15, 1 to 20, or 1 to 25, for example from 1 to 15.
In some embodiments, L1 and L2 are independently alkylene, alkenylene or alkynylene. In some embodiments, L1 and L2 are independently C3-C10 alkylene or alkenylene, for example C3-C6 alkylene or alkenylene. For example, L is
In some embodiments, L is
for example
In some embodiments, R1 and R2 are H. In some embodiments, R1 and R2 are independently alkyl, for example methyl.
In some embodiments, the present invention provides a peptidomimetic macrocycle having the formula
wherein:
L′ is a macrocycle-forming linker of the formula -L1′-L2′- or the formula
L1′ and L2′ are independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, cycloarylene, heterocycloarylene, or [—R4—K—R4—]n, each being optionally substituted with R5;
R8′ is —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, cycloaryl, or heterocycloaryl, each of which except for —H is optionally substituted with R5, or part of a cyclic structure with an E residue;
R9′ is alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, heteroaryl, or heterocyclyl group, unsubstituted or optionally substituted with Ra′ and/or Rb′;
Ra′ and Rb′ are independently alkyl, OCH3, CF3, NH2, CH2NH2, F, Br, I,
and x′, y′, and z′ are independently integers from 0-10.
In some embodiments, the sum of x+y+z and the sum of x′+y′+z′ are independently 2, 3 or 6, for example 3.
In some embodiments, each of v, w, v′ and w′ is independently an integer from 1 to 10, 1 to 15, 1 to 20, or 1 to 25.
In some embodiments, each of v, w, v′ and w′ is independently an integer from 1 to 15.
In some embodiments, L1, L2, L1′, and L2′ are independently alkylene, alkenylene or alkynylene. In some embodiments, L1, L2, L1′, and L2′ are independently C3-C10 alkylene or alkenylene, for example C3-C6 alkylene or alkenylene. In some embodiments, L and L′ are both
In some embodiments, L is
For example, L and L′ are independently
In some embodiments, R1 and R2 are H. In some embodiments, R1 and R2 are independently alkyl, for example methyl.
In some embodiments, a peptidomimetic macrocycle of the invention is
or a pharmaceutically acceptable salt thereof.
In some embodiments, a peptidomimetic macrocycle of the invention comprises a macrocycle-forming linker connecting a backbone amino group of a first amino acid to a second amino acid within the peptidomimetic macrocycle.
In some embodiments, the present invention provides a peptidomimetic macrocycle having Formula (II) or (IIa):
wherein:
each A, C, D, and E is independently an amino acid,
B is an amino acid,
[—NH-L3-CO—], [—NH-L3-SO2—], or [—NH-L3-], wherein A, B, C, D, and E, taken together with the cross-linked amino acids connected by the macrocycle-forming linker -L1-L2-, form the amino acid sequence of the peptidomimetic macrocycle which is at least about 65%, 70%, 75%, 80%, 85%, 90%, 95% or is about 100% identical to an amino acid sequence selected from the group consisting of the amino acid sequences in Tables 1a, 1b, 1c and 2;
R1 and R2 are independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, cycloalkylalkyl, heteroalkyl, or heterocycloalkyl, unsubstituted or substituted with halo-, or part of a cyclic structure with an E residue;
R3 is hydrogen, alkyl, alkenyl, alkynyl, arylalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, cycloalkylalkyl, cycloaryl, or heterocycloaryl, optionally substituted with R5;
L1 and L2 are independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, cycloarylene, heterocycloarylene, or [—R4—K—R4-]n, each being optionally substituted with R5;
each R4 is alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, arylene, or heteroarylene;
each K is O, S, SO, SO2, CO, CO2, or CONR3;
each R5 is independently halogen, alkyl, —OR6, —N(R6)2, —SR6, —SOR6, —SO2R6, —CO2R6, a fluorescent moiety, a radioisotope, or a therapeutic agent;
each R6 is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heterocycloalkyl, a fluorescent moiety, a radioisotope or a therapeutic agent;
R7 is —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, cycloaryl, or heterocycloaryl, each of which except for —H is optionally substituted with R5;
v and w are independently integers from 1-100;
u is an integer from 1 to 3;
x, y and z are independently integers from 0-10; and
n is an integer from 1-5.
In some embodiments, u is 1.
In some embodiments, the sum of x+y+z is 2, 3 or 6, for example 3.
In some embodiments, each of v and w is independently an integer from 1 to 10, 1 to 15, 1 to 20, or 1 to 25, for example from 1 to 15.
In some embodiments, L1 and L2 are independently alkylene, alkenylene or alkynylene. In some embodiments, L1 and L2 are independently C3-C10 alkylene or alkenylene, for example C3-C6 alkylene or alkenylene. For example, L is
In some embodiments, L is
for example
In some embodiments, R1 and R2 are H. In some embodiments, R1 and R2 are independently alkyl, for example methyl.
In some embodiments, the present invention provides a peptidomimetic macrocycle comprising an amino acid sequence of the formula:
X1-X2-X3-X4-X5-X6-X7-X8-X9-X10-X11-X12-X13-X14-X15-X16-X17-X18-X19-X20-X21-X22-X23-X24-X25-X26-X27-X28-X29-X30-X31-X32 (SEQ ID NO: 2)
wherein:
X1 is a hydrophobic amino acid, or absent;
X2 is a hydrophobic amino acid, or absent;
X3 is a negatively charged amino acid, a positively charged amino acid, or absent;
X4 is an uncharged polar amino acid, or absent;
X5 is a negatively charged amino acid, or absent;
X6 is a hydrophobic amino acid, a negatively charged amino acid, a positively charged amino acid, an uncharged polar amino acid, or absent;
X7 is a hydrophobic amino acid, a negatively charged amino acid, or absent;
X8 is a negatively charged amino acid, a positively charged amino acid, or absent;
X9 is a negatively charged amino acid, absent, or a cross-linked amino acid;
X10 is a negatively charged amino acid, a positively charged amino acid, an uncharged polar amino acid, or a cross-linked amino acid;
X11 is a hydrophobic amino acid, a negatively charged amino acid, a positively charged amino acid, or a cross-linked amino acid;
X12 is a hydrophobic amino acid, a negatively charged amino acid, or a cross-linked amino acid;
X13 is a hydrophobic amino acid, a hydrophobic amino acid, a negatively charged amino acid, or a cross-linked amino acid;
X14 is a cross-linked amino acid;
X15 is a hydrophobic amino acid, a negatively charged amino acid, or a cross-linked amino acid;
X16 is a hydrophobic amino acid, a negatively charged amino acid, or a cross-linked amino acid;
X17 is a hydrophobic amino acid, a negatively charged amino acid, a positively charged amino acid, or a cross-linked amino acid;
X18 is a cross-linked amino acid;
X19 is a hydrophobic amino acid, a negatively charged amino acid, a positively charged amino acid, or a cross-linked amino acid;
X20 is a negatively charged amino acid, a hydrophobic amino acid, or a cross-linked amino acid;
X21 is a hydrophobic amino acid, or a negatively charged amino acid;
X22 is a negatively charged amino acid, or absent;
X23 is a positively charged amino acid, a negatively charged amino acid, or absent;
X24 is a hydrophobic amino acid, a negatively charged amino acid, or absent;
X25 is a hydrophobic amino acid, a negatively charged amino acid, or absent;
X26 is a negatively charged amino acid, or absent;
X27 is a hydrophobic amino acid, or absent;
X28 is a hydrophobic amino acid, or absent;
X29 is a negatively charged amino acid, an uncharged polar amino acid, or absent;
X30 is a hydrophobic amino acid, or absent;
X31 is a hydrophobic amino acid, or absent; and
X32 is a hydrophobic amino acid, or absent;
wherein the peptidomimetic macrocycle comprises at least one macrocycle-forming linker connecting at least one pair of amino acids selected from X1-X28;
L is a macrocycle-forming linker of the formula -L1-L2- or the formula
L1 and L2 are independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, cycloarylene, heterocycloarylene, or [—R4—K—R4-]n, each being optionally substituted with R5;
each the cross-linked amino acid is optionally substituted at the alpha carbon position with R1 or R2, wherein R1 and R2 are independently alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, cycloalkylalkyl, heteroalkyl, or heterocycloalkyl, each being optionally substituted with halo-;
each R4 is alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, arylene, or heteroarylene;
each K is O, S, SO, SO2, CO, or CO2;
each R5 is independently halogen, alkyl, —OR6—N(R6)2, —SR6, —SOR6, —SO2R6, —CO2R6, a fluorescent moiety, a radioisotope, or a therapeutic agent;
each R6 is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heterocycloalkyl, a fluorescent moiety, a radioisotope, or a therapeutic agent;
R9 is alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, heteroaryl, or heterocyclyl group, unsubstituted or optionally substituted with R. and/or Rb; and
Ra and Rb are independently alkyl, OCH3, CF3, NH2, CH2NH2, F, Br, I,
In some embodiments, the present invention provides a peptidomimetic macrocycle comprising an amino acid sequence of the formula:
X1-X2-X3-X4-X5-X6-X7-X8-X9-X10-X11-X12-X13-X14-X15-X16-X17-X18-X19-X20-X21-X22-X23-X24-X25-X26-X27-X28-X29-X30-X31-X32 (SEQ ID NO: 3)
wherein:
X1 is Val or absent;
X2 is Ile, Phe, or absent;
X3 is Asp, Arg, or absent;
X4 is Thr or absent;
X5 is Asp or absent;
X6 is Phe, Ala, Glu, Ser, Dpr, Asn, or absent;
X7 is Ile, Ala, Glu, Ser, or absent;
X8 is Asp, Ala, Ser, Dpr, or absent;
X9 is Glu, Ala, absent, or a cross-linked amino acid;
X10 is Glu, Ala, Ser, Dpr, Gln, or a cross-linked amino acid;
X11 is Val, Ala, Asp, Ser, Dpr, or a cross-linked amino acid;
X12 is Leu, Ala, Glu, Ser, pL, or a cross-linked amino acid;
X13 is Met, Nle, Ala, Asp, or a cross-linked amino acid;
X14 is Ser or a cross-linked amino acid;
X15 is Leu, Ala, Asp, Ser, or a cross-linked amino acid;
X16 is Val, Ala, Glu, Ser, pL, or a cross-linked amino acid;
X17 is Ile, Ala, Glu, Ser, Dpr, Bpa, or a cross-linked amino acid;
X18 is Glu or a cross-linked amino acid;
X19 is Met, Nle, Ala, Glu, Ser, Dpr, Bpa, or a cross-linked amino acid;
X20 is Gly, Ala, Glu, Ser, or a cross-linked amino acid;
X22 is Asp, Ala, Ser, or absent;
X23 is Arg, Ala, Glu, Ser, Dpr, or absent;
X24 is Ile, Ala, Glu, Ser, or absent;
X25 is Lys, Glu, or absent;
X26 is Glu or absent;
X27 is Leu or absent;
X28 is Pro or absent;
X29 is Glu, Gln, or absent;
X30 is Leu or absent;
X31 is Trp or absent; and
X32 is Leu or absent;
wherein the peptidomimetic macrocycle comprises at least one macrocycle-forming linker connecting at least one pair of amino acids selected from X1-X28;
L is a macrocycle-forming linker of the formula -L1-L2- or the formula
L1 and L2 are independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, cycloarylene, heterocycloarylene, or [—R4—K—R4-]n, each being optionally substituted with R5;
each the cross-linked amino acid is optionally substituted at the alpha carbon position with R1 or R2, wherein R1 and R2 are independently alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, cycloalkylalkyl, heteroalkyl, or heterocycloalkyl, each being optionally substituted with halo-;
each R4 is alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, arylene, or heteroarylene;
each K is O, S, SO, SO2, CO, or CO2;
each R5 is independently halogen, alkyl, —OR6, —N(R6)2, —SR6, —SOR6, —SO2R6, —CO2R6, a fluorescent moiety, a radioisotope, or a therapeutic agent;
each R6 is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heterocycloalkyl, a fluorescent moiety, a radioisotope, or a therapeutic agent;
R9 is alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, heteroaryl, or heterocyclyl group, unsubstituted or optionally substituted with Ra and/or Rb; and
Ra and Rb are independently alkyl, OCH3, CF3, NH2, CH2NH2, F, Br, I,
A peptidomimetic macrocycle comprising an amino acid sequence of the formula:
X1-X2-X3-X4-X5-X6-X7-X8-X9-X10-X11-X12-X13-X14-X15-X16-X17-X18-X19-X20-X21-X22-X23-X24-X25-X26-X27-X28-X29-X30-X31-X32 (SEQ ID NO: 4)
wherein:
X1 is Val or absent;
X2 is Ile, Phe, or absent;
X3 is Asp, Arg, or absent;
X4 is Thr or absent;
X5 is Asp or absent;
X6 is Phe, Ala, Glu, Ser, Dpr, Asn, or absent;
X7 is Ile, Ala, Glu, Ser, or absent;
X8 is Asp, Ala, Ser, Dpr, or absent;
X9 is Glu, Ala, absent, or a cross-linked amino acid;
X10 is Glu, Ala, Ser, Dpr, Gln, or a cross-linked amino acid;
X11 is Val, Ala, Asp, Ser, Dpr, or a cross-linked amino acid;
X12 is Leu, Ala, Glu, Ser, pL, or a cross-linked amino acid;
X13 is Met, Nle, Ala, Asp, or a cross-linked amino acid;
X14 is Ser or a cross-linked amino acid;
X15 is Leu, Ala, Asp, Ser, or a cross-linked amino acid;
X16 is Val, Ala, Glu, Ser, pL, or a cross-linked amino acid;
X17 is Ile, Ala, Glu, Ser, Dpr, Bpa, or a cross-linked amino acid;
X18 is Glu or a cross-linked amino acid;
X19 is Met, Nle, Ala, Glu, Ser, Dpr, Bpa, or a cross-linked amino acid;
X20 is Gly, Ala, Glu, Ser, or a cross-linked amino acid;
X22 is Asp, Ala, Ser, or absent;
X23 is Arg, Ala, Glu, Ser, Dpr, or absent;
X24 is Ile, Ala, Glu, Ser, or absent;
X25 is Lys, Glu, or absent;
X26 is Glu or absent;
X27 is Leu or absent;
X28 is Pro or absent;
X29 is Glu, Gln, or absent;
X30 is Leu or absent;
X31 is Trp or absent; and
X32 is Leu or absent;
wherein the peptidomimetic macrocycle comprises at least one macrocycle-forming linker connecting at least one pair of amino acids selected from X1-X28;
L is a macrocycle-forming linker of the formula -L1-L2- or the formula
L1 and L2 are independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, cycloarylene, heterocycloarylene, or [—R4—K—R4-]n, each being optionally substituted with R5;
each the cross-linked amino acid is optionally substituted at the alpha carbon position with R1 or R2, wherein R1 and R2 are independently alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, cycloalkylalkyl, heteroalkyl, or heterocycloalkyl, each being optionally substituted with halo-;
each R4 is alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, arylene, or heteroarylene;
each K is O, S, SO, SO2, CO, or CO2;
each R5 is independently halogen, alkyl, —OR6, —N(R6)2, —SR6, —SOR6, —SO2R6, —CO2R6, a fluorescent moiety, a radioisotope, or a therapeutic agent;
each R6 is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heterocycloalkyl, a fluorescent moiety, a radioisotope, or a therapeutic agent;
R9 is alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, heteroaryl, or heterocyclyl group, unsubstituted or optionally substituted with Ra and/or Rb; and
Ra and Rb are independently alkyl, OCH3, CF3, NH2, CH2NH2, F, Br, I,
In some embodiments, the peptidomimetic macrocycle of the invention comprises one macrocycle-forming linker.
In some embodiments, the macrocycle-forming linker of the peptidomimetic macrocycle of the invention connects one of the following pairs of amino acids: X9 and X14, X9 and X16, X10 and X14, X10 and X17, X11 and X15, X11 and X18, X12 and X16, X12 and X19, X13 and X17, X13 and X20, X14 and X18, and X14 and X19. In some embodiments, the macrocycle-forming linker connects amino acids: X10 and X14. In some embodiments, the macrocycle-forming linker connects amino acids: X14 and X18.
In some embodiments, X9 is Glu. In some embodiments, X12 is Leu. In some embodiments, X13 is Nle or Met. In some embodiments, X16 is Val. In some embodiments, X18 is Glu. In some embodiments, X19 is Nle or Met. In some embodiments, X20 is Ala. In some embodiments, X21 is Leu. In some embodiments, X22 is Asp. In some embodiments, X24 is Ile. In some embodiments, X30 is Leu. In some embodiments, X31 is Trp.
In some embodiments, L1 and L2 are independently alkylene, alkenylene or alkynylene. In some embodiments, L1 and L2 are independently C3-C10 alkylene or alkenylene, for example C3-C6 alkylene or alkenylene. For example, L is
In some embodiments, L is
for example
In some embodiments, R1 and R2 are H. In some embodiments, R1 and R2 are independently alkyl, for example methyl.
In some embodiments, the present invention provides a peptidomimetic macrocycle comprising an amino acid sequence which is about 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% identical to an amino acid sequence of FIDEEVLMSLVIEMALDRI (SEQ ID NO: 5), for example an amino acid sequence of FIDEEVLM-Z-LVI-Z-MALDRI (SEQ ID NO: 6), wherein each Z is independently a cross-linked amino acid. In some embodiments, the peptidomimetic macrocycle is
or a pharmaceutically acceptable salt thereof.
In some embodiments, the present invention provides a peptidomimetic macrocycle comprising an amino acid sequence which is about 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% identical to an amino acid sequence of FIDEEVLNleSLVIENleALDRI (SEQ ID NO: 7), for example an amino acid sequence of FIDEEVLNle-Z-LVI-Z-NleALDRI (SEQ ID NO: 8), wherein each Z is independently a cross-linked amino acid. In some embodiments, the peptidomimetic macrocycle is
or a pharmaceutically acceptable salt thereof.
In some embodiments, the present invention provides a peptidomimetic macrocycle comprising an amino acid sequence which is about 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% identical to an amino acid sequence of FIDEEVLMSLVIEMGLDRIKELPELWL (SEQ ID NO: 9), for example an amino acid sequence of FIDEEVLM-Z-LVI-Z-MGLDRIKELPELWL (SEQ ID NO: 10), wherein each Z is independently a cross-linked amino acid.
In some embodiments, a peptidomimetic macrocycle of the invention has a formula X6-X7-X8-X9-X10-X11-X12-X13-X14-X15-X16-X17-X18-X19-X20-X21-X22-X23-X24-X25-X26-X27-X28 (SEQ ID NO: 11). In some embodiments, a macrocycle-forming linker of the peptidomimetic macrocycle of the invention connects one of the following pairs of amino acids: X10 and X14, X10 and X17, X11 and X18, X12 and X16, X12 and X19, and X14 and X18, for example X14 and X18. In some embodiments, X13 is Nle. In some embodiments, X19 is Nle. In some embodiments, X20 is Ala.
In some embodiments, a peptidomimetic macrocycle of the invention further comprises an amino acid sequence which is about 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% identical to an amino acid sequence of LLQGEELLRALDQV (SEQ ID NO: 12). In some embodiments, the peptidomimetic macrocycle comprises an amino acid sequence of LLQGEEL-Z-RAL-Z-QV (SEQ ID NO: 13), wherein each Z is independently a cross-linked amino acid. In some embodiments, X6 is linked to the amino acid sequence of LLQGEEL-Z-RAL-Z-QV (SEQ ID NO: 13). In some embodiments, the peptidomimetic macrocycle comprises an amino acid sequence of LLQGE-Z-LLRALD-Z-V (SEQ ID NO: 14), wherein each Z is independently a cross-linked amino acid. In some embodiments, X6 is linked to the amino acid sequence of LLQGEEL-Z-RAL-Z-QV (SEQ ID NO: 13).
In some embodiments, a peptidomimetic macrocycle of the invention further comprises an amino acid sequence which is about 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% identical to an amino acid sequence of QLTSYDCEVNA (SEQ ID NO: 15), for example an amino acid sequence of QLT-Z-YDAbu-Z-VNA (SEQ ID NO: 16), wherein each Z is independently a cross-linked amino acid. In some embodiments, X28 is linked to the amino acid sequence of QLT-Z-YDAbu-Z-VNA (SEQ ID NO: 16).
In some embodiments, the present invention provides a pharmaceutical composition comprising a peptidomimetic macrocycle of the invention and a pharmaceutically acceptable carrier.
In some embodiments, the present invention provides a method of reducing transcription of a gene in a cell, wherein transcription of the gene is mediated by interaction of Hypoxia-Inducible Factor 1α (HIF1α) with CREB-binding protein and/or p300, comprising contacting the cell with an effective amount of a peptidomimetic macrocycle of the invention. In some embodiments, the gene is selected from the group consisting of adenylate kinase 3, aldolase A, aldolase C, enolase 1, glucose transporter 1, glucose transporter 3, glyceraldehyde-3-phosphate dehydrogenase, hexokinase 1, hexokinase 2, insulin-like growth factor 2, IGF binding protein 1, IGF binding protein 3, lactate dehydrogenase A, phosphoglycerate kinase 1, pyruvate kinase M, p21, transforming growth factor β3, ceruloplasmin, erythropoietin, transferrin, transferrin receptor, αiB-adrenergic receptor, adrenomedullin, endothelin-1, heme oxygenase 1, nitric oxide synthase 2, plasminogen activator inhibitor 1, vascular endothelial growth factor, vascular endothelial growth factor receptor FLT-1, vascular endothelial growth factor receptor KDR/Flk-1, and p35srg.
In some embodiments, the present invention provides a method of treating or preventing in a subject in need thereof a disorder mediated by interaction of HIF1α with CREB-binding protein and/or p300, comprising administering to the subject an effective amount of a peptidomimetic macrocycle of the invention. In some embodiments, the disorder is selected from the group consisting of retinal ischemia, pulmonary hypertension, intrauterine growth retardation, diabetic retinopathy, age-related macular degeneration, diabetic macular edema, and cancer.
In some embodiments, the present invention provides a method of reducing or preventing angiogenesis in a tissue, comprising contacting the tissue with an effective amount of a peptidomimetic macrocycle of the invention. In some embodiments, the method is carried out in vivo. In some embodiments, the tissue is a tumor.
In some embodiments, the present invention provides a method of inducing apoptosis in a cell, comprising contacting the cell with an effective amount of a peptidomimetic macrocycle of the invention.
In some embodiments, the present invention provides a method of decreasing survival and/or proliferation of a cell, comprising contacting the cell with an effective amount of a peptidomimetic macrocycle of the invention. In some embodiments, the cell is cancerous or is contained in the endothelial vasculature of a tissue that contains cancerous cells.
In some embodiments, the present invention provides a method of treating cancer in a subject comprising administering to the subject an effective amount of a peptidomimetic macrocycle of the invention.
In some embodiments, the present invention provides a method of treating age-related macular degeneration or diabetic retinopathy in a subject comprising administering to the subject an effective amount of a peptidomimetic macrocycle of the invention.
In some embodiments, the present invention provides a method of treating a disorder caused by excessive angiogenesis in a subject comprising administering to the subject an effective amount of a peptidomimetic macrocycle of the invention.
In some embodiments, the present invention provides a method of modulating the activity of HIF1α in a subject comprising administering to the subject a peptidomimetic macrocycle of the invention.
In some embodiments, the present invention provides a method of antagonizing the interaction between CBP/p300 and HIF1α proteins in a subject comprising administering to the subject an effective amount of a peptidomimetic macrocycle of the invention.
In some embodiments, the present invention provides a method of identifying a potential ligand of CREB-binding protein and/or p300, comprising: providing a peptidomimetic macrocycle of the invention, contacting the peptidomimetic macrocycle with a test agent, and detecting whether the test agent selectively binds to the peptidomimetic macrocycle, wherein a test agent that selectively binds to the peptidomimetic macrocycle is identified as a potential ligand of CREB-binding protein and/or p300.
The novel features of the invention are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which:
The term “about” has the meaning as commonly understood by one of ordinary skill in the art. In some embodiments, the term “about” refers to ±10%. In some embodiments, the term “about” refers to ±5%.
As used herein, the term “macrocycle” refers to a molecule having a chemical structure including a ring or cycle formed by at least 9 covalently bonded atoms.
