The COVID-19 pandemic is having a major impact on public health worldwide, and there is
an urgent need for the creation of an armamentarium of effective therapeutics, including
vaccines, biologics, and small-molecule therapeutics, to combat SARS-CoV-2 and emerging
variants. Inspection of the virus life cycle reveals multiple viral- and host-based
choke points that can be exploited to combat the virus. SARS-CoV-2 3C-like protease
(3CLpro), an enzyme essential for viral replication, is an attractive target for
therapeutic intervention, and the design of inhibitors of the protease may lead to the
emergence of effective SARS-CoV-2-specific antivirals. We describe herein the results of
our studies related to the application of X-ray crystallography, the
Thorpe–Ingold effect, deuteration, and stereochemistry in the design of highly
potent and nontoxic inhibitors of SARS-CoV-2 3CLpro.