Before entering the cell, the SARS-CoV-2 spike glycoprotein receptor-binding domain (RBD) binds to the human angiotensin-converting enzyme 2 (hACE2) receptor. Hence, this RBD is a critical target for the development of antiviral agents. Recent studies have discovered that SARS-CoV-2 variants with mutations in the RBD have spread globally. The purpose of this in silico study was to determine the potential of a fruit bromelain-derived peptide. DYGAVNEVK. to inhibit the entry of various SARS-CoV-2 variants into human cells by targeting the hACE binding site within the RBD. Molecular docking analysis revealed that DYGAVNEVK interacts with several critical RBD binding residues responsible for the adhesion of the RBD to hACE2. Moreover, 100 ns MD simulations revealed stable interactions between DYGAVNEVK and RBD variants derived from the trajectory of root-mean-square deviation (RMSD), radius of gyration (Rg), and root-mean-square fluctuation (RMSF) analysis, as well as free binding energy calculations. Overall, our computational results indicate that DYGAVNEVK warrants further investigation as a candidate for preventing SARS-CoV-2 due to its interaction with the RBD of SARS-CoV-2 variants.
【저자키워드】 COVID-19, peptide, in silico, Molecular dynamics simulation, Receptor-binding domain, SARS-CoV-2 variants, Bromelain, RBD mutation, peptide-protein interaction, 【초록키워드】 SARS-CoV-2, Mutation, spike glycoprotein, SARS-CoV-2 variant, docking, MD simulation, binding site, hACE2, binding energy, Spread, RBD, Antiviral agents, trajectory, receptor, Critical, RMSD, RMSF, Interaction, Analysis, residue, domain, human Angiotensin-converting enzyme, RBD binding, radius of gyration, human cell, deviation, recent, Cell, fluctuation, bind, responsible, inhibit, determine, interact, the RBD, RBD variant, the SARS-CoV-2, 【제목키워드】 SARS-CoV-2, fruit, attachment,