Probing the Dynamic Structure–Function and Structure-Free Energy Relationships of the Coronavirus Main Protease with Biodynamics Theory

[Image: see text] The SARS-CoV-2 main protease (M(pro)) is of major interest as an antiviral drug target. Structure-based virtual screening efforts, fueled by a growing list of apo and inhibitor-bound SARS-CoV/CoV-2 M(pro) crystal structures, are underway in many laboratories. However, little is known about the dynamic enzyme mechanism, which is needed to inform both assay development and structure-based inhibitor design. Here, we apply biodynamics theory to characterize the structural dynamics of substrate-induced M(pro) activation under nonequilibrium conditions. The catalytic cycle is governed by concerted dynamic structural rearrangements of domain 3 and the m-shaped loop (residues 132–147) on which Cys145 (comprising the thiolate nucleophile and half of the oxyanion hole) and Gly143 (comprising the second half of the oxyanion hole) reside. In particular, we observed the following: (1) Domain 3 undergoes dynamic rigid-body rotation about the domain 2–3 linker, alternately visiting two primary conformational states (denoted as M(1)(pro) ↔ M(2)(pro)); (2) The Gly143-containing crest of the m-shaped loop undergoes up and down translations caused by conformational changes within the rising stem of the loop (Lys137–Asn142) in response to domain 3 rotation and dimerization (denoted as M(1/down)(pro) ↔ 2·M(2/up)(pro)) (noting that the Cys145-containing crest is fixed in the up position). We propose that substrates associate to the M(1/down)(pro) state, which promotes the M(2/down)(pro) state, dimerization (denoted as 2·M(2/up)(pro)–substrate), and catalysis. Here, we explore the state transitions of M(pro) under nonequilibrium conditions, the mechanisms by which they are powered, and the implications thereof for efficacious inhibition under in vivo conditions.