Polymeric oligonucleotide prodrugs

1. An oligonucleotide prodrug of the formula:

X 1 -(L 2 ) n -(L 1 ) o -R 1

wherein:

R 1 is a polyalkylene oxide;

L 1 is a releasable linking moiety;

L 2 is a selected bifuntional spacing group comprising from about 2 to about 10 carbon atoms;

X 1 is a single or double stranded oligonucleotide residue wherein the oligonucleotide ranges in size from 10 to 1,000 nucleotides;

n, and o are independently a positive integer; and

provided that (o+n)≧2,

wherein

L 2 is selected from the group consisting of:

—(CR 50′ R 51′ ) q′ Q′-,

—(CR 52′ R 53′ ) r′ O(CR 50′ R 51′ ) q′ Q′-,

—(CR 52′ R 53′ ) r′ (OCH 2 CH 2 )Q′-,

 and

wherein

Q′ is O, S or NH;

R 50′-53′ are independently selected from the group consisting of hydrogen, C 1-6 alkyls, C 3-12 branched alkyls, C 3-8 cycloalkyls, aryls, C 1-6 heteroalkyls, C 1-6 alkoxy, phenoxy and C 1-6 heteroalkoxy; and

q′ and r′ are each a positive integer.

2. The prodrug of claim 1 , wherein the oligonucleotide comprises a nucleotide that is selected from the group consisting of

wherein

M is O or S;

B 1 and B 2 are independently selected from the group consisting of A (adenine), G (guanine), C (cytosine), T (thymine), U (uracil) and modified bases;

R 100 and R 101 are independently selected from the group consisting of H, OR′ where R′ is H, a C 1-6 alkyl, substituted alkyls, nitro, halo and aryl.

3. The prodrug of claim 2 , wherein M is S.

4. The prodrug of claim 1 , wherein the oligonucleotide residue is a phosphorothioate oligonucleotide residue.

5. The prodrug of claim 1 , wherein said oligonucleotide residue is an antisense oligonucleotide residue or oligodeoxynucleotide residue.

6. The prodrug of claim 5 , wherein said antisense oligonucleotide residue or oligodeoxynucleotide residue is selected from the group consisting of oligonucleotides and oligodeoxynucleotides with phosphorodiester backbones or phosphorothioate backbones, LNA, PNA, tricyclo-DNA, decoy ODN, ribozymes, spiegelmers, and CpG oligomers.

7. The prodrug of claim 5 , wherein said antisense oligonucleotide has a sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, and SEQ ID NO: 4, wherein n of SEQ ID NO: 4 is any nucleotide.

8. The prodrug of claim 1 , wherein R 1 is a polyalklene oxide having a capping group A, selected from the group consisting of OH, NH 2 , SH, CO 2 H, C 1-6 alkyls, and

X 2 L 2 n L 1 o   (II)

wherein X 2 is a single stranded or double stranded oligonucleotide residues, wherein the oligonucleotide ranges in size from 10 to 1,000 nucleotides.

9. A prodrug of claim 8 , selected from the group consisting of:

H—X 1 L 2 n L 1 o R 1 L 1 o L 2 n X 2 —H

wherein X 2 is a 3′ oligonucleotide or 5′ oligonucleotide.

10. The prodrug of claim 1 , wherein L 1 is selected from the group consisting of:

wherein,

Y 1′ -Y 25′ are independently selected from the group consisting of O, S or NR 9 ;

R 6′-7′ , R 9′-13′ , R 16′-25′ , R 9 and R 27′-41′ are independently selected from the group consisting of hydrogen, C 1-6 alkyls, C 3-12 branched alkyls, C 3-8 cycloalkyls, aryls, C 1-6 heteroalkyls, C 1-6 alkoxy, phenoxy and C 1-6 heteroalkoxy;

L 5′-12′ are independently selected bifunctional spacers;

Ar is a moiety which forms a multi-substituted aromatic hydrocarbon or a multi-substituted heterocyclic group;

c, h, k, l, r, s, v, w, v′, w′, c′, and h′ are independently selected positive integers;

a, e, g, j, t, z, a′, z′, e′ and g′ are independently either zero or a positive integer; and

b, d, f, i, u, b′, d′ and f′ are independently zero or one.

11. The prodrug of claim 1 , wherein R 1 is a polyethylene glycol.

12. The prodrug of claim 1 , wherein R 1 is selected from the group consisting of:

J-O—(CH 2 CH 2 O) n′ —

J-O—(CH 2 CH 2 O) n′ —CH 2 C(O)—O—,

J-O—(CH 2 CH 2 O) n′ —CH 2 CH 2 NR 48 —,

J-O—(CH 2 CH 2 O) n′ —CH 2 CH 2 SH,

—O—C(O)CH 2 —O—(CH 2 CH 2 O) n′ —CH 2 C(O)—O—,

—NR 48 CH 2 CH 2 —O—(CH 2 CH 2 O) n′ —CH 2 CH 2 NR 48 —,

—SHCH 2 CH 2 —O—(CH 2 CH 2 O) n′ —CH 2 CH 2 SH—,

wherein

n′ is the degree of polymerization;

R 48 is selected from the group consisting of hydrogen, C 1-6 alkyls, C 3-12 branched alkyls, C 3-8 cycloalkyls, aryls, C 1-6 heteroalkyls, C 1-6 alkoxy, phenoxy and C 1-6 heteroalkoxy; and

J is a capping group.

