1
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Nocentini A, Di Porzio A, Bonardi A, Bazzicalupi C, Petreni A, Biver T, Bua S, Marzano S, Amato J, Pagano B, Iaccarino N, De Tito S, Amente S, Supuran CT, Randazzo A, Gratteri P. Development of a multi-targeted chemotherapeutic approach based on G-quadruplex stabilisation and carbonic anhydrase inhibition. J Enzyme Inhib Med Chem 2024; 39:2366236. [PMID: 38905127 PMCID: PMC11195807 DOI: 10.1080/14756366.2024.2366236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 06/02/2024] [Indexed: 06/23/2024] Open
Abstract
A novel class of compounds designed to hit two anti-tumour targets, G-quadruplex structures and human carbonic anhydrases (hCAs) IX and XII is proposed. The induction/stabilisation of G-quadruplex structures by small molecules has emerged as an anticancer strategy, disrupting telomere maintenance and reducing oncogene expression. hCAs IX and XII are well-established anti-tumour targets, upregulated in many hypoxic tumours and contributing to metastasis. The ligands reported feature a berberine G-quadruplex stabiliser scaffold connected to a moiety inhibiting hCAs IX and XII. In vitro experiments showed that our compounds selectively stabilise G-quadruplex structures and inhibit hCAs IX and XII. The crystal structure of a telomeric G-quadruplex in complex with one of these ligands was obtained, shedding light on the ligand/target interaction mode. The most promising ligands showed significant cytotoxicity against CA IX-positive HeLa cancer cells in hypoxia, and the ability to stabilise G-quadruplexes within tumour cells.
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Affiliation(s)
- Alessio Nocentini
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Anna Di Porzio
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Alessandro Bonardi
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Carla Bazzicalupi
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Andrea Petreni
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Pisa, Italy
| | - Silvia Bua
- Research Institute of the University of Bucharest (ICUB), Bucharest, Romania
| | - Simona Marzano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Stefano De Tito
- Molecular Cell Biology of Autophagy, The Francis Crick Institute, London, UK
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples, Italy
| | - Claudiu T. Supuran
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Paola Gratteri
- NEUROFARBA Department, Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Sesto Fiorentino, Florence, Italy
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2
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Vlad IM, Nuță DC, Ancuceanu RV, Costea T, Coanda M, Popa M, Marutescu LG, Zarafu I, Ionita P, Pirvu CED, Bleotu C, Chifiriuc MC, Limban C. Insights into the Microbicidal, Antibiofilm, Antioxidant and Toxicity Profile of New O-Aryl-Carbamoyl-Oxymino-Fluorene Derivatives. Int J Mol Sci 2023; 24:ijms24087020. [PMID: 37108183 PMCID: PMC10138554 DOI: 10.3390/ijms24087020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
The unprecedented increase in microbial resistance rates to all current drugs raises an acute need for the design of more effective antimicrobial strategies. Moreover, the importance of oxidative stress due to chronic inflammation in infections with resistant bacteria represents a key factor for the development of new antibacterial agents with potential antioxidant effects. Thus, the purpose of this study was to bioevaluate new O-aryl-carbamoyl-oxymino-fluorene derivatives for their potential use against infectious diseases. With this aim, their antimicrobial effect was evaluated using quantitative assays (minimum inhibitory/bactericidal/biofilms inhibitory concentrations) (MIC/MBC/MBIC), the obtained values being 0.156-10/0.312-10/0.009-1.25 mg/mL), while some of the involved mechanisms (i.e., membrane depolarization) were investigated by flow cytometry. The antioxidant activity was evaluated by studying the scavenger capacity of DPPH and ABTS•+ radicals and the toxicity was tested in vitro on three cell lines and in vivo on the crustacean Artemia franciscana Kellog. The four compounds derived from 9H-fluoren-9-one oxime proved to exhibit promising antimicrobial features and particularly, a significant antibiofilm activity. The presence of chlorine induced an electron-withdrawing effect, favoring the anti-Staphylococcus aureus and that of the methyl group exhibited a +I effect of enhancing the anti-Candida albicans activity. The IC50 values calculated in the two toxicity assays revealed similar values and the potential of these compounds to inhibit the proliferation of tumoral cells. Taken together, all these data demonstrate the potential of the tested compounds to be further used for the development of novel antimicrobial and anticancer agents.
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Affiliation(s)
- Ilinca Margareta Vlad
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - Diana Camelia Nuță
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - Robert Viorel Ancuceanu
- Department of Pharmaceutical Botany and Cell Biology, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 6 TraianVuia, 020956 Bucharest, Romania
| | - Teodora Costea
- Department of Pharmacognosy, Phytochemistry and Phytotherapy, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - Maria Coanda
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - Marcela Popa
- Research Institute of the University of Bucharest-ICUB, University of Bucharest, 50567 Bucharest, Romania
| | - Luminita Gabriela Marutescu
- Research Institute of the University of Bucharest-ICUB, University of Bucharest, 50567 Bucharest, Romania
- Department of Botany & Microbiology, University of Bucharest, 050095 Bucharest, Romania
| | - Irina Zarafu
- Department of Organic Chemistry, Biochemistry and Catalysis, Faculty of Chemistry, University of Bucharest, 050663 Bucharest, Romania
| | - Petre Ionita
- Department of Organic Chemistry, Biochemistry and Catalysis, Faculty of Chemistry, University of Bucharest, 050663 Bucharest, Romania
| | - Cristina Elena Dinu Pirvu
- Department of Physical and Colloidal Chemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 020956 Bucharest, Romania
| | - Coralia Bleotu
- Research Institute of the University of Bucharest-ICUB, University of Bucharest, 50567 Bucharest, Romania
- Ştefan S. Nicolau Institute of Virology, 285 Mihai Bravu Avenue, 030304 Bucharest, Romania
| | - Mariana-Carmen Chifiriuc
- Department of Botany & Microbiology, University of Bucharest, 050095 Bucharest, Romania
- Romanian Academy, 050044 Bucharest, Romania
| | - Carmen Limban
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, "Carol Davila" University of Medicine and Pharmacy, 020956 Bucharest, Romania
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3
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Banerjee N, Panda S, Chatterjee S. Frontiers in G-Quadruplex Therapeutics in Cancer: Selection of Small Molecules, Peptides and Aptamers. Chem Biol Drug Des 2021; 99:1-31. [PMID: 34148284 DOI: 10.1111/cbdd.13910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/27/2021] [Accepted: 06/07/2021] [Indexed: 11/28/2022]
Abstract
G-quadruplex, a unique secondary structure in nucleic acids found throughout human genome, elicited widespread interest in the field of therapeutic research. Being present in key regulatory regions of oncogenes, RNAs and telomere, G-quadruplex structure regulates transcription, translation, splicing etc. Changes in its structure and stability leads to differential expression of oncogenes causing cancer. Thus, targeting G-Quadruplex structures with small molecules/other biologics has shown elevated research interest. Covering previous reports, in this review we try to enlighten the facts on the structural diversity in G-quadruplex ligands aiming to provide newer insights to design first-in-class drugs for the next generation cancer treatment.
