Backbone modified oligonucleotide analogs

• US 5,602,240 A
• Filed: 04/25/1994
• Issued: 02/11/1997
• Est. Priority Date: 07/27/1990
• Status: Expired due to Term

• Current Assignee: ISIS Pharmaceuticals Incorporated, Novartis Ag
• Original Assignee: ISIS Pharmaceuticals Incorporated, Ciba-Geigy AG (Novartis Ag)
• Inventors: Lebreton, Jacques, De Mesmaeker, Alain, Cook, Phillip D., Waldner, Adrian
• Primary Examiner(s): Wilson, James O.
• Application Number:
  US08/140,206
• Time in Patent Office: 1,023 Days
• Field of Search: 536/22.1, 536/25.34, 536/25.3, 536/23.1, 536/25.5, 536/25.6, 514/44
• US Class Current: 536/22.1
• CPC Class Codes: A61K 47/549 Sugars, nucleosides, nucleotides or nucleic acids
• 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

Oligonucleotide analogs are provided wherein phosphodiester inter-sugar linkages are replaced with four atom linking groups. Such linking groups include NR--C(O)--CH₂ --CH₂, NR--C(S)--CH₂ --CH₂, CH₂ --NR--C(O)--CH₂, CH₂ --NR--C(S)--CH₂, CH₂ --CH₂ --NR--C(O)--R--CH₂, and CH₂ --C(S)--NR--CH₂. Methods for preparing and using these oligonucleotide analogs are also provided.

Claims

1. An oligonucleotide analog comprising the structure:

##STR16## wherein;

B_x is a variable base moiety;

Q is 0, CH₂, CHF or CF₂ ;

X is H;

OH;

C₁ to C₁₀ lower alkyl, substituted lower alkyl, alkaryl or aralkyl;

F;

Cl;

Br;

CN;

CF₃ ;

OCF₃ ;

OCN;

O--, S--, or N-alkyl;

O--, S--, or N-alkenyl;

SOCH₃ ;

SO₂ CH₃ ;

ONO₂ ;

NO₂ ;

N₃ ;

NH₂ ;

heterocycloalkyl;

heterocycloalkaryl;

aminoalkylamino;

polyalkylamino;

or substituted silyl;

L₁ --L₂ --L₃ --L₄ is selected from NR--C(O)--CH₂ --CH₂ --, NR--C(S)--CH₂ --CH₂, CH₂ --NR--C(O)--CH₂, CH₂ --NR--C(S)--CH₂, CH₂ --CH₂ --NR--C(O), CH₂ --CH₂ --NR--C(S), C(O)--NR--CH₂ --CH₂, C(S)--NR--CH₂ --CH₂, CH₂ --C(O)--NR--CH₂, and CH₂ --C(S)--NR--CH₂ where R is hydrogen, alkyl, substituted alkyl, aralkyl, alkenyl, alkaryl, aminoalkyl, hydroxyalkyl, heterocycloalkyl, or heterocycloaralkyl; and

the remaining subunits are natural or synthetic.

2. The oligonucleotide analog of claim 1 wherein Q is 0.

3. The oligonucleotide analog of claim 1 wherein X is H.

4. The oligonucleotide analog of claim 1 wherein X is OH.

5. The oligonucleotide analog of claim 1 wherein X is H, OH, F, O-alkyl or O-alkenyl and Q is 0.

6. The oligonucleotide analog of claim 1 wherein B_x is adenine, guanine, uracil, thymine, cytosine, 2-aminoadenosine or 5-methylcytosine.

7. The oligonucleotide analog of claim 1 comprising from about 4 to about 50 subunits having said structure.

8. The oligonucleotide analog of claim 1 wherein substantially all of the subunits have said structure.

9. The oligonucleotide analog of claim 1 wherein substantially alternating subunits have said structure.

17. The oligonucleotide analog of claim 1 wherein L₁ --L₂ --L₃ --L₄ is CH₂ --NR--C(O)--CH₂.

18. The oligonucleotide analog of claim 1 wherein L₁ --L₂ --L₃ --L₄ is CH₂ --C(O)--NR--CH₂.

10. A compound having the structure:

##STR17## wherein;

B_x is a variable base moiety;

Q is 0, CH₂, CHF or CF₂ ;

X is H;

OH;

