Discovery of baicalin and baicalein as novel, natural product inhibitors of SARS-CoV-2 3CL protease in vitro

Haixia Su; Sheng Yao; Wenfeng Zhao; Minjun Li; Jia Liu; Weijuan Shang; Hang Xie; Changqiang Ke; Meina Gao; Kunqian Yu; Hong Liu; Jingshan Shen; Wei Tang; Leike Zhang; Jianping Zuo; Hualiang Jiang; Fang Bai; Yan Wu; Yang Ye; Yechun Xu

In view of the long history of TCMs in treating viral infections and the urgent need of drug development against COVID-19, we investigated the anti-SARS-CoV-2 potential of natural products isolated from S. baicalensis, a long-term used TCM. S. baicalensis is also the major component of Chinese traditional patent medicines such as "Shuanghuanglian" and "Qingfei Paidutang" which have proven effective in curing patients of COVID-19 in China (22) . As a result, we identified two small natural products, baicalin and baicalein, as the first class of noncovalent, non-peptidomimetic inhibitors of SARS-CoV-2 3CLpro by the enzymatic assay in combination with the ITC, ESI-MS, and X-ray protein crystallography studies. In contrast to most available covalent, peptidomimetic inhibitors of the 3CL proteases, the ITC measurement also revealed that these two compounds are non-covalent inhibitors with a high ligand-binding efficiency. The binding mode of baicalein with the protease revealed by the crystal structure demonstrates that a unique protein-ligand interaction pattern is utilized by baicalein to block the proteolytic activity of SARS-CoV-2 3CLpro. The crystal structure of baicalein-bound SARS-CoV-2 3CLpro thus reported the first demonstration, to the best of our knowledge, of