US2010144641A1PendingUtilityA1
Compositions Having Antiangiogenic Activity and Uses Thereof
Individually held — no corporate assignee on recordPriority: Sep 12, 2005Filed: Sep 12, 2006Published: Jun 10, 2010
Est. expirySep 12, 2025(expired)· nominal 20-yr term from priority
A61P 37/02A61P 35/02A61P 43/00A61P 9/10A61P 9/00A61P 37/08A61P 27/02A61P 3/04A61P 31/12A61P 35/00A61P 31/04A61P 29/00C12N 9/6489C07K 14/472A61P 11/00C07K 14/475A61P 15/00C07K 14/47C07K 14/78C12N 9/6421A61P 17/06A61P 13/00A61P 1/04A61P 17/00A61P 11/06A61P 19/02
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Claims
Abstract
The invention generally features compositions and methods that are useful for modulating blood vessel formation, as well as methods that provide for the systematic and efficient identification of angiogenesis modulators. As described in more detail below, a systematic computational methodology based on bioinformatics was used to identify novel peptide modulators of angiogenesis that have been characterized in vitro and/or in vivo.
Claims
exact text as granted — not AI-modified1 . An isolated peptide or analog thereof comprising the amino acid sequence W-X 2 -C-X 3 -C-X 2 -G (SEQ ID NO: 161, wherein X denotes a variable amino acid; W is tryptophan; C is cysteine, G is glycine; and wherein the peptide reduces blood vessel formation in a cell, tissue or organ.
2 . The isolated peptide of claim 1 , wherein the peptide comprises at least 11 amino acids of a thrombospondin-1 domain or thrombospondin-2 domain.
3 . The isolated peptide of claim 1 , wherein the peptide comprises at least 15 amino acids of a thrombospondin-1 domain or thrombospondin-2 domain.
4 . The isolated peptide of claim 1 , wherein the peptide comprises at least 20 amino acids of a thrombospondin-1 domain or thrombospondin-2 domain.
5 . The isolated peptide of claim 1 , wherein the peptide comprises or consists essentially of 10 amino acids of a thrombospondin containing protein of Table 1 (SEQ ID Nos: 1-76).
6 . The isolated peptide of claim 5 , wherein the peptide comprises or consists essentially of 12 amino acids of a thrombospondin containing protein of Table 1 (SEQ ID Nos: 1-76).
7 . The isolated peptide of claim 6 , wherein the peptide comprises or consists essentially of at least 15 amino acids of the thrombospondin containing protein.
8 - 9 . (canceled)
10 . An isolated peptide or analog thereof comprising a 20 amino acid (AA) sequence having positions AA1-AA20 (SEQ ID NO: 162), wherein:
AA1 is X, S, T, G, Q, or A; AA2 is X, P, E, S, A, Q, or K; AA3 is W; AA4 is X, S, T, G, E, D, R, or A; AA5 is X, P, A, Q, D, E, K, R, or V; AA6 is C; AA7 is X, S, N, or T; AA8 is X, V, A, R, K, G, S, T, or E; AA9 is X, T, S, R, or N; AA10 is C; AA11 is X, G, S, or N; AA12 is X, G, K, R, M, T, L, D, S, or P; AA13 is G; AA14 is X, V, I, M, T, H, A, E, F, K, R, S, Q, W, or Y; AA15 is X, Q, S, R, K, Y, or A; AA16 is X, T, F, K, Q, S, L, E, M, N, or V; AA17 is X, R, S, or Q; AA18 is X, S, T, V, R, H, E, Q, A, or I; AA19 is X, R, or V; and AA20 is R;
wherein X denotes a variable amino acid; W is tryptophan; C is cysteine, T is threonine, S is serine; N is asparagine; G is glycine; R is arginine; V is valine, P is proline, and Q is glutamine; and wherein the peptide reduces blood vessel formation in a cell, tissue or organ.
