Discovery and Crystallographic Studies of Nonpeptidic Piperazine Derivatives as Covalent SARS-CoV-2 Main Protease Inhibitors.
Gao S, Song L, Claff T, Woodson M, Sylvester K, Jing L, Weiße RH, Cheng Y, Sträter N, Schäkel L, Gütschow M, Ye B, Yang M, Zhang T, Kang D, Toth K, Tavis J, Tollefson AE, Müller CE, Zhan P, Liu X.
The spread of SARS-CoV-2 keeps threatening human life and health, and small-molecule antivirals are in demand. The main protease (M<sup>pro</sup>) 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 M<sup>pro</sup> inhibitors. A series of covalent compounds with a piperazine scaffold containing different warheads were designed and synthesized. Among them, <b>GD-9</b> was identified as the most potent compound with a significant enzymatic inhibition of M<sup>pro</sup> (IC<sub>50</sub> = 0.18 μM) and good antiviral potency against SARS-CoV-2 (EC<sub>50</sub> = 2.64 μM), similar to that of remdesivir (EC<sub>50</sub> = 2.27 μM). Additionally, <b>GD-9</b> presented favorable target selectivity for SARS-CoV-2 M<sup>pro</sup> versus human cysteine proteases. The X-ray co-crystal structure confirmed our original design concept showing that <b>GD-9</b> covalently binds to the active site of M<sup>pro</sup>. Our nonpeptidic covalent inhibitors provide a basis for the future development of more efficient COVID-19 therapeutics.