Stablized EZH2 peptides

• US 10,308,926 B2
• Filed: 03/13/2014
• Issued: 06/04/2019
• Est. Priority Date: 03/15/2013
• Status: Active Grant

• Current Assignee: Dana-Farber Cancer Institute
• Original Assignee: Dana-Farber Cancer Institute
• Inventors: Walensky, Loren D., Bird, Gregory H., Kim, Woojin, Orkin, Stuart
• Primary Examiner(s): Miknis, Zachary J
• Application Number:
  US14/772,143
• Publication Number:
  US 20160068834A1
• Time in Patent Office: 1,909 Days
• CPC Class Codes: A61K 38/00 Medicinal preparations containing peptides peptides containing beta-lactam rings A61K31/00; cyclic dipeptides not having in their molecule any other peptide link than those which form their ring, e.g. piperazine-2,5-diones, A61K31/00; ergot alkaloids of the cyclic peptide type A61K31/48; containing macromolecular compounds having statistically distributed amino acid units A61K31/74; medicinal preparations containing antigens or antibodies A61K39/00; medicinal preparations characterised by the non-active ingredients, e.g. peptides as drug carriers, A61K47/00
• CPC Class Codes: C07K 14/47 from mammals
• CPC Class Codes: C12N 9/1007 Methyltransferases (general) (2.1.1.)
• CPC Class Codes: C12N 9/96 Stabilising an enzyme by forming an adduct or a composition; Forming enzyme conjugates
• CPC Class Codes: C12Y 201/01043 Histone-lysine N-methyltransferase (2.1.1.43)

Abstract

Provided herein are polypeptides containing stabilized therapeutic peptides related to enhancer of zeste homolog 2 (EZH2), histone lysine N-methyltransferase. Also provided are compositions containing these polypeptides and methods of using such peptides in the treatment of cancer that include administering to a subject one of the polypeptides.

Claims

1. An internally cross-linked polypeptide that inhibits the interaction between Enhancer of Zeste Homolog 2 (EZH2) and Embryonic Ectoderm Development (EED), the internally cross-linked polypeptide comprising the amino acid sequence FSSNRX₁KILX₂RTEILNQEWKQRRIQPV (SEQ ID NO:

26), wherein X₁ and X₂ are each a non-natural amino acid with an olefinic side chain, and wherein the internally cross-linked polypeptide is cell penetrant.

2. The internally cross-linked polypeptide of claim 1, wherein X₁ and X₂ are each (S)-2-(4′

-pentenyl) alanine (S5).

3. The internally cross-linked polypeptide of claim 2, wherein the internally cross-linked polypeptide consists of the amino acid sequence set forth in SEQ ID NO:

26.

4. A pharmaceutical composition comprising the internally cross-linked polypeptide of claim 3 and a pharmaceutically acceptable carrier.

5. The pharmaceutical composition of claim 4, further comprising an inhibitor of EZH2 enzymatic activity.

6. The pharmaceutical composition of claim 5, wherein the inhibitor of EZH2 enzymatic activity is GSK126.

7. A method of treating an EZH2-overexpressing or EZH2-dependent cancer in a human subject in need thereof, the method comprising administering to the human subject an effective amount of the internally cross-linked polypeptide of claim 1.

8. The method of claim 7, further comprising administering to the human subject an inhibitor of EZH2 enzymatic activity.

9. An internally cross-linked polypeptide that inhibits the interaction between Enhancer of Zeste Homolog 2 (EZH2) and Embryonic Ectoderm Development (EED), the internally cross-linked polypeptide comprising the amino acid sequence FSSNRX₁KILX₂RTQILNQEWKQRRIQPV (SEQ ID NO:

27), wherein X₁ and X₂ are each a non-natural amino acid with an olefinic side chain, and wherein the internally cross-linked polypeptide is cell penetrant.

10. The internally cross-linked polypeptide of claim 9, wherein X₁ and X₂ are each (S)-2-(4′

-pentenyl) alanine (S5).

11. The internally cross-linked polypeptide of claim 10, wherein the internally cross-linked polypeptide consists of the amino acid sequence set forth in SEQ ID NO:

27.

12. A pharmaceutical composition comprising the internally cross-linked polypeptide of claim 11, and a pharmaceutically acceptable carrier.

13. The pharmaceutical composition of claim 12, further comprising an inhibitor of EZH2 enzymatic activity.

14. The pharmaceutical composition of claim 13, wherein the inhibitor of EZH2 enzymatic activity is GSK126.

15. A method of treating an EZH2-overexpressing or EZH2-dependent cancer in a human subject in need thereof, the method comprising administering to the human subject an effective amount of the internally cross-linked polypeptide of claim 10.

16. The method of claim 15, further comprising administering to the human subject an inhibitor of EZH2 enzymatic activity.

