Identification of pyrogallol as a warhead in design of covalent inhibitors for the SARS-CoV-2 3CL protease
Haixia Su, Sheng Yao, Wenfeng Zhao, Yumin Zhang, Jia Liu, Qiang Shao, Qingxing Wang, Minjun Li, Hang Xie, Weijuan Shang, Chang‐Qiang Ke, Lu Feng, Xiangrui Jiang, Jingshan Shen, Gengfu Xiao, Hualiang Jiang, Leike Zhang, Yang Ye, Yechun Xu
Abstract
Abstract The ongoing pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) urgently needs an effective cure. 3CL protease (3CL pro ) is a highly conserved cysteine proteinase that is indispensable for coronavirus replication, providing an attractive target for developing broad-spectrum antiviral drugs. Here we describe the discovery of myricetin, a flavonoid found in many food sources, as a non-peptidomimetic and covalent inhibitor of the SARS-CoV-2 3CL pro . Crystal structures of the protease bound with myricetin and its derivatives unexpectedly revealed that the pyrogallol group worked as an electrophile to covalently modify the catalytic cysteine. Kinetic and selectivity characterization together with theoretical calculations comprehensively illustrated the covalent binding mechanism of myricetin with the protease and demonstrated that the pyrogallol can serve as an electrophile warhead. Structure-based optimization of myricetin led to the discovery of derivatives with good antiviral activity and the potential of oral administration. These results provide detailed mechanistic insights into the covalent mode of action by pyrogallol-containing natural products and a template for design of non-peptidomimetic covalent inhibitors against 3CL pro s, highlighting the potential of pyrogallol as an alternative warhead in design of targeted covalent ligands.