Discovery of a potent covalent inhibitor that unusually distorts the catalytic dyad of SARS-CoV-2 main protease
Juan Wang, Xiaohong Sang, Wenyan Zheng, Jasper Fuk‐Woo Chan, Jiao Zhou, Yan Xu, Pu Han, Yong Feng, Lifeng Fu, Jessica Oi‐Ling Tsang, Shuofeng Yuan, Aaron J. Ciechanover, Jing An, Kwok-Yung Yuen, Jianxun Qi, Ziwei Huang · Journal of Virology · 2025
ABSTRACT 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 pro ) 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 pro 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 pro inhibition with IC 50 of 8.8 nM and strongly prevented SARS-CoV-2 replication in VeroE6 cells. The co-crystal structure of H102 bound to M pro determined at 1.50 Å 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 pro 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 pro 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. IMPORTANCE A nanomolar potent small-molecule inhibitor, H102 , of SARS-CoV-2 M pro was developed and exhibited strong anti-SARS-CoV-2 infection activity in cells. Co-crystal structure determination of its complex with M pro 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 pro inhibition and potentially different type of lead for developing antiviral agents for treating disease caused by novel coronavirus SARS-CoV-2.