1
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Pirota V, Rey F, Esposito L, Fantini V, Pandini C, Maghraby E, Di Gerlando R, Doria F, Mella M, Pansarasa O, Gandellini P, Freccero M, Carelli S, Cereda C. Effective lowering of α-synuclein expression by targeting G-quadruplex structures within the SNCA gene. Int J Biol Macromol 2024:134417. [PMID: 39098688 DOI: 10.1016/j.ijbiomac.2024.134417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 07/22/2024] [Accepted: 07/30/2024] [Indexed: 08/06/2024]
Abstract
Alpha-synuclein, encoded by the SNCA gene, is a pivotal protein implicated in the pathogenesis of synucleinopathies, including Parkinson's disease. Current approaches for modulating alpha-synuclein levels involve antisense nucleotides, siRNAs, and small molecules targeting SNCA's 5'-UTR mRNA. Here, we propose a groundbreaking strategy targeting G-quadruplex structures to effectively modulate SNCA gene expression and lowering alpha-synuclein amount. Novel G-quadruplex sequences, identified on the SNCA gene's transcription starting site and 5'-UTR of SNCA mRNAs, were experimentally confirmed for their stability through biophysical assays and in vitro experiments on human genomic DNA. Biological validation in differentiated SH-SY5Y cells revealed that well-known G-quadruplex ligands remarkably stabilized these structures, inducing the modulation of SNCA mRNAs expression, and the effective decrease in alpha-synuclein amount. Besides, a novel peptide nucleic acid conjugate, designed to selectively disrupt of G-quadruplex within the SNCA gene promoter, caused a promising lowering of both SNCA mRNA and alpha-synuclein protein. Altogether our findings highlight G-quadruplexes' key role as intriguing biological targets in achieving a notable and successful reduction in alpha-synuclein expression, pointing to a novel approach against synucleinopathies.
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Affiliation(s)
- Valentina Pirota
- Department of Chemistry, University of Pavia, Pavia, Italy; G4-INTERACT, USERN, Pavia, Italy.
| | - Federica Rey
- G4-INTERACT, USERN, Pavia, Italy; Pediatric Clinical Research Center "Fondazione Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy; Center of Functional Genomics and Rare diseases, Buzzi Children's Hospital, Milan, Italy
| | - Letizia Esposito
- Pediatric Clinical Research Center "Fondazione Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy; Center of Functional Genomics and Rare diseases, Buzzi Children's Hospital, Milan, Italy
| | - Valentina Fantini
- Laboratory of Neurobiology and Neurogenetic, Golgi-Cenci Foundation, Abbiategrasso, Italy
| | - Cecilia Pandini
- Department of Biosciences, University of Milan, Milan, Italy
| | - Erika Maghraby
- Center of Functional Genomics and Rare diseases, Buzzi Children's Hospital, Milan, Italy; Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy
| | - Rosalinda Di Gerlando
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy; Molecular Biology and Transcriptomic Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia, Pavia, Italy
| | - Mariella Mella
- Department of Chemistry, University of Pavia, Pavia, Italy
| | - Orietta Pansarasa
- Cellular Models and Neuroepigenetics Unit, IRCCS Mondino Foundation, Pavia, Italy
| | | | - Mauro Freccero
- Department of Chemistry, University of Pavia, Pavia, Italy
| | - Stephana Carelli
- Pediatric Clinical Research Center "Fondazione Romeo ed Enrica Invernizzi", Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, Milan, Italy; Center of Functional Genomics and Rare diseases, Buzzi Children's Hospital, Milan, Italy.
| | - Cristina Cereda
- Center of Functional Genomics and Rare diseases, Buzzi Children's Hospital, Milan, Italy
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2
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Zhang X, Li Y, Chen Y, Liu Z, Li Z, Wang Z, Wang Y, Liu M. Design and synthesis of dual functional NBD-fluorophore-incorporated naphthalene diimide derivatives as G-quadruplex ligands. Bioorg Med Chem Lett 2024; 111:129903. [PMID: 39053704 DOI: 10.1016/j.bmcl.2024.129903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 07/27/2024]
Abstract
Nitrobenzoxadiazole (NBD)-incorporated naphthalene diimide derivatives were designed and synthesized as candidates of antitumor agents with cytotoxicity against human pancreatic cancer cell MIA PaCa-2. Among these, compounds 1NND and 3NND exhibited fluorescent "turn-off" property toward human telomeric G-quadruplex (G4), which allows the direct measurement of dissociation constant (Kd) of ligands against G4 by fluorescence titration method. Notably, the compound 1NND not only exhibited great cytotoxic activity against MIA PaCa-2 with a half maximal inhibitory concentration (IC50) of 77.9 nM, but also exhibited high affinity against G4 with Kd of 1.72 μM. Furthermore, the target binding properties were investigated by circular dichroism (CD) spectra and further studied by molecular docking methods.
