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Avagyan NA, Lemport PS, Roznyatovsky VA, Evsiunina MV, Matveev PI, Gerasimov MA, Lyssenko KA, Goncharenko VE, Khrustalev VN, Dorovatovskii PV, Tarasevich BN, Yakushev AA, Averin AD, Gloriozov IP, Petrov VG, Ustynyuk YA, Nenajdenko VG. 4-Oxo-7-fluoro-1,10-phenanthroline-2,9-diamides: Synthesis, Structural Features, Lanthanide Complexes, and Am(III)/Ln(III) Solvent Extraction. Inorg Chem 2023; 62:17721-17735. [PMID: 37847197 DOI: 10.1021/acs.inorgchem.3c02371] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
A highly efficient synthetic approach was developed for the synthesis of unsymmetrical 1,10-phenanthroline-2,9-diamides with two different substituents in the fourth and seventh positions of the phenanthroline core. The structures of these ligands were confirmed using various spectral methods including 2D-NMR and X-ray analysis. Quantum chemical calculations supported the presence of tautomeric forms of these ligands. Furthermore, it was discovered that these compounds exhibit polydentate ligand behavior toward lanthanide nitrates. The structural characteristics of the complexes formed between these ligands and lanthanide nitrates were investigated both in the solid state and in solution. To further understand the binding properties of these novel unsymmetrical ligands, the binding constants for potential complexes were quantitatively measured by using UV-vis spectrophotometric titration. This allowed for a comprehensive analysis of the binding affinity and stability of these complexes. Extraction experiments of f-elements were performed for symmetrical and unsymmetrical diamides. Overall, this study presents significant advancement in the synthesis and characterization of unsymmetrical 1,10-phenanthroline-2,9-diamides and provides valuable insights into their potential applications as polydentate ligands for lanthanide nitrates.
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Affiliation(s)
- Nane A Avagyan
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
| | - Pavel S Lemport
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
| | - Vitaly A Roznyatovsky
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
| | - Mariia V Evsiunina
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
| | - Petr I Matveev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
| | - Mikhail A Gerasimov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
| | - Konstantin A Lyssenko
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
| | - Victoria E Goncharenko
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
| | - Victor N Khrustalev
- N.D. Zelinsky Institute of Organic Chemistry of Russian Academy of Sciences, Moscow 119991, Russia
- Department of Inorganic Chemistry, Peoples' Friendship University of Russia (RUDN University), Moscow 115419, Russia
| | | | - Boris N Tarasevich
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
| | - Alexei A Yakushev
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
| | - Alexei D Averin
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
| | - Igor P Gloriozov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
| | - Vladimir G Petrov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
| | - Yuri A Ustynyuk
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
| | - Valentine G Nenajdenko
- Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1 bld. 3, Moscow 119991, Russia
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2
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Ugwu DI, Conradie J. Anticancer properties of complexes derived from bidentate ligands. J Inorg Biochem 2023; 246:112268. [PMID: 37301166 DOI: 10.1016/j.jinorgbio.2023.112268] [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: 03/30/2023] [Revised: 05/09/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023]
Abstract
Cancer is the abnormal division and multiplication of cells in an organ or tissue. It is the second leading cause of death globally. There are various types of cancer such as prostate, breast, colon, lung, stomach, liver, skin, and many others depending on the tissue or organ where the abnormal growth originates. Despite the huge investment in the development of anticancer agents, the transition of research to medications that improve substantially the treatment of cancer is less than 10%. Cisplatin and its analogs are ubiquitous metal-based anticancer agents notable for the treatment of various cancerous cells and tumors but unfortunately accompanied by large toxicities due to low selectivity between cancerous and normal cells. The improved toxicity profile of cisplatin analogs bearing bidentate ligands has motivated the synthesis of vast metal complexes of bidentate ligands. Complexes derived from bidentate ligands such as β-diketones, diolefins, benzimidazoles and dithiocarbamates have been reported to possess 20 to 15,600-fold better anticancer activity, when tested on cell lines, than some known antitumor drugs currently on the market, e.g. cisplatin, oxaliplatin, carboplatin, doxorubicin, and 5-fluorouracil. This work discusses the anticancer properties of various metal complexes derived from bidentate ligands, for possible application in chemotherapy. The results discussed were evaluated by the IC50 values as obtained from cell line tests on various metal-bidentate complexes. The structure-activity relationship study of the complexes discussed, revealed that hydrophobicity is a key factor that influences anticancer properties of molecules.
