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

Ying Li Weng, Shiv Naik, Nadia Dingelstad, Subha Kalyaanamoorthy, Aravindhan Ganesan

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Received date: 31st October 2020

The 2019 novel coronavirus pandemic caused by SARS-CoV-2 remains a serious health threat to humans and a number of countries are already in the middle of the second wave of infection. There is an urgent need to develop therapeutics against this deadly virus. Recent scientific evidences have suggested that the main protease (Mpro) 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 Mprothat resulted in hundreds of X-ray crystal structures of ligand bound Mprocomplexes in the protein data bank (PDB) that describe structural details of different chemotypes of fragments binding within different sites in Mpro. In this work, we performed rigorous molecular dynamics (MD) simulation of 62 reversible ligand-Mprocomplexes in the PDB, corresponding to a cumulative simulation time of ~2.25 µs, and gained mechanistic insights about their interactions at atomic level. Weidentified and characterized different pockets and their conformational dynamics in the apo Mprostructure. Later, we analyzed the dynamic interactions and binding affinity of small ligands within those pockets. Our results identified the key residues that stabilize the ligands in the catalytic sites and other pockets in Mpro. Our analyses unraveled the role of a lateral pocket in the catalytic site in Mprothat is critical for enhancing the ligand binding to the enzyme. We also highlighted the important contribution from HIS163 in this lateral pocket towards ligand binding and affinity against Mprothrough computational mutation analyses. Further, we revealed the effects of explicit water molecules and Mprodimerization 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 Mpro.

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This is an abstract of a preprint hosted on a preprint server, which is currently undergoing peer review at Scientific Reports. The findings have yet to be thoroughly evaluated, nor has a decision on ultimate publication been made. Therefore, the results reported should not be considered conclusive, and these findings should not be used to inform clinical practice, or public health policy, or be promoted as verified information.

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