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(12) United States Patent (10) Patent No.: US 9,677,055 B2 Jones Et Al USOO96770.55B2 (12) United States Patent (10) Patent No.: US 9,677,055 B2 Jones et al. (45) Date of Patent: Jun. 13, 2017 (54) MODIFIED FORMS OF PSEUDOMONAS 2008.0125363 A1 5/2008 Filpula et al. EXOTOXINA 2008/O193976 A1 8, 2008 Harding 2009, O142341 A1 6/2009 Pastan et al. 2009/0305411 A1 12/2009 FitzGerald et al. (71) Applicant: Intrexon Corporation, Blacksburg, VA 2010, 0215656 A1 8, 2010 Pastan et al. (US) 2012/0263674 A1 10, 2012 Pastan et al. (72) Inventors: Timothy David Jones, Cambs (GB); FOREIGN PATENT DOCUMENTS Francis Joseph Carr, Aberdeen (GB) WO WO 88,02401 A1 4f1988 Assignee: Interxon Corporation, Blacksburg, VA WO WO 89.10971 A1 11, 1989 (73) WO WO 90,12592 A1 11, 1990 (US) WO WO 91,09949 A1 7, 1991 WO WO 91,09965 A1 7, 1991 (*) Notice: Subject to any disclaimer, the term of this WO WO 91 18018 A1 11F1991 patent is extended or adjusted under 35 WO WO91f18099 A1 11, 1991 U.S.C. 154(b) by 0 days. WO WO 91.18100 A1 11F1991 WO WO92fO9613 A1 6, 1992 WO WO 93.07.286 A1 4f1993 (21) Appl. No.: 15/234,297 WO WO 93,25690 A1 12, 1993 WO WO 94,04689 A1 3, 1994 (22) Filed: Aug. 11, 2016 WO WO 97,13529 A1 4f1997 WO WO 98/20135 A2 5, 1998 (65) Prior Publication Data WO WO 98/41641 A1 9, 1998 WO WO 99,28471 A2 6, 1999 US 2017/OO37386 A1 Feb. 9, 2017 WO WO O2/40545 A2 5, 2002 WO WO 2004/050849 A2 6, 2004 Related U.S. Application Data (Continued) (63) Continuation of application No. 14/984,006, filed on Dec. 30, 2015, now Pat. No. 9,447,387, which is a OTHER PUBLICATIONS continuation of application No. 14/561,707, filed on Siegall et al., “Cell-Specific Toxicity of a Chimeric Protein Com Dec. 5, 2014, now Pat. No. 9,371,517, which is a posed of Interleukin-6 and Pseudomonas Exotoxin (IL6-PE40) on continuation of application No. 13/604,173, filed on Tumor Cells.” Mol. Cell. Biol., vol. 10, No. 6, pp. 2443-2447, Sep. 5, 2012, now Pat. No. 8,932,586. American Society for Microbiology, Jun. 1990. Pastan et al., “Recombinant Toxins for Cancer Treatment,” Science (60) Provisional application No. 61/531,576, filed on Sep. Mag., vol. 254, pp. 1173-1177, Nov. 22, 1991. Retrieved on Aug. 6, 2011. 29, 2011 from www.sciencemag.org. Siegallet al., “Analysis of Sequences in Domain II of Pseudomonas Exotoxin A Which Mediate Translocation,” Biochem., vol. 30, No. (51) Int. C. 29, pp. 7154-7159. American Chemical Society, 1991. CI2N 9/10 (2006.01) Theuer et al., “Immunotoxins Made with a Recombinant Form of (52) U.S. C. Pseudomonas Exotoxin A That Do Not Require Proteolysis for CPC. CI2N 9/1077 (2013.01); CI2Y 204/02036 Activity.” Cancer Res., vol. 53, pp. 340-347, American Assoc. for Cancer Research, Jan. 15, 1993. Retrieved on Jan. 9, 2014 from (2013.01) www.cancerres.aacjournals.org. (58) Field of Classification Search None (Continued) See application file for complete search history. Primary Examiner — Amber D Steele (56) References Cited Assistant Examiner — Schuyler Milton (74) Attorney, Agent, or Firm — Intrexon Corporation U.S. PATENT DOCUMENTS (57) ABSTRACT 4,545,985 A 10, 1985 Pastan et al. 4,892,827 A 1/1990 Pastan et al. Pseudomonas exotoxin A or “PE is a 66 kD. highly potent, 5,458,878 A 10, 1995 Pastan et al. cytotoxic protein secreted by the bacterium Pseudomonas 5,512,658 A 4, 1996 Pastan et al. 5,602,095 A 2f1997 Pastan et al. aeruginosa. Various forms of PE have been coupled to other 5,696,237 A 12/1997 FitzGerald et al. proteins, such as antibodies, to generate therapeutically 5,705,156 A 1/1998 Pastan et al. useful cytotoxin conjugates that selectively target cells of a 5,705,163 A 1/1998 Pastan et al. desired phenotype (Such as tumor cells). In the present 5,821,238 A 10, 1998 Pastan et al. invention, peptides spanning the sequence of an approxi 5,854,044 A 12/1998 Pastan et al. 5,863,745 A 1/1999 Fitzgerald et al. mately 38 kD form of Pseudomonas exotoxin A protein were 5,980,895 A 11/1999 Pastan et al. analyzed for the presence of immunogenic CD4+ T cell 5,981,726 A 11/1999 Pastan et al. epitopes. Six immunogenic T cell epitopes were identified. 