Deciphering the binding mechanism of inhibitors of the SARS-CoV-2 main protease through multiple replica accelerated molecular dynamics simulations and free energy landscapes

The pneumonia outbreak caused by the SARS-CoV-2 virus poses a serious threat to human health and the world economy. The development of safe and highly effective antiviral drugs is of great significance for the treatment of COVID-19. The main protease (M-pro) of SARS-CoV-2 is a key enzyme for viral replication and transcription and has no homolog in humans. Therefore, the M-pro is an ideal target for the design of drugs against COVID-19. Insights into the inhibitor-M-pro binding mechanism and conformational changes of the M-pro are essential for the design of potent drugs that target the M-pro. In this study, we analyzed the conformational changes of the M-pro that are induced by the binding of three inhibitors, YTV, YSP and YU4, using multiple replica accelerated molecular dynamics (MR-aMD) simulations, dynamic cross-correlation map (DCCM) calculations, principal component analysis (PCA), and free energy landscape (FEL) analysis. The results from DCCM calculations and PCA show that the binding of inhibitors significantly affects the kinetic behavior of the M-pro and induces a conformational rearrangement of the M-pro. The binding ability and binding mechanism of YTV, YSP and YU4 to the M-pro were investigated using the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method. The results indicate that substitution of the tert-butanol group by methylbenzene and trifluoromethyl groups enhances the binding ability of YSP and YU4 to the M-pro compared with YTV; moreover, massive hydrophobic interactions are detected between the inhibitors and the M-pro. Meanwhile, T25, L27, H41, M49, N142, G143, C145, M165, E166 and Q189 are identified as the key residues for inhibitor-M-pro interactions using residue-based free energy decomposition calculations, which can be employed as efficient targets in the design of drugs that inhibit the activity of the M-pro.