Supports for oligomer synthesis

• US 20050208588A1
• Filed: 11/15/2004
• Published: 09/22/2005
• Est. Priority Date: 01/31/2003
• Status: Active Grant

• Current Assignee: Ionis Pharmaceuticals, Inc.
• Original Assignee: ISIS Pharmaceuticals Incorporated
• Inventors: Manoharan, Muthiah, Guzaev, Andrei P., Wang, Zhiwei, Ravikumar, Vasulinga, Kumar, Raju Krishna
• Granted Patent: US 7,202,264 B2
• Time in Patent Office: Days
• US Class Current: 435/7.100
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C07D 491/08 Bridged systems
• CPC Class Codes: C07D 491/18 Bridged systems
• CPC Class Codes: C07D 493/18 Bridged systems

Abstract

Universal linkers, their facile processes of manufacture and methods of using the same are provided.

Claims

1. A compound of formula (I) or (II):

2. A compound of claim 1, wherein for formula (I) when one of Q or W is SM or L-SM, the other of Q or W is not —

SM or -L-SM.

3. A compound of claim 1, wherein for formula (II) when one of A, Q, or W is SM or L-SM, the other two of A, Q or W are not SM or L-SM.

4. A compound of claim 1, wherein Q and W are each hydrogen and G₁ is O.

5. A compound of claim 1, wherein one of Q and W is hydrogen and the other is hydrogen or a blocking group, and G₁, Y₁ and Y₂ are each O.

6. A compound of claim 5, wherein the blocking group is selected from 4,4′

-dimethoxytrityl, monomethoxytrityl, 9-phenylxanthen-9-yl, 9-([-methoxyphenyl)xanthen-9-yl, t-butyl, t-butoxymethyl, methoxymethyl, tetrahydropyranyl, 1-ethoxyethyl, 1-(2-chloroethoxy)ethyl, 2-trimethylsilylethyl, p-chlorophenyl, 2,-dinitrophenyl, benzyl, 2,6-dichlorobenzyl, diphenylmethyl, p,p-dinitrobenzhydryl, p-nitrobenzyl, triphenylmethyl, trimethylsilyl, triethylsilyl, t-butyldimethylsilyl, t-butyldiphenylsilyl, triphenylsilyl, benzoylformate, mesyl, tosyl, 4,4′

,4″

-tris- (benzyloxy)trityl 4,4′

,4″

-tris-(4,5-dichlorophthalimido)trityl, 4,4′

,4′

-tris(levulinyloxy)trityl, 3(indazolylmethyl)-4,4′

-dimethoxytrityl, 4-decyloxytrityl, 4-hexadecyloxytrityl, 9-(4-octadecyloxyphenyl)xanthene-9-yl, 1,1-bis-(4-methoxyphenyl)-1-pyrenylmethyl, p-phenylazophenyloxycarbonyl, 9-fluorenylmethoxycarbonyl, 2,4-dinitrophenylethoxycarbonyl, 4-(methylthiomethoxy)butyryl, 2-(methylthiomethoxymethyl)-benzoyl, 2-isopropylthiomethoxymethyl)benzoyl,

     2)2,4-dinitrobenzenesulphenyloxymethyl)benzoyl, levulinyl, trimethylsilyl, triethylsilyl, t-butyldimethylsilyl, t-butyldiphenylsilyl, triphenylsilyl, benzoylformyl, acetyl, chloroacetyl, dichloroacetyl, trichloroacetyl, trifluoroacetyl, pivaloyl, benzoyl, p-phenylbenzoyl, or acetoacetyl.

7. A compound of claim 1, wherein one of Q and W is (C═

O)—

(CH₂)_n—

(C═

O)O⁻

, wherein n is an integer from 1-20, and the other is a blocking group.

8. A compound of claim 7, wherein n is 2.

9. A compound of claim 1, wherein one of Q and W is hydrogen, blocking group, a protected or unprotected nucleosidyl moiety or a protected or unprotected oliponucleotide moiety and the other is selected from L, SM or L-SM.

