Compositions and Methods for Modulating Immunodeficiency Virus Transcription

• US 20120108500A1
• Filed: 10/04/2011
• Published: 05/03/2012
• Est. Priority Date: 10/07/2010
• Status: Abandoned Application

• Current Assignee: The J. David Gladstone Institutes
• Original Assignee: The J. David Gladstone Institutes
• Inventors: Ott, Melanie, Sakane, Naoki
• Application Number:
  US13/252,624
• Publication Number:
  US 20120108500A1
• Time in Patent Office: Days
• US Class Current: 514/3.8
• CPC Class Codes: A61K 31/00 Medicinal preparations containing organic active ingredients
• CPC Class Codes: A61K 31/137 Arylalkylamines, e.g. amphetamine, epinephrine, salbutamol, ephedrine or methadone
• CPC Class Codes: A61K 31/4525 containing a five-membered ring with oxygen as a ring hetero atom
• CPC Class Codes: A61K 31/7088 Compounds having three or more nucleosides or nucleotides
• CPC Class Codes: A61K 31/785 Polymers containing nitrogen
• CPC Class Codes: A61K 38/1709 from mammals
• CPC Class Codes: A61P 31/18 for HIV
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C07K 14/005 from viruses
• CPC Class Codes: C12N 2740/16311 concerning HIV regulatory proteins
• CPC Class Codes: C12N 2740/16322 New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
• CPC Class Codes: C12N 9/0022 with oxygen as acceptor (1.4.3)
• CPC Class Codes: C12N 9/0071 acting on paired donors with incorporation of molecular oxygen (1.14)
• CPC Class Codes: C12Q 1/26 involving oxidoreductase
• CPC Class Codes: C12Y 104/03004 Monoamine oxidase (1.4.3.4)
• CPC Class Codes: C12Y 114/11 with 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (1.14.11)
• CPC Class Codes: G01N 2333/163 Regulatory proteins, e.g. tat, nef, rev, vif, vpu, vpr, vpt, vpx
• CPC Class Codes: G01N 2333/90245 acting on paired donors with incorporation of molecular oxygen (1.14)
• CPC Class Codes: G01N 2500/02 Screening involving studying the effect of compounds C on the interaction between interacting molecules A and B (e.g. A = enzyme and B = substrate for A, or A = receptor and B = ligand for the receptor)

Abstract

The present disclosure provides methods of modulating immunodeficiency virus transcription, involving modulating enzymatic activity and/or levels of a lysine-specific demethylase-1 (LSD1) polypeptide and/or LSD1-mediated demethylation of methylated Tat. The present disclosure also provides method of identifying agents that modulate LSD1-mediated demethylation of a human immunodeficiency virus (HIV) Tat polypeptide.

Claims

1. A method of inhibiting transcription of a human immunodeficiency virus (HIV) in a cell infected with the HIV, the method comprising contacting the cell with an agent that inhibits enzymatic activity of a lysine-specific demethylase-1 (LSD1) polypeptide, that reduces the level of the LSD1 polypeptide in the cell, that reduces LSD1-mediated demethylation of a Tat polypeptide in the cell, or that reduces the level or activity of a CoREST polypeptide, wherein said contacting results in inhibition of HIV transcription.

2. The method of claim 1, wherein the agent is a monoamine oxidase inhibitor selected from selegiline, selegiline hydrochloride, dimethylselegilene, brofaromine, phenelzine, tranylcypromine, moclobemide, befloxatone, safinamide, isocarboxazid, nialamide, rasagiline, iproniazide, iproclozide, toloxatone, bifemelane, desoxypeganine, harmine, harmaline, linezolid, and pargyline.

4. The method of claim 1, wherein the agent is a polyamine compound of the formula:

5. The method of claim 1, wherein the agent is a phenylcyclopropylamine derivative of the formula:

6. The method of claim 1, wherein the agent is an interfering nucleic acid that specifically reduces the level of LSD1 in the cell or that specifically reduces the level of a CoREST polypeptide in the cell.

7. The method of claim 1, wherein the agent inhibits interaction of an LSD1 polypeptide with a CoREST polypeptide.

8. The method of claim 7, wherein the agent is a CoREST polypeptide that binds LSD1 but does not increase enzymatic activity of LSD1.

11. The method of claim 1, wherein the agent is a BHC80 polypeptide.

12. The method of claim 1, wherein the agent is a histone deacetylase-1 or -2 inhibitor.

3. (canceled)

9-10. -10. (canceled)

13. (canceled)

14. A method of treating a human immunodeficiency virus (HIV) infection in an individual having an HIV infection, the method comprising administering to the individual an effective amount of an agent that inhibits enzymatic activity of a lysine-specific demethylase-1 (LSD1) polypeptide, that reduces the level of the LSD1 polypeptide in a cell, or that reduces LSD1-mediated demethylation of a Tat polypeptide in a cell.

15. The method of claim 14, wherein the agent inhibits enzymatic activity of an LSD1 polypeptide, and wherein the agent is a polyamine compound, a phenylcyclopropylamine derivative, or a monoamine oxidase inhibitor.

20. The method of claim 14, wherein the agent is an interfering nucleic acid that specifically reduces the level of LSD1 in a cell or that specifically reduces the level of a CoREST polypeptide in a cell.

21. The method of claim 14, wherein the agent inhibits interaction of an LSD1 polypeptide with a CoREST polypeptide, wherein the agent is a CoREST polypeptide that binds LSD1 but does not increase enzymatic activity of LSD1.

25. The method of claim 14, wherein the agent is a BHC80 polypeptide.

26. The method of claim 14, wherein the agent is a histone deacetylase-1 or -2 inhibitor.

16-19. -19. (canceled)

22-24. -24. (canceled)

27-29. -29. (canceled)

30. A method of treating a human immunodeficiency virus (HIV) infection in an individual, the method comprising:

administering to an individual an effective amount of a first active agent, wherein the first active agent increases lysine-specific demethylase-1 (LSD1) enzymatic activity and/or levels, wherein said first active agent reactivates latent HIV integrated into the genome of a cell in the individual; and

administering to the individual an effective amount of a second active agent, wherein the second active agent inhibits an immunodeficiency virus function selected from viral replication, viral protease activity, viral reverse transcriptase activity, viral entry into a cell, viral integrase activity, viral Rev activity, viral Tat activity, viral Nef activity, viral Vpr activity, viral Vpu activity, and viral Vif activity.

31. (canceled)

32. An in vitro method for identifying an agent that inhibits transcription of human immunodeficiency virus (HIV), the method comprising:

a) contacting an LSD1 polypeptide and a methylated HIV Tat polypeptide, with a test agent; and

b) determining the effect, if any, of the test agent on the methylation of the Tat polypeptide,

wherein a test agent that inhibits demethylation of the methylated Tat polypeptide by the LSD1 polypeptide, compared to the level of methylation of the Tat polypeptide in the absence of the test agent, is considered a candidate agent for inhibition of HIV transcription.

33. The method of claim 32, wherein the methylated Tat polypeptide comprises a methylated Lys-51 or a methylated lysine at a position corresponding to Lys-51 of the amino acid sequence depicted in FIG. 12 (SEQ ID NO:

5), wherein the methylated Lys-51 is monomethylated or dimethylated.

35. The method of claim 32, wherein the methylated Tat polypeptide comprises the amino acid sequence SYGRKK^meRRQR.

37. The method of claim 32, wherein the methylated Tat polypeptide comprises a radiolabelled methyl group.

34. (canceled)

36. (canceled)

38-39. -39. (canceled)