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Affiliation(s)
- David Izuchukwu Ugwu
- Department of Chemistry, University of the Free State, South Africa; Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
| | - Jeanet Conradie
- Department of Chemistry, University of the Free State, South Africa.
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3
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Reznichenko O, Leclercq D, Franco Pinto J, Mouawad L, Gabelica V, Granzhan A. Optimization of G-Quadruplex Ligands through a SAR Study Combining Parallel Synthesis and Screening of Cationic Bis(acylhydrazones). Chemistry 2023; 29:e202202427. [PMID: 36286608 PMCID: PMC10099395 DOI: 10.1002/chem.202202427] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 11/06/2022]
Abstract
G-quadruplexes (G4s), secondary structures adopted by guanine-rich DNA and RNA sequences, are implicated in numerous biological processes and have been suggested as potential drug targets. Accordingly, there is an increasing interest in developing high-throughput methods that allow the generation of congeneric series of G4-targeting molecules ("ligands") and investigating their interactions with the targets. We have developed an operationally simple method of parallel synthesis to generate "ready-to-screen" libraries of cationic acylhydrazones, a motif that we have previously identified as a promising scaffold for potent, biologically active G4 ligands. Combined with well-established screening techniques, such as fluorescence melting, this method enables the rapid synthesis and screening of combinatorial libraries of potential G4 ligands. Following this protocol, we synthesized a combinatorial library of 90 bis(acylhydrazones) and screened it against five different nucleic acid structures. This way, we were able to analyze the structure-activity relationships within this series of G4 ligands, and identified three novel promising ligands whose interactions with G4-DNAs of different topologies were studied in detail by a combination of several biophysical techniques, including native mass spectrometry, and molecular modeling.
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Affiliation(s)
- Oksana Reznichenko
- CMBC, CNRS UMR9187Inserm U1196, Institut CuriePSL Research University91405OrsayFrance
- CMBC, CNRS UMR9187Inserm U1196Université Paris Saclay91405OrsayFrance
| | - Denis Leclercq
- CMBC, CNRS UMR9187Inserm U1196, Institut CuriePSL Research University91405OrsayFrance
- CMBC, CNRS UMR9187Inserm U1196Université Paris Saclay91405OrsayFrance
| | - Jaime Franco Pinto
- CMBC, CNRS UMR9187Inserm U1196, Institut CuriePSL Research University91405OrsayFrance
- CMBC, CNRS UMR9187Inserm U1196Université Paris Saclay91405OrsayFrance
| | - Liliane Mouawad
- CMBC, CNRS UMR9187Inserm U1196, Institut CuriePSL Research University91405OrsayFrance
- CMBC, CNRS UMR9187Inserm U1196Université Paris Saclay91405OrsayFrance
| | - Valérie Gabelica
- Univ. BordeauxCNRS, INSERM, ARNAUMR 5320, U1212, IECB33600PessacFrance
| | - Anton Granzhan
- CMBC, CNRS UMR9187Inserm U1196, Institut CuriePSL Research University91405OrsayFrance
- CMBC, CNRS UMR9187Inserm U1196Université Paris Saclay91405OrsayFrance
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Synthesis and evaluation of 2,9-disubstituted-1,10-phenanthroline derivatives as G-quadruplex binders. Bioorg Med Chem 2022; 73:116971. [DOI: 10.1016/j.bmc.2022.116971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 08/14/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022]
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A rapid and high sensitivity RNA detection based on NASBA and G4-ThT fluorescent biosensor. Sci Rep 2022; 12:10076. [PMID: 35710925 PMCID: PMC9203706 DOI: 10.1038/s41598-022-14107-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/01/2022] [Indexed: 11/15/2022] Open
Abstract
In recent years, various newly emerged and re-emerged RNA viruses have seriously threatened the global public health. There is a pressing need for rapid and reliable nucleic acid–based assays for detecting viral RNA. Here, we successfully developed a highly sensitive, easy-to-operate G4-ThT-NASBA system to detect viral RNA that no need for labeled primers and probes. Next, we tested the system for detecting the Classical Swine Fever Virus (CSFV), an RNA virus that causes a highly contagious disease in domestic pigs and wild boar and easily causes huge economic losses. Results showed that the system, integrated the G4-ThT fluorescent biosensor and NASBA (Nuclear acid sequence-based amplification),is capable to detect as little as 2 copies/μL of viral RNA without interfering by other swine viral RNA. Moreover, we were able to detect CSFV RNA within 2 h in serum samples taken from the field in a real-time mode. These findings indicate that the G4-ThT-NASBA system is a rapid, high sensitivity and easy-to-operate technique for RNA detection. The method also has the real-time detection capability which may be easily integrated in a highly automated system such as microfluidic chips.