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Affiliation(s)
- Nilanjan Banerjee
- Department of Biophysics, Bose Institute, P-1/12 CIT Road, Scheme VIIM, Kankurgachi, Kolkata, 700054, India
| | - Suman Panda
- Department of Biophysics, Bose Institute, P-1/12 CIT Road, Scheme VIIM, Kankurgachi, Kolkata, 700054, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, P-1/12 CIT Road, Scheme VIIM, Kankurgachi, Kolkata, 700054, India
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4
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Nimbarte VD, Wirmer‐Bartoschek J, Gande SL, Alshamleh I, Seibert M, Nasiri HR, Schnütgen F, Serve H, Schwalbe H. Synthesis and in Vitro Evaluation of Novel 5-Nitroindole Derivatives as c-Myc G-Quadruplex Binders with Anticancer Activity. ChemMedChem 2021; 16:1667-1679. [PMID: 33508167 PMCID: PMC8252724 DOI: 10.1002/cmdc.202000835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/26/2021] [Indexed: 01/05/2023]
Abstract
Lead-optimization strategies for compounds targeting c-Myc G-quadruplex (G4) DNA are being pursued to develop anticancer drugs. Here, we investigate the structure-activity- relationship (SAR) of a newly synthesized series of molecules based on the pyrrolidine-substituted 5-nitro indole scaffold to target G4 DNA. Our synthesized series allows modulation of flexible elements with a structurally preserved scaffold. Biological and biophysical analyses illustrate that substituted 5-nitroindole scaffolds bind to the c-Myc promoter G-quadruplex. These compounds downregulate c-Myc expression and induce cell-cycle arrest in the sub-G1/G1 phase in cancer cells. They further increase the concentration of intracellular reactive oxygen species. NMR spectra show that three of the newly synthesized compounds interact with the terminal G-quartets (5'- and 3'-ends) in a 2 : 1 stoichiometry.
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Affiliation(s)
- Vijaykumar D. Nimbarte
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue-Straße 760438Frankfurt am MainGermany
| | - Julia Wirmer‐Bartoschek
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue-Straße 760438Frankfurt am MainGermany
| | - Santosh L. Gande
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue-Straße 760438Frankfurt am MainGermany
- German Cancer Research Center and German Cancer ConsortiumIm Neuenheimer Feld 28069120HeidelbergGermany
| | - Islam Alshamleh
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue-Straße 760438Frankfurt am MainGermany
| | - Marcel Seibert
- Department of Medicine 2Hematology/OncologyUniversity Hospital FrankfurtGoethe UniversityTheodor-Stern-Kai 760596Frankfurt am MainGermany
| | - Hamid Reza Nasiri
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue-Straße 760438Frankfurt am MainGermany
| | - Frank Schnütgen
- German Cancer Research Center and German Cancer ConsortiumIm Neuenheimer Feld 28069120HeidelbergGermany
- Department of Medicine 2Hematology/OncologyUniversity Hospital FrankfurtGoethe UniversityTheodor-Stern-Kai 760596Frankfurt am MainGermany
- Frankfurt Cancer Institute (FCI)Theodor-Stern-Kai 760596Frankfurt am MainGermany
| | - Hubert Serve
- German Cancer Research Center and German Cancer ConsortiumIm Neuenheimer Feld 28069120HeidelbergGermany
- Department of Medicine 2Hematology/OncologyUniversity Hospital FrankfurtGoethe UniversityTheodor-Stern-Kai 760596Frankfurt am MainGermany
- Frankfurt Cancer Institute (FCI)Theodor-Stern-Kai 760596Frankfurt am MainGermany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Goethe University FrankfurtMax-von-Laue-Straße 760438Frankfurt am MainGermany
- German Cancer Research Center and German Cancer ConsortiumIm Neuenheimer Feld 28069120HeidelbergGermany
- Frankfurt Cancer Institute (FCI)Theodor-Stern-Kai 760596Frankfurt am MainGermany
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5
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Fluorene/fluorenone carboxamide derivatives as selective light-up fluorophores for c-myc G-quadruplex. Bioorg Med Chem Lett 2021; 36:127824. [PMID: 33513388 DOI: 10.1016/j.bmcl.2021.127824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/01/2021] [Accepted: 01/19/2021] [Indexed: 12/11/2022]
Abstract
The development of fluorescent dyes capable of selective recognition of G-quadruplexes is essential for studying its localization and biological functions. However, considering the G-quadruplex topologies may vary significantly, the synthesis of compounds showing both selectivity and strong fluorescence properties still remains a great challenge. Recently we have developed fluorene/fluorenone derivatives with structure-specific binding towards dsRNA, indicating its potential for structure-selective ligands. Herein, we report the synthesis of novel fluorene/fluorenone derivatives and their selectivity towards various DNA structures, particularly G-quadruplexes, two of which showed strong affinity to the proto-oncogene c-myc promoter G-quadruplex.