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Affiliation(s)
- Xinhang Zhang
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China; Department of Organic Chemistry, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Yashu Li
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China; Department of Organic Chemistry, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Yuchen Chen
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China; Department of Organic Chemistry, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Ziqi Liu
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China; Department of Organic Chemistry, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Zijin Li
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China; Department of Organic Chemistry, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Ziyin Wang
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China; Department of Organic Chemistry, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Yu Wang
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China; Department of Organic Chemistry, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China
| | - Mingzhe Liu
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China; Department of Organic Chemistry, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, China.
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3
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Nadai M, Doria F, Frasson I, Perrone R, Pirota V, Bergamaschi G, Freccero M, Richter SN. Naphthalene Diimide-Tetraazacycloalkane Conjugates Are G-Quadruplex-Based HIV-1 Inhibitors with a Dual Mode of Action. ACS Infect Dis 2024; 10:489-499. [PMID: 38175706 PMCID: PMC10862543 DOI: 10.1021/acsinfecdis.3c00453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/06/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024]
Abstract
Human immunodeficiency virus 1 (HIV-1) therapeutic regimens consist of three or more drugs targeting different steps of the viral life cycle to limit the emergence of viral resistance. In line with the multitargeting strategy, here we conjugated a naphthalene diimide (NDI) moiety with a tetraazacycloalkane to obtain novel naphthalene diimide (NDI)-tetraazacycloalkane conjugates. The NDI inhibits the HIV-1 promoter activity by binding to LTR G-quadruplexes, and the tetraazacycloalkane mimics AMD3100, which blocks HIV entry into cells by interfering with the CXCR4 coreceptor. We synthesized, purified, and tested the metal-free NDI-tetraazacycloalkane conjugate and the two derived metal-organic complexes (MOCs) that incorporate Cu2+ and Zn2+. The NDI-MOCs showed enhanced binding to LTR G4s as assessed by FRET and CD assays in vitro. They also showed enhanced activity in cells where they dose-dependently reduced LTR promoter activity and inhibited viral entry only of the HIV-1 strain that exploited the CXCR4 coreceptor. The time of addition assay confirmed the dual targeting at the different HIV-1 steps. Our results indicate that the NDI-MOC conjugates can simultaneously inhibit viral entry, by targeting the CXCR4 coreceptor, and LTR promoter activity, by stabilizing the LTR G-quadruplexes. The approach of combining multiple targets in a single compound may streamline treatment regimens and improve the overall patient outcomes.
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Affiliation(s)
- Matteo Nadai
- Department
of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Filippo Doria
- Department
of Chemistry, University of Pavia, V.le Taramelli 10, 27100 Pavia, Italy
| | - Ilaria Frasson
- Department
of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
| | - Rosalba Perrone
- Buck
Institute for Research on Aging, Novato, California 94945, United States
| | - Valentina Pirota
- Department
of Chemistry, University of Pavia, V.le Taramelli 10, 27100 Pavia, Italy
| | - Greta Bergamaschi
- National
Research Council of Italy, Istituto di Scienze e Tecnologie Chimiche
“Giulio Natta” (SCITEC–CNR), Via Mario Bianco 9, 20131 Milano, Italy
| | - Mauro Freccero
- Department
of Chemistry, University of Pavia, V.le Taramelli 10, 27100 Pavia, Italy
| | - Sara N. Richter
- Department
of Molecular Medicine, University of Padua, Via Gabelli 63, 35121 Padua, Italy
- Microbiology
and Virology Unit, Padua University Hospital, 35121 Padua, Italy
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4
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Singh K, Sharma S, Tyagi R, Sagar R. Recent progress in the synthesis of natural product inspired bioactive glycohybrids. Carbohydr Res 2023; 534:108975. [PMID: 37871479 DOI: 10.1016/j.carres.2023.108975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/25/2023]
Abstract
Carbohydrates are a basic structural component that are indispensable to all cellular processes. In addition to being employed as chiral starting materials in the synthesis of a variety of natural products, carbohydrates are recognized as naturally occurring molecules having an enormous variety of functional, stereochemical, and structural properties. The understanding and biological roles of carbohydrate derived molecules can be greatly improved by selectively synthesizing functional carbohydrates through incorporating them with privileged scaffolds. For a deeper understanding of their roles and the development of functional materials based on sugar, it is crucial to develop new techniques for efficiently synthesizing, functionalizing, and modifying carbohydrates. Glycohybrids have a wide range of structural and functional characteristics along with protein-carbohydrate interactions that are crucial to mammalian biology and a number of disease states. This review, consisting the literature from January 2017 to July 2023 and provide an overview of recent developments in the chemical synthesis of glycohybrids based on natural product scaffolds of coumarin, quinolone, naphthalene diimide, indole, isatin, naphthoquinone, imidazole and pyrimidine. The biological activity of active glycohybrids are discussed in this review.
