US2020231638A1PendingUtilityA1
Stabilized anti-microbial peptides
Assignee: DANA FARBER CANCER INST INCPriority: Jul 2, 2015Filed: Aug 26, 2019Published: Jul 23, 2020
Est. expiryJul 2, 2035(~9 yrs left)· nominal 20-yr term from priority
C07K 14/463A61P 31/00A61K 38/1729A01N 43/90A61K 38/00A61P 31/04Y02A50/30
57
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Claims
Abstract
The present invention provides methods of designing and making structurally stabilized anti-microbial peptides for the prophylaxis and treatment of infection. Methods are also disclosed for designing stabilized anti-microbial peptides that are selectively lytic/cytotoxic to bacteria, allowing for internal use of anti-microbial peptides without mammalian membrane disruption and cytotoxicity.
Claims
exact text as granted — not AI-modified1 . A therapeutic compound comprising a cross-linked amino acid sequence having the formula:
or a pharmaceutically acceptable salt thereof,
wherein:
each R 1 and R 2 is independently H, alkyl, alkenyl, alkynyl, arylalkyl, cycloalkylalkyl, heteroarylalkyl, or heterocyclylalkyl, any of which is substituted or unsubstituted;
each R 3 is independently alkylene, alkenylene, or alkynylene, any of which is substituted or unsubstituted;
each x is independently 2, 3, or 6;
each w and y is independently 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20;
z is 1 or 2; and
each Xaa is independently an amino acid,
wherein the cross-linked amino acid sequence has at least three and up to 9 amino acid substitutions relative to the sequence set forth in SEQ ID NO:3; wherein two of the at least three amino acid substitutions are substitutions of two amino acids of SEQ ID NO:3 with stapling amino acids,
and wherein one of the at least three amino acid substitutions are substitutions at any of positions 1, 2, 3, 7, 8, 9, 18, 19, 21, 22, or 23 of SEQ ID NO: 3 and is selected from the group consisting of G1K, 12K, G3K, G3E, H7K, H7E, S8K, S8E, A9K, G18E, E19K, M21B (where B is norleucine), N22K, N22E, and S23K;
wherein the cross-linked amino acid sequence has an alpha helical conformation; and wherein the compound or the pharmaceutically acceptable salt thereof exhibits an increased antibacterial effect against at least one bacterium relative to an un-cross-linked corresponding sequence set forth in SEQ ID NO:3.
2 - 3 . (canceled)
4 . The therapeutic compound or the pharmaceutically acceptable salt thereof of claim 1 , wherein x is 3; R 3 is C 8 alkylene, C 8 alkenylene, or C 8 alkynylene; and the sum of x, w, and y is at least 10.
5 . The therapeutic compound or the pharmaceutically acceptable salt thereof of claim 1 , wherein R 3 is substituted with 1, 2, 3, or 4 R 4 , and each R 4 is independently —NH 3 or —OH, wherein each —NH 3 is optionally coupled with another chemical entity.
6 . The therapeutic compound or the pharmaceutically acceptable salt thereof of claim 5 , wherein R 3 is substituted with 2 R 4 , and both R 4 are —OH.
7 . The therapeutic compound or the pharmaceutically acceptable salt thereof of claim 5 , wherein R 3 is substituted with 2 R 4 , and one R 4 is an optionally substituted —NH 3 and the other R 4 is —OH.
8 . The therapeutic compound or the pharmaceutically acceptable salt thereof of claim 1 , wherein at least one Xaa is an amino acid that is a non-natural amino acid.
9 .- 10 . (canceled)
11 . The therapeutic compound or the pharmaceutically acceptable salt thereof of claim 1 , wherein x is 6 and R 3 spans from one to two turns on an α-helix.
12 .- 23 . (canceled)
24 . The therapeutic compound or the pharmaceutically acceptable salt thereof of claim 1 , wherein the at least one bacterium is Mycobacterium tuberculosis or Pseudomonas aeruginosa.
25 .- 53 . (canceled)
54 . The therapeutic compound or the pharmaceutically acceptable salt thereof of claim 1 , wherein the therapeutic compound comprises a cross-linked amino acid sequence selected from the group consisting of:
(SEQ ID NO: 48)
(a)
Mag(i + 4)15(G1K) KIGKFLHSAKKFGKAXVGEXBNS;
(SEQ ID NO: 47)
(b)
Mag(i + 4)15(I2K) GKGKFLHSAKKFGKAXVGEXBNS;
(SEQ ID NO: 46)
(c)
Mag(i + 4)15(G3K) GIRKFLHSAKKFGKAXVGEXBNS;
(SEQ ID NO: 43)
(d)
Mag(i + 4)15(H7K) GIGKFLKSAKKFGKAXVGEXBNS;
(SEQ ID NO: 42)
(e)
Mag(i + 4)15(S8K) GIGKFLHKAKKFGKAXVGEXBNS;
(SEQ ID NO: 41)
(f)
Mag(i + 4)15(A9K) GIGKFLHSAKKFGKAXVGEXENS;
(SEQ ID NO: 35)
(g)
Mag(i + 4)15(E19K) GIGKFLHSAKKFGKAXVGKXBNS;
(SEQ ID NO: 33)
(h)
Mag(i + 4)15(N22K) GIGKFLHSAKKFGKAXVGEXBKS;
(SEQ ID NO: 32)
(i)
Mag(i + 4)15(S23K) GIGKFLHSAKKFGKAXVGEXBNK;
(SEQ ID NO: 51)
(j)
Mag(i + 4)15(G3E) GIBKFLHSAKKFGKAXVGEXBNS;
(SEQ ID NO: 55)
(k)
Mag(i + 4)15 (H7E) GIGKFLESAKKFGKAXVGEXBNS;
(SEQ ID NO: 56)
(l)
Mag(i + 4)15(S8E) GIGKFLHEAKKFGKAXVGEXBNS;
(SEQ ID NO: 65)
(m)
Mag(i + 4)15(G18E) GIGKFLHSAKKFGKAXVEEXBNS;
and
(SEQ ID NO: 67)
(n)
Mag(i + 4)15(N22E) GIGKFLHSAKKFGKAXVGEXBES;
wherein X is a stapling amino acid; and
wherein B is norleucine.
