2'-methoxy substituted oligomeric compounds and compositions for use in gene modulations

• US 20040147022A1
• Filed: 11/04/2003
• Published: 07/29/2004
• Est. Priority Date: 06/06/1996
• Status: Abandoned Application

• Current Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Original Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Inventors: Bhat, Balkrishen, Griffey, Richard H., Swayze, Eric E., Baker, Brenda F., Manoharan, Muthiah, Crooke, Stanley T., Eldrup, Anne B.
• Application Number:
  US10/701,264
• Publication Number:
  US 20040147022A1
• Time in Patent Office: Days
• US Class Current: 435/375
• 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: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• 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 15/1135 against oncogenes or tumor suppressor genes
• CPC Class Codes: C12N 2310/311 Phosphotriesters
• CPC Class Codes: C12N 2310/312 Phosphonates
• CPC Class Codes: C12N 2310/314 Phosphoramidates
• CPC Class Codes: C12N 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/316 Phosphonothioates
• CPC Class Codes: C12N 2310/318 where the PO2 is completely replaced, e.g. MMI or formacetal
• CPC Class Codes: C12N 2310/3181 Peptide nucleic acid, PNA
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2310/3341 5-Methylcytosine
• CPC Class Codes: C12N 2310/335 Modified T or U
• 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 2310/3521 Methyl
• CPC Class Codes: C12N 2310/3525 MOE, methoxyethoxy
• CPC Class Codes: C12N 2310/3527 Other alkyl chain
• CPC Class Codes: C12N 9/22 : Ribonucleases RNAses, DNAses catalytic nucleic acids C12N15/113

Abstract

Compositions comprising first and second oligomers are provided wherein at least a portion of the first oligomer is capable of hybridizing with at least a portion of the second oligomer, at least a portion of the first oligomer is complementary to and capable of hybridizing to a selected target nucleic acid, and at least one of the first or second oligomers includes a modified sugar and/or backbone modification. In some embodiments the modification is a 2′-OCH₃ substituent group on a sugar moiety. Oligomer/protein compositions are also provided comprising an oligomer complementary to and capable of hybridizing to a selected target nucleic acid and at least one protein comprising at least a portion of an RNA-induced silencing complex (RISC), wherein at least one nucleotide of the oligomer has a modified sugar and/or backbone modification.

Claims

1. A composition comprising a first oligomer and a second oligomer, wherein:

at least a portion of said first oligomer is capable of hybridizing with at least a portion of said second oligomer,

at least a portion of said first oligomer is complementary to and capable of hybridizing with a selected target nucleic acid,

at least one of said first or said second oligomers includes at least one nucleoside having a 2′

-OCH₃ substituent group.

2. The composition of claim 1 wherein said first and said second oligomers are a complementary pair of siRNA oligomers.

3. The composition of claim 1 wherein said first and said second oligomers are an antisense/sense pair of oligomers.

4. The composition of claim 1 wherein each of said first and second oligomers comprise from about 10 to about 40 linked nucleosides.

5. The composition of claim 1 wherein each of said first and second oligomers comprise from about 18 to about 30 linked nucleosides.

6. The composition of claim 1 wherein each of said first and second oligomers compirse from about 21 to about 24 linked nucleosides.

7. The composition of claim 1 wherein said first oligomer is an antisense oligomer.

8. The composition of claim 7 wherein said second oligomer comprises a sense oligomer.

9. The composition of claim 7 wherein said second oligomer has a plurality of ribose nucleoside subunits.

10. The composition of claim 1 wherein said first oligomer includes said 2′

-OCH₃ substituent group.

11. The composition of claim 10 wherein said first oligomer comprises a plurality of linked nucleosides having a 5′

-terminal hydroxyl group 12. The composition of claim 11 wherein nucleosides with said 2′

-OCH₃ substitutent group extend from the 3′

terminus of the first oligomer through the fourth, third, or penultimate nucleoside from the 5′

terminus.

16. The composition of claim 1 wherein said first oligomer comprises a plurality of linked nucleosides wherein said 5′

-terminal nucleoside comprises a 2′

-OCH₃ substitutent group.

17. The composition of claim 16 wherein said nucleoside at said 5′

-terminal nucleoside comprises a 3′

-phosphate terminal group.

18. The composition of claim 1 wherein said first oligomer is a chimeric oligomeric compound.

19. The composition of claim 18 wherein said chimeric oligomeric compound is a gapmer, an inverted gapmer, a 3′

-hemimer, a 5′

-hemimer or a blockmer.

20. The composition of claim 19 wherein said chimeric oligomeric compound is a gapmer.

21. The composition of claim 20 wherein said gapmer comprises two terminal RNA segments having nucleosides of a first type and an internal RNA segment having nucleosides of a second type and where said nucleosides of said first type are different from said nucleosides of said second type.

