Discovery and Crystallographic Studies of Nonpeptidic Piperazine Derivatives as Covalent SARS-CoV‑2 Main Protease Inhibitors

The
spread of SARS-CoV-2 keeps threatening human life and health,
and small-molecule antivirals are in demand. The main protease (Mpro) is an effective and highly conserved target for anti-SARS-CoV-2
drug design. Herein, we report the discovery of potent covalent non-peptide-derived
Mpro inhibitors. A series of covalent compounds with a
piperazine scaffold containing different warheads were designed and
synthesized. Among them, GD-9 was identified as the most
potent compound with a significant enzymatic inhibition of Mpro (IC50 = 0.18 μM) and good antiviral potency against
SARS-CoV-2 (EC50 = 2.64 μM), similar to that of remdesivir
(EC50 = 2.27 μM). Additionally, GD-9 presented favorable target selectivity for SARS-CoV-2 Mpro versus human cysteine proteases. The X-ray co-crystal structure
confirmed our original design concept showing that GD-9 covalently binds to the active site of Mpro. Our nonpeptidic
covalent inhibitors provide a basis for the future development of
more efficient COVID-19 therapeutics.