13. The prodrug of claim 1 , wherein R 1 comprises

—O—(CH 2 CH 2 O) x —

wherein x is a positive integer selected so that the weight average molecular weight is at least about 2,000 Da to about 136,000 Da.

14. The prodrug of claim 1 , wherein R 1 has a weight average molecular weight of from about 3,000 Da to about 100,000 Da.

15. The prodrug of claim 1 , wherein R 1 has a weight average molecular weight of from about 5,000 Da to about 40,000 Da.

16. The prodrug of claim 7 , wherein said antisense oligonucleotide is oblimersen (SEQ ID NO: 1).

17. A prodrug of claim 1 selected from the group consisting of:

wherein all of which comprise an oligonucleotide of SEQ ID NO: 1.

18. A method of making a prodrug comprising:

reacting a compound of the formula:

R 1 -L 1 -leaving group

with a compound of the formula:

H-L 2 -X 1

under conditions sufficient to form a prodrug of the formula

X 1 -L 2 -L 1 -R 1 ,

wherein:

R 1 is a polyalkylene oxide;

L 1 is a releasable linking moiety;

L 2 is a bifunctional spacing group comprising from about 2 to about 10 carbon atoms; and

X 1 is a single or double stranded oligonucleotide residue wherein the oligonucleotide ranges in size from 10 to 1,000 nucleotides,

wherein L 2 is selected from the group consisting of

—(CR 50′ R 51′ ) q′ Q′-,

—(CR 52′ R 53′ ) r′ O(CR 50′ R 51′ ) q′ Q′-,

—(CR 52′ R 53′ ) r′ (OCH 2 CH 2 )Q′-, and

—(CH 2 ) r′ —S—S—(CH 2 ) q′ Q′-,

wherein

Q′ is O, S or NH;

R 50′-53′ are independently selected from the group consisting of hydrogen, C 1-6 alkyls, C 3-12 branched alkyls, C 3-8 cycloalkyls, aryls, C 1-6 heteroalkyls, C 1-6 alkoxy, phenoxy and C 1-6 heteroalkoxy; and

q′ and r′ are each a positive integer.

19. An oligonucleotide prodrug prepared by a process comprising:

reacting a compound of the formula:

R 1 -L 1 -leaving group

with a compound of the formula:

H-L 2 -X 1

under conditions sufficient to form a prodrug of the formula

X 1 -L 2 -L 1 -R 1 ,

wherein

R 1 is a polyalkylene oxide;

L 1 is a releasable linking moiety;

L 2 is a bifunctional spacing group comprising from about 2 to about 10 carbon atoms; and

X 1 is a single or double stranded oligonucleotide residue wherein the oligonucleotide ranges in size from 10 to 1,000 nucleotides,

wherein L 2 is selected from the group consisting of:

—(CR 50′ R 51′ ) q′ Q′-,

—(CR 52′ R 53′ ) r′ O(CR 50′ R 51′ ) q′ Q′-,

—(CR 52′ R 53′ ) r′ (OCH 2 CH 2 )Q′-, and

—(CH 2 ) r′ —S—S—(CH 2 ) q′ Q′-,

wherein

Q′ is O, S or NH;

R 50′-53′ are independently selected from the group consisting of hydrogen, C 1-6 alkyls, C 3-12 branched alkyls, C 3-8 cycloalkyls, aryls, C 1-6 heteroalkyls, C 1-6 alkoxy, phenoxy and C 1-6 heteroalkoxy; and

q′ and r′ are each a positive integer.

20. The prodrug of claim 19 , wherein X 1 comprises a nucleotide selected from the group consisting of

wherein

M is O or S;

B 1 and B 2 are independently selected from the group consisting of A (adenine), G (guanine), C (cytosine), T (thymine), U (uracil) and modified bases thereof;

R 100 and R 101 are independently selected from the group consisting of H, OR′ where R′ is H, a C 1-6 alkyl, substituted alkyls, nitro, halo and aryl.

21. The prodrug of claim 19 , wherein X 1 is selected from the group consisting of oligonucleotides with phosphorodiester backbones or phosphorothioate backbones, LNA, PNA, tricyclo-DNA, decoy ODN, ribozymes, spiegelmers, and CpG oligomers.

22. The prodrug of claim 19 , wherein X 1 includes a phosphorothioate backbone.

23. The prodrug of claim 19 , wherein X 1 is an antisense oligonucleotide.

24. The prodrug of claim 23 , wherein the antisense oligonucleotide has a sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, and SEQ ID NO: 4, wherein n of SEQ ID NO: 4 is any nucleotide.

25. The prodrug of claim 19 , wherein R 1 is a polyalkylene glycol.

26. The prodrug of claim 19 , wherein R 1 has a weight average molecular weight of from about 3,000 Da to about 100,000 Da.

27. The prodrug of claim 25 , wherein R 1 has a weight average molecular weight of from about 5,000 Da to about 40,000 Da.

28. The prodrug of claim 19 selected from the group consisting of

wherein

 represents an oligonucleotide and point of terminal phosphate modification; and

mPEG is CH 3 O(CH 2 CH 2 O) x -, wherein x is a positive integer selected from about 10 to about 2300.