Compositions and use of EPAS1 inhibitors

• US 8,114,983 B2
• Filed: 04/03/2009
• Issued: 02/14/2012
• Est. Priority Date: 04/04/2008
• Status: Expired due to Fees

• Current Assignee: Calando Pharmaceuticals, Inc. (Arrowhead Pharmaceuticals, Inc.)
• Original Assignee: Calando Pharmaceuticals, Inc. (Arrowhead Pharmaceuticals, Inc.)
• Inventors: Davis, Mark E., Heidel, Jeremy D., Liu, Joanna Yi-Ching
• Primary Examiner(s): VIVLEMORE, TRACY ANN
• Application Number:
  US12/384,475
• Publication Number:
  US 20100010071A1
• Time in Patent Office: 1,047 Days
• Field of Search: None
• US Class Current: 536/24.5
• CPC Class Codes: A61K 31/713 Double-stranded nucleic acids or oligonucleotides
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 35/04 specific for metastasis
• CPC Class Codes: C12N 15/113 Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing when used in plants C12N15/8218
• CPC Class Codes: C12N 2310/14 interfering N.A.

Abstract

The present invention relates to inhibitors of endothelial PAS domain protein 1 (EPAS1), and methods and compositions related to the EPAS1 inhibitors. In certain embodiments, the EPAS1 inhibitors include nucleic acids, such as for example siRNAs.

Claims

1. A nucleic acid comprising:

(i) a first strand of about 15 to about 30 nucleotides in length that comprises a sequence selected from SEQ ID NOs;

11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39 and 41, and

(ii) a second strand of about 15 to about 30 nucleotides in length that comprises a sequence selected from SEQ ID NOs;

12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32,34, 36, 38, 40, and 42,

wherein at least 12 nucleotides of the first and second strands are complementary to each other and form a double-stranded nucleic acid under physiological conditions, and wherein the double-stranded nucleic acid can reduce the expression of endothelial PAS domain protein 1 (EPAS1) in a cell by an RNA interference mechanism.

2. The nucleic acid of claim 1, wherein the double-stranded portion is about 15 to about 30 nucleotides in length.

3. The nucleic acid of claim 1, wherein the nucleic acid is a hairpin RNA and the hairpin RNA comprises a loop region having about 4 to about 10 nucleotides in length.

4. The nucleic acid of claim 1, wherein the first strand is a DNA polynucleotide and the second strand is an RNA polynucleotide.

5. The nucleic acid of claim 1, wherein the first and/or second strand further comprises a 3′

overhang region, a 5′

overhang region, or both 3′ and

5′

overhang regions.

6. The nucleic acid of claim 5, wherein the overhang region contains about 1 to about 10 nucleotides in length.

7. The nucleic acid of claim 1, further comprising one or more modified backbone or base moieties selected from the group consisting of alkylphosphonates, phosphorothioates, phosphorodithioates, alkylphosphonothioates, phosphoramidates, phosphate esters, carbamates, acetamidate, carboxylmethyl esters, carbonates, and phosphate trimesters.

8. The nucleic acid of claim 7, wherein the modified backbone or base moieties comprise at least one 2′

O-alkylated ribonucleotide.

9. The nucleic acid of claim 1, wherein the nucleic acid inhibits EPAS 1 expression in cells by 50% or greater, when contacted with the cells under physiological conditions at a concentration of 10 nanomolar.

10. The nucleic acid of claim 1, wherein the first strand comprises SEQ ID NO:

29, and the second strand comprises SEQ ID NO;

30.

11. The nucleic acid of claim 1, wherein the first strand consists of SEQ ID NO:

29, and the second strand consists of SEQ ID NO;

30.

28. A pharmaceutical composition comprising the nucleic acid according to claim 1 or claim 12, and a pharmaceutically acceptable carrier.

29. The pharmaceutical composition of claim 28, wherein the pharmaceutically-acceptable carrier includes a cationic polymer.

