WO2010039137A1 - Immune regulatory oligonucleotide (iro) compounds to modulate toll-like receptor based immune response - Google Patents

Abstract

The invention provides the use of immune regulatory oligonucleotides (IRO) as antagonist of TLRs in the prevention and treatment of a disease caused by a pathogen, for example, a DNA or RNA virus.

Description

IMMUNE REGULATORY OLIGONUCLEOTIDE (IRO) COMPOUNDS TO MODULATE TOLL-LIKE RECEPTOR BASED IMMUNE RESPONSE

(Attorney Docket No. IDR-036PC4)

BACKGROUND OF THE INVENTION

Field of the invention

[0001] The invention generally relates to the field of immunology and immunotherapy, and more specifically to immune regulatory oligonucleotide (IRO) compositions and their use for inhibition and/or suppression of Toll-like Receptor- mediated immune responses.

Summary of the related art

[0002] Toll-like receptors (TLRs) are present on many cells of the immune system and have been shown to be involved in the innate immune response (Hornung, V. et al, (2002) J. Immunol. 168:4531-4537). In vertebrates, this family consists of ten proteins called TLRl to TLRlO, which are known to recognize pathogen associated molecular patterns from bacteria, fungi, parasites and viruses (Poltorak, a. et al. (1998) Science 282:2085-2088; Underhill, D.M., et al. (1999) Nature 401 :811- 815; Hayashi, F. et. al (2001) Nature 410:1099-1103; Zhang, D. et al. (2004) Science 303:1522-1526; Meier, A. et al. (2003) Cell. Microbiol. 5:561-570; Campos, M. A. et al. (2001) J. Immunol. 167: 416-423; Hoebe, K. et al. (2003) Nature 424: 743-748; Lund, J. (2003) J. Exp. Med. 198:513-520; Heil, F. et al. (2004) Science 303:1526- 1529; Diebold, S.S., et al. (2004) Science 303:1529-1531; Hornung, V. et al. (2004) J. Immunol. 173:5935-5943). TLRs are a key means by which mammals recognize and mount an immune response to foreign molecules and also provide a means by which the innate and adaptive immune responses are linked (Akira, S. et al. (2001) Nature Immunol. 2:675-680; Medzhitov, R. (2001) Nature Rev. Immunol. 1 :135-145). TLRs have also been shown to play a role in the pathogenesis of many diseases, including autoimmunity, infectious disease, and inflammation (Cook, D.N. et al. (2004) Nature Immunol. 5:975-979) and the regulation of TLR-mediated activation using appropriate agents may provide a means for disease intervention. [0003] Some TLRs are located on the cell surface to detect and initiate a response to extracellular pathogens and other TLRs are located inside the cell to detect and initiate a response to intracellular pathogens. Table 1 provides a representation of TLRs, the cell types containing the receptor and the known agonists therefore (Diebold, S. S. et al. (2004) Science 303:1529-1531; Liew, F. et al. (2005) Nature 5:446-458; Hemmi H et al. (2002) Nat Immunol 3:196-200; Jurk M et al., (2002) Nat Immunol 3:499; Lee J et al. (2003) Proc. Natl. Acad. Sci. USA 100:6646- 6651); (Alexopoulou, L. (2001) Nature 413:732-738).

Table 1:

[0004] Certain unmethylated CpG motifs present in bacterial and synthetic

DNA have been shown to activate the immune system and induce antitumor activity. (Tokunaga T et al., J. Natl. Cancer Inst. (1984) 72:955-962; Shimada S, et al., Jpn. H cancer Res, 1986, 77, 808-816; Yamamoto S, et al., Jpn. J. Cancer Res., 1986, 79, 866-73). Other studies using antisense oligonucleotides containing CpG dinucleotides have been shown to stimulate immune responses (Zhao Q, et al. (1996) Biochem.Pharmacol. 26 : 173- 182). Subsequent studies demonstrated that TLR9 recognizes unmethylated CpG motifs present in bacterial and synthetic DNA (Hemmi, H. et al. (2000) Nature 408:740-745). Other modifications of CpG-containing phosphorothioate oligonucleotides can also affect their ability to act as modulators of immune response through TLR9 (see, e.g., Zhao et al., Biochem. Pharmacol. (1996) 51 :173-182; Zhao et al. (1996) Biochem Pharmacol. 52:1537-1544; Zhao et al. (1997) Antisense Nucleic Acid Drug Dev. 7:495-502; Zhao et al (1999) Bioorg. Med. Chem. Lett. 9:3453-3458; Zhao et al. (2000) Bioorg. Med. Chem. Lett. 10:1051- 1054; Yu, D. et al. (2000) Bioorg. Med. Chem. Lett. 10:2585-2588; Yu, D. et al. (2001) Bioorg. Med. Chem. Lett. 11 :2263-2267; and Kandimalla, E. et al. (2001) Bioorg. Med. Chem. 9:807-813). In addition, structure activity relationship studies have allowed identification of synthetic motifs and novel DNA-based compounds that induce specific immune response profiles that are distinct from those resulting from unmethylated CpG dinucleotides. (Kandimalla, E. et al. (2005) Proc. Natl. Acad. Sci. U S A 102:6925-6930. Kandimalla, E. et al. (2003) Proc. Nat. Acad. Sci. U S A 100:14303-14308; Cong, Y. et al. (2003) Biochem Biophys Res. Commun.310:1133- 1139; Kandimalla, E. et al. (2003) Biochem. Biophys. Res. Commun. 306:948-953; Kandimalla, E. et al. (2003) Nucleic Acids Res. 31 :2393-2400; Yu, D. et al. (2003) Bioorg. Med. Chem.11 :459-464; Bhagat, L. et al. (2003) Biochem. Biophys. Res. Commun.300:853-861; Yu, D. et al. (2002) Nucleic Acids Res.30:4460-4469; Yu, D. et al. (2002) J. Med. Chem.45:4540-4548. Yu, D. et al. (2002) Biochem. Biophys. Res. Commun.297:83-90; Kandimalla. E. et al. (2002) Bioconjug. Chem.13:966-974; Yu, D. et al. (2002) Nucleic Acids Res. 30:1613-1619; Yu, D. et al. (2001) Bioorg. Med. Chem. 9:2803-2808; Yu, D. et al. (2001) Bioorg. Med. Chem. Lett. 11 :2263- 2267; Kandimalla, E. et al. (2001) Bioorg. Med. Chem. 9:807-813; Yu, D. et al. (2000) Bioorg. Med. Chem. Lett. 10:2585-2588; Putta, M. et al. (2006) Nucleic Acids Res. 34:3231-3238).

[0005] The selective localization of TLRs and the signaling generated therefrom, provides some insight into their role in the immune response. The immune response involves both an innate and an adaptive response based upon the subset of cells involved in the response. For example, the T helper (Th) cells involved in classical cell-mediated functions such as delayed-type hypersensitivity and activation of cytotoxic T lymphocytes (CTLs) are ThI cells. This response is the body's innate response to antigen (e.g. viral infections, intracellular pathogens, and tumor cells), and results in a secretion of IFN-gamma and a concomitant activation of CTLs. Alternatively, the Th cells involved as helper cells for B-cell activation are Th2 cells. Th2 cells have been shown to be activated in response to bacteria and parasites and may mediate the body's adaptive immune response (e.g. IgE production and eosinophil activation) through the secretion of IL-4 and IL-5. The type of immune response is influenced by the cytokines produced in response to antigen exposure and the differences in the cytokines secreted by ThI and Th2 cells may be the result of the different biological functions of these two subsets.

[0006] As a result of their involvement in regulating an inflammatory response, TLRs have been shown to play a role in the pathogenesis of many diseases, including autoimmunity, infectious disease and inflammation (Papadimitraki et al.

(2007) J. Autoimmun. 29: 310-318; Sun et al. (2007) Infiam. Allergy Drug Targets 6:223-235; Diebold (2008) Adv. Drug Deliv. Rev. 60:813-823; Cook, D.N. et al. (2004) Nature Immunol. 5:975-979; Tse and Homer (2008) Semin. Immunopathol. 30:53-62; Tobias & Curtiss (2008) Semin. Immunopathol. 30:23-27; Ropert et al.

(2008) Semin. Immunopathol. 30:41-51; Lee et al. (2008) Semin. Immunopathol. 30:3-9; Gao et al. (2008) Semin. Immunopathol. 30:29-40; Vijay-Kumar et al. (2008) Semin. Immunopathol. 30:11-21). . While activation of TLRs is involved in mounting an immune response, an uncontrolled stimulation of the immune system through TLRs may exacerbate certain diseases in immune compromised subjects. In recent years, several groups have shown the use of synthetic oligodeoxyoligonucleotides (ODNs) as inhibitors of inflammatory cytokines (Lenert, P. et al. (2003) DNA Cell Biol. 22(10):621-631).

