ArticleJournal of biomolecular structure & dynamics2021
Drug repurposing studies targeting SARS-CoV-2: an ensemble docking approach on drug target 3C-like protease (3CL
Article in Journal of biomolecular structure & dynamics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers, 1 of them a synthesis that pooled it.
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Who cites it
37 citing papers in PubMed, 1 synthesis or guideline pooled it, 54 citations in OpenAlex.
- Phytochemicals against SARS-CoV as potential drug leads.Biomedical journal · 2021Pooled it
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- Evaluating therapeutic potential of AYUSH-64 constituents against omicron variant of SARS-CoV-2 using ensemble docking and simulations.Current research in structural biology · 2024Article
- Drug repurposing to tackle parainfluenza 3 based on multi-similarities and network proximity analysis.Frontiers in pharmacology · 2024Article
- Inhibition of SARS-CoV-2 3CL protease by the anti-viral chimeric protein RetroMAD1.Scientific reports · 2023Article
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- Inhibitory Activity ofPlants (Basel, Switzerland) · 2023Article
- The Discovery of Potential SARS-CoV-2 Natural Inhibitors among 4924 African Metabolites Targeting the Papain-like Protease: A Multi-Phase In Silico Approach.Metabolites · 2022Article
- Virtual screening of substances used in the treatment of SARS-CoV-2 infection and analysis of compounds with known action on structurally similar proteins from other viruses.Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 2022Review
- Interaction of the new inhibitor paxlovid (PF-07321332) and ivermectin with the monomer of the main protease SARS-CoV-2: A volumetric study based on molecular dynamics, elastic networks, classical thermodynamics and SPT.Computational biology and chemistry · 2022Article
- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
- Functional nucleic acids as modular components against SARS-CoV-2: From diagnosis to therapeutics.Biosensors & bioelectronics · 2022Review
- A global picture: therapeutic perspectives for COVID-19.Immunotherapy · 2022Review
- Herbal Remedies, Nutraceuticals, and Dietary Supplements for COVID-19 Management: An Update.Clinical complementary medicine and pharmacology · 2022Review
- Molecular Docking as a Potential Approach in Repurposing Drugs Against COVID-19: a Systematic Review and Novel Pharmacophore Models.Current pharmacology reports · 2022Review
- Proposition of a new allosteric binding site for potential SARS-CoV-2 3CL protease inhibitors by utilizing molecular dynamics simulations and ensemble docking.Journal of biomolecular structure & dynamics · 2022Article
- Combination Therapy of Ledipasvir and Itraconazole in the Treatment of COVID-19 Patients Coinfected with Black Fungus: AnBioMed research international · 2022Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The COVID-19 pandemic has been responsible for several deaths worldwide. The causative agent behind this disease is the Severe Acute Respiratory Syndrome - novel Coronavirus 2 (SARS-CoV-2). SARS-CoV-2 belongs to the category of RNA viruses. The main protease, responsible for the cleavage of the viral polyprotein is considered as one of the hot targets for treating COVID-19. Earlier reports suggest the use of HIV anti-viral drugs for targeting the main protease of SARS-CoV, which caused SARS in the year 2002-2003. Hence, drug repurposing approach may prove to be useful in targeting the main protease of SARS-CoV-2. The high-resolution crystal structure of the main protease of SARS-CoV-2 (PDB ID: 6LU7) was used as the target. The Food and Drug Administration approved and SWEETLEAD database of drug molecules were screened. The apo form of the main protease was simulated for a cumulative of 150 ns and 10 μs open-source simulation data was used, to obtain conformations for ensemble docking. The representative structures for docking were selected using RMSD-based clustering and Markov State Modeling analysis. This ensemble docking approach for the main protease helped in exploring the conformational variation in the drug-binding site of the main protease leading to the efficient binding of more relevant drug molecules. The drugs obtained as top hits from the ensemble docking possessed anti-bacterial and anti-viral properties. This
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