55 . The therapeutic compound or the pharmaceutically acceptable salt thereof of claim 54 , wherein the stapling amino acid is an α,α-disubstituted amino acid.
56 . The therapeutic compound or the pharmaceutically acceptable salt thereof of claim 54 , wherein the stapling amino acid is S5 [(S)-2-(4-pentenyl)Alanine] or R5 [(R)-2-(4-pentenyl)Alanine].
57 . The therapeutic compound or the pharmaceutically acceptable salt thereof of claim 1 , wherein the at least one bacterium is Escherichia coli ( E. coli ).
58 . A pharmaceutical composition comprising the therapeutic compound or the pharmaceutically acceptable salt thereof of claim 54 .
59 . A method of treating an infection caused by a bacterium, the method comprising administering a therapeutically-effective amount of the therapeutic compound or the pharmaceutically acceptable salt thereof of claim 54 to a subject having, or at risk of having, the infection caused by the bacterium.
60 . The method of claim 59 , wherein the subject is a human.
61 . The method of claim 59 , wherein the bacterium is Gram-positive.
62 . The method of claim 59 , wherein the bacterium is Gram-negative.
63 . The method of claim 59 , wherein the bacterium is Mycobacterium tuberculosis or Pseudomonas aeruginosa.
64 . The method of claim 59 , wherein the infection is a bacterial vaginal infection.
65 . The method of claim 59 , wherein the infection is a bacterial pneumonia.
66 . The method of claim 59 , wherein the infection comprises a bacterial biofilm.
67 . A method of inhibiting the growth of a bacterium, the method comprising contacting the bacterium with an effective amount of the therapeutic compound or the pharmaceutically acceptable salt thereof of claim 54 .
68 . The method of claim 67 , wherein the contacting occurs in a subject harboring the bacterium.
69 . A method of making an internally cross-linked peptide, the method comprising:
(i) providing a peptide having a sequence set forth in any one of (a) through (n):
(SEQ ID NO: 48)
(a)
Mag(i + 4)15(G1K) KIGKFLHSAKKFGKAXVGEXBNS;
(SEQ ID NO: 47)
(b)
Mag(i + 4)15(I2K) GKGKFLHSAKKFGKAXVGEXBNS;
(SEQ ID NO: 46)
(c)
Mag(i + 4)15(G3K) GIRKFLHSAKKFGKAXVGEXBNS;
(SEQ ID NO: 43)
(d)
Mag(i + 4)15(H7K) GIGKFLKSAKKFGKAXVGEXBNS;
(SEQ ID NO: 42)
(e)
Mag(i + 4)15(S8K) GIGKFLHKAKKFGKAXVGEXBNS;
(SEQ ID NO: 41)
(f)
Mag(i + 4)15(A9K) GIGKFLHSAKKFGKAXVGEXENS;
(SEQ ID NO: 35)
(g)
Mag(i + 4)15(E19K) GIGKFLHSAKKFGKAXVGKXBNS;
(SEQ ID NO: 33)
(h)
Mag(i + 4)15(N22K) GIGKFLHSAKKFGKAXVGEXBKS;
(SEQ ID NO: 32)
(i)
Mag(i + 4)15(S23K) GIGKFLHSAKKFGKAXVGEXBNK;
(SEQ ID NO: 51)
(j)
Mag(i + 4)15(G3E) GIBKFLHSAKKFGKAXVGEXBNS;
(SEQ ID NO: 55)
(k)
Mag(i + 4)15(H7E) GIGKFLESAKKFGKAXVGEXBNS;
(SEQ ID NO: 56)
(l)
Mag(i + 4)15(S8E) GIGKFLHEAKKFGKAXVGEXBNS;
(SEQ ID NO: 65)
(m)
Mag(i + 4)15(G18E) GIGKFLHSAKKFGKAXVEEXBNS;
and
(SEQ ID NO: 67)
(n)
Mag(i + 4)15(N22E) GIGKFLHSAKKFGKAXVGEXBES;
wherein X is a stapling amino acid and B is norleucine; and
(ii) cross-linking the peptide.
70 . The method of claim 69 , wherein X is S5 [(S)-2-(4-pentenyl)Alanine] or R5 [(R)-2-(4-pentenyl)Alanine].
71 . A method of treating an infection caused by a coronavirus, the method comprising administering a therapeutically-effective amount of the therapeutic compound or the pharmaceutically acceptable salt thereof of claim 1 to a subject having, or at risk of having, the infection caused by the coronavirus.
72 . A method of treating an infection caused by a coronavirus, the method comprising administering a therapeutically-effective amount of the therapeutic compound or the pharmaceutically acceptable salt thereof of claim 54 to a subject having, or at risk of having, the infection caused by the coronavirus.Cited by (0)
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