11 . The isolated peptide of claim 10 , comprising or consisting an amino acid sequence selected from the group consisting of:
(SEQ ID NO: 163)
W-X 2 -C-(T/S/N)-X 2 -C-X 2 -G;
(SEQ ID NO: 164)
W-X 2 -C-S-X 2 -C-G-X-G-X 3 -R-X 3 ;
(SEQ ID NO: 165)
W-X 2 -C-S-X 2 -C-G-X 1 -G-X 3 -R-X 1 -(R/V);
(SEQ ID NO: 166)
W-X 2 -C-S-X-(S/R/T)-C-G-X-G-X 3 -R-X-(R/V)-X;
(SEQ ID NO: 167)
W-X 2 -C-(T/S/N)-X2-C-X2-G-XS-(R/V);
(SEQ ID NO: 168)
P-W-X 2 -C-X 3 -C-X 2 -G;
and
(SEQ ID NO: 169)
(S/G/Q)-P-W-X 2 -C-(T/S)-X 2 -G-(G/S)-X 1 -G-X 3 -(R/S).
12 . An isolated peptide or analog thereof comprising:
(i) at least a fragment of a thrombospondin containing protein, wherein the peptide reduces blood vessel formation in a tissue or organ and comprises a sequence having at least 85% amino acid sequence identity to an amino acid sequence selected from the thrombospondin containing protein listed in Table 1 (SEQ ID Nos: 1-76); or. (ii) a sequence having at least 85% amino acid sequence identity to an amino acid sequence selected from the group consisting of:
THSD-1:
QPWSQCSATCGDGVRERRR;
(SEQ ID NO: 64)
THSD-3:
SPWSPCSGNCSTGKQQRTR;
(SEQ ID NO: 65)
THSD-6:
WTRCSSSCGRGVSVRSR;
(SEQ ID NO: 66)
CILP:
SPWSKCSAACGQTGVQTRTR;
(SEQ ID NO: 39)
WISP-1:
SPWSPCSTSCGLGVSTRI;
(SEQ ID NO: 74)
WISP-2:
TAWGPCSTTCGLGMATRV;
(SEQ ID NO: 75)
WISP-3:
TKWTPCSRTCGMGISNRV;
(SEQ ID NO: 76)
F-spondin:
SEWSDCSVTCGKGMRTRQR;
(SEQ ID NO: 73)
F-spondin:
WDECSATCGMGMKKRHR;
(SEQ ID NO: 72)
CTGF:
TEWSACSKTCGMGISTRV;
(SEQ ID NO: 41)
fibulin-6:
ASWSACSVSCGGGARQRTR;
(SEQ ID NO: 45)
fibulin-6:
QPWGTCSESCGKGTQTRAR;
(SEQ ID NO: 44)
fibulin-6:
SAWRACSVTCGKGIQKRSR;
(SEQ ID NO: 43)
CYR61:
TSWSQCSKTCGTGISTRV;
(SEQ ID NO: 42)
NOVH:
TEWTACSKSCGMGFSTRV;
(SEQ ID NO: 46)
UNC5-C:
TEWSVCNSRCGRGYQKRTR;
(SEQ ID NO: 79)
UNC5-D:
TEWSACNVRCGRGWQKRSR;
(SEQ ID NO: 71)
SCO-spondin:
GPWEDCSVSCGGGEQLRSR;
(SEQ ID NO: 63)
Properdin:
GPWEPCSVTCSKGTRTRRR;
(SEQ ID NO: 49)
C6:
TQWTSCSKTCNSGTQSRHR;
(SEQ ID NO: 38)
ADAMTS-like-4:
SPWSQCSVRCGRGQRSRQVR;
(SEQ ID NO: 69)
ADAMTS4:
GPWGDCSRTCGGGVQFSSR;
(SEQ ID NO: 7)
ADAMTS-8:
GPWGECSRTCGGGVQFSHR;
(SEQ ID NO: 14)
ADAMTS-16:
SPWSQCTASCGGGVQTR;
(SEQ ID NO: 24)
ADAMTS-18:
SKWSECSRTCGGGVKFQER;
(SEQ ID NO: 29)
semaphorin 5A:
GPWERCTAQCGGGIQARRR;
(SEQ ID NO: 60)
semaphorin 5A:
SPWTKCSATCGGGHYMRTR;
(SEQ ID NO: 61)
semaphoring 5B:
TSWSPCSASCGGGHYQRTR;
(SEQ ID NO: 62)
papilin:
GPWAPCSASCGGGSQSRS;
(SEQ ID NO: 48)
papilin:
SQWSPCSRTGGGGVSFRER;
(SEQ ID NO: 47)
ADAM-9:
KCHGHGVCNS;
(SEQ ID NO: 157)
and
ADAM-12:
MQCHGRGVCNNRKN,
(SEQ ID NO: 2)
wherein A is alanine; I is isoleucine; M is methionine; H is histidine; Y is tyrosine; K is lysine; W is tryptophan; C is cysteine, T is threonine, S is serine; N is asparagine; G is glycine; R is arginine; V is valine, P is proline, and Q is glutamine wherein the peptide reduces blood vessel formation in a cell, tissue or organ; or