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6
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Yalçin E, Matković M, Jukić M, Obrovac LG, Piantanida I, Seferoğlu Z. Novel fluorene/fluorenone DNA and RNA binders as efficient non-toxic ds-RNA selective fluorescent probes. Tetrahedron 2018. [DOI: 10.1016/j.tet.2017.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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7
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Li D, Hou JQ, Long W, Lu YJ, Wong WL, Zhang K. A study on a telo21 G-quadruplex DNA specific binding ligand: enhancing the molecular recognition ability via the amino group interactions. RSC Adv 2018; 8:20222-20227. [PMID: 35541662 PMCID: PMC9080739 DOI: 10.1039/c8ra03833c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 06/22/2018] [Accepted: 05/27/2018] [Indexed: 02/02/2023] Open
Abstract
A symmetric ligand is synthesized composed of a core N-methylpyridinium scaffold and two para-substituted benzyl groups through a flexible ethylene bridge to form a novel three-ring-conjugated system. The ligand system was found to have only weak background fluorescent signal in aqueous or physiological conditions and exhibited strong fluorescent signal enhancement targeting at telo21 G-quadruplex structure rather than other types of nucleic acids. The comparison study with two terminal groups (–N(CH3)2versus –SCH3) indicates that the stimulated signal enhancement of specific binding is probably attributed to the hydrogen-bonding interactions through the amino groups in the G-quartets. The docking result illuminates the experimental observation that the ligand system showed only weak fluorescent signals in aqueous or physiological conditions while exhibiting a strong fluorescent signal upon binding to the telo21 G-quadruplex structure (binding energy: −6.2 kcal mol−1). A significant fluorescent signal enhancement attributed to hydrogen-bonding interactions through the amino groups of a small binding ligand in the G-quartets (binding energy: −6.2 kcal mol−1).![]()
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Affiliation(s)
- Dongli Li
- School of Chemical and Environmental Engineering
- Wuyi University
- Jiangmen 529020
- P. R. China
- International Healthcare Innovation Institute (Jiangmen)
| | - Jin-Qiang Hou
- Institute of Natural Medicine and Green Chemistry
- School of Chemical Engineering and Light Industry
- Guangdong University of Technology
- Guangzhou 510006
- P. R. China
| | - Wei Long
- Institute of Natural Medicine and Green Chemistry
- School of Chemical Engineering and Light Industry
- Guangdong University of Technology
- Guangzhou 510006
- P. R. China
| | - Yu-Jing Lu
- International Healthcare Innovation Institute (Jiangmen)
- Jiangmen 529040
- P. R. China
- Institute of Natural Medicine and Green Chemistry
- School of Chemical Engineering and Light Industry
| | - Wing-Leung Wong
- School of Chemical and Environmental Engineering
- Wuyi University
- Jiangmen 529020
- P. R. China
- International Healthcare Innovation Institute (Jiangmen)
| | - Kun Zhang
- School of Chemical and Environmental Engineering
- Wuyi University
- Jiangmen 529020
- P. R. China
- International Healthcare Innovation Institute (Jiangmen)
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8
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Rocca R, Talarico C, Moraca F, Costa G, Romeo I, Ortuso F, Alcaro S, Artese A. Molecular recognition of a carboxy pyridostatin toward G-quadruplex structures: Why does it prefer RNA? Chem Biol Drug Des 2017; 90:919-925. [PMID: 28459507 DOI: 10.1111/cbdd.13015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 04/21/2017] [Accepted: 04/25/2017] [Indexed: 01/21/2023]
Abstract
The pyridostatin (PDS) represents the lead compound of a family of G-quadruplex (G4) stabilizing synthetic small molecules based on a N,N'-bis(quinolinyl)pyridine-2,6-dicarboxamide scaffold. Its mechanism of action involves the induction of telomere dysfunction by competing for binding with telomere-associated proteins, such as human POT1. Recently, through a template-directed "in situ" click chemistry approach, a PDS derivative, the carboxypyridostatin (cPDS), was discovered. It has the peculiarity to exhibit high molecular specificity for RNA over DNA G4, while PDS is a good generic RNA and DNA G4-interacting small molecule. Structural data on the binding modes of these compounds are not available, and the selectivity mode of cPDS toward TERRA G4 is unknown too. Therefore, this work is aimed at rationalizing the selectivity of cPDS versus TERRA G4 by means of molecular dynamics and docking simulations, coupled to better understand the binding mode of these compounds to telomeric G4 structures. The comprehensive analysis of cPDS binding mode and its conformational behavior demonstrates the importance of the ligand conformation properties coupled with a remarkable solvation contribution. This work is expected to provide valuable clues for further rational design of novel and selective TERRA G4 binders.
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Affiliation(s)
- Roberta Rocca
- Laboratory of Medicinal Chemistry, Department of Health Sciences, University of Catanzaro, Catanzaro, Italy
| | - Carmine Talarico
- Laboratory of Medicinal Chemistry, Department of Health Sciences, University of Catanzaro, Catanzaro, Italy
| | - Federica Moraca
- Laboratory of Medicinal Chemistry, Department of Health Sciences, University of Catanzaro, Catanzaro, Italy
| | - Giosuè Costa
- Laboratory of Medicinal Chemistry, Department of Health Sciences, University of Catanzaro, Catanzaro, Italy
| | - Isabella Romeo
- Laboratory of Medicinal Chemistry, Department of Health Sciences, University of Catanzaro, Catanzaro, Italy
| | - Francesco Ortuso
- Laboratory of Medicinal Chemistry, Department of Health Sciences, University of Catanzaro, Catanzaro, Italy
| | - Stefano Alcaro
- Laboratory of Medicinal Chemistry, Department of Health Sciences, University of Catanzaro, Catanzaro, Italy
| | - Anna Artese
- Laboratory of Medicinal Chemistry, Department of Health Sciences, University of Catanzaro, Catanzaro, Italy
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9
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Rocca R, Costa G, Artese A, Parrotta L, Ortuso F, Maccioni E, Pinato O, Greco ML, Sissi C, Alcaro S, Distinto S, Moraca F. Hit Identification of a Novel Dual Binder for h-telo/c-myc G-Quadruplex by a Combination of Pharmacophore Structure-Based Virtual Screening and Docking Refinement. ChemMedChem 2016; 11:1721-33. [PMID: 27008476 DOI: 10.1002/cmdc.201600053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 02/29/2016] [Indexed: 12/28/2022]
Abstract
It is well known that G-quadruplexes are targets of great interest for their roles in crucial biological processes, such as aging and cancer. Hence, a promising strategy for anticancer drug therapy is the stabilization of these structures by small molecules. We report a high-throughput in silico screening of commercial libraries from several different vendors by means of a combined structure-based pharmacophore model approach followed by docking simulations. The compounds selected by the virtual screening procedure were then tested for their ability to interact with human telomeric G-quadruplex folding by circular dichroism, fluorescence spectroscopy, and fluorescence intercalator displacement. Our approach resulted in the identification of a 13-[(dimethylamino)methyl]-12-hydroxy-8H-benzo[c]indolo[3,2,1-ij][1,5]naphthyridin-8-one derivative as a novel promising stabilizer of G-quadruplex structures within the human telomeric and the c-myc promoter sequences.
