Screening of M Protease (SARS-CoV-2) Covalent Inhibitors from an Anthocyanin-Rich Blueberry Extract Using an HRMS-Based Analytical Platform.

Background: The viral main protease (M) of SARS-CoV-2 has been recently proposed as a key target to inhibit virus replication in the host. Therefore, molecules that can bind the catalytic site of M could be considered as potential drug candidates in the treatment of SARS-CoV-2 infections. Here we proposed the application of a state-of-the-art analytical platform which combines metabolomics and protein structure analysis to fish-out potential active compounds deriving from a natural matrix, i.e., a blueberry extract.

Methods: The experiments focus on finding MS covalent inhibitors of M that contain in their structure a catechol/pyrogallol moiety capable of binding to the nucleophilic amino acids of the enzyme's catalytic site.

Results: Among the potential candidates identified, the delphinidin-3-glucoside showed the most promising results. Its antiviral activity has been confirmed in vitro on Vero E6 cells infected with SARS-CoV-2, showing a dose-dependent inhibitory effect almost comparable to the known M inhibitor baicalin. The interaction of delphinidin-3-glucoside with the M pocket observed was also evaluated by computational studies.

Conclusions: The HRMS analytical platform described proved to be effective in identifying compounds that covalently bind M and are active in the inhibition of SARS-CoV-2 replication, such as delphinidin-3-glucoside.