[0007] Using certain synthetic ODNs, Lenert et al. report the ability to produce inhibitory ODNs (Lenert, P. et al. (2003) DNA Cell Biol. 22(10):621-631). These inhibitory ODN require two triplet sequences, a proximal "CCT" triplet and a distal "GGG" triplet. In addition to these triplet-containing inhibitory ODNs, several groups have reported other specific DNA sequences that could inhibit TLR-9- mediated activation by CpG-containing ODNs. These "inhibitory" or "suppressive" motifs are rich in "G" (e.g. "GGG" or "GGGG") or "GC" sequences, tend to be methylated, and are present in the DNA of mammals and certain viruses (see e.g.,; Chen, Y., et al., Gene Ther. 8: 1024-1032 (2001); Stunz, L.L., Eur. J. Immunol. 32: 1212-1222 (2002). Duramad, O., et al., J. Immunol, 174: 5193-5200 (2005) and Jurk et. al (US 2005/0239733), describe a structure for inhibitory DNA oligonucleotides containing a GGGG motif within the sequences. Patole et al. demonstrate that GGGG containing ODNs will suppress systemic lupus (Patole, P. et al. (2005) J. Am. Soc. Nephrol. 16:3273-3280). Additionally, Gursel, L, et al., J. Immunol, 171 : 1393-1400 (2003), describe repetitive TTAGGG elements, which are present at high frequency in mammalian telomeres, down-regulate CpG-induced immune activation. Shirota, H., et al, J. Immunol, 173: 5002-5007 (2004), demonstrate that synthetic oligonucleotides containing the TTAGGG element mimic this activity and could be effective in the prevention/treatment of certain ThI -dependent autoimmune diseases.

[0008] In contrast, recent studies have called into question the view that poly

G containing ODNs are acting as antagonists of TLRs. For example, US 6,426,334, Agrawal et al., demonstrate that administering CpG oligonucleotides containing GGGG strings have potent antiviral and anticancer activity, and further that administration of these compounds will cause an increase in serum IL- 12 concentration. Further, CpG oligos containing polyG sequences are known to induce immune responses through TLR9 activation (Verthelyi D et al, J Immunol. 166, 2372, 2001; Gursel M et al, J Leukoc Biol, 71, 813, 2001, Krug A et al, Eur J Immunol, 31, 2154, 2001) and show antitumor and antiviral activities (Ballas GK et al, J Immunol, 167, 4878, 2001; Verthelyi D et al, J Immunol, 170, 4717, 2003). In addition, polyG oligonucleotides are also known to inhibit HIV and ReI A (McShan WM, et al, J Biol Chem., 267(8):5712-21, 1992; Rando, RF et al., J Biol Chem, 270(4): 1754-60, 1995; Benimetskaya L, et al., Nucleic Acids Res., 25(13):2648-56, 1997). In addition, ODNs containing an immune stimulatory CpG motif and 4 consecutive G nucleotides (class A ODNs) induce interferon-γ production and a ThI shift in the immune response. Moreover, in preclinical disease models, Class A ODN have been shown to induce a TLR-mediated immune response.

[0009] In addition, oligonucleotides containing guanosine strings have been shown to form tetraplex structures, act as aptamers and inhibit thrombin activity (Bock LC et al., Nature, 355:564-6, 1992; Padmanabhan, K et al., J Biol Chem., 268(24): 17651-4, 1993). Thus, it is not clear whether single-stranded or multiple- stranded structures are effective at suppressing TLR9 activation. Thus, there is a need for effective antagonist of TLRs without a concern that they will form secondary structures. BRIEF SUMMARY OF THE INVENTION

[0010] The invention provides novel immune regulatory oligonucleotides

(IRO) compounds as antagonists of TLRs and methods of use thereof. These IROs have one or more chemical modifications in the sequence flanking an immune stimulatory motif and/or in an oligonucleotide motif that would be immune stimulatory but for the modification.

[0011] The invention provides a method for therapeutically treating a vertebrate having a disease caused by a pathogen mediated by a TLR, wherein the pathogen is selected from the group consisting of 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 metapneumovirus, 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 and Venezuelan equine encephalitis virus, such method comprising administering to the mammal an IRO compound in a pharmaceutically effective amount.

[0012] The invention further provides a method for preventing a disease caused by a pathogen mediated by a TLR, wherein the pathogen is selected from the group consisting of 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 metapneumovirus, 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 and Venezuelan equine encephalitis virus, such method comprising administering to the mammal an IRO compound in a pharmaceutically effective amount

[0013] The IRO compounds, according to the invention, have the structure 5-

N_m - N₃N₂N₁CGN¹N²N³ - N^m -3', wherein CG is an oligonucleotide motif and C is cytosine or a pyrimidine nucleotide derivative or non-nucleotide linkage, and G is guanosine a purine nucleotide derivative or non-nucleotide linkage; N₁-N₃ and N^!-N³, at each occurrence, is independently a nucleotide, nucleotide derivative or non- nucleotide linkage; N_m and N^m, at each occurrence, is independently a nucleotide, nucleotide derivative or non-nucleotide linkage; provided that at least one N₁ to N₃ and/or C and/or G is a nucleotide derivative or non-nucleotide linkage; and further provided that compound contains less than 3 consecutive guanosine nucleotides wherein the oligonucleotide motif would be immune stimulatory but for the nucleotide derivative or non-nucleotide linkage; and wherein m is a number from 0 to about 30.

[0014] In some preferred embodiments, 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, antimalarial drugs, or co -stimulatory molecules or combinations thereof. In some preferred embodiments, 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.

BRIEF DESCRIPTION OF THE DRAWINGS

[0015] Figure 1 depicts IRO inhibition of the TLR9 agonist activity of an IMO in cells treated according to Example 2.

[0016] Figure 2 depicts the specificity of an exemplar IRO compound as an antagonist of TLR9 vs TLR3 in cells treated according to Example 3.

[0017] Figure 3 depicts dose-dependent inhibition of TLR activation by an

IRO following in vivo administration according to Example 4.

[0018] Figures 4 A - 4D depicts pre-administration and simultaneous administration of IRO inhibition of the activity of an agonist of TLR9 following in vivo administration according to Example 5.

[0019] Figures 5 A and 5B depicts the TLR-inhibitory properties of an IRO having two CpG oligonucleotides linked at their 5 ' ends administered in vivo according to Example 6.

[0020] Figure 6 depicts the TLR9 inhibitory activity of an IRO in human cells treated according to Example 7.

[0021] Figure 7 depicts the in vivo activity of an IRO on OVA induced Th2 and ThI immune responses.

[0022] Figure 8 depicts that an IRO can, in vivo, reverse Th2 inhibitory properties and inhibit ThI immune responses induced by an IMO.

[0023] Figure 9 depicts antibody responses to an IMO and an IRO following in vivo administration according to Example 10.

[0024] Figure 10 depicts early inhibitory activity of an IRO on TLR2, TLR3,

TLR4, TLR5, TLR7, TLR8, and TLR9 following in vivo administration according to

Example 12.

[0025] Figure 11 depicts early inhibitory activity of an IRO on TLR2, TLR3,

TLR4, TLR5, TLR7, TLR8, and TLR9 following in vivo administration according to

Example 12.

[0026] Figure 12 depicts early inhibitory activity of an IRO on TLR2, TLR3,

TLR4, TLR5, TLR7, TLR8, and TLR9 following in vivo administration according to

Example 12.

[0027] Figure 13 depicts long-term antagonist activity of an IRO on TLR2,

TLR3, TLR4, TLR5, TLR7, TLR8, and TLR9 following in vivo administration according to Example 12. [0028] Figure 14 depicts long-term antagonist activity of selected IROs on

TLR2, TLR3, TLR4, TLR5, TLR7, TLR8, and TLR9 following in vivo administration according to Example 11.

[0029] Figure 15 depicts long-term antagonist activity of selected IROs on

TLR2, TLR3, TLR4, TLR5, TLR7, TLR8, and TLR9 following in vivo administration according to Example 11.

[0030] Figure 16 depicts the antiviral activity of an exemplar IRO following infection with an exemplar pathogen, HIV-I, according to example 14. Briefly, human PBMCs were infected with HIV-I and then treated with different concentrations of an exemplar IRO. The data represent the percentage of virus remaining as compared to control following seven days of IRO treatment. The data demonstrate that administration of IRO following HIV-I infection will reduce the amount of virus present. More generally, the data demonstrate that administration of IRO following pathogen or viral infection will reduce the amount of pathogen or virus present.

