title: Computational design of an epitope-specific Keap1 binding antibody using hotspot residues grafting and CDR loop swapping.
abstract: Therapeutic and diagnostic applications of monoclonal antibodies often require careful selection of binders that recognize specific epitopes on the target molecule to exert a desired modulation of biological function. Here we present a proof-of-concept application for the rational design of an epitope-specific antibody binding with the target protein Keap1, by grafting pre-defined structural interaction patterns from the native binding partner protein, Nrf2, onto geometrically matched positions of a set of antibody scaffolds. The designed antibodies bind to Keap1 and block the Keap1-Nrf2 interaction in an epitope-specific way. One resulting antibody is further optimised to achieve low-nanomolar binding affinity by in silico redesign of the CDRH3 sequences. An X-ray co-crystal structure of one resulting design reveals that the actual binding orientation and interface with Keap1 is very close to the design model, despite an unexpected CDRH3 tilt and VH/VLinterface deviation, which indicates that the modelling precision may be improved by taking into account simultaneous CDR loops conformation and VH/VLorientation optimisation upon antibody sequence change. Our study confirms that, given a pre-existing crystal structure of the target protein-protein interaction, hotspots grafting with CDR loop swapping is an attractive route to the rational design of an antibody targeting a pre-selected epitope.
authors.affiliation: UCB Celltech, 216 Bath Road, Slough, United Kingdom.
authors.forename: Xiaofeng
authors.initials: X
authors.lastname: Liu
authors.affiliation: UCB Celltech, 216 Bath Road, Slough, United Kingdom.
authors.forename: Richard D
authors.initials: RD
authors.lastname: Taylor
authors.affiliation: UCB Celltech, 216 Bath Road, Slough, United Kingdom.
authors.forename: Laura
authors.initials: L
authors.lastname: Griffin
authors.affiliation: UCB Celltech, 216 Bath Road, Slough, United Kingdom.
authors.forename: Shu-Fen
authors.initials: SF
authors.lastname: Coker
authors.affiliation: UCB Celltech, 216 Bath Road, Slough, United Kingdom.
authors.forename: Ralph
authors.initials: R
authors.lastname: Adams
authors.affiliation: UCB Celltech, 216 Bath Road, Slough, United Kingdom.
authors.forename: Tom
authors.initials: T
authors.lastname: Ceska
authors.affiliation: UCB Pharma, Chemin du Foriest 1, B-1420 Braine-l'Alleud, Belgium.
authors.forename: Jiye
authors.initials: J
authors.lastname: Shi
authors.affiliation: UCB Celltech, 216 Bath Road, Slough, United Kingdom.
authors.forename: Alastair D G
authors.initials: AD
authors.lastname: Lawson
authors.affiliation: UCB Celltech, 216 Bath Road, Slough, United Kingdom.
authors.forename: Terry
authors.initials: T
authors.lastname: Baker
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D000911:Antibodies, Monoclonal / Q000737:chemistry / Q000276:immunology*; D000915:Antibody Affinity / Q000276:immunology; D022801:Complementarity Determining Regions / Q000737:chemistry / Q000276:immunology; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D000939:Epitopes / Q000737:chemistry* / Q000276:immunology; D006801:Humans; D000072019:Kelch-Like ECH-Associated Protein 1 / Q000737:chemistry* / Q000235:genetics / Q000276:immunology; D051267:NF-E2-Related Factor 2 / Q000737:chemistry* / Q000235:genetics / Q000276:immunology; D011485:Protein Binding / Q000235:genetics / Q000276:immunology
chemical_list: D000911:Antibodies, Monoclonal; D022801:Complementarity Determining Regions; D000939:Epitopes; D000072019:Kelch-Like ECH-Associated Protein 1; D051267:NF-E2-Related Factor 2; C495635:NFE2L2 protein, human