(12) United States Patent (10) Patent No.: US 7.427.405 B2 Agrawal Et Al

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(12) United States Patent (10) Patent No.: US 7.427.405 B2 Agrawal Et Al USOO7427405B2 (12) United States Patent (10) Patent No.: US 7.427.405 B2 Agrawal et al. (45) Date of Patent: Sep. 23, 2008 (54) IMMUNOSTIMULATORY Tokunaga et al., “Antitumor Activity of Deoxyribonucleic Acid Frac OLGONUCLEOTDE MULTIMERS tion from Mycobaterium bovis BCG. I. Isolation. Physicochemical Characterization, and Antitumor Activity”. J. Natl. Cancer Inst. 72: (75) Inventors: Sudhir Agrawal, Shrewsbury, MA (US); 955-962(1984). Pisetsky et al., “Stimulation of in vitro proliferation of murine lym Ekambar Kandimala, Southboro, MA phocytes by synthetic oligodeoxynucleotides'. Molecular Biology (US); Dong Yu, Westboro, MA (US) Reports 18:217-221 (1993). Krieg et al., “CpG motifs in bacterial DNA trigger direct B-cell (73) Assignee: Idera Pharmaceuticals, Inc., activation”, Nature 374: 546-549 (1995). Cambridge, MA (US) Sato et al., “Immunostimulatory DNA Sequence Necessary for Effective Intradermal Gene Immunization', Science 273: 352-354 (*) Notice: Subject to any disclaimer, the term of this (1996). patent is extended or adjusted under 35 Krieg et al., “CpG Motifs in Bacterial DNA and their Immune U.S.C. 154(b) by 209 days. Effects”, Annu. Rev. Immunol. 20: 709-760 (2002). Dalpke et al., “Immunopharmacology of CpG DNA'. Biol. Chem. (21) Appl. No.: 11/174,282 383: 1491-1500 (2002). Kandimala et al., “Towards Optimal Design of Second-Generation (22) Filed: Jul. 1, 2005 Immunomodulatory Oligonucleotides'. Curr. Opin. Mol. Ther. 4(2): 122-129 (2002). (65) Prior Publication Data Kandimala et al., “Immunomers-novel 3'-3'-Linked CpG Oligodeoxyribonucleotides as Potent Immunomodulatory Agents'. US 2006/OO19919 A1 Jan. 26, 2006 Nucleic Acids Res. 30: 4460-4469 (2002). Kandimala et al. “Secondary Structures in CpG Oligonucleotides Related U.S. Application Data affect Immunostimulatory Activity”. Biochem. Biophys. Res. Com mun. 306:948-953 (2003). (63) Continuation of application No. 10/892,550, filed on Remington's Pharmaceutical Sciences, 18th Edition, ed. A. Gennaro, Jul. 15, 2004, and a continuation of application No. Mack Publishing Co., Easton, PA, 1990, ISBN: 0-912734-04-3. 11/153,054, filed on Jun. 15, 2005. Burgstaller, P. et al., "Aptamers and AptaZymes: Accelerating Small (60) Provisional application No. 60/579,985, filed on Jun. Molecule Drug Discovery'. Curr Opin Drug Discov Devel. 5(5): 15, 2004, provisional application No. 60/599,362, 690-700 (2002). Iyer R.P. et al., “3H-1,2-Benzodithiole-3-one 1,1-Dioxide as an filed on Aug. 6, 2004. Improved Sulfurizing Reagent in the Solid-Phase Synthesis of Oligodeoxyribonucleoside Phosphorothioates'. J. Am. Chem. Soc. (51) Int. Cl. 112: 1253-1254 (1990). A6 IK 39/00 (2006.01) Zhao, Q., et al., “Effect of Different Chemically Modified C7H 2L/02 (2006.01) Oligodeoxynucleotides on Immune Stimulation'. Biochem (52) U.S. Cl. ................. 424/277.1; 424/277.1536/23.1 Pharmacol. 51: 173-182 (1996). (58) Field of Classification Search .............. 424/277.1; Branda, R.F., et al., “Immune Stimulation by an antisense oligomer 536/23.1 complementary to the rev Gene of HIV-1'. Biochem. Pharmacol. See application file for complete search history. 