2.7 Covalent docking simulations
The MOE (Molecular Operating Environment 2019.01, Chemical Computing Group Inc., Montreal, Canada) was used to perform covalent docking simulations to analyze the potential binding modes of gallic acid and quercetin to Mpro30. First, the crystal structure of SARS-CoV-2 Mpro (PDB Code: 7NBY) was prepared using the QuickPrep module, which involved adding hydrogen atoms, removing water and hetero molecules, and energy minimization. Gallic acid and quercetin were generated as ligands, with Cys85 and Cys128 selected as reactive sites for gallic acid and Cys22 for quercetin, as indicated in Table 1. Afterwards, MarvinSketch was used to define the covalent reaction formula for cysteine residuals and compounds. The protein structure was set as rigid receptor, and binding scores were evaluated using GBVI/WSA dG. The poses with the lowest S-score were chosen for the ligand-Mprointeraction analysis.