10. A compound of claim 9, wherein the blocking group is selected from 4,4′

-dimethoxytrityl, monomethoxytrityl, 9-phenylxanthen-9-yl, 9 methoxyphenyl)xanthen-9-yl, t-butyl, t-butoxymethyl, methoxymethyl, tetrahydropyranyl, 1-ethoxyethyl, 1-(2-chloroethoxy)ethyl, 2-trimethylsilylethyl, p-chlorophenyl, 2,4-dinitrophenyl, benzyl, 2,6-dichlorotrityl, diphenylmethyl, p,p-dinitrobenzhydryl, p-nitrobenzyl, triphenylmethyl, trimethylsilyl, triethylsilyl, t-butyldimethylsilyl, t-butyldiphenylsilyl, triphenylsilyl, benzoylformate, mesyl, tosyl, 4,4′

,4″

-tris- (benzyloxy)trityl, 4,4′

,4″

-tris{4,5-dichlorophthalimido)trityl, 4,4′

,4″

-tris(levulinyloxy)trityl, 3-(imidazolylmethyl)4,4′

-dimethoxytrityl, 4-decyloxytrityl, 4-hexadecyloxytrityl 9-(4-octadecyloxyphenyl)xantheno 9-yl, 1,1-bis-(4-methoxyphenyl)1′

-pyrenylmethyl, p-phenylazophenyloxycarbonyl, 9-fluorenylmethoxycarbonyl, 2,-dinitrophenylethoxycarbonyl, 4-(methylthiomethoxy)butyryl, 2-(methylthiomethoxymethyl)benzoyl, 2-(isopropylthiomethoxymethyl)benzoyl, 2-(2,4-dinitrobenzenesulphenyloxymethyl)benzoyl, levulinyl, trimethylsilyl, triethylsilyl, t-butyldimethylsilyl, t-butyldiphenylsilyl, triphenylsilyl, benzoylformyl, acetyl, chloroacetyl, dichloroacetyl, trichloroacetyl, trifluoroacetyl, pivaloyl, benzoyl, p-phenylbenzoyl, or acetoacetyl.

11. A compound of claim 9, wherein L is (C═

O)—

(CH₂)—

(C═

O)O—

, where n is an integer from 1-20.

12. A compound of claim 11, wherein n is 2.

13. A compound of claim 11, wherein said support medium is selected from a controlled pore glass, oxalyl-controlled pore glass, silica-containing particles, polymers of polystyrene, copolymers of polystyrene, and divinylbenzene, copolymers of dimethylacrylamide and N,N-bisacryloylethylenediamine, a soluble support medium, or PEPS.

14. A compound of claim 9, wherein Q is hydrogen, a blocking group, a protected or unprotected nucleosidyl moiety, or a protected or unprotected oligonucleotidyl moiety.

15. A compound of claim 1, according to formula (II).

16. A compound of claim 15, wherein A is selected from a substituted or unsubstituted aromatic, substituted or unsubstituted heteroaromatic, or a substituted or unsubstituted heterocyclic.

17. A compound of claim 15, wherein A is substituted or unsubstituted aromatic.

18. A compound of claim 16, wherein A is substituted or unsubstituted phenyl.

19. A compound of claim 15, wherein one of Q and W is hydrogen, blocking group, a protected or unprotected nucleosidyl moiety or a protected or unprotected oligonucleotidyl moiety and the other is selected from L, SM or L-SM.

20. A compound of claim 19, wherein the blocking group is selected from 4,4′

-dimethoxytrityl, monomethoxytrityl, 9-phenylxanthen-9-yl, 9-(p-methoxyphenyl)xanthen-9-yl, t-butyl, t-butoxymethyl, methoxymethyl, tetrahydropyranyl, 1-ethoxyethyl, 1-(2-chloroethoxy)ethyl, 2-trimethylsilylethyl, p-chlorophenyl, 2,4-dinitrophenyl, benzyl, 2,6-dichlorobenzyl, diphenylmethyl, p,p-dinitrobenzhydryl, p-nitrobenzyl, triphenylmethyl, trimethylsilyl, triethylsilyl, t-butyldimethylsilyl, t-butyldiphenylsilyl, triphenylsilyl, benzoylformate, mesyl, tosyl, 4,4′

,4″

-tis (benzyloxy)trityl, 4,4′

,4″

-tris-(4,5-dichlorophthalimido)trityl, 4,4′

,4″

-tris(levulinyloxy)trityl, 3-(imidazolylmethyl)-4,4′

-dimethoxytrityl, 4-decyloxytrityl, 4-hexadecyloxytrityl, 9-(4-octadecyloxyphenyl)xanthene-9-yl, 1,1-bis-(4methoxyphenyl)-1′

