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 mu M) and good antiviral potency against SARS-CoV-2 (EC50 = 2.64 mu M), similar to that of remdesivir (EC50 = 2.27 mu M). 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.

Automated summary

This study reports the discovery of potent non-peptide covalent Mpro inhibitors that can combat SARS-CoV-2. Among them, GD-9 exhibits significant enzymatic inhibition of Mpro and good antiviral potency against SARS-CoV-2, with favorable selectivity for the virus. The X-ray co-crystal structure confirms the covalent binding of GD-9 to the active site of Mpro. These findings provide a foundation for the development of more efficient COVID-19 therapeutics.