PMID- 24475232
OWN - NLM
STAT- MEDLINE
DCOM- 20140929
LR  - 20211021
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 9
IP  - 1
DP  - 2014
TI  - Affinity improvement of a therapeutic antibody by structure-based computational 
      design: generation of electrostatic interactions in the transition state 
      stabilizes the antibody-antigen complex.
PG  - e87099
LID - 10.1371/journal.pone.0087099 [doi]
LID - e87099
AB  - 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.
FAU - Kiyoshi, Masato
AU  - Kiyoshi M
AD  - Medical Genome Sciences, Graduate School of Frontier Sciences, The University of 
      Tokyo, Kashiwa, Chiba, Japan.
FAU - Caaveiro, Jose M M
AU  - Caaveiro JM
AD  - Department of Bioengineering, Graduate School of Engineering, The University of 
      Tokyo, Bunkyo-ku, Tokyo, Japan ; Laboratory of Medical Proteomics, Institute of 
      Medical Science, The University of Tokyo, Minato-ku, Tokyo, Japan.
FAU - Miura, Eri
AU  - Miura E
AD  - Medical Genome Sciences, Graduate School of Frontier Sciences, The University of 
      Tokyo, Kashiwa, Chiba, Japan.
FAU - Nagatoishi, Satoru
AU  - Nagatoishi S
AD  - Department of Bioengineering, Graduate School of Engineering, The University of 
      Tokyo, Bunkyo-ku, Tokyo, Japan.
FAU - Nakakido, Makoto
AU  - Nakakido M
AD  - Laboratory of Medical Proteomics, Institute of Medical Science, The University of 
      Tokyo, Minato-ku, Tokyo, Japan.
FAU - Soga, Shinji
AU  - Soga S
AD  - Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas 
      Pharma Inc., Tsukuba, Ibaraki, Japan.
FAU - Shirai, Hiroki
AU  - Shirai H
AD  - Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas 
      Pharma Inc., Tsukuba, Ibaraki, Japan.
FAU - Kawabata, Shigeki
AU  - Kawabata S
AD  - Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas 
      Pharma Inc., Tsukuba, Ibaraki, Japan.
FAU - Tsumoto, Kouhei
AU  - Tsumoto K
AD  - Medical Genome Sciences, Graduate School of Frontier Sciences, The University of 
      Tokyo, Kashiwa, Chiba, Japan ; Department of Bioengineering, Graduate School of 
      Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan ; Laboratory of 
      Medical Proteomics, Institute of Medical Science, The University of Tokyo, 
      Minato-ku, Tokyo, Japan ; Department of Chemistry and Biotechnology, Graduate 
      School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20140127
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
RN  - 0 (Antibodies)
RN  - 0 (Antigen-Antibody Complex)
RN  - 0 (Antigens)
RN  - 0 (Chemokine CCL2)
RN  - 0 (Immunoglobulin Fab Fragments)
SB  - IM
MH  - Antibodies/genetics/*immunology/*therapeutic use
MH  - Antibody Affinity/*immunology
MH  - Antigen-Antibody Complex/immunology/*metabolism
MH  - Antigens/*immunology
MH  - Chemokine CCL2/immunology
MH  - Humans
MH  - Immunoglobulin Fab Fragments/*chemistry/genetics
MH  - *Models, Molecular
MH  - Mutagenesis
MH  - Mutation/genetics
MH  - Static Electricity
MH  - Thermodynamics
PMC - PMC3903617
COIS- Competing Interests: SS, HS, and SK are full-time employees of Astellas Pharma 
      Inc. KT serves as a consultant for Astellas Pharma Inc. This does not alter the 
      authors' adherence to all the PLOS ONE policies on sharing data and materials.
EDAT- 2014/01/30 06:00
MHDA- 2014/09/30 06:00
PMCR- 2014/01/27
CRDT- 2014/01/30 06:00
PHST- 2013/07/26 00:00 [received]
PHST- 2013/12/19 00:00 [accepted]
PHST- 2014/01/30 06:00 [entrez]
PHST- 2014/01/30 06:00 [pubmed]
PHST- 2014/09/30 06:00 [medline]
PHST- 2014/01/27 00:00 [pmc-release]
AID - PONE-D-13-30962 [pii]
AID - 10.1371/journal.pone.0087099 [doi]
PST - epublish
SO  - PLoS One. 2014 Jan 27;9(1):e87099. doi: 10.1371/journal.pone.0087099. eCollection 
      2014.