Discovery of Non-Covalent Inhibitors for SARS-CoV‑2 PLpro: Integrating Virtual Screening, Synthesis, and Experimental Validation

The SARS-CoV-2 pandemic has significantly challenged
global public
health, highlighting the need for effective therapeutic options. This
study focuses on the papain-like protease (PLpro) of SARS-CoV-2, which
is a critical enzyme for viral polyprotein processing, maturation,
and immune evasion. We employed a combined approach that began with
computational models in a virtual screening campaign, prioritizing
compounds from our in-house chemical library against PLpro. Out of
81 virtual hits evaluated through enzymatic and biophysical assays,
we identified a modest inhibitor featuring a naphthyridine core with
an IC50 of 73.61 μM and a Ki of 22 μM. Expanding our exploration, we synthesized
and assessed 30 naphthyridine analogues, three of which emerged as
promising noncovalent, nonpeptidomimetic inhibitors with IC50 values between 15.06 and 51.81 μM. Furthermore, in
vitro ADMET assays revealed these compounds to possess moderate
aqueous solubility, low cytotoxicity, and high microsomal stability,
making them excellent candidates for further development targeting
SARS-CoV-2 PLpro.