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In Silico Studies of the Biomolecular Interactions Between Natural Products and SARS-CoV-2 Main Protease
preprintsubmitted on 08.10.2020, 06:50 and posted on 08.10.2020, 09:28 by Wilmar Puma-Zamora, Fabian Jimenez, Jesus Antonio Alvarado-Huayhuaz, Gerson Cordova-Serrano, Pierre-Marie Allard, Mariano Prado Acosta, Gustavo E. Olivos-Ramirez, Héctor Condori-Alagón, Ihosvany Camps
The rapid global spread of SARS-CoV-2, the causative agent of COVID-19, has set off the alarms of healthcare systems all over the world, the situation is exacerbated as no effective treatment is available to date. One therapeutic strategy consists in stopping the replication of the virus by inhibiting SARS-CoV-2 main protease, an important enzyme in the processing of polyproteins from viral RNA. Applying techniques like virtual screening, molecular docking and molecular dynamics simulations, our study evaluated the biomolecular interactions generated between more than 200 thousand natural products structures collected from the Universal Natural Product Database and the main protease active site. Through successive docking filters, we identified 3 molecules with a good affinity profile for the enzyme. These were subjected to molecular dynamics simulations and their binding free energies were calculated. Structures of the best natural products identified could be a starting point for developing novel antiviral candidates targeting SARS-CoV-2 Mpro