-pyrenylmethyl, p-phenylazophenyloxycarbonyl, 9-fluorenylmethoxycarbonyl, 2,4-dinitrophenylethoxycatonyl, 4-(methylthiomethoxy)butyryl, 2-(methylthiomethoxymethyl)-benzoyl, 2-(isopropylthiomethoxymethyl)benzoyl, 2-(2,4-dinitrobenzenesulphenyloxymethyl)benzoyl, levulinyl, triethylsilyl, triethylsilyl, t-butyldimethylsilyl, t-butyldiphenylsilyl, triphenylsilyl, benzoylformyl, acetyl, chloroacetyl, dichloroacetyl, trichloroacetyl, trifluoroacetyl, pivaloyl, benzoyl, p-phenylbenzoyl, or acetoacetyl.

21. A compound of claim 19, wherein L is (C═

O)—

(CH₂)_n(CO)O—

, where n is an integer from 1-20.

22. A compound of claim 21, wherein n is 2.

23. A compound of claim 19, wherein SM is selected from a controlled pore glass, oxalyl-controlled pore glass, silica-containing particles, polymers of polystene, copolymers of polystyrene, and divinylbenzene, copolymers of dimethylacrylamide and N,N-bisacryloylethylenediamine, a soluble support medium, or PEPS.

24. A compound of claim 1 having the formula:

25. A compound of claim 24 wherein:

W is hydrogen, a blocking group, L, SM or L-SM;

wherein L is (C═

O)—

(CH₂)₂—

(C═

O)O—

;

Q is hydrogen, a blocking group, a protected or unprotected nucleosidyl moiety, a protected or unprotected nucleosidyl moiety attached through a phospholinker, or a protected or unprotected oligonucleotidyl moiety; and

A is a substituted or unsubstituted aromatic group.

26. A compound of claim 25 wherein W and Q are each hydrogen.

27. A compound of claim 25 wherein A is phenyl.

28. A compound of claim 25 wherein W is L, SM or L-SM;

Q is hydrogen, a protected or unprotected nucleosidyl moiety, a protected or unprotected nucleosidyl moiety attached through a phospholinker, or a protected or unprotected oligonucleotidyl moiety, and A is phenyl.

29. (canceled)

30. A process of making a compound of formula (VI):

31. The process of claim 30, further comprising the step of protecting the hydroxyl groups of the compound of formula (VI).

32. The process of claim 31, further comprising the step of selectively deprotecting one of the hydroxyl groups to yield a reactive hydroxyl;

and reacting said reactive hydroxyl with a solid support or a bifunctional linker bound to a solid support to give a support bound compound of formula (I).

33. A process of making a compound of formula (II):

34. The process of claim 33, further comprising reacting the compound of formula (II) wherein O, W or A are not SM or L-SM. with a support medium or a bifunctional linking moiety bound to a solid medium to give a support-bound compound of formula (II).

35. A process for functionalizing a support medium with a first monomeric subunit, the process comprising:

providing a support-bound compound of formula (I) or (II);

wherein;

A is independently selected from hydrogen;

a blocking group;

SM;

L-SM;

a substituted or unsubstituted aliphatic group;

a substituted or unsubstituted aliphatic ether;

unsaturated a substituted or unsubstituted aromatic;

substituted or unsubstituted heteroaromatic;

or a substituted or unsubstituted heterocyclic;

SM is a support medium;

L is a bifunctional linking moiety,

G₁ is independently selected from O, S, CR₁R₂, or NR₃;

each of R₁ and R₂ is independently selected from hydrogen, a substituted or unsubstituted, saturated, partially saturated or unsaturated aliphatic group, substituted or unsubstituted aromatic, substituted or unsubstituted heteroaromatic, or substituted or unsubstituted heterocyclic;

R₃ is independently selected from hydrogen, a blocking group, substituted or unsubstituted aliphatic group, substituted or unsubstituted aromatic, substituted or unsubstituted heteroaromatic, or substituted or unsubstituted heterocyclic;

each of R_U, R_V, R_W, R_X, R_Y, and R_Z is independently selected from hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted alkenyl, or substituted or unsubstituted alkynyl;

one of Q or W is SM or L-SM, and the other of Q or W is a blocking group;

X is independently selected from O or S; and

each of Y₁ and Y₂ is independently selected from O, S, N, or CR₁R₂;

deblocking one of Q or W to give a reactive hydroxyl; and

treating said reactive hydroxyl with a first monomeric subunit having a further protected hydroxyl group to form a monomer-functionalized support medium.

