title: A novel antibody humanization method based on epitopes scanning and molecular dynamics simulation.
abstract: 1-17-2 is a rat anti-human DEC-205 monoclonal antibody that induces internalization and delivers antigen to dendritic cells (DCs). The potentially clinical application of this antibody is limited by its murine origin. Traditional humanization method such as complementarity determining regions (CDRs) graft often leads to a decreased or even lost affinity. Here we have developed a novel antibody humanization method based on computer modeling and bioinformatics analysis. First, we used homology modeling technology to build the precise model of Fab. A novel epitope scanning algorithm was designed to identify antigenic residues in the framework regions (FRs) that need to be mutated to human counterpart in the humanization process. Then virtual mutation and molecular dynamics (MD) simulation were used to assess the conformational impact imposed by all the mutations. By comparing the root-mean-square deviations (RMSDs) of CDRs, we found five key residues whose mutations would destroy the original conformation of CDRs. These residues need to be back-mutated to rescue the antibody binding affinity. Finally we constructed the antibodies in vitro and compared their binding affinity by flow cytometry and surface plasmon resonance (SPR) assay. The binding affinity of the refined humanized antibody was similar to that of the original rat antibody. Our results have established a novel method based on epitopes scanning and MD simulation for antibody humanization.
authors.affiliation: MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
authors.forename: Ding
authors.initials: D
authors.lastname: Zhang
authors.forename: Cai-Feng
authors.initials: CF
authors.lastname: Chen
authors.forename: Bin-Bin
authors.initials: BB
authors.lastname: Zhao
authors.forename: Lu-Lu
authors.initials: LL
authors.lastname: Gong
authors.forename: Wen-Jing
authors.initials: WJ
authors.lastname: Jin
authors.forename: Jing-Jun
authors.initials: JJ
authors.lastname: Liu
authors.forename: Jing-Fei
authors.initials: JF
authors.lastname: Wang
authors.forename: Tian-Tian
authors.initials: TT
authors.lastname: Wang
authors.forename: Xiao-Hui
authors.initials: XH
authors.lastname: Yuan
authors.forename: You-Wen
authors.initials: YW
authors.lastname: He
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D022801:Complementarity Determining Regions; D017931:DNA Primers; D000939:Epitopes / Q000737:chemistry / Q000276:immunology*; D006801:Humans; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D009154:Mutation; D017386:Sequence Homology, Amino Acid; D020349:Surface Plasmon Resonance
chemical_list: D022801:Complementarity Determining Regions; D017931:DNA Primers; D000939:Epitopes