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In Silico Studies of the Biomolecular Interactions Between Natural Products and SARS-CoV-2 Main Protease

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