ArticleChemMedChem2021
Inspecting the Mechanism of Fragment Hits Binding on SARS-CoV-2 M
Article in ChemMedChem, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Structuring Disorder via Supervised Molecular Dynamics: Uncovering Arginine-Glycine-Glycine-Mediated Ribonucleic Acid-Intrinsically Disordered Region Recognition Mechanisms.Journal of chemical information and modeling · 2026Article
- FMOPhore for hotspot identification and efficient fragment-to-lead growth strategies.Nature communications · 2026Article
- Structural Basis and Inhibitor Development of SARS-CoV-2 Papain-like Protease.Molecules (Basel, Switzerland) · 2026Review
- P2YACS pharmacology & translational science · 2025Article
- Thermal Titration Molecular Dynamics: The Revenge of the Fragments.Journal of chemical information and modeling · 2025Article
- Accurate prediction of dynamic protein-ligand binding using P-score ranking.Journal of computational chemistry · 2024Article
- Fighting Antimicrobial Resistance: Insights on How theJournal of chemical information and modeling · 2023Article
- Article
- Lessons Learnt from COVID-19: Computational Strategies for Facing Present and Future Pandemics.International journal of molecular sciences · 2023Review
- Discovery of the 3-Amino-1,2,4-triazine-Based Library as Selective PDK1 Inhibitors with Therapeutic Potential in Highly Aggressive Pancreatic Ductal Adenocarcinoma.International journal of molecular sciences · 2023Article
- "Dual Anta-Inhibitors" of the APharmaceuticals (Basel, Switzerland) · 2023Article
- Bat coronaviruses related to SARS-CoV-2: what about their 3CL proteases (MPro)?Journal of enzyme inhibition and medicinal chemistry · 2022Article
- Investigating RNA-protein recognition mechanisms through supervised molecular dynamics (SuMD) simulations.NAR genomics and bioinformatics · 2022Article
- From the Wuhan-Hu-1 strain to the XD and XE variants: is targeting the SARS-CoV-2 spike protein still a pharmaceutically relevant option against COVID-19?Journal of enzyme inhibition and medicinal chemistry · 2022Article
- Supervised Molecular Dynamics (SuMD) Insights into the mechanism of action of SARS-CoV-2 main protease inhibitor PF-07321332.Journal of enzyme inhibition and medicinal chemistry · 2021Article
- Inspecting the Mechanism of Fragment Hits Binding on SARS-CoV-2 MChemMedChem · 2021Article
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Authors and funding
6 authors.
Funding
Abstract
Computational approaches supporting the early characterization of fragment molecular recognition mechanism represent a valuable complement to more expansive and low-throughput experimental techniques. In this retrospective study, we have investigated the geometric accuracy with which high-throughput supervised molecular dynamics simulations (HT-SuMD) can anticipate the experimental bound state for a set of 23 fragments targeting the SARS-CoV-2 main protease. Despite the encouraging results herein reported, in line with those previously described for other MD-based posing approaches, a high number of incorrect binding modes still complicate HT-SuMD routine application. To overcome this limitation, fragment pose stability has been investigated and integrated as part of our in-silico pipeline, allowing us to prioritize only the more reliable predictions.
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Registered trials
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