PYRROLIDINYL GROUPS FOR ATTACHING CONJUGATES TO OLIGOMERIC COMPOUNDS

• US 20090203132A1
• Filed: 09/01/2005
• Published: 08/13/2009
• Est. Priority Date: 09/09/2004
• Status: Abandoned Application

• Current Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Original Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Inventors: Robinson, Dale E. JR., Bhat, Balkrishen, Allerson, Charles, Swayze, Eric E., Prakash, Thazha P., Dande, Prasad, Jefferson, Elizabeth Anne
• Application Number:
  US11/574,396
• Publication Number:
  US 20090203132A1
• Time in Patent Office: Days
• US Class Current: 435/375
• CPC Class Codes: C07D 207/12 Oxygen or sulfur atoms

Abstract

The present invention provides pyrrolidinyl compounds that are useful for preparing conjugated oligomeric compounds. The conjugated pyrrolidinyl compounds can be attached to support medium and provide a free hydroxyl for oligomer synthesis to prepare an oligmeric compound having a 3′-conjugate. Alternatively, the pyrrolidinyl compound can be prepared as a phosphoramidite which can be placed internally or at the 5′-position of an oligomeric compound. These two strategies can be used together to prepare oligomeric compounds having 2 or more conjugates at any selected positions. The present invention also provides methods for modulating gene expression using the conjugated oligomeric compounds.

Claims

1. A compound having the formula:

2. The compound of claim 1 wherein R₁ is hydroxyl or a protected hydroxyl.

3. The compound of claim 2 wherein said protected hydroxyl comprises a protecting group selected from trityl, monomethoxytrityl, dimethoxytrityl, trimethoxytrityl, 9-phenylxanthin-9-yl (Pixyl) or 9-(p-methoxyphenyl)xanthin-9-yl (MOX).

4. The compound of claim 1 wherein R₁ is J-SM.

5. The compound of claim 4 wherein J-SM has the formula:

C(═

O)—

R₄—

C(═

O)—

SM

wherein

R₄ is C₁-C₁₂ alkyl or substituted C₁-C₁₂ alkyl, wherein said alkyl group can be interrupted by one or more heteroatoms selected from N(R_a), S and O;

R_a is H, C₁-C₁₂ alkyl or substituted C₁-C₁₂ alkyl; and

SM is a support medium.

6. The compound of claim 5 wherein R₄ is C₁-C₁₂ alkyl.

7. The compound of claim 6 wherein R₄ is CH₂CH₂.

8. The compound of claim 1 wherein R₁ is X₁-Y.

9. The compound of claim 8 wherein X₁ is phosphodiester, phosphorothioate or chiral phosphorothioate.

10. The compound of claim 9 wherein Y is an oligomeric compound.

11. The compound of claim 4 wherein SM is aminoalkyl controlled pore glass (CPG).

12. The compound of claim 1 wherein R₂ is hydroxyl or a protected hydroxyl.

13. The compound of claim 1 wherein R₂ is X₂-Y.

14. The compound of claim 13 wherein X₂ is a phosphodiester, phosphorothioate or a chiral phosphorothioate.

15. The compound of claim 14 wherein Y is an oligomeric compound.

16. The compound of claim 1 wherein said bivalent tethering moiety T has the formula:

*-C(═

O)-E-N(R_a)—

wherein

* is attached to the N atom of the pyrrolidinyl group; and

E is a C₁-C₁₂ alkyl or substituted C₁-C₁₂ alkyl, wherein said alkyl groups are optionally further interrupted with from 1 to 5 heteroatoms selected from O, S or N(R_a), said substituent groups are selected from ═

O and N(R_a).

each R_a is, independently, H or C₁-C₁₂ alkyl.

17. The compound of claim 16 wherein said bivalent tethering moiety is selected from —

C(═

O)—

CH₂—

O—

(CH₂)₂—

O—

(CH₂)₂—

N(R_a)— and

—

C(═

O)—

(CH₂)₅—

N(R_a)—

.

18. The compound of claim 1 wherein said activated phosphite moiety comprises a phosphoramidite, H-phosphonate, phosphate triester or a chiral auxiliary.

19. The compound of claim 1 having at least one Y group and wherein said at least one Y group is an oligomeric compound.

20. An oligomeric compound having the formula:

21. The oligomeric compound of claim 20 wherein m is 0.

22. The oligomeric compound of claim 20 wherein mm is 0.

23. The oligomeric compound of claim 20 wherein m is at least 1 and mm is at least 1.

24. The oligomeric compound of claim 20 wherein each L is independently, a phosphodiester or phosphorothioate internucleoside linking group.

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

at least a portion of said first oligomeric compound is capable of hybridizing with at least a portion of said second oligomeric compound;

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

wherein at least one of said first and second oligomeric compounds is an oligomeric compound of claim 20; and

said first and said second oligomeric compounds optionally further comprise one or more overhangs, phosphate moieties or capping groups.

26. The composition of claim 25 wherein said first and said second oligomeric compounds comprise a siRNA duplex.

27. The oligomeric compound of claims 20 wherein Q is a lipophilic moiety, vitamin, polymer, peptide, protein, nucleic acid, small molecule, oligosaccharide, carbohydrate cluster, intercalator, minor groove binder, cleaving agent, or cross-linking agent.

28. The oligomeric compound of claim 20 wherein Q is a steroid.

29. The oligomeric compound of claim 20 wherein Q is cholesterol or a cholesterol derivative.

30. The oligomeric compound of claim 20 wherein Q binds to low-density lipoprotein.

31. The oligomeric compound of claim 20 wherein Q is folate or folate derivative.

32. The oligomeric compound of claim 20 comprising a water-soluble polymer.

33. The oligomeric compound of claim 20 wherein Q comprises polyethylene glycol or copolymer thereof.

34. The oligomeric compound of claim 20 wherein said polyentylene glycol or copolymer thereof has a molecular weight of about 20,000 daltons.

35. The oligomeric compound of claim 20 wherein Q comprises a fusogenic peptide or delivery peptide.

36. The oligomeric compound of claim 20 wherein Q comprises a drug.

37. The oligomeric compound of claim 20 wherein Q binds to human serum albumin.

38. The oligomeric compound of claim 20 wherein Q comprises a reporter group.

39. A method of inhibiting gene expression comprising contacting one or more cells, a tissue or an animal with an oligomeric compound of claim 20.

40. A method of inhibiting gene expression comprising contacting one or more cells, a tissue or an animal with a composition of claim 25.

41. The composition of claim 25 wherein said second oligomeric compound is the oligomeric compound of claim 20.