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Mooney DT, Donkin BDT, Demirel N, Moore PR, Lee AL. Direct C-H Functionalization of Phenanthrolines: Metal- and Light-Free Dicarbamoylations. J Org Chem 2021; 86:17282-17293. [PMID: 34792370 DOI: 10.1021/acs.joc.1c02425] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A direct method for C-H dicarbamoylations of phenanthrolines has been developed, which is capable of directly installing primary, secondary as well as tertiary amides. This is a significant improvement on the previous direct method, which was limited to primary amides. The metal-, light-, and catalyst-free Minisci-type reaction is cheap, operationally simple, and scalable. We demonstrate that the step efficiency toward dicarbamoylated phenanthroline targets can now be significantly improved.
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Affiliation(s)
- David T Mooney
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, Scotland EH14 4AS, U.K
| | - Benjamin D T Donkin
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, Scotland EH14 4AS, U.K
| | - Nemrud Demirel
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, Scotland EH14 4AS, U.K
| | - Peter R Moore
- Early Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Macclesfield SK10 2NA, U.K
| | - Ai-Lan Lee
- Institute of Chemical Sciences, Heriot-Watt University, Edinburgh, Scotland EH14 4AS, U.K
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7
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Craciun AM, Rotaru A, Cojocaru C, Mangalagiu II, Danac R. New 2,9-disubstituted-1,10-phenanthroline derivatives with anticancer activity by selective targeting of telomeric G-quadruplex DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 249:119318. [PMID: 33360205 DOI: 10.1016/j.saa.2020.119318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/26/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Fifteen new 1,10-phenanthrolines disubstituted at positions 2 and 9 via amide bonds with different heterocycles have been designed and synthesized as G-quadruplex DNA stabilizers. Ten compounds were evaluated for the in vitro anticancer activity against 60 human tumor cell lines panel, four of them showing a very good inhibitory activity on several cell lines. To assess the ability of the most active compounds to interact with G-quadruplex DNA (G4-DNA), circular dichroism experiments were performed. The potency of the compounds to stabilize the G4-DNA has been shown from the thermal denaturation experiments. The mechanism of compounds binding to DNA and to G4-DNA was theoretically investigated by molecular docking studies. The experimental results demonstrated excellent capacity of the two compounds bearing two pyridin-3-yl residues (methylated and non-methylated) to act as selective G-quadruplex binders with promising anticancer activity.
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Affiliation(s)
- Anda-Mihaela Craciun
- Chemistry Department, Faculty of Chemistry, "Al. I. Cuza" University of Iasi, 11 Carol I, Iasi 700506, Romania; "Petru Poni" Institute of Macromolecular Chemistry, 41A, Grigore Ghica Voda Alley, Iasi 700487, Romania
| | - Alexandru Rotaru
- "Petru Poni" Institute of Macromolecular Chemistry, 41A, Grigore Ghica Voda Alley, Iasi 700487, Romania
| | - Corneliu Cojocaru
- "Petru Poni" Institute of Macromolecular Chemistry, 41A, Grigore Ghica Voda Alley, Iasi 700487, Romania
| | - Ionel I Mangalagiu
- Chemistry Department, Faculty of Chemistry, "Al. I. Cuza" University of Iasi, 11 Carol I, Iasi 700506, Romania
| | - Ramona Danac
- Chemistry Department, Faculty of Chemistry, "Al. I. Cuza" University of Iasi, 11 Carol I, Iasi 700506, Romania.
