Heteroatomic oligonucleoside linkages

• US 5,777,092 A
• Filed: 02/04/1997
• Issued: 07/07/1998
• Est. Priority Date: 07/27/1990
• Status: Expired due to Term

• Current Assignee: ISIS Pharmaceuticals Incorporated
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Sanghvi, Yogesh Shantilal, Cook, Phillip Dan
• Primary Examiner(s): Elliott, George C.
• Assistant Examiner(s): LARSON, THOMAS GEORGE
• Application Number:
  US08/795,282
• Time in Patent Office: 518 Days
• Field of Search: 435/6, 435/375, 514/44, 536/23.1, 536/24.3, 536/24.31, 536/24.32, 536/24.5
• US Class Current: 536/23.1
• CPC Class Codes: A61K 31/70 Carbohydrates; Sugars; Derivatives thereof sorbitol A61K31/047
• CPC Class Codes: A61K 47/59 obtained otherwise than by reactions only involving carbon-to-carbon unsaturated bonds, e.g. polyureas or polyurethanes
• CPC Class Codes: A61K 47/605 the macromolecule containing phosphorus in the main chain, e.g. poly-phosphazene
• 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-mimicking macromolecules that have improved nuclease resistance are provided. Replacement of the normal phosphorodiester inter-sugar linkages found in natural oligonucleotides with three or four atom linking groups provide unique oligonucleotide-mimicking macromolecules that are useful in regulating RNA expression and in therapeutics. Methods of synthesis and use also are disclosed.

Claims

1. A macromolecule, at least a portion of which is of the structure:

##STR4## wherein one of L₁ or L₂ is O or S, and the other of L.sub. or L₂ is N--R; and

L₃ and L₄, combined, are CH₂, or L₃ is CH₂ and L₄ is CR'"'"'R";

or

one of L₃ or L₄ is O or S, and the other of L₃ or L₄ is N--R; and

L.sub. and L₂, combined, are CH₂, or L₂ is CH₂ and L₁ is CR'"'"'R";

or

one of L₁ and L₄ is O, S or N--R, and the other of L₁ and L₄ is CR'"'"'R"; and

L₂ and L₃ are CH₂ ;

or

L₁, L₂, L₃ and L₄, together, are O--N═

CH--CH₂ or CH₂ --CH═

2 N--O;

or

L₁ is O;

L₂ is N;

L₃ is CH₂ ; and

L₄ is C or CH; and

together with at least two additional carbon or hetero atoms, L₂, L₃ and L₄ form a 5 or 6 membered ring;

or

L₁ is C or CH;

L₂ is CH₂ ;

L₃ is N; and

L₄ is O; and

together with at least two additional carbon or hetero atoms, L₁, L₂ and L₃ form a 5 or 6 membered ring;

R is H;

C₁ to C₁₀ straight or branched chain lower alkyl or substituted lower alkyl;

C₂ to C₁₀ straight or branched chain lower alkenyl or substituted lower alkenyl;

C₂ to C₁₀ straight or branched chain lower alkynyl or substituted lower alkynyl;

a ¹⁴ C containing lower alkyl, lower alkenyl or lower alkynyl;

C₇ to C₁₄ alkaryl or aralkyl;

a ⁴ C containing C₇ to C₁₄ alkaryl or aralkyl;

alicyclic;

heterocyclic;

a reporter molecule;

or an RNA cleaving group;

R'"'"' and R" are H;

or R'"'"' is H and R" is O--R;

or R'"'"' and R", combined, are ═

O;

X is H;

O--R;

S--R;

NH--R;

F, Cl;

Br;

CN;

CF₃ ;

OCF₃ ;

OCN;

SOCH₃ ;

SO₂ CH₃ ;

ONO₂ ;

NO₂ ;

N₃ ;

NH₂ ;

heterocycloalkyl;

heterocycloalkaryl;

aminoalkylamino;

polyalkylamino;

substituted silyl;

a reporter molecule;

or an RNA cleaving group;

Q is O or CH₂ ;

n is an integer greater than 0; and

Bx is a variable heterocyclic base moiety.