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Affiliation(s)
- Roberta Rocca
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy.
| | - Anna Artese
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Lucia Parrotta
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Elias Maccioni
- Department of Life and Environment Sciences, University of Cagliari, Via Ospedale 72, 09124, Cagliari, Italy
| | - Odra Pinato
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Maria Laura Greco
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Simona Distinto
- Department of Life and Environment Sciences, University of Cagliari, Via Ospedale 72, 09124, Cagliari, Italy
| | - Federica Moraca
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
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10
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Cogoi S, Zorzet S, Shchekotikhin AE, Xodo LE. Potent Apoptotic Response Induced by Chloroacetamidine Anthrathiophenediones in Bladder Cancer Cells. J Med Chem 2015; 58:5476-85. [DOI: 10.1021/acs.jmedchem.5b00409] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Susanna Cogoi
- Department
of Medical and Biological Sciences, University of Udine, P.le Kolbe
4, 33100 Udine, Italy
| | - Sonia Zorzet
- Department
of Life Science, University of Trieste, Via Giorgieri 7-9, 34100 Trieste, Italy
| | | | - Luigi E. Xodo
- Department
of Medical and Biological Sciences, University of Udine, P.le Kolbe
4, 33100 Udine, Italy
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11
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Lavrado J, Brito H, Borralho PM, Ohnmacht SA, Kim NS, Leitão C, Pisco S, Gunaratnam M, Rodrigues CMP, Moreira R, Neidle S, Paulo A. KRAS oncogene repression in colon cancer cell lines by G-quadruplex binding indolo[3,2-c]quinolines. Sci Rep 2015; 5:9696. [PMID: 25853628 PMCID: PMC5382548 DOI: 10.1038/srep09696] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 03/05/2015] [Indexed: 01/29/2023] Open
Abstract
KRAS is one of the most frequently mutated oncogenes in human cancer, yet remaining undruggable. To explore a new therapeutic strategy, a library of 5-methyl-indolo[3,2-c]quinoline derivatives (IQc) with a range of alkyldiamine side chains was designed to target DNA and RNA G-quadruplexes (G4) in the promoter and 5′-UTR mRNA of the KRAS gene. Biophysical experiments showed that di-substituted IQc compounds are potent and selective KRAS G4 stabilizers. They preferentially inhibit the proliferation of KRAS mutant cancer cell lines (0.22 < IC50 < 4.80 μM), down-regulate KRAS promoter activity in a luciferase reporter assay, and reduce both KRAS mRNA and p21KRAS steady-state levels in mutant KRAS colon cancer cell lines. Additionally, IQcs induce cancer cell death by apoptosis, explained in part by their capacity to repress KRAS expression. Overall, the results suggest that targeting mutant KRAS at the gene level with G4 binding small molecules is a promising anticancer strategy.
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Affiliation(s)
- João Lavrado
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Hugo Brito
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Pedro M Borralho
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Stephan A Ohnmacht
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Nam-Soon Kim
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-333, Republic of Korea
| | - Clara Leitão
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Sílvia Pisco
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Mekala Gunaratnam
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Cecília M P Rodrigues
- Cell Function and Therapeutic Targeting Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Rui Moreira
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
| | - Stephen Neidle
- The School of Pharmacy, University College London. 29/39 Brunswick Square, London WC1N 1AX, United Kingdom
| | - Alexandra Paulo
- Medicinal Chemistry Group, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal, Av. Prof. Gama Pinto, 1649-003 Lisbon, Portugal
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12
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Pagano B, Amato J, Iaccarino N, Cingolani C, Zizza P, Biroccio A, Novellino E, Randazzo A. Looking for efficient G-quadruplex ligands: evidence for selective stabilizing properties and telomere damage by drug-like molecules. ChemMedChem 2015; 10:640-9. [PMID: 25694275 DOI: 10.1002/cmdc.201402552] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Indexed: 01/02/2023]
Abstract
There is currently significant interest in the development of G-quadruplex-interactive compounds, given the relationship between the ability to stabilize these non-canonical DNA structures and anticancer activity. In this study, a set of biophysical assays was applied to evaluate the binding of six drug-like ligands to DNA G-quadruplexes with different folding topologies. Interestingly, two of the investigated ligands showed selective G-quadruplex-stabilizing properties and biological activity. These compounds may represent useful leads for the development of more potent and selective ligands.
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Affiliation(s)
- Bruno Pagano
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Napoli (Italy)
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Structure-based virtual screening of novel natural alkaloid derivatives as potential binders of h-telo and c-myc DNA G-quadruplex conformations. Molecules 2014; 20:206-23. [PMID: 25547724 PMCID: PMC6272608 DOI: 10.3390/molecules20010206] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/15/2014] [Indexed: 01/08/2023] Open
Abstract
Several ligands can bind to the non-canonical G-quadruplex DNA structures thereby stabilizing them. These molecules can act as effective anticancer agents by stabilizing the telomeric regions of DNA or by regulating oncogene expression. In order to better interact with the quartets of G-quadruplex structures, G-binders are generally characterized by a large aromatic core involved in π-π stacking. Some natural flexible cyclic molecules from Traditional Chinese Medicine have shown high binding affinity with G-quadruplex, such as berbamine and many other alkaloids. Using the structural information available on G-quadruplex structures, we performed a high throughput in silico screening of commercially available alkaloid derivative databases by means of a structure-based approach based on docking and molecular dynamics simulations against the human telomeric sequence d[AG3(T2AG3)3] and the c-myc promoter structure. We identified 69 best hits reporting an improved theoretical binding affinity with respect to the active set. Among them, a berberine derivative, already known to remarkably inhibit telomerase activity, was related to a better theoretical affinity versusc-myc.
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Parrotta L, Ortuso F, Moraca F, Rocca R, Costa G, Alcaro S, Artese A. Targeting unimolecular G-quadruplex nucleic acids: a new paradigm for the drug discovery? Expert Opin Drug Discov 2014; 9:1167-87. [PMID: 25109710 DOI: 10.1517/17460441.2014.941353] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
INTRODUCTION G-quadruplexes (G4s) are targets of great interest because of their roles in crucial biological processes, such as aging and cancer. G4s are based on the formation of G-quartets, stabilised by Hoogsteen-type hydrogen bonds and by interaction with cations between the tetrads. These biologically relevant conformations were first discovered in eukaryotic chromosomal telomeric DNA, but have also been found in the proximal location of promoters in a number of human genes. Therefore, the extensive analysis of an intriguing target could move towards the rational drug design of new selective anticancer agents. AREAS COVERED The authors review G4 structural characterisation, with detailed insight related to the polymorphism issue. The authors describe the topologically distinct G4 structural forms and the factors involved in their interconversion mechanisms, such as the sequence of the oligonucleotides, the strand stoichiometry and orientation, the syn-anti conformation of the guanine glycosidic bonds and the G4 loop types and the environmental factors. Furthermore, the authors report several studies related to folding and unfolding kinetic profiles in order to understand the conformational view of monomolecular G4 formations. EXPERT OPINION G4 unimolecular nucleic acids can be considered as valid targets for the rational drug development of novel anticancer agents. Structural biology represents an essential link between the biology and medicinal chemistry knowledge in this field. In silico methods have already been demonstrated to be useful, especially if well integrated with biophysical tests. If this proves successful, the G4-targeting paradigm could also be extended to drug discovery beyond neoplastic pathologies.