(iii) the amino acid sequence G-X 3 -C-L-X-P-X 10 -K-X-L (SEQ ID NO: 170), wherein X denotes a variable amino acid; G denotes Glycine; C denotes cysteine; L denotes leucine; P denotes proline; K is lysine; and the peptide reduces blood vessel formation in a cell, tissue or organ; or
(iv) a 22 amino acid sequence having positions AA1-AA22 (SEQ ID NO: 171), wherein:
AA1 is X, N or D;
AA2 is G;
AA3 is X, R or K;
AA4 is X, K, E, or Q;
AA5 is X, A, I, L, or V;
AA6 is C;
AA7 is L;
AA8 is X, D or N;
AA9 is P;
AA10 is X, A, E, D, or K;
AA11 is X, A, S, or E;
AA12 is P;
AA13 is X, F, I, M, R, or W;
AA14 is X, V, L, or I;
AA15 is X, K or Q;
AA16 is X, K or R;
AA17 is X, I or V;
AA18 is X, I or V;
AA19 is X, E or Q;
AA20 is K;
A21 is X, I, F, K, or M; and
AA22 is L;
wherein X denotes a variable amino acid; A is alanine; I is isoleucine; F is phenylalanine; D is aspartic acid; M is methionine; H is histidine; Y is tyrosine; K is lysine; W is tryptophan; C is cysteine, T is threonine, S is serine; N is asparagine; G is glycine; R is arginine; V is valine, P is proline, and Q is glutamine; and wherein the peptide reduces blood vessel formation in a cell, tissue or organ; or
(v) an amino acid sequence selected from the group consisting of:
G-X 3 -C-L-X-P-X 10 -K-X-L;
(SEQ ID NO: 170)
(N/D/K)-G-X 3 -C-L-(D/N)-(P/L)-X 5 -(K/Q)-(K/R/N)-(I/V/L)-(I/V/L)-X 6 ;
(SEQ ID NO: 172)
and
(N/D)-G-(R/K)-X 2 -C-L-(N/D)-P-X 2 -(P/N)-X 2 -(K/Q)-(K/Q)-(I/V)-(I/V)-(E/Q)-K-X-L;
(SEQ ID NO: 173)
or
(vi a sequence that has at least 85% amino acid sequence identity to a CXC Chemokine protein listed in Table 1 (SEQ ID Nos: 95-116); or
(vii) a sequence having at 85% identity to an amino acid sequence selected from the group consisting of:
ENA-78:
NGKEICLDPEAPFLKKVIQKILD;
(SEQ ID NO: 95)
CXCL6:
NGKQVCLDPEAPFLKKVIQKILDS;
(SEQ ID NO: 98)
CXCL1:
NGRKACLNPASPIVKKIIEKMLNS;
(SEQ ID NO: 102)
Gro-γ:
NGKKACLNPASPMVQKIIEKIL;
(SEQ ID NO: 106)
Beta thromboglobulin/CXCL7:
DGRKICLDPDAPRIKKIVQKKL,
(SEQ ID NO: 114)
Interleukin 8(IL-8)/CXCL8:
DGRELCLDPKENWVQRVVEKFLK,
(SEQ ID NO: 110)
GCP-2:
NGKQVCLDPLAPFLKKVIQKILDS,
(SEQ ID NO: 98)
wherein A is alanine; I is isoleucine; F is phenylalanine; D is aspartic acid; M is methionine; H is histidine; Y is tyrosine; K is lysine; W is tryptophan; C is cysteine, T is threonine, S is serine; N is asparagine; G is glycine; R is arginine; V is valine, P is proline, and Q is glutamine; and wherein the peptide reduces blood vessel formation in a cell, tissue or organ, or
(viii) a peptide comprises at least a fragment of a C-X-C chemokine protein of Table 1.
