Affinity improvement of a therapeutic antibody by structure-based computational design: generation of electrostatic interactions in the transition state stabilizes the antibody-antigen complex

Masato Kiyoshi, Jose M.M. Caaveiro, Eri Miura, Satoru Nagatoishi, Makoto Nakakido, Shinji Soga, Hiroki Shirai, Shigeki Kawabata, Kouhei Tsumoto

Research output: Contribution to journalArticle

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Abstract

The optimization of antibodies is a desirable goal towards the development of better therapeutic strategies. The antibody 11K2 was previously developed as a therapeutic tool for inflammatory diseases, and displays very high affinity (4.6 pM) for its antigen the chemokine MCP-1 (monocyte chemo-attractant protein-1). We have employed a virtual library of mutations of 11K2 to identify antibody variants of potentially higher affinity, and to establish benchmarks in the engineering of a mature therapeutic antibody. The most promising candidates identified in the virtual screening were examined by surface plasmon resonance to validate the computational predictions, and to characterize their binding affinity and key thermodynamic properties in detail. Only mutations in the light-chain of the antibody are effective at enhancing its affinity for the antigen in vitro, suggesting that the interaction surface of the heavy-chain (dominated by the hot-spot residue Phe101) is not amenable to optimization. The single-mutation with the highest affinity is L-N31R (4.6-fold higher affinity than wild-type antibody). Importantly, all the single-mutations showing increase affinity incorporate a charged residue (Arg, Asp, or Glu). The characterization of the relevant thermodynamic parameters clarifies the energetic mechanism. Essentially, the formation of new electrostatic interactions early in the binding reaction coordinate (transition state or earlier) benefits the durability of the antibody-antigen complex. The combination of in silico calculations and thermodynamic analysis is an effective strategy to improve the affinity of a matured therapeutic antibody.
Original languageEnglish
Article numbere87099
Number of pages9
JournalPLoS One
Volume9
Issue number1
DOIs
Publication statusPublished - 2014

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antigen-antibody complex
electrostatic interactions
Coulomb interactions
Antigen-Antibody Complex
Static Electricity
therapeutics
antibodies
Antibodies
Thermodynamics
Mutation
thermodynamics
mutation
Therapeutics
Digital Libraries
Antigens
Benchmarking
Antibody Affinity
Surface Plasmon Resonance
antigens
surface plasmon resonance

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Affinity improvement of a therapeutic antibody by structure-based computational design: generation of electrostatic interactions in the transition state stabilizes the antibody-antigen complex. / Kiyoshi, Masato; Caaveiro, Jose M.M.; Miura, Eri; Nagatoishi, Satoru; Nakakido, Makoto; Soga, Shinji; Shirai, Hiroki; Kawabata, Shigeki; Tsumoto, Kouhei.

In: PLoS One, Vol. 9, No. 1, e87099, 2014.

Research output: Contribution to journalArticle

Kiyoshi, Masato ; Caaveiro, Jose M.M. ; Miura, Eri ; Nagatoishi, Satoru ; Nakakido, Makoto ; Soga, Shinji ; Shirai, Hiroki ; Kawabata, Shigeki ; Tsumoto, Kouhei. / Affinity improvement of a therapeutic antibody by structure-based computational design: generation of electrostatic interactions in the transition state stabilizes the antibody-antigen complex. In: PLoS One. 2014 ; Vol. 9, No. 1.
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