Structure-based discovery of inhibitors of the SARS-CoV-2 Nsp14N7-methyltransferase

Abstract

AbstractAn under-explored target for SARS-CoV-2 is non-structural protein 14 (Nsp14), a crucial enzyme for viral replication that catalyzes the methylation ofN7-guanosine of the viral RNA at 5′-end; this enables the virus to evade the host immune response by mimicking the eukaryotic post-transcriptional modification mechanism. We sought new inhibitors of the S-adenosyl methionine (SAM)-dependent methyltransferase (MTase) activity of Nsp14 with three large library docking strategies. First, up to 1.1 billion make-on-demand (“tangible”) lead-like molecules were docked against the enzyme’s SAM site, seeking reversible inhibitors. On de novo synthesis and testing, three inhibitors emerged with IC50values ranging from 6 to 43 μM, each with novel chemotypes. Structure-guided optimization andin vitrocharacterization supported their non-covalent mechanism. In a second strategy, docking a library of 16 million tangible fragments revealed nine new inhibitors with IC50values ranging from 12 to 341 μM and ligand efficiencies from 0.29 to 0.42. In a third strategy, a newly created library of 25 million tangible, virtual electrophiles were docked to covalently modify Cys387 in the SAM binding site. Seven inhibitors emerged with IC50values ranging from 3.2 to 39 μM, the most potent being a reversible aldehyde. Initial optimization of a second series yielded a 7 μM acrylamide inhibitor. Three inhibitors characteristic of the new series were tested for selectivity against 30 human protein and RNA MTases, with one showing partial selectivity and one showing high selectivity. Overall, 32 inhibitors encompassing eleven chemotypes had IC50values <50 μM and 5 inhibitors in four chemotypes had IC50values <10 μM. These molecules are among the first non-SAM-like inhibitors of Nsp14, providing multiple starting points for optimizing towards antiviral activity.