Discovery of the potent covalent inhibitor with an acrylate warhead for SARS-CoV-2 3CL protease

COVID-19 has caused severe consequences in terms of public health and economy worldwide since its outbreak in December 2019. SARS-CoV-2 3C-like protease (3CL^pro), crucial for the viral replications, is an attractive target for the development of antiviral drugs. In this study, several kinds of Michael acceptor warheads were utilized to hunt for potent covalent inhibitors against 3CL^pro. Meanwhile, novel 3CL^pro inhibitors with the P3-3,5-dichloro-4-(2-(dimethylamino)ethoxy)phenyl moiety were designed and synthesized which may form salt bridge with residue Glu166. Among them, two compounds 12b and 12c exhibited high inhibitory activities against SARS-CoV-2 3CL^pro. Further investigations suggested that 12b with an acrylate warhead displayed potent activity against HCoV-OC43 (EC₅₀ = 97 nM) and SARS-CoV-2 replicon (EC₅₀ = 45 nM) and low cytotoxicity (CC₅₀ > 10 μM) in Huh7 cells. Taken together, this study devised two series of 3CL^pro inhibitors and provided the potent SARS-CoV-2 3CL^pro inhibitor (12b) which may be used for treating coronavirus infections.