Coronavirus disease 2019 (COVID-19) has caused huge deaths and economic losses worldwide in the current pandemic. The main
protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is thought to be an ideal
drug target for treating
COVID-19.
Leupeptin, a broad-spectrum covalent inhibitor of
serine,
cysteine, and
threonine proteases, showed inhibitory activity against Mpro, with a 50% inhibitory concentration (IC50) value of 127.2 μM in vitro in our study here. In addition,
leupeptin can also inhibit SARS-CoV-2 in Vero cells, with 50% effective concentration (EC50) values of 42.34 μM. More importantly, various strains of streptomyces that have a broad symbiotic relationship with medicinal plants can produce
leupeptin and
leupeptin analogs to regulate autogenous
proteases. Fingerprinting and structure elucidation using high-performance liquid chromatography (HPLC) and high-resolution mass spectrometry (HRMS), respectively, further proved that the Qing-Fei-Pai-Du (QFPD) decoction, a
traditional Chinese medicine (TCM) formula for the effective treatment of
COVID-19 during the period of the Wuhan outbreak, contains
leupeptin. All these results indicate that
leupeptin at least contributes to the
antiviral activity of the QFPD decoction against SARS-CoV-2. This also reminds us to pay attention to the microbiomes in TCM herbs as streptomyces in the soil might produce
leupeptin that will later infiltrate the medicinal plant. We propose that plants, microbiome, and microbial metabolites form an ecosystem for the effective components of TCM herbs. IMPORTANCE A TCM formula has played an important role in the treatment of
COVID-19 in China. However, the mechanism of TCM action is still unclear. In this study, we identified
leupeptin, a metabolite produced by plant-symbiotic actinomyces (PSA), which showed
antiviral activity in both cell culture and
enzyme assays. Moreover,
leupeptin found in the QFPD decoction was confirmed by both HPLC fingerprinting and HRMS. These results suggest that
leupeptin likely contributes to the
antiviral activity of the QFPD decoction against SARS-CoV-2. This result gives us important insight into further studies of the PSA metabolite and medicinal plant ecosystem for future TCM modernization research.