Immune regulatory oligonucleotide (IRO) compounds to modulate toll-like receptor based immune response

1. A method for therapeutically treating a vertebrate having a disease mediated by TLR7, TLR8 and/or TLR9 that is Lyme disease, ocular infections, conjunctivitis, scleroderma, cardiovascular disease, chronic fatigue syndrome, transplant rejection, chronic inflammation, behçet's disease, hypersensitivities, reperfusion injury, or uveitis, such method comprising administering to the vertebrate a pharmaceutically effective amount of an immune regulatory oligonucleotide (IRO) compound comprising at least two oligonucleotides linked by a non-nucleotide linker at their 3′ ends or by a functionalized sugar or by a functionalized nucleobase via a non-nucleotide linker, wherein at least one oligonucleotide has the structure

5-N m -N 3 N 2 N 1 CGN 1 N 2 N 3 -N m -3′:

wherein:

CG is an oligonucleotide motif that is CpG, C*pG, C*pG* or CpG*, wherein C is cytosine, C* is a pyrimidine nucleotide derivative, G is guanosine, and G* is a purine nucleotide derivative; N 1 is a modified nucleotide that suppresses the activity of the oligonucleotide motif selected from the group consisting of 2′-substituted ribonucleoside, 2′-O-substituted ribonucleoside, 2′-substituted arabinoside, and 2′-O-substituted arabinoside;

N 2 -N 3 , at each occurrence, is independently i) a nucleotide, ii) a nucleotide derivative, or iii) a modified nucleotide that suppresses the activity of the oligonucleotide motif selected from the group consisting of 2′-substituted ribonucleoside, 2′-O-substituted ribonucleoside, 2′-substituted arabinoside, and 2′-O-substituted arabinoside;

N 1 -N 3 , at each occurrence, is independently i) a nucleotide or ii) a nucleotide derivative; N m and N m , at each occurrence, is independently a nucleotide, nucleotide derivative or non-nucleotide linkage;

and provided that the compound contains less than 3 consecutive guanosine nucleotides;

wherein the oligonucleotide motif would be immune stimulatory but for the one or more modified nucleotides that suppress the activity of the oligonucleotide motif;

wherein m is a number from 0 to about 30; and

wherein the IRO is an antagonist of an agonist of TLR7, TLR8 and/or TLR9;

provided that the at least two oligonucleotides are not antisense oligonucleotides.

2. The method according to claim 1 , wherein the IRO compound is administered in combination with one or more vaccines, antigens, antibodies, cytotoxic agents, allergens, antibiotics, antisense oligonucleotides, TLR agonists, TLR antagonists, peptides, proteins, gene therapy vectors, DNA vaccines, adjuvants, kinase inhibitors or co-stimulatory molecules.

3. The method according to claim 1 , wherein the route of administration is parenteral, mucosal delivery, oral, sublingual, transdermal, topical, inhalation, intranasal, aerosol, intraocular, intratracheal, intrarectal, vaginal, by gene gun, dermal patch or in eye drop or mouthwash form.

4. The method according to claim 1 , wherein the non-nucleotide linker linking the at least two oligonucleotides at their 3′ ends or by a functionalized sugar or by a functionalized nucleobase is Glycerol(1,2,3-Propanetriol), 1,2,4, Butanetriol, 2-(hydroxymethyl)-1,3-propanediol, 2-(hydroxymethyl)1,4-butanediol, 1,3,5-Pentanetriol, 1,1,1-Tris(hydroxymethyl)ethane, 1,1,1-Tris(hydroxymethyl)nitromethane, 1,1,1-Tris(hydroxymethyl)propane, 1,2,6-Hexanetriol, 3-Methyl-1,3,5-pentanetriol, 1,2,3-Heptanetriol, 2-Amino-2-(hydroxymethyl)-1,3-propanediol, N-[Tris(hydroxymethyl)methyl]acrylamide, Cis-1,3,5-Cyclohexanetriol, Cis-1,3,5-Tri(hydroxymethyl)cyclohexane, 3,5-Di(hydroxymethyl)phenol, 1,3,5-Trihydroxyl-benzene, 3,5-Di(hydroxymethyl)benzene, 1,3-Di(hydroxyethoxy)-2-hydroxyl-propane, 1,3-Di(hydroxypropoxy)-2-hydroxyl-propane, 2-Deoxy-D-ribose, 1,2,4-Trihydroxyl-benzene, D-Galactoal, 1,6-anhydro-β-D-Glucose, 1,3,5-Tris(2-hydroxyethyl)-Cyanuric acid, Gallic acid, 3,5,7-Trihydroxyflavone, 4,6-Nitropyrogallol, Ethylene glycol, 1,3-Propanediol, 1,2-Propanediol, 1,4-Butanediol, 1,3-Butanediol, 2,3-Butanediol, 1,4-Butanediol, 1,5-Pentanediol, 2,4-Pentanediol, 1,6-Hexanediol, 1,2-Hexanediol, 1,5-Hexanediol, 2,5-Hexanediol, 1,7-Heptanediol, 1,8-Octanediol, 1,2-Octanediol, 1,9-Nonanediol, 1,12-Dodecanediol, Triethylene glycol, Tetraethylene glycol, 2-(1-Aminopropyl)-1,3-propanediol, or 1,2-Dideoxyribose.

