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

• US 8,357,665 B2
• Filed: 10/12/2006
• Issued: 01/22/2013
• Est. Priority Date: 10/12/2005
• Status: Active Grant

• Current Assignee: Idera Pharmaceuticals, Inc. (Aceragen Incorporated)
• Original Assignee: Idera Pharmaceuticals, Inc. (Aceragen Incorporated)
• Inventors: Kandimalla, Ekambar R., Wang, Daqing, Li, Yukui, Yu, Dong, Zhu, FuGang, Bhagat, Lakshmi, Agrawal, Sudhir
• Primary Examiner(s): OGUNBIYI, OLUWATOSIN A
• Application Number:
  US11/549,048
• Publication Number:
  US 20090060898A1
• Time in Patent Office: 2,294 Days
• Field of Search: None
• US Class Current: 514/44
• CPC Class Codes: A61K 2039/55561 CpG containing adjuvants; Oligonucleotide containing adjuvants
• CPC Class Codes: A61K 31/713 Double-stranded nucleic acids or oligonucleotides
• CPC Class Codes: A61K 45/06 Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
• CPC Class Codes: A61K 48/00 Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
• CPC Class Codes: A61K 9/0019 Injectable compositions; Intramuscular, intravenous, arterial, subcutaneous administration; Compositions to be administered through the skin in an invasive manner non-active ingredients are additionally classified in A61K47/00
• CPC Class Codes: A61P 11/00 Drugs for disorders of the respiratory system
• CPC Class Codes: A61P 11/06 Antiasthmatics
• CPC Class Codes: A61P 17/00 Drugs for dermatological disorders
• CPC Class Codes: A61P 29/00 Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
• CPC Class Codes: A61P 31/00 Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 37/02 Immunomodulators
• CPC Class Codes: A61P 37/04 Immunostimulants
• CPC Class Codes: A61P 37/06 Immunosuppressants, e.g. drugs for graft rejection
• CPC Class Codes: A61P 37/08 Antiallergic agents antiasthmatic agents A61P11/06; ophthalmic antiallergics A61P27/14
• CPC Class Codes: C12N 15/117 Nucleic acids having immunomodulatory properties, e.g. containing CpG-motifs
• CPC Class Codes: C12N 2310/17 Immunomodulatory nucleic acids
• CPC Class Codes: C12N 2310/314 Phosphoramidates
• CPC Class Codes: C12N 2310/321 2'-O-R Modification
• CPC Class Codes: C12N 2310/33 of the base
• CPC Class Codes: C12N 2310/335 : Modified T or U
• CPC Class Codes: C12N 2320/31 : Combination therapy

Abstract

The invention provides novel immune regulatory oligonucleotides (IRO) as antagonist of TLRs and methods of use thereof. These IROs have unique sequences that inhibit or suppress TLR-mediated signaling in response to a TLR ligand or TLR agonist. The methods may have use in the prevention and treatment of cancer, an autoimmune disorder, airway inflammation, inflammatory disorders, infectious disease, skin disorders, allergy, asthma or a disease caused by a pathogen.

Claims

1. 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 base via a non-nucleotide linker, wherein at least one oligonucleotide has the structure

5′

-N_m—

N₃N₂N₁CGN¹N²N³—

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;

N₁ is a modified nucleoside 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;

N₂-N₃, at each occurrence, is independently i) a nucleotide, ii) a nucleotide derivative, or iii) a modified nucleoside 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;

N¹-N³, at each occurrence, is independently i) a nucleotide, or ii) a nucleotide derivative;

N_n, and N^m, at each occurrence, is independently a nucleotide, nucleotide derivative or non-nucleotide linkage;

and further 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 nucleosides that suppress the activity of the oligonucleotide motif;

wherein m is a number from 0 to about 30;

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

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

2. A pharmaceutical composition comprising an IRO according to claim 1 and a pharmaceutically acceptable carrier.

3. The IRO according to claim 1, wherein the non-nucleotide linker linking the at least two oligonucleotides at their 3′

ends or functionalized base or sugar 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.

4. The IRO according to claim 1, wherein the non-nucleotide linker linking the at least two oligonucleotides at their 3′

ends or functionalized base or sugar is Glycerol (1,2,3-Propanetriol).

