title: Protein deimmunization via structure-based design enables efficient epitope deletion at high mutational loads.
abstract: Anti-drug immune responses are a unique risk factor for biotherapeutics, and undesired immunogenicity can alter pharmacokinetics, compromise drug efficacy, and in some cases even threaten patient safety. To fully capitalize on the promise of biotherapeutics, more efficient and generally applicable protein deimmunization tools are needed. Mutagenic deletion of a protein's T cell epitopes is one powerful strategy to engineer immunotolerance, but deimmunizing mutations must maintain protein structure and function. Here, EpiSweep, a structure-based protein design and deimmunization algorithm, has been used to produce a panel of seven beta-lactamase drug candidates having 27-47% reductions in predicted epitope content. Despite bearing eight mutations each, all seven engineered enzymes maintained good stability and activity. At the same time, the variants exhibited dramatically reduced interaction with human class II major histocompatibility complex proteins, key regulators of anti-drug immune responses. When compared to 8-mutation designs generated with a sequence-based deimmunization algorithm, the structure-based designs retained greater thermostability and possessed fewer high affinity epitopes, the dominant drivers of anti-biotherapeutic immune responses. These experimental results validate the first structure-based deimmunization algorithm capable of mapping optimal biotherapeutic design space. By designing optimal mutations that reduce immunogenic potential while imparting favorable intramolecular interactions, broadly distributed epitopes may be simultaneously targeted using high mutational loads.
authors: Thayer School of Engineering, Dartmouth, 14 Engineering Dr., Hanover, New Hampshire, 03755.
authors: Regina S
authors: RS
authors: Salvat
authors: Department of Computer Science, Dartmouth, 6211 Sudikoff Laboratory, Hanover, New Hampshire, 03755.
authors: Yoonjoo
authors: Y
authors: Choi
authors: Colby College, Waterville, Maine.
authors: Alexandra
authors: A
authors: Bishop
authors: Department of Computer Science, Dartmouth, 6211 Sudikoff Laboratory, Hanover, New Hampshire, 03755. cbk@cs.dartmouth.edu.
authors: Chris
authors: C
authors: Bailey-Kellogg
authors: Thayer School of Engineering, Dartmouth, 14 Engineering Dr., Hanover, New Hampshire, 03755. karl.e.griswold@dartmouth.edu.|Program in Molecular and Cellular Biology, Dartmouth, Hanover, New Hampshire. karl.e.griswold@dartmouth.edu.
authors: Karl E
authors: KE
authors: Griswold
mesh_terms: D000941:Antigens / Q000235:genetics / Q000276:immunology*; D001688:Biological Products / Q000276:immunology*; D019295:Computational Biology / Q000379:methods*; D015195:Drug Design; D018984:Epitopes, T-Lymphocyte / Q000235:genetics*; D006801:Humans; D011506:Proteins / Q000235:genetics / Q000276:immunology*; D017384:Sequence Deletion; D001618:beta-Lactamases / Q000235:genetics / Q000276:immunology / Q000378:metabolism
chemical_list: D000941:Antigens; D001688:Biological Products; D018984:Epitopes, T-Lymphocyte; D011506:Proteins; D001618:beta-Lactamases
keywords: T cell epitope deletion; biotherapeutics; computational protein design; deimmunization; immunogenicity
references: Med Health R I. 2007 Oct;90(10):301-3
references: 18019185
references: Bioinformatics. 2001 Dec;17(12):1236-7
references: 11751237
references: Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8577-82
references: 24843166
references: Immunol Res. 2009 Dec;45(2-3):123-43
references: 19198764
references: PLoS Comput Biol. 2015 Jan 08;11(1):e1003988
references: 25568954
references: Nat Rev Drug Discov. 2002 Jun;1(6):457-62
references: 12119747
references: Self Nonself. 2010 Oct;1(4):314-322
references: 21487506
references: Cell Mol Life Sci. 2014 Dec;71(24):4869-80
references: 24880662
references: J Bioinform Comput Biol. 2011 Apr;9(2):207-29
references: 21523929
references: Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):8571-6
references: 24799704
references: J Clin Invest. 1997 Jul 15;100(2):339-49
references: 9218510
references: PLoS Comput Biol. 2012 Jan;8(1):e1002335
references: 22279426
references: MAbs. 2010 May-Jun;2(3):256-65
references: 20400861
references: Immunology. 2010 Jul;130(3):319-28
references: 20408898
references: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D138-41
references: 14681378
references: Proteins. 2012 Mar;80(3):790-806
references: 22180081
references: PLoS Comput Biol. 2008 Apr 04;4(4):e1000048
references: 18389056
references: Curr Opin Biotechnol. 2007 Aug;18(4):305-11
references: 17644370
references: Proc Natl Acad Sci U S A. 2012 Dec 18;109(51):E3597-603
references: 23213206
references: Nat Biotechnol. 1999 Jun;17(6):555-61
references: 10385319
references: J Exp Med. 2006 Apr 17;203(4):961-71
references: 16585267
references: Trends Immunol. 2007 Nov;28(11):482-90
references: 17964218
references: BMC Bioinformatics. 2010 Apr 09;11:180
references: 20380721
references: Discov Med. 2010 Jun;9(49):560-4
references: 20587346
references: Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1272-7
references: 21209329
references: Circulation. 1996 Jul 15;94(2):197-206
references: 8674179
references: J Chem Theory Comput. 2018 Oct 9;14(10):5273-5289
references: 30176213
references: J Immunol. 2002 Nov 1;169(9):5098-108
references: 12391226
references: Nat Biotechnol. 2014 Jan;32(1):32-9
references: 24406926
references: Clin Immunol. 2012 Mar;142(3):320-31
references: 22222093
references: J Immunol. 2004 Jun 1;172(11):6658-65
references: 15153481
references: Clin Dev Immunol. 2013;2013:467852
references: 24222776
references: Proteins. 2000 Aug 15;40(3):389-408
references: 10861930
references: Proteins. 1988;4(2):99-122
references: 3227018
references: J Comput Biol. 2013 Feb;20(2):152-65
references: 23384000
references: Drug Discov Today. 2011 Apr;16(7-8):345-53
references: 21300174
references: Annu Rev Immunol. 2005;23:975-1028
references: 15771591
references: Protein Eng Des Sel. 2012 Oct;25(10):613-23
references: 22898588
references: BioDrugs. 2010 Feb 1;24(1):1-8
references: 20055528
references: J Vis Exp. 2014 Mar 25;(85):
references: 24686319
references: J Comput Chem. 2013 Apr 5;34(10):879-91
references: 23299435
references: Proteins. 2006 Nov 15;65(3):712-25
references: 16981200
references: BMC Bioinformatics. 2007 Jul 04;8:238
references: 17608956
references: Mol Cancer Ther. 2005 Nov;4(11):1791-800
references: 16276001
references: Arthritis Res Ther. 2003;5(1):R40-8
references: 12716452
references: J Immunother. 2009 Jul-Aug;32(6):574-84
references: 19483652
references: J Immunol. 1998 Apr 1;160(7):3363-73
references: 9531296