[0031] Figure 17 depicts antiviral activity of an exemplar IRO plus azidothymidine (AZT), or AZT alone, against an exemplar pathogen, HIV-I, in cells treated according to example 15. Briefly, human PBMCs were pretreated with the exemplar IRO for 2 hours and then infected with HIV-I . Following IRO pretreatment and viral infection, the PBMCs were incubated with AZT for 7 days. The data demonstrate that pretreatment with IRO increased the potency of AZT against HIV-I . More generally, the data demonstrate that administration of IRO prior to pathogen or viral infection enhances the activity of antiviral compounds. In addition, the data generally demonstrate that administering an IRO prior to pathogen or viral infection can decrease the amount of virus present following infection.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0032] The present invention relates to the therapeutic use of novel oligonucleotides as immune modulatory agents for immunotherapy applications. Specifically, the invention provides Immune Regulatory Oligonucleotide (IRO) compounds as antagonists of toll-like receptors (TLRs) to inhibit and/or suppress a TLR-mediated immune response. These IROs have unique sequences that inhibit or suppress TLR-mediated signaling in response to endogenous and/or exogenous TLR ligands or agonists. The references cited herein reflect the level of knowledge in the field and are hereby incorporated by reference in their entirety. Any conflicts between the teachings of the cited references and this specification shall be resolved in favor of the latter.

[0033] The invention provides methods for suppressing an immune response caused by TLRs and can be used for immunotherapy applications such as, but not limited to, treatment of cancer, autoimmune disorders, asthma, respiratory allergies, food allergies, skin allergies, systemic lupus erythematosus (SLE), arthritis, pleurisy, chronic infections, inflammatory diseases, inflammatory bowl syndrome, sepsis, and bacteria, parasitic, and viral infections in adult and pediatric human and veterinary applications. Thus, the invention further provides IRO compounds having optimal levels of immune modulatory effect for immunotherapy and methods for making and using such compounds. In addition, IRO compounds of the invention are useful in combination with, for example, DNA vaccines, antigens, antibodies, antiviral agents, antimalarial drugs (for example, chloroquine and hydroxychloroquine) and allergens; and in combination with chemotherapeutic agents (both traditional chemotherapy and modern targeted therapies) and/or antisense oligonucleotides for prevention and treatment of diseases.

[0034] The term "oligonucleotide" generally refers to a polynucleoside comprising a plurality of linked nucleoside units. Such oligonucleotides can be obtained from existing nucleic acid sources, including genomic or cDNA, but are preferably produced by synthetic methods. In preferred embodiments each nucleoside unit can encompass various chemical modifications and substitutions as compared to wild-type oligonucleotides, including but not limited to modified nucleoside base and/or modified sugar unit. Examples of chemical modifications are known to the person skilled in the art and are described, for example, in Uhlmann E et al. (1990) Chem. Rev. 90:543; "Protocols for Oligonucleotides and Analogs" Synthesis and Properties & Synthesis and Analytical Techniques, S. Agrawal, Ed, Humana Press, Totowa, USA 1993; and Hunziker, J. et al. (1995) Mod. Syn. Methods 7:331-417; and Crooke, S. et al. (1996) Ann.Rev. Pharm. Tox. 36:107-129. The nucleoside residues can be coupled to each other by any of the numerous known internucleoside linkages. Such internucleoside linkages include, without limitation, phosphodiester, phosphorothioate, phosphorodithioate, alkylphosphonate, alkylphosphonothioate, phosphotriester, phosphoramidate, siloxane, carbonate, carboalkoxy, acetamidate, carbamate, morpholino, borano, thioether, bridged phosphoramidate, bridged methylene phosphonate, bridged phosphorothioate, and sulfone internucleoside linkages. The term "oligonucleotide" also encompasses polynucleosides having one or more stereospecifϊc internucleoside linkage (e.g., (R_P)- or (5^*p)-phosphorothioate, alkylphosphonate, or phosphotriester linkages). As used herein, the terms "oligonucleotide" and "dinucleotide" are expressly intended to include polynucleosides and dinucleosides having any such internucleoside linkage, whether or not the linkage comprises a phosphate group. In certain preferred embodiments, these internucleoside linkages may be phosphodiester, phosphorothioate, or phosphorodithioate linkages, or combinations thereof. [0035] The term "2'-substituted ribonucleoside" or "2 '-substituted arabinoside" generally includes ribonucleosides or arabinonucleosides in which the hydroxyl group at the 2' position of the pentose moiety is substituted to produce a 2'- substituted or 2'-O-substituted ribonucleoside. In certain embodiments, such substitution is with a lower hydrocarbyl group containing 1-6 saturated or unsaturated carbon atoms, with a halogen atom, or with an aryl group having 6-10 carbon atoms, wherein such hydrocarbyl, or aryl group may be unsubstituted or may be substituted, e.g., with halo, hydroxy, trifluoromethyl, cyano, nitro, acyl, acyloxy, alkoxy, carboxyl, carboalkoxy, or amino groups. Examples of 2'-O-substituted ribonucleosides or 2'-O-substituted-arabinosides include, without limitation 2 '-amino, 2'-fluoro, 2'-allyl, 2'-O-alkyl and 2'-propargyl ribonucleosides or arabinosides, 2'-O- methylribonucleosides or 2'-O-methylarabinosides and 2'-O- methoxyethoxyribonucleosides or 2'-O-methoxyethoxyarabinosides. [0036] The term " 3' " , when used directionally, generally refers to a region or position in a polynucleotide or oligonucleotide 3' (downstream) from another region or position in the same polynucleotide or oligonucleotide. [0037] The term " 5' " , when used directionally, generally refers to a region or position in a polynucleotide or oligonucleotide 5' (upstream) from another region or position in the same polynucleotide or oligonucleotide.

[0038] The term "about" generally means that the exact number is not critical.

Thus, the number of nucleoside residues in the oligonucleotides is not critical, and oligonucleotides having one or two fewer nucleoside residues, or from one to several additional nucleoside residues are contemplated as equivalents of each of the embodiments described above.

[0039] The term "agonist" generally refers to a substance that binds to a receptor of a cell and induces a response. Such response may be an increase in the activity mediated by the receptor. An agonist often mimics the action of a naturally occurring substance such as a ligand.

[0040] The term "antagonist" generally refers to a substance that can bind to a receptor, but does not produce a biological response upon binding. The antagonist can block, inhibit or attenuate the response mediated by an agonist and may compete with agonist for binding to a receptor. Such antagonist activity may be reversible or irreversible.

[0041] The term "adjuvant" generally refers to a substance which, when added to an immunogenic agent such as vaccine or antigen, enhances or potentiates an immune response to the agent in the recipient host upon exposure to the mixture. [0042] The term "airway inflammation" generally includes, without limitation, asthma.

[0043] The term "allergen" generally refers to an antigen or antigenic portion of a molecule, usually a protein, which elicits an allergic response upon exposure to a subject. Typically the subject is allergic to the allergen as indicated, for instance, by the wheal and flare test or any method known in the art. A molecule is said to be an allergen even if only a small subset of subjects exhibit an allergic immune response upon exposure to the molecule.

[0044] The term "allergy" generally refers to an inappropriate immune response characterized by inflammation and includes, without limitation, food allergies and respiratory allergies.

[0045] The term "antigen" generally refers to a substance that is recognized and selectively bound by an antibody or by a T cell antigen receptor, resulting in induction of an immune response. Antigens may include but are not limited to peptides, proteins, nucleosides, nucleotides, and combinations thereof. Antigens may be natural or synthetic and generally induce an immune response that is specific for that antigen.

[0046] The term "antiviral agent" generally refers to an agent that has the capacity to kill viruses, suppress their replication, cell binding or other essential functions and, hence, inhibits their capacity to multiply and reproduce. Such agents may act by stimulating cellular defenses against viruses.

[0047] The term "autoimmune disorder" generally refers to disorders in which

"self components undergo attack by the immune system.

[0048] The term "TLR-mediated disease" or TLR-mediated disorder" generally means any pathological condition for which activation of one or more TLRs is a contributing factor. Such conditions include but are not limited, cancer, an autoimmune disorder, airway inflammation, inflammatory disorders, infectious disease, skin disorders, allergy, asthma or a disease caused by a pathogen.

