Stabilized polypeptides as regulators of RAB GTPase function

• US 9,487,562 B2
• Filed: 06/15/2012
• Issued: 11/08/2016
• Est. Priority Date: 06/17/2011
• Status: Active Grant

• Current Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Original Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Inventors: Moellering, Raymond E., Verdine, Gregory L.
• Primary Examiner(s): LIEB, JEANETTE M
• Application Number:
  US14/126,642
• Publication Number:
  US 20140235549A1
• Time in Patent Office: 1,607 Days
• Field of Search: None
• US Class Current: 1/1
• 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: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C07K 14/001 by chemical synthesis
• CPC Class Codes: C07K 14/4702 Regulators; Modulating activity

Abstract

The present invention provides inventive polypeptides comprising a C terminal RAB binding domain (RabBD) of RAB family interacting proteins (FIPs) stabilized by peptide stapling, and pharmaceutical compositions thereof. Also provided are methods for modulating RAB function comprising contacting an inventive stapled polypeptide with a RAB protein, and methods of treatment associated with modulation of RAB activity. The present invention also provides methods of making the inventive stapled polypeptides by ring closing metathesis of unstapled polypeptide precursors.

Claims

1. An unstapled polypeptide of Formula (I):

R^f-[X_AA]_s-[X_1-26]-[X_AA]_t-R^e 

 

(I)

or a pharmaceutically acceptable salt thereof;

wherein;

each instance of X_AA is a natural amino acid or an unnatural amino acid;

s is 0 or an integer between 1 and 100, inclusive;

t is 0 or an interger between 1 and 100, inclusive;

R^f is an N-terminal group selected from the group consisting of hydrogen;

optionally substituted aliphatic;

optionally substituted heteroaliphatic;

optionally substituted aryl;

optionally substituted heteroaryl;

acyl;

a resin;

an amino protecting group; and

a label optionally joined by a linker, wherein the linker is selected from the group consisting of optionally substituted alkylene;

optionally substituted alkenylene;

optionally substituted alkynylene;

optionally substituted heteroalkylene;

optionally substituted heteroalkenylene;

optionally substituted heteroalkynylene;

optionally substituted arylene;

optionally substituted heteroarylene; and

acylene;

R^e is a C-terminal group selected from the group consisting of hydrogen;

optionally substituted aliphatic;

optionally substituted heteroaliphatic;

optionally substituted aryl;

optionally substituted heteroaryl;

—

OR^E, —

N(R^E)₂, or —

SR^E, wherein each instance of R^E is, independently, hydrogen;

optionally substituted aliphatic;

optionally substituted heteroaliphatic;

optionally substituted aryl;

optionally substituted heteroaryl;

acyl;

a resin;

a protecting group;

or two R^E groups taken together form an optionally substituted heterocyclic or optionally substituted heteroaryl ring;

-[X_1-26]- is an unstapled amino acid sequence of the formula;

25. The polypeptide of claim 1, wherein the amino acid sequence comprises at least two independent occurrences of an amino acid of Formula (i) or (ii) separated by two or three amino acids.

26. The polypeptide of claim 1, wherein the alpha carbon of the amino acid of Formula (i) is in the (S) configuration.

27. The polypeptide of claim 1, wherein the alpha carbon of the amino acid of Formula (i) is in the (R) configuration.

28. The polypeptide of claim 1, wherein K is unsubstituted C_1-6alkylene.

29. The polypeptide of claim 1, wherein the amino acid of Formula (i) is selected from the group consisting of:

30. The polypeptide of claim 29, wherein the amino acid of Formula (i) is:

31. The polypeptide of claim 1, wherein each instance of L₁ and L₂ is independently unsubstituted C_1-6alkylene.

32. The polypeptide of claim 1, wherein the amino acid of Formula (ii) is selected from the group consisting of:

2. A stapled polypeptide of the Formula (II):

R^f-[X_AA]_s-[X_1-26]-[X_AA]_t-R^e 

 

(II)

or a pharmaceutically acceptable salt thereof;

wherein;

each instance of X_AA is a natural amino acid or unnatural amino acid;

s is 0 or an integer between 1 and 100, inclusive;

t is 0 or an integer between 1 and 100, inclusive;

R^f is an N-terminal group selected from the group consisting of hydrogen;

optionally substituted aliphatic;

optionally substituted heteroaliphatic;

optionally substituted aryl;

optionally substituted heteroaryl;

acyl;

a resin;

an amino protecting group; and

a label optionally joined by a linker, wherein the linker is selected from the group consisting of optionally substituted alkylene;

optionally substituted alkenylene;

optionally substituted alkynylene;

optionally substituted heteroalkylene;

optionally substituted heteroalkenylene;

optionally substituted heteroalkynylene;

optionally substituted arylene;

optionally substituted heteroarylene; and

acylene;