22. The composition of claim 21 wherein each of said nucleosides of said first type includes a 2′

-OCH₃ substitutent group.

23. The composition of claim 19 wherein said chimeric oligomeric compound is an inverted gapmer.

24. The composition of claim 23 wherein said inverted gapmer comprises two terminal RNA segments having nucleosides of a second type and an internal RNA segment having nucleosides of a first type and where said nucleosides of said first type are different from said nucleosides of said second type.

25. The composition of claim 24 wherein each of said nucleosides of said first type includes a 2′

-OCH₃ sugar substituent group.

26. The composition of claim 19 wherein said chimeric oligomeric compound is 3′

-hemimer.

27. The composition of claim 26 wherein said 3′

-hemimer comprises a terminal RNA segment having nucleosides of a first type and a further RNA segment having nucleosides of a second type and where said nucleosides of said first type are different from said nucleosides of said second type.

28. The composition of claim 27 wherein each of said nucleosides of said first type includes a 2′

-OCH₃ substitutent group.

29. The composition of claim 19 wherein said chimeric oligomeric compound is 5′

-hemimer.

30. The composition of claim 29 wherein said 5′

-hemimer comprises a terminal RNA segment having nucleosides of a first type and a further RNA segment having nucleosides of a second type and where said nucleosides of said first type are different from said nucleosides of said second type.

31. The composition of claim 30 wherein each of said nucleosides of said first type includes a 2′

-OCH₃ substituent group.

32. The composition of claim 19 wherein the chimeric oligomeric compound comprises a blockmer.

33. The composition of claim 32 wherein said blockmer comprises an oligonucleoside having at least two consecutive nucleosides of a first type located immediately adjacent at least one nucleoside of a second type and

where said nucleosides of said first type are different from said nucleosides of said second type.

34. The composition of claim 33 wherein each of said nucleosides of said first type includes a 2′

-OCH₃ substituent group.

73. A pharmaceutical composition comprising the composition of claim 1 and a pharmaceutically acceptable carrier.

76. A method of modulating the expression of a target nucleic acid in a cell comprising contacting said cell with a composition of claim 1.

79. A method of treating or preventing a disease or disorder associated with a target nucleic acid comprising administering to an animal having or predisposed to said disease or disorder a therapeutically effective amount of a composition of claim 1.

13. The composition of claim 12 wherein nucleosides with said 2′

-OCH₃ substitutent group extend from the 3′

terminus of the first oligomer through the fourth nucleoside from the 5′

terminus.

14. The composition of claim 12 wherein nucleosides with said 2′

-OCH₃ substitutent group extend from the 3′

terminus of the first oligomer through the third nucleoside from the 5′

terminus.

15. The composition of claim 12 wherein nucleosides with said 2′

-OCH₃ substitutent group extend from the 3′

terminus of the first oligomer through the penultimate nucleoside from the 5′

terminus.

35. A composition comprising an oligomer complementary to and capable of hybridizing to a selected target nucleic acid and at least one protein, said protein comprising at least a portion of a RNA-induced silencing complex (RISC), wherein:

said oligomer includes includes at least one sugar moiety having a 2′

-OCH₃ substituent group.

36. The composition of claim 35 wherein said oligomer is an antisense oligomer.

37. The composition of claim 35 wherein said oligomer comprises from about 10 to about 40 linked nucleosides.

38. The composition of claim 35 wherein said oligomer comprises from about 18 to about 30 linked nucleosides.

39. The composition of claim 35 wherein said oligomer comprises from about 21 to about 24 linked nucleosides.

40. The composition of claim 35 further including a further oligomer, wherein said further oligomer is complementary to said oligomer.

41. The composition of claim 40 wherein said further oligomer is a sense oligomer.

42. The composition of claim 40 wherein said further oligomer is an oligomer having a plurality of ribose nucleoside subunits.

43. The composition of claim 35 wherein said oligomer comprises a plurality of linked nucleosides having a 5′

-terminal hydroxyl group

44. The composition of claim 43 wherein nucleosides with said 2′

-OCH₃ substitutent group extend from the 3′

terminus of the oligomer through the fourth, third, or penultimate nucleoside from the 5′

terminus.

45. The composition of claim 44 wherein nucleosides with said 2′

-OCH₃ substitutent group extend from the 3′

terminus of said oligomer through the fourth nucleoside from the 5′

terminus.

46. The composition of claim 44 wherein nucleosides with said 2′

-OCH₃ substitutent group extend from the 3′

terminus of said oligomer through the third nucleoside from the 5′

terminus.

