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Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis

The generation of a wide range of candidate antibodies is important for the successful development of drugs that simultaneously satisfy multiple requirements. To find cooperative mutations and increase the diversity of mutants, an in silico double-point mutation approach, in which 3D models of all p...

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Autores principales: Chiba, Shuntaro, Tanabe, Aki, Nakakido, Makoto, Okuno, Yasushi, Tsumoto, Kouhei, Ohta, Masateru
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7567794/
https://www.ncbi.nlm.nih.gov/pubmed/33067496
http://dx.doi.org/10.1038/s41598-020-74545-4
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author Chiba, Shuntaro
Tanabe, Aki
Nakakido, Makoto
Okuno, Yasushi
Tsumoto, Kouhei
Ohta, Masateru
author_facet Chiba, Shuntaro
Tanabe, Aki
Nakakido, Makoto
Okuno, Yasushi
Tsumoto, Kouhei
Ohta, Masateru
author_sort Chiba, Shuntaro
collection PubMed
description The generation of a wide range of candidate antibodies is important for the successful development of drugs that simultaneously satisfy multiple requirements. To find cooperative mutations and increase the diversity of mutants, an in silico double-point mutation approach, in which 3D models of all possible double-point mutant/antigen complexes are constructed and evaluated using interaction analysis, was developed. Starting from an antibody with very high affinity, four double-point mutants were designed in silico. Two of the double-point mutants exhibited improved affinity or affinity comparable to that of the starting antibody. The successful identification of two active double-point mutants showed that a cooperative mutation could be found by utilizing information regarding the interactions. The individual single-point mutants of the two active double-point mutants showed decreased affinity or no expression. These results suggested that the two active double-point mutants cannot be obtained through the usual approach i.e. a combination of improved single-point mutants. In addition, a triple-point mutant, which combines the distantly located active double-point mutation and an active single-point mutation collaterally obtained in the process of the double-point mutation strategy, was designed. The triple-point mutant showed improved affinity. This finding suggested that the effects of distantly located mutations are independent and additive. The double-point mutation approach using the interaction analysis of 3D structures expands the design repertoire for mutants, and hopefully paves a way for the identification of cooperative multiple-point mutations.
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spelling pubmed-75677942020-10-19 Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis Chiba, Shuntaro Tanabe, Aki Nakakido, Makoto Okuno, Yasushi Tsumoto, Kouhei Ohta, Masateru Sci Rep Article The generation of a wide range of candidate antibodies is important for the successful development of drugs that simultaneously satisfy multiple requirements. To find cooperative mutations and increase the diversity of mutants, an in silico double-point mutation approach, in which 3D models of all possible double-point mutant/antigen complexes are constructed and evaluated using interaction analysis, was developed. Starting from an antibody with very high affinity, four double-point mutants were designed in silico. Two of the double-point mutants exhibited improved affinity or affinity comparable to that of the starting antibody. The successful identification of two active double-point mutants showed that a cooperative mutation could be found by utilizing information regarding the interactions. The individual single-point mutants of the two active double-point mutants showed decreased affinity or no expression. These results suggested that the two active double-point mutants cannot be obtained through the usual approach i.e. a combination of improved single-point mutants. In addition, a triple-point mutant, which combines the distantly located active double-point mutation and an active single-point mutation collaterally obtained in the process of the double-point mutation strategy, was designed. The triple-point mutant showed improved affinity. This finding suggested that the effects of distantly located mutations are independent and additive. The double-point mutation approach using the interaction analysis of 3D structures expands the design repertoire for mutants, and hopefully paves a way for the identification of cooperative multiple-point mutations. Nature Publishing Group UK 2020-10-16 /pmc/articles/PMC7567794/ /pubmed/33067496 http://dx.doi.org/10.1038/s41598-020-74545-4 Text en © The Author(s) 2020, corrected publication 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Chiba, Shuntaro
Tanabe, Aki
Nakakido, Makoto
Okuno, Yasushi
Tsumoto, Kouhei
Ohta, Masateru
Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis
title Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis
title_full Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis
title_fullStr Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis
title_full_unstemmed Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis
title_short Structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis
title_sort structure-based design and discovery of novel anti-tissue factor antibodies with cooperative double-point mutations, using interaction analysis
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7567794/
https://www.ncbi.nlm.nih.gov/pubmed/33067496
http://dx.doi.org/10.1038/s41598-020-74545-4
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