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Pont I, Galiana-Roselló C, Sabater-Arcis M, Bargiela A, Frías JC, Albelda MT, González-García J, García-España E. Development of potent tripodal G-quadruplex DNA binders and their efficient delivery to cancer cells by aptamer functionalised liposomes. Org Biomol Chem 2023; 21:1000-1007. [PMID: 36541358 DOI: 10.1039/d2ob01911f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Two new ligands (TPB3P and TPB3Py) showing a strong stabilisation effect and good selectivity for G4 over duplex DNAs have been synthesised. The ligands hold three analogous polyamine pendant arms (TPA3P and TPA3Py) but differ in the central aromatic core, which is a triphenylbenzene moiety instead of a triphenylamine moiety. Both TPB3P and TPB3Py exhibit high cytotoxicity in MCF-7, LN229 and HeLa cancer cells in contrast to TPA-based ligands, which exhibit no significant cytotoxicity. Moreover, the most potent G4 binders have been encapsulated in liposomes and AS1411 aptamer-targeted liposomes reaching nanomolar IC50 values for the most cytotoxic systems.
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Affiliation(s)
- Isabel Pont
- Instituto de Ciencia Molecular (ICMol), Departamento de Química Inorgánica, Universidad de Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain.
| | - Cristina Galiana-Roselló
- Instituto de Ciencia Molecular (ICMol), Departamento de Química Inorgánica, Universidad de Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain.
| | - Maria Sabater-Arcis
- Translational Genomics Group, Incliva Health Research Institute, Valencia, Spain.,Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), University of Valencia, Valencia, Spain.,CIPF-INCLIVA Joint Unit, Valencia, Spain
| | - Ariadna Bargiela
- Neuromuscular Research Unit, Neurology Department, Hospital La Fe, Instituto de Investigación Sanitaria La Fe (IISLAFE), Valencia, Spain
| | - Juan Carlos Frías
- Department of Biomedical Sciences, CEU Cardenal Herrera University, Ramón y Cajal s/n, 46115 Alfara del Patriarca, Spain
| | - M Teresa Albelda
- Instituto de Ciencia Molecular (ICMol), Departamento de Química Inorgánica, Universidad de Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain.
| | - Jorge González-García
- Instituto de Ciencia Molecular (ICMol), Departamento de Química Inorgánica, Universidad de Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain.
| | - Enrique García-España
- Instituto de Ciencia Molecular (ICMol), Departamento de Química Inorgánica, Universidad de Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain.
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2
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Bağda E, Bağda E, Kocak A, Durmuş M. Investigation of Binding behaviour of a water-soluble gallium (III) phthalocyanine with double-stranded and G-quadruplex DNA via experimental and computational methods. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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3
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4
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Wei YF, Wang Y, Wei XR, Sun R, Xu YJ, Ge JF. Adenine-based small molecule fluorescent probe for imaging mitochondrial nucleic acid. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 229:117865. [PMID: 31813730 DOI: 10.1016/j.saa.2019.117865] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
A small molecule fluorescent probe (probe 1) based on adenine-coumarin derivative was designed and synthesized in this paper. Probe 1 exhibited a significant fluorescence-enhancing response to nucleic acids at 495 nm (for DNA) and 487 nm (for RNA). The fluorescence enhancement of probe 1 for DNA and RNA was 5.68 and 9.73 times respectively, the fluorescence quantum yield was changed from 2.5% to 11.7% and 22.5% accordingly. Meanwhile, an excellent linear relationship of fluorescence intensity at 495 nm or 487 nm versus the nucleic acid concentration (1 μM for probe 1, 0-350 μg/mL for DNA and 0-300 μg/mL for RNA) was obtained. Co-staining and nucleic acid digestion experiments showed that probe 1 could selectively image nucleic acids in mitochondria and nucleoli in HeLa cells.
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Affiliation(s)
- Yu-Fang Wei
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China
| | - Yue Wang
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China
| | - Xue-Rui Wei
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Ru Sun
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China.
| | - Yu-Jie Xu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, China
| | - Jian-Feng Ge
- College of Chemistry, Chemical Engineering and Material Science, Soochow University, 199 Ren'Ai Road, Suzhou 215123, China; Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China.
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5
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Wang MQ, Liao YF, Zhang SH, Yu QQ, Huang JQ. Synthesis, G-Quadruplex DNA binding and cytotoxic properties of naphthalimide substituted styryl dyes. Bioorg Med Chem 2020; 28:115325. [PMID: 31982241 DOI: 10.1016/j.bmc.2020.115325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 01/07/2020] [Accepted: 01/12/2020] [Indexed: 02/06/2023]
Abstract
G-Quadruplex DNAs, formed by G-rich DNA sequences in human genes, are promising targets for design of cancer drugs. In this study, two naphthalimide substituted styryl dyes with different sizes of aromatic groups were synthesized. The spectral analysis showed that the dye X-2 with a large aromatic group formed aggregates in buffer solution displaying very weak fluorescence intensity, and disaggregated in the presence of G-Quadruplex DNAs with large intensity enhancements (up to ~1800 fold). Moreover, X-2 displayed good selectivity to G-Quadruplex DNAs. In contrast, dye X-3 with the smaller aromatic group had much lower fluorescence enhancements and poor selectivity to G-Quadruplex DNAs, suggesting that the suitably sized aromatic ring was essential for the interaction with G-Quadruplex. Further binding studies suggested that X-2 mainly bound on G-quartet surface through end-stacking mode. Cytotoxicity assay showed that both of the two dyes showed good anti-proliferative activities against the cancer cell lines and less cytotoxicity in non-malignant cell lines, which were better than a standard drug 5-fluorouracil. In addition, living cell imaging was also studied and demonstrated the potential applications of the new dye X-2 in bioassays and cell imaging.