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Andreeva DV, Tikhomirov AS, Shchekotikhin AE. Ligands of G-quadruplex nucleic acids. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4968] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Dhamodharan V, Pradeepkumar PI. Specific Recognition of Promoter G-Quadruplex DNAs by Small Molecule Ligands and Light-up Probes. ACS Chem Biol 2019; 14:2102-2114. [PMID: 31532996 DOI: 10.1021/acschembio.9b00475] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
G-Quadruplexes (G4s) are four-stranded nucleic acid structures whose underlying G-rich sequences are present across the chromosome and transcriptome. These highly structured elements are known to regulate many key biological functions such as replication, transcription, translation, and genomic stability, thereby providing an additional layer of gene regulation. G4s are structurally dynamic and diverse, and they can fold into numerous topologies. They are potential targets for small molecules, which can modulate their functions. To this end, myriad classes of small molecules have been developed and studied for their ability to bind and stabilize these unique structures. Though many of them can selectively target G4s over duplex DNA, only a few of them can distinguish one G4 topology from others. Design and development of G4-specific ligands are challenging owing to the subtle structural variations among G4 structures. However, screening assays and computational methods have identified a few classes of ligands that preferentially or specifically target the G4 topology of interest over others. This review focuses on the small molecules and fluorescent probes that specifically target human promoter G4s associated with oncogenes. Targeting promoter G4s could circumvent the issues such as undruggability and development of drug resistance associated with the protein targets. The ligands discussed here highlight that development of G4-specific ligands is an achievable goal in spite of the limited structural data available. The future goal is to pursue the development of G4-specific ligands endowed with drug-like properties for G4-based therapeutics and diagnostics.
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Affiliation(s)
- V. Dhamodharan
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Okinawa Institute of Science and Technology Graduate University, Okinawa 9040495, Japan
| | - P. I. Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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Aksakal NE, Tanrıverdi Eçik E, Kazan HH, Yenilmez Çiftçi G, Yuksel F. Novel ruthenium(ii) and iridium(iii) BODIPY dyes: insights into their application in photodynamic therapy in vitro. Photochem Photobiol Sci 2019; 18:2012-2022. [PMID: 31282525 DOI: 10.1039/c9pp00201d] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Organic-metal complexes are promising molecules for use in photodynamic therapy (PDT). The aim of this study was to investigate in vitro effects of novel Ru(ii) and Ir(iii) BODIPY complexes for PDT. These hybrid organic-metal molecules (Ru-BD and Ir-BD) have been synthesized via reactions of a BODIPY precursor (BD) with a phenanthroline unit bearing Ru(ii) (3) and novel Ir(iii) (4) compounds. The crystal structures of the new distyryl BODIPY (BD) and Ru(ii) complex (3) are also reported. The photophysical and singlet oxygen generation properties of Ru-BD and Ir-BD were investigated in comparison with unsubstituted BODIPY (BD). Moreover, Ru-BD and Ir-BD have been biologically evaluated in vitro in chronic myeloid leukemia and cervical cancer cell lines in terms of photodynamic therapy efficacy in the presence of BD control. These complexes were not toxic in the dark but red light was needed to induce cell death. These data support the fact that Ru-BD could be accepted as a valuable photosensitizer-drug for further PDT treatment.
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Affiliation(s)
- Nuray Esra Aksakal
- Department of Chemistry, Faculty of Science, Gebze Technical University, Gebze, Kocaeli, Turkey.