6,051.405 A 4/2000 FitzGerald et al. Residues were identified within each epitope for introduc 6,074,644 A 6, 2000 Pastan et al. 6.426,075 B1 7/2002 Fitzgerald et al. tion of targeted amino acid Substitutions to reduce or prevent 7,314.632 B1 1/2008 Fitzgerald immunogenic T-cell responses in PE molecules which may 7,750,136 B2 7, 2010 Baker et al. be administered to a heterologous host. 8,092,809 B2 1/2012 FitzGerald 2006/0051359 A1 3, 2006 Pastan et al. 23 Claims, 12 Drawing Sheets US 9,677,055 B2 Page 2 (56) References Cited mor Activity in Mice,” J Immunother; vol. 33, No. 3, pp. 297-304. Lippincott Williams & Wilkins, Apr. 2010. Hwang et al., “Functional Domains of Pseudomonas Exotoxin FOREIGN PATENT DOCUMENTS Identified by Deletion Analysis of the Gene Expressed in E. coli,” Cell, vol. 48, pp. 129-136, Cell Press, Jan. 16, 1987. WO WO 2006/065867 A2 6, 2006 Kreitman et al., “Recombinant immunotoxins and other therapies WO WO 2007/O16150 A2 2, 2007 for relapsed/refractory hairy cell leukemia,” Leukemia & Lym WO WO 2009/032954 A1 3, 2009 WO WO 2011/032022 A1 3, 2011 phoma, vol. 52, No. S2, pp. 82-86, Informa UK. Ltd., Jun. 2011. WO WO 2012/154530 A1 11, 2012 Shapira et al., “An Immunoconjugate of Anti-CD24 and WO WO 2012/170617 A1 12/2012 Pseudomonas Exotoxin Selectively Kills Human Colorectal Tumors WO WO 2013/040141 A1 3, 2013 in Mice,” Gastroenterology, vol. 140, No. 3, pp. 935-946, Mar. 2011. Chaudhary et al., “Pseudomonas exotoxin contains a specific OTHER PUBLICATIONS sequence at the carboxyl terminus that is required for cytotoxicity.” Benhar et al., “Pseudomonas Exotoxin A Mutants.” The Journal of Proc. Natl. Acad. Sci. USA, vol. 87, pp. 308-312, Jan. 1990. Biol. Chem., vol. 269, No. 18, pp. 13398-13404, May 6, 1994. Hu et al., “Investigation of a plasmid containing a novel Thomas et al., “Abrogation of Head and Neck Squamous Cell immunotoxin VEGF165-PE38 gene for antiangiogenic therapy in a Carcinoma Growth by Epidermal Growth Factor Receptor Ligand malignant glioma model.” Int. J. Cancer, vol. 127, pp. 2222-2229, Fused to Pseudomonas Exotoxin Transforming Growth Factor 2010. O-PE38.” Clin. Cancer Res., vol. 10, pp. 7079-7087, American Itoi et al., “Targeting of Locus Ceruleus Noradrenergic Neurons Assoc. for Cancer Research, Oct. 15, 2004. Retrieved on Aug. 29. Expressing Human Interleukin-2 Receptor O-Subunit in Transgenic 2012 from www.clincancerres.aacjournals.org. Mice by a Recombinant Immunotoxin anti-Tac(Fv)-PE38: A Study Bang et al., “HA22 (R490A) Is a Recombinant Immunotoxin with for Exploring Noradrenergic Influence upon Anxiety-Like and Increased Antitumor Activity without an Increase in Animal Tox Depression-Like Behaviors.” The Journal of Neuroscience, vol. 31. icity.” Clin. 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Nagata, S. and Pastan, I., “Removal of B cell epitopes as a practical Retrieved on Jan. 9, 2014 from www.bloodjournal. approach for reducing the immunogenicity of foreign protein-based hematologylibrary.org. therapeutics.” Adv. Drug Deliv Rey, vol. 61, No. 11, pp. 977-985, Baker et al., “Pre-Clinical Considerations in the Assessment of Elsevier Science Publishers B.V., Sep. 30, 2009. Immunogenicity for Protein Therapeutics.” Current Drug Safety, Seetharam et al., “Increased Cytotoxic Activity of Pseudomonas vol. 5, No. 4, pp. 1-6, Bentham Science Publishers Ltd., Feb. 19. Exotoxin and Two Chimeric Toxins Ending in KDEL.” The Journal 2010. of Biological Chemistry, vol. 266, No. 26, pp. 17376-17381, Ameri Kreitman et al., “Antibody Fusion Proteins: Anti-CD22 Recombi can Society for Biochemistry and Molecular Biology, Sep. 15, 1991. nant Immunotoxin Moxetumomab Pasudotox,” Clin. 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