ArticlePhytotherapy research : PTR2020
The natural way forward: Molecular dynamics simulation analysis of phytochemicals from Indian medicinal plants as potential inhibitors of SARS-CoV-2 targets.
Article in Phytotherapy research : PTR, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed, 81 citations in OpenAlex.
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- Designing and Evaluation of a Novel IL-1RA Fusion Cytokine to Enhance the Pharmacokinetics and Receptor Affinity for Better Therapeutic Intervention in Inflammatory Disorders.Current computer-aided drug design · 2026Article
- Allosteric Coupling in Full-Length Lyn Kinase Revealed by Molecular Dynamics and Network Analysis.International journal of molecular sciences · 2025Article
- The Dynamical Asymmetry in SARS-CoV2 Protease Reveals the Exchange Between Catalytic Activity and Stability in Homodimers.Molecules (Basel, Switzerland) · 2025Article
- Repurposing of Compounds fromCurrent computer-aided drug design · 2025Article
- Revolutionizing Chikungunya Vaccines: mRNA Breakthroughs With Molecular and Immune Simulations.Bioinformatics and biology insights · 2025Article
- In-silico identification of COX-2 inhibitory phytochemicals from traditional medicinal plants: molecular docking, dynamics, and safety predictions.In silico pharmacology · 2025Article
- Identification of novel potential cathepsin-B inhibitors through pharmacophore-based virtual screening, molecular docking, and dynamics simulation studies for the treatment of Alzheimer's disease.Molecular diversity · 2024Article
- Regulation of NS5B Polymerase Activity of Hepatitis C Virus by Target Specific Phytotherapeutics: An In-Silico Molecular Dynamics Approach.Cell biochemistry and biophysics · 2024Article
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- Nigella sativa and its chemical constituents: pre-clinical and clinical evidence for their potential anti-SARS-CoV-2 effects.Inflammopharmacology · 2024Review
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- Identification of novel drug targets forFrontiers in bioinformatics · 2024Article
- Exploring Lead-Like Molecules of Traditional Chinese Medicine for Treatment Quest againstBioMed research international · 2024Article
- Molecular dynamics simulation analysis of structural dynamic cross correlation induced by odorant hydrogen-bonding in mouse eugenol ol- factory receptor.Biophysics and physicobiology · 2024Article
- Molecular modeling and simulations of some antiviral drugs, benzylisoquinoline alkaloid, and coumarin molecules to investigate the effects on Mpro main viral protease inhibition.Biochemistry and biophysics reports · 2023Article
- A Comprehensive Update of Various Attempts by Medicinal Chemists to Combat COVID-19 through Natural Products.Molecules (Basel, Switzerland) · 2023Review
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The pandemic COVID-19 has become a global panic-forcing life towards a compromised "new normal." Antiviral therapy against SARS-CoV-2 is still lacking. Thus, development of natural inhibitors as a prophylactic measure is an attractive strategy. In this context, this work explored phytochemicals as potential inhibitors for SARS-CoV-2 by performing all atom molecular dynamics simulations using high performance computing for 8 rationally screened phytochemicals from Withania somnifera and Azadirachta indica and two repurposed drugs docked with the spike glycoprotein and the main protease of SARS-CoV-2. These phytochemicals were rationally screened from 55 Indian medicinal plants in our previous work. MM/PBSA, principal component analysis (PCA), dynamic cross correlation matrix (DCCM) plots and biological pathway enrichment analysis were performed to reveal the therapeutic efficacy of these phytochemicals. The results revealed that Withanolide R (-141.96 KJ/mol) and 2,3-Dihydrowithaferin A (-87.60 KJ/mol) were with the lowest relative free energy of binding for main protease and the spike proteins respectively. It was also observed that the phytochemicals exhibit a remarkable multipotency with the ability to modulate various human biological pathways especially pathways in cancer. Conclusively we suggest that these compounds need further detailed in vivo experimental evaluation and clinical validation to implement them as potent therapeutic agents for combating SARS-CoV-2.
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