C₁ to C₁₀ lower alkyl, substituted lower alkyl, alkaryl or aralkyl;

F;

Cl;

Br;

CN;

CF₃ ;

OCF₃ ;

OCN;

O--, S--, or N-alkyl;

O--, S--, or N-alkenyl;

SOCH₃ ;

SO₂ CH₃ ;

ONO₂ ;

NO₂ ;

N₃ ;

NH₂ ;

heterocycloalkyl;

heterocycloalkaryl;

or aminoalkylamino;

polyalkylamino;

substituted silyl;

L₁ --L₂ --L₃ --L₄ is selected from NR--C(O)--CH₂ --CH₂, NR--C(S)--CH₂ --CH₂, CH₂ --NR--C(O)--CH₂, CH₂ --NR--C(S)--CH₂, CH₂ --CH₂ --NR--C(O), CH₂ --CH₂ --NR--C(S), C(O)--NR--CH₂ --CH₂, C(S)--NR--CH₂ --CH₂, CH₂ --C(O)--NR--CH₂, and CH₂ --C(S)--NR--CH₂ where R is hydrogen, alkyl, substituted alkyl, aralkyl, alkenyl, alkaryl, aminoalkyl, hydroxyalkyl, heterocycloalkyl, or heterocycloaralkyl; and

R_HP1 and R_HP2 are, independently, H or a hydroxyl protecting group.

11. The compound of claim 10 wherein Q is 0.

12. The compound of claim 10 wherein X is H.

13. The compound of claim 10 wherein X is OH.

14. The compound of claim 10 wherein X is H, OH, F, O-alkyl or O-alkenyl and Q is 0.

15. The compound claim 10 wherein B_x is adenine, guanine, uracil, thymine, cytosine, 2-aminoadenosine or 5-methylcytosine.

19. The compound of claim 10 wherein L₁ --L₂ --L₃ --L₄ is CH₂ --NR--C(O)--CH₂.

20. The compound of claim 10 wherein L₁ --L₂ --L₃ --L₄ is CH₂ --C(O)--NR--CH₂.

16. A process for preparing a compound having the structure:

##STR18## wherein;

B_x is a variable base moiety;

Q is 0, CH₂, CHF or CF₂ ;

X is H;

OH;

C₁ to C₁₀ lower alkyl, substituted lower alkyl, alkaryl or aralkyl;

F;

Cl;

Br;

CN;

CF₃ ;

OCF₃ ;

OCN;

O--, S--, or N-alkyl;

O--, S--, or N-alkenyl;

SOCH₃ ;

SO₂ CH₃ ;

ONO₂ ;

NO₂ ;

N₃ ;

NH₂ ;

heterocycloalkyl;

heterocycloalkaryl;

aminoalkylamino;

polyalkylamino;

or substituted silyl;

L₁ --L₂ --L₃ --L₄ is selected from NR--C(O)--CH₂ --CH₂, NR--C(S)--CH₂ --CH₂, CH₂ --NR--C(O)--CH₂, CH₂ --NR--C(S)--CH₂, CH₂ --CH₂ --NR--C(O), CH₂ --CH₂ --NR--C(S), C(O)--NR--CH₂ --CH₂, C(S)--NR--CH₂ --CH₂, CH₂ --C(O)--NR--CH₂, and CH₂ --C(S)--NR--CH₂ where R is hydrogen, alkyl, substituted alkyl, aralkyl, alkenyl, alkaryl, aminoalkyl, hydroxyalkyl, heterocycloalkyl, or heterocycloaralkyl; and

R_HP1 and R_HP2 are, independently, H or a hydroxyl protecting group.

comprising the steps of;

providing a first synthon having structure (I) and second synthon having structure (II);

##STR19## wherein;

(a) R_T is NH₂ and R_B is R_A --CH₂ --CH₂ ;

(b) R_T is CH₂ --NH₂ and R_B is R_A --CH₂ ;

(c) R_T is CH₂ --CH₂ --NH₂ and R_B is R_A ;

(d) R_T is R_A and R_B is NH₂ --CH₂ --CH₂ ;

or

(e) R_T is CH₂ --R_A and R_B is NH₂ --CH₂ ;

where R_A is C(O) OH, C(S)OH, or an activated derivative thereof; and

coupling said first synthon and said second synthon to form an amide or thioamide linkage through said R_T and R_B groups.