5. The method according to claim 1 , wherein the non-nucleotide linker linking the at least two oligonucleotides at their 3′ ends or by a functionalized sugar or by a functionalized nucleobase is Glycerol(1,2,3-Propanetriol).

6. The method according to claim 1 , wherein the pyrimidine nucleotide derivative is 2′-deoxythymidine, 1-(2′-deoxy-β-D-ribofuranosyl)-2-oxo-7-deaza-8-methyl-purine, 2′-dideoxy-5-halocytosine, 2′-dideoxy-5-nitrocytosine, arabinocytidine, 2′-deoxy-5-hydroxycytidine, 2′-deoxy-N4-alkyl-cytidine, 2′-deoxy-4-thiouridine, or other pyrimidine nucleoside analogs.

7. The method according to claim 1 , wherein the purine nucleotide derivative is 2′-deoxy-7-deazaguanosine, 2′-deoxy-6-thioguanosine, arabinoguanosine, 2′-deoxyinosine, or other purine nucleoside analogs.

8. The method according to claim 1 , wherein at least one of the oligonucleotides of the IRO has the sequence TCT GA CGTTCT (SEQ ID NO: 86), TCT GA CG 1 TTCT (SEQ ID NO: 87), TCT GA CG 4 TTCT (SEQ ID NO: 88), TCTCT GA CGTT (SEQ ID NO: 89), TCT GU CGTTCT (SEQ ID NO: 93), TCT GU CG 1 TTCT (SEQ ID NO: 94), TCT GA CG 4 TTCT (SEQ ID NO: 95), TCT GA CG 1 TT (SEQ ID NO: 96), UGU CG 1 TTCT (SEQ ID NO: 100) or UGA CG 1 TTCT (SEQ ID NO: 101), wherein G 1 =7-deaza, G 4 =araG, and G , A or U =2′-OMe.

9. The method according to claim 1 , wherein the IRO is

5′-(TCT GA CGTTCT) 2 X 2 (5′-SEQ ID NO: 86-3′-X 2 -3′-SEQ ID NO: 86-5′),

5′-(TCT GA CG 1 TTCT) 2 X 2 (5′-SEQ ID NO: 87-3′-X 2 -3′-SEQ ID NO: 87-5′),

5′-(TCT GA CG 4 TTCT) 2 X 2 (5′-SEQ ID NO: 88-3′-X 2 -3′-SEQ ID NO: 88-5′),

5′-(TCTCT GA CGTT) 2 X 2 (5′-SEQ ID NO: 89-3′-X 2 -3′-SEQ ID NO: 89-5′),

5′-(TCT GU CGTTCT) 2 X 2 (5′-SEQ ID NO: 93-3′-X 2 -3′-SEQ ID NO: 93-5′),

5′-(TCT GU CG 1 TTCT) 2 X 2 (5′-SEQ ID NO: 94-3′-X 2 -3′-SEQ ID NO: 94-5′),

5′-(TCT GA CG 4 TTCT) 2 X 2 (5′-SEQ ID NO: 95-3′-X 2 -3′-SEQ ID NO: 95-5′),

5′-(TCT GA CG 1 TT) 2 X 2 (5′-SEQ ID NO: 96-3′-X 2 -3′-SEQ ID NO: 96-5′),

5′-( UGU CG 1 TTCT) 2 X 2 (5′-SEQ ID NO: 100-3′-X 2 -3′-SEQ ID NO: 100-5′) or

5′-( UGA CG 1 TTCT) 2 X 2 (5′-SEQ ID NO: 101-3′-X 2 -3′-SEQ ID NO: 101-5′),

wherein G 1 =7-deaza, G 4 =araG, G , A or U =2′-OMe and X 2 =glycerol linker.

10. The method according to claim 1 , wherein the 2′-O-substituted ribonucleoside is a 2′-OMe-ribonucleoside.

11. The method according to claim 1 , wherein the non-nucleotide linker may be attached to the 3′hydroxyl.

12. The method according to claim 1 , wherein CG is an oligonucleotide motif that is C*pG, C*pG* or CpG*.

13. The method according to claim 1 , wherein the chronic inflammation is selected from sarcoidosis, chronic prostatitis, glomerulonephritis, inflammatory bowel disease, or pelvic inflammatory disease.

14. The method according to claim 13 , wherein the inflammatory bowel disease is ulcerative colitis.

15. The method according to claim 1 , wherein the cardiovascular disease is atherosclerosis.