R^e is a C-terminal group selected from the group consisting of hydrogen;

optionally substituted aliphatic;

optionally substituted heteroaliphatic;

optionally substituted aryl;

optionally substituted heteroaryl;

—

OR^E, —

N(R^E)₂, or —

SR^E, wherein each instance of R^E is, independently, hydrogen;

optionally substituted aliphatic;

optionally substituted heteroaliphatic;

optionally substituted aryl;

optionally substituted heteroaryl;

acyl;

a resin;

a protecting group;

or two R^E groups taken together form an optionally substituted heterocyclic or optionally substituted heteroaryl ring; and

-[X_1-26]- is a stapled amino sequence of the Formula;

3. The polypeptide of claim 2, wherein the amino acid sequence is alpha helical.

4. The polypeptide of claim 2, wherein the amino acid sequence comprises a Rab binding domain (RabBD).

5. The polypeptide of claim 2, wherein the amino acid sequence is a modified amino acid sequence corresponding to residues 1247-1272 of Fip1:

6. The polypeptide of claim 2, wherein the amino acid sequence is a modified amino acid sequence corresponding to residues 473-498 of Fip2:

7. The polypeptide of claim 2, wherein the amino acid sequence is a modified amino acid sequence corresponding to residues 730-757 of Fip3:

8. The polypeptide of claim 2, wherein the amino acid sequence is a modified amino acid sequence corresponding to residues 610-635 of Fip4:

9. The polypeptide of claim 2, wherein the amino acid sequence is selected from the group consisting of:

10. The polypeptide of claim 2, wherein the amino acid sequence is selected from the group consisting of:

11. A composition comprising a polypeptide of claim 2, or a pharmaceutically acceptable salt thereof, and optionally a pharmaceutically acceptable excipient.

12. A method of modulating RAB function comprising contacting a polypeptide of claim 2, or a pharmaceutically acceptable salt thereof, and a RAB protein, wherein the polypeptide or salt thereof, binds to the RAB protein.

13. The method of claim 12, wherein the polypeptide is a RAB family interacting protein (FIP) polypeptide.

14. The method of claim 12, wherein the polypeptide substantially inhibits RAB function.

15. The method of claim 12, wherein the polypeptide is derived from FIP1, FIP2, FIP3, or FIP4 protein.

16. The method of claim 12, wherein the polypeptide is selected from the group consisting of:

17. The method of claim 12, wherein the RAB protein is RAB11 or RAB25.

18. A method of treating a condition associated with aberrant RAB protein levels or activity comprising administering an effective amount of a polypeptide of claim 2 or a pharmaceutically acceptable salt thereof to a subject in need thereof.

19. The method of claim 18, wherein the condition associated with aberrant RAB protein levels or activity is cancer.

20. The method of claim 19, wherein the cancer is breast or ovarian cancer.

21. The method of claim 18, wherein the condition associated with aberrant RAB protein levels or activity is Griscelli syndrome, Charcot-Marie-Tooth, tuberous sclerosis, or choroideremia.

22. The method of claim 19, wherein the cancer associated with aberrant RAB protein levels or activity is squamous cell carcinomas, neuroendocrine tumors, lung cancer, hepatoma, Medullary thyroid cancer, pancreatic carcinoma, hepatocellular carcinoma, gastric cancer, prostate cancer, liver cancer, ovarian cancer, or breast cancer.

23. The method of claim 18, wherein the condition associated with aberrant RAB protein levels or activity is a proliferative, a neurological, an immunological, an endocrinologic, a cardiovascular, a hematologic, or an inflammatory condition associated with aberrant RAB protein levels or activity.

24. A method of inhibiting a RAB protein from binding to a RAB Family Interacting Protein (FIP), the method comprising administering an effective amount of a polypeptide of claim 2 or a pharmaceutically acceptable salt thereof to a subject in need thereof.

33. The method of claim 12, wherein the polypeptide is positively charged.

34. The method of claim 12, wherein the polypeptide has a hydrocarbon staple corresponding to a) amino acid positions 1253 and 1257, 1254 and 1258, 1258 and 1261, or 1261 and 1265 of the FIP1 protein;

b) amino acid positions 479 and 483, 480 and 484, 484 and 487, or 487 and 491 of the FIP2 protein;

c) amino acid positions 736 and 740, 737 and 741, 741 and 744, or 744 and 748 of the FIP3 protein;

or

d) amino acid positions 616 and 620, 617 and 621, 621 and 624, 624 and 628 of the FIP4 protein.