Expedited Approach toward the Rational Design of Noncovalent SARS-CoV‑2 Main Protease Inhibitors

The main protease (Mpro) of SARS-CoV-2 is a validated
antiviral drug target. Several Mpro inhibitors have been
reported with potent enzymatic inhibition and cellular antiviral activity,
including GC376, boceprevir, calpain
inhibitors II, and XII, with each containing a
reactive warhead that covalently modifies the catalytic Cys145. Coupling
structure-based drug design with the one-pot Ugi four-component reaction,
we discovered one of the most potent noncovalent inhibitors, 23R (Jun8-76-3A) that is structurally distinct
from the canonical Mpro inhibitor GC376. Significantly, 23R is highly selective compared with covalent inhibitors
such as GC376, especially toward host proteases. The
cocrystal structure of SARS-CoV-2 Mpro with 23R revealed a previously unexplored binding site located in between
the S2 and S4 pockets. Overall, this study discovered 23R, one of the most potent and selective noncovalent SARS-CoV-2 Mpro inhibitors reported to date, and a novel binding pocket
in Mpro that can be explored for inhibitor design.