title: Identification of G-quadruplex DNA/RNA binders: Structure-based virtual screening and biophysical characterization.
abstract: Recent findings demonstrated that, in mammalian cells, telomere DNA (Tel) is transcribed into telomeric repeat-containing RNA (TERRA), which is involved in fundamental biological processes, thus representing a promising anticancer target. For this reason, the discovery of dual (as well as selective) Tel/TERRA G-quadruplex (G4) binders could represent an innovative strategy to enhance telomerase inhibition.
  
  
  
  Initially, docking simulations of known Tel and TERRA active ligands were performed on the 3D coordinates of bimolecular G4 Tel DNA (Tel2) and TERRA (TERRA2). Structure-based pharmacophore models were generated on the best complexes and employed for the virtual screening of ~257,000 natural compounds. The 20 best candidates were submitted to biophysical assays, which included circular dichroism and mass spectrometry at different K+concentrations.
  
  
  
  Three hits were here identified and characterized by biophysical assays. Compound 7 acts as dual Tel2/TERRA2G4-ligand at physiological KCl concentration, while hits 15 and 17 show preferential thermal stabilization for Tel2DNA. The different molecular recognition against the two targets was also discussed.
  
  
  
  Our successful results pave the way to further lead optimization to achieve both increased selectivity and stabilizing effect against TERRA and Tel DNA G4s.
  
  
  
  The current study combines for the first time molecular modelling and biophysical assays applied to bimolecular DNA and RNA G4s, leading to the identification of innovative ligand chemical scaffolds with a promising anticancer profile. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
authors.affiliation: Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", viale Europa, 88100, Catanzaro, Italy.
authors.forename: Roberta
authors.initials: R
authors.lastname: Rocca
authors.affiliation: Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", viale Europa, 88100, Catanzaro, Italy.
authors.forename: Federica
authors.initials: F
authors.lastname: Moraca
authors.affiliation: Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", viale Europa, 88100, Catanzaro, Italy. Electronic address: gcosta@unicz.it.
authors.forename: Giosuè
authors.initials: G
authors.lastname: Costa
authors.affiliation: Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Nadai
authors.affiliation: Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy.
authors.forename: Matteo
authors.initials: M
authors.lastname: Scalabrin
authors.affiliation: Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", viale Europa, 88100, Catanzaro, Italy.
authors.forename: Carmine
authors.initials: C
authors.lastname: Talarico
authors.affiliation: Dipartimento di Scienze della Vita e dell'Ambiente, Università degli Studi di Cagliari, via Ospedale 72, Cagliari 09124, Italy.
authors.forename: Simona
authors.initials: S
authors.lastname: Distinto
authors.affiliation: Dipartimento di Scienze della Vita e dell'Ambiente, Università degli Studi di Cagliari, via Ospedale 72, Cagliari 09124, Italy.
authors.forename: Elias
authors.initials: E
authors.lastname: Maccioni
authors.affiliation: Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", viale Europa, 88100, Catanzaro, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Ortuso
authors.affiliation: Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", viale Europa, 88100, Catanzaro, Italy.
authors.forename: Anna
authors.initials: A
authors.lastname: Artese
authors.affiliation: Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", viale Europa, 88100, Catanzaro, Italy. Electronic address: alcaro@unicz.it.
authors.forename: Stefano
authors.initials: S
authors.lastname: Alcaro
authors.affiliation: Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy.
authors.forename: Sara N
authors.initials: SN
authors.lastname: Richter
mesh_terms: D000970:Antineoplastic Agents / Q000737:chemistry / Q000378:metabolism* / Q000494:pharmacology; D001665:Binding Sites; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry / Q000187:drug effects / Q000235:genetics / Q000378:metabolism*; D015195:Drug Design; D054856:G-Quadruplexes / Q000187:drug effects; D006151:Guanosine / Q000737:chemistry / Q000378:metabolism*; D057166:High-Throughput Screening Assays; D008024:Ligands; D062105:Molecular Docking Simulation; D009691:Nucleic Acid Denaturation; D011188:Potassium / Q000737:chemistry; D012313:RNA / Q000737:chemistry / Q000187:drug effects / Q000235:genetics / Q000378:metabolism*; D020871:RNA Stability; D021241:Spectrometry, Mass, Electrospray Ionization; D013329:Structure-Activity Relationship; D019098:Telomerase / Q000737:chemistry / Q000187:drug effects / Q000235:genetics / Q000378:metabolism*; D013696:Temperature
chemical_list: D000970:Antineoplastic Agents; D008024:Ligands; D006151:Guanosine; D012313:RNA; D004247:DNA; D019098:Telomerase; D011188:Potassium
keywords: Circular dichroism; G-quadruplex DNA; Mass spectrometry; TERRA; Virtual screening