Chimeric oligomeric compounds for modulation of splicing

• US 8,501,703 B2
• Filed: 08/29/2006
• Issued: 08/06/2013
• Est. Priority Date: 08/30/2005
• Status: Active Grant

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: ISIS Pharmaceuticals Incorporated, Sarepta Therapeutics, Inc.
• Inventors: Bennett, C. Frank, Dean, Nicholas M., Kole, Ryszard, Kopczynski, Casey C.
• Primary Examiner(s): Chong, Kimberly
• Application Number:
  US12/065,250
• Publication Number:
  US 20110039334A1
• Time in Patent Office: 2,534 Days
• Field of Search: None
• US Class Current: 514/44
• 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 15/1135 against oncogenes or tumor suppressor genes
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 2'-R Modification
• 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: C12N 2310/3531 Hydrogen
• CPC Class Codes: C12N 2310/3533 Halogen
• CPC Class Codes: C12N 2320/33 Alteration of splicing

Abstract

Disclosed herein are compounds, compositions and methods for modulating splicing of a selected target mRNA. Further provided are uses of the disclosed compounds and compositions in the manufacture of a medicament for treatment of diseases and disorders. Methods of enhancing cellular uptake, modulating tissue distribution and enhancing pharmacological activity of RNase H-independent antisense oligonucleotides are also provided.

Claims

1. A method of modulating splicing of a selected target pre-mRNA in a cell comprising contacting the cell with an oligomeric compound comprising an oligonucleotide consisting of 13 to 30 linked nucleosides which is complementary to the selected target pre-mRNA, and wherein the oligonucleotide has 7-11 separate regions, wherein:

the 5′

-most region consists of 1-5 linked modified nucleosides, each comprising a modified sugar moiety;

the 3′

-most region consists of 1-5 linked modified nucleosides, each comprising a modified sugar moiety; and

the internal regions alternate between regions of 1-5 linked 2′

-deoxyribonucleosides and regions of 1-5 linked modified nucleosides, each comprising a modified sugar moiety,

wherein splicing of the selected target pre-mRNA is modulated.

2. The method of claim 1, wherein said oligonucleotide comprises 3 separate regions of 2′

-deoxyribonucleosides.

3. The method of claim 1, wherein said oligonucleotide comprises 4 separate regions of 2′

-deoxyribonucleosides.

4. The method of claim 1, wherein each region of 2′

-deoxyribonucleosides of said oligonucleotide consists of 2 or 3 nucleosides.

5. The method of claim 1, wherein the 5′

most region of the oligonucleotide consists of 3 or 4 linked modified nucleosides each comprising a modified sugar moiety.

6. The method of claim 1, wherein the 3′

most region of the oligonucleotide consists of 4 or 5 linked modified nucleosides each comprising a modified sugar moiety.

7. The method of claim 1, wherein each sugar modification of each modified nucleoside is selected from the group consisting of 2′

-O-methoxyethyl, 2′

-fluoro, 2′

-dimethylaminooxyethoxy, 2′

-dimethylaminoethoxyethoxy, 2′

-guanidinium, 2′

-O-guanidinium ethyl, 2′

-carbamate, 2′

-aminooxy, 2′

-acetamido and locked nucleic acid.

8. The method of claim 7, wherein each sugar modification of each modified nucleoside is 2′

-O-methoxyethyl.

9. The method of claim 1, wherein the oligonucleotide consists of 20 to 30 linked nucleosides.

10. The method of claim 1, wherein the oligonucleotide consists of 15 to 25 linked nucleosides.

11. The method of claim 1, wherein the oligonucleotide consists of 20 linked nucleosides.

12. The method of claim 11, wherein the oligonucleotide has 2′

-deoxyribonucleosides at positions 3, 4, 5, 7, 8, 9, 11, 12, 13, 15, 16 and 17.

13. The method of claim 11, wherein the oligonucleotide has 2′

-deoxyribonucleosides at positions 4, 5, 6, 9, 10, 11, 14, 15 and 16.

14. The method of claim 11, wherein the oligonucleotide has 2′

-deoxyribonucleosides at positions 4, 5, 8, 9, 10, 13, 14 and 15.

15. The method of claim 11, wherein the oligonucleotide has 2′

-deoxyribonucleosides at positions 5, 6, 7, 9, 10, 11, 13, 14 and 15.

16. The method of claim 11, wherein the oligonucleotide has 2′

-deoxyribonucleosides at positions 5, 6, 7, 9, 10, 13, 14 and 15.

17. The method of claim 11, wherein the oligonucleotide has 2′

-deoxyribonucleosides at positions 5, 6, 7, 10, 11, 12, 15, 16 and 17.

18. The method of claim 11, wherein the oligonucleotide has 2′

-deoxyribonucleosides at positions 6, 7, 8, 10, 11, 12, 14, 15 and 16.

19. The method of claim 11, wherein the oligonucleotide has 2′

-deoxyribonucleosides at positions 6, 7, 8, 11, 12, 13, 16 and 17.

20. The method of claim 1, wherein the cell is derived from adipose.

21. The method of claim 1, wherein the cell is derived from liver.

22. The method of claim 1, wherein the oligonucleotide is complementary to a splice site.

23. The method of claim 22, wherein the splice site is an aberrant splice site.

24. The method of claim 22, wherein the splice site is a cryptic splice site.