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Affiliation(s)
- Kavita Singh
- Glycochemistry Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Sunil Sharma
- Glycochemistry Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Rajdeep Tyagi
- Glycochemistry Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Ram Sagar
- Glycochemistry Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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5
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Cebrián R, Belmonte-Reche E, Pirota V, de Jong A, Morales JC, Freccero M, Doria F, Kuipers OP. G-Quadruplex DNA as a Target in Pathogenic Bacteria: Efficacy of an Extended Naphthalene Diimide Ligand and Its Mode of Action. J Med Chem 2021; 65:4752-4766. [PMID: 34928608 PMCID: PMC8958502 DOI: 10.1021/acs.jmedchem.1c01905] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Guanidine DNA quadruplex
(G4-DNA) structures convey a distinctive
layer of epigenetic information that is critical for regulating key
biological activities and processes as transcription, replication,
and repair in living cells. The information regarding their role and
use as therapeutic drug targets in bacteria is still scarce. Here,
we tested the biological activity of a G4-DNA ligand library, based
on the naphthalene diimide (NDI) pharmacophore, against both Gram-positive
and Gram-negative bacteria. For the best compound identified, NDI-10, a different action mechanism was described for Gram-positive
or negative bacteria. This asymmetric activity profile could be related
to the different prevalence of putative G4-DNA structures in each
group, the influence that they can exert on gene expression, and the
different roles of the G4 structures in these bacteria, which seem
to promote transcription in Gram-positive bacteria and repress transcription
in Gram-negatives.
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Affiliation(s)
- Rubén Cebrián
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Efres Belmonte-Reche
- Advanced (magnetic) Theranostic Nanostructures Lab, International Iberian Nanotechnology Laboratory, Nanomedicine unit, Avenida Mestre José Veiga, s/n 4715-310 Braga, Portugal
| | - Valentina Pirota
- Department of Chemistry, University of Pavia, via Taramelli 10, I-27100 Pavia (PV), Italy
| | - Anne de Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
| | - Juan Carlos Morales
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, via Taramelli 10, I-27100 Pavia (PV), Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia, via Taramelli 10, I-27100 Pavia (PV), Italy
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands
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6
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Naphthalene diimides (NDI) in highly stable pH-neutral aqueous organic redox flow batteries. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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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: 0.7] [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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8
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Platella C, Napolitano E, Riccardi C, Musumeci D, Montesarchio D. Disentangling the Structure-Activity Relationships of Naphthalene Diimides as Anticancer G-Quadruplex-Targeting Drugs. J Med Chem 2021; 64:3578-3603. [PMID: 33751881 PMCID: PMC8041303 DOI: 10.1021/acs.jmedchem.1c00125] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
In the context of
developing efficient anticancer therapies aimed
at eradicating any sort of tumors, G-quadruplexes represent excellent
targets. Small molecules able to interact with G-quadruplexes can
interfere with cell pathways specific of tumors and common to all
cancers. Naphthalene diimides
(NDIs) are among the most promising, putative anticancer G-quadruplex-targeting
drugs, due to their ability to simultaneously target multiple G-quadruplexes
and their strong, selective in vitro and in vivo anticancer activity.
Here, all the available biophysical, biological, and structural data
concerning NDIs targeting G-quadruplexes were systematically analyzed.
Structure–activity correlations were obtained by analyzing
biophysical data of their interactions with G-quadruplex targets and
control duplex structures, in parallel to biological data concerning
the antiproliferative activity of NDIs on cancer and normal cells.
In addition, NDI binding modes to G-quadruplexes were discussed in
consideration of the structures and properties of NDIs by in-depth
analysis of the available structural models of G-quadruplex/NDI complexes.