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Gueddouda NM, Hurtado MR, Moreau S, Ronga L, Das RN, Savrimoutou S, Rubio S, Marchand A, Mendoza O, Marchivie M, Elmi L, Chansavang A, Desplat V, Gabelica V, Bourdoncle A, Mergny JL, Guillon J. Design, Synthesis, and Evaluation of 2,9-Bis[(substituted-aminomethyl)phenyl]-1,10-phenanthroline Derivatives as G-Quadruplex Ligands. ChemMedChem 2017; 12:146-160. [DOI: 10.1002/cmdc.201600511] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/29/2016] [Indexed: 11/09/2022]
Affiliation(s)
| | | | - Stéphane Moreau
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Luisa Ronga
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Rabindra Nath Das
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Solène Savrimoutou
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Sandra Rubio
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Adrien Marchand
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Oscar Mendoza
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | | | - Lilian Elmi
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Albain Chansavang
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Vanessa Desplat
- Univ. Bordeaux; UFR des Sciences Pharmaceutiques; Biothérapie des Maladies Génétiques Inflammatoires et Cancers; INSERM U1035; 33076 Bordeaux cedex France
| | - Valérie Gabelica
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Anne Bourdoncle
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Jean-Louis Mergny
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
| | - Jean Guillon
- Univ. Bordeaux; ARNA laboratory; CNRS UMR 5320, INSERM U1212; 33076 Bordeaux France
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12
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Medeiros-Silva J, Guédin A, Salgado GF, Mergny JL, Queiroz JA, Cabrita EJ, Cruz C. Phenanthroline-bis-oxazole ligands for binding and stabilization of G-quadruplexes. Biochim Biophys Acta Gen Subj 2016; 1861:1281-1292. [PMID: 27865994 DOI: 10.1016/j.bbagen.2016.11.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 10/29/2016] [Accepted: 11/15/2016] [Indexed: 01/01/2023]
Abstract
BACKGROUND G-quadruplexes (G4) are found at important genome regions such as telomere ends and oncogene promoters. One prominent strategy to explore the therapeutic potential of G4 is stabilized it with specific ligands. METHODS We report the synthesis of new phenanthroline, phenyl and quinoline acyclic bisoxazole compounds in order to explore and evaluate the targeting to c-myc and human telomeric repeat 22AG G4 using FRET-melting, CD-melting, NMR, fluorescence titrations and FID assays. RESULTS The design strategy has led to potent compounds (Phen-1 and Phen-2) that discriminate different G4 structures (human telomeric sequences and c-myc promoter) and selectively stabilize G4 over duplex DNA. CD studies show that Phen-2 binds and induces antiparallel topologies in 22AG quadruplex and also binds c-myc promotor, increasing their Tm in about 12°C and 30°C respectively. In contrast, Phen-1 induces parallel topologies in 22AG and c-myc, with a moderate stabilization of 4°C for both sequences. Consistent with a CD melting study, Phen-2 binds strongly (K=106 to 107M-1) to c-myc and 22AG quadruplexes. CONCLUSIONS Phen-1 and Phen-2 discriminated among various quadruplex topologies and exhibited high selectivity for quadruplexes over duplexes. Phen-2 retains antiparallel topologies for quadruplex 22AG and does not induce conformational changes on the parallel c-myc quadruplex although Phen-1 favors the parallel topology. NMR studies also showed that the Phen-2 binds to the c-myc quadruplex via end stacking. GENERAL SIGNIFICANCE Overall, the results suggest the importance of Phen-2 as a scaffold for the fine-tuning with substituents in order to enhance binding and stabilization to G4 structures. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- João Medeiros-Silva
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal; UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Aurore Guédin
- INSERM, U1212, CNRS, UMR 5320, IECB, F-33600 Pessac, France; Univ. Bordeaux, ARNA laboratory, F-33000 Bordeaux, France
| | - Gilmar F Salgado
- INSERM, U1212, CNRS, UMR 5320, IECB, F-33600 Pessac, France; Univ. Bordeaux, ARNA laboratory, F-33000 Bordeaux, France
| | - Jean-Louis Mergny
- INSERM, U1212, CNRS, UMR 5320, IECB, F-33600 Pessac, France; Univ. Bordeaux, ARNA laboratory, F-33000 Bordeaux, France
| | - João A Queiroz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal
| | - Eurico J Cabrita
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
| | - Carla Cruz
- CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal.