As used herein, the term “peptidomimetic macrocycle” or “crosslinked polypeptide” refers to a compound comprising a plurality of amino acid residues joined by a plurality of peptide bonds and at least one macrocycle-forming linker which forms a macrocycle between a first naturally-occurring or non-naturally-occurring amino acid residue (or analog) and a second naturally-occurring or non-naturally-occurring amino acid residue (or analog) within the same molecule. Peptidomimetic macrocycles include embodiments where the macrocycle-forming linker connects the α carbon of the first amino acid residue (or analog) to the α carbon of the second amino acid residue (or analog). The peptidomimetic macrocycles optionally include one or more non-peptide bonds between one or more amino acid residues and/or amino acid analog residues, and optionally include one or more non-naturally-occurring amino acid residues or amino acid analog residues in addition to any which form the macrocycle. A “corresponding uncrosslinked polypeptide” when referred to in the context of a peptidomimetic macrocycle is understood to relate to a polypeptide of the same length as the macrocycle and comprising the equivalent natural amino acids of the wild-type sequence corresponding to the macrocycle.
As used herein, the term “stability” refers to the maintenance of a defined secondary structure in solution by a peptidomimetic macrocycle of the invention as measured by circular dichroism, NMR or another biophysical measure, or resistance to proteolytic degradation in vitro or in vivo. Non-limiting examples of secondary structures contemplated in this invention are α-helices, 310 helices, β-turns, and β-pleated sheets.
As used herein, the term “helical stability” refers to the maintenance of a helical structure by a peptidomimetic macrocycle of the invention as measured by circular dichroism or NMR. For example, in some embodiments, the peptidomimetic macrocycles of the invention exhibit at least a 1.25, 1.5, 1.75 or 2-fold increase in α-helicity as determined by circular dichroism compared to a corresponding uncrosslinked macrocycle.
The term “amino acid” refers to a molecule containing both an amino group and a carboxyl group. Suitable amino acids include, without limitation, both the D- and L-isomers of the naturally-occurring amino acids, as well as non-naturally occurring amino acids prepared by organic synthesis or other metabolic routes. The term amino acid, as used herein, includes without limitation, α-amino acids, natural amino acids, non-natural amino acids, and amino acid analogs.
The term “α-amino acid” refers to a molecule containing both an amino group and a carboxyl group bound to a carbon which is designated the α-carbon.
The term “β-amino acid” refers to a molecule containing both an amino group and a carboxyl group in a β configuration.
The term “naturally occurring amino acid” refers to any one of the twenty amino acids commonly found in peptides synthesized in nature, and known by the one letter abbreviations A, R, N, C, D, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y and V.
The following table shows a summary of the properties of natural amino acids:
“Hydrophobic amino acids” include small hydrophobic amino acids and large hydrophobic amino acids. “Small hydrophobic amino acids” are glycine, alanine, proline, and analogs thereof. “Large hydrophobic amino acids” are valine, leucine, isoleucine, phenylalanine, methionine, tryptophan, tyrosine, and analogs thereof. “Polar amino acids” are serine, threonine, asparagine, glutamine, cysteine, and analogs thereof. “Charged amino acids” include positively charged amino acids and negatively charged amino acids. “Positively charged amino acids” include lysine, arginine, histidine, and analogs thereof. “Negatively charged amino acids” include aspartate, glutamate, and analogs thereof.
The term “amino acid analog” refers to a molecule which is structurally similar to an amino acid and which can be substituted for an amino acid in the formation of a peptidomimetic macrocycle. Amino acid analogs include, without limitation, f-amino acids and amino acids where the amino or carboxy group is substituted by a similarly reactive group (e.g., substitution of the primary amine with a secondary or tertiary amine, or substitution of the carboxy group with an ester).
The term “non-natural amino acid” refers to an amino acid which is not one of the twenty amino acids commonly found in peptides synthesized in nature, and known by the one letter abbreviations A, R, N, C, D, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y and V. Non-natural amino acids or amino acid analogs include, without limitation, structures according to the following:
Amino acid analogs include β-amino acid analogs. Examples of 1-amino acid analogs include, but are not limited to, the following: cyclic β-amino acid analogs; β-alanine; (R)-β-phenylalanine; (R)-1,2,3,4-tetrahydro-isoquinoline-3-acetic acid; (R)-3-amino-4-(1-naphthyl)-butyric acid; (R)-3-amino-4-(2,4-dichlorophenyl)butyric acid; (R)-3-amino-4-(2-chlorophenyl)-butyric acid; (R)-3-amino-4-(2-cyanophenyl)-butyric acid; (R)-3-amino-4-(2-fluorophenyl)-butyric acid; (R)-3-amino-4-(2-furyl)-butyric acid; (R)-3-amino-4-(2-methylphenyl)-butyric acid; (R)-3-amino-4-(2-naphthyl)-butyric acid; (R)-3-amino-4-(2-thienyl)-butyric acid; (R)-3-amino-4-(2-trifluoromethylphenyl)-butyric acid; (R)-3-amino-4-(3,4-dichlorophenyl)butyric acid; (R)-3-amino-4-(3,4-difluorophenyl)butyric acid; (R)-3-amino-4-(3-benzothienyl)-butyric acid; (R)-3-amino-4-(3-chlorophenyl)-butyric acid; (R)-3-amino-4-(3-cyanophenyl)-butyric acid; (R)-3-amino-4-(3-fluorophenyl)-butyric acid; (R)-3-amino-4-(3-methylphenyl)-butyric acid; (R)-3-amino-4-(3-pyridyl)-butyric acid; (R)-3-amino-4-(3-thienyl)-butyric acid; (R)-3-amino-4-(3-trifluoromethylphenyl)-butyric acid; (R)-3-amino-4-(4-bromophenyl)-butyric acid; (R)-3-amino-4-(4-chlorophenyl)-butyric acid; (R)-3-amino-4-(4-cyanophenyl)-butyric acid; (R)-3-amino-4-(4-fluorophenyl)-butyric acid; (R)-3-amino-4-(4-iodophenyl)-butyric acid; (R)-3-amino-4-(4-methylphenyl)-butyric acid; (R)-3-amino-4-(4-nitrophenyl)-butyric acid; (R)-3-amino-4-(4-pyridyl)-butyric acid; (R)-3-amino-4-(4-trifluoromethylphenyl)-butyric acid; (R)-3-amino-4-pentafluoro-phenylbutyric acid; (R)-3-amino-5-hexenoic acid; (R)-3-amino-5-hexynoic acid; (R)-3-amino-5-phenylpentanoic acid; (R)-3-amino-6-phenyl-5-hexenoic acid; (S)-1,2,3,4-tetrahydro-isoquinoline-3-acetic acid; (S)-3-amino-4-(1-naphthyl)-butyric acid; (S)-3-amino-4-(2,4-dichlorophenyl)butyric acid; (S)-3-amino-4-(2-chlorophenyl)-butyric acid; (S)-3-amino-4-(2-cyanophenyl)-butyric acid; (S)-3-amino-4-(2-fluorophenyl)-butyric acid; (S)-3-amino-4-(2-furyl)-butyric acid; (S)-3-amino-4-(2-methylphenyl)-butyric acid; (S)-3-amino-4-(2-naphthyl)-butyric acid; (S)-3-amino-4-(2-thienyl)-butyric acid; (S)-3-amino-4-(2-trifluoromethylphenyl)-butyric acid; (S)-3-amino-4-(3,4-dichlorophenyl)butyric acid; (S)-3-amino-4-(3,4-difluorophenyl)butyric acid; (S)-3-amino-4-(3-benzothienyl)-butyric acid; (S)-3-amino-4-(3-chlorophenyl)-butyric acid; (S)-3-amino-4-(3-cyanophenyl)-butyric acid; (S)-3-amino-4-(3-fluorophenyl)-butyric acid; (S)-3-amino-4-(3-methylphenyl)-butyric acid; (S)-3-amino-4-(3-pyridyl)-butyric acid; (S)-3-amino-4-(3-thienyl)-butyric acid; (S)-3-amino-4-(3-trifluoromethylphenyl)-butyric acid; (S)-3-amino-4-(4-bromophenyl)-butyric acid; (S)-3-amino-4-(4-chlorophenyl)-butyric acid; (S)-3-amino-4-(4-cyanophenyl)-butyric acid; (S)-3-amino-4-(4-fluorophenyl)-butyric acid; (S)-3-amino-4-(4-iodophenyl)-butyric acid; (S)-3-amino-4-(4-methylphenyl)-butyric acid; (S)-3-amino-4-(4-nitrophenyl)-butyric acid; (S)-3-amino-4-(4-pyridyl)-butyric acid; (S)-3-amino-4-(4-trifluoromethylphenyl)-butyric acid; (S)-3-amino-4-pentafluoro-phenylbutyric acid; (S)-3-amino-5-hexenoic acid; (S)-3-amino-5-hexynoic acid; (S)-3-amino-5-phenylpentanoic acid; (S)-3-amino-6-phenyl-5-hexenoic acid; 1,2,5,6-tetrahydropyridine-3-carboxylic acid; 1,2,5,6-tetrahydropyridine-4-carboxylic acid; 3-amino-3-(2-chlorophenyl)-propionic acid; 3-amino-3-(2-thienyl)-propionic acid; 3-amino-3-(3-bromophenyl)-propionic acid; 3-amino-3-(4-chlorophenyl)-propionic acid; 3-amino-3-(4-methoxyphenyl)-propionic acid; 3-amino-4,4,4-trifluoro-butyric acid; 3-aminoadipic acid; D-β-phenylalanine; β-leucine; L-β-homoalanine; L-β-homoaspartic acid γ-benzyl ester; L-β-homoglutamic acid δ-benzyl ester; L-β-homoisoleucine; L-β-homoleucine; L-β-homomethionine; L-β-homophenylalanine; L-β-homoproline; L-β-homotryptophan; L-β-homovaline; L-Nω-benzyloxycarbonyl-β-homolysine; Nω-L-β-homoarginine; O-benzyl-L-β-homohydroxyproline; O-benzyl-L-β-homoserine; O-benzyl-L-β-homothreonine; O-benzyl-L-β-homotyrosine; γ-trityl-L-β-homoasparagine; (R)-β-phenylalanine; L-β-homoaspartic acid γ-t-butyl ester; L-β-homoglutamic acid δ-t-butyl ester; L-Nω-β-homolysine; Nδ-trityl-L-β-homoglutamine; Nω-2,2,4,6,7-pentamethyl-dihydrobenzofuran-5-sulfonyl-L-β-homoarginine; O-t-butyl-L-β-homohydroxy-proline; O-t-butyl-L-β-homoserine; O-t-butyl-L-β-homothreonine; O-t-butyl-L-β-homotyrosine; 2-aminocyclopentane carboxylic acid; and 2-aminocyclohexane carboxylic acid.
Amino acid analogs include analogs of alanine, valine, glycine or leucine. Examples of amino acid analogs of alanine, valine, glycine, and leucine include, but are not limited to, the following: α-methoxyglycine; α-allyl-L-alanine; α-aminoisobutyric acid; α-methyl-leucine; β-(1-naphthyl)-D-alanine; β-(1-naphthyl)-L-alanine; β-(2-naphthyl)-D-alanine; β-(2-naphthyl)-L-alanine; β-(2-pyridyl)-D-alanine; β-(2-pyridyl)-L-alanine; β-(2-thienyl)-D-alanine; β-(2-thienyl)-L-alanine; β-(3-benzothienyl)-D-alanine; β-(3-benzothienyl)-L-alanine; β-(3-pyridyl)-D-alanine; β-(3-pyridyl)-L-alanine; β-(4-pyridyl)-D-alanine; β-(4-pyridyl)-L-alanine; β-chloro-L-alanine; β-cyano-L-alanin; β-cyclohexyl-D-alanine; β-cyclohexyl-L-alanine; β-cyclopenten-1-yl-alanine; β-cyclopentyl-alanine; β-cyclopropyl-L-Ala-OH.dicyclohexylammonium salt; β-t-butyl-D-alanine; β-t-butyl-L-alanine; γ-aminobutyric acid; L-α,β-diaminopropionic acid; 2,4-dinitro-phenylglycine; 2,5-dihydro-D-phenylglycine; 2-amino-4,4,4-trifluorobutyric acid; 2-fluoro-phenylglycine; 3-amino-4,4,4-trifluoro-butyric acid; 3-fluoro-valine; 4,4,4-trifluoro-valine; 4,5-dehydro-L-leu-OH.dicyclohexylammonium salt; 4-fluoro-D-phenylglycine; 4-fluoro-L-phenylglycine; 4-hydroxy-D-phenylglycine; 5,5,5-trifluoro-leucine; 6-aminohexanoic acid; cyclopentyl-D-Gly-OH.dicyclohexylammonium salt; cyclopentyl-Gly-OH.dicyclohexylammonium salt; D-α,β-diaminopropionic acid; D-α-aminobutyric acid; D-α-t-butylglycine; D-(2-thienyl)glycine; D-(3-thienyl)glycine; D-2-aminocaproic acid; D-2-indanylglycine; D-allylglycine*dicyclohexylammonium salt; D-cyclohexylglycine; D-norvaline; D-phenylglycine; β-aminobutyric acid; β-aminoisobutyric acid; (2-bromophenyl)glycine; (2-methoxyphenyl)glycine; (2-methylphenyl)glycine; (2-thiazoyl)glycine; (2-thienyl)glycine; 2-amino-3-(dimethylamino)-propionic acid; L-α,β-diaminopropionic acid; L-α-aminobutyric acid; L-α-t-butylglycine; L-(3-thienyl)glycine; L-2-amino-3-(dimethylamino)-propionic acid; L-2-aminocaproic acid dicyclohexyl-ammonium salt; L-2-indanylglycine; L-allylglycine*dicyclohexyl ammonium salt; L-cyclohexylglycine; L-phenylglycine; L-propargylglycine; L-norvaline; N-α-aminomethyl-L-alanine; D-α,γ-diaminobutyric acid; L-α,γ-diaminobutyric acid; β-cyclopropyl-L-alanine; (N-β-(2,4-dinitrophenyl))-L-α,β-diaminopropionic acid; (N-β-1-(4,4-dimethyl-2,6-dioxocyclohex-1-ylidene)ethyl)-D-α,β-diaminopropionic acid; (N-β-1-(4,4-dimethyl-2,6-dioxocyclohex-1-ylidene)ethyl)-L-α,β-diaminopropionic acid; (N-β-4-methyltrityl)-L-α,β-diaminopropionic acid; (N-3-allyloxycarbonyl)-L-α,β-diaminopropionic acid; (N-γ-1-(4,4-dimethyl-2,6-dioxocyclohex-1-ylidene)ethyl)-D-α,γ-diaminobutyric acid; (N-γ-1-(4,4-dimethyl-2,6-dioxocyclohex-1-ylidene)ethyl)-L-α,γ-diaminobutyric acid; (N-γ-4-methyltrityl)-D-α,γ-diaminobutyric acid; (N-γ-4-methyltrityl)-L-α,γ-diaminobutyric acid; (N-7-allyloxycarbonyl)-L-α,γ-diaminobutyric acid; D-α,γ-diaminobutyric acid; 4,5-dehydro-L-leucine; cyclopentyl-D-Gly-OH; cyclopentyl-Gly-OH; D-allylglycine; D-homocyclohexylalanine; L-1-pyrenylalanine; L-2-aminocaproic acid; L-allylglycine; L-homocyclohexylalanine; and N-(2-hydroxy-4-methoxy-Bzl)-Gly-OH.
Amino acid analogs include analogs of arginine or lysine. Examples of amino acid analogs of arginine and lysine include, but are not limited to, the following: citrulline; L-2-amino-3-guanidinopropionic acid; L-2-amino-3-ureidopropionic acid; L-citrulline; Lys(Me)2-OH; Lys(N3)—OH; Nδ-benzyloxycarbonyl-L-omithine; Nω-nitro-D-arginine; Nω-nitro-L-arginine; α-methyl-omithine; 2,6-diaminoheptanedioic acid; L-omithine; (Nδ-1-(4,4-dimethyl-2,6-dioxo-cyclohex-1-ylidene)ethyl)-D-omithine; (Nδ-1-(4,4-dimethyl-2,6-dioxo-cyclohex-1-ylidene)ethyl)-L-omithine; (N6-4-methyltrityl)-D-omithine; (N6-4-methyltrityl)-L-omithine; D-omithine; L-omithine; Arg(MeXPbf)-OH; Arg(Me)2-OH (asymmetrical); Arg(Me)2-OH (symmetrical); Lys(ivDde)-OH; Lys(Me)2-OH.HCl; Lys(Me3)-OH chloride; Nω-nitro-D-arginine; and Nω-nitro-L-arginine.
Amino acid analogs include analogs of aspartic or glutamic acids. Examples of amino acid analogs of aspartic and glutamic acids include, but are not limited to, the following: α-methyl-D-aspartic acid; α-methyl-glutamic acid; α-methyl-L-aspartic acid; γ-methylene-glutamic acid; (N-γ-ethyl)-L-glutamine; [N-α-(4-aminobenzoyl)]-L-glutamic acid; 2,6-diaminopimelic acid; L-α-aminosuberic acid; D-2-aminoadipic acid; D-α-aminosuberic acid; α-aminopimelic acid; iminodiacetic acid; L-2-aminoadipic acid; threo-β-methyl-aspartic acid; γ-carboxy-D-glutamic acid γ,γ-di-t-butyl ester; γ-carboxy-L-glutamic acid γ,γ-di-t-butyl ester; Glu(OAll)-OH; L-Asu(OtBu)—OH; and pyroglutamic acid.
Amino acid analogs include analogs of cysteine and methionine. Examples of amino acid analogs of cysteine and methionine include, but are not limited to, Cys(famesyl)-OH, Cys(famesyl)-OMe, α-methyl-methionine, Cys(2-hydroxyethyl)-OH, Cys(3-aminopropyl)-OH, 2-amino-4-(ethylthio)butyric acid, buthionine, buthioninesulfoximine, ethionine, methionine methylsulfonium chloride, selenomethionine, cysteic acid, [2-(4-pyridyl)ethyl]-DL-penicillamine, [2-(4-pyridyl)ethyl]-L-cysteine, 4-methoxybenzyl-D-penicillamine, 4-methoxybenzyl-L-penicillamine, 4-methylbenzyl-D-penicillamine, 4-methylbenzyl-L-penicillamine, benzyl-D-cysteine, benzyl-L-cysteine, benzyl-DL-homocysteine, carbamoyl-L-cysteine, carboxyethyl-L-cysteine, carboxymethyl-L-cysteine, diphenylmethyl-L-cysteine, ethyl-L-cysteine, methyl-L-cysteine, t-butyl-D-cysteine, trityl-L-homocysteine, trityl-D-penicillamine, cystathionine, homocystine, L-homocystine, (2-aminoethyl)-L-cysteine, seleno-L-cystine, cystathionine, Cys(StBu)—OH, and acetamidomethyl-D-penicillamine.
Amino acid analogs include analogs of phenylalanine and tyrosine. Examples of amino acid analogs of phenylalanine and tyrosine include β-methyl-phenylalanine, β-hydroxyphenylalanine, α-methyl-3-methoxy-DL-phenylalanine, α-methyl-D-phenylalanine, α-methyl-L-phenylalanine, 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid, 2,4-dichloro-phenylalanine, 2-(trifluoromethyl)-D-phenylalanine, 2-(trifluoromethyl)-L-phenylalanine, 2-bromo-D-phenylalanine, 2-bromo-L-phenylalanine, 2-chloro-D-phenylalanine, 2-chloro-L-phenylalanine, 2-cyano-D-phenylalanine, 2-cyano-L-phenylalanine, 2-fluoro-D-phenylalanine, 2-fluoro-L-phenylalanine, 2-methyl-D-phenylalanine, 2-methyl-L-phenylalanine, 2-nitro-D-phenylalanine, 2-nitro-L-phenylalanine, 2;4;5-trihydroxy-phenylalanine, 3,4,5-trifluoro-D-phenylalanine, 3,4,5-trifluoro-L-phenylalanine, 3,4-dichloro-D-phenylalanine, 3,4-dichloro-L-phenylalanine, 3,4-difluoro-D-phenylalanine, 3,4-difluoro-L-phenylalanine, 3,4-dihydroxy-L-phenylalanine, 3,4-dimethoxy-L-phenylalanine, 3,5,3′-triiodo-L-thyronine, 3,5-diiodo-D-tyrosine, 3,5-diiodo-L-tyrosine, 3,5-diiodo-L-thyronine, 3-(trifluoromethyl)-D-phenylalanine, 3-(trifluoromethyl)-L-phenylalanine, 3-amino-L-tyrosine, 3-bromo-D-phenylalanine, 3-bromo-L-phenylalanine, 3-chloro-D-phenylalanine, 3-chloro-L-phenylalanine, 3-chloro-L-tyrosine, 3-cyano-D-phenylalanine, 3-cyano-L-phenylalanine, 3-fluoro-D-phenylalanine, 3-fluoro-L-phenylalanine, 3-fluoro-tyrosine, 3-iodo-D-phenylalanine, 3-iodo-L-phenylalanine, 3-iodo-L-tyrosine, 3-methoxy-L-tyrosine, 3-methyl-D-phenylalanine, 3-methyl-L-phenylalanine, 3-nitro-D-phenylalanine, 3-nitro-L-phenylalanine, 3-nitro-L-tyrosine, 4-(trifluoromethyl)-D-phenylalanine, 4-(trifluoromethyl)-L-phenylalanine, 4-amino-D-phenylalanine, 4-amino-L-phenylalanine, 4-benzoyl-D-phenylalanine, 4-benzoyl-L-phenylalanine, 4-bis(2-chloroethyl)amino-L-phenylalanine, 4-bromo-D-phenylalanine, 4-bromo-L-phenylalanine, 4-chloro-D-phenylalanine, 4-chloro-L-phenylalanine, 4-cyano-D-phenylalanine, 4-cyano-L-phenylalanine, 4-fluoro-D-phenylalanine, 4-fluoro-L-phenylalanine, 4-iodo-D-phenylalanine, 4-iodo-L-phenylalanine, homophenylalanine, thyroxine, 3,3-diphenylalanine, thyronine, ethyl-tyrosine, and methyl-tyrosine.
Amino acid analogs include analogs of proline. Examples of amino acid analogs of proline include, but are not limited to, 3,4-dehydro-proline, 4-fluoro-proline, cis-4-hydroxy-proline, thiazolidine-2-carboxylic acid, and trans-4-fluoro-proline.
Amino acid analogs include analogs of serine and threonine. Examples of amino acid analogs of serine and threonine include, but are not limited to, 3-amino-2-hydroxy-5-methylhexanoic acid, 2-amino-3-hydroxy-4-methylpentanoic acid, 2-amino-3-ethoxybutanoic acid, 2-amino-3-methoxybutanoic acid, 4-amino-3-hydroxy-6-methylheptanoic acid, 2-amino-3-benzyloxypropionic acid, 2-amino-3-benzyloxypropionic acid, 2-amino-3-ethoxypropionic acid, 4-amino-3-hydroxybutanoic acid, and α-methylserine.
Amino acid analogs include analogs of tryptophan. Examples of amino acid analogs of tryptophan include, but are not limited to, the following: α-methyl-tryptophan; 3-(3-benzothienyl)-D-alanine; β-(3-benzothienyl)-L-alanine; 1-methyl-tryptophan; 4-methyl-tryptophan; 5-benzyloxy-tryptophan; 5-bromo-tryptophan; 5-chloro-tryptophan; 5-fluoro-tryptophan; 5-hydroxy-tryptophan; 5-hydroxy-L-tryptophan; 5-methoxy-tryptophan; 5-methoxy-L-tryptophan; 5-methyl-tryptophan; 6-bromo-tryptophan; 6-chloro-D-tryptophan; 6-chloro-tryptophan; 6-fluoro-tryptophan; 6-methyl-tryptophan; 7-benzyloxy-tryptophan; 7-bromo-tryptophan; 7-methyl-tryptophan; D-1,2,3,4-tetrahydro-norharman-3-carboxylic acid; 6-methoxy-1,2,3,4-tetrahydronorharman-1-carboxylic acid; 7-azatryptophan; L-1,2,3,4-tetrahydro-norharman-3-carboxylic acid; 5-methoxy-2-methyl-tryptophan; and 6-chloro-L-tryptophan.
In some embodiments, amino acid analogs are racemic. In some embodiments, the D isomer of the amino acid analog is used. In some embodiments, the L isomer of the amino acid analog is used. In other embodiments, the amino acid analog comprises chiral centers that are in the R or S configuration. In still other embodiments, the amino group(s) of a β-amino acid analog is substituted with a protecting group, e.g., tert-butyloxycarbonyl (BOC group), 9-fluorenylmethyloxycarbonyl (FMOC), tosyl, and the like. In yet other embodiments, the carboxylic acid functional group of a β-amino acid analog is protected, e.g., as its ester derivative. In some embodiments the salt of the amino acid analog is used.
A “non-essential” amino acid residue is a residue that can be altered from the wild-type sequence of a polypeptide without abolishing or substantially abolishing its essential biological or biochemical activity (e.g., receptor binding or activation). An “essential” amino acid residue is a residue that, when altered from the wild-type sequence of the polypeptide, results in abolishing or substantially abolishing the polypeptide's essential biological or biochemical activity.
