Short Lecture “Natural products against SARS-CoV-2 or how to catch a butterfly?”

Abstract

There is still an unmet medical need for agents to overcome severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study, we applied an integrated in silico – in vitro approach to explore the potential role of natural products (NP) acting against SARS-CoV-2. The two SARS-CoV-2 viral proteases, the main protease (MPro) and the papain-like protease (PLPro) [1], were selected as targets for the in silico study. Virtual hits (VHs) were determined by molecular docking using GOLD [2] from databases containing > 140,000 molecules from in-house and commercially available natural products. For experimental validation 35 VHs were selected and subjected to enzyme-based assays. The protease inhibitory activity was confirmed for 11 VHs showing > 50% enzyme inhibition at 20 µM. These target-based hits were further evaluated for their antiviral activity against SARS-CoV-2 in a Caco-2 cell model. The results from the cell-based assay revealed several VHs not only as Mpro inhibitors but also as promising anti-SARS-CoV-2 agents with IC50 values in the low µM range without having cytotoxic effects (CC50 > 20 µM). The docking poses of SARS-CoV-2 MPro proposed a butterfly-shaped substrate binding pocket for the bioactive VHs similar to the already known synthetic inhibitor X77 ([Fig. 1]). In addition, saturation transfer difference – nuclear magnetic resonance (STD-NMR) experiments were performed to validate the predicted molecular interactions of in the MPro and support our proposed binding hypothesis.