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Livendahl M, Jamroskovic J, Ivanova S, Demirel P, Sabouri N, Chorell E. Design and Synthesis of 2,2′-Diindolylmethanes to Selectively Target Certain G-Quadruplex DNA Structures. Chemistry 2016; 22:13004-9. [DOI: 10.1002/chem.201602416] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Indexed: 11/11/2022]
Affiliation(s)
| | - Jan Jamroskovic
- Department of Medical Biochemistry and Biophysics; Umeå University; 901 87 Umeå Sweden
| | | | - Peter Demirel
- Department of Chemistry; Umeå University; 901 87 Umeå Sweden
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics; Umeå University; 901 87 Umeå Sweden
| | - Erik Chorell
- Department of Chemistry; Umeå University; 901 87 Umeå Sweden
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14
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Recent advances in targeting the telomeric G-quadruplex DNA sequence with small molecules as a strategy for anticancer therapies. Future Med Chem 2016; 8:1259-90. [PMID: 27442231 DOI: 10.4155/fmc-2015-0017] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Human telomeric DNA (hTelo), present at the ends of chromosomes to protect their integrity during cell division, comprises tandem repeats of the sequence d(TTAGGG) which is known to form a G-quadruplex secondary structure. This unique structural formation of DNA is distinct from the well-known helical structure that most genomic DNA is thought to adopt, and has recently gained prominence as a molecular target for new types of anticancer agents. In particular, compounds that can stabilize the intramolecular G-quadruplex formed within the human telomeric DNA sequence can inhibit the activity of the enzyme telomerase which is known to be upregulated in tumor cells and is a major contributor to their immortality. This provides the basis for the discovery and development of small molecules with the potential for selective toxicity toward tumor cells. This review summarizes the various families of small molecules reported in the literature that have telomeric quadruplex stabilizing properties, and assesses the potential for compounds of this type to be developed as novel anticancer therapies. A future perspective is also presented, emphasizing the need for researchers to adopt approaches that will allow the discovery of molecules with more drug-like properties in order to improve the chances of lead molecules reaching the clinic in the next decade.
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Duskova K, Sierra S, Arias-Pérez MS, Gude L. Human telomeric G-quadruplex DNA interactions of N-phenanthroline glycosylamine copper(II) complexes. Bioorg Med Chem 2015; 24:33-41. [PMID: 26678174 DOI: 10.1016/j.bmc.2015.11.037] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 01/12/2023]
Abstract
We report in this article the interactions of five N-(1,10-phenanthrolin-5-yl)-β-glycopyranosylamine copper(II) complexes with G-quadruplex DNA. Specifically, the interactions of these compounds with a human telomeric oligonucleotide have been assessed by fluorescence-based assays (FRET melting and G4-FID), circular dichroism and competitive equilibrium dialysis experiments. The metal complexes bind and stabilize G-quadruplex DNA structures with apparent association constants in the order of 10(4)-10(5)M(-1) and the affinity observed is dependent on the ionic conditions utilized and the specific nature of the carbohydrate moiety tethered to the 1,10-phenanthroline system. The compounds showed only a slight preference to bind G-quadruplex DNA over duplex DNA when the quadruplex DNA was folded in sodium ionic conditions. However, the binding affinity and selectivity, although modest, were notably increased when the G-quadruplex DNA was folded in the presence of potassium metal ions. Moreover, the study points towards a significant contribution of groove and/or loop binding in the recognition mode of quadruplex structures by these non-classical quadruplex ligands. The results reported herein highlight the potential and the versatility of carbohydrate bis-phenanthroline metal-complex conjugates to recognize G-quadruplex DNA structures.
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Affiliation(s)
- Katerina Duskova
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares (Madrid), Spain
| | - Sara Sierra
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares (Madrid), Spain
| | - María-Selma Arias-Pérez
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares (Madrid), Spain
| | - Lourdes Gude
- Departamento de Química Orgánica y Química Inorgánica, Universidad de Alcalá, 28805 Alcalá de Henares (Madrid), Spain.
