Structure-guided discovery of a small molecule inhibitor of SARS-CoV-2 main protease with potent in vitro and in vivo antiviral activities.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease (Mpro) is a clinically validated target for the treatment of coronavirus disease 2019 (COVID-19). Here, we report the hit-to-lead discovery of a new nitrile-based inhibitor, H135, of SARS-CoV-2 Mpro from a series of chemical modifications of a nitrile-warhead-containing compound guided by its 1.8 Å high-resolution crystal structure in complex with SARS-CoV-2 Mpro. H135 exhibited potent and selective inhibition of SARS-CoV-2 Mpro with IC50 of 12.7 nM and exerted broad anti-SARS-CoV-2 activity in VeroE6-TMPRSS2 cells. Furthermore, H135-treated golden Syrian hamsters demonstrated significantly lower respiratory tract viral burden compared with solvent-treated control hamsters. H135 may serve as a new lead for developing antiviral therapeutics for SARS-CoV-2 infection.IMPORTANCEIn this study, a structure-guided hit-to-lead strategy was employed to develop a nanomolar potent small molecule inhibitor H135 of SARS-CoV-2 Mpro with strong anti-SARS-CoV-2 infection activity in cell cultures and animals. H135 may serve as a new lead for developing antiviral agents targeting the virus's main protease Mpro.