2. The macromolecule of claim 1 wherein R is H.

3. The macromolecule of claim 1 wherein R is C₁ to C₁₀ straight or branched chain lower alkyl or substituted lower alkyl;

C₂ to C₁₀ straight or branched chain lower alkenyl or substituted lower alkenyl;

C₂ to C₁₀ straight or branched chain lower alkynyl or substituted lower alkynyl;

or C₇ to C₁₄ alkaryl or aralkyl.

4. The macromolecule of claim 1 wherein R is a ¹⁴ C containing lower alkyl, lower alkenyl or lower alkynyl;

or a ¹⁴ C containing C₇ to C₁₄ alkaryl or aralkyl.

5. The macromolecule of claim 1 wherein R is a reporter molecule;

or an RNA cleaving group.

6. The macromolecule of claim 1 wherein Q is O .

7. The macromolecule of claim 1 wherein X is H or OH.

8. A macromolecule, at least a portion of which is of the structure:

##STR5## wherein one of L₁ or L₂ is O or S, and the other of L₁ or L₂ is N--R; and

L₃ and L₄, combined, are CH₂ ;

or

one of L₃ or L₄ is O or S, and the other of L₃ or L₄ is N--R; and

L₁ and L₂, combined, are CH₂ ; and

R is H;

C₁ to C₁₀ straight or branched chain lower alkyl or substituted lower alkyl;

C₂ to C₁₀ straight or branched chain lower alkenyl or substituted lower alkenyl;

C₂ to C₁₀ straight or branched chain lower alkynyl or substituted lower alkynyl;

a ¹⁴ C containing lower alkyl, lower alkenyl or lower alkynyl;

C₇ to C₁₄ alkaryl or aralkyl;

a ¹⁴ C containing C₇ to C₁₄ alkaryl or aralkyl;

alicyclic;

heterocyclic;

a reporter molecule;

or an RNA cleaving group;

X is H;

O--R;

S--R;

NH--R;

F, Cl;

Br;

CN;

CF₃ ;

OCF₃ ;

OCN;

SOCH₃ ;

SO₂ CH₃ ;

ONO₂ ;

NO₂ ;

N₃ ;

NH₂ ;

heterocycloalkyl;

heterocycloalkaryl;

aminoalkylamino;

polyalkylamino;

substituted silyl;

a reporter molecule;

or an RNA cleaving group;

Q is O or CH₂ ;

n is an integer greater than 0; and

Bx is a variable heterocyclic base moiety.

9. The macromolecule of claim 8 wherein L₃ and L₄, combined, are CH₂.

10. The macromolecule of claim 9 wherein L₁ is O and L₂ is N--R.

11. A macromolecule, at least a portion of which is of the structure:

##STR6## wherein one of L₁ and L₄ is O , S or N--R, and the other of L₁ and L₄ is CR'"'"'R"; and

L₂ and L₃ are CH₂ ;

R is H;

C₁ to C₁₀ straight or branched chain lower alkyl or substituted lower alkyl;

C₂ to C₁₀ straight or branched chain lower alkenyl or substituted lower alkenyl;

C₂ to C₁₀ straight or branched chain lower alkynyl or substituted lower alkynyl;

a ¹⁴ C containing lower alkyl, lower alkenyl or lower alkynyl;

C₇ to C₁₄ alkaryl or aralkyl;

a ¹⁴ C containing C₇ to C₁₄ alkaryl or aralkyl;

alicyclic;

heterocyclic;

a reporter molecule;

or an RNA cleaving group;

R'"'"' and R" are H;

or R'"'"' is H and R" is O--R;

or R'"'"' and R", combined, are ═

O;

X is H;

O--R;

S--R;

NH--R;

F, Cl;

Br;

CN;

CF₃ ;

OCF₃ ;

OCN;

SOCH₃ ;

SO₂ CH₃ ;

ONO₂ ;

NO₂ ;

N₃ ;

NH₂ ;

heterocycloalkyl;

heterocycloalkaryl;

aminoalkylamino;

polyalkylamino;

substituted silyl;

a reporter molecule;

or an RNA cleaving group;

Q is O or CH₂ ;

n is an integer greater than 0; and

Bx is a variable heterocyclic base moiety.

12. The macromolecule of claim 11 wherein R'"'"' and R" are H.

13. The macromolecule of claim 11 wherein R'"'"' is H;

R" is O--R; and

R is H.

