ArticleComputers in biology and medicine2022
Combined deep learning and molecular docking simulations approach identifies potentially effective FDA approved drugs for repurposing against SARS-CoV-2.
Article in Computers in biology and medicine, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- AI-driven drug-target interaction prediction: current progress, challenges, and future roadmap for precision medicine.Journal of computer-aided molecular design · 2026Review
- A Computational Framework to Evaluate Interactions of BPA and Its Analogs with Human Liver X Receptor-Beta for Health Risk Assessment.Chemical research in toxicology · 2026Article
- An Interpretable Deep Learning and Molecular Docking Framework for Repurposing Existing Drugs as Inhibitors of SARS-CoV-2 Main Protease.Molecules (Basel, Switzerland) · 2025Article
- Potential association between COVID-19 and neurological disorders: analysis of common genes and therapeutics.Frontiers in neurology · 2024Article
- Staying Ahead of the Game: How SARS-CoV-2 has Accelerated the Application of Machine Learning in Pandemic Management.BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy · 2023Review
- AiKPro: deep learning model for kinome-wide bioactivity profiling using structure-based sequence alignments and molecular 3D conformer ensemble descriptors.Scientific reports · 2023Article
- Cyclic lipopeptides as membrane fusion inhibitors against SARS-CoV-2: New tricks for old dogs.Antiviral research · 2023Article
- A review of SARS-CoV-2 drug repurposing: databases and machine learning models.Frontiers in pharmacology · 2023Review
- Drug Repurposing against KRAS Mutant G12C: A Machine Learning, Molecular Docking, and Molecular Dynamics Study.International journal of molecular sciences · 2022Article
- Identification of Diosmin and Flavin Adenine Dinucleotide as Repurposing Treatments for Monkeypox Virus: A Computational Study.International journal of molecular sciences · 2022Article
- Combined use of the hepatitis C drugs and amentoflavone could interfere with binding of the spike glycoprotein of SARS-CoV-2 to ACE2: the results of a molecular simulation study.Journal of biomolecular structure & dynamics · 2022Article
- Deep learning-based molecular dynamics simulation for structure-based drug design against SARS-CoV-2.Computational and structural biotechnology journal · 2022Review
- Riboflavin for COVID-19 Adjuvant Treatment in Patients With Mental Health Disorders: Observational Study.Frontiers in pharmacology · 2022Article
- Molecular Docking and Dynamics Investigations for Identifying Potential Inhibitors of the 3-Chymotrypsin-like Protease of SARS-CoV-2: Repurposing of Approved Pyrimidonic Pharmaceuticals for COVID-19 Treatment.Molecules (Basel, Switzerland) · 2021Article
- Proteomics advances towards developing SARS-CoV-2 therapeutics using in silico drug repurposing approaches.Drug discovery today. Technologies · 2021Review
- New Insights Into Drug Repurposing for COVID-19 Using Deep Learning.IEEE transactions on neural networks and learning systems · 2021Review
- Identification of FDA approved drugs against SARS-CoV-2 RNA dependent RNA polymerase (RdRp) and 3-chymotrypsin-like protease (3CLpro), drug repurposing approach.Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie · 2021Article
- A molecular modelling approach for identifying antiviral selenium-containing heterocyclic compounds that inhibit the main protease of SARS-CoV-2: an in silico investigation.Briefings in bioinformatics · 2021Article
- Machine and Deep Learning towards COVID-19 Diagnosis and Treatment: Survey, Challenges, and Future Directions.International journal of environmental research and public health · 2021Review
- Targeting SARS-CoV-2 RNA-dependent RNA polymerase: AnF1000Research · 2020Article
Corrections and comments
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Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ongoing pandemic of Coronavirus Disease 2019 (COVID-19) has posed a serious threat to global public health. Drug repurposing is a time-efficient approach to finding effective drugs against SARS-CoV-2 in this emergency. Here, we present a robust experimental design combining deep learning with molecular docking experiments to identify the most promising candidates from the list of FDA-approved drugs that can be repurposed to treat COVID-19. We have employed a deep learning-based Drug Target Interaction (DTI) model, called DeepDTA, with few improvements to predict drug-protein binding affinities, represented as KIBA scores, for 2440 FDA-approved and 8168 investigational drugs against 24 SARS-CoV-2 viral proteins. FDA-approved drugs with the highest KIBA scores were selected for molecular docking simulations. We ran around 50,000 docking simulations for 168 selected drugs against 285 total predicted and/or experimentally proven active sites of all 24 SARS-CoV-2 viral proteins. A list of 49 most promising FDA-approved drugs with the best consensus KIBA scores and binding affinity values against selected SARS-CoV-2 viral proteins was generated. Most importantly, 16 drugs including anidulafungin, velpatasvir, glecaprevir, rifapentine, flavin adenine dinucleotide (FAD), terlipressin, and selinexor demonstrated the highest predicted inhibitory potential against key SARS-CoV-2 viral proteins. We further measured the inhibitory activity of 5 compounds (rifapentine, velpatasvir, glecaprevir, anidulafungin, and FAD disodium) on SARS-CoV-2 PLpro using Ubiquitin-Rhodamine 110 Gly fluorescent intensity assay. The highest inhibition of PLpro activity was seen with rifapentine (IC50: 15.18 μM) and FAD disodium (IC50: 12.39 μM), the drugs with high predicted KIBA scores and binding affinities.
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