Antisense modulation of apolipoprotein B expression

• US 7,511,131 B2
• Filed: 11/13/2003
• Issued: 03/31/2009
• Est. Priority Date: 11/13/2002
• Status: Expired due to Fees

• Current Assignee: Kastle Therapeutics, LLC.
• Original Assignee: Genzyme Corporation (Sanofi )
• Inventors: Graham, Mark, Crooke, Roseanne M., Freier, Susan M.
• Primary Examiner(s): EPPS -SMITH, JANET L
• Application Number:
  US10/712,795
• Publication Number:
  US 20040214325A1
• Time in Patent Office: 1,965 Days
• Field of Search: None
• US Class Current: 536/24.5
• 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: A61K 48/00 Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
• 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 15/85 for animal cells
• CPC Class Codes: C12N 2310/13 Decoys
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/3341 5-Methylcytosine
• CPC Class Codes: C12N 2310/341 Gapmers, i.e. of the type ===---===
• CPC Class Codes: C12N 2310/346 having a combination of backbone and sugar modifications
• CPC Class Codes: C12N 2310/3525 MOE, methoxyethoxy
• CPC Class Codes: Y02P 20/582 Recycling of unreacted starting or intermediate materials

Abstract

Antisense compounds, compositions and methods are provided for modulating the expression of apolipoprotein B. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding apolipoprotein B. Methods of using these compounds for modulation of apolipoprotein B expression and for treatment of diseases associated with expression of apolipoprotein B are provided.

Claims

1. An antisense oligonucleotide 20 to 30 nucleobases in length, or a pharmaceutically acceptable salt form thereof, wherein the antisense oligonucleotide has a nucleobase sequence comprising the nucleobase sequence of SEQ ID NO:

247.

2. The antisense oligonucleotide of claim 1, wherein the antisense oligonucleotide is 20 nucleobases in length and has a nucleobase sequence consisting of the nucleobase sequence of SEQ ID NO:

247.

3. The antisense oligonucleotide of claim 1, wherein the antisense oligonucleotide comprises at least one modified internucleoside linkage.

4. The antisense oligonucleotide of claim 3, wherein the modified internucleoside linkage is a phosphorothioate linkage.

5. The antisense oligonucleotide of claim 1, wherein the antisense oligonucleotide comprises at least one modified sugar moiety.

6. The antisense oligonucleotide of claim 5, wherein the modified sugar moiety is a 2′

-O-methoxyethyl sugar moiety.

7. The antisense oligonucleotide of claim 5, wherein the modified sugar moiety is a bicyclic sugar moiety.

8. The antisense oligonucleotide of claim 1, wherein the antisense oligonucleotide is a chimeric oligonucleotide having a plurality of 2′

-deoxynucleotides flanked on each side by at least one nucleotide having a modified sugar moiety.

9. The antisense oligonucleotide of claim 8, wherein the modified sugarmoiety is a 2′

-O-methoxyethyl sugar moiety.

10. The antisense oligonucleotide of claim 8, wherein the modified sugar moiety is a bicyclic sugar moiety.

11. The antisense oligonucleotide of claim 1, wherein the antisense oligonucleotide comprises at least one modified nucleobase.

12. The antisense oligonucleotide of claim 11, wherein the modified nucleobase is a 5-methylcytosine.

13. The antisense oligonucleotide of claim 1, wherein the antisense oligonucleotide is a pharmaceutically acceptable salt form.

14. The antisense oligonucleotide of claim 13, wherein the salt form is a sodium salt form.

15. A formulation comprising the antisense oligonucleotide of any one of claims 1-14 and a pharmaceutically acceptable carrier or diluent.

16. An antisense oligonucleotide 20 nucleotides in length having the sequence of nucleobases as set forth in SEQ ID NO:

247 and comprising 5-methylcytosine at nucleobases 2, 3, 5, 9, 12, 15, 17, 19, and 20, wherein every internucleoside linkage is a phosphorothioate linkage, nucleotides 1-5 and 16-20 are 2′

-O-methoxyethyl nucleotides, and nucleotides 6-15 are 2′

-deoxynucleotides, or wherein said antisense oligonucleotide is a pharmaceuticallv acceptable salt form thereof.

17. The antisense oligonucleotide of claim 16, wherein the antisense oligonucleotide is said pharmaceutically acceptable salt form.

18. The antisense oligonucleotide of claim 17, wherein the pharmaceutically acceptable salt form is a sodium salt form.

19. A formulation comprising the antisense oligonucleotide of any of claims 16-18 and a pharmaceutically acceptable carrier or diluent.

20. An antisense compound 12 to 30 nucleobases in length and fully complementary to SEQ ID NO:

3, wherein said compound specifically hybridizes to the range of nucleotides 3230-3287 as set forth in SEQ ID NO;

3, or a pharmaceutically acceptable salt thereof.

