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(12) United States Patent (10) Patent No.: US 9,669,108 B2 Williams Et Al

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(12) United States Patent (10) Patent No.: US 9,669,108 B2 Williams Et Al USOO9669.108B2 (12) United States Patent (10) Patent No.: US 9,669,108 B2 Williams et al. (45) Date of Patent: Jun. 6, 2017 (54) MEDITOPES AND MEDITOPE-BINDING (56) References Cited ANTIBODIES AND USES THEREOF U.S. PATENT DOCUMENTS (71) Applicant: City of Hope, Duarte, CA (US) 7.754,853 B2 7/2010 Hellendoorn et al. 8,592,149 B2 11/2013 Ramakrishnan (72) Inventors: John C. Williams, Monrovia, CA (US); 8,658,774 B2 2/2014 Williams et al. David A. Horne, Duarte, CA (US); 2004/0001842 A1 1/2004 Michaeli ............ A61K 39,0005 Yuelong Ma, Duarte, CA (US); Heng 2004, OO67503 A1 4, 2004 Tan et all 424,185.1 Wei Chang, Foster City, CA (US); 2005, OO42664 A1 2/2005 Wua etC al.a. Joshua M. Donaldson, Lumberton, NJ 2005, OO69549 A1 3/2005 Herman (US); Cindy Zer, Duarte, CA (US); 2005/026O711 A1 11/2005 Datta et al. Krzysztof Bzymek, Pasadena, CA 2008, OO38260 A1 2/2008 Ponath et al. (US); Kendra N. Avery Pasadena, CA 39925. A 299 ElC a (US); Jun Xie, Duarte, CA (US) 2009/0202568 A1 8/2009 Eriksson et al. 2010.0068135 A1 3/2010 Rock (73) Assignee: City of Hope,s Duarte,s CA (US) 2010/0076178 A1 3/2010 Ghayur et al. (*) Notice: Subject to any disclaimer, the term of this FOREIGN PATENT DOCUMENTS patent is extended or adjusted under 35 U.S.C. 154(b) by 0 days. WO WO-96.40210 12/1996 WO WOO 132207 A1 * 5, 2001 ........ A61K 39,385 WO WO-O2/O72832 9, 2002 (21) Appl. No.: 14/453,586 WO WO-2004/101790 11 2004 WO WO-2005/056606 6, 2005 (22) Filed: Aug. 6, 2014 WO WO-2007/O19541 2, 2007 WO WO-2009/062051 5, 2009 (65) Prior Publication Data WO WO 2009099651 A1 * 8, 2009 ......... A61K 31/44 WO WO-2010, 114940 10, 2010 US 2015/OO30535 A1 Jan. 29, 2015 OTHER PUBLICATIONS Related U.S. Application Data Riemer et al., Journal of the National Cancer Institute, 2005, (60) Division- - - of application No. 13/443,804, filed O Apr. Carter97(22): et 1663-1670.* al., Endocrine-Related Cancer, 2004, 11:659-687. 10, 2012, now Pat. No. 8,962,804, which is a Albanell et al., “Trastuzumab, a humanized anti-HER2 monoclonal continuation-in-part of application No. 13/270.207, antibody, for the treatment of breast cancer.” Drugs Today (Barc) filed on Oct. 10, 2011, now Pat. No. 8,658,774. (1999) 35(12):931-946. International Preliminary Report on Patentability for PCT/US2011/ 55656 issued Jun. 4, 2013, 8 pages. (60) Provisional application No. 61/391,558, filed on Oct. Notice of the First Office Action (including translation) for CN 8, 2010, provisional application No. 61/597,708, filed 201280060888.7, mailed Jul. 17, 2015, 24 pages. on Feb. 10, 2012. Smith et al., Sequence of the full-length immunoglobulin kappa chain of mouse myeloma MPC 11, Biochem. J. (1978) 171:337-347. (51) Int. Cl. Supplementary European Search Report for EP 11831753.6, mailed May 12, 2015, 9 pages. C07K 6/8 (2006.01) Supplementary European Search Report for EP 12839868.2, mailed C07K 700 (2006.01) May 12, 2015, 10 pages. A6 IK 47/48 (2006.01) Accardi et al., “Antibodies in single-chain format against tumour A6 IK 38/00 (2006.01) associated antigens: present and future applications.” Curr Med A6 IK 39/00 (2006.01) Chem (2010) 17(17): 1730-1755. A6 IK 5L/It (2006.01) Adams et al., “High affinity restricts the localization and tumor C07K 6/28 (2006.01) penetration of single-chain fiv antibody molecules, Cancer Res C07K 6/32 (2006.01) (2001) 61(12):4750-4755. B825/00 (2011.01) (Continued) (52) U.S. Cl. CPC. A61K 47/48746 (2013.01); A61K 47/48346 Primary Examiner — Hong Sang (2013.01); A61K 47/48669 (2013.01); A61 K (74) Attorney, Agent, or Firm — Sheppard Mullin Richter 51/1087 (2013.01); B82Y5/00 (2013.01); & Hampton LLP C07K 16/18 (2013.01); C07K 16/2863 (2013.01); C07K 16/32 (2013.01); C07K (57) ABSTRACT 2299/00 (2013.01); C07K 23.17/34 (2013.01); Antibodies and meditopes that bind to the antibodies are C07K 2317/40 (2013.01); C07K 231 7/55 provided, as well as complexes, compositions and combi (2013.01); C07K 231 7/567 (2013.01); C07K nations containing the meditopes and antibodies, and meth 2317/622 (2013.01); C07K 2317/92 (2013.01) ods of producing, using, testing, and Screening the same, (58) Field of Classification Search including therapeutic and diagnostic methods and uses. None See application file for complete search history. 