ArticlePloS one2013
A novel antibody humanization method based on epitopes scanning and molecular dynamics simulation.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Structural Basis for TGF-β Mimetic Peptide-Induced Signaling Activation Through Molecular Dynamics Simulations.International journal of molecular sciences · 2025Article
- Plasticity of BioPhi-driven humanness optimization in ScFv-CD99 binding affinity validated through AlphaFold, HADDOCK, and MD simulations.Computational and structural biotechnology journal · 2025Article
- Design and synthesis of novel main protease inhibitors of COVID-19: quinoxalino[2,1-RSC advances · 2024Article
- Rapid Generation and Molecular Docking Analysis of Single-Chain Fragment Variable (scFv) Antibody Selected by Ribosome Display Targeting Cholecystokinin B Receptor (CCK-BR) for Reduction of Chronic Neuropathic Pain.International journal of molecular sciences · 2023Article
- Current Trends and Changes in Use of Membrane Molecular Dynamics Simulations within Academia and the Pharmaceutical Industry.Membranes · 2023Review
- Immunoglobulin somatic hypermutation in a defined biochemical system recapitulates affinity maturation and permits antibody optimization.Nucleic acids research · 2022Article
- Article
- Inhibition of SARS-CoV-2 3CL MFrontiers in molecular biosciences · 2021Article
- Sagacity in antibody humanization for therapeutics, diagnostics and research purposes: considerations of antibody elements and their roles.Antibody therapeutics · 2020Review
- Surprisingly Fast Interface and Elbow Angle Dynamics of Antigen-Binding Fragments.Frontiers in molecular biosciences · 2020Article
- Molecular Docking and Molecular Dynamics (MD) Simulation of Human Anti-Complement Factor H (CFH) Antibody Ab42 and CFH Polypeptide.International journal of molecular sciences · 2019Article
- Identifying the Epitope Regions of Therapeutic Antibodies Based on Structure Descriptors.International journal of molecular sciences · 2017Article
- Design and Generation of Humanized Single-chain Fv Derived from Mouse Hybridoma for Potential Targeting Application.Monoclonal antibodies in immunodiagnosis and immunotherapy · 2015Article
- Functional and Structural Consequences of Damaging Single Nucleotide Polymorphisms in Human Prostate Cancer Predisposition Gene RNASEL.BioMed research international · 2015Article
- OptMAVEn--a new framework for the de novo design of antibody variable region models targeting specific antigen epitopes.PloS one · 2014Article
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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