14. A macromolecule, at least a portion of which is of the structure:

##STR7## wherein one of L₁ or L₂ is CH ₂, O or S, and the other of L₁ or L₂ is N--R; and

L₃ is CH₂ and L₄ is CR'"'"'R";

or

one of L₃ or L₄ is CH₂, O or S, and the other of L₃ or L₄ is N--R; and

L₂ CH₂ and L₁ is CR'"'"'R"; and

R is H;

C₁ to C₁₀ straight or branched chain lower alkyl or substituted lower alkyl;

C₂ to C₁₀ straight or branched chain lower alkenyl or substituted lower alkenyl;

C₂ to C₁₀ straight or branched chain lower alkynyl or substituted lower alkynyl;

a ¹⁴ C containing lower alkyl, lower alkenyl or lower alkynyl;

C₇ to C₁₄ alkaryl or aralkyl;

a ¹⁴ C containing C₇ to C₁₄ alkaryl or aralkyl;

alicyclic;

heterocyclic;

a reporter molecule;

or an RNA cleaving group;

R'"'"' and R" are H;

or R'"'"' is H and R" is O--R;

or R'"'"' and R", combined, are ═

O;

X is H;

O--R;

S--R;

NH--R;

F, Cl;

Br;

CN;

CF₃ ;

OCF₃ ;

OCN;

SOCH₃ ;

SO₂ CH₃ ;

ONO₂ ;

NO₂ ;

N₃ ;

NH₂ ;

heterocycloalkyl;

heterocycloalkaryl;

aminoalkylamino;

polyalkylamino;

substituted silyl;

a reporter molecule;

or an RNA cleaving group;

Q is O or CH₂ ;

n is an integer greater than 0; and

Bx is a variable heterocyclic base moiety.

15. The macromolecule of claim 14 wherein L₃ and L₄ are CH₂.

16. The macromolecule of claim 15 wherein L₁ is O or S and L₂ is N--R.

17. The macromolecule of claim 16 wherein L₁ is O .

18. The macromolecule of claim 16 wherein L₁ is S.

24. The macromolecule of claim 14 wherein one of L₁ or L₄ is CR'"'"'R", R'"'"' is H, and R" is O--R.

25. The macromolecule of claim 24 wherein R is H.

26. The macromolecule of claim 14 wherein L₄ is CR'"'"'R", R'"'"' is H, and R" is O--R.

27. The macromolecule of claim 26 wherein R is H.

28. The macromolecule of claim 27 wherein L₁ is O or S and L₂ is N--R.

19. The macromolecule of claim 19 wherein L₁ is N--R.

20. The macromolecule of claim 19 wherein L₂ is CH₂, O or S.

21. The macromolecule of claim 19 wherein L₂ is CH₂.

22. The macromolecule of claim 19 wherein L₂ is O or S.

23. The macromolecule of claim 22 wherein L₂ is O .

29. A macromolecule, at least a portion of which is of the structure:

##STR8## wherein L₁, L₂, L₃ and L₄, together, are O--N═

CH--CH₂ or CH₂ --CH═

N--O;

X is H;

O--R;

S--R;

NH--R;

F, Cl;

Br;

CN;

CF₃ ;

OCF₃ ;

OCN;

SOCH₃ ;

SO₂ CH₃ ;

ONO₂ ;

NO₂ ;

N₃ ;

NH₂ ;

heterocycloalkyl;

heterocycloalkaryl;

aminoalkylamino;

polyalkylamino;

substituted silyl;

a reporter molecule;

or an RNA cleaving group;

Q is O or CH₂ ;

n is an integer greater than 0; and

Bx is a variable heterocyclic base moiety.

30. A macromolecule, at least a portion of which is of the structure:

##STR9## wherein L₁ is O;

L₂ is N;

L₃ is CH₂ ; and

L₄ is C or CH; and

together with at least two additional carbon or hetero atoms, L₂, L₃ and L₄ form a 5 or 6 membered ring;

or

L₁ is C or CH;

L₂ is CH₂ ;

L₃ is N; and

L₄ is O; and

together with at least two additional carbon or hetero atoms, L₁, L₂ and L₃ form a 5 or 6 membered ring; and

X is H;

O--R;

S--R;

NH--R;

F, Cl;

Br;

CN;

CF₃ ;

OCF₃ ;

OCN;

SOCH₃ ;

SO₂ CH₃ ;

ONO₂ ;

NO₂ ;

N₃ ;

NH₂ ;

heterocycloalkyl;

heterocycloalkaryl;

aminoalkylamino;

polyalkylamino;

substituted silyl;

a reporter molecule;

or an RNA cleaving group;

Q is O or CH₂ ;

n is an integer greater than 0; and

Bx is a variable heterocyclic base moiety.