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Affiliation(s)
- Lucia Parrotta
- Università degli Studi "Magna Græcia", Dipartimento di Scienze della Salute , Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro , Italy
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15
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Ungvarsky J, Plsikova J, Janovec L, Koval J, Mikes J, Mikesová L, Harvanova D, Fedorocko P, Kristian P, Kasparkova J, Brabec V, Vojtickova M, Sabolova D, Stramova Z, Rosocha J, Imrich J, Kozurkova M. Novel trisubstituted acridines as human telomeric quadruplex binding ligands. Bioorg Chem 2014; 57:13-29. [PMID: 25171773 DOI: 10.1016/j.bioorg.2014.07.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/25/2014] [Accepted: 07/27/2014] [Indexed: 11/24/2022]
Abstract
A novel series of trisubstituted acridines were synthesized with the aim of mimicking the effects of BRACO19. These compounds were synthesized by modifying the molecular structure of BRACO19 at positions 3 and 6 with heteroacyclic moieties. All of the derivatives presented in the study exhibited stabilizing effects on the human telomeric DNA quadruplex. UV-vis spectroscopy, circular dichroism, linear dichroism and viscosimetry were used in order to study the nature of the DNA binding in more detail. The results show that all of the novel derivatives were able to fold the single-stranded DNA sequences into antiparallel G-quadruplex structures, with derivative 15 exhibiting the highest stabilizing capability. Cell cycle analysis revealed that a primary trend of the "braco"-like derivatives was to arrest the cells in the S- and G2M-phases of the cell cycle within the first 72h, with derivative 13 and BRACO19 proving particularly effective in suppressing cell proliferation. All studies derivatives were less toxic to human fibroblast cell line in comparison with HT 29 cancer cell line.
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Affiliation(s)
- Jan Ungvarsky
- Department of Organic Chemistry, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Jana Plsikova
- Department of Biochemistry, Moyzesova 11, 04001 Kosice, Slovak Republic; Associated Tissue Bank of Faculty of Medicine, L. Pasteur University Hospital, Trieda SNP 1, 04166 Kosice, Slovak Republic
| | - Ladislav Janovec
- Department of Organic Chemistry, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Jan Koval
- Department of Cellular Biology, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Jaromir Mikes
- Department of Cellular Biology, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Lucia Mikesová
- Department of Cellular Biology, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Denisa Harvanova
- Associated Tissue Bank of Faculty of Medicine, L. Pasteur University Hospital, Trieda SNP 1, 04166 Kosice, Slovak Republic
| | - Peter Fedorocko
- Department of Cellular Biology, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Pavol Kristian
- Department of Organic Chemistry, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Jana Kasparkova
- Institute of Biophysics, Department of Molecular Biophysics and Pharmacology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Viktor Brabec
- Institute of Biophysics, Department of Molecular Biophysics and Pharmacology, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Maria Vojtickova
- Department of Organic Chemistry, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Danica Sabolova
- Department of Biochemistry, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Zuzana Stramova
- Department of Biochemistry, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Jan Rosocha
- Associated Tissue Bank of Faculty of Medicine, L. Pasteur University Hospital, Trieda SNP 1, 04166 Kosice, Slovak Republic
| | - Jan Imrich
- Department of Organic Chemistry, Moyzesova 11, 04001 Kosice, Slovak Republic
| | - Maria Kozurkova
- Department of Biochemistry, Moyzesova 11, 04001 Kosice, Slovak Republic.
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16
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Hepatitis C virus genetic variability and the presence of NS5B resistance-associated mutations as natural polymorphisms in selected genotypes could affect the response to NS5B inhibitors. Antimicrob Agents Chemother 2014; 58:2781-97. [PMID: 24590484 DOI: 10.1128/aac.02386-13] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Because of the extreme genetic variability of hepatitis C virus (HCV), we analyzed the NS5B polymerase genetic variability in circulating HCV genotypes/subtypes and its impact on the genetic barrier for the development of resistance to clinically relevant nucleoside inhibitors (NIs)/nonnucleoside inhibitors (NNIs). The study included 1,145 NS5B polymerase sequences retrieved from the Los Alamos HCV database and GenBank. The genetic barrier was calculated for drug resistance emergence. Prevalence and genetic barrier were calculated for 1 major NI and 32 NNI resistance variants (13 major and 19 minor) at 21 total NS5B positions. Docking calculations were used to analyze sofosbuvir affinity toward the diverse HCV genotypes. Overall, NS5B polymerase was moderately conserved among all HCV genotypes, with 313/591 amino acid residues (53.0%) showing ≤1% variability and 83/591 residues (14.0%) showing high variability (≥25.1%). Nine NNI resistance variants (2 major variants, 414L and 423I; 7 minor variants, 316N, 421V, 445F, 482L, 494A, 499A, and 556G) were found as natural polymorphisms in selected genotypes. In particular, 414L and 423I were found in HCV genotype 4 (HCV-4) (n = 14/38, 36.8%) and in all HCV-5 sequences (n = 17, 100%), respectively. Regardless of HCV genotype, the 282T major NI resistance variant and 10 major NNI resistance variants (316Y, 414L, 423I/T/V, 448H, 486V, 495L, 554D, and 559G) always required a single nucleotide substitution to be generated. Conversely, the other 3 major NNI resistance variants (414T, 419S, and 422K) were associated with a different genetic barrier score development among the six HCV genotypes. Sofosbuvir docking analysis highlighted a better ligand affinity toward HCV-2 than toward HCV-3, in agreement with the experimental observations. The genetic variability among HCV genotypes, particularly with the presence of polymorphisms at NNI resistance positions, could affect their responsiveness to NS5B inhibitors. A pretherapy HCV NS5B sequencing could help to provide patients with the full efficacy of NNI-containing regimens.
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Sattin G, Artese A, Nadai M, Costa G, Parrotta L, Alcaro S, Palumbo M, Richter SN. Conformation and stability of intramolecular telomeric G-quadruplexes: sequence effects in the loops. PLoS One 2013; 8:e84113. [PMID: 24367632 PMCID: PMC3867476 DOI: 10.1371/journal.pone.0084113] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 11/12/2013] [Indexed: 01/15/2023] Open
Abstract
Telomeres are guanine-rich sequences that protect the ends of chromosomes. These regions can fold into G-quadruplex structures and their stabilization by G-quadruplex ligands has been employed as an anticancer strategy. Genetic analysis in human telomeres revealed extensive allelic variation restricted to loop bases, indicating that the variant telomeric sequences maintain the ability to fold into G-quadruplex. To assess the effect of mutations in loop bases on G-quadruplex folding and stability, we performed a comprehensive analysis of mutant telomeric sequences by spectroscopic techniques, molecular dynamics simulations and gel electrophoresis. We found that when the first position in the loop was mutated from T to C or A the resulting structure adopted a less stable antiparallel topology; when the second position was mutated to C or A, lower thermal stability and no evident conformational change were observed; in contrast, substitution of the third position from A to C induced a more stable and original hybrid conformation, while mutation to T did not significantly affect G-quadruplex topology and stability. Our results indicate that allelic variations generate G-quadruplex telomeric structures with variable conformation and stability. This aspect needs to be taken into account when designing new potential anticancer molecules.