21. The antisense compound of claim 20, which is 12 to 20 nucleobases in length.

22. The antisense compound of claim 20, which is an antisense oligonucleotide.

23. The antisense oligonucleotide of claim 22, wherein the antisense oligonucleotide comprises at least one modified intemucleoside linkage.

24. The antisense oligonucleotide of claim 23, wherein the modified internucleoside linkage is a phosphorothioate linkage.

25. The antisense oligonucleotide of claim 22, wherein the antisense oligonucleotide comprises at least one modified sugar moiety.

26. The antisense oligonucleotide of claim 25, wherein the modified sugar moiety is a 2′

-O-methoxyethyl sugar moiety.

27. The antisense oligonucleotide of claim 25, wherein the modified sugar moiety is a bicyclic sugar moiety.

28. The antisense oligonucleotide of claim 22, wherein the antisense oligonucleotide is a chimeric oligonucleotide having a plurality of 2′

-deoxynucleotides flanked on each side by at least one nucleotide having a modified sugar moiety.

29. The antisense oligonucleotide of claim 28, wherein the modified sugar moiety is a 2′

-O-methoxyethyl sugar moiety.

30. The antisense oligonucleotide of claim 28, wherein the modified sugar moiety is a bicyclic sugar moiety.

31. The antisense oligonucleotide of claim 22, wherein the antisense oligonucleotide comprises at least one modified nucleobase.

32. The antisense oligonucleotide of claim 31, wherein the modified nucleobase is a 5-methylcytosine.

33. The antisense compound of claim 20, wherein the antisense compound is a salt form.

34. The antisense compound of claim 33, wherein the salt form is a sodium salt form.

35. A formulation comprising the antisense compound of any one of claims 20-34 and a pharmaceutically acceptable carrier or diluent.

36. A formulation comprising the antisense oligonucleotide of claim 1 and a penetration enhancer.

37. The formulation of claim 36, wherein the penetration enhancer is capric acid or lauric acid.

38. A formulation comprising the antisense oligonucleotide of claim 1 and at least one additional pharmaceutically active material.

39. The formulation of claim 38, wherein the at least one additional pharmaceutically active material is an anti-inflammatory agent.

40. The formulation of claim 19, further comprising at least one additional pharmaceutically active material.

41. The formulation of claim 19, wherein the at least one additional pharmaceutically active material is an anti-inflammatory agent.

42. The antisense oligonucleotide of claim 20, which is 20 nucleobases in length.

43. The antisense oligonucleotide of claim 42, having

a gap segment often linked 2′

-deoxynucleosides,

a 5′

wing segment of five linked nucleosides, and

a 3′

wing segment of five linked nucleosides,

wherein the gap segment is positioned between the 5′

wing segment and the 3′

wing segment, wherein each nucleoside of each wing segment comprises a 2′

-O-methoxyethyl sugar modification, and wherein each intemucleoside linkage is a phosphorothioate intemucleoside linkage.

44. The antisense oligonucleotide of claim 43, wherein the antisense oligonucleotide comprises at least one modified nucleobase.

45. The antisense oligonucleotide of claim 44, comprising at least one modified cytosine, wherein the cytosine is a 5-methylcytosine.

46. The antisense oligonucleotide of claim 45, wherein each cytosine is a 5-methyl cytosine.

47. An oral formulation comprising the antisense compound of claim 20 and a pharmaceutically acceptable diluent or carrier.

48. The formulation of claim 47, wherein said formulation comprises a penetration enhancer.

49. The formulation of claim 48, wherein the penetration enhancer is capric acid or lauric acid.

50. A formulation comprising the antisense oligonucleotide of claim 20 and at least one additional pharmaceutically active material.

51. The formulation of claim 50, wherein the at least one additional pharmaceutically active material therapeutic agent is an anti-inflammatory agent.

52. The antisense oligonucleotide of claim 7, wherein the bicyclic sugar moiety has a (—

CH2—

)n group forming a bridge between the 2′

oxygen and the 4′

carbon atoms of the sugar ring, wherein n is 1 or 2.

53. The antisense oligonucleotide of claim 10, wherein the bicyclic sugar moiety has a (—

CH2—

)n group forming a bridge between the 2′

oxygen and the 4′

carbon atoms of the sugar ring, wherein n is 1 or 2.

54. The antisense oligonucleotide of claim 27 wherein the bicyclic sugar moiety has a (—

CH2—

)n group forming a bridge between the 2′

oxygen and the 4′

carbon atoms of the sugar ring, wherein n is 1 or 2.

55. The antisense oligonucleotide of claim 30 wherein the bicylic sugar moiety has a (—

CH2—

)n group forming a bridge between the 2′

oxygen and the 4′

carbon atoms of the sugar ring, wherein n is 1 or 2.

56. A formulation comprising the antisense oligonucleotide of claim 16 and a penetration enhancer.

57. The formulation of claim 56, wherein the penetration enhancer is capric acid or lauric acid.