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Affiliation(s)
- Ming-Qi Wang
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China.
| | - Yi-Fan Liao
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China
| | - Shu-Hui Zhang
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China
| | - Quan-Qi Yu
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China
| | - Jin-Qiu Huang
- School of Pharmacy, Jiangsu University, Zhenjiang 212013, PR China
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6
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In-Gel Probing Polymorphic Structures of G-Quadruplexes Derived from c-Myc Promoter. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60002-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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7
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Pont I, Martínez-Camarena Á, Galiana-Roselló C, Tejero R, Albelda MT, González-García J, Vilar R, García-España E. Development of Polyamine-Substituted Triphenylamine Ligands with High Affinity and Selectivity for G-Quadruplex DNA. Chembiochem 2020; 21:1167-1177. [PMID: 31701633 DOI: 10.1002/cbic.201900678] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Indexed: 01/01/2023]
Abstract
Currently, significant efforts are devoted to designing small molecules able to bind selectively to guanine quadruplexes (G4s). These noncanonical DNA structures are implicated in various important biological processes and have been identified as potential targets for drug development. Previously, a series of triphenylamine (TPA)-based compounds, including macrocyclic polyamines, that displayed high affinity towards G4 DNA were reported. Following this initial work, herein a series of second-generation compounds, in which the central TPA has been functionalised with flexible and adaptive linear polyamines, are presented with the aim of maximising the selectivity towards G4 DNA. The acid-base properties of the new derivatives have been studied by means of potentiometric titrations, UV/Vis and fluorescence emission spectroscopy. The interaction with G4s and duplex DNA has been explored by using FRET melting assays, fluorescence spectroscopy and circular dichroism. Compared with previous TPA derivatives with macrocyclic substituents, the new ligands reported herein retain the G4 affinity, but display two orders of magnitude higher selectivity for G4 versus duplex DNA; this is most likely due to the ability of the linear substituents to embrace the G4 structure.
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Affiliation(s)
- Isabel Pont
- Department of Inorganic Chemistry, Institute of Molecular Science, University of Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain.,Department of Chemistry, Imperial College London, White City Campus, London, W12 OBZ, UK
| | - Álvaro Martínez-Camarena
- Department of Inorganic Chemistry, Institute of Molecular Science, University of Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain
| | - Cristina Galiana-Roselló
- Department of Inorganic Chemistry, Institute of Molecular Science, University of Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain
| | - Roberto Tejero
- Department of Physical Chemistry, University of Valencia, Dr. Moliner s/n, 46100, Burjassot, Spain
| | - M Teresa Albelda
- Department of Inorganic Chemistry, Institute of Molecular Science, University of Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain
| | - Jorge González-García
- Department of Inorganic Chemistry, Institute of Molecular Science, University of Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain.,Department of Chemistry, Imperial College London, White City Campus, London, W12 OBZ, UK
| | - Ramón Vilar
- Department of Chemistry, Imperial College London, White City Campus, London, W12 OBZ, UK
| | - Enrique García-España
- Department of Inorganic Chemistry, Institute of Molecular Science, University of Valencia, Catedrático José Beltrán 2, 46980, Paterna, Spain
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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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9
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Manna S, Srivatsan SG. Fluorescence-based tools to probe G-quadruplexes in cell-free and cellular environments. RSC Adv 2018; 8:25673-25694. [PMID: 30210793 PMCID: PMC6130854 DOI: 10.1039/c8ra03708f] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 07/08/2018] [Indexed: 12/26/2022] Open
Abstract
Biophysical and biochemical investigations provide compelling evidence connecting the four-stranded G-quadruplex (GQ) structure with its role in regulating multiple cellular processes. Hence, modulating the function of GQs by using small molecule binders is being actively pursued as a strategy to develop new chemotherapeutic agents. However, sequence diversity and structural polymorphism of GQs have posed immense challenges in terms of understanding what conformation a G-rich sequence adopts inside the cell and how to specifically target a GQ motif amidst several other GQ-forming sequences. In this context, here we review recent developments in the applications of biophysical tools that use fluorescence readout to probe the GQ structure and recognition in cell-free and cellular environments. First, we provide a detailed discussion on the utility of covalently labeled environment-sensitive fluorescent nucleoside analogs in assessing the subtle difference in GQ structures and their ligand binding abilities. Furthermore, a detailed discussion on structure-specific antibodies and small molecule probes used to visualize and confirm the existence of DNA and RNA GQs in cells is provided. We also highlight the open challenges in the study of tetraplexes (GQ and i-motif structures) and how addressing these challenges by developing new tools and techniques will have a profound impact on tetraplex-directed therapeutic strategies.
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Affiliation(s)
- Sudeshna Manna
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), PuneDr. Homi Bhabha RoadPune 411008India
| | - Seergazhi G. Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), PuneDr. Homi Bhabha RoadPune 411008India
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Suseela YV, Narayanaswamy N, Pratihar S, Govindaraju T. Far-red fluorescent probes for canonical and non-canonical nucleic acid structures: current progress and future implications. Chem Soc Rev 2018; 47:1098-1131. [DOI: 10.1039/c7cs00774d] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Our review presents the recent progress on far-red fluorescent probes of canonical and non-canonical nucleic acid (NA) structures, critically discusses the design principles, applications, limitations and outline the future prospects of developing newer probes with target-specificity for different NA structures.
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Affiliation(s)
- Y. V. Suseela
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Nagarjun Narayanaswamy
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Sumon Pratihar
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory
- New Chemistry Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
- Bengaluru 560064
- India
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