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Dhamodharan V, Harikrishna S, Bhasikuttan AC, Pradeepkumar PI. Topology specific stabilization of promoter over telomeric G-quadruplex DNAs by bisbenzimidazole carboxamide derivatives. ACS Chem Biol 2015; 10:821-33. [PMID: 25495750 DOI: 10.1021/cb5008597] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Various potential G-quadruplex forming sequences present in the genome offer a platform to modulate their function by means of stabilizing molecules. Though G-quadruplex structures exhibit diverse structural topologies, the presence of G-quartets as a common structural element makes the design of topology specific ligands a daunting task. To address this, the subtle structural variations of loops and grooves present in the quadruplex structures can be exploited. To this end, we report the design and synthesis of quadruplex stabilizing agents based on bisbenzimidazole carboxamide derivatives of pyridine, 1,8-naphthyridine, and 1,10-phenanthroline. The designed ligands specifically bind to and stabilize promoter quadruplexes having parallel topology over any of the human telomeric quadruplex topologies (parallel, hybrid, or antiparallel) and duplex DNAs. CD melting studies indicate that ligands could impart higher stabilization to c-MYC and c-KIT promoter quadruplexes (up to 21 °C increment in Tm) than telomeric and duplex DNAs (ΔTm ≤ 2.5 °C). Consistent with a CD melting study, ligands bind strongly (Kb = ∼10(4) to 10(5) M(-1)) to c-MYC quadruplex DNA. Molecular modeling and dynamics studies provide insight into how the specificity is achieved and underscore the importance of flexible N-alkyl side chains attached to the benzimidazole-scaffold in recognizing propeller loops of promoter quadruplexes. Overall, the results reported here demonstrate that the benzimidazole scaffold represents a potent and powerful side chain, which could judiciously be assembled with a suitable central core to achieve specific binding to a particular quadruplex topology.
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Affiliation(s)
- V. Dhamodharan
- Department
of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - S. Harikrishna
- Department
of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | | | - P. I. Pradeepkumar
- Department
of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Stafford VS, Suntharalingam K, Shivalingam A, White AJP, Mann DJ, Vilar R. Syntheses of polypyridyl metal complexes and studies of their interaction with quadruplex DNA. Dalton Trans 2015; 44:3686-700. [DOI: 10.1039/c4dt02910k] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A series of metal complexes with substituted terpyridines show high affinity towards quadruplex DNA, particularly bimetallic (trpy)Pt/M(cyclen) complexes.
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Affiliation(s)
| | | | | | | | - David J. Mann
- Department of Life Sciences
- Imperial College London
- London SW7 2AZ
- UK
| | - Ramon Vilar
- Department of Chemistry
- Imperial College London
- London SW7 2AZ
- UK
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18
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Kataoka Y, Fujita H, Kasahara Y, Yoshihara T, Tobita S, Kuwahara M. Minimal Thioflavin T Modifications Improve Visual Discrimination of Guanine-Quadruplex Topologies and Alter Compound-Induced Topological Structures. Anal Chem 2014; 86:12078-84. [DOI: 10.1021/ac5028325] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yuka Kataoka
- Graduate School of Science and Technology, Gunma University, 1-5-1
Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Hiroto Fujita
- Graduate School of Science and Technology, Gunma University, 1-5-1
Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Yuuya Kasahara
- Graduate School of Science and Technology, Gunma University, 1-5-1
Tenjin-cho, Kiryu, Gunma 376-8515, Japan
- National Institute of Biomedical Innovation (NIBIO), 7-6-8 Asagi, Saito, Ibaraki, Osaka 567-0085, Japan
| | - Toshitada Yoshihara
- Graduate School of Science and Technology, Gunma University, 1-5-1
Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Seiji Tobita
- Graduate School of Science and Technology, Gunma University, 1-5-1
Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Masayasu Kuwahara
- Graduate School of Science and Technology, Gunma University, 1-5-1
Tenjin-cho, Kiryu, Gunma 376-8515, Japan
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19
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DNA binders in clinical trials and chemotherapy. Bioorg Med Chem 2014; 22:4506-21. [DOI: 10.1016/j.bmc.2014.05.030] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 05/09/2014] [Accepted: 05/14/2014] [Indexed: 01/09/2023]
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21
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Maji B, Bhattacharya S. Advances in the molecular design of potential anticancer agents via targeting of human telomeric DNA. Chem Commun (Camb) 2014; 50:6422-38. [DOI: 10.1039/c4cc00611a] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Telomerase is an attractive drug target to develop new generation drugs against cancer.
