Identification of Natural Products Inhibiting SARS-CoV-2 by Targeting Viral Proteases: A Combined in Silico and in Vitro Approach

  • J Nat Prod. 2023 Feb 24;86(2):264-275. doi: 10.1021/acs.jnatprod.2c00843.
Andreas Wasilewicz  1  2 ,  Benjamin Kirchweger  1 ,  Denisa Bojkova  3 ,  Marie Jose Abi Saad  1  2 ,  Julia Langeder  1  2 ,  Matthias Bütikofer  4 ,  Sigrid Adelsberger  1  2 ,  Ulrike Grienke  1 ,  Jindrich Cinatl Jr  3 ,  Olivier Petermann  5  6 ,  Leonardo Scapozza  5  6 ,  Julien Orts  1 ,  Johannes Kirchmair  1 ,  Holger F Rabenau  3 ,  Judith M Rollinger  1
Affiliations
  • 1. Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
  • 2. Vienna Doctoral School of Pharmaceutical, Nutritional and Sport Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria.
  • 3. Institute of Medical Virology, University Hospital Frankfurt, Paul-Ehrlich-Straße 40, 60596 Frankfurt am Main, Germany.
  • 4. Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 1-5/10, 8093 Zurich, Switzerland.
  • 5. Pharmaceutical Biochemistry Group, School of Pharmaceutical Sciences, University of Geneva, 1205 Geneva, Switzerland.
  • 6. Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1205 Geneva, Switzerland.
PMID: 36651644 DOI: 10.1021/acs.jnatprod.2c00843
Abstract

In this study, an integrated in silico-in vitro approach was employed to discover natural products (NPs) active against SARS-CoV-2. The two SARS-CoV-2 viral proteases, i.e., main protease (Mpro) and papain-like protease (PLpro), were selected as targets for the in silico study. Virtual hits were obtained by docking more than 140,000 NPs and NP derivatives available in-house and from commercial sources, and 38 virtual hits were experimentally validated in vitro using two enzyme-based assays. Five inhibited the enzyme activity of SARS-CoV-2 Mpro by more than 60% at a concentration of 20 μM, and four of them with high potency (IC50 < 10 μM). These hit compounds were further evaluated for their Antiviral activity against SARS-CoV-2 in Calu-3 cells. The results from the cell-based assay revealed three mulberry Diels-Alder-type adducts (MDAAs) from Morus alba with pronounced anti-SARS-CoV-2 activities. Sanggenons C (12), O (13), and G (15) showed IC50 values of 4.6, 8.0, and 7.6 μM and selectivity index values of 5.1, 3.1 and 6.5, respectively. The docking poses of MDAAs in SARS-CoV-2 Mpro proposed a butterfly-shaped binding conformation, which was supported by the results of saturation transfer difference NMR experiments and competitive 1H relaxation dispersion NMR spectroscopy.