ArticleNucleic acids research2014
Mechanistic insight into ligand binding to G-quadruplex DNA.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed, 86 citations in OpenAlex.
- Recovering Small Molecule Ligand-RNA Binding Pocket Binding Modes and Exploring Potential Binding Pathways Using Metadynamics.Molecules (Basel, Switzerland) · 2026Article
- Water-Soluble Heptacyclic Oligo-Heteroaryls Targeting G‑Quadruplex DNA via Groove-Binding Interactions.ACS omega · 2026Article
- Modulating G-quadruplexes for therapeutic intervention: Structural diversity, stability, and emerging nucleic-acid-based strategies.Molecular therapy. Nucleic acids · 2026Review
- Comparative Analysis of Crystal Violet-Binding Aptamers as Potential Cores for Binary Sensors.International journal of molecular sciences · 2025Article
- Thermodynamics and Kinetics of the Deintercalation of a Novel Anthracycline from Double-Stranded Oligonucleotide DNA.The journal of physical chemistry. B · 2025Article
- Three- and four-stranded nucleic acid structures and their ligands.RSC chemical biology · 2025Review
- Bioactive nutraceuticals as G4 stabilizers: potential cancer prevention and therapy-a critical review.Naunyn-Schmiedeberg's archives of pharmacology · 2024Review
- Binding free energy decomposition and multiple unbinding paths of buried ligands in a PreQ1 riboswitch.PLoS computational biology · 2021Article
- Recognition of single-stranded nucleic acids by small-molecule splicing modulators.Nucleic acids research · 2021Article
- Enhanced sampling molecular dynamics simulations correctly predict the diverse activities of a series of stiff-stilbene G-quadruplex DNA ligands.Chemical science · 2020Article
- Structure of a DNA G-Quadruplex Related to Osteoporosis with a G-A Bulge Forming aMolecules (Basel, Switzerland) · 2020Article
- Ligand binding free-energy calculations with funnel metadynamics.Nature protocols · 2020Article
- Spiro-Indole-Coumarin Hybrids: Synthesis, ADME, DFT, NBO Studies and In Silico Screening through Molecular Docking on DNA G-Quadruplex.ChemistrySelect · 2020Article
- Folding intermediate states of the parallel human telomeric G-quadruplex DNA explored using Well-Tempered Metadynamics.Scientific reports · 2020Article
- Article
- Assessment of a Single Decoupling Alchemical Approach for the Calculation of the Absolute Binding Free Energies of Protein-Peptide Complexes.Frontiers in molecular biosciences · 2018Article
- Binding of anticancer drug daunomycin to a TGGGGT G-quadruplex DNA probed by all-atom molecular dynamics simulations: additional pure groove binding mode and implications on designing more selective G-quadruplex ligands.Journal of molecular modeling · 2017Article
- High-resolution three-dimensional NMR structure of theThe Journal of biological chemistry · 2017Article
- Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Chelerythrine down regulates expression of VEGFA, BCL2 and KRAS by arresting G-Quadruplex structures at their promoter regions.Scientific reports · 2017Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 2 countries.
Funding
Abstract
Specific guanine-rich regions in human genome can form higher-order DNA structures called G-quadruplexes, which regulate many relevant biological processes. For instance, the formation of G-quadruplex at telomeres can alter cellular functions, inducing apoptosis. Thus, developing small molecules that are able to bind and stabilize the telomeric G-quadruplexes represents an attractive strategy for antitumor therapy. An example is 3-(benzo[d]thiazol-2-yl)-7-hydroxy-8-((4-(2-hydroxyethyl)piperazin-1-yl)methyl)-2H-chromen-2-one (compound 1: ), recently identified as potent ligand of the G-quadruplex [d(TGGGGT)]4 with promising in vitro antitumor activity. The experimental observations are suggestive of a complex binding mechanism that, despite efforts, has defied full characterization. Here, we provide through metadynamics simulations a comprehensive understanding of the binding mechanism of 1: to the G-quadruplex [d(TGGGGT)]4. In our calculations, the ligand explores all the available binding sites on the DNA structure and the free-energy landscape of the whole binding process is computed. We have thus disclosed a peculiar hopping binding mechanism whereas 1: is able to bind both to the groove and to the 3' end of the G-quadruplex. Our results fully explain the available experimental data, rendering our approach of great value for further ligand/DNA studies.
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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.