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.