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Affiliation(s)
- Giovanna Sattin
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Anna Artese
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, Catanzaro, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, Catanzaro, Italy
| | - Lucia Parrotta
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università "Magna Græcia" di Catanzaro, Catanzaro, Italy
| | - Manlio Palumbo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Sara N. Richter
- Department of Molecular Medicine, University of Padua, Padua, Italy
- * E-mail:
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18
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Artese A, Costa G, Ortuso F, Parrotta L, Alcaro S. Identification of new natural DNA G-quadruplex binders selected by a structure-based virtual screening approach. Molecules 2013; 18:12051-70. [PMID: 24084014 PMCID: PMC6270229 DOI: 10.3390/molecules181012051] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 09/18/2013] [Accepted: 09/22/2013] [Indexed: 02/06/2023] Open
Abstract
The G-quadruplex DNA structures are mainly present at the terminal portion of telomeres and can be stabilized by ligands able to recognize them in a specific manner. The recognition process is usually related to the inhibition of the enzyme telomerase indirectly involved and over-expressed in a high percentage of human tumors. There are several ligands, characterized by different chemical structures, already reported in the literature for their ability to bind and stabilize the G-quadruplex structures. Using the structural and biological information available on these structures; we performed a high throughput in silico screening of commercially natural compounds databases by means of a structure-based approach followed by docking experiments against the human telomeric sequence d[AG₃(T₂AG₃)₃]. We identified 12 best hits characterized by different chemical scaffolds and conformational and physicochemical properties. All of them were associated to an improved theoretical binding affinity with respect to that of known selective G-binders. Among these hits there is a chalcone derivative; structurally very similar to the polyphenol butein; known to remarkably inhibit the telomerase activity.
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Affiliation(s)
- Anna Artese
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia", Campus "S. Venuta", Viale Europa, Germaneto, Catanzaro 88100, Italy.
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19
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Lee CC, Chang DM, Huang KF, Chen CL, Chen TC, Lo Y, Guh JH, Huang HS. Design, synthesis and antiproliferative evaluation of fluorenone analogs with DNA topoisomerase I inhibitory properties. Bioorg Med Chem 2013; 21:7125-33. [PMID: 24094433 DOI: 10.1016/j.bmc.2013.09.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 09/03/2013] [Accepted: 09/03/2013] [Indexed: 11/29/2022]
Abstract
A series of 2,7-diamidofluorenones were designed, synthesized, and screened by SRB assay. Some synthesized compounds exhibited antitumor activities in submicromolar range. Ten compounds (3a, 3b, 3c, 3g, 3j, 3l, 4a, 4h, 4i, and 4j) were also selected by NCI screening system and 3c (GI50=1.66 μM) appeared to be the most active agent of this series. Furthermore, 3c attenuated topoisomerase I-mediated DNA relaxation at low micromolar concentrations. These results indicated that fluorenones have potential to be further developed into anticancer drugs.
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Affiliation(s)
- Chia-Chung Lee
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan; School of Pharmacy, National Defense Medical Center, Taipei 114, Taiwan
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20
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Lavrado J, Borralho PM, Ohnmacht SA, Castro RE, Rodrigues CMP, Moreira R, dos Santos DJVA, Neidle S, Paulo A. Synthesis, G-quadruplex stabilisation, docking studies, and effect on cancer cells of indolo[3,2-b]quinolines with one, two, or three basic side chains. ChemMedChem 2013; 8:1648-61. [PMID: 23960016 DOI: 10.1002/cmdc.201300288] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Indexed: 11/07/2022]
Abstract
G-quadruplex (G4) DNA structures in telomeres and oncogenic promoter regions are potential targets for cancer therapy, and G4 ligands have been shown to modulate telomerase activity and oncogene transcription. Herein we report the synthesis and G4 thermal stabilisation effects, determined by FRET melting assays, of 20 indolo[3,2-b]quinolines mono-, di-, and trisubstituted with basic side chains. Molecular modelling studies were also performed in an attempt to rationalise the ligands' binding poses with G4. Overall, the results suggest that ligand binding and G4 DNA thermal stabilisation increase with an N5-methyl or a 7-carboxylate group and propylamine side chains, whereas selectivity between G4 and duplex DNA appears to be modulated by the number and relative position of basic side chains. From all the indoloquinoline derivatives studied, the novel trisubstituted compounds 3 d and 4 d, bearing a 7-(aminoalkyl)carboxylate side chain, stand out as the most promising compounds; they show high G4 thermal stabilisation (ΔTm values between 17 and 8 °C) with an inter-G4 ΔTm trend of Hsp90A>KRas21R≈F21T>c-Kit2, 10-fold selectivity for G4 over duplex DNA, and 100-fold selectivity for the HCT116 cancer cell line (IC50 and IC90: <10 μM) over primary rat hepatocytes. Compounds 3 d and 4 d also decreased protein expression levels of Hsp90 and KRas in HCT116 cancer cells.
