Repurposing of the herbal formulations: molecular docking and molecular dynamics simulation studies to validate the efficacy of phytocompounds against SARS-CoV-2 proteins
Authors
Chinmayi Joshi
aGujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
Armi Chaudhari
aGujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
Chaitanya Joshi
aGujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
Madhvi Joshi
aGujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
Snehal Bagatharia
bGujarat State Biotechnology Mission, Gandhinagar, Gujarat, India
Keywords:
COVID-19, traditional medicine, polyherbal formulations, validation
Abstract
Herbal formulations mentioned in traditional medicinal texts were investigated for in silico effect against SARS-COV-2 proteins involved in various functions of a virus such as attachment, entry, replication, transcription, etc. To repurpose and validate polyherbal formulations, molecular docking was performed to study the interactions of more than 150 compounds from various formulations against the SARS-CoV-2 proteins. Molecular dynamics (MD) simulation was performed to evaluate the interaction of top scored ligands with the various receptor proteins. The docking results showed that Liquiritic acid, Liquorice acid, Terchebulin, Glabrolide, Casuarinin, Corilagin, Chebulagic acid, Neochebulinic acid, Daturataturin A, and Taraxerol were effective against SARS-COV-2 proteins with higher binding affinities with different proteins. Results of MD simulations validated the stability of ligands from potent formulations with various receptors of SARS-CoV-2. Binding free energy analysis suggested the favourable interactions of phytocompounds with the recpetors. Besides, in silico comparison of the various formulations determined that Pathyadi kwath, Sanjeevani vati, Yashtimadhu, Tribhuvan Keeratiras, and Septillin were more effective than Samshamni vati, AYUSH-64, and Trikatu. Polyherbal formulations having anti-COVID-19 potential can be used for the treatment with adequate monitoring. New formulations may also be developed for systematic trials based on ranking from these studies.
Communicated by Ramaswamy H. Sarma.
Keywords: COVID-19, traditional medicine, polyherbal formulations, validation
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