A “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., K, R, H), acidic side chains (e.g., D, E), uncharged polar side chains (e.g., G, N, Q, S, T, Y, C), nonpolar side chains (e.g., A, V, L, I, P, F, M, W), beta-branched side chains (e.g., T, V, I) and aromatic side chains (e.g., Y, F, W, H). Thus, a predicted nonessential amino acid residue in a polypeptide, for example, is replaced with another amino acid residue from the same side chain family. Other examples of acceptable substitutions are substitutions based on isosteric considerations (e.g. norleucine for methionine) or other properties (e.g. 2-thienylalanine for phenylalanine).
The term “capping group” refers to the chemical moiety occurring at either the carboxy or amino terminus of the polypeptide chain of the subject peptidomimetic macrocycle. The capping group of a carboxy terminus includes an unmodified carboxylic acid (ie —COOH) or a carboxylic acid with a substituent. For example, the carboxy terminus can be substituted with an amino group to yield a carboxamide at the C-terminus. Various substituents include but are not limited to primary and secondary amines, including pegylated secondary amines. Representative secondary amine capping groups for the C-terminus include:
The capping group of an amino terminus includes an unmodified amine (ie —NH2) or an amine with a substituent. For example, the amino terminus can be substituted with an acyl group to yield a carboxamide at the N-terminus. Various substituents include but are not limited to substituted acyl groups, including C1-C6 carbonyls, C7-C30 carbonyls, and pegylated carbamates. Representative capping groups for the N-terminus include:
The term “member” as used herein in conjunction with macrocycles or macrocycle-forming linkers refers to the atoms that form or can form the macrocycle, and excludes substituent or side chain atoms. By analogy, cyclodecane, 1,2-difluoro-decane and 1,3-dimethyl cyclodecane are all considered ten-membered macrocycles as the hydrogen or fluoro substituents or methyl side chains do not participate in forming the macrocycle.
The symbol “” when used as part of a molecular structure refers to a single bond or a trans or cis double bond.
The term “amino acid side chain” refers to a moiety attached to the α-carbon (or another backbone atom) in an amino acid. For example, the amino acid side chain for alanine is methyl, the amino acid side chain for phenylalanine is phenylmethyl, the amino acid side chain for cysteine is thiomethyl, the amino acid side chain for aspartate is carboxymethyl, the amino acid side chain for tyrosine is 4-hydroxyphenylmethyl, etc. Other non-naturally occurring amino acid side chains are also included, for example, those that occur in nature (e.g., an amino acid metabolite) or those that are made synthetically (e.g., an α,α di-substituted amino acid).
The term “α,α di-substituted amino” acid refers to a molecule or moiety containing both an amino group and a carboxyl group bound to a carbon (the α-carbon) that is attached to two natural or non-natural amino acid side chains.
The term “polypeptide” encompasses two or more naturally or non-naturally-occurring amino acids joined by a covalent bond (e.g., an amide bond). Polypeptides as described herein include full length proteins (e.g., fully processed proteins) as well as shorter amino acid sequences (e.g., fragments of naturally-occurring proteins or synthetic polypeptide fragments).
The term “macrocyclization reagent” or “macrocycle-forming reagent” as used herein refers to any reagent which may be used to prepare a peptidomimetic macrocycle of the invention by mediating the reaction between two reactive groups. Reactive groups may be, for example, an azide and alkyne, in which case macrocyclization reagents include, without limitation, Cu reagents such as reagents which provide a reactive Cu(I) species, such as CuBr, CuI or CuOTf, as well as Cu(II) salts such as Cu(CO2CH3)2, CuSO4, and CuCl2 that can be converted in situ to an active Cu(I) reagent by the addition of a reducing agent such as ascorbic acid or sodium ascorbate. Macrocyclization reagents may additionally include, for example, Ru reagents known in the art such as Cp*RuCl(PPh3)2, [Cp*RuCl]4 or other Ru reagents which may provide a reactive Ru(II) species. In other cases, the reactive groups are terminal olefins. In such embodiments, the macrocyclization reagents or macrocycle-forming reagents are metathesis catalysts including, but not limited to, stabilized, late transition metal carbene complex catalysts such as Group VIII transition metal carbene catalysts. For example, such catalysts are Ru and Os metal centers having a +2 oxidation state, an electron count of 16 and pentacoordinated. In other examples, catalysts have W or Mo centers. Various catalysts are disclosed in Grubbs et al., “Ring Closing Metathesis and Related Processes in Organic Synthesis” Acc. Chem. Res. 1995, 28, 446-452, and U.S. Pat. Nos. 5,811,515; 7,932,397; U.S. Application No. 2011/0065915; U.S. Application No. 2011/0245477; Yu et al., “Synthesis of Macrocyclic Natural Products by Catalyst-Controlled Stereoselective Ring-Closing Metathesis,” Nature 2011, 479, 88; and Peryshkov et al., “Z-Selective Olefin Metathesis Reactions Promoted by Tungsten Oxo Alkylidene Complexes,” J. Am. Chem. Soc. 2011, 133, 20754. In yet other cases, the reactive groups are thiol groups. In such embodiments, the macrocyclization reagent is, for example, a linker functionalized with two thiol-reactive groups such as halogen groups.
The term “halo” or “halogen” refers to fluorine, chlorine, bromine or iodine or a radical thereof.
The term “alkyl” refers to a hydrocarbon chain that is a straight chain or branched chain, containing the indicated number of carbon atoms. For example, C1-C10 indicates that the group has from 1 to 10 (inclusive) carbon atoms in it. In the absence of any numerical designation, “alkyl” is a chain (straight or branched) having 1 to 20 (inclusive) carbon atoms in it.
The term “alkylene” refers to a divalent alkyl (i.e., —R—).
The term “alkenyl” refers to a hydrocarbon chain that is a straight chain or branched chain having one or more carbon-carbon double bonds. The alkenyl moiety contains the indicated number of carbon atoms. For example, C2-C10 indicates that the group has from 2 to 10 (inclusive) carbon atoms in it. The term “lower alkenyl” refers to a C2-C6 alkenyl chain. In the absence of any numerical designation, “alkenyl” is a chain (straight or branched) having 2 to 20 (inclusive) carbon atoms in it.
The term “alkynyl” refers to a hydrocarbon chain that is a straight chain or branched chain having one or more carbon-carbon triple bonds. The alkynyl moiety contains the indicated number of carbon atoms. For example, C2-C10 indicates that the group has from 2 to 10 (inclusive) carbon atoms in it. The term “lower alkynyl” refers to a C2-C6 alkynyl chain. In the absence of any numerical designation, “alkynyl” is a chain (straight or branched) having 2 to 20 (inclusive) carbon atoms in it.
The term “aryl” refers to a 6-carbon monocyclic or 10-carbon bicyclic aromatic ring system wherein 0, 1, 2, 3, or 4 atoms of each ring are substituted by a substituent. Examples of aryl groups include phenyl, naphthyl and the like. The term “arylalkoxy” refers to an alkoxy substituted with aryl.
“Arylalkyl” refers to an aryl group, as defined above, wherein one of the aryl group's hydrogen atoms has been replaced with a C1-C5 alkyl group, as defined above. Representative examples of an arylalkyl group include, but are not limited to, 2-methylphenyl, 3-methylphenyl, 4-methylphenyl, 2-ethylphenyl, 3-ethylphenyl, 4-ethylphenyl, 2-propylphenyl, 3-propylphenyl, 4-propylphenyl, 2-butylphenyl, 3-butylphenyl, 4-butylphenyl, 2-pentylphenyl, 3-pentylphenyl, 4-pentylphenyl, 2-isopropylphenyl, 3-isopropylphenyl, 4-isopropylphenyl, 2-isobutylphenyl, 3-isobutylphenyl, 4-isobutylphenyl, 2-sec-butylphenyl, 3-sec-butylphenyl, 4-sec-butylphenyl, 2-t-butylphenyl, 3-t-butylphenyl and 4-t-butylphenyl.
“Arylamido” refers to an aryl group, as defined above, wherein one of the aryl group's hydrogen atoms has been replaced with one or more —C(O)NH2 groups. Representative examples of an arylamido group include 2-C(O)NH2-phenyl, 3-C(O)NH2-phenyl, 4-C(O)NH2-phenyl, 2-C(O)NH2-pyridyl, 3-C(O)NH2-pyridyl, and 4-C(O)NH2-pyridyl,
“Alkylheterocycle” refers to a C1-C5 alkyl group, as defined above, wherein one of the C1-C5 alkyl group's hydrogen atoms has been replaced with a heterocycle. Representative examples of an alkylheterocycle group include, but are not limited to, —CH2CH2-morpholine, —CH2CH2-piperidine, —CH2CH2CH2-morpholine, and —CH2CH2CH2-imidazole.
“Alkylamido” refers to a C1-C5 alkyl group, as defined above, wherein one of the C1-C5 alkyl group's hydrogen atoms has been replaced with a —C(O)NH2 group. Representative examples of an alkylamido group include, but are not limited to, —CH2—C(O)NH2, —CH2CH2—C(O)NH2, —CH2CH2CH2C(O)NH2, —CH2CH2CH2CH2C(O)NH2, —CH2CH2CH2CH2CH2C(O)NH2, —CH2CH(C(O)NH2)CH3, —CH2CH(C(O)NH2)CH2CH3, —CH(C(O)NH2)CH2CH3, —C(CH3)2CH2C(O)NH2, —CH2—CH2—NH—C(O)—CH3, —CH2—CH2—NH—C(O)—CH3—CH3, and —CH2—CH2—NH—C(O)—CH═CH2.
“Alkanol” refers to a C1-C5 alkyl group, as defined above, wherein one of the C1-C5 alkyl group's hydrogen atoms has been replaced with a hydroxyl group. Representative examples of an alkanol group include, but are not limited to, —CH2OH, —CH2CH2OH, —CH2CH2CH2OH, —CH2CH2CH2CH2OH, —CH2CH2CH2CH2CH2OH, —CH2CH(OH)CH3, —CH2CH(OH)CH2CH3, —CH(OH)CH3 and —C(CH3)2CH2OH.
“Alkylcarboxy” refers to a C1-C5 alkyl group, as defined above, wherein one of the C1-C5 alkyl group's hydrogen atoms has been replaced with a —COOH group. Representative examples of an alkylcarboxy group include, but are not limited to, —CH2COOH, —CH2CH2COOH, —CH2CH2CH2COOH, —CH2CH2CH2CH2COOH, —CH2CH(COOH)CH3, —CH2CH2CH2CH2CH2COOH, —CH2CH(COOH)CH2CH3, —CH(COOH)CH2CH3 and —C(CH3)2CH2COOH.
The term “cycloalkyl” as employed herein includes saturated and partially unsaturated cyclic hydrocarbon groups having 3 to 12 carbons, preferably 3 to 8 carbons, and more preferably 3 to 6 carbons, wherein the cycloalkyl group additionally is optionally substituted. Some cycloalkyl groups include, without limitation, cyclopropyl, cyclobutyl, cyclopentyl, cyclopentenyl, cyclohexyl, cyclohexenyl, cycloheptyl, and cyclooctyl.
The term “heteroaryl” refers to an aromatic 5-8 membered monocyclic, 8-12 membered bicyclic, or 11-14 membered tricyclic ring system having 1-3 heteroatoms if monocyclic, 1-6 heteroatoms if bicyclic, or 1-9 heteroatoms if tricyclic, said heteroatoms selected from O, N, or S (e.g., carbon atoms and 1-3, 1-6, or 1-9 heteroatoms of O, N, or S if monocyclic, bicyclic, or tricyclic, respectively), wherein 0, 1, 2, 3, or 4 atoms of each ring are substituted by a substituent. Examples of heteroaryl groups include pyridyl, furyl or furanyl, imidazolyl, benzimidazolyl, pyrimidinyl, thiophenyl or thienyl, quinolinyl, indolyl, thiazolyl, and the like.
The term “heteroarylalkyl” or the term “heteroaralkyl” refers to an alkyl substituted with a heteroaryl. The term “heteroarylalkoxy” refers to an alkoxy substituted with heteroaryl.
The term “heteroarylalkyl” or the term “heteroaralkyl” refers to an alkyl substituted with a heteroaryl. The term “heteroarylalkoxy” refers to an alkoxy substituted with heteroaryl.
The term “heterocyclyl” refers to a nonaromatic 5-8 membered monocyclic, 8-12 membered bicyclic, or 11-14 membered tricyclic ring system having 1-3 heteroatoms if monocyclic, 1-6 heteroatoms if bicyclic, or 1-9 heteroatoms if tricyclic, said heteroatoms selected from O, N, or S (e.g., carbon atoms and 1-3, 1-6, or 1-9 heteroatoms of O, N, or S if monocyclic, bicyclic, or tricyclic, respectively), wherein 0, 1, 2 or 3 atoms of each ring are substituted by a substituent. Examples of heterocyclyl groups include piperazinyl, pyrrolidinyl, dioxanyl, morpholinyl, tetrahydrofuranyl, and the like.
The term “substituent” refers to a group replacing a second atom or group such as a hydrogen atom on any molecule, compound or moiety. Suitable substituents include, without limitation, halo, hydroxy, mercapto, oxo, nitro, haloalkyl, alkyl, alkaryl, aryl, aralkyl, alkoxy, thioalkoxy, aryloxy, amino, alkoxycarbonyl, amido, carboxy, alkanesulfonyl, alkylcarbonyl, and cyano groups.
In some embodiments, the compounds of this invention contain one or more asymmetric centers and thus occur as racemates and racemic mixtures, single enantiomers, individual diastereomers and diastereomeric mixtures. All such isomeric forms of these compounds are included in the present invention unless expressly provided otherwise. In some embodiments, the compounds of this invention are also represented in multiple tautomeric forms, in such instances, the invention includes all tautomeric forms of the compounds described herein (e.g., if alkylation of a ring system results in alkylation at multiple sites, the invention includes all such reaction products). All such isomeric forms of such compounds are included in the present invention unless expressly provided otherwise. All crystal forms of the compounds described herein are included in the present invention unless expressly provided otherwise.
As used herein, the terms “increase” and “decrease” mean, respectively, to cause a statistically significantly (i.e., p<0.1) increase or decrease of at least 5%.
As used herein, the recitation of a numerical range for a variable is intended to convey that the variable is equal to any of the values within that range. Thus, for a variable which is inherently discrete, the variable is equal to any integer value within the numerical range, including the end-points of the range. Similarly, for a variable which is inherently continuous, the variable is equal to any real value within the numerical range, including the end-points of the range. As an example, and without limitation, a variable which is described as having values between 0 and 2 takes the values 0, 1 or 2 if the variable is inherently discrete, and takes the values 0.0, 0.1, 0.01, 0.001, or any other real values ≥0 and ≤2 if the variable is inherently continuous.
As used herein, unless specifically indicated otherwise, the word “or” is used in the inclusive sense of “and/or” and not the exclusive sense of “either/or.”
The term “on average” represents the mean value derived from performing at least three independent replicates for each data point.
The term “biological activity” encompasses structural and functional properties of a macrocycle of the invention. Biological activity is, for example, structural stability, alpha-helicity, affinity for a target, resistance to proteolytic degradation, cell penetrability, intracellular stability, in vivo stability, or any combination thereof.
The details of one or more particular embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.
Peptidomimetic Macrocycles of the InventionThe present invention provides pharmaceutical formulations comprising an effective amount of peptidomimetic macrocycles or pharmaceutically acceptable salts thereof. The peptidomimetic macrocycles of the invention are cross-linked (e.g., stapled or stitched) and possess improved pharmaceutical properties relative to their corresponding uncross-linked peptidomimetic macrocycles. These improved properties include improved bioavailability, enhanced chemical and in vivo stability, increased potency, and reduced immunogenicity (i.e., fewer or less severe injection site reactions).
In some embodiments, the peptide sequences are derived from a Cited2 peptide. For example, the peptide sequences are derived from human Cited2 (222-244) or human Cited2 (217-248).
In some embodiments, the peptide sequences are derived from a Cited2 peptide and a HIF1α peptide. For example, the peptide sequences are derived from human Cited2 (222-244) and human HIF1α (812-826). For example, the peptide sequences are derived from human Cited2 (222-244) and human HIF1α (794-804).
Non-limiting exemplary lists of suitable Cited2-derived peptides for use in the present invention are given in Tables 1a, 1b, and 1c below; and a non-limiting exemplary list of suitable hybrid peptides derived from Cited2 and HIF1α for use in the present invention is given in Table 2.
In the sequences shown above and elsewhere, the following abbreviations are used: amino acids represented as “$” are alpha-Me S5-pentenyl-alanine olefin amino acids connected by an all-carbon i to i+4 crosslinker comprising one double bond. Amino acids represented as “$r8” are alpha-Me R8-octenyl-alanine olefin amino acids connected by an all-carbon i to i+7 crosslinker comprising one double bond. “Ne” represents norleucine. “Aib” represents 2-aminoisobutyric acid. “Ac” represents acetyl. Amino acids represented as “Ba” are beta-alanine. Amino acids designated as “Cba” represent cyclobutyl alanine. Amino acids designated as “F4cooh” represent 4-carboxy phenylalanine. Amino acids represented as “$1” are alpha-Me S5-pentenyl-alanine olefin amino acids that are not connected by any crosslinker. “$r5” are alpha-Me R5-pentenyl-alanine olefin amino acids connected by an all-carbon comprising one double bond. Amino acids represented as “$/r5” are alpha-Me R5-pentenyl-alanine olefin amino acids that are not connected by any crosslinker. Amino acids represented as “St” are amino acids comprising two pentenyl-alanine olefin side chains, each of which is crosslinked to another amino acid as indicated. Amino acids represented as “Sta5” are amino acids comprising two R5-pentenyl-alanine olefin side chains, each of which is crosslinked to another amino acid as indicated. Other amino acids are described below.
Additionally, “Bpa” represents 4-benzyoyl-phenylalanine, a photoreactive amino acid analog useful in making photoreactive stapled peptides that covalently capture their physiologic targets, as described for example Braun et al. Chem Biol. 2010 Dec. 22; 17(12):1325-33 and Leshchiner et al. Proc Nal Acad Sci USA. 2013 Feb. 12.
Amino acids which are used in the formation of triazole cross-linkers are represented according to the legend indicated below. Stereochemistry at the alpha position of each amino acid is S unless otherwise indicated. For azide amino acids, the number of carbon atoms indicated refers to the number of methylene units between the alpha carbon and the terminal azide. For alkyne amino acids, the number of carbon atoms indicated is the number of methylene units between the alpha position and the triazole moiety plus the two carbon atoms within the triazole group derived from the alkyne.
In some embodiments, the present invention provides a peptidomimetic macrocycle comprising an amino acid sequence which is at least about 60% identical to an amino acid sequence selected from the group consisting of the amino acid sequences in Tables 1a, 1b and 1c, further comprising at least one macrocycle-forming linker, wherein the macrocycle-forming linker connects a first amino acid to a second amino acid. In some embodiments, the peptidomimetic macrocycle comprises an amino acid sequence which is at least about 65%, 70%, 75%, 80%, 85%, 90% or 95% an amino acid sequence identical to selected from the group consisting of the amino acid sequences in Tables 1a, 1b and 1c. In some embodiments, the peptidomimetic macrocycle comprises an amino acid sequence selected from the group consisting of the amino acid sequences in Tables 1a, 1b and 1c. In some embodiments, a macrocycle-forming linker of the peptidomimetic macrocycle of the invention connects one of the following pairs of amino acids: 9 and 13, 9 and 16, 10 and 14, 10 and 17, 11 and 15, 11 and 18, 12 and 16, 12 and 19, 13 and 17, 13 and 20, 14 and 18, and 15 and 19. In some embodiments, the macrocycle-forming linker connects amino acids 10 and 14. In some embodiments, the macrocycle-forming linker connects amino acids 14 and 18.
In some embodiments, the present invention provides a peptidomimetic macrocycle comprising an amino acid sequence which is at least about 60% identical to an amino acid sequence selected from the group consisting of the amino acid sequences in Table 2, further comprising at least one macrocycle-forming linker, wherein the macrocycle-forming linker connects a first amino acid to a second amino acid. In some embodiments, the peptidomimetic macrocycle comprises an amino acid sequence which is at least about 65%, 70%, 75%, 80%, 85%, 90% or 95% identical to an amino acid sequence selected from the group consisting of the amino acid sequences in Table 2. In some embodiments, the peptidomimetic macrocycle comprises an amino acid sequence selected from the group consisting of the amino acid sequences in Table 2. In some embodiments, one or more macrocycle-forming linkers of the peptidomimetic macrocycle of the invention connect one or more of the following pairs of amino acids: 4 and 8, 4 and 11, 5 and 9, 5 and 12, 6 and 10, 6 and 13, 7 and 11, 8 and 12, 9 and 13, 19 and 23, 19 and 26, 20 and 27, 21 and 25, 21 and 28, 23 and 27, and 41 and 45. In some embodiments, the peptidomimetic macrocycle comprise two macrocycle-forming linkers. In some embodiments, the macrocycle-forming linkers connect amino acids 6 and 13 and amino acids 23 and 27. In some embodiments, the macrocycle-forming linkers connect amino acids 8 and 12 and amino acids 19 and 26. In some embodiments, the macrocycle-forming linkers connect amino acids 8 and 12 and amino acids 23 and 27. In some embodiments, the macrocycle-forming linkers connect amino acids 23 and 27 and amino acids 41 and 45.
In some embodiments, a peptidomimetic macrocycle of the invention comprises a helix, for example an α-helix. In some embodiments, a peptidomimetic macrocycle of the invention comprises an α,α-disubstituted amino acid. In some embodiments, each amino acid connected by the macrocycle-forming linker is an α,α-disubstituted amino acid.
In some embodiments, a peptidomimetic macrocycle of the invention has Formula (I):
wherein: each A, C, D, and E is independently an amino acid (including natural or non-natural amino acids and amino acid analogs) and the terminal D and E independently optionally include a capping group, B is an amino acid (including natural or non-natural amino acids and amino acid analogs)
[—NH-L3-CO—], [—NH-L3-SO2—], or [—NH-L3-],
wherein A, B, C, D, and E, taken together with the crosslinked amino acids connected by the macrocycle-forming linker L, form the amino acid sequence of the peptidomimetic macrocycle;
L is a macrocycle-forming linker of the formula -L1-L2- or the formula
R1 and R2 are independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, cycloalkylalkyl, heteroalkyl, or heterocycloalkyl, unsubstituted or substituted with halo-;
R3 is hydrogen, alkyl, alkenyl, alkynyl, arylalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, cycloalkylalkyl, cycloaryl, or heterocycloaryl, optionally substituted with R5;
L1, L2 and L3 are independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, cycloarylene, heterocycloarylene, or [—R4—K—R4-]n, each being optionally substituted with R5;
each R4 is alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, arylene, or heteroarylene;
each K is O, S, SO2, CO CO2 or CONR3;
each R5 is independently halogen, alkyl, —OR6, —N(R6)2, —SR6, —SOR6, —SO2R6, —CO2R6, a fluorescent moiety, a radioisotope or a therapeutic agent;
each R6 is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heterocycloalkyl, a fluorescent moiety, a radioisotope or a therapeutic agent;
R7 is —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, cycloaryl, or heterocycloaryl, optionally substituted with R5, or part of a cyclic structure with a D residue;
R8 is —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, cycloaryl, or heterocycloaryl, optionally substituted with R5, or part of a cyclic structure with an E residue;
R9 is alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, heteroaryl, or heterocyclyl group, unsubstituted or optionally substituted with Ra and/or Rb;
Ra and Rb are independently alkyl, OCH3, CF3, NH2, CH2NH2, F, Br, I,
v from 1-1000, for example 1-500, 1-200, 1-100, 1-50, 1-40, 1-25, 1-20, i to 15, or 1 to 10;
u, x, y and z are independently integers from 0-10, for example u is 1, 2, or 3; and
n is an integer from 1-5, for example 1.
In some embodiments, u is 1.
In some embodiments, the sum of x+y+z is 2, 3 or 6, for example 3 or 6.
In some embodiments, L1 and L2 are independently alkylene, alkenylene or alkynylene. In some embodiments, L1 and L2 are independently C3-C10 alkylene or alkenylene, for example C3-C6 alkylene or alkenylene.
In some embodiments, R1 and R2 are H. In some embodiments, R1 and R2 are independently alkyl, for example methyl.
In some embodiments, A, B, C, D, and E, taken together with the crosslinked amino acids connected by the macrocycle-forming linker L, form the amino acid sequence of the peptidomimetic macrocycle which is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to an amino acid sequence chosen from the group consisting of the amino acid sequences in Tables 1a, 1b, 1c and 2.
