Discovery of Novel Isofunctional SARS-CoV‑2 NSP14 RNA Cap Methyltransferase Inhibitors by Structure-Based Virtual Screening

In early 2020, SARS-CoV-2 spread into a worldwide pandemic,
causing
more than 7 million deaths. Direct-acting antivirals (DAAs) complementing
vaccines and mitigating severe disease in at-risk populations remain
important. Here, we used a structure-based virtual screening (SBVS)
workflow to identify new SAH-dependent inhibitors of the SARS-CoV-2
RNA cap methyltransferase NSP14. We virtually screened the Enamine
and Sigma in-stock screening collections as well as the 3 orders of
magnitude larger Enamine REAL make-on-demand compound library, which
produced better docking scores and higher virtual hit rates. While
biochemical testing of 145 in-stock library compounds yielded a single
NSP14-specific inhibitor, 123 chemically synthesized Enamine REAL
SBVS compounds contained 10 hits specifically inhibiting NSP14 with
half-maximal inhibitory concentrations (IC50) below 10
μM. The new compounds were chemically distinct in atomic composition
from any NSP14 inhibitors previously identified by conventional biochemical
high-throughput screening (HTS) and may serve as starting points to
develop novel SARS-CoV-2 DAAs.