Molecular dynamics and in silico mutagenesis on the reversible inhibitor-bound SARS-CoV-2 main protease complexes reveal the role of lateral pocket in enhancing the ligand affinity

Weng, Ying Li; Naik, Shiv Rakesh; Dingelstad, Nadia; Lugo, Miguel R.; Kalyaanamoorthy, Subha; Ganesan, Aravindhan

The 2019 novel coronavirus pandemic caused by SARS-CoV-2 remains a serious health threat to humans and there is an urgent need to develop therapeutics against this deadly virus. Recent scientific evidences have suggested that the main protease (M(pro)) enzyme in SARS-CoV-2 can be an ideal drug target due to its crucial role in the viral replication and transcription processes. Therefore, there are ongoing research efforts to identify drug candidates against SARS-CoV-2 M(pro) that resulted in hundreds of X-ray crystal structures of ligand-bound M(pro) complexes in the Protein Data Bank (PDB) describing the interactions of different fragment chemotypes within different sites of the M(pro). In this work, we performed rigorous molecular dynamics (MD) simulation of 62 reversible ligand–M(pro) complexes in the PDB to gain mechanistic insights about their interactions at the atomic level. Using a total of over 3 µs long MD trajectories, we characterized different pockets in the apo M(pro) structure, and analyzed the dynamic interactions and binding affinity of ligands within those pockets. Our results identified the key residues that stabilize the ligands in the catalytic sites and other pockets of M(pro). Our analyses unraveled the role of a lateral pocket in the catalytic site in M(pro) that is critical for enhancing the ligand binding to the enzyme. We also highlighted the important contribution from HIS163 in the lateral pocket towards ligand binding and affinity against M(pro) through computational mutation analyses. Further, we revealed the effects of explicit water molecules and M(pro) dimerization in the ligand association with the target. Thus, comprehensive molecular-level insights gained from this work can be useful to identify or design potent small molecule inhibitors against SARS-CoV-2 M(pro).