4'-thionucleosides and oligomeric compounds

• US 20050130923A1
• Filed: 09/20/2004
• Published: 06/16/2005
• Est. Priority Date: 09/18/2003
• Status: Active Grant

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Bhat, Balkrishen, Allerson, Charles, Griffey, Richard H., Swayze, Eric E., Prakash, Thazha P., Dande, Prasad
• Granted Patent: US 7,875,733 B2
• Time in Patent Office: Days
• US Class Current: 514/44.A
• 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 2310/11 Antisense
• CPC Class Codes: C12N 2310/14 interfering N.A.
• CPC Class Codes: C12N 2310/32 of the sugar
• CPC Class Codes: Y02P 20/55 Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Abstract

The present invention provides modified oligomeric compounds and compositions of oligomeric compounds for use in the RNA interference pathway of gene modulation. The modified oligomeric compounds include siRNA and asRNA having at least one affinity modification.

Claims

1. A compound of formula (I):

2. The compound of claim 1, wherein X is a group of formula Ia or Ib:

3. The compound of claim 1, wherein one of T₁ or T₂ is an activated phosphorous group.

4. The compound of claim 1, wherein one of T₁ or T₂ is -L_s-SS.

5. The compound of claim 1, wherein X is selected from fluoro, substituted or unsubstituted alkoxy, substituted or unsubstituted —

O—

C₁-C₁₂ alkenyl, or substituted or unsubstituted —

O—

C₁-C₁₂ alkynyl.

6. The compound of claim 1, wherein X is selected from fluoro, —

O—

CH₃, or —

O—

CH₂CH₂—

O—

CH₃.

7. The compound of claim 1, wherein X is allyl, amino, azido, O—

CH₃, O-allyl, O—

CH₂CH₂—

O—

CH₃, O—

(CH₂)_ma—

O—

N(R_m)(R_n) or O—

CH₂—

C(═

O)—

N(R_m)(R_n);

wherein;

each R_m and Rn is, independently, H, an amino protecting group, substituted or unsubstituted C₁-C₁₀ alkyl, substituted or unsubstituted C₂-C₁₀ alkenyl, substituted or unsubstituted C₂-C₁₀ alkynyl; and

ma is from 1 to about 10.

8. An oligomeric having at least one nucleoside of compound of formula II:

9. The oligomeric compound of claim 8, wherein X is a group of formula Ia or Ib:

10. The oligomeric compound of claim 8, wherein at least one of L₁ or L₂ is a phosphodiester internucleoside linkage.

11. The oligomeric compound of claim 8, wherein at least one of L₁ or L₂ is a phosphorothioate internucleoside linkage.

12. The oligomeric compound of claim 8, wherein X is selected from fluoro, substituted or unsubstituted alkoxy, substituted or unsubstituted —

O—

C₁-C₁₂ alkenyl, or substituted or unsubstituted —

O—

C₁-C₁₂ alkynyl.

13. The oligomeric compound of claim 8, wherein X is selected from fluoro, —

O—

CH₃, or —

O—

CH₂CH₂—

O—

CH₃.

14. The oligomeric compound of claim 8, wherein X is allyl, amino, azido, O—

CH₃, O-allyl, O—

CH₂CH₂—

O—

CH₃, O—

(CH₂)_ma—

O—

N(R_m)(R_n) or O—

CH₂—

C(═

O)—

N(R_m)(R_n);

wherein;

each R_m and R_n is, independently, H, an amino protecting group, substituted or unsubstituted C₁-C₁₀ alkyl, substituted or unsubstituted C₂-C₁₀ alkenyl, substituted or unsubstituted C₂-C₁₀ alkynyl; and

ma is from 1 to about 10.

15. The oligomeric compound of claim 8 comprising between 8 and 80 nucleotides.

16. The oligomeric compound of claim 8 comprising between 8 and 50 nucleotides.

17. The oligomeric compound of claim 8 comprising between 8 and 30 nucleotides.

18. The oligomeric compound of claim 8 comprising between 10 and 30 nucleotides.

19. The oligomeric compound of claim 8 comprising between 15 and 30 nucleotides.

20. The oligomeric compound of claim 8 comprising between 15 and 25 nucleotides.

21. A composition comprising a first oligonucleotide and a second oligonucleotide, wherein:

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

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

at least one of said first or said second oligonucleotides includes at least one nucleoside having a modification comprising a 4′

-thionucleoside of the formula;

wherein

L₁ and L₂ are independently an internucleoside linkage;

Bx is hydrogen or a nucleobase;

X is halogen, amino, azido, substituted or unsubstituted C₁-C₁₂ alkyl, substituted or unsubstituted C₂-C₁₂ alkenyl, substituted or unsubstituted C₂-C₁₂ alkynyl, substituted or unsubstituted alkoxy, substituted or unsubstituted —

C₂-C₁₂ alkenyl, or substituted or unsubstituted —

O—

C₂-C₁₂ alkynyl.

