Discovery and Mechanism Study of SARS-CoV-2 3C-like Protease Inhibitors with a New Reactive Group

Pengxuan Ren; Hui Li; Tianqing Nie; Xiaoqin Jian; Changyue Yu; Jian Li; Haixia Su; Xianglei Zhang; Shiwei Li; Xin Yang; Chao Peng; Yue Yin; Leike Zhang; Yechun Xu; Hong Liu; Fang Bai

doi:10.1021/acs.jmedchem.3c00818

Discovery and Mechanism Study of SARS-CoV-2 3C-like Protease Inhibitors with a New Reactive Group

J Med Chem. 2023 Sep 14;66(17):12266-12283. doi: 10.1021/acs.jmedchem.3c00818. Epub 2023 Aug 18.

Authors

Pengxuan Ren¹, Hui Li^{2

3}, Tianqing Nie³, Xiaoqin Jian⁴, Changyue Yu³, Jian Li³, Haixia Su³, Xianglei Zhang¹, Shiwei Li¹, Xin Yang¹, Chao Peng⁵, Yue Yin⁵, Leike Zhang⁴, Yechun Xu^{3

6}, Hong Liu^{2

3

6}, Fang Bai^{1

7

8}

Affiliations

¹ School of Life Science and Technology, and Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.
² School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China.
³ State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
⁴ State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan 430071, China.
⁵ National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China.
⁶ School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
⁷ School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China.
⁸ Shanghai Clinical Research and Trial Center, Shanghai 201210, China.

PMID: 37594952
DOI: 10.1021/acs.jmedchem.3c00818

Abstract

3CL^pro is an attractive target for the treatment of COVID-19. Using the scaffold hopping strategy, we identified a potent inhibitor of 3CL^pro (3a) that contains a thiocyanate moiety as a novel warhead that can form a covalent bond with Cys145 of the protein. Tandem mass spectrometry (MS/MS) and X-ray crystallography confirmed the mechanism of covalent formation between 3a and the protein in its catalytic pocket. Moreover, several analogues of compound 3a were designed and synthesized. Among them, compound 3h shows the best inhibition of 3CL^pro with an IC₅₀ of 0.322 μM and a k_inact/K_i value of 1669.34 M^-1 s^-1, and it exhibits good target selectivity for 3CL^pro against host proteases. Compound 3c inhibits SARS-CoV-2 in Vero E6 cells (EC₅₀ = 2.499 μM) with low cytotoxicity (CC₅₀ > 200 μM). These studies provide ideas and insights to explore and develop new 3CL^pro inhibitors in the future.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

COVID-19*
Humans
Molecular Targeted Therapy
Protease Inhibitors / pharmacology
SARS-CoV-2*
Tandem Mass Spectrometry

Substances

Protease Inhibitors