Prior to running the binding free energy calculations, we performed 10-ns MD simulations on the model complexes to determine the preferred protonation state of His41. The protonation states of His41 in the model structures were assigned either as HID (N ! protonated) or HIE (N " protonated), according to amber force field naming convention. All the other histidines were left unaltered in their default protonation states as chosen by the pdb2gmx program of GROMACS MD engine (see Supporting Information). The difference in structure and binding interactions of the inhibitors with the M pro target in the structures were analyzed upon detailed visual inspection of their contacts. Also, the root-mean-square deviation, or RMSD, between select corresponding atoms (𝛼-carbon of the protein and heavy atoms of the ligand) in the simulated complexes and the crystallographic starting structures were measured after alignment of the structures. Our results indicate that the inhibitorbound complexes of 11a, GC373, and MI-30 favour the HID states of His41, while the PF-231 inhibitor-bound complex favours the HIE state of His41. Figure depicts snapshots of the structural environment of the catalytic dyad configurations in the M pro target complexes taken from the equilibrated MD simulation.