In some embodiments, the present invention provides a peptidomimetic macrocycle having the formula
wherein:
L′ is a macrocycle-forming linker of the formula -L1′-L2′- or the formula
L1′ and L2′ are independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, cycloarylene, heterocycloarylene, or [—R4—K—R4-]n, each being optionally substituted with R5;
R8′ is —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, cycloaryl, or heterocycloaryl, each of which except for —H is optionally substituted with R5, or part of a cyclic structure with an E residue;
R9 is alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, heteroaryl, or heterocyclyl group, unsubstituted or optionally substituted with Ra′ and/or Rb′;
Ra′ and Rb′ are independently alkyl, OCH3, CF3, NH2, CH2NH2, F, Br, I,
and x′, y′, and z′ are independently integers from 0-10.
In some embodiments, the sum of x+y+z and the sum of x′+y′+z′ are independently 2, 3 or 6, for example 3.
In some embodiments, each of v, w, v′ and w′ is independently an integer from 1 to 10, 1 to 15, 1 to 20, or 1 to 25.
In some embodiments, each of v, w, v′ and w′ is independently an integer from 1 to 15.
In some embodiments, L1, L2, L1′, and L2′ are independently alkylene, alkenylene or alkynylene. In some embodiments, L1, L2, L1′, and L2′ are independently C3-C10 alkylene or alkenylene, for example C3-C6 alkylene or alkenylene. In some embodiments, L and L′ are both
In some embodiments, L is
For example, L and L are independently
In some embodiments, R1 and R2 are H. In some embodiments, R1 and R2 are independently alkyl, for example methyl.
In some embodiments, the peptidomimetic macrocycle is
or a pharmaceutically acceptable salt thereof.
In some embodiments, u is 2.
In some embodiments, the peptidomimetic macrocycle of Formula (I) has the Formula:
wherein each A, C, D, and E is independently an amino acid;
B is an amino acid,
[—NH-L3-CO—], [—NH-L3-SO2—], or [—NH-L3-];
L′ is a macrocycle-forming linker of the formula -L1′-L2′- or the formula
and wherein A, B, C, D, and E, taken together with the crosslinked amino acids connected by the macrocycle-forming linkers L and L′, form the amino acid sequence of the peptidomimetic macrocycle;
R1′ and R2′ are independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, cycloalkylalkyl, heteroalkyl, or heterocycloalkyl, unsubstituted or substituted with halo-;
L1′ and L2′ are independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, cycloarylene, heterocycloarylene, or [—R4—K—R4-]n, each being optionally substituted with R5;
each K is independently O, S, SO, SO2, CO, CO2, or CONR3;
R7′ is —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, cycloaryl, or heterocycloaryl, optionally substituted with R5, or part of a cyclic structure with a D residue;
R8′ is —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, cycloaryl, or heterocycloaryl, optionally substituted with R5, or part of a cyclic structure with an E residue;
v′ and w′ are independently integers from 1-1000, for example 1-500, 1-200, 1-100, 1-50, 1-40, 1-25, 1-20, i to 15, orn to 10;
x′, y′ and z′ are independently integers from 0-10; and
n is an integer from 1-5. In some embodiments, the sum of x′+y′+z′ is 2, 3 or 6, for example 3 or 6.
In some embodiments of any of the peptidomimetic macrocycles described herein, each K is O, S, SO, SO2, CO, or CO2.
In one example, at least one of R1 and R2 is alkyl, unsubstituted or substituted with halo-. In another example, both R1 and R2 are independently alkyl, unsubstituted or substituted with halo-. In some embodiments, at least one of R1 and R2 is methyl. In other embodiments, R1 and R2 are methyl.
In some embodiments of the invention, the sum of the sum of x+y+z is at least 3, and/or the su of x′+y′+z′ is at least 3. In other embodiments of the invention, the sum of the sum ofx+y+z is 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 (for example 2, 3 or 6) and/or the sum ofx′+y′+z′ is 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 (for example 2, 3 or 6).
Each occurrence of A, B, C, D or E in a macrocycle or macrocycle precursor of the invention is independently selected. For example, a sequence represented by the formula [A]x, when x is 3, encompasses embodiments where the amino acids are not identical, e.g. Gln-Asp-Ala as well as embodiments where the amino acids are identical, e.g. Gln-Gln-Gln. This applies for any value of x, y, or z in the indicated ranges. Similarly, when u is greater than 1, each compound of the invention may encompass peptidomimetic macrocycles which are the same or different. For example, a compound of the invention may comprise peptidomimetic macrocycles comprising different linker lengths or chemical compositions.
In some embodiments, the peptidomimetic macrocycle of the invention comprises a secondary structure which is an α-helix and R8 is —H, allowing intrahelical hydrogen bonding. In some embodiments, at least one of A, B, C, D or E is an α,α-disubstituted amino acid. In one example, B is an α,α-disubstituted amino acid. For instance, at least one of A, B, C, D or E is 2-aminoisobutyric acid. In other embodiments, at least one of A, B, C, D or E is
In other embodiments, the length of the macrocycle-forming linker L as measured from a first Cα to a second Cα is selected to stabilize a desired secondary peptide structure, such as an α-helix formed by residues of the peptidomimetic macrocycle including, but not necessarily limited to, those between the first Cα to a second Cα.
In one embodiment, the peptidomimetic macrocycle of Formula (I) is:
wherein each R1 and R2 is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, cycloalkylalkyl, heteroalkyl, or heterocycloalkyl, unsubstituted or substituted with halo-.
In related embodiments, the peptidomimetic macrocycle comprises a structure of Formula (I) which is:
In other embodiments, the peptidomimetic macrocycle of Formula (I) is a compound of any of the formulas shown below:
wherein “AA” represents any natural or non-natural amino acid side chain and “” is [D]v, [E]w as defined above, and n is an integer between 0 and 20, 50, 100, 200, 300, 400 or 500. In some embodiments, the substituent “n” shown in the preceding paragraph is 0. In other embodiments, the substituent “n” shown in the preceding paragraph is less than 50, 40, 30, 20, 10, or 5.
Exemplary embodiments of the macrocycle-forming linker L are shown below.
In other embodiments, D and/or E in the compound of Formula I are further modified in order to facilitate cellular uptake. In some embodiments, lipidating or PEGylating a peptidomimetic macrocycle facilitates cellular uptake, increases bioavailability, increases blood circulation, alters pharmacokinetics, decreases immunogenicity and/or decreases the needed frequency of administration.
In other embodiments, at least one of [D] and [E] in the compound of Formula I represents a moiety comprising an additional macrocycle-forming linker such that the peptidomimetic macrocycle comprises at least two macrocycle-forming linkers. In a specific embodiment, a peptidomimetic macrocycle comprises two macrocycle-forming linkers.
In the peptidomimetic macrocycles of the invention, any of the macrocycle-forming linkers described herein may be used in any combination with any of the sequences shown in Tables 1a, 1b, 1c, and 2 and also with any of the R-substituents indicated herein.
In some embodiments, the peptidomimetic macrocycle comprises at least one α-helix motif. For example, A, B and/or C in the compound of Formula I include one or more α-helices. As a general matter, α-helices include between 3 and 4 amino acid residues per turn. In some embodiments, the α-helix of the peptidomimetic macrocycle includes 1 to 5 turns and, therefore, 3 to 20 amino acid residues. In specific embodiments, the α-helix includes 1 turn, 2 turns, 3 turns, 4 turns, or 5 turns. In some embodiments, the macrocycle-forming linker stabilizes an α-helix motif included within the peptidomimetic macrocycle. Thus, in some embodiments, the length of the macrocycle-forming linker L from a first Cα to a second Cα is selected to increase the stability of an α-helix. In some embodiments, the macrocycle-forming linker spans from 1 turn to 5 turns of the α-helix. In some embodiments, the macrocycle-forming linker spans approximately 1 turn, 2 turns, 3 turns, 4 turns, or 5 turns of the α-helix. In some embodiments, the length of the macrocycle-forming linker is approximately 5 Å to 9 Å per turn of the α-helix, or approximately 6 Å to 8 Å per turn of the α-helix. Where the macrocycle-forming linker spans approximately 1 turn of an α-helix, the length is equal to approximately 5 carbon-carbon bonds to 13 carbon-carbon bonds, approximately 7 carbon-carbon bonds to 11 carbon-carbon bonds, or approximately 9 carbon-carbon bonds. Where the macrocycle-forming linker spans approximately 2 turns of an α-helix, the length is equal to approximately 8 carbon-carbon bonds to 16 carbon-carbon bonds, approximately 10 carbon-carbon bonds to 14 carbon-carbon bonds, or approximately 12 carbon-carbon bonds. Where the macrocycle-forming linker spans approximately 3 turns of an α-helix, the length is equal to approximately 14 carbon-carbon bonds to 22 carbon-carbon bonds, approximately 16 carbon-carbon bonds to 20 carbon-carbon bonds, or approximately 18 carbon-carbon bonds. Where the macrocycle-forming linker spans approximately 4 turns of an α-helix, the length is equal to approximately 20 carbon-carbon bonds to 28 carbon-carbon bonds, approximately 22 carbon-carbon bonds to 26 carbon-carbon bonds, or approximately 24 carbon-carbon bonds. Where the macrocycle-forming linker spans approximately 5 turns of an α-helix, the length is equal to approximately 26 carbon-carbon bonds to 34 carbon-carbon bonds, approximately 28 carbon-carbon bonds to 32 carbon-carbon bonds, or approximately 30 carbon-carbon bonds. Where the macrocycle-forming linker spans approximately 1 turn of an α-helix, the linkage contains approximately 4 atoms to 12 atoms, approximately 6 atoms to 10 atoms, or approximately 8 atoms. Where the macrocycle-forming linker spans approximately 2 turns of the α-helix, the linkage contains approximately 7 atoms to 15 atoms, approximately 9 atoms to 13 atoms, or approximately 11 atoms. Where the macrocycle-forming linker spans approximately 3 turns of the α-helix, the linkage contains approximately 13 atoms to 21 atoms, approximately 15 atoms to 19 atoms, or approximately 17 atoms. Where the macrocycle-forming linker spans approximately 4 turns of the α-helix, the linkage contains approximately 19 atoms to 27 atoms, approximately 21 atoms to 25 atoms, or approximately 23 atoms. Where the macrocycle-forming linker spans approximately 5 turns of the α-helix, the linkage contains approximately 25 atoms to 33 atoms, approximately 27 atoms to 31 atoms, or approximately 29 atoms. Where the macrocycle-forming linker spans approximately 1 turn of the α-helix, the resulting macrocycle forms a ring containing approximately 17 members to 25 members, approximately 19 members to 23 members, or approximately 21 members. Where the macrocycle-forming linker spans approximately 2 turns of the α-helix, the resulting macrocycle forms a ring containing approximately 29 members to 37 members, approximately 31 members to 35 members, or approximately 33 members. Where the macrocycle-forming linker spans approximately 3 turns of the α-helix, the resulting macrocycle forms a ring containing approximately 44 members to 52 members, approximately 46 members to 50 members, or approximately 48 members. Where the macrocycle-forming linker spans approximately 4 turns of the α-helix, the resulting macrocycle forms a ring containing approximately 59 members to 67 members, approximately 61 members to 65 members, or approximately 63 members. Where the macrocycle-forming linker spans approximately 5 turns of the α-helix, the resulting macrocycle forms a ring containing approximately 74 members to 82 members, approximately 76 members to 80 members, or approximately 78 members.
In some embodiments, L is a macrocycle-forming linker of the formula
Exemplary embodiments of such macrocycle-forming linkers L are shown below.
In some embodiments, a peptidomimetic macrocycle of the invention comprises a macrocycle-forming linker connecting a backbone amino group of a first amino acid to a second amino acid within the peptidomimetic macrocycle.
In other embodiments, the invention provides peptidomimetic macrocycles of Formula (II) or (IIa):
wherein:
each A, C, D, and E is independently an amino acid;
B is an amino acid,
[—NH-L3-CO—], [—NH-L3-SO2—], or [—NH-L3-];
R1 and R2 are independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, cycloalkylalkyl, heteroalkyl, or heterocycloalkyl, unsubstituted or substituted with halo-, or part of a cyclic structure with an E residue;
R3 is hydrogen, alkyl, alkenyl, alkynyl, arylalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, cycloalkylalkyl, cycloaryl, or heterocycloaryl, optionally substituted with R5;
L1, L2 and L3 are independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, cycloarylene, heterocycloarylene, or [—R4—K—R4-]n, each being optionally substituted with R5;
and wherein A, B, C, D, and E, taken together with the crosslinked amino acids connected by the macrocycle-forming linker -L1-L2-, form the amino acid sequence of the peptidomimetic macrocycle which is at least about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identical to an amino acid sequence chosen from the group consisting of the amino acid sequences in Tables 1a, 1b, 1c and 2;
each R4 is alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, arylene, or heteroarylene;
each K is O, S, SO, SO2, CO, CO2, or CONR3;
each R5 is independently halogen, alkyl, —OR6, —N(R6)2, —SR6, —SOR6, —SO2R6, —CO2R6, a fluorescent moiety, a radioisotope or a therapeutic agent;
each R6 is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heterocycloalkyl, a fluorescent moiety, a radioisotope or a therapeutic agent;
R7 is —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, cycloaryl, or heterocycloaryl, optionally substituted with R5;
v and w are independently integers from 1-1000, for example 1-100;
u, x, y and z are independently integers from 0-10, for example u is 1-3; and
n is an integer from 1-5.
In some embodiments, u is 1.
In some embodiments, the sum of x+y+z is 2, 3 or 6, for example 3.
In some embodiments, each of v and w is independently an integer from 1 to 10, 1 to 15, to 20, or to 25, for example from 1 to 15.
In some embodiments, L1 and L2 are independently alkylene, alkenylene or alkynylene. In some embodiments, L1 and L2 are independently C3-C10 alkylene or alkenylene, for example C3-C6 alkylene or alkenylene.
In some embodiments, R1 and R2 are H.
In some embodiments, at least one of R1 and R2 is alkyl, unsubstituted or substituted with halo-. In another example, both R1 and R2 are independently alkyl, unsubstituted or substituted with halo-. In some embodiments, at least one of R1 and R2 is methyl. In other embodiments, R1 and R2 are methyl.
In some embodiments of the invention, the sum of x+y+z is at least 1. In other embodiments of the invention, the sum of x+y+z is at least 2. In other embodiments of the invention, the su of x+y+z is 1,2,3,4,5,6, 7, 8, 9 or 10. Each occurrence of A, B, C, D or E in a macrocycle or macrocycle precursor of the invention is independently selected. For example, a sequence represented by the formula [A]x, when x is 3, encompasses embodiments where the amino acids are not identical, e.g. Gln-Asp-Ala as well as embodiments where the amino acids are identical, e.g. Gln-Gln-Gln. This applies for any value of x, y, or z in the indicated ranges.
In some embodiments, the peptidomimetic macrocycle of the invention comprises a secondary structure which is an α-helix and R8 is —H, allowing intrahelical hydrogen bonding. In some embodiments, at least one of A, B, C, D or E is an α,α-disubstituted amino acid. In one example, B is an α,α-disubstituted amino acid. For instance, at least one of A, B, C, D or E is 2-aminoisobutyric acid. In other embodiments, at least one of A, B, C, D or E is
In some embodiments, the present invention provides a peptidomimetic macrocycle comprising an amino acid sequence of the formula:
X1-X2-X3-X4-X5-X6-X7-X8-X9-X10-X11-X12-X13-X14-X15-X16-X17-X18-X19-X20-X21-X22-X23-X24-X25-X26-X27-X28-X29-X30-X31-X32 (SEQ ID NO: 2)
wherein:
X1 is a hydrophobic amino acid, or absent;
X2 is a hydrophobic amino acid, or absent;
X3 is a negatively charged amino acid, a positively charged amino acid, or absent;
X4 is an uncharged polar amino acid, or absent;
X5 is a negatively charged amino acid, or absent;
X6 is a hydrophobic amino acid, a negatively charged amino acid, a positively charged amino acid, an uncharged polar amino acid, or absent;
X7 is a hydrophobic amino acid, a negatively charged amino acid, or absent;
X8 is a negatively charged amino acid, a positively charged amino acid, or absent;
X9 is a negatively charged amino acid, absent, or a cross-linked amino acid;
X10 is a negatively charged amino acid, a positively charged amino acid, an uncharged polar amino acid, or a cross-linked amino acid;
X11 is a hydrophobic amino acid, a negatively charged amino acid, a positively charged amino acid, or a cross-linked amino acid;
X12 is a hydrophobic amino acid, a negatively charged amino acid, or a cross-linked amino acid;
X13 is a hydrophobic amino acid, a hydrophobic amino acid, a negatively charged amino acid, or a cross-linked amino acid;
X14 is a cross-linked amino acid;
X15 is a hydrophobic amino acid, a negatively charged amino acid, or a cross-linked amino acid;
X16 is a hydrophobic amino acid, a negatively charged amino acid, or a cross-linked amino acid;
X17 is a hydrophobic amino acid, a negatively charged amino acid, a positively charged amino acid, or a cross-linked amino acid;
X18 is a cross-linked amino acid;
X19 is a hydrophobic amino acid, a negatively charged amino acid, a positively charged amino acid, or a cross-linked amino acid;
X20 is a negatively charged amino acid, a hydrophobic amino acid, or a cross-linked amino acid;
X21 is a hydrophobic amino acid, or a negatively charged amino acid;
X22 is a negatively charged amino acid, or absent;
X23 is a positively charged amino acid, a negatively charged amino acid, or absent;
X24 is a hydrophobic amino acid, a negatively charged amino acid, or absent;
X25 is a hydrophobic amino acid, a negatively charged amino acid, or absent;
X26 is a negatively charged amino acid, or absent;
X27 is a hydrophobic amino acid, or absent;
X28 is a hydrophobic amino acid, or absent;
absent;
X29 is a negatively charged amino acid, an uncharged polar amino acid, or absent;
X30 is a hydrophobic amino acid, or absent;
X31 is a hydrophobic amino acid, or absent; and
X32 is a hydrophobic amino acid, or absent;
wherein the peptidomimetic macrocycle comprises at least one macrocycle-forming linker connecting at least one pair of amino acids selected from X1-X28;
L is a macrocycle-forming linker of the formula -L1-L2- or the formula
L1 and L2 are independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, cycloarylene, heterocycloarylene, or [—R4—K—R4-]n, each being optionally substituted with R5;
each the cross-linked amino acid is optionally substituted at the alpha carbon position with R1 or R2, wherein R1 and R2 are independently alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, cycloalkylalkyl, heteroalkyl, or heterocycloalkyl, each being optionally substituted with halo-;
each R4 is alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, arylene, or heteroarylene;
each K is O, S, SO, SO2, CO, or CO2;
each R5 is independently halogen, alkyl, —OR6, —N(R6)2, —SR6, —SOR6, —SO2R6, —CO2R6, a fluorescent moiety, a radioisotope, or a therapeutic agent;
each R6 is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heterocycloalkyl, a fluorescent moiety, a radioisotope, or a therapeutic agent;
R9 is alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, heteroaryl, or heterocyclyl group, unsubstituted or optionally substituted with Ra and/or Rb; and
Ra and Rb are independently alkyl, OCH3, CF3, NH2, CH2NH2, F, Br, I,
In some embodiments, the present invention provides a peptidomimetic macrocycle comprising an amino acid sequence of the formula:
X1-X2-X3-X4-X5-X6-X7-X8-X9-X10-X11-X12-X13-X14-X15-X16-X17-X18-X19-X20-X21-X22-X23-X24-X25-X26-X27-X28-X29-X30-X31-X32 (SEQ ID NO: 3)
X1 is Val or absent;
X2 is Ile, Phe, or absent;
X3 is Asp, Arg, or absent;
X4 is Thr or absent;
X5 is Asp or absent;
X6 is Phe, Ala, Glu, Ser, Dpr, Asn, or absent;
X7 is Ile, Ala, Glu, Ser, or absent;
X8 is Asp, Ala, Ser, Dpr, or absent;
X9 is Glu, Ala, absent, or a cross-linked amino acid;
X10 is Glu, Ala, Ser, Dpr, Gln, or a cross-linked amino acid;
X11 is Val, Ala, Asp, Ser, Dpr, or a cross-linked amino acid;
X12 is Leu, Ala, Glu, Ser, pL, or a cross-linked amino acid;
X13 is Met, Nle, Ala, Asp, or a cross-linked amino acid;
X14 is Ser or a cross-linked amino acid;
X15 is Leu, Ala, Asp, Ser, or a cross-linked amino acid;
X16 is Val, Ala, Glu, Ser, pL, or a cross-linked amino acid;
X17 is Ile, Ala, Glu, Ser, Dpr, Bpa, or a cross-linked amino acid;
X18 is Glu or a cross-linked amino acid;
X19 is Met, Nle, Ala, Glu, Ser, Dpr, Bpa, or a cross-linked amino acid;
X20 is Gly, Ala, Glu, Ser, or a cross-linked amino acid;
X22 is Asp, Ala, Ser, or absent;
X23 is Arg, Ala, Glu, Ser, Dpr, or absent;
X24 is Ile, Ala, Glu, Ser, or absent;
X25 is Lys, Glu, or absent;
X26 is Glu or absent;
X27 is Leu or absent;
X28 is Pro or absent;
X29 is Glu, Gln, or absent;
X30 is Leu or absent;
X31 is Trp or absent; and
X32 is Leu or absent;
wherein the peptidomimetic macrocycle comprises at least one macrocycle-forming linker connecting at least one pair of amino acids selected from X1-X28;
L is a macrocycle-forming linker of the formula -L1-L2- or the formula
L1 and L2 are independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, cycloarylene, heterocycloarylene, or [—R4—K—R4-]n, each being optionally substituted with R5;
each the cross-linked amino acid is optionally substituted at the alpha carbon position with R1 or R2, wherein R1 and R2 are independently alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, cycloalkylalkyl, heteroalkyl, or heterocycloalkyl, each being optionally substituted with halo-;
each R4 is alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, arylene, or heteroarylene;
each K is O, S, SO, SO2, CO, or CO2;
each R5 is independently halogen, alkyl, —OR6, —N(R6)2, —SR6, —SORE, —SO2R6, —CO2R6, a fluorescent moiety, a radioisotope, or a therapeutic agent;
each R6 is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heterocycloalkyl, a fluorescent moiety, a radioisotope, or a therapeutic agent;
R9 is alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, heteroaryl, or heterocyclyl group, unsubstituted or optionally substituted with Ra and/or Rb; and
Ra and Rb are independently alkyl, OCH3, CF3, NH2, CH2NH2, F, Br, I,
A peptidomimetic macrocycle comprising an amino acid sequence of the formula:
X1-X2-X3-X4-X5-X6-X7-X8-X9-X10-X11-X12-X13-X14-X15-X16-X17-X18-X19-X20-X21-X22-X23-X24-X25-X26-X27-X28-X29-X30-X31-X32 (SEQ ID NO: 4)
wherein:
X1 is Val or absent;
X2 is Ile, Phe, or absent;
X3 is Asp, Arg, or absent;
X4 is Thr or absent;
X5 is Asp or absent;
X6 is Phe, Ala, Glu, Ser, Dpr, Asn, or absent;
X7 is Ile, Ala, Glu, Ser, or absent;
X8 is Asp, Ala, Ser, Dpr, or absent;
X9 is Glu, Ala, absent, or a cross-linked amino acid;
X10 is Glu, Ala, Ser, Dpr, Gln, or a cross-linked amino acid;
X11 is Val, Ala, Asp, Ser, Dpr, or a cross-linked amino acid;
X12 is Leu, Ala, Glu, Ser, pL, or a cross-linked amino acid;
X13 is Met, Nle, Ala, Asp, or a cross-linked amino acid;
X14 is Ser or a cross-linked amino acid;
X15 is Leu, Ala, Asp, Ser, or a cross-linked amino acid;
X16 is Val, Ala, Glu, Ser, pL, or a cross-linked amino acid;
X17 is Ile, Ala, Glu, Ser, Dpr, Bpa, or a cross-linked amino acid;
X18 is Glu or a cross-linked amino acid;
X19 is Met, Nle, Ala, Glu, Ser, Dpr, Bpa, or a cross-linked amino acid;
X20 is Gly, Ala, Glu, Ser, or a cross-linked amino acid;
X22 is Asp, Ala, Ser, or absent;
X23 is Arg, Ala, Glu, Ser, Dpr, or absent;
X24 is Ile, Ala, Glu, Ser, or absent;
X25 is Lys, Glu, or absent;
X26 is Glu or absent;
X27 is Leu or absent;
X28 is Pro or absent;
X29 is Glu, Gln, or absent;
X30 is Leu or absent;
X31 is Trp or absent; and
X32 is Leu or absent;
wherein the peptidomimetic macrocycle comprises at least one macrocycle-forming linker connecting at least one pair of amino acids selected from X1-X28;
L is a macrocycle-forming linker of the formula -L1-L2- or the formula
L1 and L2 are independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, cycloarylene, heterocycloarylene, or [—R4—K—R4-]6, each being optionally substituted with R5;
each the cross-linked amino acid is optionally substituted at the alpha carbon position with R1 or R2, wherein R1 and R2 are independently alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, cycloalkylalkyl, heteroalkyl, or heterocycloalkyl, each being optionally substituted with halo-;
each R4 is alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, arylene, or heteroarylene;
each K is O, S, SO, SO2, CO, or CO2;
each R5 is independently halogen, alkyl, —OR6, —N(R6)2, —SR6, —SORE, —SO2R6, —CO2R6, a fluorescent moiety, a radioisotope, or a therapeutic agent;
each R6 is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heterocycloalkyl, a fluorescent moiety, a radioisotope, or a therapeutic agent;
R9 is alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, heteroaryl, or heterocyclyl group, unsubstituted or optionally substituted with Ra and/or Rb; and
Ra and Rb are independently alkyl, OCH3, CF3, NH2, CH2NH2, F, Br, I,
In some embodiments, the peptidomimetic macrocycle of the invention comprises one macrocycle-forming linker.