17. The method of claim 16, wherein the inhibitor of EZH2 enzymatic activity is GSK126.

18. The method of claim 15, wherein the cancer is a leukemia, a breast cancer, a prostate cancer, a sarcoma, or a neuroblastoma.

19. A method of treating an EZH2-overexpressing or EZH2-dependent cancer in a human subject in need thereof, the method comprising administering to the human subject an effective amount of the pharmaceutical composition of claim 12.

20. The method of claim 19, further comprising administering to the human subject an inhibitor of EZH2 enzymatic activity.

21. The method of claim 20, wherein the inhibitor of EZH2 enzymatic activity is GSK126.

22. The method of claim 19, wherein the cancer is a leukemia, a breast cancer, a prostate cancer, a sarcoma, or a neuroblastoma.

23. An internally cross-linked polypeptide that inhibits the interaction between Enhancer of Zeste Homolog 2 (EZH2) and Embryonic Ectoderm Development (EED), the internally cross-linked polypeptide comprising the amino acid sequence FSSNRX₁KILX₂RTX₃ILNX₄EWKQRRIQPV (SEQ ID NO:

56), wherein X₁, X₂, X₃, and X₄ are each a non-natural amino acid with an olefinic side chain, and wherein the internally cross-linked polypeptide is cell penetrant.

24. The internally cross-linked polypeptide of claim 23, wherein X₁, X₂, X₃, and X₄ are each (S)-2-(4′

-pentenyl) alanine (S5).

25. The internally cross-linked polypeptide of claim 23, wherein the internally cross-linked polypeptide consists of the amino acid sequence set forth in SEQ ID NO:

56.

26. A pharmaceutical composition comprising the internally cross-linked polypeptide of claim 25 and a pharmaceutically acceptable carrier.

27. The pharmaceutical composition of claim 26, further comprising an inhibitor of EZH2 enzymatic activity.

28. The pharmaceutical composition of claim 27, wherein the inhibitor of EZH2 enzymatic activity is GSK126.

29. A method of treating an EZH2-overexpressing or EZH2-dependent cancer in a human subject in need thereof, the method comprising administering to the human subject an effective amount of the internally cross-linked polypeptide of claim 23.

30. The method of claim 29, further comprising administering to the human subject an inhibitor of EZH2 enzymatic activity.

31. The method of claim 30, wherein the inhibitor of EZH2enzymatic activity is GSK126.

32. An internally cross-linked polypeptide that inhibits the interaction between Enhancer of Zeste Homolog 2 (EZH2) and Embryonic Ectoderm Development (EED), the internally cross-linked polypeptide comprising an amino acid sequence set forth in FSSNRX₁KILX₂RTEILNQEWKQRRIQPV (SEQ ID NO:

26), except that one or more amino acids at positions 2, 3, 9, 13, 14, 17, 21 or 23 of SEQ ID NO;

26 are substituted, and wherein X₁, and X₂, are each a non-natural amino acid with an olefinic side chain, and wherein the internally cross-linked polypeptide is cell penetrant.

33. The internally cross-linked polypeptide of claim 32, wherein the amino acids at positions 13 and 17, are each substituted with a non-natural amino acid with an olefinic side chain.

34. The internally cross-linked polypeptide of claim 32, wherein the internally cross-linked polypeptide consists of an amino acid sequence set forth in SEQ ID NO:

26, but with 1 to 6 amino acid substitutions at positions selected from the group consisting of positions;

2, 3, 9, 13, 14, 17, 21, and 23, of SEQ ID NO;

26.

35. The internally cross-linked polypeptide of claim 32, wherein the internally cross-linked polypeptide comprises an amino acid sequence set forth in SEQ ID NO:

26 but with 1 to 4 amino acid substitutions at positions 2, 3, 9, 13, 14, 17, 21 or 23.

36. The internally cross-linked polypeptide of claim 32, wherein the internally cross-linked polypeptide comprises an amino acid sequence set forth in SEQ ID NO:

26 but with 1 amino acid substitution at position 2, 3, 9, 13, 14, 17, 21 or 23.

37. The internally cross-linked polypeptide of claim 32, wherein the non-natural amino acid is S5 [(S)-2-4′

-pentenyl) alanine].

38. A pharmaceutical composition comprising the internally cross-linked polypeptide of claim 32 and a pharmaceutically acceptable carrier.

39. The pharmaceutical composition of claim 38, further comprising an inhibitor of EZH2 enzymatic activity.

40. The pharmaceutical composition of claim 39, wherein the inhibitor of EZH2 enzymatic activity is GSK126.

41. A method of treating an EZH2-overexpressing or EZH2-dependent cancer in a human subject in need thereof, the method comprising administering to the human subject an effective amount of the internally cross-linked polypeptide of claim 32.

42. The method of claim 41, further comprising administering to the human subject an inhibitor of EZH2 enzymatic activity.

43. The method of claim 42, wherein the inhibitor of EZH2 enzymatic activity is GSK126.