Integratively screening SARS-CoV-2 3CLpro inhibitors from Coptidis Rhizoma applying activity fingerprinting and molecular docking program.

The 3-chymotrypsin like protease (3CLpro), a key enzyme essential for coronavirus replication, is recognized as a critical target for developing broad-spectrum anti-coronavirus therapeutics. Coptidis Rhizoma (CR), as a famous traditional Chinese medicine, showed significant therapeutic efficacy against viral pneumonia. This study proposed a strategy integrating activity fingerprinting and molecular docking process to identify anti-3CLpro active compounds from CR. An activity fingerprinting of CR was firstly established by integrating the information of chemical compounds obtained by HPLC-DAD and anti-3CLpro activity by fluorescent assay. The results showed that 16 fractions of CR exhibited strong anti-3CLpro activity, which also were identified by UPLC-Q-TOF-MS/MS. In addition, the binding energy between the potential active compounds and 3CLpro were investigated by molecular docking program, which showed that all the components in CR had binding energies of ≤ - 5.85 kcal/mol to the active pocket of 3CLpro. Finally, eight components (including chlorogenic acid, groenlandicine, coptisine, epiberberine, jatrorrhizine, columbamine, berberine and palmatine) was screened with significant inhibitory activities against 3CLpro, whose binding energies to 3CLpro were of ≤ -5.85 kcal/mol, and half-inhibitory concentrations (IC50) ranged from 0.055 to 0.328 μM. An anti-3CLpro activity fingerprints was established for CR, which was successfully applyed to screen 3CLpro inhibitors. It will also provide scientific evidence to elucidate the therapeutic basis of the antiviral effects of CR.