[0049] The term "physiologically acceptable" generally refers to a material that does not interfere with the effectiveness of an IRO compound and that is compatible with a biological system such as a cell, cell culture, tissue, or organism. Preferably, the biological system is a living organism, such as a mammal.

[0050] The term "carrier" generally encompasses any excipient, diluent, filler, salt, buffer, stabilizer, solubilizer, oil, lipid, lipid containing vesicle, microspheres, liposomal encapsulation, or other material well known in the art for use in pharmaceutical formulations. It will be understood that the characteristics of the carrier, excipient, or diluent will depend on the route of administration for a particular application. The preparation of pharmaceutically acceptable formulations containing these materials is described in, e.g., Remington 's Pharmaceutical Sciences, 18th Edition, ed. A. Gennaro, Mack Publishing Co., Easton, PA, 1990.

[0051] The term "co-administration" generally refers to the administration of at least two different substances sufficiently close in time to modulate an immune response. Co-administration refers to simultaneous administration, as well as temporally spaced order of up to several days apart, of at least two different substances in any order, either in a single dose or separate doses. [0052] The term "complementary" generally means having the ability to hybridize to a nucleic acid. Such hybridization is ordinarily the result of hydrogen bonding between complementary strands, preferably to form Watson-Crick or Hoogsteen base pairs, although other modes of hydrogen bonding, as well as base stacking can also lead to hybridization.

[0053] The term an "effective amount" or a "sufficient amount" generally refers to an amount sufficient to affect a desired biological effect, such as beneficial results. Thus, an "effective amount" or "sufficient amount" will depend upon the context in which it is being administered. In the context of administering a composition that modulates an immune response to a co -administered antigen, an effective amount of an IRO compound and antigen is an amount sufficient to achieve the desired modulation as compared to the immune response obtained when the antigen is administered alone. An effective amount may be administered in one or more administrations.

[0054] The term "in combination with" generally means in the course of treating a disease or disorder in a patient, administering an IRO compound and an agent useful for treating the disease or disorder that does not diminish the immune modulatory effect of the IRO compound. Such combination treatment may also include more than a single administration of an IRO compound and/or independently an agent. The administration of the IRO compound and/or the agent may be by the same or different routes.

[0055] The term "individual" or "subject" or "mammal" generally refers to but is not limited to, humans, non-human primates, rats, mice, cats, dogs, horses, cattle, cows, pigs, sheep, and rabbits.

[0056] The term "kinase inhibitor" generally refers to molecules that antagonize or inhibit phosphorylation-dependent cell signaling and/or growth pathways in a cell. Kinase inhibitors may be naturally occurring or synthetic and include small molecules that have the potential to be administered as oral therapeutics. Kinase inhibitors have the ability to rapidly and specifically inhibit the activation of the target kinase molecules. Protein kinases are attractive drug targets, in part because they regulate a wide variety of signaling and growth pathways and include many different proteins. As such, they have great potential in the treatment of diseases involving kinase signaling, including cancer, cardiovascular disease, inflammatory disorders, diabetes, macular degeneration and neurological disorders. Examples of kinase inhibitors include sorafenib (Nexavar®), Sutent®, dasatinib, Dasatinib™, Zactima™, Tykerb™ and STI571.

[0057] The term "nucleoside" generally refers to compounds consisting of a sugar, usually ribose or deoxyribose, and a purine or pyrimidine base.

[0058] The term "nucleotide" generally refers to a nucleoside comprising a phosphate group attached to the sugar.

[0059] As used herein, the term "pyrimidine nucleoside" refers to a nucleoside wherein the base component of the nucleoside is a pyrimidine base (e.g., cytosine (C) or thymine (T) or Uracil (U)). Similarly, the term "purine nucleoside" refers to a nucleoside wherein the base component of the nucleoside is a purine base (e.g., adenine (A) or guanine (G)).

[0060] The terms "analog" or "derivative" can be used interchangeable to generally refer to any purine and/or pyrimidine nucleotide or nucleoside that has a modified base and/or sugar. A modified base is a base that is not guanine, cytosine, adenine, thymine or uracil. A modified sugar is any sugar that is not ribose or 2 'deoxyribose and can be used in the backbone for an oligonucleotide.

[0061] The term "inhibiting" or "suppressing" generally refers to a decrease in a response or qualitative difference in a response, which could otherwise arise from eliciting and/or stimulation of a response.

[0062] The term "non-nucleotide linker" generally refers to any linkage or moiety that can link or be linked to the oligonucleotides other than through a phosphorous-containing linkage. Preferably such linker is from about 2 angstroms to about 200 angstroms in length.

[0063] The term "nucleotide linkage" generally refers to a direct 3 '-5' linkage that directly connects the 3' and 5' hydroxyl groups of two nucleosides through a phosphorous-containing linkage.

[0064] The terms "oligonucleotide motif generally refers to an oligonucleotide sequence, including a dinucleotide. An "oligonucleotide motif that would be immune stimulatory, but for one or more modifications" means an oligonucleotide motif which is immune stimulatory in a parent oligonucleotide, but not in a derivative oligonucleotide, wherein the derivative oligonucleotide is based upon the parent oligonucleotide, but has one or more modifications that reduce or eliminate immune stimulation.

[0065] The terms CpG, C*pG, C*pG* and CpG* refer to oligonucleotide motifs that are immune stimulatory and comprise cytosine or a cytosine analog and a guanine or a guanine analog.

[0066] The term "treatment" generally refers to an approach intended to obtain a beneficial or desired results, which may include alleviation of symptoms, or delaying or ameliorating a disease progression.

[0067] In a first aspect, the invention provides an immune regulatory oligonucleotide (IRO) compound. The term "IRO" refers to an immune regulatory oligonucleotide compound that is an antagonist for one or more TLR, wherein the compound comprises an oligonucleotide motif and at least one modification, wherein the oligonucleotide motif would be immune stimulatory (e.g., unmethylated CpG), but for the one or more modifications that suppress the activity of the oligonucleotide motif, provided that the compound contains less than 3 consecutive guanosine nucleotides. Such modifications may be in the oligonucleotide 5' terminus, in a sequence flanking the oligonucleotide motif, and/or within the oligonucleotide motif. These modifications result in an IRO compound that suppresses TLR-modulated immune stimulation. Such modifications can be to the bases, sugar residues and/or the phosphate backbone of the nucleotides/nucleosides flanking the oligonucleotide motif or within the oligonucleotide motif.

[0068] In preferred embodiments, when the modification is a 2' alkylation or alkoxylation then the modification is not 5' adjacent to the oligonucleotide motif; when the modification is a non-charged internucleoside linkage then the modification is not 5' adjacent to the oligonucleotide motif; and when the modification is a 3' alkylation or alkoxylation then the modification is not 5' or 3' adjacent to the oligonucleotide motif.

[0069] In preferred embodiments the IRO compound is not an antisense oligonucleotide. [0070] The general structure of the IRO compounds may be represented as 5'-

N_m - N₃N₂N₁CGN¹N²N³ - N^m -3' wherein CG is an immune stimulatory motif and C is cytosine or a pyrimidine nucleotide derivative or non-nucleotide linker, and G is guanosine, a purine nucleotide derivative or non-nucleotide linker; N₁-N₃ and N^!-N³, at each occurrence, is independently a nucleotide, nucleotide derivative or non- nucleotide linker; N_m and N^m, at each occurrence, is independently a nucleotide, nucleotide derivative or non-nucleotide linker; provided that at least one N₁ to N₃ and/or C and/or G is a nucleotide derivative or non-nucleotide linker; and further provided that compound contains less than 4 consecutive guanosine nucleotides and preferably less than 3 consecutive guanosines, wherein the immune stimulatory activity of the CG is suppressed by the nucleotide derivative or non-nucleotide linker; and wherein m is a number from 0 to about 30.

[0071] In certain embodiments of the invention, IRO compounds may comprise at least two oligonucleotides covalently linked by a nucleotide linkage, or a non-nucleotide linker, at their 5'-, 3'- or 2'-ends or by functionalized sugar or by functionalized nucleobase via a non-nucleotide linker or a nucleotide linkage. Such IRO compounds may be linear or branched. As a non-limiting example, the linker may be attached to the 3'-hydroxyl. In such embodiments, the linker comprises a functional group, which is attached to the 3'-hydroxyl by means of a phosphate -based linkage like, for example, phosphodiester, phosphorothioate, phosphorodithioate, methylphosphonate, or by non-phosphate-based linkages. Possible sites of conjugation for the ribonucleotide are indicated in Formula I, below, wherein B represents a heterocyclic base and wherein the arrow pointing to P indicates any attachment to phosphorous.