(ix) an amino acid sequence C-N-X 3 -V-C (SEQ ID NO: 174) or P-F-X-E-C-X-G-X 5 -A-N (SEQ ID NO: 175), wherein X denotes a variable amino acid; F is phenylalanine; C is cysteine, N is asparagine; G is glycine; V is valine, P is proline, and Q is glutamine wherein the peptide reduces blood vessel formation in a cell, tissue or organ;
(x) a sequence comprising at least a fragment of a type IV collagen C4 polypeptide, wherein the peptide reduces blood vessel formation in a cell, tissue or organ and comprises a sequence having at least 85% identity to an amino acid sequence selected from collagen proteins listed in Table 1;
(xi) one of the following amino acid sequences,
C-N-X 3 -V-C-X2-A-X-R-N-D-X-S-Y-W-L (SEQ ID NO: 176); or
L-X2-F-S-T-X-P-F-X 2 -C-N-X 3 -V-C (SEQ ID NO: 177), wherein the peptide reduces blood vessel formation in a cell, tissue or organ; or
(xii) an amino acid sequence P-F-(I/L)-E-C-X-G-X-(R/G)-X-(Y/F)-(Y/F)-A-N (SEQ ID NO: 178), wherein the peptide reduces blood vessel formation in a cell, tissue or organ;
(xiii) a sequence having at least 85% amino acid sequence identity to an amino acid sequence selected from the group consisting of
Alpha 6 fibril of type 4 collagen:
YCNINEVCHYARRNDKSYWL;
(SEQ ID NO: 93)
Alpha 5 fibril of type 4 collagen:
LRRFSTMPFMFCNINNVCNF;
(SEQ ID NO: 89)
Alpha 4 fibril of type 4 collagen:
AAPFLECQGRQGTCHFFAN;
(SEQ ID NO. 87)
Alpha 4 fibril of type 4 collagen:
LPVFSTLPFAYCNIHQVCHY;
(SEQ ID NO: 85)
and
Alpha 4 fibril of type 4 collagen:
YCNIHQVCHYAQRNDRSYWL,
(SEQ ID NO: 86)
wherein A is alanine; I is isoleucine; F is phenylalanine; D is aspartic acid; M is methionine; H is histidine; Y is tyrosine; K is lysine; W is tryptophan; C is cysteine, T is threonine, S is serine; N is asparagine; G is glycine; R is arginine; V is valine, P is proline, and Q is glutamine wherein the peptide reduces blood vessel formation in a cell, tissue or organ
(xiv) an amino acid sequence E-C-L-W-X-D-X 8 -G-X-Y-X 5 -C (SEQ ID NO: 179), wherein the peptide reduces blood vessel formation in a cell, tissue or organ;
(xv) a peptide comprising or consisting essentially of twenty-three amino acids of a TIMP protein listed in Table 1; or
(xvi) a peptide comprising or consisting essentially of at least twenty-four amino acids of a TIMP protein listed in Table 1; or
(xvii) a peptide comprising or consisting essentially of 30 amino acids of a TIMP protein listed in Table 1; or
(xviii) a peptide comprising or consisting essentially of an amino acid sequence having at least 85% amino acid sequence identity to ECLWTDMLSNFGYPGYQSKHYACI (SEQ ID NO: 155), wherein the peptide reduces blood vessel formation in a cell, tissue or organ; or
(xiv) a fragment of a TIMP, wherein the peptide comprises a sequence having at least 85% amino acid sequence identity to an amino acid sequence selected from TIMP protein listed in Table 1, and wherein the peptide reduces blood vessel formation in a cell, tissue or organ; or
(xv) a fragment of an amino acid sequence selected from the group consisting of SEQ ID Nos. 1-156; or
(xvi) a peptide comprising or consisting essentially of an amino acid sequence having at least 85% identity to an amino acid sequence selected from the group consisting of SEQ ID Nos. 1-156.
