title: Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations.
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 (d[AG3(T2AG3)3]), computing also the binding free-energy landscape. Two ligand binding modes have been identified as the lowest energy states. Furthermore, we have found prebinding sites, which are preparatory to reach the final binding mode. In our simulations, the ions and the water molecules have been explicitly represented and the energetic contribution of the solvent during ligand binding evaluated. Our theoretical results provide an accurate estimate of the absolute ligand/DNA binding free energy ([Formula: see text] = -10.3 ± 0.5 kcal/mol) that we validated through steady-state fluorescence binding assays. The good agreement between the theoretical and experimental value demonstrates that FM is a most powerful method to investigate ligand/DNA interaction and can be a useful tool for the rational design also of G4 ligands.
authors.affiliation: Dipartimento di Scienze della Salute, University of Catanzaro "Magna Græcia," I-88100 Catanzaro, Italy.
authors.forename: Federica
authors.initials: F
authors.lastname: Moraca
authors.affiliation: Department of Pharmacy, University of Naples "Federico II," I-80131 Naples, Italy.
authors.forename: Jussara
authors.initials: J
authors.lastname: Amato
authors.affiliation: Dipartimento di Scienze della Salute, University of Catanzaro "Magna Græcia," I-88100 Catanzaro, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Ortuso
authors.affiliation: Dipartimento di Scienze della Salute, University of Catanzaro "Magna Græcia," I-88100 Catanzaro, Italy.
authors.forename: Anna
authors.initials: A
authors.lastname: Artese
authors.affiliation: Department of Pharmacy, University of Naples "Federico II," I-80131 Naples, Italy.
authors.forename: Bruno
authors.identifier: 0000-0002-7716-9010
authors.initials: B
authors.lastname: Pagano
authors.affiliation: Department of Pharmacy, University of Naples "Federico II," I-80131 Naples, Italy.
authors.forename: Ettore
authors.initials: E
authors.lastname: Novellino
authors.affiliation: Dipartimento di Scienze della Salute, University of Catanzaro "Magna Græcia," I-88100 Catanzaro, Italy.
authors.forename: Stefano
authors.initials: S
authors.lastname: Alcaro
authors.affiliation: Department of Chemistry and Applied Biosciences, Eidgenössische Technische Hochschule Zürich, CH-8093 Zurich, Switzerland.|Università della Svizzera Italiana (USI), Faculty of Informatics, Institute of Computational Science, CH-6900 Lugano, Switzerland.
authors.forename: Michele
authors.initials: M
authors.lastname: Parrinello
authors.affiliation: Department of Pharmacy, University of Naples "Federico II," I-80131 Naples, Italy; vittoriolimongelli@gmail.com.|Università della Svizzera Italiana (USI), Faculty of Informatics, Institute of Computational Science - Center for Computational Medicine in Cardiology, CH-6900 Lugano, Switzerland.
authors.forename: Vittorio
authors.initials: V
authors.lastname: Limongelli
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D054856:G-Quadruplexes; D008024:Ligands; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D015394:Molecular Structure; D012997:Solvents; D013050:Spectrometry, Fluorescence; D016615:Telomere / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D008024:Ligands; D012997:Solvents; D004247:DNA
keywords: DNA G-quadruplex; free-energy calculations; funnel-metadynamics; ligand binding free energy; ligand docking