ArticleProceedings of the National Academy of Sciences of the United States of America2017
Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Metadynamics Simulations Meet Ligand Design for the Reversible Inhibition of Human Peroxiredoxin 5.ACS omega · 2026Article
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- Unraveling the Molecular Basis for G-Quadruplex-Binders to ALS/FTD-Associated G4C2 Repeats of the C9orf72 Gene.Chembiochem : a European journal of chemical biology · 2025Article
- Stabilization of Hoogsteen H-bonds in G-quartet sheets by coordinated KBioImpacts : BI · 2025Article
- Insights into the Molecular Structure, Stability, and Biological Significance of Non-Canonical DNA Forms, with a Focus on G-Quadruplexes and i-Motifs.Molecules (Basel, Switzerland) · 2024Review
- Synthesis, biological evaluation and metadynamics simulations of novelRSC medicinal chemistry · 2024Article
- Structural biology in the age of X-ray free-electron lasers and exascale computing.Current opinion in structural biology · 2024Review
- Towards Computational Modeling of Ligand Binding to the ILPR G-Quadruplex.Molecules (Basel, Switzerland) · 2023Article
- Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design.International journal of molecular sciences · 2022Article
- Binding Properties of RNA Quadruplex of SARS-CoV-2 to Berberine Compared to Telomeric DNA Quadruplex.International journal of molecular sciences · 2022Article
- Major Achievements in the Design of Quadruplex-Interactive Small Molecules.Pharmaceuticals (Basel, Switzerland) · 2022Review
- Thiophen urea derivatives as a new class of hepatitis C virus entry inhibitors.Journal of enzyme inhibition and medicinal chemistry · 2021Article
- Article
- Berberine Molecular Recognition of the Parallel MYC G-Quadruplex in Solution.Journal of medicinal chemistry · 2021Article
- An Integrated Mass Spectrometry and Molecular Dynamics Simulations Approach Reveals the Spatial Organization Impact of Metal-Binding Sites on the Stability of Metal-Depleted Metallothionein-2 Species.Journal of the American Chemical Society · 2021Article
- Solution Structure of Ternary Complex of Berberine Bound to a dGMP-Fill-In Vacancy G-Quadruplex Formed in the PDGFR-β Promoter.Journal of the American Chemical Society · 2021Article
- Combining Electrospray Mass Spectrometry (ESI-MS) and Computational Techniques in the Assessment of G-Quadruplex Ligands: A Hybrid Approach to Optimize Hit Discovery.Journal of medicinal chemistry · 2021Article
- Recognition of single-stranded nucleic acids by small-molecule splicing modulators.Nucleic acids research · 2021Article
- Current Updates on Naturally Occurring Compounds Recognizing SARS-CoV-2 Druggable Targets.Molecules (Basel, Switzerland) · 2021Review
- Berberine Inhibits Telomerase Activity and Induces Cell Cycle Arrest and Telomere Erosion in Colorectal Cancer Cell Line, HCT 116.Molecules (Basel, Switzerland) · 2021Article
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Authors and funding
9 authors.
Funding
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Abstract
G-quadruplexes (G4s) are higher-order DNA structures typically present at promoter regions of genes and telomeres. Here, the G4 formation decreases the replicative DNA at each cell cycle, finally leading to apoptosis. The ability to control this mitotic clock, particularly in cancer cells, is fascinating and passes through a rational understanding of the ligand/G4 interaction. We demonstrate that an accurate description of the ligand/G4 binding mechanism is possible using an innovative free-energy method called funnel-metadynamics (FM), which we have recently developed to investigate ligand/protein interaction. Using FM simulations, we have elucidated the binding mechanism of the anticancer alkaloid berberine to the human telomeric G4 (
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