SLAS Discov . Discovery of SARS-CoV-2 Main Protease Covalent Inhibitors from a DNA-Encoded Library Selection

[tetano]

SLAS Discov


. 2022 Jan 18;S2472-5552(22)00006-5.
doi: 10.1016/j.slasd.2022.01.001. Online ahead of print.
Discovery of SARS-CoV-2 Main Protease Covalent Inhibitors from a DNA-Encoded Library Selection


Rui Ge ¹ , Zuyuan Shen ¹ , Jian Yin ¹ , Wenhua Chen ¹ , Qi Zhang ¹ , Yulong An ¹ , Dewei Tang ¹ , Alexander L Satz ² , Wenji Su ³ , Letian Kuai ⁴



Affiliations

• PMID: 35063690
• DOI: 10.1016/j.slasd.2022.01.001

Abstract

Covalent inhibitors targeting the main protease (M^pro, or 3CLpro) of SARS-CoV-2 have shown promise in preclinical investigations. Herein, we report the discovery of two new series of molecules that irreversibly bind to SARS-CoV-2 M^pro. These acrylamide containing molecules were discovered using our DNA-encoded library (DEL) screening platform. Following selection against SARS-CoV-2 M^pro, off-DNA compounds were synthesized and investigated to determine their inhibitory effects, the nature of their binding, and generate preliminary structure-activity relationships. LC-MS analysis indicates a 1:1 (covalent) binding stoichiometry between our hit molecules and SARS-CoV-2 M^pro. Fluorescent staining assay for covalent binding in the presence of cell lysate suggests reasonable selectivity for SARS-CoV-2 M^pro. And lastly, inhibition of enzymatic activity was also observed against a panel of 3CLpro enzymes from different coronavirus strains, with IC₅₀ values ranging from inactive to single digit micromolar. Our results indicate that DEL selection is a useful approach for identifying covalent inhibitors of cysteine proteases.

Keywords: COVID-19; Covalent inhibitor; SARS-CoV-2 M(pro); covalent DEL selection.