2′-O-aminoethyloxyethyl-modified oligonucleotides

• US 6,600,032 B1
• Filed: 08/06/1999
• Issued: 07/29/2003
• Est. Priority Date: 08/07/1998
• Status: Expired due to Term

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Manoharan, Muthiah, Cook, Phillip Dan
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US09/370,625
• Time in Patent Office: 1,453 Days
• Field of Search: 435/6, 536/26.6
• US Class Current: 536/26.6
• CPC Class Codes: A61P 1/18 for pancreatic disorders, e.g. pancreatic enzymes
• CPC Class Codes: A61P 31/14 for RNA viruses
• 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 2310/315 Phosphorothioates
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/3341 5-Methylcytosine
• CPC Class Codes: C12N 2310/341 Gapmers, i.e. of the type ===---===
• CPC Class Codes: C12N 2310/3527 Other alkyl chain

Abstract

2′-O-Modified ribosyl nucleosides and modified oligomeric compounds containing such nucleosidic monomers are disclosed. Oligomeric compounds are disclosed that have increased binding affinity as shown by molecular modeling experiments. The 2′-O-modified nucleosides of the invention include ring structures that position the sugar moiety of the nucleosides preferentially in 3′ endo geometries.

Claims

1. An oligomeric compound having at least one nucleoside of the formula:

wherein

Bx is a heterocyclic base;

each R₁ and R₂ is, independently, H, a nitrogen protecting group, substituted or unsubstituted C₁-C₁₀ alkyl, substituted or unsubstituted C₂-C₁₀ alkenyl, substituted or unsubstituted C₂-C₁₀ alkynyl, wherein said substitution is OR₃, SR₃, NH₃⁺, N(R₃)(R₄), guanidino or acyl where said acyl is an acid, amide or an ester;

or R₁ and R₂, together, are a nitrogen protecting group or are joined in a ring structure that optionally includes an additional heteroatom selected from N and O; and

each R₃ and R₄ is, independently, H, C₁-C₁₀ alkyl, a nitrogen protecting group, or R₃ and R₄, together, are a nitrogen protecting group;

or R₃ and R₄ are joined in a ring structure that optionally includes an additional heteroatom selected from N and O.

2. The oligomeric compound of claim 1 wherein R₁ is H, C₁-C₁₀ alkyl or C₁-C₁₀ substituted alkyl and R₂ is C₁-C₁₀ substituted alkyl.

3. The oligomeric compound of claim 2 wherein R₁ is C₁-C₁₀ alkyl.

4. The oligomeric compound of claim 2 wherein R₂ is C₁-C₁₀ substituted alkyl and the substituent is NH₃⁺ or N(R₃) (R₄).

5. The oligomeric compound of claim 2 wherein R₁ and R₂ are both C₁-C₁₀ substituted alkyl.

6. The oligomeric compound of claim 5 wherein said substituents are, independently, NH₃⁺ or N(R₃) (R₄).

7. The oligomeric compound of claim 1 wherein R₁ and R₂ are each C₁-C₁₀ alkyl.

8. The oligomeric compound of claim 1 wherein R₁ and R₂ are joined in a ring structure that can include at least one heteroatom selected from N and O.

9. The oligomeric compound of claim 8 wherein said ring structure is imidazole, piperidine, morpholine or a substituted piperazine.

10. The oligomeric compound of claim 9 wherein the substituent on said piperazine is C₁-C₁₂ alkyl.

11. The oligomeric compound of claim 1 wherein said heterocyclic base is a purine or a pyrimidine.

12. The oligomeric compound of claim 11 wherein said heterocyclic base is adenine, cytosine, 5-methylcytosine, thymine, uracil, guanine or 2-aminoadenine.

13. The oligomeric compound of claim 1 comprising from about 5 to about 50 nucleosides.

14. The oligomeric compound of claim 1 comprising from bout 8 to about 30 nucleosides.

15. The oligomeric compound of claim 1 comprising from about 15 to about 25 nucleosides.

16. A compound of the formula:

wherein;

Bx is a heterocyclic base;

T₁ and T₂, independently, are OH, a protected hydroxyl, an activated phosphorus group, a reactive group for forming an internucleotide linkage, a nucleoside, a nucleotide, an oligonucleoside an oligonucleotide or a linkage to a solid support;

each R₁ and R₂ is, independently, H, a nitrogen protecting group, substituted or unsubstituted C₁-C₁₀ alkyl, substituted or unsubstituted C₂-C₁₀ alkenyl, substituted or unsubstituted C₂-C₁₀ alkynyl, wherein said substitution is OR₃, SR₃, NH₃⁺, N(R₃) (R₄), guanidino or acyl where said acyl is an acid, amide or an ester;

or R₁ and R₂, together, are a nitrogen protecting group or are joined in a ring structure that optionally includes an additional heteroatom selected from N and O; and

each R₃ and R₄ is, independently, H, C₁-C₁₀ alkyl, a nitrogen protecting group, or R₃ and R₄, together, are a nitrogen protecting group;

or R₃ and R₄ are joined in a ring structure that optionally includes an additional heteroatom selected from N and O.

17. The compound of claim 16 wherein R₁ is H, C₁-C₁₀ alkyl or C₁-C₁₀ substituted alkyl and R₂ is C₁-C₁₀ substituted alkyl.

18. The compound of claim 17 wherein R₁ is C₁-C₁₀ alkyl.

19. The compound of claim 17 wherein R₂ is C₁-C₁₀ substituted alkyl and the substituent is NH₃⁺ or N(R₃) (R₄).

20. The compound of claim 17 wherein R₁ and R₂ are both C₁-C₁₀ substituted alkyl.

21. The compound of claim 20 wherein said substituents are, independently, NH₃⁺ or N(R₃) (R₄).

22. The compound of claim 16 wherein R₁ and R₂ are each C₁-C₁₀ alkyl.

23. The compound of claim 16 wherein R₁ and R₂ are joined in a ring structure that can include at least one heteroatom selected from N and O.

24. The compound of claim 23 wherein said ring structure is imidazole, piperidine, morpholine or a substituted piperazine.

25. The compound of claim 24 wherein said substituted piperazine is substituted with a C₁-C₁₂ alkyl.

26. The compound of claim 25 wherein said heterocyclic base is a purine or a pyrimidine.

27. The compound of claim 26 wherein said heterocyclic base is adenine, cytosine, 5-methylcytosine, thymine, uracil, guanine or 2-aminoadenine.

28. The compound of claim 16 wherein T₁ is a hydroxyl protecting group.

29. The compound of claim 16 wherein T₂ is an activated phosphorus group or a connection to a solid support.

30. The compound of claim 29 wherein said solid support material is microparticles.

31. The compound of claim 29 wherein said solid support material is CPG.