In silico screening of natural antivirals as potential inhibitors of SARS-CoV-2 virus

Coronavirus infectious disease 2019 (COVID-19) is an infectious disease of the human respiratory tract caused by the SARS-CoV-2 virus. Spike protein is a class I glycoprotein trimeric TM involved in viral entry and infection. Four major targets to inhibit the SARS-CoV-2 virus are spike protein, angiotensin-converting enzyme 2 (ACE2), main protease and the enzyme RNA-dependent RNA polymerase (RdRp). In this study, we evaluated the inhibitory potential of natural antiviral compounds against spike protein, ACE2, main protease, RdRp targets by molecular docking and molecular dynamics simulations. Lipinski Rule of Five was used to evaluate the drug-like properties of these compounds. The pkCSM tool was used to assess the pharmacokinetic parameters of prospective substances. Based on the ChemFaces database, we have collected 273 natural antiviral compounds. The results showed that the 7/273 compounds with the most potential to inhibit SARS-CoV-2 were: hinokiflavone, sotetsuflavone, mulberroside C, daphnoretin, morellic acid, digitoxin, and hypericin. Among them, sotetsuflavone is the most potent compound that inhibits four targets, with drug-like properties, good intestinal absorption, and low toxicity. The molecular dynamics simulation results of the complexes are also relatively stable. As a results, in vitro and in vivo test should be carried out to verify the potential for COVID-19 treatment of this compound.