α‑Ketoamides as Broad-Spectrum Inhibitors of Coronavirus and Enterovirus Replication: Structure-Based Design, Synthesis, and Activity Assessment

The main protease of coronaviruses
and the 3C protease of enteroviruses
share a similar active-site architecture and a unique requirement
for glutamine in the P1 position of the substrate. Because of their
unique specificity and essential role in viral polyprotein processing,
these proteases are suitable targets for the development of antiviral
drugs. In order to obtain near-equipotent, broad-spectrum antivirals
against alphacoronaviruses, betacoronaviruses, and enteroviruses,
we pursued a structure-based design of peptidomimetic α-ketoamides
as inhibitors of main and 3C proteases. Six crystal structures of
protease–inhibitor complexes were determined as part of this
study. Compounds synthesized were tested against the recombinant proteases
as well as in viral replicons and virus-infected cell cultures; most
of them were not cell-toxic. Optimization of the P2 substituent of
the α-ketoamides proved crucial for achieving near-equipotency
against the three virus genera. The best near-equipotent inhibitors, 11u (P2 = cyclopentylmethyl) and 11r (P2 = cyclohexylmethyl),
display low-micromolar EC50 values against enteroviruses,
alphacoronaviruses, and betacoronaviruses in cell cultures. In Huh7
cells, 11r exhibits three-digit picomolar activity against
the Middle East Respiratory Syndrome coronavirus.