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Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Ettore Napolitano
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy.,Institute of Biostructures and Bioimages, CNR, via Mezzocannone 16, I-80134 Naples, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, I-80126 Naples, Italy
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9
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The electrochemical response of core-functionalized naphthalene Diimides (NDI) – a combined computational and experimental investigation. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2020.137480] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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10
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Tassinari M, Zuffo M, Nadai M, Pirota V, Sevilla Montalvo AC, Doria F, Freccero M, Richter SN. Selective targeting of mutually exclusive DNA G-quadruplexes: HIV-1 LTR as paradigmatic model. Nucleic Acids Res 2020; 48:4627-4642. [PMID: 32282912 PMCID: PMC7229848 DOI: 10.1093/nar/gkaa186] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 02/28/2020] [Accepted: 03/11/2020] [Indexed: 02/06/2023] Open
Abstract
Targeting of G-quadruplexes, non-canonical conformations that form in G-rich regions of nucleic acids, has been proposed as a novel therapeutic strategy toward several diseases, including cancer and infections. The unavailability of highly selective molecules targeting a G-quadruplex of choice has hampered relevant applications. Herein, we describe a novel approach, based on naphthalene diimide (NDI)-peptide nucleic acid (PNA) conjugates, taking advantage of the cooperative interaction of the NDI with the G-quadruplex structure and hybridization of the PNA with the flanking region upstream or downstream the targeted G-quadruplex. By biophysical and biomolecular assays, we show that the NDI-PNA conjugates are able to specifically recognize the G-quadruplex of choice within the HIV-1 LTR region, consisting of overlapping and therefore mutually exclusive G-quadruplexes. Additionally, the conjugates can induce and stabilize the least populated G-quadruplex at the expenses of the more stable ones. The general and straightforward design and synthesis, which readily apply to any G4 target of choice, together with both the red-fluorescent emission and the possibility to introduce cellular localization signals, make the novel conjugates available to selectively control G-quadruplex folding over a wide range of applications.
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Affiliation(s)
- Martina Tassinari
- Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy
| | - Michela Zuffo
- Department of Chemistry, University of Pavia, v. le Taramelli 10, 27100, Pavia, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy
| | - Valentina Pirota
- Department of Chemistry, University of Pavia, v. le Taramelli 10, 27100, Pavia, Italy
| | | | - Filippo Doria
- Department of Chemistry, University of Pavia, v. le Taramelli 10, 27100, Pavia, Italy
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, v. le Taramelli 10, 27100, Pavia, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy
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11
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Trifunctionalized Naphthalene Diimides and Dimeric Analogues as G-Quadruplex-Targeting Anticancer Agents Selected by Affinity Chromatography. Int J Mol Sci 2020; 21:ijms21061964. [PMID: 32183038 PMCID: PMC7139804 DOI: 10.3390/ijms21061964] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 12/14/2022] Open
Abstract
A focused library of newly designed monomeric and dimeric naphthalene diimides (NDIs) was analyzed in its ability to recognize specific G-quadruplex (G4) structures discriminating duplex DNA. The best G4 ligands—according to an affinity chromatography-based screening method named G4-CPG—were tested on human cancer and healthy cells, inducing DNA damage at telomeres, and in parallel, showing selective antiproliferative activity on HeLa cancer cells with IC50 values in the low nanomolar range. CD and fluorescence spectroscopy studies allowed detailed investigation of the interaction in solution with different G4 and duplex DNA models of the most promising NDI of the series, as determined by combining the biophysical and biological assays’ data.
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12
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Shukla J, Mukhopadhyay P. Synthesis of Functionalized Naphthalene Diimides and their Redox Properties. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901390] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Jyoti Shukla
- School of Physical Sciences; Jawaharlal Nehru University; New Delhi India
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13
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Reiß B, Wagenknecht HA. Naphthalene diimides with improved solubility for visible light photoredox catalysis. Beilstein J Org Chem 2019; 15:2043-2051. [PMID: 31501672 PMCID: PMC6720061 DOI: 10.3762/bjoc.15.201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/12/2019] [Indexed: 12/11/2022] Open
Abstract
Five core-substituted naphthalene diimides bearing two dialkylamino groups were synthesized as potential visible light photoredox catalysts and characterized by methods of optical spectroscopy and electrochemistry in comparison with one unsubstituted naphthalene diimide as reference. The core-substituted naphthalene diimides differ by the alkyl groups at the imide nitrogens and at the nitrogens of the two substituents at the core in order to enhance their solubility in DMF and thereby enhance their photoredox catalytic potential. The 1-ethylpropyl group as rather short and branched alkyl substituent at the imide nitrogen and the n-propyl group as short and unbranched one at the core amines yielded the best solubilities. The electron-donating diaminoalkyl substituents together with the electron-deficient aromatic core of the naphthalene diimides increase the charge-transfer character of their photoexcited states and thus shift their absorption into the visible light (500-650 nm). The excited state reduction potential was estimated to be approximately +1.0 V (vs SCE) which is sufficient to photocatalyze typical organic reactions. The photoredox catalytic activity in the visible light range was tested by the α-alkylation of 1-octanal as benchmark reaction. Irradiations were performed with LEDs in the visible light range between 520 nm and 640 nm. The irradiation by visible light together with the use of an organic dye instead of a transition metal complex as photoredox catalyst improve the sustainability and make photoredox catalysis "greener".