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Affiliation(s)
- João Lavrado
- Medicinal Chemistry Group, Research Institute for Medicines and Pharmaceutical Sciences, Faculty of Pharmacy, University of Lisbon, Av. Prof. Gama Pinto, 1649-003 Lisbon (Portugal)
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21
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Artese A, Costa G, Distinto S, Moraca F, Ortuso F, Parrotta L, Alcaro S. Toward the design of new DNA G-quadruplex ligands through rational analysis of polymorphism and binding data. Eur J Med Chem 2013; 68:139-49. [PMID: 23974014 DOI: 10.1016/j.ejmech.2013.07.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 07/15/2013] [Accepted: 07/17/2013] [Indexed: 12/21/2022]
Abstract
Human telomeres play a key role in protecting chromosomal ends from fusion events; they are composed of d(TTAGGG) repeats, ranging in size from 3 to 15 kb. They form G-quadruplex DNA structures, stabilized by G-quartets in the presence of cations, and are involved in several biological processes. In particular, a telomere maintenance mechanism is provided by a specialized enzyme called telomerase, a reverse transcriptase able to add multiple copies of the 5'-GGTTAG-3' motif to the end of the G-strand of the telomere and which is over-expressed in the majority of cancer cells. The central cation has a crucial role in maintaining the stability of the structure. Based on its nature, it can be associated with different topological telomeric quadruplexes, which depend also on the orientation of the DNA strands and the syn/anti conformation of the guanines. Such a polymorphism, confirmed by the different structures deposited in the Protein Data Bank (PDB), prompted us to apply a computational protocol in order to investigate the conformational properties of a set of known G-quadruplex ligands and their molecular recognition against six different experimental models of the human telomeric sequence d[AG3(T2AG3)3]. The average AutoDock correlation between theoretical and experimental data yielded an r2 value equal to 0.882 among all the studied models. Such a result was always improved with respect to those of the single folds, with the exception of the parallel structure (r2 equal to 0.886), thus suggesting a key role of this G4 conformation in the stacking interaction network. Among the studied binders, a trisubstituted acridine and a dibenzophenanthroline derivative were well recognized by the parallel and the mixed G-quadruplex structures, allowing the identification of specific key contacts with DNA and the further design of more potent or target specific G-quadruplex ligands.
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Affiliation(s)
- Anna Artese
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Græcia", Campus "S. Venuta", Viale Europa, Germaneto, 88100 Catanzaro, Italy.
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22
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State-of-the-art and dissemination of computational tools for drug-design purposes: a survey among Italian academics and industrial institutions. Future Med Chem 2013; 5:907-27. [PMID: 23682568 DOI: 10.4155/fmc.13.59] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
During the first edition of the Computationally Driven Drug Discovery meeting, held in November 2011 at Dompé Pharma (L'Aquila, Italy), a questionnaire regarding the diffusion and the use of computational tools for drug-design purposes in both academia and industry was distributed among all participants. This is a follow-up of a previously reported investigation carried out among a few companies in 2007. The new questionnaire implemented five sections dedicated to: research group identification and classification; 18 different computational techniques; software information; hardware data; and economical business considerations. In this article, together with a detailed history of the different computational methods, a statistical analysis of the survey results that enabled the identification of the prevalent computational techniques adopted in drug-design projects is reported and a profile of the computational medicinal chemist currently working in academia and pharmaceutical companies in Italy is highlighted.
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23
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Zhou D, Tuo W, Hu H, Xu J, Chen H, Rao Z, Xiao Y, Hu X, Liu P. Synthesis and activity evaluation of tilorone analogs as potential anticancer agents. Eur J Med Chem 2013; 64:432-41. [PMID: 23665799 DOI: 10.1016/j.ejmech.2013.03.050] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/08/2013] [Accepted: 03/24/2013] [Indexed: 10/27/2022]
Abstract
Tilorone is an interferon inducer with anticancer activity. Twenty-two novel tilorone analogs were synthesized by improvements of fluorenone skeleton, side chains and amino groups to screen new anticancer agents. In vitro evaluation showed that ten new compounds had better anticancer activities than tilorone. Among them, 2c (IC50 < 7 μM against cancer cell lines and IC50 > 35 μM against non-cancer cell lines) and 5d (IC50 < 10 μM against cancer cell lines and IC50 > 53 μM against non-cancer cell lines) exhibited the best anticancer activities and selectivities. Pharmacophore modeling of highly active compounds was carried out by Molecular Operating Environment (MOE) to generate a visualized model for compound design in future study.
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Affiliation(s)
- Dingshan Zhou
- State Key Laboratory of Virology, Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China.
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24
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Alcaro S, Musetti C, Distinto S, Casatti M, Zagotto G, Artese A, Parrotta L, Moraca F, Costa G, Ortuso F, Maccioni E, Sissi C. Identification and characterization of new DNA G-quadruplex binders selected by a combination of ligand and structure-based virtual screening approaches. J Med Chem 2013; 56:843-55. [PMID: 23294188 DOI: 10.1021/jm3013486] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nowadays, it has been demonstrated that DNA G-quadruplex arrangements are involved in cellular aging and cancer, thus boosting the discovery of selective binders for these DNA secondary structures. By taking advantage of available structural and biological information on these structures, we performed a high throughput in silico screening of commercially available molecules databases by merging ligand- and structure-based approaches by means of docking experiments. Compounds selected by the virtual screening procedure were then tested for their ability to interact with the human telomeric G-quadruplex folding by circular dichroism, fluorescence spectroscopy, and photodynamic techniques. Interestingly, our screening succeeded in retrieving a new promising scaffold for G-quadruplex binders characterized by a psoralen moiety.
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Affiliation(s)
- Stefano Alcaro
- Dipartimento di Scienze della Salute, Università di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100 Catanzaro, Italy
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25
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Chen M, Svicher V, Artese A, Costa G, Alteri C, Ortuso F, Parrotta L, Liu Y, Liu C, Perno CF, Alcaro S, Zhang J. Detecting and understanding genetic and structural features in HIV-1 B subtype V3 underlying HIV-1 co-receptor usage. ACTA ACUST UNITED AC 2013; 29:451-60. [PMID: 23297034 DOI: 10.1093/bioinformatics/btt002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MOTIVATION To define V3 genetic elements and structural features underlying different HIV-1 co-receptor usage in vivo. RESULTS By probabilistically modeling mutations in the viruses isolated from HIV-1 B subtype patients, we present a unique statistical procedure that would first identify V3 determinants associated with the usage of different co-receptors cooperatively or independently, and then delineate the complicated interactions among mutations functioning cooperatively. We built a model based on dual usage of CXCR4 and CCR5 co-receptors. The molecular basis of our statistical predictions is further confirmed by phenotypic and molecular modeling analyses. Our results provide new insights on molecular basis of different HIV-1 co-receptor usage. This is critical to optimize the use of genotypic tropism testing in clinical practice and to obtain molecular-implication for design of vaccine and new entry-inhibitors.
