Chimeric Gapped Oligomeric Compounds

• US 20080261904A1
• Filed: 06/03/2004
• Published: 10/23/2008
• Est. Priority Date: 06/03/2004
• Status: Abandoned Application

• Current Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Original Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Inventors: Bhat, Balkrishen, Allerson, Charles, Griffey, Richard H., Swayze, Eric E., Prakash, Thazha P., Dande, Prasad
• Application Number:
  US11/569,941
• Publication Number:
  US 20080261904A1
• Time in Patent Office: Days
• US Class Current: 514/44
• CPC Class Codes: A61K 31/07 Retinol compounds, e.g. vitamin A retinoic acids A61K31/203
• CPC Class Codes: A61P 13/10 of the bladder
• CPC Class Codes: A61P 3/04 Anorexiants; Antiobesity agents
• CPC Class Codes: A61P 3/06 Antihyperlipidemics
• CPC Class Codes: A61P 3/10 for hyperglycaemia, e.g. antidiabetics
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C12N 15/111 General methods applicable to biologically active non-coding 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 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/32 of the sugar
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2310/341 Gapmers, i.e. of the type ===---===
• CPC Class Codes: C12N 2310/3521 Methyl
• CPC Class Codes: C12N 2320/51 modulating the chemical stability, e.g. nuclease-resistance

Abstract

The present invention provides double stranded compositions wherein the first strand comprises three different regions and the second strand is native RNA. Each region has native or modified ribofuranosyl sugar moieties that are different than those of the other two regions. At least a portion of the first oligomeric compound is complementary to and hybridizes to a nucleic acid target. The present invention also provides methods for modulating gene expression using the modified oligomeric compounds and compositions of oligomeric compounds.

Claims

1. A composition comprising first and second chemically synthesized oligomeric compounds, wherein:

at least a portion of the first oligomeric compound is capable of hybridizing with at least a portion of the second oligomeric compound,

at least a portion of the first oligomeric compound is complementary to and capable of hybridizing to a selected target nucleic acid,

the first oligomeric compound comprises a contiguous sequence of from about 12 to about 30 nucleosides linked by internucleoside linking groups wherein the sequence of the first oligomeric compound is divided into an internal region flanked by two external regions;

the sugar soups of each of the three regions differ from the sugar groups of the other two regions and each region comprises modified ribofuranosyl moieties or one region comprises β

-D-ribofuranosyl moieties and the other two regions comprise modified ribofuranosyl moieties;

the second oligomeric compound comprises a contiguous sequence of from about 12 to about 30 nucleosides linked by internucleoside linking groups; and

each of the first and second oligomeric compounds optionally comprises a phosphate group, a 3′

-overhang or a conjugate group.

2. The composition of claim 1 wherein each of the regions of modified ribofuranosyl sugar moieties is uniformly modified.

3. The composition of claim 1 wherein at least one of the regions of the first oligomeric compound comprises nucleosides having 3′

-endo conformational geometry.

4. The composition of claim 3 wherein each of the three regions of the first oligomeric compound comprises nucleosides having 3′

-endo conformational geometry.

5. The composition of claim 1 wherein at least one of the regions of the first oligomeric compound comprises 2′

-substituted ribofuranosyl moieties wherein the 2′

-substituent group is —

F, —

O—

CH₂CH₂—

O—

CH₃, —

O—

C₁-C₁₂alkyl, —

O—

CH₂—

CH₂-CH₂—

NH₂, —

O—

(CH₂)₂—

O—

N(R₁)₂, —

O—

CH₂C(═

O)—

N(R₁)₂, —

O—

(CH₂)₂—

O—

(CH₂)₂—

N(R₁)₂, —

O—

CH₂—

CH₂—

CH₂—

NHR₁, —

N₃, —

O—

CH₂—

CH═

CH₂, —

N(H)COR₁, —

N(R₁)₂, —

SR₁, —

N(R₁)OR₁ or —

O—

CH₂—

N(H)—

C(═

NR₁)N(R₁)₂;

wherein each R₁ is, independently, H, C₁-C₁₂ alkyl, a protecting group or substituted or unsubstituted C₁-C₁₂ alkyl, C₂-C₁₂ alkenyl, or C₂-C₁₂ alkynyl wherein the substituent groups are selected from halogen, hydroxyl, amino, azido, cyano, haloalkyl, alkenyl, alkoxy, thioalkoxy, haloalkoxy or aryl.

6. The composition of claim 5 wherein each of the 2′

-substituent groups is, independently, —

F, —

O—

CH₃, —

O—

CH₂CH₂—

O—

CH₃, —

O—

CH₂—

CH═

CH₂, N₃, NH₂, NHOH, —

O—

(CH₂)₂—

O—

N(R₁)₂, —

O—

CH₂C(O)—

N(R₁)₂, —

O—

CH₂—

CH₂-CH₂—

NH₂, —

O—

(CH₂)₂—

O—

(CH₂)₂—

N(R₁)₂ or —

O—

CH₂—

N(H)—

C(═

NR₁)N(R₁)₂;

wherein each R₁ is, independently, H, C₁-C₁₂ alkyl, a protecting group or substituted or unsubstituted C₁-C₁₂ alkyl, C₂-C₁₂ alkenyl, or C₂-C₁₂ alkynyl wherein the substituent groups are selected from halogen, hydroxyl, amino, azido, cyano, haloalkyl, alkenyl, alkoxy, thioalkoxy, haloalkoxy or aryl.

7. The composition of claim 6 wherein each of the 2′

-substituent groups is, independently, —

F, —

O—

CH₂CH₂—

O—

CH or —

O—

CH₃, —

O—

CH₂—

CH═

CH₂ or.

