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

The catalytic reaction in SARS-CoV-2 main protease is activated by a proton transfer (PT) from Cys145 to His41. The same PT reaction is likely also required for the covalent binding of some classes of inhibitors. Here we use a hybrid quantum/classical approach to investigate the PT thermodynamics in the apo state and in the presence of a covalent inhibitor, N3. We show that in the apo state a neutral catalytic dyad is favored whereas in the presence of N3 the PT reaction becomes thermodynamically favorable. We also show that a few key sites (including a water molecule) are able to significantly enhance or reduce the thermodynamic feasibility of the PT reaction. The approach presented is a general and cost-effective procedure to identify the enzyme regions that control the activation of the catalytic reaction. It is also useful to guide the screening and design of potential covalent inhibitors.