Identification of Inhibitors of SARS-CoV‑2 3CL-Pro Enzymatic Activity Using a Small Molecule in Vitro Repurposing Screen

Compound repurposing
is an important strategy for the identification
of effective treatment options against SARS-CoV-2 infection and COVID-19
disease. In this regard, SARS-CoV-2 main protease (3CL-Pro), also
termed M-Pro, is an attractive drug target as it plays a central role
in viral replication by processing the viral polyproteins pp1a and
pp1ab at multiple distinct cleavage sites. We here report the results
of a repurposing program involving 8.7 K compounds containing marketed
drugs, clinical and preclinical candidates, and small molecules regarded
as safe in humans. We confirmed previously reported inhibitors of
3CL-Pro and have identified 62 additional compounds with IC50 values below 1 μM and profiled their selectivity toward chymotrypsin
and 3CL-Pro from the Middle East respiratory syndrome virus. A subset
of eight inhibitors showed anticytopathic effect in a Vero-E6 cell
line, and the compounds thioguanosine and MG-132 were analyzed for
their predicted binding characteristics to SARS-CoV-2 3CL-Pro. The
X-ray crystal structure of the complex of myricetin and SARS-Cov-2
3CL-Pro was solved at a resolution of 1.77 Å, showing that myricetin
is covalently bound to the catalytic Cys145 and therefore inhibiting
its enzymatic activity.