Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations
Published 2017 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations
Authors
Keywords
-
Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 114, Issue 11, Pages E2136-E2145
Publisher
Proceedings of the National Academy of Sciences
Online
2017-02-24
DOI
10.1073/pnas.1612627114
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Hit Identification of a Novel Dual Binder forh-telo/c-mycG-Quadruplex by a Combination of Pharmacophore Structure-Based Virtual Screening and Docking Refinement
- (2016) Roberta Rocca et al. ChemMedChem
- The Free Energy Landscape of GABA Binding to a Pentameric Ligand-Gated Ion Channel and Its Disruption by Mutations
- (2016) Federico Comitani et al. Journal of Chemical Theory and Computation
- Toward the Development of Specific G-Quadruplex Binders: Synthesis, Biophysical, and Biological Studies of New Hydrazone Derivatives
- (2016) Jussara Amato et al. JOURNAL OF MEDICINAL CHEMISTRY
- Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations
- (2016) Mickaël Lelimousin et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Selective repression of RET proto-oncogene in medullary thyroid carcinoma by a natural alkaloid berberine
- (2015) Vishnu Muthuraj Kumarasamy et al. BMC CANCER
- Looking for Efficient G-Quadruplex Ligands: Evidence for Selective Stabilizing Properties and Telomere Damage by Drug-Like Molecules
- (2015) Bruno Pagano et al. ChemMedChem
- Steroidal scaffolds as FXR and GPBAR1 ligands: from chemistry to therapeutical application
- (2015) Valentina Sepe et al. Future Medicinal Chemistry
- Funnel-Metadynamics and Solution NMR to Estimate Protein–Ligand Affinities
- (2015) Laura Troussicot et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field
- (2015) Lingle Wang et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Kinetics of protein–ligand unbinding: Predicting pathways, rates, and rate-limiting steps
- (2015) Pratyush Tiwary et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Energetics and Structural Characterization of the large-scale Functional Motion of Adenylate Kinase
- (2015) Elena Formoso et al. Scientific Reports
- The Glycan Role in the Glycopeptide Immunogenicity Revealed by Atomistic Simulations and Spectroscopic Experiments on the Multiple Sclerosis Biomarker CSF114(Glc)
- (2015) Agostino Bruno et al. Scientific Reports
- Modification on Ursodeoxycholic Acid (UDCA) Scaffold. Discovery of Bile Acid Derivatives As Selective Agonists of Cell-Surface G-Protein Coupled Bile Acid Receptor 1 (GP-BAR1)
- (2014) Valentina Sepe et al. JOURNAL OF MEDICINAL CHEMISTRY
- Marine and Semi-Synthetic Hydroxysteroids as New Scaffolds for Pregnane X Receptor Modulation
- (2014) Valentina Sepe et al. Marine Drugs
- Structure-Based Virtual Screening of Novel Natural Alkaloid Derivatives as Potential Binders of h-telo and c-myc DNA G-Quadruplex Conformations
- (2014) Roberta Rocca et al. MOLECULES
- Mechanistic insight into ligand binding to G-quadruplex DNA
- (2014) Francesco Saverio Di Leva et al. NUCLEIC ACIDS RESEARCH
- Well-Tempered Metadynamics Converges Asymptotically
- (2014) James F. Dama et al. PHYSICAL REVIEW LETTERS
- The G-Triplex DNA
- (2013) Vittorio Limongelli et al. ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
- GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
- (2013) Sander Pronk et al. BIOINFORMATICS
- Toward the design of new DNA G-quadruplex ligands through rational analysis of polymorphism and binding data
- (2013) Anna Artese et al. EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
- Insights on pregnane-X-receptor modulation. Natural and semisynthetic steroids from Theonella marine sponges
- (2013) Valentina Sepe et al. EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
- Binding Mechanism of the Farnesoid X Receptor Marine Antagonist Suvanine Reveals a Strategy To Forestall Drug Modulation on Nuclear Receptors. Design, Synthesis, and Biological Evaluation of Novel Ligands
- (2013) Francesco Saverio Di Leva et al. JOURNAL OF MEDICINAL CHEMISTRY
- Identification and Characterization of New DNA G-Quadruplex Binders Selected by a Combination of Ligand and Structure-Based Virtual Screening Approaches
- (2013) Stefano Alcaro et al. JOURNAL OF MEDICINAL CHEMISTRY
- Quantitative visualization of DNA G-quadruplex structures in human cells
