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Computational design of an epitope-specific Keap1 binding antibody using hotspot residues grafting and CDR loop swapping

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 epito...

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Autores principales: Liu, Xiaofeng, Taylor, Richard D., Griffin, Laura, Coker, Shu-Fen, Adams, Ralph, Ceska, Tom, Shi, Jiye, Lawson, Alastair D. G., Baker, Terry
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5269676/
https://www.ncbi.nlm.nih.gov/pubmed/28128368
http://dx.doi.org/10.1038/srep41306
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author Liu, Xiaofeng
Taylor, Richard D.
Griffin, Laura
Coker, Shu-Fen
Adams, Ralph
Ceska, Tom
Shi, Jiye
Lawson, Alastair D. G.
Baker, Terry
author_facet Liu, Xiaofeng
Taylor, Richard D.
Griffin, Laura
Coker, Shu-Fen
Adams, Ralph
Ceska, Tom
Shi, Jiye
Lawson, Alastair D. G.
Baker, Terry
author_sort Liu, Xiaofeng
collection PubMed
description 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 V(H)/V(L) interface deviation, which indicates that the modelling precision may be improved by taking into account simultaneous CDR loops conformation and V(H)/V(L) orientation 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.
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spelling pubmed-52696762017-02-01 Computational design of an epitope-specific Keap1 binding antibody using hotspot residues grafting and CDR loop swapping Liu, Xiaofeng Taylor, Richard D. Griffin, Laura Coker, Shu-Fen Adams, Ralph Ceska, Tom Shi, Jiye Lawson, Alastair D. G. Baker, Terry Sci Rep Article 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 V(H)/V(L) interface deviation, which indicates that the modelling precision may be improved by taking into account simultaneous CDR loops conformation and V(H)/V(L) orientation 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. Nature Publishing Group 2017-01-27 /pmc/articles/PMC5269676/ /pubmed/28128368 http://dx.doi.org/10.1038/srep41306 Text en Copyright © 2017, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Liu, Xiaofeng
Taylor, Richard D.
Griffin, Laura
Coker, Shu-Fen
Adams, Ralph
Ceska, Tom
Shi, Jiye
Lawson, Alastair D. G.
Baker, Terry
Computational design of an epitope-specific Keap1 binding antibody using hotspot residues grafting and CDR loop swapping
title Computational design of an epitope-specific Keap1 binding antibody using hotspot residues grafting and CDR loop swapping
title_full Computational design of an epitope-specific Keap1 binding antibody using hotspot residues grafting and CDR loop swapping
title_fullStr Computational design of an epitope-specific Keap1 binding antibody using hotspot residues grafting and CDR loop swapping
title_full_unstemmed Computational design of an epitope-specific Keap1 binding antibody using hotspot residues grafting and CDR loop swapping
title_short Computational design of an epitope-specific Keap1 binding antibody using hotspot residues grafting and CDR loop swapping
title_sort computational design of an epitope-specific keap1 binding antibody using hotspot residues grafting and cdr loop swapping
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5269676/
https://www.ncbi.nlm.nih.gov/pubmed/28128368
http://dx.doi.org/10.1038/srep41306
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