8 Claims, 76 Drawing Sheets US 9,669.108 B2 Page 2 (56) References Cited Chung et al., “Cetuximab-induced anaphylaxis and IgE specific for galactose-alpha-1,3-galactose." N Eng J Med (2008) 358(11): 1109 1117. OTHER PUBLICATIONS Collis et al., “Analysis of the antigen combining site: correlations between length and sequence composition of the hypervariable Adams et al., “PHENIX: Building new software for automated loops and the nature of the antigen.” J Mol Biol (2003)325(2):337 354. crystallographic structure determination.” Acta Crystallogr D Biol Colman, “Effects of amino acid sequence changes on antibody Crystallogr (2002) 58:1948-1954. antigen interactions.” Res Immunol (1994) 145:33-36. 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Derksen et al., “Antimicrobial leucocin analogues with a disulfide Alley et al., “Antibody-drug conjugates: targeted drug delivery for bridge replaced by a carbocycle or by noncovalent interactions of cancer.” Curr Opin Chem Biol (2010) 14(4):529-537. allyl glycine residues,” J Am Chem Soc (2006) 128(44): 14252 Auffinger et al., “Halogen bonds in biological molecules.” Proc Natl 14253. Acad Sci USA (2004) 101(48): 16789-16794. Donaldson et al., “Design and development of masked therapeutic Beck et al., “Trends in glycosylation, glycoanalysis and antibodies to limit off-target effects: application to anti-EGFR glycoengineering of therapeutic antibodies and Fc-fusion proteins.” antibodies.” Cancer Biol Ther (2009) 8(22):2147-2152. Curr Pharm Biotechnol (2008) 9(6):482-501. Donaldson et al., “Identification and grafting of a unique peptide Beck et al., “Strategies and challenges for the next generation of binding site in the Fab framework of monoclonal antibodies.” Proc therapeutic antibodies.” Nat Rev Immunol (2010) 10(5):345-352. Natl AcadSci USA (2013) 110(43): 17456-17461 (Published online Bendig, “Humanization of rodent monoclonal antibodies by CDR before print Oct. 7, 2013, doi:10.1073/pnas. 1307309110, supple grafting” Methods: A Companion to Methods in Enzymology mental information included, 38 pages). (1995) 8:83-93. 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Clin Oncol (2009). 27(5):663-671. antibody Rituximab,” J Biol Chem (2007) 282(20): 15073-15080. Bowie et al., “Deciphering the message in protein sequences: Emsley et al., "Coot: model-building tools for molecular graphics.” tolerance to amino acid substitutions.” Science (1990) Acta Crystallogr D Biol Crystallogr (2004) 60(Pt 12 Pr 1):2126 247(4948): 1306-1310. 2132. Bretscher et al., “Structural characterization and kinetics of nitric Erlanson et al., “Discovery of a potent and highly selective PDK1 oxide synthase inhibition by novel N5-(iminoalkyl)- and inhibitor via fragment-based drug discovery,” Bioorg Med Chem N5-(iminoalkenyl)-ornithines,” J Biol Chem (2003)278(47):46789 Lett (2011) 21(10):3078-3083. 46.797. Ferenczy et al., “Thermodynamics guided lead discovery and opti Burgess et al., “Possible dissociation of the heparin-binding and mization.” Drug Discov Today (2010) 15:919-932. mitogenic activities of heparin-binding (acidic fibroblast) growth Gencoglan et al., “Two cases of acneiform eruption induced by factor-1 from its receptor-binding activities by site-directed inhibitor of epidermal growth factor receptor.” Skin Pharmacol mutagenesis of a single lysine residue.” J Cell Biol (1990) 111(5 Pt Physiol (2007) 2005):260-262. 1):2129-2138. Goodwin et al., “Pretargeted peptide imaging and therapy,” Cancer Butlin et al., “Antibodies with infinite affinity: origins and applica Biother Radiopharm (1999) 14(3):145-152.
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