- (2013) Giulia Biffi et al. Nature Chemistry
- Proton transfer through the water gossamer
- (2013) Ali Hassanali et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Funnel metadynamics as accurate binding free-energy method
- (2013) V. Limongelli et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- DNA Repair at Telomeres: Keeping the Ends Intact
- (2013) C. J. Webb et al. Cold Spring Harbor Perspectives in Biology
- Spectroscopic, Molecular Modeling, and NMR-Spectroscopic Investigation of the Binding Mode of the Natural Alkaloids Berberine and Sanguinarine to Human Telomeric G-Quadruplex DNA
- (2012) Irene Bessi et al. ACS Chemical Biology
- The Polymorphisms of DNA G-Quadruplex Investigated by Docking Experiments with Telomestatin Enantiomers
- (2012) Stefano Alcaro et al. CURRENT PHARMACEUTICAL DESIGN
- Spectroscopic probing of recognition of the G-quadruplex in c-kit promoter by small-molecule natural products
- (2012) Xiaojie Cui et al. INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
- New insights from molecular dynamic simulation studies of the multiple binding modes of a ligand with G-quadruplex DNA
- (2012) Jin-Qiang Hou et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- The crystal structure of human telomeric DNA complexed with berberine: an interesting case of stacked ligand to G-tetrad ratio higher than 1:1
- (2012) Carla Bazzicalupi et al. NUCLEIC ACIDS RESEARCH
- Sampling protein motion and solvent effect during ligand binding
- (2012) V. Limongelli et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A structural analysis of G-quadruplex/ligand interactions
- (2011) Shozeb M. Haider et al. BIOCHIMIE
- Insight into G-DNA Structural Polymorphism and Folding from Sequence and Loop Connectivity through Free Energy Analysis
- (2011) Xiaohui Cang et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Absolute Binding Free Energy Calculations of Sparsomycin Analogs to the Bacterial Ribosome
- (2010) Xiaoxia Ge et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Structural and Conformational Requisites in DNA Quadruplex Groove Binding: Another Piece to the Puzzle
- (2010) Sandro Cosconati et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition
- (2010) V. Limongelli et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A systematic review of the anticancer properties of berberine, a natural product from Chinese herbs
- (2009) Yiyi Sun et al. ANTI-CANCER DRUGS
- Synthesis and evaluation of 9-O-substituted berberine derivatives containing aza-aromatic terminal group as highly selective telomeric G-quadruplex stabilizing ligands
- (2009) Yan Ma et al. BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
- PLUMED: A portable plugin for free-energy calculations with molecular dynamics
- (2009) Massimiliano Bonomi et al. COMPUTER PHYSICS COMMUNICATIONS
- Computational Analysis of Human Immunodeficiency Virus (HIV) Type-1 Reverse Transcriptase Crystallographic Models Based on Significant Conserved Residues Found in Highly Active Antiretroviral Therapy (HAART)-Treated Patients (Supplementary Material)
- (2009) Stefano Alcaro et al. CURRENT MEDICINAL CHEMISTRY
- G-quadruplex nucleic acids as therapeutic targets
- (2009) Shankar Balasubramanian et al. CURRENT OPINION IN CHEMICAL BIOLOGY
- Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics
- (2009) M. Bonomi et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- 9-N-Substituted berberine derivatives: Stabilization of G-quadruplex DNA and down-regulation of oncogene c-myc
- (2008) Yan Ma et al. BIOORGANIC & MEDICINAL CHEMISTRY
- Natural products in drug discovery
- (2008) A HARVEY DRUG DISCOVERY TODAY
- Binding of berberine to human telomeric quadruplex - spectroscopic, calorimetric and molecular modeling studies
- (2008) Amit Arora et al. FEBS Journal
- Structural Basis of DNA Quadruplex Recognition by an Acridine Drug
- (2008) Nancy H. Campbell et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Dissociation of minor groove binders from DNA: insights from metadynamics simulations
- (2008) A. V. Vargiu et al. NUCLEIC ACIDS RESEARCH
- Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
- (2008) Alessandro Barducci et al. PHYSICAL REVIEW LETTERS
- A hitchhiker's guide to G-quadruplex ligands
- (2007) David Monchaud et al. ORGANIC & BIOMOLECULAR CHEMISTRY
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now