[0072] In some embodiments, the non-nucleotide linker is a small molecule, macromolecule or biomolecule, including, without limitation, polypeptides, antibodies, lipids, antigens, allergens, and oligosaccharides. In some other embodiments, the non-nucleotidic linker is a small molecule. For purposes of the invention, a small molecule is an organic moiety having a molecular weight of less than 1,000 Da. In some embodiments, the small molecule has a molecular weight of less than 750 Da.

[0073] In some embodiments, the small molecule is an aliphatic or aromatic hydrocarbon, either of which optionally can include, either in the linear chain connecting the oligoribonucleotides or appended to it, one or more functional groups including, but not limited to, hydroxy, amino, thiol, thioether, ether, amide, thioamide, ester, urea, or thiourea. The small molecule can be cyclic or acyclic. Examples of small molecule linkers include, but are not limited to, amino acids, carbohydrates, cyclodextrins, adamantane, cholesterol, haptens and antibiotics. However, for purposes of describing the non-nucleotidic linker, the term "small molecule" is not intended to include a nucleoside.

[0074] In some embodiments, the non-nucleotidic linker is an alkyl linker or amino linker. The alkyl linker may be branched or unbranched, cyclic or acyclic, substituted or unsubstituted, saturated or unsaturated, chiral, achiral or racemic mixture. The alkyl linkers can have from about 2 to about 18 carbon atoms. In some embodiments such alkyl linkers have from about 3 to about 9 carbon atoms. Some alkyl linkers include one or more functional groups including, but not limited to, hydroxy, amino, thiol, thioether, ether, amide, thioamide, ester, urea, and thioether. Such alkyl linkers can include, but are not limited to, 1,2 propanediol, 1,2,3 propanediol, 1,3 propanediol, triethylene glycol hexaethylene glycol, polyethylene glycollinkers (e.g. [-O-CH2-CH2-]_n (n= l-9)),methyl linkers, ethyl linkers, propyl linkers, butyl linkers, or hexyl linkers. In some embodiments, such alkyl linkers may include peptides or amino acids.

[0075] In some embodiments, the non-nucleotide linker may include, but are not limited to, those listed in Table 2.

[0076] In some embodiments, the small molecule linker is glycerol or a glycerol homolog of the formula HO-(CH₂)_O-CH(OH)-(CH₂)_?-OH, wherein o and/? independently are integers from 1 to about 6, from 1 to about 4, or from 1 to about 3. In some other embodiments, the small molecule linker is a derivative of 1,3-diamino- 2-hydroxypropane. Some such derivatives have the formula HO-(CH₂)_m-C(O)NH-CH₂-CH(OH)-CH₂-NHC(O)-(CH₂)_m-OH, wherein m is an integer from O to about 10, from 0 to about 6, from 2 to about 6, or from 2 to about 4

[0077] Some non-nucleotide linkers according to the invention permit attachment of more than two oligonucleotides. For example, the small molecule linker glycerol has three hydroxyl groups to which oligonucleotides may be covalently attached. Some IROs according to the invention, therefore, comprise two or more oligonucleotides linked to a nucleotide or a non-nucleotide linker. Such IROs are referred to as being "branched".

[0078] IRO compounds may comprise at least two oligonucleotides non- covalently linked, such as by electrostatic interactions, hydrophobic interactions, π-stacking interactions, hydrogen bonding and combinations thereof. Non-limiting examples of such non-covalent linkage includes Watson-Crick base pairing, Hoogsteen base pairing and base stacking.

[0079] Some of the ways in which two or more oligonucleotides can be linked are shown in Table 3.

[0080] In certain embodiments, pyrimidine nucleosides in the immune regulatory oligonucleotides used in the compositions and methods according to the invention have the structure (II):

wherein:

D is a hydrogen bond donor;

D' is selected from the group consisting of hydrogen, hydrogen bond donor, hydrogen bond acceptor, hydrophilic group, hydrophobic group, electron withdrawing group and electron donating group;

A is a hydrogen bond acceptor or a hydrophilic group; A' is selected from the group consisting of hydrogen bond acceptor, hydrophilic group, hydrophobic group, electron withdrawing group and electron donating group;

X is carbon or nitrogen; and

S' is a pentose or hexose sugar ring, or a sugar analog.

[0081] In certain embodiments, the sugar ring is derivatized with a phosphate moiety, modified phosphate moiety, or other linker moiety suitable for linking the pyrimidine nucleoside to another nucleoside or nucleoside analog.

[0082] In some embodiments hydrogen bond donors include, without limitation, -NH-, -NH₂, -SH and -OH. Preferred hydrogen bond acceptors include, without limitation, C=O, C=S, and the ring nitrogen atoms of an aromatic heterocycle, e.g., N3 of cytosine.

[0083] In some embodiments, (II) is a pyrimidine nucleoside derivative.

Examples of pyrimidine nucleoside derivatives include, without limitation, 5- hydroxycytosine, 5-hydroxymethylcytosine, N4-alkylcytosine, or N4-ethylcytosine, araC, 5-OH-dC, N3-Me-dC, and 4-thiouracil. Chemical modified derivatives also include, but are not limited to, thymine or uracil analogues. In some embodiments, the sugar moiety S' in (II) is a sugar derivative. Suitable sugar derivatives include, but are not limited to, trehalose or trehalose derivatives, hexose or hexose derivatives, arabinose or arabinose derivatives.

[0084] In some embodiments, the purine nucleosides in immune regulatory oligonucleotides used in the compositions and methods according to the invention have the structure (III):

wherein:

D is a hydrogen bond donor; D' is selected from the group consisting of hydrogen, hydrogen bond donor, and hydrophilic group;

A is a hydrogen bond acceptor or a hydrophilic group;

X is carbon or nitrogen; each L is independently selected from the group consisting of C, O, N and S; and

S' is a pentose or hexose sugar ring, or a sugar analog.

[0085] In certain embodiments, the sugar ring is derivatized with a phosphate moiety, modified phosphate moiety, or other linker moiety suitable for linking the pyrimidine nucleoside to another nucleoside or nucleoside analog.

[0086] In certain embodiments hydrogen bond donors include, without limitation, -NH-, -NH₂, -SH and -OH. In certain embodiments hydrogen bond acceptors include, without limitation, C=O, C=S, -NO₂ and the ring nitrogen atoms of an aromatic heterocycle, e.g., Nl of guanine.

[0087] In some embodiments, (III) is a purine nucleoside derivative.

Examples of purine nucleoside derivatives include, without limitation, guanine analogues such as 7-deaza-G, 7-deaza-dG, ara-G, 6-thio-G, Inosine, Iso-G, loxoribine, TOG(7-thio-8-oxo)-G, 8-bromo-G, 8-hydroxy-G, 5-aminoformycin B, Oxoformycin, 7-methyl-G, 9-p-chlorophenyl-8-aza-G, 9-phenyl-G, 9-hexyl-guanine, 7-deaza-9- benzyl-G, 6-Chloro-7-deazaguanine, 6-methoxy-7-deazaguanine, 8-Aza-7-deaza- G(PPG), 2-(Dimethylamino)guanosine, 7-Methyl-6-thioguanosine, 8- Benzyloxyguanosine, 9-Deazaguanosine, 1 -(B-D-ribofuranosyl)-2-oxo-7-deaza-8- methyl-purine, l-(2'-deoxy-β-D-ribofuranosyl)-2-oxo-7-deaza-8-methyl-purine. Chemically modified derivatives also include, but are not limited to, adenine analogues such as 9-benzyl-8-hydroxy-2-(2-methoxyethoxy)adenine, 2-Amino-N2-O- , methyladenosine, 8-Aza-7-deaza-A, 7-deaza-A, Vidarabine, 2-Aminoadenosine, Nl- Methyladenosine, 8-Azaadenosine, 5-Iodotubercidin, and Nl-Me-dG. In some embodiments, the sugar moiety S' in (III) is a sugar derivative as defined for Formula II.

