Dyad orientation-dependent regulation of SARS-CoV 2 protease: towards informed structure-based drug discovery

NOTE - A significant portion of the text from this preprint is drawn from a previous submission (https://doi.org/10.26434/chemrxiv.12967655.v2). This is a later version of the previous submission with a new title and updated results. The Coronavirus Disease of 2019 (COVID-19) is caused by a novel coronavirus known as the Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV 2). The main protease (MPro) of SARS-CoV 2 mediates viral replication through proteolytic activity and the subsequent generation of infectious virus particles. Current computational efforts towards SARS-CoV 2 MPro inhibitor design generally neglect an allosteric mechanism linked to His41-Cys145 catalytic dyad disruption and thus do not target the open conformational state. Using both empirical and computational evidence, it was found that the rotation of the His41 imidazole side chain along the His41 backbone dihedral from 0.5 rads to -0.25 or -0.6 rads provides a conformational pathway for mediating MPro activity. In this work, the importance of enhanced sampling methods such as metadynamics when performing computer-aided MPro inhibitor design is demonstrated via the sampling of the dyad disruption pathway in a computationally feasible timescale. We calculate an MPro dyad-open against dyad-closed free energy difference of 3.55 ± 1.21kJ/mol, which is compensated by His41 imidazole-ligand interactions. The implications of this result for MPro inhibitor design are discussed