5. The IRO according to claim 1, wherein the pyrimidine nucleotide derivative is 2-deoxythymidine, 1-(2′

-deoxy-α

-D-ribofuranosyl)-2-oxo-7-deaza-8-methyl-purine, 2′

-dideoxy-5-halocytosine, 2′

-dideoxy-5-nitrocytosine, arabinocytidine, T-deoxy-5-hydroxycytidine, 2′

-deoxy-N4-alkyl-cytidine, 2′

-deoxy-4-thiouridine, or other pyrimidine nucleoside analogs.

6. The IRO 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.

7. The IRO according to claim 1, wherein at least one of the oligonucleotides has the sequence selected from TCTGACGTTCT (SEQ ID NO:

86), TCTGACG₁TTCT (SEQ ID NC);

     87), TCTGACG₄TTCT (SEQ ID NO;

     88), TCTCTGACGTT (SEQ ID NO;

     89), TCTGUCGTTCT (SEQ ID NO;

     93), TCTGUCG₁TTCT (SEQ ID NO;

     94), TCTGACG₄TTCT (SEQ ID NO;

     95), TCTGACG₁TT (SEQ ID NO;

     96), UGUCG₁TTCT (SEQ ID NO;

     100) and UGACG₁TTCT (SEQ ID NO;

     101), wherein G₁=7-deaza, G₄=araG, and G, A or U=2′

-OMe.

8. The IRO according to claim 1, wherein the IRO is selected from 5′

-(TCTGACGTTCT)₂X₂(5′

-SEQ ID NO;

86-3′

-X₂-3′

-SEQ ID NO;

86-5′

), 5′

-(TCTGACG₁TTCT)₂X₂(5′

-SEQ ID NO;

87-3′

-X₂-3′

-SEQ ID NO;

87-5′

), 5′

-(TCTGACG₄TTCT)₂X₂(5′

-SEQ ID NO;

88-3′

-X₂-3′

-SEQ ID NO;

88-5′

), 5′

-(TCTCTGACGTT)₂X₂(5′

-SEQ ID NO;

89-3′

-X₂-3′

-SEQ ID NO;

89-5′

), 5′

-(TCTGUCGTTCT)₂X₂(5′

-SEQ ID NO;

93-3′

-X₂-3′

-SEQ ID NO;

93-5′

), 5′

-(TCTGUCG₁TTCT)₂X₂(5″

-SEQ ID NO;

94-3′

-X₂-3′

-SEQ ID NO;

94-5′

), 5′

-(TCTGACG₄TTCT)₂×

2(5′

-SEQ ID NO;

95-3′

-X₂-3′

-SEQ ID NO;

95-5′

), 5′

-(TCTGACG₁TT)₂X₂(5′

-SEQ ID NO;

96-3′

-X₂-3′

-SEQ ID NO;

96-5′

), 5′

-(UGUCG₁TTCT)₂X₂(5′

-SEQ ID NO;

100-3′

-X₂-3′

-SEQ ID NO;

100-5′

) and 5′

-(UGACG₁TTCT)₂X₂(5′

-SEQ ID NO;

101-3′

-X₂-3′

-SEQ ID NO;

101-5′

), wherein G₁=7-deaza, G₄=araG, G, A or U=2′

-OMe and X₂=glycerol linker.

9. A pharmaceutical composition comprising an IRO according to claim 7 and a pharmaceutically acceptable carrier.

10. A pharmaceutical composition comprising an IRO according to claim 8 and a pharmaceutically acceptable carrier.

11. The IRO according to claim 1, wherein N₂ is a 2′

-substituted ribonucleoside, 2′

-O-substituted ribonucleoside, 2′

-substituted arabinoside, or 2′

-O-substituted arabinoside.

12. The IRO according to claim 1, wherein the 2′

-O-substituted ribonucleoside of N₁ is a 2′

-OMe-ribonucleoside.

13. The IRO according to claim 11, wherein the 2′

-O-substituted ribonucleoside is a 2′

-OMe-ribonucleoside.

14. The IRO according to claim 1, wherein the non-nucleotide linker may be attached to the 3′

hydroxyl.

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