[0088] In certain embodiments of the invention, the immune regulatory nucleic acid comprises a nucleic acid sequence containing at least one B-L-deoxy nucleoside or 3'-deoxy nucleoside. [0089] In certain embodiments of the invention, the immune regulatory oligonucleotide comprises a nucleic acid sequence containing at least one dinucleotide selected from CpG, C*pG, C*pG* and CpG*, wherein C is cytosine or T- deoxycytidine, G is guanosine or 2'-deoxyguanosine, C* is 2'-deoxythymidine, l-(2'- deoxy-β-D-ribofuranosyl)-2-oxo-7-deaza-8-methyl-purine, 2'-dideoxy-5- halocytosine, 2'-dideoxy-5-nitrocytosine, arabinocytidine, 2'-deoxy-2'-substituted arabinocytidine, 2'-O-substituted arabinocytidine, 2'-deoxy-5-hydroxycytidine, T- deoxy-N4-alkyl-cytidine, 2'-deoxy-4-thiouridine, or other pyrimidine nucleoside analogs, G* is 2'-deoxy-7-deazaguanosine, 2'-deoxy-6-thioguanosine, arabinoguanosine, 2'-deoxy-2'substituted-arabinoguanosine, 2'-O-substituted- arabinoguanosine, T- deoxyinosine, or other purine nucleoside analogs, and p is an internucleoside linkage selected from the group consisting of phosphodiester, phosphorothioate, and phosphorodithioate, and wherein the activity of the at least one dinucleotide is regulated by the flanking sequence.

[0090] The sequences of specific IRO within these general structures used in the present study include, but are not limited to, those shown in Table 4a.

Table 4

Underlined G, A or U = 2'-0Me; Underlined T = 3'-0Me; Ai = 3'-0Me; Gi=7- deaza-dG; m= P-Me; A₂, T₂, C₂, and G₂ = B-L-deoxy nucleoside; Xi = abasic; X₂ = glycerol linker, X3 = C3-linker; C3 and G3 = 3'-deoxy-nucleoside; G₄ = araG; C₄ = araC; C₅ = 5-OH-dC; C₆ = l-(2'-deoxy-β-D-ribofuranosyl)-2-oxo-7-deaza-8-methyl- purine; G₅ = Nl-Me-dG; C₇ = N3-Me-dC; Ui=3'-0Me; U₂=dU

[0091] The sequences of control oligonucleotides used in the present studies include those shown in Table 4b.

Underlined U = 2'-0Me; Underlined T = 3'-0Me; Gi=7-deaza-dG; X₂ = glycerol linker

[0092] In some embodiments, the oligonucleotides each have from about 6 to about 35 nucleoside residues, preferably from about 9 to about 30 nucleoside residues, more preferably from about 11 to about 23 nucleoside residues. In some embodiments, the oligonucleotides have from about 6 to about 18. [0093] In a second aspect, the invention provides pharmaceutical formulations comprising an IRO compound according to the invention and a physiologically acceptable carrier.

[0094] In a third aspect, the invention provides methods for inhibiting or suppressing TLR-mediated induction of an immune response in a vertebrate, such methods comprising administering to the vertebrate a IRO compound according to the invention. In some embodiments, the vertebrate is a mammal. In preferred embodiments, IRO compound is administered to a vertebrate in need of immune suppression.

[0095] According to this aspect of the invention, an IRO compound is capable of suppressing a TLR-based immune response to a further TLR ligand or TLR agonist. As discussed further in the Examples below, the activation of a TLR-based immune response by a TLR agonist or TLR ligand (e.g. an immune modulatory oligonucleotide) can be suppressed/inhibited by the simultaneous, pre- or post- administration of an IRO compound, and such suppression/inhibition may be maintained for an extended period of time (e.g. days) after administration. This beneficial property of the current invention has a unique advantage for the prevention and/or treatment of a disease or disorder. For example, application of certain TLR- agonists in the course of treating the disease may cause unwanted immune stimulation that an IRO compound could suppress/inhibit. Administration of the IRO simultaneously, pre and/or post administration of the TLR-agonist may allow therapeutic benefits from the TLR-agonist while suppressing/inhibiting the unwanted side effect(s). Additionally, pre-administration of an IRO could prevent an immune response (e.g., allergic reaction) to a subsequent or later challenge by a TLR-agonist.

[0096] In the methods according to this aspect of the invention, administration of IRO compound can be by any suitable route, including, without limitation, 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. Administration of the therapeutic compositions of IRO compound can be carried out using known procedures at dosages and for periods of time effective to reduce symptoms or surrogate markers of the disease. When administered systemically, the therapeutic composition is preferably administered at a sufficient dosage to attain a blood level of IRO compound from about 0.0001 micromolar to about 10 micromolar. For localized administration, much lower concentrations than this may be effective, and much higher concentrations may be tolerated. Preferably, a total dosage of IRO compound ranges from about 0.001 mg per patient per day to about 200 mg per kg body weight per day. It may be desirable to administer simultaneously, or sequentially a therapeutically effective amount of one or more of the therapeutic compositions of the invention to an individual as a single treatment episode.

[0097] The IRO compound may optionally be linked to one or more allergens and/or antigens (self or foreign), an immunogenic protein, such as keyhole limpet hemocyanin (KLH), cholera toxin B subunit, or any other immunogenic carrier protein. IRO can also be used in combination with other compounds (e.g. adjuvants) including, without limitation, TLR agonists (e.g. TLR2 agonists and TLR9 agonists), Freund's incomplete adjuvant, KLH, monophosphoryl lipid A (MPL), alum, and saponins, including QS-21 and imiquimod, or combinations thereof. [0098] The methods according to this aspect of the invention are useful for model studies of the immune system. The methods are also useful for the prophylactic or therapeutic treatment of human or animal disease. For example, the methods are useful for pediatric and veterinary vaccine applications. [0099] In a fourth aspect, the invention provides methods for therapeutically treating a patient having a disease or disorder, such methods comprising administering to the patient a IRO compound according to the invention. In various embodiments, the disease or disorder to be treated is cancer, an autoimmune disorder, airway inflammation, inflammatory disorders, infectious disease, malaria, Lyme disease, ocular infections, conjunctivitis, skin disorders, psoriasis, scleroderma, cardiovascular disease, atherosclerosis, chronic fatigue syndrome, sarcoidosis, transplant rejection, allergy, asthma or a disease caused by a pathogen. Pathogens include bacteria, parasites, fungi, viruses, viroids and prions. Preferred viruses include DNA or RNA virus such as, but not limited to, double stranded DNA viruses (for example Herpesviruses, Poxviruses, Hepadnaviruses), single-stranded DNA viruses (for example Parvoviruses), single stranded RNA viruses (for example Picornaviruses, Togaviruses, Orthomyanviruses and Rhabdoviruses) and those listed in Table 5. Administration is carried out as described for in the third aspect of the invention.

[00100] In a fifth aspect, the invention provides methods for preventing a disease or disorder, such methods comprising administering to the patient IRO compound according to the invention. In various embodiments, the disease or disorder to be prevented is cancer, an autoimmune disorder, airway inflammation, inflammatory disorders, infectious disease, malaria, Lyme disease, ocular infections, conjunctivitis, skin disorders, psoriasis, scleroderma, cardiovascular disease, atherosclerosis, chronic fatigue syndrome, sarcoidosis, transplant rejection, allergy, asthma or a disease caused by a pathogen. Pathogens include bacteria, parasites, fungi, viruses, viroids and prions. Preferred viruses include DNA or RNA virus such as, but not limited to, those listed in Table 5. Administration is carried out as described for the third aspect of the invention.

[00101] In any of the methods according to this aspect of the invention, the

IRO compound can be administered in combination with any other agent useful for treating the disease or condition that does not diminish the immune modulatory effect of the IRO compound. In any of the methods according to the invention, the agent useful for treating the disease or condition includes, but is not limited to, one or more vaccines, antigens, antibodies, cytotoxic agents, allergens, antibiotics, antisense oligonucleotides, TLR agonist, TLR antagonist, peptides, proteins, gene therapy vectors, DNA vaccines, adjuvants, antiviral agents, antimalarial drugs (for example chloroquine and hydroxychloroquine) or kinase inhibitors to enhance the specificity or magnitude of the immune response, or co -stimulatory molecules such as cytokines, chemokines, protein ligands, trans-activating factors, peptides and peptides comprising modified amino acids. For example, in the treatment of cancer, it is contemplated that the IRO compound may be administered in combination with one or more chemotherapeutic compound, targeted therapeutic agent and/or monoclonal antibody. Alternatively, the agent can include DNA vectors encoding for antigen or allergen. In these embodiments, the IRO compounds of the invention can variously act as adjuvants and/or produce direct immune modulatory effects. [00102] The following examples are intended to further illustrate certain exemplary embodiments of the invention and are not intended to limit the scope of the invention. For example, representative TLR-ligands are shown in the following examples, but do not limit the scope of ligands to which the IROs of the invention act as antagonists.

Example 1

Synthesis of Oligonucleotides Containing Immune regulatory Moieties. [00103] All IRO were synthesized according to standard procedures (see e.g.

