Backbone modified oligonucleotide analogs and preparation thereof through radical coupling

• US 5,969,118 A
• Filed: 02/04/1997
• Issued: 10/19/1999
• Est. Priority Date: 07/27/1990
• Status: Expired due to Fees

• Current Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Original Assignee: ISIS Pharmaceuticals Incorporated (Ionis Pharmaceuticals, Inc.)
• Inventors: Sanghvi, Yogesh S., Cook, Phillip Dan
• Primary Examiner(s): Marschel, Ardin H.
• Assistant Examiner(s): Riley, Jezia
• Application Number:
  US08/794,493
• Time in Patent Office: 987 Days
• Field of Search: 536/22.1, 536/23.1, 536/28.54, 536/25.3
• US Class Current: 536/22.1
• CPC Class Codes: C07D 405/04 directly linked by a ring-member-to-ring-member bond
• CPC Class Codes: C07D 405/14 containing three or more hetero rings
• CPC Class Codes: C07F 7/1804 Compounds having Si-O-C linkages Si-O-acyl linkages C07F7/1896
• 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 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

Abstract

Methods for preparing oligonucleotide analogs which have improved nuclease resistance and improved cellular uptake are provided. In preferred embodiments, the methods involve radical coupling of 3'"'"'- and 5'"'"'-substituted or 5'"'"'- and 3'"'"'-subutituted nucleosidic synthons.

Claims

1. A compound having structure:

##STR8## wherein;

Z₁ is CH₂ --R_B, R_B, CH₂ --R_A N═

CH₂, or R_A N═

CH₂, provided that Z₁ is not R_A N═

CH₂ when X₁ is H or OH, and Z₁ is not R_B when R_B is OC(O)O--C₆ H₅ ;

R_A is O or NH;

R_B is a radical generating group selected from I, OC(O)O--C₆ H₅, OC(O)S--C₆ H₅, Se--C₆ H₅, O--C(S)O--C₆ F₅, O--C(S)O--C₆ Cl₅, O--C(S)O--(2,4,6--C₆ Cl₃), NO₂, C(S)S--Me, C(S)O--(p--CH₄ F), bis-dimethylglyoximato-pyridine cobalt, O--C(S)C₆ H₅, O--C(S)SCH₃, O--C(S)-imidazole, and C(O)O-pyridin-2-thione;

Y₁ is H, hydroxymethyl, a nucleoside, a nucleotide, an oligonucleotide, an oligonucleoside, or a hydroxyl-protected or amine-protected derivative thereof;

B_X1 is a nucleosidic base;

Q₁ is O, S, CH₂, CHF or CF₂ ; and

X₁ is H, OH, C₁ to C₁₀ lower alkyl, substituted lower alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SOCH₃, SO₂ CH₃, ONO₂, NO₂, N₃, NH₂, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino or substituted silyl.

2. The compound of claim 1 wherein R_A is O.

3. The compound of claim 1 wherein R_A is NH.

4. The compound of claim 1 wherein Z₁ is CH₂ --R_S or R_S.

5. The compound of claim 1 wherein Z₁ is R_A --N═

CH₂ or CH₂ --R_a -N═

CH₂.

6. The compound of claim 1 wherein said radical generating group is I.

7. A compound having structure:

##STR9## wherein;

Y₂ is CH₂ --R_B, R_B, CH₂ --R_A N═

CH₂, or R_A N═

CH₂ ;

R_A is O or NH;

R_B is a radical generating group selected from I, OC(O)O--C₆ H₅, OC(O)S--C₆ H₅, Se--C₆ H₅, O--(S)O--C₆ F₅, O--(S)O--C₆ Cl₅, O--(S)O--(2,4,6--C₆ Cl₃), Br, NO₂, Cl, C(S)S--Me, C(S)O--(p--CH₄ F), bis-dimethylglyoximato-pyridine cobalt, O(S)C₆ H₅, O(S)SCH₃, O(S)-imidazole, and C(O)O-pyridin-2-thione;

Z₂ is H, hydroxyl, a nucleoside, a nucleotide, an oligonucleotide, an oligonucleoside, or a hydroxyl-protected or amine-protected derivative thereof;

B_X2 is a nucleosidic base;

Q₂ is O, S, CH₂, CHF or CF₂ ; and

X₂ is H, OH, C₁ to C₁₀ lower alkyl, substituted lower alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF₃, OCF₃, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SOCH₃, SO₂ CH₃, ONO₂, NO₂, N₃, NH₂, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino or substituted silyl;

provided that R_B is not I, Br, or Cl when Z₂ is hydroxyl, Q₂ is O, and X₂ is H or OH.

8. The compound of claim 7 wherein R_A is O.

9. The compound of claim 7 wherein R_A is NH.

10. The compound of claim 7 wherein Y₂ is CH₂ --R_S or R_S.

11. The compound of claim 7 wherein Y₂ is CH₂ --R_A --N═

CH₂ or R_A --N═

CH₂.

12. The compound of claim 7 wherein said radical generating group is I.