The catalytic reaction in the main protease (Mpro) of SARS-CoV-2 is activated by a proton transfer (PT) from cystein 145 to histidine 41. The same PT reaction is also believed to be required for the covalent binding of some classes of inhibitors. Here we present a hybrid quantum mechanical/classical mechanical approach to investigate the PT thermodynamics in the apo state of Mpro and in the presence of two covalent inhibitors, namely the peptidomimetic N3 and the α-ketoamide <b>13b</b>. We show that in the presence of the inhibitors the free energy cost to reach the charge-separated state of the active-site dyad is lower than in the apo state, with N3 inducing the most significant reduction in the free energy change upon PT. We also show that a few key sites (including specific water molecules) are able to significantly enhance or reduce the thermodynamic feasibility of the PT reaction, with selective desolvation of the active site playing a crucial role. In general, the presented approach is a cost-effective procedure to identify the enzyme regions that control the activation of the catalytic reaction and, more specifically, is also useful to guide the screening and design of potential covalent inhibitors.

Tuning proton transfer thermodynamics in SARS-Cov-2 main protease: Implications for catalysis and inhibitor design

ACS Spring Meeting 2021

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