30. The pharmaceutical composition of claim 28, wherein the pharmaceutically acceptable carrier includes a cyclodextrin polymer.

31. The pharmaceutical composition of claim 30, wherein the cyclodextrin structure is im-CDP.

32. The pharmaceutical composition of claim 30, wherein the cyclodextrin polymer is PEGylated.

33. The pharmaceutical composition of claim 30, wherein the carrier comprises adamantine.

34. The pharmaceutical composition of claim 30, wherein the carrier comprises a ligand that targets a particular tissue or cell type.

35. The pharmaceutical composition of claim 34, wherein the ligand is transferrin.

36. The pharmaceutical composition of claim 28, wherein the pharmaceutical composition comprises nanoparticles from about 10 to about 100 nm in diameter.

37. The pharmaceutical composition of claim 28, wherein the pharmaceutically acceptable carrier comprises an imidazole modified cyclodextrin-containing cationic polymer, and a targeting moiety comprising adamantane-PEG-ligand, wherein the polymer and targeting moiety form nanoparticles that encapsulate the nucleic and wherein the nanoparticles have a diameter of about 50 to about 120 nm.

38. The pharmaceutical composition of claim 37, wherein the targeting ligand is galactose.

39. The pharmaceutical composition of claim 37, wherein the targeting ligand is transferrin.

12. An isolated nucleic acid comprising a sequence that hybridizes to a region of an EPAS1 transcript corresponding to nucleotides 655-718 of SEQ ID NO:

1 under physiological conditions and decreases the expression of EPAS 1 in a cell, comprising a first strand of about 15 to about 50 nucleotides in length that comprises a sequence selected from SEQ ID NOs;

11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39 and 41, and a second strand of about 15 to about 30 nucleotides in length that comprises a sequence selected from SEQ ID NOs;

14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, and 42.

13. The isolated nucleic acid of claim 12, wherein the nucleic acid is single-stranded.

14. The isolated nucleic acid of claim 12, wherein the nucleic acid is double-stranded.

15. The isolated nucleic acid of claim 12, wherein the nucleic acid is a DNA. molecule, comprising one or more modified backbone or base moieties.

16. The isolated nucleic acid of claim 12, wherein the nucleic acid is an RNA molecule, comprising one or more modified backbone or base moieties.

17. The isolated nucleic acid of claim 12, wherein the nucleic acid comprises a DNA strand and an RNA strand and one or more modified backbone or base moieties.

18. The isolated nucleic acid of claim 12, wherein the nucleic acid is an RNAi construct.

19. The isolated nucleic acid of claim 18, wherein the RNAi construct is a dsRNA comprising one more modified backbone or base moieties.

20. The isolated nucleic acid of claim 18, wherein the RNAi construct is a hairpin RNA, comprising one or more modified backbone or base moieties.

21. The isolated nucleic acid of claim 18, wherein the duplex portion of the RNAi construct is from about 15 to about 30 nucleotides in length.

22. The isolated nucleic acid of claim 12, further comprising at least one internucleotide linkage selected from the group consisting of alkylphosphonates, phosphorothioates, phosphorodithioates, alkylphosphonothioates, phosphoramidates, phosphate esters, carbamates, acetamidate, carboxylmethyl esters, carbonates, and phosphate trimesters.

23. The isolated nucleic acid of claim 12, further comprising at least one 2′

-O -alkylated ribonucleotide.

24. The isolated nucleic acid of claim 12, wherein the nucleic acid is an enzymatic nucleic acid.

25. The isolated nucleic acid of claim 24, wherein the enzymatic. nucleic acid is a ribozyme.

26. The isolated nucleic acid of claim 24, wherein the enzymatic nucleic acid is a DNA enzyme.

27. The isolated nucleic acid of claim 12, wherein the nucleic acid inhibits EPAS 1 expression in cells by 50% or greater, when contacted with the cells under physiological conditions at a concentration of 10 nanomalar.