In some embodiments, the macrocycle-forming linker of the peptidomimetic macrocycle of the invention connects one of the following pairs of amino acids: X9 and X14, X9 and X16, X10 and X14, X10 and X17, X11 and X15, X11 and X18, X12 and X16, X12 and X19, X13 and X17, X13 and X20, X14 and X18, and X14 and X19. In some embodiments, the macrocycle-forming linker connects amino acids: X10 and X14. In some embodiments, the macrocycle-forming linker connects amino acids: X14 and X18.
In some embodiments, X9 is Glu. In some embodiments, X12 is Leu. In some embodiments, X13 is Nle or Met. In some embodiments, X16 is Val. In some embodiments, X18 is Glu. In some embodiments, X19 is Nle or Met. In some embodiments, X20 is Ala. In some embodiments, X21 is Leu. In some embodiments, X22 is Asp. In some embodiments, X24 is Ile. In some embodiments, X30 is Leu. In some embodiments, X31 is Trp.
In some embodiments, L1 and L2 are independently alkylene, alkenylene or alkynylene. In some embodiments, L1 and L2 are independently C3-C10 alkylene or alkenylene, for example C3-C6 alkylene or alkenylene. For example, L is
In some embodiments, L is
for example
In some embodiments, R1 and R2 are H. In some embodiments, R1 and R2 are independently alkyl, for example methyl.
In some embodiments, the present invention provides a peptidomimetic macrocycle comprising an amino acid sequence which is about 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% identical to an amino acid sequence of FIDEEVLMSLVIEMALDRI (SEQ ID NO: 5), for example an amino acid sequence of FIDEEVLM-Z-LVI-Z-MALDRI (SEQ ID NO: 6), wherein each Z is independently a cross-linked amino acid. In some embodiments, the peptidomimetic macrocycle is
or a pharmaceutically acceptable salt thereof.
In some embodiments, the present invention provides a peptidomimetic macrocycle comprising an amino acid sequence which is about 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% identical to an amino acid sequence of FIDEEVLNleSLVIENleALDRI (SEQ ID NO: 7), for example an amino acid sequence of FIDEEVLNle-Z-LVI-Z-NleALDRI (SEQ ID NO: 8), wherein each Z is independently a cross-linked amino acid. In some embodiments, the peptidomimetic macrocycle is
or a pharmaceutically acceptable salt thereof.
In some embodiments, the present invention provides a peptidomimetic macrocycle comprising an amino acid sequence which is about 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% identical to an amino acid sequence of FIDEEVLMSLVIEMGLDRIKELPELWL (SEQ ID NO: 9), for example an amino acid sequence of FIDEEVLM-Z-LVI-Z-MGLDRIKELPELWL (SEQ ID NO: 10), wherein each Z is independently a cross-linked amino acid.
In some embodiments, a peptidomimetic macrocycle of the invention has a formula X6-X7-X8-X9-X10-X11-X2-X13-X14-X15-X16-X17-X18-X19-X20-X21-X22-X23-X24-X25-X26-X27-X28 (SEQ ID NO: 11). In some embodiments, a macrocycle-forming linker of the peptidomimetic macrocycle of the invention connects one of the following pairs of amino acids: X10 and X14, X10 and X17, X11 and X18, X12 and X16, X12 and X19, and X14 and X18, for example X14 and X18. In some embodiments, X13 is Nle. In some embodiments, X19 is Nle. In some embodiments, X20 is Ala.
In some embodiments, a peptidomimetic macrocycle of the invention further comprises an amino acid sequence which is about 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% identical to an amino acid sequence of LLQGEELLRALDQV (SEQ ID NO: 12). In some embodiments, the peptidomimetic macrocycle comprises an amino acid sequence of LLQGEEL-Z-RAL-Z-QV (SEQ ID NO: 13), wherein each Z is independently a cross-linked amino acid. In some embodiments, X6 is linked to the amino acid sequence of LLQGEEL-Z-RAL-Z-QV (SEQ ID NO: 13). In some embodiments, the peptidomimetic macrocycle comprises an amino acid sequence of LLQGE-Z-LLRALD-Z-V (SEQ ID NO: 14), wherein each Z is independently a cross-linked amino acid. In some embodiments, X6 is linked to the amino acid sequence of LLQGEEL-Z-RAL-Z-QV (SEQ ID NO: 13).
In some embodiments, a peptidomimetic macrocycle of the invention further comprises an amino acid sequence which is about 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% identical to an amino acid sequence of QLTSYDCEVNA (SEQ ID NO: 15), for example an amino acid sequence of QLT-Z-YDAbu-Z-VNA (SEQ ID NO: 16), wherein each Z is independently a cross-linked amino acid. In some embodiments, X28 is linked to the amino acid sequence of QLT-Z-YDAbu-Z-VNA (SEQ ID NO: 16).
In other embodiments, the length of the macrocycle-forming linker -L1-L2- as measured from a first Cα to a second Cα is selected to stabilize a desired secondary peptide structure, such as an α-helix formed by residues of the peptidomimetic macrocycle including, but not necessarily limited to, those between the first Cα to a second Cα.
Exemplary embodiments of the macrocycle-forming linker -L1-L2- are shown below.
Peptidomimetic macrocycles of the invention may be prepared by any of a variety of methods known in the art. For example, any of the cross-linked amino acids in Tables 1a, 1b, 1c and 2 may be substituted with a residue capable of forming a crosslinker with a second residue in the same molecule or a precursor of such a residue.
Various methods to effect formation of peptidomimetic macrocycles are known in the art. For example, the preparation of peptidomimetic macrocycles of Formula (I) is described in Schafeister et al., J. Am. Chem. Soc. 122:5891-5892 (2000); Schafmeister & Verdine, J. Am. Chem. Soc. 122:5891 (2005); Walensky et al., Science 305:1466-1470 (2004); U.S. Pat. No. 7,192,713 and PCT application WO 2008/121767. The α,α-disubstituted amino acids and amino acid precursors disclosed in the cited references may be employed in synthesis of the peptidomimetic macrocycle precursor polypeptides. For example, the “S5-olefin amino acid” is (S)-α-(2′-pentenyl) alanine and the “R8 olefin amino acid” is (R)-α-(2′-octenyl) alanine. Following incorporation of such amino acids into precursor polypeptides, the terminal olefins are reacted with a metathesis catalyst, leading to the formation of the peptidomimetic macrocycle. In various embodiments, the following amino acids may be employed in the synthesis of the peptidomimetic macrocycle:
In some embodiments, x+y+z is 3, and A, B and C are independently natural or non-natural amino acids. In other embodiments, x+y+z is 6, and A, B and C are independently natural or non-natural amino acids.
In some embodiments, the contacting step is performed in a solvent selected from the group consisting of protic solvent, aqueous solvent, organic solvent, and mixtures thereof. For example, the solvent may be chosen from the group consisting of H2O, THF, THF/H2O, tBuOH/H2O, DMF, DIPEA, CH3CN or CH2Cl2, ClCH2CH2Cl or a mixture thereof. The solvent may be a solvent which favors helix formation.
Alternative but equivalent protecting groups, leaving groups or reagents are substituted, and certain of the synthetic steps are performed in alternative sequences or orders to produce the desired compounds. Synthetic chemistry transformations and protecting group methodologies (protection and deprotection) useful in synthesizing the compounds described herein include, for example, those such as described in Larock, Comprehensive Organic Transformations, VCH Publishers (1989); Greene and Wuts, Protective Groups in Organic Synthesis, 2d. Ed., John Wiley and Sons (1991); Fieser and Fieser, Fieser and Fieser's Reagents for Organic Synthesis, John Wiley and Sons (1994); and Paquette, ed., Encyclopedia of Reagents for Organic Synthesis, John Wiley and Sons (1995), and subsequent editions thereof.
The peptidomimetic macrocycles disclosed herein are made, for example, by chemical synthesis methods, such as described in Fields et al., Chapter 3 in Synthetic Peptides: A User's Guide, ed. Grant, W. H. Freeman & Co., New York, N.Y., 1992, p. 77. Hence, for example, peptides are synthesized using the automated Merrifield techniques of solid phase synthesis with the amine protected by either tBoc or Fmoc chemistry using side chain protected amino acids on, for example, an automated peptide synthesizer (e.g., Applied Biosystems (Foster City, Calif.), Model 430A, 431, or 433).
One manner of producing the peptidomimetic precursors and peptidomimetic macrocycles described herein uses solid phase peptide synthesis (SPPS). The C-terminal amino acid is attached to a cross-linked polystyrene resin via an acid labile bond with a linker molecule. This resin is insoluble in the solvents used for synthesis, making it relatively simple and fast to wash away excess reagents and by-products. The N-terminus is protected with the Fmoc group, which is stable in acid, but removable by base. Side chain functional groups are protected as necessary with base stable, acid labile groups.
Longer peptidomimetic precursors are produced, for example, by conjoining individual synthetic peptides using native chemical ligation. Alternatively, the longer synthetic peptides are biosynthesized by well known recombinant DNA and protein expression techniques. Such techniques are provided in well-known standard manuals with detailed protocols. To construct a gene encoding a peptidomimetic precursor of this invention, the amino acid sequence is reverse translated to obtain a nucleic acid sequence encoding the amino acid sequence, preferably with codons that are optimum for the organism in which the gene is to be expressed. Next, a synthetic gene is made, typically by synthesizing oligonucleotides which encode the peptide and any regulatory elements, if necessary. The synthetic gene is inserted in a suitable cloning vector and transfected into a host cell. The peptide is then expressed under suitable conditions appropriate for the selected expression system and host. The peptide is purified and characterized by standard methods.
The peptidomimetic precursors are made, for example, in a high-throughput, combinatorial fashion using, for example, a high-throughput polychannel combinatorial synthesizer (e.g., Thuraed TETRAS multichannel peptide synthesizer from CreoSalus, Louisville, Ky. or Model Apex 396 multichannel peptide synthesizer from AAPPTEC, Inc., Louisville, Ky.).
In some embodiments, the peptidomimetic macrocycles of the invention comprise triazole macrocycle-forming linkers. For example, the synthesis of such peptidomimetic macrocycles involves a multi-step process that features the synthesis of a peptidomimetic precursor containing an azide moiety and an alkyne moiety; followed by contacting the peptidomimetic precursor with a macrocyclization reagent to generate a triazole-linked peptidomimetic macrocycle. Such a process is described, for example, in U.S. application Ser. No. 12/037,041, filed on Feb. 25, 2008. Macrocycles or macrocycle precursors are synthesized, for example, by solution phase or solid-phase methods, and can contain both naturally-occurring and non-naturally-occurring amino acids. See, for example, Hunt, “The Non-Protein Amino Acids” in Chemistry and Biochemistry of the Amino Acids, edited by G. C. Barrett, Chapman and Hall, 1985.
In some embodiments, an azide is linked to the α-carbon of a residue and an alkyne is attached to the α-carbon of another residue. In some embodiments, the azide moieties are azido-analogs of amino acids L-lysine, D-lysine, alpha-methyl-L-lysine, alpha-methyl-D-lysine, L-omithine, D-omithine, alpha-methyl-L-ornithine or alpha-methyl-D-omithine. In another embodiment, the alkyne moiety is L-propargylglycine. In yet other embodiments, the alkyne moiety is an amino acid selected from the group consisting of L-propargylglycine, D-propargylglycine, (S)-2-amino-2-methyl-4-pentynoic acid, (R)-2-amino-2-methyl-4-pentynoic acid, (S)-2-amino-2-methyl-5-hexynoic acid, (R)-2-amino-2-methyl-5-hexynoic acid, (S)-2-amino-2-methyl-6-heptynoic acid, (R)-2-amino-2-methyl-6-heptynoic acid, (S)-2-amino-2-methyl-7-octynoic acid, (R)-2-amino-2-methyl-7-octynoic acid, (S)-2-amino-2-methyl-8-nonynoic acid and (R)-2-amino-2-methyl-8-nonynoic acid.
The following synthetic schemes are provided solely to illustrate the present invention and are not intended to limit the scope of the invention, as described herein. To simplify the drawings, the illustrative schemes depict azido amino acid analogs ε-azido-α-methyl-L-lysine and 8-azido-1-methyl-D-lysine, and alkyne amino acid analogs L-propargylglycine, (S)-2-amino-2-methyl-4-pentynoic acid, and (S)-2-amino-2-methyl-6-heptynoic acid. Thus, in the following synthetic schemes, each R1, R2, R7 and R8 is —H; each L1 is —(CH2)4—; and each L2 is —(CH2)—. However, as noted throughout the detailed description above, many other amino acid analogs can be employed in which R1, R2, R7, R8, L1 and L2 can be independently selected from the various structures disclosed herein.
Synthetic Scheme 1 describes the preparation of several compounds of the invention. Ni(II) complexes of Schiff bases derived from the chiral auxiliary (S)-2-[N—(N′-benzylprolyl)amino]benzophenone (BPB) and amino acids such as glycine or alanine are prepared as described in Belokon et al. (1998), Tetrahedron Asymm. 9:4249-4252. The resulting complexes are subsequently reacted with alkylating reagents comprising an azido or alkynyl moiety to yield enantiomerically enriched compounds of the invention. If desired, the resulting compounds can be protected for use in peptide synthesis.
In the general method for the synthesis of peptidomimetic macrocycles shown in Synthetic Scheme 2, the peptidomimetic precursor contains an azide moiety and an alkyne moiety and is synthesized by solution-phase or solid-phase peptide synthesis (SPPS) using the commercially available amino acid N-α-Fmoc-L-propargylglycine and the N-α-Fmoc-protected forms of the amino acids (S)-2-amino-2-methyl-4-pentynoic acid, (S)-2-amino-6-heptynoic acid, (S)-2-amino-2-methyl-6-heptynoic acid, N-methyl-ε-azido-L-lysine, and N-methyl-ε-azido-D-lysine. The peptidomimetic precursor is then deprotected and cleaved from the solid-phase resin by standard conditions (e.g., strong acid such as 95% TFA). The peptidomimetic precursor is reacted as a crude mixture or is purified prior to reaction with a macrocyclization reagent such as a Cu(I) in organic or aqueous solutions (Rostovtsev et al. (2002), Angew. Chem. Int. Ed. 41:2596-2599; Tomoe et al. (2002), J. Org. Chem. 67:3057-3064; Deiters et al. (2003), J. Am. Chem. Soc. 125:11782-11783; Punna et al. (2005), Angew. Chem. Int. Ed. 44:2215-2220). In one embodiment, the triazole forming reaction is performed under conditions that favor α-helix formation. In one embodiment, the macrocyclization step is performed in a solvent chosen from the group consisting of H2O, THF, CH3CN, DMF, DIPEA, tBuOH or a mixture thereof. In another embodiment, the macrocyclization step is performed in DMF. In some embodiments, the macrocyclization step is performed in a buffered aqueous or partially aqueous solvent.
In the general method for the synthesis of peptidomimetic macrocycles shown in Synthetic Scheme 3, the peptidomimetic precursor contains an azide moiety and an alkyne moiety and is synthesized by solid-phase peptide synthesis (SPPS) using the commercially available amino acid N-α-Fmoc-L-propargylglycine and the N-α-Fmoc-protected forms of the amino acids (S)-2-amino-2-methyl-4-pentynoic acid, (S)-2-amino-6-heptynoic acid, (S)-2-amino-2-methyl-6-heptynoic acid, N-methyl-ε-azido-L-lysine, and N-methyl-ε-azido-D-lysine. The peptidomimetic precursor is reacted with a macrocyclization reagent such as a Cu(I) reagent on the resin as a crude mixture (Rostovtsev et al. (2002), Angew. Chem. Int. Ed. 41:2596-2599; Tomoe et al. (2002), J. Org. Chem. 67:3057-3064; Deiters et al. (2003), J. Am. Chem. Soc. 125:11782-11783; Punna et al. (2005), Angew. Chem. Int. Ed. 44:2215-2220). The resultant triazole-containing peptidomimetic macrocycle is then deprotected and cleaved from the solid-phase resin by standard conditions (e.g., strong acid such as 95% TFA). In some embodiments, the macrocyclization step is performed in a solvent chosen from the group consisting of CH2Cl2, ClCH2CH2Cl, DMF, THF, NMP, DIPEA, 2,6-lutidine, pyridine, DMSO, H2O or a mixture thereof. In some embodiments, the macrocyclization step is performed in a buffered aqueous or partially aqueous solvent
In the general method for the synthesis of peptidomimetic macrocycles shown in Synthetic Scheme 4, the peptidomimetic precursor contains an azide moiety and an alkyne moiety and is synthesized by solution-phase or solid-phase peptide synthesis (SPPS) using the commercially available amino acid N-α-Fmoc-L-propargylglycine and the N-α-Fmoc-protected forms of the amino acids (S)-2-amino-2-methyl-4-pentynoic acid, (S)-2-amino-6-heptynoic acid, (S)-2-amino-2-methyl-6-heptynoic acid, N-methyl-ε-azido-L-lysine, and N-methyl-ε-azido-D-lysine. The peptidomimetic precursor is then deprotected and cleaved from the solid-phase resin by standard conditions (e.g., strong acid such as 95% TFA). The peptidomimetic precursor is reacted as a crude mixture or is purified prior to reaction with a macrocyclization reagent such as a Ru(II) reagents, for example Cp*RuCl(PPh3)2 or [Cp*RuCl]4 (Rasmussen et al. (2007), Org. Lett. 9:5337-5339; Zhang et al. (2005), J. Am. Chem. Soc. 127:15998-15999). In some embodiments, the macrocyclization step is performed in a solvent chosen from the group consisting of DMF, CH3CN and THF.
In the general method for the synthesis of peptidomimetic macrocycles shown in Synthetic Scheme 5, the peptidomimetic precursor contains an azide moiety and an alkyne moiety and is synthesized by solid-phase peptide synthesis (SPPS) using the commercially available amino acid N-α-Fmoc-L-propargylglycine and the N-α-Fmoc-protected forms of the amino acids (S)-2-amino-2-methyl-4-pentynoic acid, (S)-2-amino-6-heptynoic acid, (S)-2-amino-2-methyl-6-heptynoic acid, N-methyl-ε-azido-L-lysine, and N-methyl-ε-azido-D-lysine. The peptidomimetic precursor is reacted with a macrocyclization reagent such as a Ru(II) reagent on the resin as a crude mixture. For example, the reagent can be Cp*RuCl(PPh3)2 or [Cp*RuCl]4 (Rasmussen et al. (2007), Org. Lett. 9:5337-5339; Zhang et al. (2005), J. Am. Chem. Soc. 127:15998-15999). In some embodiments, the macrocyclization step is performed in a solvent chosen from the group consisting of CH2Cl2, ClCH2CH2Cl, CH3CN, DMF, and THF.
In some embodiments, a peptidomimetic macrocycle of Formula I comprises a halogen group substitution on a triazole moiety, for example an iodo substitution. Such peptidomimetic macrocycles may be prepared from a precursor having the partial structure and using the cross-linking methods taught herein. Crosslinkers of any length, as described herein, may be prepared comprising such substitutions. In one embodiment, the peptidomimetic macrocycle is prepared according to the scheme shown below. The reaction is performed, for example, in the presence of Cu and an amine ligand such as TEA or TTTA. See, e.g., Hein et al. Angew. Chem., Int. Ed. 2009, 48, 8018-8021.
In other embodiments, an iodo-substituted triazole is generated according to the scheme shown below. For example, the second step in the reaction scheme below is performed using, for example, CuI and N-bromosuccinimide (NBS) in the presence of THF (see, e.g. Zhang et al., J. Org. Chem. 2008, 73, 3630-3633). In other embodiments, the second step in the reaction scheme shown below is performed, for example, using CuI and an iodinating agent such as ICl (see, e.g. Wu et al., Synthesis 2005, 1314-1318.)
In some embodiments, an iodo-substituted triazole moiety is used in a cross-coupling reaction, such as a Suzuki or Sonogashira coupling, to afford a peptidomimetic macrocycle comprising a substituted crosslinker. Sonogashira couplings using an alkyne as shown below may be performed, for example, in the presence of a palladium catalyst such as Pd(PPh3)2Cl2, CuI, and in the presence of a base such as triethylamine. Suzuki couplings using an arylboronic or substituted alkenyl boronic acid as shown below may be performed, for example, in the presence of a catalyst such as Pd(PPh3)4, and in the presence of a base such as K2CO3.
Any suitable triazole substituent groups which reacts with the iodo-substituted triazole can be used in Suzuki couplings described herein. Example triazole substituents for use in Suzuki couplings are shown below:
wherein “Cyc” is a suitable aryl, cycloalkyl, cycloalkenyl, heteroaryl, or heterocyclyl group, unsubstituted or optionally substituted with an Ra or Rb, group as described below.
In some embodiments, the substituent is:
Any suitable substituent group which reacts with the iodo-substituted triazole can be used in Sonogashira couplings described herein. Example triazole substituents for use in Sonogashira couplings are shown below:
wherein “Cyc” is a suitable aryl, cycloalkyl, cycloalkenyl, heteroaryl, or heterocyclyl group, unsubstituted or optionally substituted with an Ra or Rb group as described below.
In some embodiments, the triazole substituent is:
In some embodiments, the Cyc group shown above is further substituted by at least one Ra or Rb substituent. In some embodiments, at least one of Ra and Rb is independently:
In other embodiments, the triazole substituent is
and at least one of Ra and Rb is alkyl (including hydrogen, methyl, or ethyl), or:
The present invention contemplates the use of non-naturally-occurring amino acids and amino acid analogs in the synthesis of the peptidomimetic macrocycles described herein. Any amino acid or amino acid analog amenable to the synthetic methods employed for the synthesis of stable triazole containing peptidomimetic macrocycles can be used in the present invention. For example, L-propargylglycine is contemplated as a useful amino acid in the present invention. However, other alkyne-containing amino acids that contain a different amino acid side chain are also useful in the invention. For example, L-propargylglycine contains one methylene unit between the α-carbon of the amino acid and the alkyne of the amino acid side chain. The invention also contemplates the use of amino acids with multiple methylene units between the α-carbon and the alkyne. Also, the azido-analogs of amino acids L-lysine, D-lysine, alpha-methyl-L-lysine, and alpha-methyl-D-lysine are contemplated as useful amino acids in the present invention. However, other terminal azide amino acids that contain a different amino acid side chain are also useful in the invention. For example, the azido-analog of L-lysine contains four methylene units between the α-carbon of the amino acid and the terminal azide of the amino acid side chain. The invention also contemplates the use of amino acids with fewer than or greater than four methylene units between the α-carbon and the terminal azide. Table 3 shows some amino acids useful in the preparation of peptidomimetic macrocycles disclosed herein.
-
- Table 3 shows exemplary amino acids useful in the preparation of peptidomimetic macrocycles disclosed herein.
In some embodiments the amino acids and amino acid analogs are of the D-configuration. In other embodiments they are of the L-configuration. In some embodiments, some of the amino acids and amino acid analogs contained in the peptidomimetic are of the D-configuration while some of the amino acids and amino acid analogs are of the L-configuration. In some embodiments the amino acid analogs are α,α-disubstituted, such as α-methyl-L-propargylglycine, α-methyl-D-propargylglycine, ε-azido-alpha-methyl-L-lysine, and ε-azido-alpha-methyl-D-lysine. In some embodiments the amino acid analogs are N-alkylated, e.g., N-methyl-L-propargylglycine, N-methyl-D-propargylglycine, N-methyl-ε-azido-L-lysine, and N-methyl-ε-azido-D-lysine.