45(10): 2037-2043 (1993). Bhagat L., et al., "CpG penta- and Hexadeoxyribonucleotides as (56) References Cited potent immunomodulatory agents'. Biochem. BiophyS. Res. Com mun. 300: 853-861 (2003). U.S. PATENT DOCUMENTS Hemmi H., et al., “A Toll-Like Receptor Recognizes Bacterial DNA'. 5,366,878 A 11/1994 Pederson et al. Nature 408: 740–745 (2000). 5,635,377 A 6, 1997 Pederson et al. Yi A.K., et al., “Rapid Induction of Mitogen-Activated Protein 5,652,355 A 7, 1997 Metelev et al. Kinases by Immune Stimulatory CpG DNA'. J. Immunol. 161:4493 5,912,332 A 6/1999 Agrawal et al. 4497 (1998). 6,143,881 A 11/2000 Metelev et al. Stacey, K.J., et al., “Macrophages Ingest and Are Activated by Bac 6,346,614 B1 2/2002 Metelev et al. terial DNA”, J. Immunol. 157: 21 16-2122 (1996). Yu D., et al., “Potent CpG Oligonucleotides Containing OTHER PUBLICATIONS Phosphodiester Linkages: in vitro and in vivo immunostimulatory properties”. Biochem. Biophys. Res. Commun. 297: 83-90 (2002). Moldoveanu et al (Vaccine 16:1216-1224, 1998).* Kuramoto etal (Jpn. J. Cancer Res. 83:1128-1131, 1992).* * cited by examiner Krieg etal (Nature 371:546-549, 1995).* Liang etal (J. Clin. Invest. 98: 1119-1129, 1996).* Primary Examiner Brandon J Fetterolf McCluskie and Davis (J. Immunol. 161:4463-4466, 1998).* (74) Attorney, Agent, or Firm—Keown & Zucchero, LLP: Baral et al (Cancer Immunol. Immunother. 52(3):317-327, 2003).* Wayne A. Keown; Joseph C. Zucchero Kandimala et al (Bioconjugate Chem. 13, 966-974, 2002; Nucleic Acid Research vol. 31, No. 9, 2003).* (57) ABSTRACT Kandimala et al (PNAS 100(24): 14303-14308, 2003).* Donnelly et al (Nature Medicine, 9(11): 1354-1356, 2003).* The invention provides an immunostimulatory nucleic acid. DeGruijl et al. Nature Medicine, 51.10: 1124-1125, 1999.* Bitton R.J. (Current Opinion in Molecular Therapeutics 611: 17-26, In certain embodiments according to this aspect of the inven 2004).* tion, the sequence of the immunostimulatory oligonucleotide Weiner (J. Leukoc. Biol. 68: 455-463, 2000).* and/or immunomer is at least partially self-complementary. Ballas et al (J. Immunol. 167: 4878-4886, 2001).* Agrawaletal (Trends in Molecular Medicine 8(3): 114-120, 2002).* 7 Claims, 6 Drawing Sheets U.S. Patent Sep. 23, 2008 Sheet 1 of 6 US 7.427.405 B2 U.S. Patent Sep. 23, 2008 Sheet 2 of 6 US 7.427.405 B2 U.S. Patent US 7.427.405 B2 U.S. Patent US 7.427.405 B2 U.S. Patent Sep. 23, 2008 Sheet 6 of 6 US 7.427.405 B2 US 7,427,405 B2 1. 2 IMMUNOSTIMULATORY ythymidine, 1-(2'-deoxy-f-D-ribofuranosyl)-2-oxo-7-deaza OLGONUCLEOTDE MULTIMERS 8-methyl-purine, 2-dideoxy-5-halocytosine, 2'-dideoxy-5- nitrocytosine, arabinocytidine, 2'-deoxy-2-substituted RELATED APPLICATIONS arabinocytidine, 2'-O-substituted arabinocytidine, 2'-deoxy 5-hydroxycytidine, 2'-deoxy-N4-alkyl-cytidine, 2'-deoxy-4- This application is a continuation-in-part of U.S. patent thiouridine, or other pyrimidine nucleoside analogs, G is application Ser. No. 10/892,550, filed Jul. 15, 2004 and a 2'-deoxy-7-deazaguanosine, 2'-deoxy-6-thioguanosine, ara continuation of U.S. patent application Ser. No. 1 1/153,054, binoguanosine. 2'-deoxy-2'substituted-arabinoguanosine, filed Jun. 15, 2005, which claims the benefit of U.S. Provi 2'-O-substituted-arabinoguanosine. 