Peptide derivatives as inhibitors of SARS-CoV-2-S protein: Molecular docking study

Molecular docking study was performed to identify new lead inhibitor of SARS-CoV-2 spike glycoprotein (S protein) from the set of 62 peptide derivatives and evaluate their interactions with the receptor. Peptide-type compounds are previously proven peptide-type SARS- CoV 3CL protease inhibitors. However, highest binding affinity towards S protein has compound 21 (E = -127.2 kcal/mol), which showed the very low inhibitory activity against SARS- CoV 3CL protease. Compound 21 is in conformation that tightly fits along only the subunit S1, making the interactions with RBD and SD2 residues. Formation of a cluster of H- atom acceptor (O and N atoms), allows stronger binding to S1 subdomain. Antiviral drug Remdesivir demonstrated low binding affinity toward the S protein. Compounds that interact with receptor binding domain of SARS-CoV-2 spike glycoprotein may be potential therapeutic targets for drug design against COVID-19.