In some embodiments, the —NH moiety of the amino acid is protected using a protecting group, including without limitation -Fmoc and -Boc. In other embodiments, the amino acid is not protected prior to synthesis of the peptidomimetic macrocycle.
Additional methods of forming peptidomimetic macrocycles which are envisioned as suitable to perform the present invention include those disclosed by Mustapa, M. Firouz Mohd et al., J. Org. Chem (2003), 68, pp. 8193-8198; Yang, Bin et al. Bioorg Med. Chem. Lett. (2004), 14, pp. 1403-1406; U.S. Pat. Nos. 5,364,851; 5,446,128; 5,824,483;
6,713,280; and 7,202,332. In such embodiments, amino acid precursors are used containing an additional substituent R— at the alpha position. Such amino acids are incorporated into the macrocycle precursor at the desired positions, which may be at the positions where the crosslinker is substituted or, alternatively, elsewhere in the sequence of the macrocycle precursor. Cyclization of the precursor is then performed according to the indicated method.
For example, a peptidomimetic macrocycle of Formula (II) is prepared as indicated:
-
- wherein each AA1, AA2, AA3 is independently an amino acid side chain.
In other embodiments, a peptidomimetic macrocycle of Formula (II) is prepared as indicated:
-
- wherein each AA1, AA2, AA3 is independently an amino acid side chain.
In some embodiments, a peptidomimetic macrocycle is obtained in more than one isomer, for example due to the configuration of a double bond within the structure of the crosslinker (E vs Z). Such isomers can or can not be separable by conventional chromatographic methods. In some embodiments, one isomer has improved biological properties relative to the other isomer. In one embodiment, an E crosslinker olefin isomer of a peptidomimetic macrocycle has better solubility, better target affinity, better in vivo or in vitro efficacy, higher helicity, or improved cell permeability relative to its Z counterpart. In another embodiment, a Z crosslinker olefin isomer of a peptidomimetic macrocycle has better solubility, better target affinity, better in vivo or in vitro efficacy, higher helicity, or improved cell permeability relative to its E counterpart.
AssaysThe properties of the peptidomimetic macrocycles of the invention are assayed, for example, by using the methods described below. In some embodiments, a peptidomimetic macrocycle of the invention has improved biological properties relative to a corresponding polypeptide lacking the substituents described herein.
Assay to Determine α-Helicity.In solution, the secondary structure of polypeptides with α-helical domains will reach a dynamic equilibrium between random coil structures and α-helical structures, often expressed as a “percent helicity”. Thus, for example, alpha-helical domains are predominantly random coils in solution, with α-helical content usually under 25%. Peptidomimetic macrocycles with optimized linkers, on the other hand, possess, for example, an alpha-helicity that is at least two-fold greater than that of a corresponding uncrosslinked polypeptide. In some embodiments, macrocycles of the invention will possess an alpha-helicity of greater than 50%. To assay the helicity of peptidomimetic macrocycles of the invention, the compounds are dissolved in an aqueous solution (e.g. 50 mM potassium phosphate solution at pH 7, or distilled H2O, to concentrations of 25-50 μM). Circular dichroism (CD) spectra are obtained on a spectropolarimeter (e.g., Jasco J-710) using standard measurement parameters (e.g. temperature, 20° C.; wavelength, 190-260 nm step resolution, 0.5 nm speed, 20 nm/sec; accumulations, 10; response, 1 sec; bandwidth, 1 nm path length, 0.1 cm). The α-helical content of each peptide is calculated by dividing the mean residue ellipticity (e.g. [Φ]222obs) by the reported value for a model helical decapeptide (Yang et al. (1986), Methods Enzymol. 130:208)).
Assay to Determine Melting Temperature (Tm).A peptidomimetic macrocycle of the invention comprising a secondary structure such as an α-helix exhibits, for example, a higher melting temperature than a corresponding uncrosslinked polypeptide. Typically peptidomimetic macrocycles of the invention exhibit Tm of >60° C. representing a highly stable structure in aqueous solutions. To assay the effect of macrocycle formation on melting temperature, peptidomimetic macrocycles or unmodified peptides are dissolved in distilled H2O (e.g. at a final concentration of 50 μM) and the Tm is determined by measuring the change in ellipticity over a temperature range (e.g. 4 to 95° C.) on a spectropolarimeter (e.g., Jasco J-710) using standard parameters (e.g. wavelength 222 nm step resolution, 0.5 nm; speed, 20 nm/sec; accumulations, 10; response, 1 sec; bandwidth, 1 nm; temperature increase rate: 1° C./min; path length, 0.1 cm).
Protease Resistance Assay.The amide bond of the peptide backbone is susceptible to hydrolysis by proteases, thereby rendering peptidic compounds vulnerable to rapid degradation in vivo. Peptide helix formation, however, typically buries the amide backbone and therefore may shield it from proteolytic cleavage. The peptidomimetic macrocycles of the present invention may be subjected to in vitro trypsin proteolysis to assess for any change in degradation rate compared to a corresponding uncrosslinked polypeptide. For example, the peptidomimetic macrocycle and a corresponding uncrosslinked polypeptide are incubated with trypsin agarose and the reactions quenched at various time points by centrifugation and subsequent HPLC injection to quantitate the residual substrate by ultraviolet absorption at 280 n Briefly, the peptidomimetic macrocycle and peptidomimetic precursor (5 mcg) are incubated with trypsin agarose (Pierce) (S/E˜125) for 0, 10, 20, 90, and 180 minutes. Reactions are quenched by tabletop centrifugation at high speed; remaining substrate in the isolated supernatant is quantified by HPLC-based peak detection at 280 nm. The proteolytic reaction displays first order kinetics and the rate constant, k, is determined from a plot of ln[S] versus time (k=−1Xslope).
Ex Vivo Stability Assay.Peptidomimetic macrocycles with optimized linkers possess, for example, an ex vivo half-life that is at least two-fold greater than that of a corresponding uncrosslinked polypeptide, and possess an ex vivo half-life of 12 hours or more. For ex vivo serum stability studies, a variety of assays may be used. For example, a peptidomimetic macrocycle and a corresponding uncrosslinked polypeptide (2 mcg) are incubated with fresh mouse, rat and/or human serum (2 mL) at 37° C. for 0, 1, 2, 4, 8, and 24 hours. To determine the level of intact compound, the following procedure may be used: The samples are extracted by transferring 100 μl of sera to 2 ml centrifuge tubes followed by the addition of 10 μL of 50% formic acid and 500 μL acetonitrile and centrifugation at 14,000 RPM for 10 min at 4±2° C. The supernatants are then transferred to fresh 2 ml tubes and evaporated on Turbovap under N2<10 psi, 37° C. The samples are reconstituted in 100 μL of 50:50 acetonitrile:water and submitted to LC-MS/MS analysis.
In Vitro Binding Assays.To assess the binding and affinity of peptidomimetic macrocycles and peptidomimetic precursors to acceptor proteins, a fluorescence polarization assay (FPA) is used, for example. The FPA technique measures the molecular orientation and mobility using polarized light and fluorescent tracer. When excited with polarized light, fluorescent tracers (e.g., FITC) attached to molecules with high apparent molecular weights (e.g. FITC-labeled peptides bound to a large protein) emit higher levels of polarized fluorescence due to their slower rates of rotation as compared to fluorescent tracers attached to smaller molecules (e.g. FITC-labeled peptides that are free in solution).
For example, fluoresceinated peptidomimetic macrocycles (25 nM) are incubated with the acceptor protein (25-1000 nM) in binding buffer (140 mM NaCl, 50 mM Tris-HCL, pH 7.4) for 30 minutes at room temperature. Binding activity is measured, for example, by fluorescence polarization on a luminescence spectrophotometer (e.g. Perkin-Elmer LS50B). Kd values may be determined by nonlinear regression analysis using, for example, Graphpad Prism software (GraphPad Software, Inc., San Diego, Calif.). A peptidomimetic macrocycle of the invention shows, in some instances, similar or lower Kd than a corresponding uncrosslinked polypeptide.
In Vitro Displacement Assays to Characterize Antagonists of Peptide-Protein Interactions.To assess the binding and affinity of compounds that antagonize the interaction between a peptide and an acceptor protein, a fluorescence polarization assay (FPA) utilizing a fluoresceinated peptidomimetic macrocycle derived from a peptidomimetic precursor sequence is used, for example. The FPA technique measures the molecular orientation and mobility using polarized light and fluorescent tracer. When excited with polarized light, fluorescent tracers (e.g., FITC) attached to molecules with high apparent molecular weights (e.g. FITC-labeled peptides bound to a large protein) emit higher levels of polarized fluorescence due to their slower rates of rotation as compared to fluorescent tracers attached to smaller molecules (e.g. FITC-labeled peptides that are free in solution). A compound that antagonizes the interaction between the fluoresceinated peptidomimetic macrocycle and an acceptor protein will be detected in a competitive binding FPA experiment.
For example, putative antagonist compounds (1 nM to 1 mM) and a fluoresceinated peptidomimetic macrocycle (25 nM) are incubated with the acceptor protein (50 nM) in binding buffer (140 mM NaCl, 50 mM Tris-HCL, pH 7.4) for 30 minutes at room temperature. Antagonist binding activity is measured, for example, by fluorescence polarization on a luminescence spectrophotometer (e.g. Perkin-Elmer LS50B). Kd values may be determined by nonlinear regression analysis using, for example, Graphpad Prism software (GraphPad Software, Inc., San Diego, Calif.).
Any class of molecule, such as small organic molecules, peptides, oligonucleotides or proteins can be examined as putative antagonists in this assay.
Assay for Protein-Ligand Binding by Affinity Selection-Mass SpectrometryTo assess the binding and affinity of test compounds for proteins, an affinity-selection mass spectrometry assay is used, for example. Protein-ligand binding experiments are conducted according to the following representative procedure outlined for a system-wide control experiment using 1 μM peptidomimetic macrocycle plus 5 μM target protein. A 1 μL DMSO aliquot of a 40 μM stock solution of peptidomimetic macrocycle is dissolved in 19 μL of PBS (Phosphate-buffered saline: 50 mM, pH 7.5 Phosphate buffer containing 150 mM NaCl). The resulting solution is mixed by repeated pipetting and clarified by centrifugation at 10 000 g for 10 min. To a 4 μL aliquot of the resulting supernatant is added 4 μL of 10 μM target protein in PBS. Each 8.0 μL experimental sample thus contains 40 pmol (1.5 μg) of protein at 5.0 μM concentration in PBS plus 1 μM peptidomimetic macrocycle and 2.5% DMSO. Duplicate samples thus prepared for each concentration point are incubated for 60 min at room temperature, and then chilled to 4° C. prior to size-exclusion chromatography-LC-MS analysis of 5.0 μL injections. Samples containing a target protein, protein-ligand complexes, and unbound compounds are injected onto an SEC column, where the complexes are separated from non-binding component by a rapid SEC step. The SEC column eluate is monitored using UV detectors to confirm that the early-eluting protein fraction, which elutes in the void volume of the SEC column, is well resolved from unbound components that are retained on the column. After the peak containing the protein and protein-ligand complexes elutes from the primary UV detector, it enters a sample loop where it is excised from the flow stream of the SEC stage and transferred directly to the LC-MS via a valving mechanism. The (M+3H)3+ ion of the peptidomimetic macrocycle is observed by ESI-MS at the expected m/z, confirming the detection of the protein-ligand complex.
Assay for Protein-Ligand Kd Titration Experiments.To assess the binding and affinity of test compounds for proteins, a protein-ligand Kd titration experiment is performed. Protein-ligand Kd titrations experiments are conducted as follows: 2 μL DMSO aliquots of a serially diluted stock solution of titrant peptidomimetic macrocycle (5, 2.5, . . . , 0.098 mM) are prepared then dissolved in 38 μL of PBS. The resulting solutions are mixed by repeated pipetting and clarified by centrifugation at 10 000 g for 10 min. To 4.0 μL aliquots of the resulting supernatants is added 4.0 μL of 10 μM target protein in PBS. Each 8.0 μL experimental sample thus contains 40 pmol (1.5 μg) of protein at 5.0 μM concentration in PBS, varying concentrations (125, 62.5, . . . , 0.24 μM) of the titrant peptide, and 2.5% DMSO. Duplicate samples thus prepared for each concentration point are incubated at room temperature for 30 min, then chilled to 4° C. prior to SEC-LC-MS analysis of 2.0 μL injections. The (M+H)1+, (M+2H)2+, (M+3H)3+, and/or (M+Na)1+ ion is observed by ESI-MS; extracted ion chromatograms are quantified, then fit to equations to derive the binding affinity Kd as described in “A General Technique to Rank Protein-Ligand Binding Affinities and Determine Allosteric vs. Direct Binding Site Competition in Compound Mixtures.” Annis, D. A.; Nazef, N.; Chuang, C. C.; Scott, M. P.; Nash, H. M. J. Am. Chem. Soc. 2004, 126, 15495-15503; also in “ALIS: An Affinity Selection-Mass Spectrometry System for the Discovery and Characterization of Protein-Ligand Interactions” D. A. Annis, C.-C. Chuang, and N. Nazef. In Mass Spectromety in Medicinal Chemistry. Edited by Wanner K, Höfner G: Wiley-VCH; 2007:121-184. Mannhold R, Kubinyi H, Folkers G (Series Editors): Methods and Principles in Medicinal Chemistry.
Assay for Competitive Binding Experiments by Affinity Selection-Mass SpectrometryTo determine the ability of test compounds to bind competitively to proteins, an affinity selection mass spectrometry assay is performed, for example. A mixture of ligands at 40 μM per component is prepared by combining 2 μL aliquots of 400 μM stocks of each of the three compounds with 14 μL of DMSO. Then, 1 μL aliquots of this 40 μM per component mixture are combined with 1 μL DMSO aliquots of a serially diluted stock solution of titrant peptidomimetic macrocycle (10, 5, 2.5, . . . , 0.078 mM). These 2 μL samples are dissolved in 38 μL of PBS. The resulting solutions were mixed by repeated pipetting and clarified by centrifugation at 10 000 g for 10 m. To 4.0 μL aliquots of the resulting supernatants is added 4.0 μL of 10 μM target protein in PBS. Each 8.0 μL experimental sample thus contains 40 pmol (1.5 μg) of protein at 5.0 μM concentration in PBS plus 0.5 μM ligand, 2.5% DMSO, and varying concentrations (125, 62.5, . . . , 0.98 μM) of the titrant peptidomimetic macrocycle. Duplicate samples thus prepared for each concentration point are incubated at room temperature for 60 min, then chilled to 4° C. prior to SEC-LC-MS analysis of 2.0 L injections. Additional details on these and other methods are provided in “A General Technique to Rank Protein-Ligand Binding Affinities and Determine Allosteric vs. Direct Binding Site Competition in Compound Mixtures.” Annis, D. A.; Nazef, N.; Chuang, C. C.; Scott, M. P.; Nash, H. M. J. Am. Chem. Soc. 2004, 126, 15495-15503; also in “ALIS: An Affinity Selection-Mass Spectrometry System for the Discovery and Characterization of Protein-Ligand Interactions” D. A. Annis, C.-C. Chuang, and N. Nazef. In Mass Spectrometry in Medicinal Chemistry. Edited by Wanner K, Höfner G: Wiley-VCH; 2007:121-184. Mannhold R, Kubinyi H, Folkers G (Series Editors): Methods and Principles in Medicinal Chemistry.
Binding Assays in Intact Cells.It is possible to measure binding of peptides or peptidomimetic macrocycles to their natural acceptors in intact cells by immunoprecipitation experiments. For example, intact cells are incubated with fluoresceinated (FITC-labeled) compounds for 4 hrs in the absence of serum, followed by serum replacement and further incubation that ranges from 4-18 hrs. Cells are then pelleted and incubated in lysis buffer (50 mM Tris [pH 7.6], 150 mM NaCl, 1% CHAPS and protease inhibitor cocktail) for 10 minutes at 4° C. Extracts are centrifuged at 14,000 rpm for 15 minutes and supernatants collected and incubated with 10 μl goat anti-FITC antibody for 2 hrs, rotating at 4° C. followed by further 2 hrs incubation at 4° C. with protein A/G Sepharose (50 μl of 50% bead slurry). After quick centrifugation, the pellets are washed in lysis buffer containing increasing salt concentration (e.g. 150, 300, 500 mM). The beads are then re-equilibrated at 150 mM NaCl before addition of SDS-containing sample buffer and boiling. After centrifugation, the supemrnatants are optionally electrophoresed using 4-12% gradient Bis-Tris gels followed by transfer into Immobilon-P membranes. After blocking, blots are optionally incubated with an antibody that detects FITC and also with one or more antibodies that detect proteins that bind to the peptidomimetic macrocycle.
Cellular Penetrability Assays.To measure the cell penetrability of peptidomimetic macrocycles and corresponding uncrosslinked macrocycle, intact cells are incubated with fluoresceinated peptidomimetic macrocycles or corresponding uncrosslinked macrocycle (10 μM) for 4 hrs in serum free media at 37° C., washed twice with media and incubated with trypsin (0.25%) for 10 min at 37° C. The cells are washed again and resuspended in PBS. Cellular fluorescence is analyzed, for example, by using either a FACSCalibur flow cytometer or Cellomics' KineticScan® HCS Reader.
In Vivo Stability Assay.To investigate the in vivo stability of the peptidomimetic macrocycles, the compounds are, for example, administered to mice and/or rats by IV, IP, PO or inhalation routes at concentrations ranging from 0.1 to 50 mg/kg and blood specimens withdrawn at 0′, 5′, 15′, 30′, 1 hr, 4 hrs, 8 hrs and 24 hours post-injection. Levels of intact compound in 25 μL of fresh serum are then measured by LC-MS/MS as above.
Clinical Trials.To determine the suitability of the peptidomimetic macrocycles of the invention for treatment of humans, clinical trials are performed. For example, patients diagnosed with a muscle wasting disease or lipodystrophy and in need of treatment are selected and separated in treatment and one or more control groups, wherein the treatment group is administered a peptidomimetic macrocycle of the invention, while the control groups receive a placebo or a known HIF drug. The treatment safety and efficacy of the peptidomimetic macrocycles of the invention can thus be evaluated by performing comparisons of the patient groups with respect to factors such as survival and quality-of-life. In this example, the patient group treated with a peptidomimetic macrocycle show improved long-term survival compared to a patient control group treated with a placebo.
Pharmaceutical Compositions and Routes of AdministrationIn some embodiments, the present invention provides a pharmaceutical composition comprising a peptidomimetic macrocycle of the invention and a pharmaceutically acceptable carrier.
The peptidomimetic macrocycles of the invention also include pharmaceutically acceptable derivatives or prodrugs thereof. A “pharmaceutically acceptable derivative” means any pharmaceutically acceptable salt, ester, salt of an ester, pro-drug or other derivative of a compound of this invention which, upon administration to a recipient, is capable of providing (directly or indirectly) a compound of this invention. Particularly favored pharmaceutically acceptable derivatives are those that increase the bioavailability of the compounds of the invention when administered to a mammal (e.g., by increasing absorption into the blood of an orally administered compound) or which increases delivery of the active compound to a biological compartment (e.g., the brain or lymphatic system) relative to the parent species. Some pharmaceutically acceptable derivatives include a chemical group which increases aqueous solubility or active transport across the gastrointestinal mucosa.
In some embodiments, the peptidomimetic macrocycles of the invention are modified by covalently or non-covalently joining appropriate functional groups to enhance selective biological properties. Such modifications include those which increase biological penetration into a given biological compartment (e.g. blood, lymphatic system, central nervous system), increase oral availability, increase solubility to allow administration by injection, alter metabolism, and alter rate of excretion.
Pharmaceutically acceptable salts of the compounds of this invention include those derived from pharmaceutically acceptable inorganic and organic acids and bases. Examples of suitable acid salts include acetate, adipate, benzoate, benzenesulfonate, butyrate, citrate, digluconate, dodecylsulfate, formate, fumarate, glycolate, hemisulfate, heptanoate, hexanoate, hydrochloride, hydrobroide, hydroiodide, lactate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, palmoate, phosphate, picrate, pivalate, propionate, salicylate, succinate, sulfate, tartrate, tosylate and undecanoate. Salts derived from appropriate bases include alkali metal (e.g., sodium), alkaline earth metal (e.g., magnesium), ammonium and N-(alkyl)4+ salts.
For preparing pharmaceutical compositions from the compounds of the present invention, pharmaceutically acceptable carriers include either solid or liquid carriers. Solid form preparations include powders, tablets, pills, capsules, cachets, suppositories, and dispersible granules. A solid carrier can be one or more substances, which also acts as diluents, flavoring agents, binders, preservatives, tablet disintegrating agents, or an encapsulating material. Details on techniques for formulation and administration are well described in the scientific and patent literature, see, e.g., the latest edition of Remington's Pharmaceutical Sciences, Maack Publishing Co, Easton Pa.
In powders, the carrier is a finely divided solid, which is in a mixture with the finely divided active component. In tablets, the active component is mixed with the carrier having the necessary binding properties in suitable proportions and compacted in the shape and size desired.
Suitable solid excipients are carbohydrate or protein fillers include, but are not limited to sugars, including lactose, sucrose, mannitol, or sorbitol; starch from corn, wheat, rice, potato, or other plants; cellulose such as methyl cellulose, hydroxypropylmethyl-cellulose, or sodium carboxymethylcellulose; and gums including arabic and tragacanth; as well as proteins such as gelatin and collagen. If desired, disintegrating or solubilizing agents are added, such as the cross-linked polyvinyl pyrrolidone, agar, alginic acid, or a salt thereof, such as sodium alginate.
Liquid form preparations include solutions, suspensions, and emulsions, for example, water or water/propylene glycol solutions. For parenteral injection, liquid preparations can be formulated in solution in aqueous polyethylene glycol solution.
The pharmaceutical preparation is preferably in unit dosage form. In such form the preparation is subdivided into unit doses containing appropriate quantities of the active component. The unit dosage form can be a packaged preparation, the package containing discrete quantities of preparation, such as packeted tablets, capsules, and powders in vials or ampoules. Also, the unit dosage form can be a capsule, tablet, cachet, or lozenge itself, or it can be the appropriate number of any of these in packaged form.
When the compositions of this invention comprise a combination of a peptidomimetic macrocycle and one or more additional therapeutic or prophylactic agents, both the compound and the additional agent should be present at dosage levels of between about 1 to 100%, and more preferably between about 5 to 95% of the dosage normally administered in a monotherapy regimen. In some embodiments, the additional agents are administered separately, as part of a multiple dose regimen, from the compounds of this invention. Alternatively, those agents are part of a single dosage form, mixed together with the compounds of this invention in a single composition.
In some embodiments, the compositions are present as unit dosage forms that can deliver, for example, from about 0.0001 mg to about 1,000 mg of the peptidomimetic macrocycles, salts thereof, prodrugs thereof, derivatives thereof, or any combination of these. Thus, the unit dosage forms can deliver, for example, in some embodiments, from about 1 mg to about 900 mg, from about 1 mg to about 800 mg, from about 1 mg to about 700 mg, from about 1 mg to about 600 mg, from about 1 mg to about 500 mg, from about 1 mg to about 400 mg, from about 1 mg to about 300 mg, from about 1 mg to about 200 mg, from about 1 mg to about 100 mg, from about 1 mg to about 10 mg, from about 1 mg to about 5 mg, from about 0.1 mg to about 10 mg, from about 0.1 mg to about 5 mg, from about 10 mg to about 1,000 mg, from about 50 mg to about 1,000 mg, from about 100 mg to about 1,000 mg, from about 200 mg to about 1,000 mg, from about 300 mg to about 1,000 mg, from about 400 mg to about 1,000 mg, from about 500 mg to about 1,000 mg, from about 600 mg to about 1,000 mg, from about 700 mg to about 1,000 mg, from about 800 mg to about 1,000 mg, from about 900 mg to about 1,000 mg, from about 10 mg to about 900 mg, from about 100 mg to about 800 mg, from about 200 mg to about 700 mg, or from about 300 mg to about 600 mg of the peptidomimetic macrocycles, salts thereof, prodrugs thereof, derivatives thereof, or any combination of these.
