Discovery of a potent covalent inhibitor that unusually distorts the catalytic dyad of SARS-CoV-2 main protease.

Publication date: Sep 15, 2025

Proteases are versatile therapeutic targets for a wide variety of human diseases, including cancer, cardiovascular diseases, and infections by viruses, bacteria, and parasites. The main protease (M) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has been one of the major drug targets for the treatment of COVID-19. In this study, a small-molecule covalent inhibitor, H102, of SARS-CoV-2 M was developed from serial structural modifications on a compound previously reported by us to have anti-SARS-CoV-2 activity. H102 exhibited very high potency in SARS-CoV-2 M inhibition with IC of 8. 8 nM and strongly prevented SARS-CoV-2 replication in VeroE6 cells. The co-crystal structure of H102 bound to M determined at 1. 50 A resolution provided a structural mechanism of H102’s action and revealed an unusual distortion of the catalytic dyad of the viral enzyme which was caused by the benzyl ring of P2 position of H102 interacting with the side chain of catalytic dyad His41 residue of M and pulling His41 side chain away from the other catalytic dyad Cys145 residue. This structural mechanism of H102 is very different from that of other reported covalent M inhibitors for which His41 side chain orientation and its close proximity to Cys145 remain unchanged with the binding of a covalent inhibitor. As such, H102 may serve as a biochemical probe for investigating further an unusual mechanism of the viral enzyme’s catalytic dyad disruption and inhibition, and as a prototype distinct from other reported covalent inhibitors for the development of novel antiviral agents. IMPORTANCEA nanomolar potent small-molecule inhibitor, H102, of SARS-CoV-2 M was developed and exhibited strong anti-SARS-CoV-2 infection activity in cells. Co-crystal structure determination of its complex with M provided a structural mechanism of H102’s action and revealed an interesting structural feature: the benzyl ring at the P2 position of H102 interacts with the reorientated His41 side chain, accompanied by a significant increase of the distance between the catalytic dyad Cys145-His41 residues, which is uncommon in reported covalent inhibitors. Compound H102 may be used as a biochemical probe to further investigate mechanisms of M inhibition and potentially different type of lead for developing antiviral agents for treating disease caused by novel coronavirus SARS-CoV-2.

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