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

1. A method for therapeutically treating a mammal having a disease caused by a pathogen mediated by TLR7, TLR8 and/or TLR9, wherein the pathogen is Cytomegalovirus, Hepatitis A virus, Hepatitis B virus, Hepatitis C virus, Hepatitis delta virus, Hepatitis E virus, Herpes simplex virus, Human immunodeficiency virus, Human papillomavirus, Influenzavirus A, Influenzavirus B, Influenzavirus C, Colorado Tick Fever virus, Dengue virus, Ebolavirus, Coxsackie A virus, Enterovirus 71, Varicella zoster virus, Lassa virus, Marburg virus, Epstein-Barr virus/Human herpesvirus 4, Norovirus, Rotavirus, JC virus, Rabies virus, SARS-associated coronavirus, Variola virus, Human respiratory syncytial virus, Adenoviruses, Human metapneulmovirus, West Nile virus, Yellow fever virus, Picornaviruses, Measles virus, Mumps virus, Poliovirus, Rubella virus, Japanese encephalitis virus, Chandipura virus, St. Louis encephalitis virus, Eastern equine encephalomyelitis virus, Western equine encephalitis virus or Venezuelan equine encephalitis virus, such method comprising administering to the mammal a pharmaceutically effective amount of an 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;

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 suppresses 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, antiviral agents 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)-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-3-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 TCTGACGTTCT (SEQ ID NO: 86), TCTGACG 1 TTCT (SEQ ID NO: 87), TCTGACG 4 TTCT (SEQ ID NO: 88), TCTCTGACGTT (SEQ ID NO: 89), TCTGUCGTTCT (SEQ ID NO: 93), TCTGUCGTTCT (SEQ ID NO: 94), TCTGACG 4 TTCT (SEQ ID NO: 95), TCTGACG 1 TT (SEQ ID NO: 96), UGUCG 1 TTCT (SEQ ID NO: 100) or UGACG 1 TTCT (SEQ ID NO: 101)), wherein G 1 =7-deaza, G 4 G=araG, and G, A or U=2′-OMe.

9. The method according to claim 1 , wherein two oligonucleotides are linked at their 3′-ends to a non-nucleotide linker, wherein the IRO is 5′-(TCTGACGTTCT) 2 X 2 (5′-SEQ ID NO: 86-3′-X 2 -3′-SEQ ID NO: 86-5′), 5′-(TCTGACG 1 TTCT) 2 X 2 (5′-SEQ ID NO: 87-3′-X 2 -3′-SEQ ID NO: 87-5′), 5′-(TCTGACG 4 TTCT) 2 X 2 (5′-SEQ ID NO: 88-3′-X 2 -3′-SEQ ID NO: 88-5′), 5′-(TCTCTGACGTT) 2 X 2 (5′-SEQ ID NO: 89-3′-X 2 -3′-SEQ ID NO: 89-5′), 5′-(TCTGUCGTTCT) 2 X 2 (5′-SEQ ID NO: 93-3′-X 2 -3′-SEQ ID NO: 93-5′), 5′-(TCTGUCG 1 TTCT) 2 X 2 (5′-SEQ ID NO: 94-3′-X 2 -3′-SEQ ID NO: 94-5′), 5′-(TCTGACG 4 TTCT) 2 X 2 (5′-SEQ ID NO: 95-3′-X 2 -3′-SEQ ID NO: 95-5′), 5′-(TCTGACG 1 TT) 2 X 2 (5′-SEQ ID NO: 96-3′-X 2 -3′-SEQ ID NO: 96-5′), 5′-(UGUCG 1 TTCT) 2 X 2 (5′-SEQ ID NO: 100-3′-X 2 -3′-SEQ ID NO: 100-5′) or 5′-(UGACG 1 TTCT) 2 X 2 (5′-SEQ ID NO: 101-3′-X 2 -3′-SEQ ID NO: 101-5′), wherein G 1 =7-deaza, (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*.