31. A macromolecule, at least a portion of which is of the structure:

##STR10## wherein (a) one of L₁ or L₂ is S, and the other of L₁ or L₂ is N--R; and

L₃ and L₄, combined, are CH₂, or L₃ is CH₂ and L₄ is CR'"'"'R";

or

(b) one of L₁ or L₂ is O , and the other of L₁ or L₂ is N--R; and

L₃ and L₄, combined, are CH₂, or L₃ is CH₂ and L₄ is CR'"'"'"R"";

or

(c) one of L₃ or L₄ is S, and the other of L₃ or L₄ is N--R; and

L₁ and L₂, combined, are CH₂, or L₂ is CH₂ and L₁ is CR'"'"'R";

or

(d) one of L₃ or L₄ is O , and the other of L₃ or L₄ is N--R; and

L₁ and L₂, combined, are CH₂, or L₂ is CH₂ and L₁ is CR'"'"'"R"";

or

(e) L₁ is CR'"'"'R", L₄ is S, and L₂ and L₃ are CH₂ ;

or

(f) L₁ is O , L₄ is CR'"'"'"R"", and L₂ and L₃ are CH₂ ;

or

(g) L₁, L₂, L₃ and L₄, together, are O--N═

CH--CH₂ or CH₂ --CH═

N--O;

or

(h) L₁ is O;

L₂ is N;

L₃ is CH₂ ; and

L₄ is C or CH; and

together with at least two additional carbon or hetero atoms, L₂, L₃ and L₄ form a 5 or 6 membered ring;

or

(i) L₁ is C or CH;

L₂ is CH₂ ;

L₃ is N; and

L₄ is O; and

together with at least two additional carbon or hetero atoms, L₁, L₂ and L₃ form a 5 or 6 membered ring;

where;

R is H;

C₁ to C₁₀ straight or branched chain lower alkyl or substituted lower alkyl;

C₂ to C₁₀ straight or branched chain lower alkenyl or substituted lower alkenyl;

C₂ to C₁₀ straight or branched chain lower alkynyl or substituted lower alkynyl;

a ¹⁴ C containing lower alkyl, lower alkenyl or lower alkynyl;

C₇ to C₁₄ alkaryl or aralkyl;

a ¹⁴ C containing C₇ to C₁₄ alkaryl or aralkyl;

alicyclic;

heterocyclic;

a reporter molecule;

or an RNA cleaving group;

R'"'"' and R" are H;

or R'"'"' is H and R" is O--R;

or R'"'"' and R", combined, are ═

O;

R'"'"'" is H and R"" is O--R""'"'"';

or R'"'"'" and R"", combined, are ═

O;

R""'"'"' is H;

C₁ to C₁₀ straight or branched chain lower alkyl or substituted lower alkyl;

C₂ to C₁₀ straight or branched chain lower alkenyl or substituted lower alkenyl;

C₂ to C₁₀ straight or branched chain lower alkynyl or substituted lower alkynyl;

a ¹⁴ C containing lower alkyl, lower alkenyl or lower alkynyl;

C₇ to C₁₄ alkaryl or aralkyl;

a ¹⁴ C containing C₇ to C₁₄ alkaryl or aralkyl;

alicyclic;

heterocyclic;

a reporter molecule;

or an RNA cleaving group;

X is H;

O--R;

S--R;

NH--R;

F, Cl;

Br;

CN;

CF₃ ;

OCF₃ ;

OCN;

SOCH₃ ;

SO₂ CH₃ ;

ONO₂ ;

NO₂ ;

N₃ ;

NH₂ ;

heterocycloalkyl;

heterocycloalkaryl;

aminoalkylamino;

polyalkylamino;

substituted silyl;

a reporter molecule;

or an RNA cleaving group;

Q is O or CH₂ ;

n is an integer greater than 0; and

Bx is a variable heterocyclic base moiety.