Ultralarge Virtual Screening Identifies SARS-CoV‑2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses

Drugs targeting SARS-CoV-2
could have saved millions of lives during
the COVID-19 pandemic, and it is now crucial to develop inhibitors
of coronavirus replication in preparation for future outbreaks. We
explored two virtual screening strategies to find inhibitors of the
SARS-CoV-2 main protease in ultralarge chemical libraries. First,
structure-based docking was used to screen a diverse library of 235
million virtual compounds against the active site. One hundred top-ranked
compounds were tested in binding and enzymatic assays. Second, a fragment
discovered by crystallographic screening was optimized guided by docking
of millions of elaborated molecules and experimental testing of 93
compounds. Three inhibitors were identified in the first library screen,
and five of the selected fragment elaborations showed inhibitory effects.
Crystal structures of target–inhibitor complexes confirmed
docking predictions and guided hit-to-lead optimization, resulting
in a noncovalent main protease inhibitor with nanomolar affinity,
a promising in vitro pharmacokinetic profile, and broad-spectrum antiviral
effect in infected cells.