U.S. Patent Publication No. 20040097719).

[00104] Oligonucleotides were synthesized on a 1 μM scale using an automated DNA synthesizer (Expedite 8909; PerSeptive Biosystems, Framingham, Mass.), following standard linear synthesis or parallel synthesis procedures (see e.g. FIGS. 5 and 6 of U.S. Patent Publication No. 20040097719).

[00105] Deoxyribonucleoside phosphoramidites were obtained from (Aldrich-

Sigma, St Louis, Mo). r,2'-dideoxyribose phosphoramidite, propyl- 1- phosphoramidite, 2-deoxyuridine phosphoramidite, l,3-bis-[5-(4,4'- dimethoxytrityl)pentylamidyl]-2-propanol phosphoramidite and methyl phosponamidite were obtained from Glen Research (Sterling, Va.). .beta.-L-2'- deoxyribonucleoside phosphoramidite, .alpha.-2'-deoxyribonucleoside phosphoramidite, mono-DMT-glycerol phosphoramidite and di-DMT-glycerol phosphoramidite were obtained from ChemGenes (Willmington, Mass.). (4- Aminobutyl)- 1,3 -propanediol phosphoramidite was obtained from Clontech (Palo Alto, Calif). Arabinocytidine phosphoramidite, arabinoguanosine, arabinothymidine and arabinouridine were obtained from Reliable Pharmaceutical (St. Louis, Mo.). Arabinoguanosine phosphoramidite, arabinothymidine phosphoramidite and arabinouridine phosphoramidite were synthesized at Idera Pharmaceuticals, Inc. (Cambridge, Mass.) (Noronha et al. (2000) Biochem., 39:7050-7062). [00106] All nucleoside phosphoramidites were characterized by ³¹P and ¹H

NMR spectra. Modified nucleosides were incorporated at specific sites using normal coupling cycles. After synthesis, oligonucleotides were deprotected using concentrated ammonium hydroxide and purified by reverse phase HPLC, followed by dialysis. Purified oligonucleotides as sodium salt form were lyophilized prior to use. Purity was tested by CGE and MALDI-TOF MS.

Example 2

Inhibition of TLR9 stimulation

[00107] HEK293 cells stably expressing TLR9 (Invivogen) were transiently transfected with reporter gene, Seap, (Invivogen) for 6 hr. Cells were treated with 0.5 μg/ml 5 '-CTATCTGACGTTCTCTGT-S ' (mouse CpG sequence; IMO/SEQ ID NO 1 ; 0 dose) alone and various concentrations of IRO 5 or 6 for 18 hr. TLR9-dependent reporter gene expression was determined according to the manufacturer's protocol (Invivogen) and the results are expressed as % activity of TLR9 stimulating oligonucleotide (100%). The results are shown in Figure 1. These results demonstrate that IRO 5 inhibited TLR9 agonistic activity of IMO.

Example 3

IRQ specifically inhibit TLR9 stimulation

[00108] HEK293 cells stably expressing TLR9 or TLR3 (Invivogen) were transiently transfected with reporter gene, Seap, (Invivogen) for 6 hr. Cells were treated with 0.5 mg/ml IMOl (0.5 μg/ml), IRO 5 (2.0 μg/ml), R848 (5.0 μg/ml), or poly (I).poly(C) (0.5 μg/ml) and combinations of IMO+IRO, R848+IRO, or poly(I).poly(C)+IRO for 18 hr. TLR9- or TLR3 -dependent reporter gene expression was determined according to the manufacturer's protocol (Invivogen) and the results are expressed as fold change in NF-kB activity. The results are shown in Figure 2. These results demonstrate that IRO 5 inhibits the activity of the TLR9 agonist but not agonist of TLR3, and more generally that IRO 's can selectively inhibit TLR activation.

Example 4

Dose-dependent inhibition by IRQ

[00109] C57BL/6 mice were injected subcutaneously (s.c.) at left underarm with 0.25 mg/kg stimulating 5 '-TCTGACG₁TTCT-X₂-TCTTG₁CAGTCT-S ' (IMO/SEQ ID NO 3; Gi=7-deazaG, X=glycerol) and different doses of IRO 5 at right under arm. Serum samples were taken at 2 hours after IMO3 injection and determined IL- 12 levels by ELISA. The results are shown in Figure 3. These results demonstrate dose-dependent inhibition by IRO.

Example 5

Time-dependence inhibition by IRQ

[00110] C57BL/6 mice were injected s.c. at left underarm with 0.25 mg/kg stimulating IMO 3 and 1 mg/kg IRO 5 or 5 '-CTATCTCACCTTCTCTGT-S ' (non- CpG non-stimulatory control; oligo/SEQ ID NO 4) at right under arm either one hour before (-Ih) or at the same time as stimulating IMO (Oh). Serum samples were taken at 2 hours after IMO injection and determined IL- 12 levels by ELISA. The results in Figure 4 A demonstrate a decrease in serum IL- 12 levels after administration of IRO 5 or (oligo 4) either one hour before (-Ih) or at the same time as stimulating IMO (Oh). [00111] C57BL/6 mice were injected s.c. at left underarm with 0.25 mg/kg stimulating IMO 3 and intranasal administration of 10 mg/kg IRO 101 at the same time as stimulating IMO (Oh). Serum samples were taken at 2 hours after stimulating IMO injection and determined IL- 12 levels by ELISA. The results in Figure 4B demonstrate a decrease in serum IL- 12 levels after intranasal administration of IRO 99 at the same time as s.c. of IMO.

[00112] C57BL/6 mice were injected s.c at left underarm with 0.25 mg/kg stimulating IMO 3 and 2 mg/kg or 10 mg/kg IRO 17, 99, 99 s.c. at right under arm either one hour before (-Ih), twenty- four hours before (-24) or seventy-two hours before (-72) as stimulating IMO (Oh). Serum samples were taken at 2 hours after stimulating IMO injection and determined IL- 12 levels by ELISA. The results are shown in Figure 4C-D. These results demonstrate pre-administration and simultaneous administration of IRO was able to inhibit agonist of TLR9, and more generally that IRO 's can inhibit TLR activation.

Example 6

Inhibition of TLR9 stimulation

[00113] C57BL/6 mice were injected s.c. at left underarm with 0.25 mg/kg stimulating IMO 3 and 1 mg/kg IRO 21 or control oligo 4 at right under arm either one hour before (-Ih) or at the same time as stimulating IMO (Oh). Serum samples were taken at 2 hours after stimulating IMO injection and determined IL- 12 levels by ELISA. The results are shown in Figure 5A and 5B. These results demonstrate that a CpG oligonucleotide linked at its 5' ends show inhibitory properties, and more generally that immune stimulatory CpG oligonucleotides linked at their 5 ' ends can inhibit TLR activation.

Example 7

Inhibition of TLR9 in human cell cultures

[00114] Human pDCs and PBMCs were incubated with 10 ug/ml 5 '-

CTATCTGTCGTTCTCTGT-3' (human CpG sequence; IMO/SEQ ID NO 2) and 40 ug IROlO for 24 hr. The results are shown in Figure 6. These results demonstrate that an IRO inhibited TLR9 agonist activity in human cell cultures, and more generally that IROs can inhibit TLRs in human cells.

Example 8

IRQ effect on OVA induced Th2 immune response

[00115] The results are shown in Figure 7. These results demonstrate that an

IRO does not have an effect on Ovalbumin ("OVA") induced Th2 immune responses, whereas IMO compounds reduce OVA induced Th2 response and cause the production of ThI cytokines. Example 9

IRQ inhibition of IMO effects on ThI and Th2 immune responses [00116] The results are shown in Figure 8. These results demonstrate that an

IRO can reverse Th2 inhibitory properties and can inhibit ThI immune responses induced by IMO.

Example 10

Antibody responses to IMO and IRQ

[00117] Mice were immunized with HBsAg in the presence and absence of

IMO 1 and IRO 5 or SEQ ID NO. 6 and combinations thereof at wk 0 and wk 2 and antibody responses were measured wk 4. The results are shown in Figure 9 and demonstrate reduction by an IRO on an IMO induced IgG2A immune response.

Example 11

Inhibition of immune stimulatory oligonucleotides

[00118] HEK293 cells stably expressing TLR9 (Invivogen) were transiently transfected with reporter gene, Seap, (Invivogen) for 6 hr. Cells were treated with 0.25 μg/ml IMO alone (IMOl; 0 dose) and various concentrations of IROs for 18 hr. TLR9-dependent reporter gene expression was determined according to the manufacturer's protocol (Invivogen) and the results are expressed as % inhibition of immune stimulating oligonucleotide activity. The results are shown in Tables 6 and 7 below. These results demonstrate that IROs inhibited activity of IMO.

