Small-molecule inhibition of SARS-CoV-2 guanine-N7 RNA cap methyltransferase

Coronavirus Disease 2019 (COVID-19) is caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The rapid development of highly effective vaccines against SARS-CoV-2 has altered the pandemic's trajectory, and antiviral therapeutics have further reduced the number of COVID-19 hospitalizations and deaths. Coronaviruses are enveloped, positive-sense, single-stranded RNA viruses that encode various structural and non-structural proteins, including those required for viral RNA replication and evasion from innate immunity. Here we report the discovery and development of a first-in-class non-covalent small-molecule inhibitor of the viral guanine-N7 methyltransferase (MTase) NSP14. High-throughput screening (HTS) identified RU-0415529, which inhibited NSP14 by forming a ternary S-adenosyl homocysteine (SAH)-bound complex. Hit-to-lead optimization of RU-0415529 resulted in TDI-015051 with a KD of 39 pM and an EC50 of 11 nM inhibiting virus replication in a cell-based infection system. TDI-015051 also inhibited viral replication in vivo in a mouse-adapted SARS-CoV-2 model with an efficacy comparable to the FDA-approved covalent protease inhibitor nirmatrelvir. The inhibition of viral cap methylases as antiviral strategy is also adaptable to other viruses of pandemic concern.