Discovery of broad-spectrum antivirals targeting viral proteases using in silico structural modeling and cellular analysis.

The development of broad-spectrum antivirals is a high-priority goal to prevent future global outbreaks. Some antiviral agents developed for specific viral protein targets may exhibit broad-spectrum antiviral activity or provide helpful information for broad-spectrum drug development. In this study, we compared the sequence- and structure-based similarity of SARS-CoV-2 3CL with proteases from other viruses and identified 24 proteases with similar active-site structures. Our in-house lead molecules, NIP-22c and CIP-1 were reported as novel peptidomimetic, reversible covalent inhibitors of SARS-CoV-2 3CL with nanomolar potency. Molecular docking of NIP-22c, CIP-1 and nirmatrelvir were performed with structurally similar proteases of different viruses, norovirus, enterovirus and rhinovirus. The predictions were validated with in vitro enzymatic and cell-based assays. As predicted, NIP-22c and CIP-1 showed broad-spectrum antiviral activity with EC values in the nanomolar range against SARS-CoV-2, norovirus, enterovirus and rhinovirus by targeting 3CL/3C. In contrast, nirmatrelvir did not show activity up to 10 μM against all three viruses and the mechanism of inactivity of nirmatrelvir was hypothesized through binding pocket analysis using molecular dynamics simulations.