Structure-Based Discovery of Inhibitors of the SARS-CoV-2 Nsp14 N7-Methyltransferase

An under-explored target for SARS-CoV-2 is the S-adenosyl methionine (SAM)-dependent methyltransferase Nsp14, which methylates the N7-guanosine of viral RNA at the 5′-end, allowing the virus to evade host immune response. We sought new Nsp14 inhibitors with three large library docking strategies. First, up to 1.1 billion lead-like molecules were docked against the enzyme’s SAM site, leading to three inhibitors with IC₅₀ values from 6 to 50 μM. Second, docking a library of 16 million fragments revealed 9 new inhibitors with IC₅₀ values from 12 to 341 μM. Third, docking a library of 25 million electrophiles to covalently modify Cys387 revealed 7 inhibitors with IC₅₀ values from 3.5 to 39 μM. Overall, 32 inhibitors encompassing 11 chemotypes had IC₅₀ values < 50 μM and 5 inhibitors in 4 chemotypes had IC₅₀ values < 10 μM. These molecules are among the first non-SAM-like inhibitors of Nsp14, providing starting points for future optimization.