47. The composition of claim 44 wherein nucleosides with said 2′

-OCH₃ substitutent group extend from the 3′

terminus of said oligomer through the penultimate nucleoside from the 5′

terminus.

48. The composition of claim 35 wherein said oligomer comprises a plurality of linked nucleosides wherein said 5′

-terminal nucleoside comprises comprises a 2′

-OCH₃ substitutent group.

49. The composition of claim 48 wherein said nucleoside at said 5′

terminus comprises a 5′

-phosphate group.

50. The composition of claim 35 wherein said first oligomer is a chimeric oligomeric compound.

51. The composition of claim 50 wherein said chimeric oligomeric compound is a gapmer, an inverted gapmer, a 3′

-hemimer, a 5′

-hemimer or a blockmer.

52. The composition of claim 51 wherein said chimeric oligomeric compound is a gapmer.

53. The composition of claim 52 wherein said gapmer comprises two terminal RNA segments having nucleosides of a first type and an internal RNA segment having nucleosides of a second type and where said nucleosides of said first type are different from said nucleosides of said second type.

54. The composition of claim 53 wherein each of said nucleosides of said first type includes a 2′

-OCH₃ substitutent group.

55. The composition of claim 51 wherein said chimeric oligomeric compound is an inverted gapmer.

56. The composition of claim 55 wherein said inverted gapmer comprises two terminal RNA segments having nucleosides of a second type and an internal RNA segment having nucleosides of a first type and where said nucleosides of said first type are different from said nucleosides of said second type.

57. The composition of claim 56 wherein each of said nucleosides of said first type includes a 2′

-OCH₃ sugar substituent group.

58. The composition of claim 51 wherein said chimeric oligomeric compound is 3′

-hemimer.

59. The composition of claim 58 wherein said 3′

-hemimer comprises a terminal RNA segment having nucleosides of a first type and a further RNA segment having nucleosides of a second type and where said nucleosides of said first type are different from said nucleosides of said second type.

60. The composition of claim 59 wherein each of said nucleosides of said first type includes a 2′

-OCH₃ substitutent group.

61. The composition of claim 51 wherein said chimeric oligomeric compound is 5′

-hemimer.

62. The composition of claim 61 wherein said 5′

-hemimer comprises a terminal RNA segment having nucleosides of a first type and a further RNA segment having nucleosides of a second type and where said nucleostides of said first type are different from said nucleosides of said second type.

63. The composition of claim 62 wherein each of said nucleosides of said first type includes a 2′

-OCH₃ substituent group.

64. The composition of claim 51 wherein the chimeric oligomeric compound comprises a blockmer.

65. The composition of claim 64 wherein said blockmer comprises an oligonucleoside having at least two consecutive nucleosides of a first type located immediately adjacent at least one nucleoside of a second type and where said nucleosides of said first type are different from said nucleosides of said second type.

66. The composition of claim 65 wherein each of said nucleosides of said first type includes a 2′

-OCH₃ substituent group.

74. A pharmaceutical composition comprising the composition of claim 35 and a pharmaceutically acceptable carrier.

77. A method of modulating the expression of a target nucleic acid in a cell comprising contacting said cell with a composition of claim 35.

80. A method of treating or preventing a disease or disorder associated with a target nucleic acid comprising administering to an animal having or predisposed to said disease or disorder a therapeutically effective amount of a composition of claim 35.

67. An oligomer having at least a first region and a second region, wherein:

said first region of said oligomer is complementary to and capable of hybridizing with said second region of said oligomer,

at least a portion of said oligomer is complementary to and capable of hybridizing to a selected target nucleic acid, and

said oligomer further includes at least one nucleoside having a 2′

-OCH₃ substituent group.

68. The oligomer of claim 67 wherein each of said first and said second regions has at least 10 nucleosides.

69. The oligomer of claim 67 wherein said first regions in a 5′

to 3′

direction is complementary to said second region in a 3′

to 5′

direction.

70. The oligomer of claim 67 wherein said oligomer includes a hairpin structure.

71. The oligomer of claim 67 wherein said first region of said oligomer is spaced from said second region of said oligomer by a third region and where said third region comprises at least two nucleosides.

72. The oligomer of claim 67 wherein said first region of said oligomer is spaced from said second region of said oligomer by a third region and where said third region comprises a non-nucleoside region.

75. A pharmaceutical composition comprising the oligomeric compound of claim 67 and a pharmaceutically acceptable carrier.

78. A method of modulating the expression of a target nucleic acid in a cell comprising contacting said cell with an oligomeric compound of claim 67.

81. A method of treating or preventing a disease or disorder associated with a target nucleic acid comprising administering to an animal having or predisposed to said disease or disorder a therapeutically effective amount of a composition of claim 67.