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Affiliation(s)
- Mengjie Chen
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
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26
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Artese A, Parrotta L, Alcaro S, Ortuso F, Costa G, Sissi C. Molecular Recognition of Human Telomeric DNA by Phenanthroline-Based G-Quadruplex Ligands. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ojmc.2013.32006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Milelli A, Tumiatti V, Micco M, Rosini M, Zuccari G, Raffaghello L, Bianchi G, Pistoia V, Fernando Díaz J, Pera B, Trigili C, Barasoain I, Musetti C, Toniolo M, Sissi C, Alcaro S, Moraca F, Zini M, Stefanelli C, Minarini A. Structure–activity relationships of novel substituted naphthalene diimides as anticancer agents. Eur J Med Chem 2012; 57:417-28. [DOI: 10.1016/j.ejmech.2012.06.045] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 06/20/2012] [Accepted: 06/21/2012] [Indexed: 01/23/2023]
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Cento V, Mirabelli C, Salpini R, Dimonte S, Artese A, Costa G, Mercurio F, Svicher V, Parrotta L, Bertoli A, Ciotti M, Di Paolo D, Sarrecchia C, Andreoni M, Alcaro S, Angelico M, Perno CF, Ceccherini-Silberstein F. HCV genotypes are differently prone to the development of resistance to linear and macrocyclic protease inhibitors. PLoS One 2012; 7:e39652. [PMID: 22792183 PMCID: PMC3391197 DOI: 10.1371/journal.pone.0039652] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 05/24/2012] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Because of the extreme genetic variability of hepatitis C virus (HCV), we analyzed whether specific HCV-genotypes are differently prone to develop resistance to linear and macrocyclic protease-inhibitors (PIs). METHODS The study includes 1568 NS3-protease sequences, isolated from PI-naive patients infected with HCV-genotypes 1a (N = 621), 1b (N = 474), 2 (N = 72), 3 (N = 268), 4 (N = 54) 5 (N = 6), and 6 (N = 73). Genetic-barrier was calculated as the sum of nucleotide-transitions (score = 1) and/or nucleotide-transversions (score = 2.5) required for drug-resistance-mutations emergence. Forty-three mutations associated with PIs-resistance were analyzed (36A/M/L/G-41R-43S/V-54A/S/V-55A-Q80K/R/L/H/G-109K-138T-155K/Q/T/I/M/S/G/L-156T/V/G/S-158I-168A/H/T/V/E/I/G/N/Y-170A/T-175L). Structural analyses on NS3-protease and on putative RNA-models have been also performed. RESULTS Overall, NS3-protease was moderately conserved, with 85/181 (47.0%) amino-acids showing <1% variability. The catalytic-triad (H57-D81-S139) and 6/13 resistance-associated positions (Q41-F43-R109-R155-A156-V158) were fully conserved (variability <1%). Structural-analysis highlighted that most of the NS3-residues involved in drug-stabilization were highly conserved, while 7 PI-resistance residues, together with selected residues located in proximity of the PI-binding pocket, were highly variable among HCV-genotypes. Four resistance-mutations (80K/G-36L-175L) were found as natural polymorphisms in selected genotypes (80K present in 41.6% HCV-1a, 100% of HCV-5 and 20.6% HCV-6; 80G present in 94.4% HCV-2; 36L present in 100% HCV-3-5 and >94% HCV-2-4; 175L present in 100% HCV-1a-3-5 and >97% HCV-2-4). Furthermore, HCV-3 specifically showed non-conservative polymorphisms (R123T-D168Q) at two drug-interacting positions. Regardless of HCV-genotype, 13 PIs resistance-mutations were associated with low genetic-barrier, requiring only 1 nucleotide-substitution (41R-43S/V-54A-55A-80R-156V/T: score = 1; 54S-138T-156S/G-168E/H: score = 2.5). By contrast, by using HCV-1b as reference genotype, nucleotide-heterogeneity led to a lower genetic-barrier for the development of some drug-resistance-mutations in HCV-1a (36M-155G/I/K/M/S/T-170T), HCV-2 (36M-80K-155G/I/K/S/T-170T), HCV-3 (155G/I/K/M/S/T-170T), HCV-4-6 (155I/S/L), and HCV-5 (80G-155G/I/K/M/S/T). CONCLUSIONS The high degree of HCV genetic variability makes HCV-genotypes, and even subtypes, differently prone to the development of PIs resistance-mutations. Overall, this can account for different responsiveness of HCV-genotypes to PIs, with important clinical implications in tailoring individualized and appropriate regimens.
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Affiliation(s)
- Valeria Cento
- Department of Experimental Medicine and Biochemical Sciences, University of Tor Vergata, Rome, Italy
| | - Carmen Mirabelli
- Department of Experimental Medicine and Biochemical Sciences, University of Tor Vergata, Rome, Italy
| | - Romina Salpini
- Department of Experimental Medicine and Biochemical Sciences, University of Tor Vergata, Rome, Italy
| | - Salvatore Dimonte
- Department of Experimental Medicine and Biochemical Sciences, University of Tor Vergata, Rome, Italy
| | - Anna Artese
- Department of Pharmacobiological Sciences, University of Catanzaro “Magna Græcia”, Catanzaro, Italy
| | - Giosuè Costa
- Department of Pharmacobiological Sciences, University of Catanzaro “Magna Græcia”, Catanzaro, Italy
| | - Fabio Mercurio
- Department of Experimental Medicine and Biochemical Sciences, University of Tor Vergata, Rome, Italy
| | - Valentina Svicher
- Department of Experimental Medicine and Biochemical Sciences, University of Tor Vergata, Rome, Italy
| | - Lucia Parrotta
- Department of Pharmacobiological Sciences, University of Catanzaro “Magna Græcia”, Catanzaro, Italy
| | - Ada Bertoli
- Complex Unit of Molecular Virology, Tor Vergata University Hospital, Rome, Italy
| | - Marco Ciotti
- Complex Unit of Molecular Virology, Tor Vergata University Hospital, Rome, Italy
| | - Daniele Di Paolo
- Department of Internal Medicine, Tor Vergata University Hospital, Rome, Italy
| | - Cesare Sarrecchia
- Department of Public Health, Tor Vergata University Hospital, Rome, Italy
| | - Massimo Andreoni
- Department of Public Health, Tor Vergata University Hospital, Rome, Italy
| | - Stefano Alcaro
- Department of Pharmacobiological Sciences, University of Catanzaro “Magna Græcia”, Catanzaro, Italy
| | - Mario Angelico
- Department of Internal Medicine, Tor Vergata University Hospital, Rome, Italy
| | - Carlo Federico Perno
- Department of Experimental Medicine and Biochemical Sciences, University of Tor Vergata, Rome, Italy
- Complex Unit of Molecular Virology, Tor Vergata University Hospital, Rome, Italy
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Conformational studies and solvent-accessible surface area analysis of known selective DNA G-Quadruplex binders. Biochimie 2011; 93:1267-74. [DOI: 10.1016/j.biochi.2011.06.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 06/14/2011] [Indexed: 12/18/2022]
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Benz A, Singh V, Mayer TU, Hartig JS. Identification of Novel Quadruplex Ligands from Small Molecule Libraries by FRET-Based High-Throughput Screening. Chembiochem 2011; 12:1422-6. [DOI: 10.1002/cbic.201100094] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Indexed: 12/11/2022]
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