Functional antibody characterization via direct structural analysis and information‐driven protein–protein docking

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2022-04, Vol.90 (4), p.919-935
• Main Authors: Depetris, Rafael S., Lu, Dan, Polonskaya, Zhanna, Zhang, Zhikai, Luna, Xenia, Tankard, Amari, Kolahi, Pegah, Drummond, Michael, Williams, Chris, Ebert, Maximilian C. C. J. C., Patel, Jeegar P., Poyurovsky, Masha V.
• Format: Article
• Language: English
• Subjects: Antibodies; antibody X‐ray structure function; antibody–antigen modeling; Antigens; Assaying; Binding; Computer applications; Growth factors; Humans; Model accuracy; model validation studies; Molecular dynamics; Molecular Dynamics Simulation; Mutagenesis; Optimization; protein complex modeling validation; Proteins; Structural analysis; Vascular endothelial growth factor; Vascular Endothelial Growth Factor A - metabolism; Vascular endothelial growth factor receptor 2; VEGF signaling; VEGFR2 clinical antibody
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.26280

Detailed description of the mechanism of action of the therapeutic antibodies is essential for the functional characterization and future optimization of potential clinical agents. We recently developed KD035, a fully human antibody targeting vascular endothelial growth factor receptor 2 (VEGFR2). KD035 blocked VEGF‐A, and VEGF‐C‐mediated VEGFR2 activation, as demonstrated by the in vitro binding and competition assays and functional cellular assays. Here, we report a computational model of the complex between the variable fragment of KD035 (KD035(Fv)) and the domains 2 and 3 of the extracellular portion of VEGFR2 (VEGFR2(D2‐3)). Our modeling was guided by a priori experimental information including the X‐ray structures of KD035 and related antibodies, binding assays, target domain mapping and comparison of KD035 affinity for VEGFR2 from different species. The accuracy of the model was assessed by molecular dynamics simulations, and subsequently validated by mutagenesis and binding analysis. Importantly, the steps followed during the generation of this model can set a precedent for future in silico efforts aimed at the accurate description of the antibody–antigen and more broadly protein–protein complexes.