Assay development and screening of inhibitors targeting the SARS-CoV-2 2′-O-methyltransferase NSP16

The coronavirus disease-2019 (COVID-19) pandemic, etiologically caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has profoundly impacted the global health. While vaccines have been developed, they have shown limited efficacy in treating patients already under infection or preventing infection with emerging SARS-CoV-2 variants. The nonstructural protein 16 (NSP16), with the assistance of the nonstructural protein 10 (NSP10), is responsible for forming the Cap-1 structure, which is critical for viral replication and immune evasion through the 5′-capping of viral mRNA. As a result, NSP16/NSP10 has emerged as a promising target for antiviral treatment of coronaviruses. In this study, we aimed to discover small molecule inhibitors of NSP16/NSP10 by leveraging recent structural insights and combined tools of virtual and experimental screenings. We designed a simple scintillation proximity assay to enable biochemical testing for NSP16/NSP10 enzymatic activity and applied it to screen inhibitors from candidate hit compounds that are derived from molecular docking-based virtual screenings. We identified potential hits that inhibit the NSP16 activity with cellular efficacy. Together with structural analysis and chemotype categorization, this study lays the groundwork for novel antiviral therapeutics development against SARS-CoV-2 and related coronaviruses.