Discovery and Mechanism of SARS-CoV‑2 Main Protease Inhibitors

The emergence of
a new coronavirus, severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2), presents an urgent public health crisis.
Without available targeted therapies, treatment options remain limited
for COVID-19 patients. Using medicinal chemistry and rational drug
design strategies, we identify a 2-phenyl-1,2-benzoselenazol-3-one
class of compounds targeting the SARS-CoV-2 main protease (Mpro). FRET-based screening against recombinant SARS-CoV-2 Mpro identified six compounds that inhibit proteolysis with nanomolar
IC50 values. Preincubation dilution experiments and molecular
docking determined that the inhibition of SARS-CoV-2 Mpro can occur by either covalent or noncovalent mechanisms, and lead
E04 was determined to inhibit Mpro competitively. Lead
E24 inhibited viral replication with a nanomolar EC50 value
(844 nM) in SARS-CoV-2-infected Vero E6 cells and was further confirmed
to impair SARS-CoV-2 replication in human lung epithelial cells and
human-induced pluripotent stem cell-derived 3D lung organoids. Altogether,
these studies provide a structural framework and mechanism of Mpro inhibition that should facilitate the design of future
COVID-19 treatments.