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Affiliation(s)
- Basudeb Maji
- Department of Organic Chemistry
- Indian Institute of Science
- Bangalore-560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry
- Indian Institute of Science
- Bangalore-560012, India
- Chemical Biology Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
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Chung WJ, Heddi B, Hamon F, Teulade-Fichou MP, Phan AT. Solution Structure of a G-quadruplex Bound to the Bisquinolinium Compound Phen-DC3. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201308063] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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23
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Chung WJ, Heddi B, Hamon F, Teulade-Fichou MP, Phan AT. Solution structure of a G-quadruplex bound to the bisquinolinium compound Phen-DC(3). Angew Chem Int Ed Engl 2013; 53:999-1002. [PMID: 24356977 DOI: 10.1002/anie.201308063] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/14/2013] [Indexed: 11/07/2022]
Abstract
Phen-DC3 is a highly promising compound that specifically targets G-quadruplexes, with potent biological effects observed in vivo. We used NMR spectroscopy to solve the structure of the complex formed between Phen-DC3 and an intramolecular G-quadruplex derived from the c-myc promoter. Structural information revealed that Phen-DC3 interacts with the quadruplex through extensive π-stacking with guanine bases of the top G-tetrad. On the basis of our structure, modifications are proposed for the development of this compound for selective targeting of a specific G-quadruplex conformation.
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Affiliation(s)
- Wan Jun Chung
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371 (Singapore)
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Roembke BT, Nakayama S, Sintim HO. Nucleic acid detection using G-quadruplex amplification methodologies. Methods 2013; 64:185-98. [PMID: 24135042 PMCID: PMC7129037 DOI: 10.1016/j.ymeth.2013.10.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/19/2013] [Accepted: 10/02/2013] [Indexed: 12/28/2022] Open
Abstract
In the last decade, there has been an explosion in the use of G-quadruplex labels to detect various analytes, including DNA/RNA, proteins, metals and other metabolites. In this review, we focus on strategies for the detection of nucleic acids, using G-quadruplexes as detection labels or as enzyme labels that amplify detection signals. Methods to detect other analytes are briefly mentioned. We highlight various strategies, including split G-quadruplex, hemin-G-quadruplex conjugates, molecular beacon G-quadruplex or inhibited G-quadruplex probes. The tandem use of G-quadruplex labels with various DNA-modifying enzymes, such as polymerases (used for rolling circle amplification), exonucleases and endonucleases, is also discussed. Some of the detection modalities that are discussed in this review include fluorescence, colorimetric, chemiluminescence, and electrochemical methods.
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Nielsen MC, Larsen AF, Abdikadir FH, Ulven T. Phenanthroline-2,9-bistriazoles as selective G-quadruplex ligands. Eur J Med Chem 2013; 72:119-26. [PMID: 24361524 DOI: 10.1016/j.ejmech.2013.11.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 11/17/2013] [Accepted: 11/25/2013] [Indexed: 02/09/2023]
Abstract
G-quadruplex (G4) ligands are currently receiving considerable attention as potential anticancer therapeutics. A series of phenanthroline-2,9-bistriazoles carrying tethered positive end groups has been synthesized and evaluated as G4 stabilizers. The compounds were efficiently assembled by copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) in CH2Cl2 and water in the presence of a complexing agent. Characterization of the target compounds on telomeric and c-KIT G4 sequences led to the identification of guanidinium-substituted compounds as potent G4 DNA ligands with high selectivity over duplex DNA. The diisopropylguanidium ligands exhibited high selectivity for the proto-oncogenic sequence c-KIT over the human telomeric sequence in the surface plasmon resonance (SPR) assay, whereas the compounds appeared potent on both G4 structures in the FRET melting temperature assay. The phenanthroline-2,9-bistriazole ligands were thus identified as potent G4 ligands with high selectivity over duplex DNA, and preliminary results indicate that the scaffold may form basis for the development of subtype-specific G4 ligands.
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Affiliation(s)
- Mads Corvinius Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Anders Foller Larsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Faisal Hussein Abdikadir
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Trond Ulven
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
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Biver T. Stabilisation of non-canonical structures of nucleic acids by metal ions and small molecules. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.04.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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27
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Wei C, Wang Y, Zhang M. Synthesis and binding studies of novel di-substituted phenanthroline compounds with genomic promoter and human telomeric DNA G-quadruplexes. Org Biomol Chem 2013; 11:2355-64. [DOI: 10.1039/c3ob27426h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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