In silico study binding affinity of regdanvimab-RBD spike protein SARS CoV-2 Omicron variant Indonesia
Lubbi Ilmiawan, Raymond Rubianto Tjandrawinata, Vivitri Dewi Prasasty.
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the responsible virus causing the COVID- 19 pandemic. Monoclonal antibodies were one of the main treatments for COVID-19, including regdanvimab. However, the efficacy of regdanvimab for Indonesian patients with the Omicron variant has yet to be published. This study was designed to investigate in silico binding affinity of regdanvimab to receptor binding domain (RBD) SARS-CoV-2 Omicron variant Indonesia. This study was performed in four stages; homology modeling, molecular docking, molecular dynamics, and protein-protein interactions analysis. We found that the mean of the interface binding score regdanvimab-RBD Omicron Indonesia was higher than that of regdanvimab-RBD wild-type (−19.881 ± 1.74 vs. −35.097 ± 1.01, respectively). Based on this in silico study, it can be concluded that the binding affinity of regdanvimab-RBD Omicron variant Indonesia was lower than that of regdanvimab-RBD wild-type.
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