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Affiliation(s)
- Barbara Reiß
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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14
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Zuffo M, Stucchi A, Campos-Salinas J, Cabello-Donayre M, Martínez-García M, Belmonte-Reche E, Pérez-Victoria J, Mergny J, Freccero M, Morales J, Doria F. Carbohydrate-naphthalene diimide conjugates as potential antiparasitic drugs: Synthesis, evaluation and structure-activity studies. Eur J Med Chem 2019; 163:54-66. [DOI: 10.1016/j.ejmech.2018.11.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/31/2018] [Accepted: 11/18/2018] [Indexed: 12/21/2022]
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15
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Naphthalene Diimides as Multimodal G-Quadruplex-Selective Ligands. Molecules 2019; 24:molecules24030426. [PMID: 30682828 PMCID: PMC6384834 DOI: 10.3390/molecules24030426] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 01/11/2019] [Accepted: 01/22/2019] [Indexed: 02/03/2023] Open
Abstract
G-quadruplexes are four-stranded nucleic acids structures that can form in guanine-rich sequences. Following the observation that G-quadruplexes are particularly abundant in genomic regions related to cancer, such as telomeres and oncogenes promoters, several G-quadruplex-binding molecules have been developed for therapeutic purposes. Among them, naphthalene diimide derivatives have reported versatility, consistent selectivity and high affinity toward the G-quadruplex structures. In this review, we present the chemical features, synthesis and peculiar optoelectronic properties (absorption, emission, redox) that make naphtalene diimides so versatile for biomedical applications. We present the latest developments on naphthalene diimides as G-quadruplex ligands, focusing on their ability to bind G-quadruplexes at telomeres and oncogene promoters with consequent anticancer activity. Their different binding modes (reversible versus irreversible/covalent) towards G-quadruplexes and their additional use as antimicrobial agents are also presented and discussed.
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16
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Seymour CP, Nakata A, Tsubaki M, Hayashi M, Matsubara R. A Fluorescent Naphthalenediimide-Alkoxyfuroxan Photoinduced Nitric Oxide Donor. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2019. [DOI: 10.1246/bcsj.20180219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
| | - Akito Nakata
- Department of Chemistry, Graduate School of Science, Kobe University, Nada, Kobe 657-8501, Japan
| | - Motonari Tsubaki
- Department of Chemistry, Graduate School of Science, Kobe University, Nada, Kobe 657-8501, Japan
| | - Masahiko Hayashi
- Department of Chemistry, Graduate School of Science, Kobe University, Nada, Kobe 657-8501, Japan
| | - Ryosuke Matsubara
- Department of Chemistry, Graduate School of Science, Kobe University, Nada, Kobe 657-8501, Japan
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17
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Cox RP, Sandanayake S, Scarborough DLA, Izgorodina EI, Langford SJ, Bell TDM. Investigation of cation binding and sensing by new crown ether core substituted naphthalene diimide systems. NEW J CHEM 2019. [DOI: 10.1039/c8nj05666h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Different modes of cation binding lead to very different optical readouts from two structurally similar sensors.