36. The process of claim 35, wherein the first monomeric subunit is an activated phosphoramidite nucleoside.

37. The process of claim 35, further comprising reacting said monomer-functionalized support medium with a capping agent;

and optionally treating said monomer-functionalized support medium with an oxidizing agent.

38. The process of claim 37, further comprising:

(a) deblocking said further protected hydroxyl group to give a reactive hydroxyl;

(b) treating said reactive hydroxyl with an additional monomeric subunit bearing a further protected hydroxyl to produce an extended compound;

(c) reacting the extended compound with a capping reagent;

(d) optionally contacting the product of step (b) with an oxidizing or sulfurizing agent;

optionally repeating steps (a)-(d) one or more times to form an oligomeric compound.

44. The process of claim 38, further comprising a step of treating said oligomeric compound with a reagent effective to cleave said oligomeric compound from said linker attached to said support medium.

46. The process of claim 44, wherein said cleaved oligomeric compound has a terminal hydroxyl group at the site of cleavage.

48. The process of claim 38, wherein said treating of said reactive hydroxyl group with a further monomeric subunit is performed in the presence of an activating agent.

49. The process of claim 35, wherein said support medium is controlled pore glass, oxalyl-controlled pore glass, silica-containing particles, polymers of polystyrene, copolymers of polystyrene, copolymers of styrene and divinylbenzene, copolymers of dimethylacrylamide and N,N′

-bisacryloylethylenediamine, soluble support medium or PEPS.

50. The process of claim 35, wherein said support medium is controlled pore glass, polymers of polystyrene or copolymers of polystyrene.

51. The process of claim 35, wherein said blocking group is 4,4′

-dimethoxytrityl, monomethoxytrityl, 9-phenylxanthen-9-yl, 9-(p-methoxyphenyl) xanthen-9-yl, t-butyl, t-butoxymethyl, methoxymethyl, tetrahydropyranyl, 1-ethoxyethyl, 1-(2-chloroethoxy)ethyl, 2-trimethylsilylethyl, p-chlorophenyl, 2,4-chlorophenyl, benzyl, 2,6-dichlorobenzyl, diphenylmethyl, p,p-dinitrobenzhydryl, p-nitrobenzyl, triphenylmethyl, trimethylsilyl, triethylsilyl, t-butyldimethylsilyl, t-butyldiphenylsilyl, triphenylsilyl, benzoylformate, acetyl, chloroacetyl, trichloroacetyl, trifluoroacetyl, pivaloyl, benzoyl, p-phenylbenzoyl, mesyl, tosyl, 4,4′

,4″

-tris- (benzyloxy)trityl, 4,4′

,4″

-tris-(4,5-dichlorophthalimido)trityl 4,4′

,4″

-tris(levulinyloxy)tityl, 3-(imidazolylmethyl)-4,4′

-dimethoxytrityl, 4-decyloxytrityl, 4-hexadecyloxytrityl, 9-(4-octadecyloxyphenyl)xanthene-9-yl, 1,1-bis-(4-methoxyphenyl)-1-pyrenyl methyl, p-phenylazophenyloxycarbonyl, 9-fluorenylmethoxycarbonyl, 2,4-dinitrophenylethoxy carbonyl, 4-(methylthiomethoxy)butyryl, 2-(methylthiomethoxymethyl)-benzoyl, 2-(isopropylthiomethoxymethyl)benzoyl, 2-(2,4 dinitobenzenesulphenyloxymethyl)benzoyl, or levulinyl groups.

52. The process of claim 38, wherein said oligomeric compound is an oligonucleotide, modified oligonucleotide, oligonucleotide analog, oligonucleoside, oligonucleotide mimetic, hemimer, gapmer or chimera.

39. (canceled)

40. (canceled)

41. (canceled)

42. (canceled)

43. (canceled)

45. (canceled)

47. (canceled)

53. (canceled)