ArticleJournal of computer-aided molecular design2021
Supervised molecular dynamics for exploring the druggability of the SARS-CoV-2 spike protein.
Article in Journal of computer-aided molecular design, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
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The trial behind it
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Who cites it
38 citing papers in PubMed, 61 citations in OpenAlex.
- Flavonoids as Structural Probes Reveal Conformationally Dependent Ligand Recognition in the SARS-CoV-2 JN.1 Spike Protein.International journal of molecular sciences · 2026Article
- Article
- Exploring SARS-CoV‑2 Spike RBD Pockets as Targets for Generic Drugs: A Combined Computational, Biophysical, and Biological Approach.ACS omega · 2025Article
- Hidden GPCR structural transitions addressed by multiple walker supervised molecular dynamics (mwSuMD).eLife · 2025Article
- Virtual Screening and Dynamic Simulation of Baloxavir Derivatives for Multitarget Breast Cancer Treatment.Anti-cancer agents in medicinal chemistry · 2025Article
- The Recognition Pathway of the SARS-CoV-2 Spike Receptor-Binding Domain to Human Angiotensin-Converting Enzyme 2.Molecules (Basel, Switzerland) · 2024Article
- Computational Drug Design Strategies for Fighting the COVID-19 Pandemic.Advances in experimental medicine and biology · 2024Article
- Comparative Study of the Mutations Observed in the SARS-CoV-2 RBD Variants of Concern and Their Impact on the Interaction with the ACE2 Protein.The journal of physical chemistry. B · 2023Article
- Multi-structural molecular docking (MOD) combined with molecular dynamics reveal the structural requirements of designing broad-spectrum inhibitors of SARS-CoV-2 entry to host cells.Scientific reports · 2023Article
- An In Silico Design of Peptides Targeting the S1/S2 Cleavage Site of the SARS-CoV-2 Spike Protein.Viruses · 2023Article
- A Computational Pipeline to Identify and Characterize Binding Sites and Interacting Chemotypes in SARS-CoV-2.ACS omega · 2023Article
- Review
- Triterpene Derivatives as Potential Inhibitors of the RBD Spike Protein from SARS-CoV-2: An In Silico Approach.Molecules (Basel, Switzerland) · 2023Article
- Identifying SARS-CoV-2 Drugs Binding to the Spike Fatty Acid Binding Pocket Using In Silico Docking and Molecular Dynamics.International journal of molecular sciences · 2023Article
- Virtual screening and molecular dynamics simulations provide insight into repurposing drugs against SARS-CoV-2 variants Spike protein/ACE2 interface.Scientific reports · 2023Article
- In Silico Approach for the Evaluation of the Potential Antiviral Activity of Extra Virgin Olive Oil (EVOO) Bioactive Constituents Oleuropein and Oleocanthal on Spike Therapeutic Drug Target of SARS-CoV-2.Molecules (Basel, Switzerland) · 2022Article
- A Pathway Model to Understand the Evolution of Spike Protein Binding to ACE2 in SARS-CoV-2 Variants.Biomolecules · 2022Article
- The impacts of 13 novel mutations of SARS-CoV-2 on protein dynamics: In silico analysis from Turkey.Human gene (Amsterdam, Netherlands) · 2022Article
- Molecular dynamics studies reveal structural and functional features of the SARS-CoV-2 spike protein.BioEssays : news and reviews in molecular, cellular and developmental biology · 2022Review
- Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2.Chemical reviews · 2022Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
The recent outbreak of the respiratory syndrome-related coronavirus (SARS-CoV-2) is stimulating an unprecedented scientific campaign to alleviate the burden of the coronavirus disease (COVID-19). One line of research has focused on targeting SARS-CoV-2 proteins fundamental for its replication by repurposing drugs approved for other diseases. The first interaction between the virus and the host cell is mediated by the spike protein on the virus surface and the human angiotensin-converting enzyme (ACE2). Small molecules able to bind the receptor-binding domain (RBD) of the spike protein and disrupt the binding to ACE2 would offer an important tool for slowing, or even preventing, the infection. Here, we screened 2421 approved small molecules in silico and validated the docking outcomes through extensive molecular dynamics simulations. Out of six drugs characterized as putative RBD binders, the cephalosporin antibiotic cefsulodin was further assessed for its effect on the binding between the RBD and ACE2, suggesting that it is important to consider the dynamic formation of the heterodimer between RBD and ACE2 when judging any potential candidate.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.