In some embodiments, the compositions are present as unit dosage forms that can deliver, for example, about 1 mg, about 2 mg, about 3 mg, about 4 mg, about 5 mg, about 6 mg, about 7 mg, about 8 mg, about 9 mg, about 10 mg, about 20 mg, about 30 mg, about 40 mg, about 50 mg, about 60 mg, about 70 mg, about 80 mg, about 90 mg, about 100 mg, about 150 mg, about 200 mg, about 250 mg, about 300 mg, about 350 mg, about 400 mg, about 500 mg, about 600 mg, about 700 mg, about 800 mg, or about 800 mg of peptidomimetic macrocycles, salts thereof, prodrugs thereof, derivatives thereof, or any combination of these.
Suitable routes of administration include, but are not limited to, oral, intravenous, rectal, aerosol, parenteral, ophthalmic, pulmonary, transmucosal, transdermal, vaginal, otic, nasal, and topical administration. In addition, by way of example only, parenteral delivery includes intramuscular, subcutaneous, intravenous, intramedullary injections, as well as intrathecal, direct intraventricular, intraperitoneal, intralymphatic, and intranasal injections.
In certain embodiments, a composition as described herein is administered in a local rather than systemic manner, for example, via injection of the compound directly into an organ. In specific embodiments, long acting formulations are administered by implantation (for example subcutaneously or intramuscularly) or by intramuscular injection. Furthermore, in other embodiments, the drug is delivered in a targeted drug delivery system, for example, in a liposome coated with organ-specific antibody. In such embodiments, the liposomes are targeted to and taken up selectively by the organ. In yet other embodiments, the compound as described herein is provided in the form of a rapid release formulation, in the form of an extended release formulation, or in the form of an intermediate release formulation. In yet other embodiments, the compound described herein is administered topically.
In another embodiment, compositions described herein are formulated for oral administration. Compositions described herein are formulated by combining a peptidomimetic macrocycle with, e.g., pharmaceutically acceptable carriers or excipients. In various embodiments, the compounds described herein are formulated in oral dosage forms that include, by way of example only, tablets, powders, pills, dragees, capsules, liquids, gels, syrups, elixirs, slurries, suspensions and the like.
In certain embodiments, pharmaceutical preparations for oral use are obtained by mixing one or more solid excipient with one or more of the peptidomimetic macrocycles described herein, optionally grinding the resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries, if desired, to obtain tablets or dragee cores. Suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as: for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methylcellulose, microcrystalline cellulose, hydroxypropylmethylcellulose, sodium carboxymethylcellulose; or others such as: polyvinylpyrrolidone (PVP or povidone) or calcium phosphate. In specific embodiments, disintegrating agents are optionally added. Disintegrating agents include, by way of example only, cross-linked croscarmellose sodium, polyvinylpyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.
In one embodiment, dosage forms, such as dragee cores and tablets, are provided with one or more suitable coating. In specific embodiments, concentrated sugar solutions are used for coating the dosage form. The sugar solutions optionally contain additional components, such as by way of example only, gum arabic, talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol, and/or titanium dioxide, lacquer solutions, and suitable organic solvents or solvent mixtures. Dyestuffs and/or pigments are also optionally added to the coatings for identification purposes. Additionally, the dyestuffs and/or pigments are optionally utilized to characterize different combinations of active compound doses.
In certain embodiments, therapeutically effective amounts of at least one of the peptidomimetic macrocycles described herein are formulated into other oral dosage forms. Oral dosage forms include push-fit capsules made of gelatin, as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. In specific embodiments, push-fit capsules contain the active ingredients in admixture with one or more filler. Fillers include, by way of example only, lactose, binders such as starches, and/or lubricants such as talc or magnesium stearate and, optionally, stabilizers. In other embodiments, soft capsules contain one or more active compound that is dissolved or suspended in a suitable liquid. Suitable liquids include, by way of example only, one or more fatty oil, liquid paraffin, or liquid polyethylene glycol. In addition, stabilizers are optionally added.
In other embodiments, therapeutically effective amounts of at least one of the peptidomimetic macrocycles described herein are formulated for buccal or sublingual administration. Formulations suitable for buccal or sublingual administration include, by way of example only, tablets, lozenges, or gels. In still other embodiments, the peptidomimetic macrocycles described herein are formulated for parenteral injection, including formulations suitable for bolus injection or continuous infusion. In specific embodiments, formulations for injection are presented in unit dosage form (e.g., in ampoules) or in multi-dose containers. Preservatives are, optionally, added to the injection formulations. In still other embodiments, pharmaceutical compositions are formulated in a form suitable for parenteral injection as a sterile suspensions, solutions or emulsions in oily or aqueous vehicles. Parenteral injection formulations optionally contain formulatory agents such as suspending, stabilizing and/or dispersing agents. In specific embodiments, pharmaceutical formulations for parenteral administration include aqueous solutions of the active compounds in water-soluble form. In additional embodiments, suspensions of the active compounds are prepared as appropriate oily injection suspensions. Suitable lipophilic solvents or vehicles for use in the pharmaceutical compositions described herein include, by way of example only, fatty oils such as sesame oil, or synthetic fatty acid esters, such as ethyl oleate or triglycerides, or liposomes. In certain specific embodiments, aqueous injection suspensions contain substances which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol, or dextran. Optionally, the suspension contains suitable stabilizers or agents which increase the solubility of the compounds to allow for the preparation of highly concentrated solutions. Alternatively, in other embodiments, the active ingredient is in powder form for constitution with a suitable vehicle, e.g., sterile pyrogen-free water, before use.
Pharmaceutical compositions herein can be administered, for example, once or twice or three or four or five or six times per day, or once or twice or three or four or five or six times per week, and can be administered, for example, for a day, a week, a month, 3 months, six months, a year, five years, or for example ten years.
Methods of UseIn one aspect, the present invention provides novel peptidomimetic macrocycles that are useful in competitive binding assays to identify agents which bind to the natural ligand(s) of the proteins or peptides upon which the peptidomimetic macrocycles are modeled. For example, in the HIF1α/CBP/p300 system, labeled peptidomimetic macrocycles based on HIF1α can be used in a CBP/p300 binding assay along with small molecules that competitively bind to CBP/p300. Competitive binding studies allow for rapid in vitro evaluation and determination of drug candidates specific for the HIF1α/CBP/p300 system. Such binding studies may be performed with any of the peptidomimetic macrocycles disclosed herein and their binding partners.
The invention further provides for the generation of antibodies against the peptidomimetic macrocycles. In some embodiments, these antibodies specifically bind both the peptidomimetic macrocycle and the precursor peptides, such as HIF1α, to which the peptidomimetic macrocycles are related. Such antibodies, for example, disrupt the native protein-protein interaction, for example, binding between HIF1α and CBP/p300.
In other aspects, the present invention provides for both prophylactic and therapeutic methods of treating a subject at risk of (or susceptible to) a disorder or having a disorder associated with aberrant (e.g., insufficient or excessive) expression or activity of the molecules including HIF-family proteins, such as HIF1α.
In another embodiment, a disorder is caused, at least in part, by an abnormal level of HIF1α, (e.g. over or under expression), or by the presence of HIF1α exhibiting abnormal activity. As such, the reduction in the level and/or activity of HIF1α, or the enhancement of the level and/or activity of HIF1α, by peptidomimetic macrocycles derived from HIF1α, is used, for example, to ameliorate or reduce the adverse symptoms of the disorder.
In another aspect, the present invention provides methods for treating or preventing a disease including hyperproliferative disease and inflammatory disorder by interfering with the interaction or binding between binding partners, for example, between HIF1α and CBP/p300. These methods comprise administering an effective amount of a compound of the invention to a warm blooded animal, including a human. In some embodiments, the administration of the compounds of the present invention induces cell growth arrest or apoptosis.
As used herein, the term “treatment” is defined as the application or administration of a therapeutic agent to a patient, or application or administration of a therapeutic agent to an isolated tissue or cell line from a patient, who has a disease, a symptom of disease or a predisposition toward a disease, with the purpose to cure, heal, alleviate, relieve, alter, remedy, ameliorate, improve or affect the disease, the symptoms of disease or the predisposition toward disease.
In some embodiments, the peptidomimetic macrocycles of the invention is used to treat, prevent, and/or diagnose cancers and neoplastic conditions. As used herein, the terms “cancer”, “hyperproliferative” and “neoplastic” refer to cells having the capacity for autonomous growth, i.e., an abnormal state or condition characterized by rapidly proliferating cell growth. Hyperproliferative and neoplastic disease states may be categorized as pathologic, i.e., characterizing or constituting a disease state, or may be categorized as non-pathologic, i.e., a deviation from normal but not associated with a disease state. The term is meant to include all types of cancerous growths or oncogenic processes, metastatic tissues or malignantly transformed cells, tissues, or organs, irrespective of histopathologic type or stage of invasiveness. A metastatic tumor can arise from a multitude of primary tumor types, including but not limited to those of breast, lung, liver, colon and ovarian origin. “Pathologic hyperproliferative” cells occur in disease states characterized by malignant tumor growth. Examples of non-pathologic hyperproliferative cells include proliferation of cells associated with wound repair. Examples of cellular proliferative and/or differentiative disorders include cancer, e.g., carcinoma, sarcoma, or metastatic disorders. In some embodiments, the peptidomimetic macrocycles are novel therapeutic agents for controlling breast cancer, ovarian cancer, colon cancer, lung cancer, metastasis of such cancers and the like.
Examples of cancers or neoplastic conditions include, but are not limited to, a fibrosarcoma, myosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewings tumor, leiomyosarcoma, rhabdomyosarcoma, gastric cancer, esophageal cancer, rectal cancer, pancreatic cancer, ovarian cancer, prostate cancer, uterine cancer, cancer of the head and neck, skin cancer, brain cancer, squamous cell carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinoma, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilm's tumor, cervical cancer, testicular cancer, small cell lung carcinoma, non-small cell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroa, oligodendroglioma, meningioma, melanoma, neuroblastoma, retinoblastoma, leukemia, lymphoma, or Kaposi sarcoma.
Examples of proliferative disorders include hematopoietic neoplastic disorders. As used herein, the term “hematopoetic neoplastic disorders” includes diseases involving hyperplastic/neoplastic cells of hematopoietic origin, e.g., arising from myeloid, lymphoid or erythroid lineages, or precursor cells thereof. Preferably, the diseases arise from poorly differentiated acute leukemias, e.g., erythroblastic leukemia and acute megakaryoblastic leukemia. Additional exemplary myeloid disorders include, but are not limited to, acute promyeloid leukemia (APML), acute myelogenous leukemia (AML) and chronic myelogenous leukemia (CML); lymphoid malignancies include, but are not limited to acute lymphoblastic leukemia (ALL) which includes B-lineage ALL and T-lineage ALL, chronic lymphocytic leukemia (CLL), prolymphocytic leukemia (PLL), haiy cell leukemia (HLL) and Waldenstrom's macroglobulinemia (WM). Additional forms of malignant lymphomas include, but are not limited to non-Hodgkin lymphoma and variants thereof, peripheral T cell lymphomas, adult T cell leukemia/lymphoma (ATL), cutaneous T-cell lymphoma (CTCL), large granular lymphocytic leukemia (LGF), Hodgkin's disease and Reed-Stemberg disease.
Examples of cellular proliferative and/or differentiative disorders of the breast include, but are not limited to, proliferative breast disease including, e.g., epithelial hyperplasia, sclerosing adenosis, and small duct papillomas; tumors, e.g., stromal tumors such as fibroadenoma, phyllodes tumor, and sarcomas, and epithelial tumors such as large duct papilloma carcinoma of the breast including in situ (noninvasive) carcinoma that includes ductal carcinoma in situ (including Pagets disease) and lobular carcinoma in situ, and invasive (infiltrating) carcinoma including, but not limited to, invasive ductal carcinoma, invasive lobular carcinoma, medullary carcinoma, colloid (mucinous) carcinoma, tubular carcinoma, and invasive papillary carcinoma, and miscellaneous malignant neoplasms. Disorders in the male breast include, but are not limited to, gynecomastia and carcinoma.
Examples of cellular proliferative and/or differentiative disorders of the lung include, but are not limited to, bronchogenic carcinoma, including paraneoplastic syndromes, bronchioloalveolar carcinoma, neuroendocrine tumors, such as bronchial carcinoid, miscellaneous tumors, and metastatic tumors; pathologies of the pleura, including inflammatory pleural effusions, noninflamatory pleural effusions, pneumothorax, and pleural tumors, including solitary fibrous tumors (pleural fibroma) and malignant mesothelioma.
Examples of cellular proliferative and/or differentiative disorders of the colon include, but are not limited to, non-neoplastic polyps, adenomas, familial syndromes, colorectal carcinogenesis, colorectal carcinoma, and carcinoid tumors.
Examples of cellular proliferative and/or differentiative disorders of the liver include, but are not limited to, nodular hyperplasias, adenomas, and malignant tumors, including primary carcinoma of the liver and metastatic tumors.
Examples of cellular proliferative and/or differentiative disorders of the ovary include, but are not limited to, ovarian tumors such as, tumors of coelomic epithelium, serous tumors, mucinous tumors, endometrioid tumors, clear cell adenocarcinoma, cystadenofibroma, Brenner tumor, surface epithelial tumors; germ cell tumors such as mature (benign) teratomas, monodermal teratomas, immature malignant teratomas, dysgerminoma, endodermal sinus tumor, choriocarcinoma sex cord-stomal tumors such as, granulosa-theca cell tumors, thecomafibromas, androblastomas, hill cell tumors, and gonadoblastoma; and metastatic tumors such as Krukenberg tumors.
In other or further embodiments, the peptidomimetic macrocycles described herein are used to treat, prevent or diagnose conditions characterized by overactive cell death or cellular death due to physiologic insult, etc. Some examples of conditions characterized by premature or unwanted cell death are or alternatively unwanted or excessive cellular proliferation include, but are not limited to hypocellular/hypoplastic, acellular/aplastic, or hypercellular/hyperplastic conditions. Some examples include hematologic disorders including but not limited to fanconi anemia, aplastic anemia, thalaessemia, congenital neutropenia, and myelodysplasia.
In other or further embodiments, the peptidomimetic macrocycles of the invention that act to decrease apoptosis are used to treat disorders associated with an undesirable level of cell death. Thus, in some embodiments, the anti-apoptotic peptidomimetic macrocycles of the invention are used to treat disorders such as those that lead to cell death associated with viral infection, e.g., infection associated with infection with human immunodeficiency virus (HIV). A wide variety of neurological diseases are characterized by the gradual loss of specific sets of neurons. One example is Alzheimer's disease (AD). Azheimer's disease is characterized by loss of neurons and synapses in the cerebral cortex and certain subcortical regions. This loss results in gross atrophy of the affected regions. Both amyloid plaques and neurofibrillary tangles are visible in brains of those afflicted by AD. Alzheimer's disease has been identified as a protein misfolding disease, due to the accumulation of abnormally folded A-beta and tau proteins in the brain. Plaques are made up of β-amyloid. β-amyloid is a fragment from a larger protein called amyloid precursor protein (APP). APP is critical to neuron growth, survival and post-injury repair. In AD, an unknown process causes APP to be cleaved into smaller fragments by enzymes through proteolysis. One of these fragments is fibrils of β-amyloid, which form clumps that deposit outside neurons in dense formations known as senile plaques. Plaques continue to grow into insoluble twisted fibers within the nerve cell, often called tangles. Disruption of the interaction between β-amyloid and its native receptor is therefore important in the treatment of AD. The anti-apoptotic peptidomimetic macrocycles of the invention are used, in some embodiments, in the treatment of AD and other neurological disorders associated with cell apoptosis. Such neurological disorders include Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis (ALS) retinitis pigmentosa, spinal muscular atrophy, and various forms of cerebellar degeneration. The cell loss in these diseases does not induce an inflammatory response, and apoptosis appears to be the mechanism of cell death.
In addition, a number of hematologic diseases are associated with a decreased production of blood cells. These disorders include anemia associated with chronic disease, aplastic anemia, chronic neutropenia, and the myelodysplastic syndromes. Disorders of blood cell production, such as myelodysplastic syndrome and some forms of aplastic anemia, are associated with increased apoptotic cell death within the bone marrow. These disorders could result from the activation of genes that promote apoptosis, acquired deficiencies in stromal cells or hematopoietic survival factors, or the direct effects of toxins and mediators of immune responses. Two common disorders associated with cell death are myocardial infarctions and stroke. In both disorders, cells within the central area of ischemia, which is produced in the event of acute loss of blood flow, appear to die rapidly as a result of necrosis. However, outside the central ischemic zone, cells die over a more protracted time period and morphologically appear to die by apoptosis. In other or further embodiments, the anti-apoptotic peptidomimetic macrocycles of the invention are used to treat all such disorders associated with undesirable cell death.
Some examples of neurologic disorders that are treated with the peptidomimetic macrocycles described herein include but are not limited to Alzheimer's Disease, Down's Syndrome, Dutch Type Hereditary Cerebral Hemorrhage Amyloidosis, Reactive Amyloidosis, Familial Amyloid Nephropathy with Urticaria and Deafness, Muckle-Wells Syndrome, Idiopathic Myeloma; Macroglobulinemia-Associated Myeloma, Familial Amyloid Polyneuropathy, Familial Amyloid Cardiomyopathy, Isolated Cardiac Amyloid, Systemic Senile Amyloidosis, Adult Onset Diabetes, Insulinoma, Isolated Atrial Amyloid, Medullary Carcinoma of the Thyroid, Familial Amyloidosis, Hereditary Cerebral Hemorrhage With Amyloidosis, Familial Amyloidotic Polyneuropathy, Scrapie, Creutzfeldt-Jacob Disease, Gerstmann Straussler-Scheinker Syndrome, Bovine Spongiform Encephalitis, a prion-mediated disease, and Huntington's Disease.
In another embodiment, the peptidomimetic macrocycles described herein are used to treat, prevent or diagnose inflammatory disorders. Numerous types of inflammatory disorders exist. Certain inflammatory diseases are associated with the immune system, for example, autoimmune diseases. Autoimmune diseases arise from an overactive immune response of the body against substances and tissues normally present in the body, i.e. self antigens. In other words, the immune system attacks its own cells. Autoimmune diseases are a major cause of immune-mediated diseases. Rheumatoid arthritis is an example of an autoimmune disease, in which the immune system attacks the joints, where it causes inflammation (i.e. arthritis) and destruction. It can also damage some organs, such as the lungs and skin. Rheumatoid arthritis can lead to substantial loss of functioning and mobility. Rheumatoid arthritis is diagnosed with blood tests especially the rheumatoid factor test. Some examples of autoimmune diseases that are treated with the peptidomimetic macrocycles described herein include, but are not limited to, acute disseminated encephalomyelitis (ADEM), Addison's disease, ankylosing spondylitis, antiphospholipid antibody syndrome (APS), autoimmune hemolytic anemia, autoimmune hepatitis, autoimmune inner ear disease, Bechet's disease, bullous pemphigoid, coeliac disease, Chagas disease, Churg-Strauss syndrome, chronic obstructive pulmonary disease (COPD), Cron's disease, dermatomyositis, diabetes mellitus type 1, endometriosis, Goodpastures syndrome, Graves' disease, Guillain-Barrd syndrome (GBS), Hashimotos disease, Hidradenitis suppurativa, idiopathic thrombocytopenic purpura, inflammatory bowl disease (IBD), interstitial cystitis, lupus erythematosus, morphea, multiple sclerosis, myasthenia gravis, narcolepsy, neuromyotonia, pemphigus vulgaris, pernicious anaemia, Polymyositis, polymyalgia rheumatica, primary biliary cirrhosis, psoriasis, rheumatoid arthritis, schizophrenia, scleroderma, Sjgrens syndrome, temporal arteritis (also known as “giant cell arteritis”), Takayasus arteritis, Vasculitis, Vitiligo, and Wegener's granulomatosis.
Some examples of other types of inflammatory disorders that are treated with the peptidomimetic macrocycles described herein include, but are not limited to, allergy including allergic rhinitis/sinusitis, skin allergies (urticaria/hives, angioedema, atopic dermatitis), food allergies, drug allergies, insect allergies, and rare allergic disorders such as mastocytosis, asthma, arthritis including osteoarthritis, rheumatoid arthritis, and spondyloarthropathies, primary angitis of the CNS, sarcoidosis, organ transplant rejection, fibromyalgia, fibrosis, pancreatitis, and pelvic inflammatory disease.
Examples of cardiovascular disorders (e.g., inflammatory disorders) that are treated or prevented with the peptidomimetic macrocycles of the invention include, but are not limited to, aortic valve stenosis, atherosclerosis, myocardial infarction, stroke, thrombosis, aneurism, heart failure, ischemic heart disease, angina pectoris, sudden cardiac death, hypertensive heart disease; non-coronary vessel disease, such as arteriolosclerosis, small vessel disease, nephropathy, hypertriglyceridemia, hypercholesterolemia, hyperlipidemia, xanthomatosis, asthma, hypertension, emphysema and chronic pulmonary disease; or a cardiovascular condition associated with interventional procedures (“procedural vascular trauma”), such as restenosis following angioplasty, placement of a shunt, stent, synthetic or natural excision grafts, indwelling catheter, valve or other implantable devices. Preferred cardiovascular disorders include atherosclerosis, myocardial infarction, aneurism, and stroke.
Other disorders that can be treated or prevented include, for example, retinal ischemia, pulmonary hypertension, intrauterine growth retardation, diabetic retinopathy, age-related macular degeneration, and diabetic macular edema. Yet another embodiment of this aspect of the present invention relates to a method of reducing or preventing angiogenesis in a tissue.
In another aspect, the compositions of the invention may be used to reduce transcription of a gene in a cell, where transcription of the gene is mediated by an interaction of HIF1α, such as interaction of HIF1α with CBP and/or p300. Genes whose transcription is mediated by interaction of HIF1α with CBP and/or p300 include adenylate kinase 3, aldolase A, aldolase C, enolase 1, glucose transporter 1, glucose transporter 3, glyceraldehyde-3-phosphate dehydrogenase, hexokinase 1, hexokinase 2, insulin-like growth factor 2, IGF binding protein 1, IGF binding protein 3, lactate dehydrogenase A, phosphoglycerate kinase 1, pyruvate kinase M, p21, transforming growth factor β3, ceruloplasmin, erythropoietin, transferrin, tranferrin receptor, alB-adrenergic receptor, adrenomedullin, endothelin-1, heme oxygenase 1, nitric oxide synthase 2, plasminogen activator inhibitor 1, vascular endothelial growth factor, vascular endothelial growth factor receptor FLT-1, vascular endothelial growth factor receptor KDR/Flk-1, and p35srg.
A second aspect of the present invention relates to inhibiting the HIF1α-p300/CBP interaction using the peptides of the present invention. One embodiment of this aspect of the present invention relates to a method of reducing transcription of a gene in a cell, where transcription of the gene is mediated by interaction of HIF1α with CREB-binding protein and/or p300. This method involves contacting the cell with a peptide of the present invention under conditions effective to cause nuclear uptake of the peptide, where the peptide disrupts interaction of HIF1α and p300/CBP and thereby reduces transcription of the gene. Genes whose transcription is mediated by interaction of HIF1α with CBP and/or p300 include adenylate kinase 3, aldolase A, aldolase C, enolase 1, glucose transporter 1, glucose transporter 3, glyceraldehyde-3-phosphate dehydrogenase, hexokinase 1, hexokinase 2, insulin-like growth factor 2, IGF binding protein 1, IGF binding protein 3, lactate dehydrogenase A, phosphoglycerate kinase 1, pyruvate kinase M, p21, transforming growth factor β3, ceruloplasmin, erythropoietin, transferrin, tranferrin receptor, alB-adrenergic receptor, adrenomedullin, endothelin-1, heme oxygenase 1, nitric oxide synthase 2, plasminogen activator inhibitor 1, vascular endothelial growth factor, vascular endothelial growth factor receptor FLT-1, vascular endothelial growth factor receptor KDR/Flk-1, and p35srg. Some uses for inhibiting transcription of these genes are shown in Table 4.
Another embodiment of this aspect of the present invention relates to a method of treating or preventing in a subject in need thereof a disorder mediated by interaction of HIF1α with CBP and/or p300. This method involves administering a peptide of the present invention to the subject under conditions effective to treat or prevent the disorder.
