2.3. Receptor grid generation and molecular docking

A grid box [co-ordinates X −10.86, Y 11.94, Z 693.32, 10 X 15 X 15] was generated around the protein (PDB: 6LZE) by selecting the co-crystallized inhibitory peptide ligand 11a in Receptor Grid Generation tool of Glide in Maestro. All docking calculations for the prepared ligand molecules were performed in Glide's extra precision (XP) mode using default settings. Prior to docking of all ligands, Glide's XP mode was used to redock the co-crystallized ligand 11a (Pubchem ID: 145343771) into the active site of the protein to ensure the reliability of docking protocol [²³]. Following Glide's best pose based on energy, post docking minimization was performed. They were then exported and analysed in the BIOVIA Discovery Studio (DS) visualizer to explore how the functional groups of ligands interact with the amino acids in the binding site of the protein to form hydrogen bonds and hydrophobic interactions. Among all docked molecules, top five metabolites with the highest binding affinity and the most interactions with amino acids that interact with the essential residues that form the catalytic dyad HIS41 and/or CYS145 of SARS-CoV2-Mpro were chosen for further examination.