2'-deoxyinosine, or other sional Application Ser. No. 60/579,985, filed Jun. 15, 2004, 10 purine nucleoside analogs, and p is an internucleoside linkage and U.S. Provisional Application Ser. No. 60/599,362, filed selected from the group consisting of phosphodiester, phos on Aug. 6, 2004. The entire teachings of the above-referenced phorothioate, and phosphorodithioate. Applications are incorporated herein by reference. In Some embodiments, the immunostimulatory nucleic acid is from about 2 to about 50 nucleotides in length. In BACKGROUND OF THE INVENTION 15 certain embodiments the immunostimulatory nucleic acid is from about 12 to about 26 nucleotides in length. In some 1. Field of the Invention embodiments, the oligonucleotides each have from about 3 to The invention relates to immune stimulation by oligo about 35 nucleoside residues, in further embodiments from nucleotide analogs. about 4 to about 30 nucleoside residues, in even further 2. Summary of the Related Art embodiments from about 4 to about 20 nucleoside residues. Tokunaga et al., J. Natl. Cancer Inst. 72 (1984) 955-96. In some embodiments, the oligonucleotides have from about Pisetsky et al.; Reich et al., Mol. Biol. Rep. 18 (1993) 217 5 to about 18, or from about 5 to about 14, nucleoside resi 221; Krieg et al., Yi et al., Nature 374 (1995) 546-549 and dues. As used herein, the term “about implies that the exact Sato et al., Science 273 (1996) 352-354 teach that bacterial number is not critical. Thus, the number of nucleoside resi DNA, synthetic oligodeoxynucleotides, and DNA vaccines 25 dues in the oligonucleotides is not critical, and oligonucle containing unmethylated CpG-dinucleotides in specific otides having one or two fewer nucleoside residues, or from sequence contexts (CpG DNA) activate the vertebrate one to several additional nucleoside residues are contem immune system. plated as equivalents of each of the embodiments described Krieg et al., Annu. Rev. Immunol. 20 (2002) 709-760; above. In some embodiments, one or more of the oligonucle Dalpke et al., Biol. Chem. 383 (2002) 1491-1500 and Kan 30 otides have 11 nucleotides. dimala et al., Curr. Opin. Mol. Ther. 4 (2002) 122-129 teach In a second aspect the invention provides an immunomer that CpG DNAS induce innate immune cells to produce Th1 comprising at least two oligonucleotides linked by a non cytokines that promote cytotoxic T lymphocyte (CTL) nucleotide linker, wherein the sequences of the immuno responses and production of immunoglobulins by B cells. stimulatory oligonucleotides are at least partially self The immunostimulatory properties of CpG DNAs have 35 complementary. In certain embodiments according to this allowed their use as therapeutic agents for a broad spectrum aspect of the invention at least one of the oligonucleotides of disease indications including cancers, viral and bacterial contains at least one dinucleotide selected from the group infections, inflammatory disorders and as adjuvant in immu consisting of CpG, CpG, CpG* and CpG*, wherein C is notherapy. cytidine or 2'-deoxycytidine, G is guanosine or 2'-deoxygua In addition to chemical modifications, a number of struc 40 nosine, C* is 2'-deoxythymidine, 1-(2'-deoxy-f-D-ribofura tural modifications influenced the activity of CpG DNAs. nosyl)-2-oxo-7-deaza-8-methyl-purine, 2-dideoxy-5-halo Kandimalla et al., Nucleic Acids Res.
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