Disorders that can be treated or prevented include, for example, retinal ischemia (Zhu et al., “Long-term Tolerance to Retinal Ischemia by Repetitive Hypoxic Preconditioning: Role of HIF-1α and Heme Oxygenase-1,” Invest. Ophthalmol. Vis. Sci. 48: 1735-43 (2007); Ding et al., “Retinal Disease in Mice. Lacking Hypoxia-inducible Transcription Factor-2a,” Invest. Ophthalmol. Vis. Sci. 46:1010-6 (2005), each of which is hereby incorporated by reference in its entirety), pulmonary hypertension (Simon et al., “Hypoxia-induced Signaling in the Cardiovascular System,” Annu. Rev. Physiol. 70:51-71 (2008); Eul et al., “Impact of HIF-1α and HIF-2α on Proliferation and Migration of Human Pulmonary Artery Fibroblasts in Hypoxia,” FASEB J. 20:163-5 (2006), each of which is hereby incorporated by reference in its entirety), intrauterine growth retardation (Caramelo et al., “Respuesta a la Hipoxia. Un Mecanismo Sistemico Basado en el Control de la Expresion Genica [Response to Hypoxia A Systemic Mechanism Based on the Control of Gene Expression],” Medicina B. Aires 66: 155-{54(2006); Tazuke et al., “Hypoxia Stimulates Insulin-like Growth Factor Binding Protein I (IGFBP-1) Gene Expression in HepG2 Cells: A Possible Model for IGFBP-1 Expression in Fetal Hypoxia,” Proc. Nat'l Acad Sci. USA 95:10188-93 (1998), each of which is hereby incorporated by reference in its entirety), diabetic retinopathy (Ritter et al., “Myeloid Progenitors Differentiate into Microglia and Promote Vascular Repair in a Model of Ischemic Retinopathy,” J. Clin Invest. 116:3266-76 (2006); Wilkinson-Berka et al., “The Role of Growth Hormone, Insulin-like Growth Factor and Somatostatin in Diabetic Retinopathy,” Curr. Med Chem. 13:3307-17 (2006); Vinores et al., “Implication of the Hypoxia Response Element of the Vegf Promoter in Mouse Models of Retinal and Choroidal Neovascularization, but Not Retinal Vascular Development,” J. Cell. Physiol. 206:749-58 (2006); Caldwell et al., “Vascular Endothelial Growth Factor and Diabetic Retinopathy: Role of Oxidative Stress,” Curr. Drug Targets 6:511-24 (2005), each of which is hereby incorporated by reference in its entirety), age-related macular degeneration (Inoue et al., “Expression of Hypoxia-inducible Factor 1a and 2a in Choroidal Neovascular Membranes Associated with Age-related Macular Degeneration,” Br. J Ophthalmol. 91:1720-1 (2007); Zuluaga et al., “Synergies of VEGF Inhibition and Photodynamic Therapy in the Treatment of Age-related Macular Degeneration,” Invest. Ophthalmol. Vis. Sci 48:1767-72 (2007); Provis, “Development of the Primate Retinal Vasculature,” Prog. Retin Eye Res. 20:799-821 (2001), each of which is hereby incorporated by reference in its entirety), diabetic macular edema (Vinores et al., “Implication of the Hypoxia Response Element of the Vegf Promoter in Mouse Models of Retinal and Choroidal Neovascularization, but Not Retinal Vascular Development,” J Cell. Physiol. 206:749-58(2006); Forooghian & Das, “Anti-angiogenic Effects of Ribonucleic Acid Interference Targeting Vascular Endothelial Growth Factor and Hypoxia-inducible Factor-1α,” Am. J Ophthalmol. 144:761-8 (2007), each of which is hereby incorporated by reference in its entirety), and cancer (Marignol et aL, “Hypoxia in Prostate Cancer: A Powerful Shield Against Tumour Destruction?” Cancer Treat. Rev. 34:313-27 (2008); Galanis et al, “Reactive Oxygen Species and HIF-Signalling in Cancer,” Cancer Lett. 266: 12-20 (2008); Ushio-Fukai & Nakamura, “Reactive Oxygen Species and Angiogenesis: NADPH Oxidase as Target for Cancer Therapy,” Cancer Lett. 266:37-52 (2008); Adaski et al, “The Cellular Adaptations to Hypoxia as Novel Therapeutic Targets in Childhood Cancer,” Cancer Treat. Rev. 34:231-46 (2008); Toffoli & Michiels, “Intermittent Hypoxia Is a Key Regulator of Cancer Cell and Endothelial Cell Interplay in Tumours,” FEBS J. 275:2991-3002 (2008), each of which is hereby incorporated by reference in its entirety).
Yet another embodiment of this aspect of the present invention relates to a method of reducing or preventing angiogenesis in a tissue. This method involves contacting the tissue with a peptide of the present invention under conditions effective to reduce or prevent angiogenesis in the tissue. Another embodiment of this aspect of the present invention relates to a method of inducing apoptosis of a cell. This method involves contacting the cell with a peptide of the present invention under conditions effective to induce apoptosis of the cell. Another embodiment of this aspect of the present invention relates to a method of decreasing survival and/or proliferation of a cell. This method involves contacting the cell with a peptide of the present invention under conditions effective to decrease survival and/or proliferation of the cell. Contacting (including administering) according to this aspect of the present invention can be carried out using methods that will be apparent to the skilled artisan and as described above, and can be done in vitro or in vivo.
Some example target cells, tissues and/or organs for the embodiments described above are shown in Table 5.
Another aspect of the present invention relates to a method of identifying an agent that potentially inhibits interaction of HIF1α with CBP and/or p300. This method involves providing a peptide of the present invention, contacting the peptide with a test agent, and determining whether the test agent selectively binds to the peptide, wherein a test agent that selectively binds to the peptide is identified as a potential inhibitor of interaction between HIF1α with CBP and/or p300.
This aspect of the present invention can be carried out in a variety of ways, which will be apparent to the skilled artisan. For example, the affinity of the test agent for the peptide of the present invention may be measured using isothermal titration calorimetry analysis, as described in Example 4 (Wiseman et al., “Rapid Measurement of Binding Constants and Heats of Binding Using a New Titration Calorimeter,” Anal. Biochem. 179: 131-7 (1989); Freire et al., “Isothermal Titration Calorimetry,” Anal. Chem. 62:A950-A959 (1990); Chervenak & Toone, “Calorimetric Analysis of the Binding of Lectins with Overlapping Carbohydrate-binding Ligand Specificities,” Biochemistry 34:5685-95 (1995); Aki et al., “Competitive Binding of Drugs to the Multiple Binding Sites on Human Serum Albumin. A Calorimetric Study,” J Thermal Anal. Calorim. 57:361-70 (1999); Graziano et al., “Linkage of Proton Binding to the Thermal Unfolding of Sso7d from the Hyperthermophilic Archaebacterium Sulfolobus solfataricus,” Int'l J Biol. Macromolecules 26:45-53 (1999): Pluschke & Mutz, “Use of Isothennal Titration Calorimetry in the Development of Molecularly Defined Vaccines,” J. Thermal Anal. Calorim. 57:377-88 (1999); Corbell et al., “A Comparison of Biological and Calorimetric Analyses of Multivalent Glycodendrimer Ligands for Concanavalin A,” Tetrahedron-Asymmetry 11:95-111 (2000), which are hereby incorporated by reference in their entirety). In one embodiment, a test agent is identified as a potential inhibitor of interaction between HIF1α with CBP and/or p300 if the dissociation constant (Kd) for the test agent and the peptide of the invention is 50 μM or less. In another embodiment, the Kd is 200 nM or less. In yet another embodiment, the Kd is 100 nM or less.
Test agents identified as potential inhibitors of HIF1α-p300/CREB interaction may be subjected to further testing to confirm their ability to inhibit interaction between HIF1α with CBP and/or p300.
As used herein, the term “treatment” is defined as the application or administration of a therapeutic agent to a patient, or application or administration of a therapeutic agent to an isolated tissue or cell line from a patient, who has a disease, a symptom of disease or a predisposition toward a disease, with the purpose to cure, heal, alleviate, relieve, alter, remedy, ameliorate, improve or affect the disease, the symptoms of disease or the predisposition toward disease.
EXAMPLES Example 1: Peptidomimetic Macrocycles of the InventionPeptidomimetic macrocycles were synthesized, purified and analyzed as previously described and as described below (Schafmeister et al., J. Am. Chem. Soc. 122:5891-5892 (2000); Schafeister & Verdine, J. Am. Chem. Soc. 122:5891 (2005); Walensky et al., Science 305:1466-1470 (2004); and U.S. Pat. No. 7,192,713). Peptidomimetic macrocycles were designed by replacing two or more naturally occurring amino acids with the corresponding synthetic amino acids. Substitutions were made at i and i+4, and i and i+7 positions. Peptide synthesis was performed either manually or on an automated peptide synthesizer (Applied Biosystems, model 433A), using solid phase conditions, rink amide AM resin (Novabiochem), and Fmoc main-chain protecting group chemistry. For the coupling of natural Fmoc-protected amino acids (Novabiochem), 10 equivalents of amino acid and a 1:1:2 molar ratio of coupling reagents HBTU/HOBt (Novabiochem)/DIEA were employed. Non-natural amino acids (4 equiv) were coupled with a 1:1:2 molar ratio of HATU (Applied Biosystems)/HOBt/DIEA. The N-termini of the synthetic peptides were acetylated, while the C-termini were amidated.
Purification of cross-linked compounds was achieved by high performance liquid chromatography (HPLC) (Varian ProStar) on a reverse phase C18 column (Varian) to yield the pure compounds. Chemical composition of the pure products was confirmed by LC/MS mass spectrometry (Micromass LCT interfaced with Agilent 1100 HPLC system) and amino acid analysis (Applied Biosystems, model 420A).
Exemplary structures of several peptidomimetic macrocycles are shown.
SP-5 (X═S) (SEQ ID NO: 21) and SP-6 (X═CH2) (SEQ ID NO: 22)The ability of peptides to displace HIF1α c-terminal trans-activation domain from p300-CH was measured by a TR FRET assay. A complex of flag-tagged HIF1α (AA 786-826) and His6-tagged p300 (AA 323-423) was co-expressed using pETDuet vector (EMDMillipore, Bellrica Mass.) and purified from E. coli in the presence of 0.1 mM ZnSO4. The complex was diluted to 300 nM final in complete assay media and competitor peptides were added. The complete assay media contained 150 mM NaCl (Sigma +S5150 or equivalent), 20 mM HEPES pH 7.4 (Boston Bioproducts, Ashland, Mass.; #BB-2076), 7.5 mM CHAPS (Thermo #28300 or equivalent), and 1 mM DTT. Protein and peptide were incubated at room temperature for 1 hour before the addition of anti-Flag-K and anti-6×HIS-D2 (CisBio, Bedford Mass.) HTRF reconstitution buffer (50 mM Phosphate pH 7, 0.8 Potassium Flouride, BSA 0.2%)1 to a final concentration of 0.5 μM and 4 nM respectively. The reaction continued for an additional two hours at room temperature. The reaction was read on a TECAN F500 plate reader with settings recommended by CisBio. The ratio of donor to acceptor fluorescence was calculated. The resulting data was analyzed with Graphpad Prism 5.0. IC50 values were calculated for both proteins using the One Site Fit-LogIC50 equation and presented in the column “IC50 (nM) (HIF1α_p300 Displacement+CHAPS)” of Table 6. 1 Cisbio USA, Bedford, Mass.; 61HISDLB (lot 007A), 61FG2KLB (024A), HTRF Buffer (62RB3RDF)
Example 3: Reporter Gene AssayThe following reagents were used:
-
- DMEM+GutaMAX: (#10569044, Invitrogen)
- Black clear bottom plates: (#3603, Costar)
- HRE-bla-ME-180 cell line: (#K1644, Invitrogen)
- Gene-Blazer reagent & protocol: (#K1096, Invitrogen)
- Plate reader: Biotek Synergy 2
- Chetomin: (C9623, Sigma)
4 hours prior to experiment: HRE-bla ME-180 cells were seeded at a density of 20,000 cells/well in a volume of 180 μl in black clear bottom 96-well plates. 180 μl of assay medium was added to the cell-free control wells. Incubation was conducted at 37° C., 5% CO2 for 4 hours.
Diluted chetomin was used as a positive control. Chetomin was diluted in 100% DMSO to a 10 mM stock concentration. A 1 mM stock of chetomin was prepared in 100% DMSO. Then the 1 mM chetomin stock was serially diluted in 1:4 in 100% DMSO. Finally, 50, 12.5, 3.125, 0.78, 0.2, 0.05 μM stock of chetomin in 5% DMSO/water were prepared by adding 114 μL water+6 μL chetomin in DMSO.
Test peptides were diluted before use. The test peptides were diluted in 100% DMSO to a 10 mM stock concentration. Then each 10 mM peptide stock was diluted in 1:3 in 100% DMSO. Finally, 300, 100, 33.3, 11.1, 3.7, 1.2 μM stock of each peptide in 5% DMSO/water were prepared by adding 129.2 μL water+4 μL peptide in DMSO.
20 μl of peptide, chetomin dilution, or DMSO/water control were added to the appropriate wells of a plate to achieve 200 μL final volumes in 0.3% DMSO/media. The plate was first incubated for 18-20 hours in normoxia incubator (37° C. in humidified 5% CO2, 20% O2 atmosphere). Then the plate was transferred to hypoxia incubator for 24 hours (37° C. in humidified 5% CO2, 1% O2 atmosphere)
Day +1: (all Work in the Absence of Strong Light)6× LiveBLAzer™-FRET B/G (CCF4-AM) Substrate Mixture was prepared according to CellSensor™ HRE-bla ME-180 Cell-based Assay Protocol (Invitrogen) and added into each well. Solution A (CCF4-AM) was reconstituted in DMSO to a working concentration of 1 mM, divided in aliquots, and stored at −20° C. The 6× LiveBLAzer-FRET B/G (CCF4-AM) Substrate mixture was prepared by mixing 6 μl of Solution A, 60 μl of Solution B, and 934 μl Solution C.
The plates were removed from incubator and equilibrated to RT for a few minutes. Then 20 μl of 6× Substrate mixture was added to each well. The plates were then incubated at room temperature for 3 hr in the dark and read at 409 Ex/460Em and 409Ex/530Em using the “GeneBlazer-Tungsten with export” program on the Synergy 2.
Results:The average percentage of maximum inhibition was obtained by comparing the peptide treated cells (30 μM) to DMSO vehicle control treated cells. The results are shown in the columns “ME-180 HIF Reporter EC50 (μM) −24 hr normoxia” and “18 h Avg % max inhibition at top conc (HIF Rptr-24 hrsnormoxia) (μM)” of Table 6.
SP-6 effectively inhibited several known HIF1α targets, including ANGPTL4, CA9 and ALDOC which regulate angiogenesis and tumor metabolism in ME-180 cervical cancer cells, as shown in
The human cervical cell line HRE-Bla ME-180 was obtained from Invitrogen. 2×104 ME-180 cells were plated in 96-well plates (costar) in Opti-MEM plus 1% FBS (Invitrogen). After 4 hr, cells were pretreated with chetomin, peptide or 0.5% DMSO (final concentration in media) vehicle control for 16 hr under normoxia (21% O2); then incubation continued under normoxia or hypoxia (1% O2) using a hypoxia incubator (Thermo Forma model). Viable cell numbers were quantified using CellTiter 96 Non-Radioactive Cell Proliferation kit (Promega, G4100). The results are presented in the column “Viability 1% FBS AVG (MTT V3-24 hr Normoxia) (μM)” of Table 6.
Example 4: qRT-PCRThe human cervical cell line HRE-Bla ME-180 was obtained from Invitrogen. 1.2×105 ME-180 cells were plated in 24-well plates (costar) in Opti-MEM plus 1% FBS (Invitrogen). 4 hrs later, cells were pretreated with chetomin, peptide or 0.5% DMSO (final concentration in media) vehicle control for 16 hrs under normoxia (21% O2); then incubation continued under normoxia or hypoxia (1% O2) for 12 hrs using a hypoxia incubator (Thermo Forma model). Total RNA was isolated with an Rneasy Plus mini Kit (Qiagen) and cDNA was synthesized with cDNA synthesis Kit and then amplified with angiopoietin-like 4 (Angpt14, Hs01101127_m1, Invitrogen); CA9 (Hs00154208_m1, Invitrogen); aldolase C (ALDOC, Hs00193059_m1, Invitrogen); SLC2A1 (Glut1, Hs00892681_m1, Invitrogen); EP300 (p300, Hs00914223_m1, Invitrogen); ARNT (HIF1b, Hs00231048_m1, Invitrogen).
Example 5: Western Blot AnalysisThe human cervical cell line HRE-Bla ME-180 was obtained from Invitrogen. 6.2×105 cells were plated in 6-well plates (costar) in Opti-MEM plus 1% FBS (Invitrogen). 4 hrs later, cells were pretreated with chetomin, peptide or 0.5% DMSO (final concentration in media) vehicle control for 16 hrs under normoxia (21% O2); then incubation continued under normoxia or hypoxia (1% O2) for 24 hrs using a hypoxia incubator (Thermo Forma model). Total cell lysate form control, chetomin treated or SP-6 treated ME-180 cells were separated by SDS-PAGE and probed with anti-CA9 (1:2000, NB100-417, Novus biologicals) and anti HSC70 (1:5000, ab19136, Abcam). The results demonstrate that the protein level of Carbonic anhydrase 9 (CA9) was down-regulated by treating with SP-6 in ME-180 cells, as shown in
Biolayer inferometry (ForteBio, Menlo Park Calif.) was used to measure competition of SP-6 for HIF1α (AAs 788-826). Biotinylated HIF1α peptide was captured on Ni-NTA biosensor tip. The association of 300 nM GST-tagged p300 CH1 domain (AAs 302-423) in the presence or absence of varying concentrations of SP-6 was measured for 240 s. Dissociation was monitored for a minimum of 200 s in the absence of free p300 or stapled peptide. Binding of p300 to biosensor immobilized HIF1α target was analyzed with instrument software and total response (R) was proportional to binding.
The results are shown in
A xenograft study was performed to test the efficacy of SP-6 in inhibiting tumor growth in athymic mice in the PC-3 human prostate carcinoma xenograft model. PC-3 tumor fragments were implanted subcutaneously (sc) in the flank of athymic nude mice. Once the implanted tumor fragments had grown sufficiently (Day 1), sc tumors were measured using calipers to determine their length and width and the mice were weighed. The tumor sizes were calculated using the formula (length×width2)/2 and expressed as cubic millimeters (mm3). Mice with tumors smaller than 108 mm3 or larger than 162 mm3 were excluded from subsequent group formation. Groups of mice, 10 mice per group, were formed by randomization such that the group mean tumor sizes were essentially equivalent (mean of groups±standard error of the means of groups=128.4±0.6 mm3).
Each group received treatment intravenously (IV) on an every other day basis starting on Day 1 for a total of 12 injections (Days 1-24); volume of dosing solution to be administered was based on the weight of the mouse taken on each dosing day. The negative control vehicle group received vehicle administered at 10 mL/kg body weight. Two groups were administered SP-6 at either 50 or 25 mg/kg per dosing day in a single IV injection on that day of 10 mL/kg of a dosing solution of SP-6 of 5 or 2.5 mg/mL, respectively.
During the treatment and tumor measurement period (Days 1-24) the mice were weighed and tumors measured two to three times per week. Treatment with SP-6 was well-tolerated as evidenced by no significant decrease in body weight in the SP-6 treated groups compared with the negative control vehicle group. Results in terms of tumor volume are shown in
SP-6 effectively inhibited tumor growth, as shown in
While preferred embodiments of the present invention have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention. It should be understood that various alternatives to the embodiments of the invention described herein may be employed in practicing the invention. It is intended that the following claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.
Claims
1-132. (canceled)
133. A method of modulating Hypoxia-Inducible Factor 1-alpha (HIF1α) activity in a cell, comprising administering to the cell an effective amount of a peptidomimetic macrocycle having Formula (I): wherein: wherein administering of the peptidomimetic macrocycle modulates HIF-1α activity in the cell.
- each A, C, D, and E is independently an amino acid,
- B is an amino acid,
- [—NH-L3-CO—], [—NH-L3-SO2—], or [—NH-L3-], wherein A, B, C, D, and E, taken together with the cross-linked amino acids connected by the macrocycle-forming linker L, form the amino acid sequence of the peptidomimetic macrocycle;
- each L is independently a macrocycle-forming linker of the formula -L1-L2- or the formula
- each R1 and R2 are independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, cycloalkylalkyl, heteroalkyl, or heterocycloalkyl, each of which except for —H is optionally substituted with halo;
- each R3 is —H, alkyl, alkenyl, alkynyl, arylalkyl, heteroalkyl, cycloalkyl, heterocycloalkyl, cycloalkylalkyl, cycloaryl, or heterocycloaryl, each of which except for —H is optionally substituted with R5;
- each L1, L2, and L3 is independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, cycloarylene, heterocycloarylene, or [—R4—K—R4-]n, each being optionally substituted with R5; each R4 is alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, arylene, or heteroarylene; each K is O, S, SO, SO2, CO, CO2, or CONR3;
- each R5 is independently halogen, alkyl, —OR6, —N(R6)2, —SR6, —SOR6, —SO2R6, —CO2R6, a fluorescent moiety, a radioisotope, or a therapeutic agent; each R6 is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heterocycloalkyl, a fluorescent moiety, a radioisotope, or a therapeutic agent;
- each R7 is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, cycloaryl, or heterocycloaryl, each of which except for —H is optionally substituted with R5, or part of a cyclic structure with a D residue;
- each R8 is independently —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, cycloaryl, or heterocycloaryl, each of which except for —H is optionally substituted with R5, or part of a cyclic structure with an E residue;
- each R9 is independently alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, heteroaryl, or heterocyclyl group, unsubstituted or optionally substituted with Ra and/or Rb;
- Ra and Rb are independently alkyl, OCH3, CF3, NH2, CH2NH2, F, Br, I,
- each v and w is independently integers from 1-100;
- u is an integer from 1 to 3;
- each x, y and z is independently integers from 0-10; and
- each n is independently an integer from 1-5,
134. The method of claim 133, wherein u is 1.
135. The method of claim 133, wherein the sum of x+y+z is 2, 3, or 6.
136. The method of claim 133, wherein the sum of x+y+z is 3.
137. The method of claim 133, wherein [A]x-[B]y-[C]z comprises Leu-Val-Ile.
138. The method of claim 133, wherein R1 and R2 are H.
139. The method of claim 133, wherein R1 and R2 are independently alkyl.
140. The method of claim 133, wherein R1 and R2 are methyl.
141. The method of claim 133, wherein L1 and L2 are independently alkylene, alkenylene, or alkynylene.
142. The method of claim 133, wherein the peptidomimetic macrocycle is or a pharmaceutically acceptable salt thereof.
143. The method of claim 133, wherein the peptidomimetic macrocycle is wherein:
- L′ is a macrocycle-forming linker of the formula -L1′-L2′- or the formula
- L1′ and L2′ are independently alkylene, alkenylene, alkynylene, heteroalkylene, cycloalkylene, heterocycloalkylene, cycloarylene, heterocycloarylene, or [—R4—K—R4-]n, each being optionally substituted with R5;
- R8′ is —H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkyl, heteroalkyl, cycloalkylalkyl, heterocycloalkyl, cycloaryl, or heterocycloaryl, each of which except for —H is optionally substituted with R5, or part of a cyclic structure with an E residue;
- R9′ is alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, heteroaryl, or heterocyclyl group, unsubstituted or optionally substituted with Ra′ and/or Rb′;
- Ra′ and Rb′ are independently alkyl, OCH3, CF3, NH2, CH2NH2, F, Br, I,
- and x′, y′, and z′ are independently integers from 0-10.
144. The method of claim 143, wherein the sum of x+y+z and the sum of x′+y′+z′ are independently 2, 3, or 6.
145. The method of claim 143, wherein the sum of x+y+z is 3, and the sum of x′+y′+z′ is 3.
146. The method of claim 143, wherein the peptidomimetic macrocycle is or a pharmaceutically acceptable salt thereof.
147. The method of claim 133, wherein the peptidomimetic macrocycle is at least about 70%, 75%, 80%, 85%, 90%, or 95% identical to an amino acid sequence of FIDEEVLMSLVIEMALDRI.
148. The method of claim 133, wherein administering of the peptidomimetic macrocycle inhibits HIF-1α activity in the cell.
149. The method of claim 133, wherein administering of the peptidomimetic macrocycle antagonizes an interaction of HIF1α with CREB-binding protein and/or p300 in the cell.
150. The method of claim 133, wherein administering of the peptidomimetic macrocycle reduces transcription of a gene that is mediated by interaction of HIF1α with CREB-binding protein and/or p300 in the cell.
151. The method of claim 133, wherein administering of the peptidomimetic macrocycle reduces angiogenesis in the cell.
152. The method of claim 133, wherein administering of the peptidomimetic macrocycle induces apoptosis in the cell.
Type: Application
Filed: Jan 30, 2019
Publication Date: Jul 25, 2019
Inventors: Vincent GUERLAVAIS (Arlington, MA), Noriyuki KAWAHATA (West Roxbury, MA), Huw M. NASH (Lexington, MA), Carl ELKIN (Arlington, MA), Eric FEYFANT (Lexington, MA)
Application Number: 16/262,121
