2'-O-amino-containing nucleoside analogs and polynucleotides

• US 6,159,951 A
• Filed: 12/02/1997
• Issued: 12/12/2000
• Est. Priority Date: 02/13/1997
• Status: Expired due to Term

• Current Assignee: Ribozyme Pharmaceuticals, Inc. (Alnylam Pharmaceuticals Incorporated)
• Original Assignee: Ribozyme Pharmaceuticals, Inc. (Alnylam Pharmaceuticals Incorporated)
• Inventors: Beigelman, Leonid, Karpeisky, Alexander
• Primary Examiner(s): Wilson, James O.
• Application Number:
  US08/982,841
• Time in Patent Office: 1,106 Days
• Field of Search: 536/26.26, 536/26.6, 536/26.7, 536/26.74, 536/27.21, 536/276, 536/17.8, 536/27.81, 536/28.1, 536/28.5, 536/28.53, 536/28.54, 536/23.1, 935/33, 935/34, 935/69.1, 435/6, 435/91.1, 435/172.1, 435/240, 435/240.2, 435/375, 435/325, 514/44, 514/43, 514/45, 514/46, 514/47, 514/48, 514/49, 514/50, 514/51
• US Class Current: 514/45
• CPC Class Codes: C07H 19/04 Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 19/16 Purine radicals
• CPC Class Codes: C07H 19/20 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• 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: C07K 14/005 from viruses
• CPC Class Codes: C12N 15/85 for animal cells
• CPC Class Codes: C12N 15/86 Viral vectors
• CPC Class Codes: C12N 2310/121 Hammerhead
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/322 2'-R Modification
• CPC Class Codes: C12N 2760/10122 New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
• CPC Class Codes: C12Q 1/701 Specific hybridization probes

Abstract

Novel nucleoside or nucleotide analogs comprising 2'"'"'-O-amino residues, processes for their synthesis and incorporation into polynucleotides.

Claims

1. A nucleoside or a nucleotide comprising a sugar portion, wherein the 2'"'"' position of said sugar has the formula:

2'"'"'-O--NHR₁, wherein R₁ is selected from a group consisting of H, aminoacyl group, peptidyl group, biotinyl group, cholesteryl group, lipoic acid residue, retinoic acid residue, folic acid residue, ascorbic acid residue, nicotinic acid residue, 6-aminopenicillanic acid residue, 7-aminocephalosporanic acid residue, alkyl, alkenyl, alkynyl, aryl, alkylaryl, carbocyclic aryl, heterocyclic aryl, amide and ester.

5. The compound of claim 1 or claim 2, wherein said compound is a nucleotide.

6. The compound of claim 1 or claim 2, wherein said compound is a nucleotide-tri-phosphate.

7. The compound of claim 1, wherein said compound is 2'"'"'-O-amino adenosine.

8. The compound of claim 1, wherein said compound is 2'"'"'-O-amino guanosine.

9. The compound of claim 1, wherein said compound is 2'"'"'-O-amino cytidine.

10. The compound of claim 1, wherein said compound is 2'"'"'-O-amino uridine.

11. A pharmaceutical composition comprising a compound of claim 1 or claim 2.

2. A nucleoside or a nucleotide comprising a sugar portion, wherein the 2'"'"' position of said sugar has the formula:

2'"'"'-O--N═

R₃, wherein R₃ is selected from a group consisting of pyridoxal residue, pyridoxal-5-phosphate residue, 13-cis-retinal residue, 9-cis-retinal residue, alkyl, alkenyl, alkynyl, alkylaryl, carbocyclic alkylaryl, and heterocyclic alkylaryl.

3. A compound having the formula 1:

##STR6## wherein, R₁ is selected from a group consisting of H, aminoacyl group, peptidyl group, biotinyl group, cholesteryl group, lipoic acid residue, retinoic acid residue, folic acid residue, ascorbic acid residue, nicotinic acid residue, alkyl, alkenyl, alkynyl, aryl, alkyaryl, carbocyclic aryl, heterocyclic aryl, amide and ester;

X is independently a nucleotide base or its analog or hydrogen;

Y is independently a phosphorus-containing group; and

R2 is independently a blocking group or a phosphorus-containing group.

4. A compound having the formula II:

##STR7## wherein, R₃ is selected from a group consisting of pyridoxal residue, pyridoxal-5-phosphate residue, 13-cis-retinal residue, 9-cis-retinal residue, alkyl, alkenyl, alkynyl, alkylaryl, carbocyclic alkylaryl, and heterocyclic alkylaryl;

X is independently a nucleotide base or its analog or hydrogen;

Y is independently a phosphorus-containing group; and

R2 is independently a blocking group or a phosphorus-containing group.

12. A process for the synthesis of a 2'"'"'-O-amino nucleoside comprising the steps of:

a) contacting a 3'"'"' and 5'"'"'-protected arabino nucleoside with sulfonylating reagent under conditions suitable for the formation of 3'"'"' and 5'"'"'-protected 2'"'"'-arabino sulfonyl nucleoside;

b) displacing the sulfonyl group from said 2'"'"'-arabino sulfonyl nucleoside with N-hydroxy-phthalimide in the presence of a strong organic base under conditions suitable for the formation of 3'"'"' and 5'"'"'-protected 2'"'"'-O-N-phthaloyl ribonucleoside;

c) deprotecting said phthaloyl ribonucleoside with a fluoride containing reagent under conditions suitable for the formation of 2'"'"'-O-N-phthaloyl ribonucleoside; and

d) contacting said 2'"'"'-O-N-phthaloyl ribonucleoside with a reagent selected from a group consisting of alkylamine, hydrazine, N-phenyl hydrazine and N-alkylhydrazine, under conditions suitable for the formation of said 2'"'"'-O-amino nucleoside.

13. The process of claim 12, wherein said sulfonylating reagent is tri-fluoromethane sulfonic anhydride.

14. The process of claim 12, wherein said sulfonylating reagent is tri-fluoromethane sulfonic chloride.

15. The process of claim 12, wherein said strong organic base is 1,8-diazabicyclo(5.4.0)undec-7-ene.

16. The process of claim 12, wherein said fluoride containing reagent is selected from a group consisting of tetrabutylammonium fluoride and triethylamine trihydrofluoride.

17. The process of claim 12, wherein said alkylamine is aqueous methylamine.

18. The process of claim 12, wherein said N-alkylhydrazine is N-methylhydrazine.