8. The composition of claim 7 wherein each of the 2′

-substituent groups is, independently, —

F, —

O—

CH₃ or —

O—

CH₂CH₂—

O—

CH₃.

9. The composition of claim 8 wherein each of the 2′

-substituent groups is, independently, —

F or —

O—

CH₃.

10. The composition of claim 1 wherein one of the regions of the first oligomeric compound comprises 4′

-thio modified nucleosides.

11. The composition of claim 1 wherein the first oligomeric compound comprises one region of β

-D-ribofuranosyl sugar moieties.

12. The composition of claim 11 wherein the region of β

-D-ribofuranosyl sugar moieties is the internal region.

13. The composition of claim 12 wherein the 5′

-external region comprises 2′

-F modified ribofuranosyl sugar moieties or 4′

-thio modified ribofuranosyl moieties and the 3′

-external region comprises 2′

-OCH₃ modified ribofuranosyl sugar moieties, 4′

-thio modified ribofuranosyl moieties, modified ribofuranosyl moieties each having a 4′

-CH₂—

O-2′

-bridge or ribofuranosyl moieties each having a 4′

-(CH₂)₂—

O-2′

-bridge.

14. The composition of claim 1 wherein each region of the first oligomeric compound comprises modified ribofuranosyl moieties selected from 2′

-F modified sugar moieties, 2′

-OCH₃ modified sugar moieties, 4′

-thio modified sugar moieties, modified sugar moieties each having a 4′

-CH₂—

O-2′

-bridge or modified sugar moieties each having a 4′

-(CH₂)₂—

O-2′

-bridge.

15. The composition of claim 14 wherein the 5′

-external region comprises 4′

-thio modified sugar moieties, the internal region comprises 2′

-F modified sugar moieties and the 3′

-external region comprises 2′

-OCH₃ modified sugar moieties, modified sugar moieties each having a 4′

-CH₂—

O-2′

-bridge or modified sugar moieties each having a 4′

-(CH₂)₂—

O-2′

-bridge.

16. The composition of claim 1 wherein each external region of the first oligomeric compound is from 1 to 6 nucleosides in length and the internal region is from 6 to 14 nucleosides in length.

17. The composition of claim 1 wherein each external region of the first oligomeric compound is from 2 to 5 nucleosides in length and the internal region is from 8 to 13 nucleosides in length.

18. The composition of claim 1 wherein each external region of the first oligomeric compound is from 2 to 3 nucleosides in length and the internal region is from 10 to 13 nucleosides in length.

19. The composition of claim 1 wherein each external region of the first oligomeric compound is from 1 to 3 nucleosides in length, the internal region is from 13 to 17 nucleosides in length and the first oligomeric compound comprises 19 nucleosides.

20. The composition of claim 1 wherein each external region of the first oligomeric compound is from 2 to 5 nucleosides in length, the internal region is from 10 to 14 nucleosides in length and the first oligomeric compound comprises 20 nucleosides.

21. The composition of claim 1 further comprising at least one 5′

-phosphate group.

22. The composition of claim 1 further comprising a terminal 3′

-OH group.

23. The composition of claim 1 further comprising at least one conjugate group.

24. The composition of claim 1 wherein the nucleosides of each of the first and the second oligomeric compounds are linked by phosphodiester internucleoside linking groups.

25. The composition of claim 1 wherein the nucleosides of each of the first and the second oligomeric compounds are linked by phosphorothioate internucleoside linking groups.

26. The composition of claim 1 wherein the nucleosides of one of the first and the second oligomeric compound are linked by phosphorothioate internucleoside linking groups and the nucleosides of the other of the first and the second oligomeric compound are linked by phosphodiester internucleoside linking groups.

27. The composition of claim 1 wherein the nucleosides of the first oligomeric compound are linked by phosphorothioate internucleoside linking groups and the nucleosides of the second oligomeric compound are linked by phosphodiester internucleoside linking groups.

28. The composition of claim 1 wherein each of the nucleosides of the first and the second oligomeric compound are independently linked by phosphorothioate or phosphodiester internucleoside linking groups.

29. The composition of claim 28 wherein at least one of the first and the second oligomeric compounds are independently linked by alternating phosphorothioate and phosphodiester internucleoside linking groups.

30. The composition of claim 1 wherein at least one of the first and the second oligomeric compounds further comprises at least one terminal cap moiety attached at the 3′

-end, the 5′

-end or both the 3′

-end and the 5′

-end.

31. The composition of claim 30 wherein the terminal cap moiety is an inverted deoxy abasic moiety.

32. The composition of claim 31 wherein the second oligomeric compound comprises a terminal cap moiety at one or both of the 3′

-terminal and the 5′

-terminal ends.

33. The composition of claim 32 wherein the terminal cap moiety is an inverted deoxy abasic moiety.

34. The composition of claim 1 wherein the first and the second oligomeric compounds are a complementary pair of siRNA oligonucleotides.

38. The composition of claim 1 wherein each of the first and the second oligomeric compounds is independently from about 12 to about 24 nucleosides in length.

39. The composition of claim 1 wherein each of the first and the second oligomeric compounds is independently from about 19 to about 23 nucleosides in length.

40. The composition of claim 1 wherein the first oligomeric compound is an antisense oligomeric compound.

41. The composition of claim 1 wherein the second oligomeric compound is a sense oligomeric compound

43. A method of inhibiting gene expression comprising contacting one or more cells, a tissue or an animal with a composition of claim 1.

35-37. -37. (canceled)

42. (canceled)

44. (canceled)