22. The composition of claim 21, in at least one of said first or second oligonucleotides, for at least one nucleoside of formula II contained therein, X is a group of formula Ia or Ib:

23. The composition of claim 21, in at least one of said first or second oligonucleotides, for at least one nucleoside of formula II contained therein, at least one of L₁ or L₂ is a phosphodiester internucleoside linkage.

24. The composition of claim 21, in at least one of said first or second oligonucleotides, for at least one nucleoside of formula II contained therein, at least one of L₁ or L₂ is a phosphorothioate internucleoside linkage.

25. The composition of claim 21, in at least one of said first or second oligonucleotides, for at least one nucleoside of formula II contained therein, at least one of L₁ or L₂ is a phosphodiester internucleoside linkage and the other is a phosphorothioate internucleoside linkage.

26. The composition of claim 21, in at least one of said first or second oligonucleotides, for at least one nucleoside of formula II contained therein, X is selected from fluoro, substituted or unsubstituted alkoxy, substituted or unsubstituted —

O—

C₁-C₁₂ alkenyl, or substituted or unsubstituted —

O—

C₁-C₁₂ alkynyl.

27. The composition of claim 21, in at least one of said first or second oligonucleotides, for at least one nucleoside of formula II contained therein, X is selected from fluoro, —

O—

CH₃, or —

O—

CH₂CH₂—

O—

CH₃.

28. The composition of claim 21, in at least one of said first or second oligonucleotides, for at least one nucleoside of formula II contained therein, X is allyl, amino, azido, O—

CH₃, O-allyl, O—

CH₂CH₂—

O—

CH₃, O—

(CH₂)_ma—

O—

N(R_m)(R_n) or O—

CH₂—

C(═

O)—

N(R_m)(R_n);

wherein;

each R_m and R_n, is, independently, H, an amino protecting group, substituted or unsubstituted C₁-C₁₀ alkyl, substituted or unsubstituted C₂-C₁₀ alkenyl, substituted or unsubstituted C₂-C₁₀ alkynyl; and

ma is from 1 to about 10.

29. The composition of claim 21, wherein said first and said second oligonucleotides are a complementary pair of siRNA oligonucleotides.

30. The composition of claim 21, wherein said first and said second oligonucleotides are an antisense/sense pair of oligonucleotides.

31. The composition of claim 21, wherein each of said first and second oligonucleotides comprises 10 to 40 nucleotides.

32. The composition of claim 21, wherein each of said first and second oligonucleotides comprises 18 to 30 nucleotides.

33. The composition of claim 21, wherein each of said first and second oligonucleotides comprises 18 to 24 nucleotides.

34. The composition of claim 21, wherein said first oligonucleotide is an antisense oligonucleotide.

35. The composition of claim 34 wherein said second oligonucleotide is a sense oligonucleotide.

36. The composition of claim 34 wherein said second oligonucleotide has a plurality of ribose nucleotide units.

37. Te composition of claim 21 wherein said first oligonucleotide includes at least one modified nucleotide of formula II.

38. A process for the preparation of 1,4-anhydro-2-O-(2,4-dimethoxybenzoyl)-3,5-O-(1,1,3,3-tetraisopropyl disiloxane-1,3-diyl)-4-sulfinyl-D-ribitol comprising:

preparing an oxidizing mixture by adding diethyl-L-tartrate to a solution of Ti(IV) isopropoxide in a suitable solvent followed by the addition of a suitable peroxide in said suitable solvent;

treating 1,4-anhydro-3,5-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)-4-thio-D-ribitol in a suitable solvent with said oxidizing mixture to form 1,4-anhydro-2-O-(2,4-dimethoxybenzoyl)-3,5-O-(1,1,3,3-tetraisopropyl disiloxane-1,3-diyl)-4-sulfinyl-D-ribitol.