Table 6. Percent inhibition of immune stimulatory oligonucleotide 1. IMOl concentration was 0.25 μg/ml and IRO concentration was 2 μg/ml

IROs containing various modifications inhibit NF-κB activation of IMO in HEK293 cells expressing TLR9, and more generally IROs containing various modifications can inhibit NF -KB activation of IMO.

IROs containing various modifications inhibit NF-κB activation of IMO in HEK293 cells expressing TLR9, and more generally IROs containing various modifications can inhibit NF-κB activation of IMO.

Example 12

Time-dependence inhibition by IRQ

[00119] C57BL/6 mice were injected subcutaneously (s.c.) at left underarm with 0.25 mg/kg to 10 mg/kg TLR agonist and 1 mg/kg to 20 mg/kg IRO 5, 17 or 37 or 5 '-TCCTGGCGGGGAAGT-S ' (poly dG control; oligo/SEQ ID NO 49) at right under arm at one hour (-Ih) or up to forty-eight hours (-48) before or at the same time as TLR agonist (Oh). Serum samples were taken at 2 hours after stimulating IMO injection and determined IL-12 levels by ELISA. The results are shown in Tables 8- 23 below. These results demonstrate that both pre-administration and simultaneous administration of an IRO inhibits agonists of TLR9, and that the inhibitory activities of an IRO were effective even when administered 48 hours prior to the administration of the IMO. More generally, these results demonstrate that pre-administration and simultaneous administration of an IRO can both inhibit TLR agonists and that the inhibitory activities of an IRO can be seen even when administered many hours prior to the administration of the TLR agonist.

Example 13

Short-term and Long-term blocking activities of IRQ against TLR agonist [00120] To assess the short term activity and selectivity of IRO compounds, mice were subcutaneously injected with 2 mg/kg IRO in their right flank one hour (- Ih) before subcutaneous administration of a TLR agonist to the left flank. Serum samples were taken at 2 hours after administration of the TLR agonist and were analyzed using multiple cytokine/chemokine detecting Luminex kits obtained from Biosource (Camarillo, CA). Manufacture recommended protocols were followed. Cytokine/chemokine values were determined from mean values falling on the standard curve determined on a Luminex 100 instrument. Luminex analysis was performed using STarStation software (Applied Cytometry Systems, Sacramento, CA). The following representative agonists were used at the indicated dose: 5'- TCTGACG₁TTCT-X₂-TCTTG₁CAGTCT-S ' (SEQ ID NO. 3; TLR9 agonist; 0.25 mg/kg, Gi=7-deaza-dG), R848 (TLR7/8 agonist, 0.1 mg/kg), Loxoribine (TLR7 agonist, 100 mg/kg), Flagellin (TLR5 agonist, 0.25 mg/kg), LPS (TLR4 agonist, 0.25 mg/kg), Polyl.PolyC (TLR3 agonist, 20 mg/kg), and MALP-2 (TLR2 agonist, 0.5 mg/kg). The results are shown in Figures 10-12. These data demonstrate that IROs can inhibit cytokine/chemokine production in response to TLR agonists. The effect is greater for intracellular TLRs (e.g. TLR3, TLR7, TLR8, and TLR9) as compared to extracellular TLRs (e.g. TLR2, TLR4, and TLR5).

[00121] To assess the long-term activity and selectivity of IRO compounds, mice were subcutaneously injected with 10 mg/kg IRO in their right flank seventy- two hours (-72h) before subcutaneous administration of a TLR agonist (as described above) to the left flank. Serum samples were taken at 2 hours after administration of the TLR agonist and were analyzed as described above. The results are shown in Figures 13-15. These results demonstrate pre-administration administration of an IRO was able to inhibit TLR agonist, and that the inhibitory activities of IRO were effective even when administered 72 hours prior to the administration of the agonist.

Example 14

Antiviral Activity of IRQ in PBMC HIV Assay

[00122] Fresh human PBMCs, seronegative for HIV and HBV, were isolated from donors and treated with phytohemagglutinin (PHA). Following PHA treatment, the cells were plated in a 96 well round bottom microplate at 5 x 104 cells/well in triplicate. The cells were infected by placing 50 μL of a HIV-I virus stock in each test well (final MOI approximately 0.1). After infection with HIV-I, the PBMCs were incubated in the presence of increasing concentrations of IRO for seven days at 37⁰C, 5% CO₂. Cell-free supernatants were then collected for analysis of reverse transcriptase activity. The results are shown in Figure 16. These results demonstrate that administration of IRO following HIV-I infection will reduce the amount of virus present. More generally, the results demonstrate that administration of IRO following pathogen or viral infection will reduce the amount of pathogen or virus present.

Example 15

Antiviral Activity of IRQ Plus AZT in PBMC HIV Assay

[00123] Fresh human PBMCs, seronegative for HIV and HBV, were isolated from donors and treated with phytohemagglutinin (PHA). Following PHA treatment, the cells were plated in a 96 well round bottom microplate at 5 x 104 cells/well in triplicate. The cells were infected by placing 50 μL of a HIV-I virus stock in each test well (final MOI approximately 0.1). Prior to infection with HIV-I , PBMCs were pretreated with IRO for two hours. After IRO pretreatment and infection, the PBMCs were incubated in the presence of increasing concentrations of AZT for seven days at 37⁰C, 5% CO₂. Cell-free supernatants were then collected for analysis of reverse transcriptase activity. The results are shown in Figure 17. These results demonstrate that the combination of antagonist plus AZT is more efficient in controlling HIV-I infection than AZT alone. These results demonstrate that pretreatment with IRO increased the potency of AZT against HIV-I . More generally, the results demonstrate that administration of IRO prior to pathogen or viral infection enhances the activity of antiviral compounds. In addition, the results generally demonstrate that administering an IRO prior to pathogen or viral infection can decrease the amount of virus present following infection.

Claims

What is claimed is:

1. A method for therapeutically treating a vertebrate having a disease caused by a pathogen mediated by a TLR, wherein the pathogen is selected from the group consisting of 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 metapneumovirus, 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 and Venezuelan equine encephalitis virus, such method comprising administering to the mammal an IRO compound in a pharmaceutically effective amount wherein the IRO contains less than 3 consecutive guanosine nucleotides.

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. A method for preventing a disease caused by a pathogen mediated by a TLR, wherein the pathogen is selected from the group consisting of 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 metapneumovirus, 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 and Venezuelan equine encephalitis virus, such method comprising administering to the mammal an IRO compound in a pharmaceutically effective amount wherein the IRO contains less than 3 consecutive guanosine nucleotides.

5. The method according to claim 4, 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, antiviral agents or co-stimulatory molecules.

6. The method according to claim 4 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.

7. The method according to claim 1, wherein the IRO compound comprises the structure

5-N_m - N₃N₂N₁CGN¹N²N³ - N^m -3 ' : wherein:

CG is an oligonucleotide motif and C is cytosine or a pyrimidine nucleotide derivative or non-nucleotide linkage, and G is guanosine a purine nucleotide derivative or non-nucleotide linkage;

N₁-N₃ and N^!-N³, at each occurrence, is independently a nucleotide, nucleotide derivative or non-nucleotide linkage;

N_m and N^m, at each occurrence, is independently a nucleotide, nucleotide derivative or non-nucleotide linkage; provided that at least one N₁ to N3 and/or C and/or G is a nucleotide derivative or non-nucleotide linkage; wherein the oligonucleotide motif would be immune stimulatory but for the nucleotide derivative or non-nucleotide linkage; and wherein m is a number from 0 to about 30.

8. The method according to claim 4, wherein the IRO compound comprises the structure

5-N_m - N₃N₂N₁CGN¹N²N³ - N^m -3 ' : wherein:

CG is an oligonucleotide motif and C is cytosine or a pyrimidine nucleotide derivative or non-nucleotide linkage, and G is guanosine a purine nucleotide derivative or non-nucleotide linkage;

N₁-N₃ and N^!-N³, at each occurrence, is independently a nucleotide, nucleotide derivative or non-nucleotide linkage;

N_m and N^m, at each occurrence, is independently a nucleotide, nucleotide derivative or non-nucleotide linkage; provided that at least one N₁ to N₃ and/or C and/or G is a nucleotide derivative or non-nucleotide linkage; wherein the oligonucleotide motif would be immune stimulatory but for the nucleotide derivative or non-nucleotide linkage; and wherein m is a number from 0 to about 30.