Crystal Structure of SARS-CoV-2 Main Protease in Complex with the Non-Covalent Inhibitor ML188

Viral proteases are critical enzymes for the maturation of many human pathogenic viruses and thus are key targets for direct acting antivirals (DAAs). The current viral pandemic caused by SARS-CoV-2 is in dire need of DAAs. The Main protease (M-pro) is the focus of extensive structure-based drug design efforts which are mostly covalent inhibitors targeting the catalytic cysteine. ML188 is a non-covalent inhibitor designed to target SARS-CoV-1 M-pro, and provides an initial scaffold for the creation of effective pan-coronavirus inhibitors. In the current study, we found that ML188 inhibits SARS-CoV-2 M-pro at 2.5 mu M, which is more potent than against SAR-CoV-1 M-pro. We determined the crystal structure of ML188 in complex with SARS-CoV-2 M-pro to 2.39 angstrom resolution. Sharing 96% sequence identity, structural comparison of the two complexes only shows subtle differences. Non-covalent protease inhibitors complement the design of covalent inhibitors against SARS-CoV-2 main protease and are critical initial steps in the design of DAAs to treat CoVID 19.

Automated summary

Viral proteases are crucial enzymes for the maturation of human pathogenic viruses, and ML188, a non-covalent inhibitor, shows more potency against SARS-CoV-2 M-pro. These non-covalent inhibitors play a critical role in the design of DAAs for treating COVID-19.