13 - 38 . (canceled)
39 . The isolated peptide of claim 12 , wherein the peptide comprises at least one modification.
40 - 42 . (canceled)
43 . A peptide conjugate comprising a peptide having an amino acid sequence selected from the group consisting of SEQ ID Nos. 1-156 conjugated to an agent that specifically binds a tumor marker or endothelial cell marker.
44 - 46 . (canceled)
47 . An isolated nucleic acid molecule encoding the peptide of claim 12 .
48 . An expression vector comprising the nucleic acid molecule of claim 47 , wherein the nucleic acid molecule is positioned for expression.
49 . (canceled)
50 . A host cell comprising the peptide of claim 1 or a nucleic acid molecule encoding the peptide.
51 - 53 . (canceled)
54 . A method of reducing blood vessel formation in a tissue or organ, the method comprising contacting an endothelial cell, or a tissue or organ comprising an endothelial cell with an effective amount of a peptide of claim 1 any one of claims 1 - 35 , thereby reducing blood vessel formation in the tissue or organ.
55 . A method of reducing endothelial cell proliferation, migration, survival, or stability in a tissue or organ, the method comprising contacting tissue or organ comprising an endothelial cell with an effective amount of a peptide of claim 1 , thereby reducing endothelial cell proliferation, migration, survival, or stability in the tissue or organ.
56 . A method of increasing endothelial cell death in a tissue or organ, the method comprising contacting a tissue or organ comprising an endothelial cell with an effective amount of a peptide of claim 1 or a peptide conjugate, thereby increasing endothelial cell death in the tissue or organ.
57 . (canceled)
58 . A method of reducing blood vessel formation in a tissue or organ the method comprising:
(a) contacting the tissue, or organ with a vector encoding a polypeptide comprising SEQ ID Nos. 1-156; and (b) expressing the polypeptide in a cell of the tissue or organ, thereby reducing blood vessel formation in the tissue or organ.
59 - 63 . (canceled)
64 . A method for decreasing blood vessel formation in a subject in need thereof, the method comprising administering an effective amount of a peptide of claim 1 or a peptide conjugate to the subject thereby decreasing blood vessel formation.
65 . A method of reducing endothelial cell proliferation, migration, survival, or stability in a subject in need thereof; the method comprising administering an effective amount of a peptide of claim 1 or a peptide conjugate to the subject thereby reducing endothelial cell proliferation, migration, survival, or stability in the tissue or organ.
66 . A method of increasing endothelial cell death in a subject in need thereof the method comprising administering an effective amount of a peptide of claim 1 or a peptide conjugate to the subject, thereby increasing endothelial cell death in the subject.
67 - 81 . (canceled)
82 . A pharmaceutical composition comprising an effective amount of an isolated peptide of claims 1 or a peptide conjugate in a pharmacologically acceptable excipient.
83 . A pharmaceutical composition comprising an effective amount of a nucleic acid molecule or portion thereof encoding a peptide of claim 1 or a peptide conjugate in a pharmacologically acceptable excipient.
84 . (canceled)
85 . A method for identifying an amino acid sequence of interest, the method comprising:
(a) identifying an initial polypeptide or fragment thereof having amino acid sequence identity to a reference sequence having a biological function of interest; (b) generating a random sequence comprising the amino acid composition of the initial polypeptide of interest and comparing the random sequence to the reference sequence to determine amino acid sequence identity, wherein said amino acid sequence identity determines a random sequence cut-off value; (c) comparing the sequence identity of step a to the random sequence cut-off value of set b, wherein a sequence identity that is significantly greater than the random sequence cut-off value identifies an amino acid sequence of interest.
86 - 91 . (canceled)Join the waitlist — get patent alerts
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