Title:In silico Exploration of Dakshina Kannada Medicinal Plants as Anti-
SARS-CoV-2 Agents by Molecular Docking and Simulation Approaches
Volume: 20
Issue: 10
Author(s): Jainey P. James*, Divya Jyothi*, Vinod Devaraji and Sneh Priya
Affiliation:
- Department of Pharmaceutical Chemistry, Nitte (Deemed to be University), NGSM Institute of Pharmaceutical Sciences
(NGSMIPS), Deralakatte, Mangaluru-575018, Karnataka, India
- Department of Pharmacognosy, Nitte (Deemed to
be University), NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Deralakatte, Mangaluru-575018, Karnataka,
India
Keywords:
Dakshina Kannada, SARS-CoV-2, molecular docking, molecular dynamics, MM/GBSA, phytochemicals.
Abstract:
Aims: The rich ethnomedicinal practices of Dakshina Kannada have received considerable
attention, and many treatment methods have been documented. This work aimed to explore the traditional
medicinal plants originating from Dakshina Kannada for their anti-SARS-CoV-2 activity by employing in
silico methodologies.
Methods: Virtual screening of Dakshina Kannada's plants was conducted, which are known for their antiviral
activities. Potent plants were shortlisted as Tinospora cordifolia, Nyctanthes arbortristis, Bacopa
monnieri, Bombax ceiba, and Curcuma longa based on molecular docking scores. Among these, the active
plant Tinospora cordifolia possessed the most potent phytochemicals. Molecular dynamics (MD)
simulation and MM/GBSA calculations have been performed on cordifolioside A, syringin, and cordioside.
Results: Initially, the selected plants were docked into the active site of SARS-CoV-2 protein. MD simulations
were performed to investigate the various conformations and validate the docking results, revealing
that cordifolioside A and syringin were more stable than cordioside. The stability of the phytoconstituents
in complex with SARS-CoV-2 protein was steady throughout the 100 ns simulation time. Finally,
the binding free energies were calculated using the MM/GBSA method. The pharmacophore model has
confirmed the hydrogen bond interactions, and PASS prediction determined their antiviral activities.
Conclusion: Thus, the present study identified the most potent plant from Dakshina Kannada against the
SARS-CoV-2 virus as Tinospora cordifolia with powerful phytochemicals (cordifolioside A, syringin and
cordioside). Furthermore, in vitro and in vivo experiments are needed to provide experimental data to
develop anti-SARS-CoV-2 drugs.