Abstract
There is an urgent need for reliable cure and preventive measures in this hour of the outbreak of SARS-CoV-2. Siddha- and Ayurvedic-based classical formulations have antiviral properties and great potential therapeutic choice in this pandemic situation. In the current study, in silico-based analysis for the binding potential of phytoconstituents from the classical formulations suggested by the Ministry of Ayush (Kabasura Kudineer, Shwas Kuthar Rasa with Kantakari and pippali churna, Talisadi churna) to the interface domain of the SARS-CoV-2 receptor-binding domain and angiotensin-converting enzyme 2 was performed. Maestro software from Schrodinger and tools like Glide Docking, induced fit docking, MM-GBSA, molecular dynamics (MD) simulation, and thermal MM-GBSA was used to analyze the binding of protein PDB ID:6VW1 and the selected 133 ligands in comparison with drug molecules like favipiravir and ribavirin. QikProp-based ADMET evaluation of all the phytoconstituents found them nontoxic and with drug-like properties. Selection of top ten ligands was made based on docking score for further MM-GBSA analysis. After performing IFD of top five molecules iso-chlorogenic acid, taxiphyllin, vasicine, catechin and caffeic acid, MD simulation and thermal MM-GBSA were done. Iso-chlorogenic acid had formed more stable interaction with key residue among all phytoconstituents. Computational-based study has highlighted the potential of the many constituents of traditional medicine to interact with the SARS-CoV-2 RBD and ACE2, which might stop the viral entry into the cell. However, in vivo experiments and clinical trials are necessary for supporting this claim.
Highlights
The emergence of the global pandemic caused by the novel coronavirus (COVID-19) with the epicenter in Wuhan, China, has claimed many lives and affected the world's population
An in silico approach is used to evaluate the traditional formulation of Siddha and Ayurveda system of medicine like Kabasura Kudineer, Shwas Kuthar Rasa with Kantakari and Pippali churna, Talisadi churna selected from the advisory issued by the ministry of Ayush for management of COVID-19 pandemic
The spike protein of COVID-19 has been proven to assist the entry of the virus into the cell more compared to its counterpart in the family of the severe acute respiratory syndrome (SARS) virus
Summary
The emergence of the global pandemic caused by the novel coronavirus (COVID-19) with the epicenter in Wuhan, China, has claimed many lives and affected the world's population. Till September 26, 2021, more than 232,349,581 people have contracted corona infection, and mortality of. 4,758,617 people has been registered in the world due to SARS-CoV-2 (2021a). Coronaviruses have already been a cause for two pandemics, i.e., Middle East respiratory syndrome (MERS) and severe acute respiratory syndrome (SARS), recently in the past two decades. SARS-CoV-2 member of β-coronavirus shares 96.2% genome sequence similarity with bat coronavirus (CoV RaTG13), 79.5% with SARS-CoV, indicating that SARS-CoV-2 might have been transmitted from bats (Guo et al 2020). CryoEM-based analysis of SARS-CoV-2 spike structure has shown the binding affinity of S-protein and ACE2 for SARS-CoV-2 is 10–20 times higher than SARS-CoV. The spike protein receptor-binding domain of SARS-CoV-2
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