COVID-19 pandemic has poses urgent health challenge, and this project aims to identify potential inhibitors to combat this virus. We screened 198 bioactive compounds from five selected medicinal plants previously reported to be antiviral against SARS-CoV-2 protease and two coreceptors followed by molecular dynamics simulations. From the screened compounds, Astragalin demonstrated very strong molecular interactions with the molecular docking binding energies −8.5, −8.0, −7.6 kcal/mol for 6LU7, 6LZG, and 6VXX proteins of SARS-CoV-2, respectively. Hydrogen bonding interaction with the active site catalytic residue HIS-41 or CYS-145 of the main protease SARS-CoV-2 was observed. Binding free energies (G bind) from MM-GBSA after 50 ns MD simulations showed that Astragalin has the highest energy of −33.00 and −34.89 kcal/mol in complex with the main protease and spike glycoprotein of SARS-CoV-2, respectively. The study identifies Astragalin as a better inhibitor for the inactivation of COVID-19 and should be pursued as a potential drug candidate for this virus.