In silico designing and optimization of anti‐epidermal growth factor receptor scaffolds by complementary‐determining regions‐grafting technique

Abstract

Monoclonal antibodies are attractive therapeutic agents in a wide range of human disorders that bind specifically to their target through their complementary‐determining regions (CDRs). Small proteins with structurally preserved CDRs are promising antibodies mimetics. In this in silico study, we presented new antibody mimetics against the cancer marker epidermal growth factor receptor (EGFR) created by the CDRs grafting technique. Ten potential graft acceptor sites that efficiently immobilize the grafted CDR loops were selected from three small protein scaffolds using a computer. The three most involved CDR loops in antibody‐receptor interactions extracted from panitumumab antibody against the EGFR domain III crystal structure were then grafted to the selected scaffolds through the loop randomization technique. The combination of three CDR loops and 10 grafting sites revealed that three of the 36 combinations showed specific binding to EGFR DIII by binding energy calculations. Thus, the present strategy and selected small protein scaffolds are promising tools in the design of new binders against EGFR with high binding energy.

Keywords

CDR grafting technique / EGFR / molecular dynamic simulation / panitumumab

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2024 The Author(s). Quantitative Biology published by John Wiley & Sons Australia, Ltd on behalf of Higher Education Press.