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## Abstract In this study, we investigated the binding affinities between the main protease of SARS-CoV-2 virus and its various ligand to identify the hot spot residues of the protease. To investigate the effect of various force fields, we performed MD simulations with three different force fields: GROMOS54a7, Amber99-SB, and CHARMM36. The total amount of MD simulation time was 1.1 μs. To investigate how known ligands interact with M^pro^ of SARS-CoV-2, the binding affinities were calculated by using the MMPBSA approach. It is identified that no single force field succeeded in predicting the relative rankings of experimental binding affinities. When compared between different force fields, Amber99-SB and GROMOS54a7 results are fairly correlated while CHARMM36 results show weak or almost no correlations with the others. Additionally, we identified specific residues of M^pro^, which contribute more importantly to the binding energies with ligands. It is identified that the residues of the S4 subsite of the binding site, N142, M165, and R188, contribute strongly to ligand binding. In addition, the terminal residues, D295, R298, and Q299 are identified to have attractive interactions w

Author

Jinyoung Byun; Juyong Lee

Publisher

Research Square Platform LLC

Published

2021

Language

EN