Azapeptide-Based SARS-CoV-2 Main Protease Inhibitors: Design, Synthesis, Enzyme Inhibition, Structural Determination, and Antiviral Activity

Mpro of SARS-CoV-2 plays a vital role in the
replication
and pathogenesis of virus. Additionally, its high conservation within
the Coronaviridae family makes it an attractive therapeutic
target for developing broad-spectrum agents. This study describes
the design, synthesis, and structure−activity relationships
of azapeptide-based SARS-CoV-2 Mpro inhibitors, leading
to several compounds with nanomolar IC50 values. Examples
include 14r (IC50 = 13.3 nM), 14s (IC50 = 30.6 nM), 20a (TPG-20a, IC50 = 28.0 nM), and 20g (IC50 = 30.4 nM). Some compounds inhibit MERS-CoV and SARS-CoV-1 Mpro but not the human protease cathepsin L. Several inhibitors,
such as 20a and 20f, exhibit antiviral activity
with potencies comparable to nirmatrelvir and activity against the
E166V-carrying SARS-CoV-2 variant (SARS-CoV-2E166V). An
Mpro cocrystal structure with 20a shows a
covalent adduct with the catalytic Cys145. Overall, these new inhibitors
are promising chemical tools that may contribute to the identification
of future pan-anticoronaviral drugs.