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Affiliation(s)
- R. P. Cox
- School of Chemistry
- Monash University
- Clayton
- Australia
| | - S. Sandanayake
- School of Chemistry
- Monash University
- Clayton
- Australia
- Addtec Pty Ltd
| | | | | | - S. J. Langford
- School of Chemistry
- Monash University
- Clayton
- Australia
- Department of Chemistry and Biotechnology
| | - T. D. M. Bell
- School of Chemistry
- Monash University
- Clayton
- Australia
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18
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Choudhury P, Sarkar S, Das PK. Tunable Aggregation-Induced Multicolor Emission of Organic Nanoparticles by Varying the Substituent in Naphthalene Diimide. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14328-14341. [PMID: 30384612 DOI: 10.1021/acs.langmuir.8b02996] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this article, we have designed l-aspartic acid-linked naphthalene diimide (NDI)-based amphiphilic molecules having a benzyl ester group at both the terminals with varying substituents (NAB-1-5). The substituent was judiciously modified from an electron-withdrawing group (EWG) like nitrobenzene to an electron-donating group (EDG), methoxybenzene, and finally to an extended aromatic residue (naphthalene) to regulate the π-electron density at the terminal of NDI derivatives. All of the synthesized NDI derivatives were molecularly dissolved in dimethyl sulfoxide (DMSO), and with an increase in the water content within the DMSO solution, the NDI derivative starts to get self-assembled through J-aggregation at and above 40% water content. Self-assembled spherical organic nanoparticles formed in 99% water in DMSO ( fw = 99%) were characterized by microscopic studies. All of the NDI derivatives showed very weak emission in the molecularly dissolved state (DMSO). Aggregation-induced emission (AIE) was observed for the NDI derivatives (except NAB-1) at the self-assembled state through excimer formation. Upon excitation at 350 nm, the emission maxima of these NDI-based AIE luminogens (AIE-gens) (NAB-2-5) get red shifted from 463 to 588 nm upon altering the substitution from EWG to EDG at the donor site. Inclusion of proper donor-acceptor moieties in the molecular backbone of the self-assembling unit can govern the AIE in combination with the intramolecular charge-transfer process. Consequently, the emission color of these AIE-gens (NAB-2-5) gets tuned from cyan blue to faint green to strong green and finally to bright orange. The tunable aggregation-induced multicolor emission was investigated by different spectroscopic techniques. These cytocompatible, multicolor-emitting fluorescent organic nanoparticles were utilized for bioimaging applications.
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Affiliation(s)
- Pritam Choudhury
- School of Biological Sciences , Indian Association for the Cultivation of Science , Jadavpur , Kolkata 700032 , India
| | - Saheli Sarkar
- School of Biological Sciences , Indian Association for the Cultivation of Science , Jadavpur , Kolkata 700032 , India
| | - Prasanta Kumar Das
- School of Biological Sciences , Indian Association for the Cultivation of Science , Jadavpur , Kolkata 700032 , India
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19
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Tassinari M, Cimino-Reale G, Nadai M, Doria F, Butovskaya E, Recagni M, Freccero M, Zaffaroni N, Richter SN, Folini M. Down-Regulation of the Androgen Receptor by G-Quadruplex Ligands Sensitizes Castration-Resistant Prostate Cancer Cells to Enzalutamide. J Med Chem 2018; 61:8625-8638. [PMID: 30188709 DOI: 10.1021/acs.jmedchem.8b00502] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Stabilization of the G-quadruplexes (G4s) within the androgen receptor (AR) gene promoter to block transcription may represent an innovative approach to interfere with aberrant AR signaling in castration resistant prostate cancer (CRPC). A library of differently functionalized naphthalene diimides (NDIs) was screened for their ability to stabilize AR G4s: the core-extended NDI (7) stood out as the most promising ligand. AR-positive cells were remarkably sensitive to 7 in comparison to AR-negative CRCP or normal prostate epithelial cells; 7 induced remarkable impairment of AR mRNA and protein amounts and significant perturbations in the expression levels of KLK3 and of genes involved in the activation of AR program via feedback mechanisms. Moreover, 7 synergistically interacted with Enzalutamide, an inhibitor of AR signaling used in second-line therapies. Overall, our data show that stabilization of AR G4s may represent an alternative treatment options for CRPC and other malignancies relying on aberrant androgen signaling.
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Affiliation(s)
- Martina Tassinari
- Department of Molecular Medicine , University of Padua , via A. Gabelli 63 , 35121 Padua , Italy
| | - Graziella Cimino-Reale
- Department of Applied Research and Technological Development , Fondazione IRCCS Istituto Nazionale dei Tumori di Milano , Via G. A. Amadeo 42 , 20133 Milan , Italy
| | - Matteo Nadai
- Department of Molecular Medicine , University of Padua , via A. Gabelli 63 , 35121 Padua , Italy
| | - Filippo Doria
- Department of Chemistry , University of Pavia , v. le Taramelli 10 , 27100 , Pavia , Italy
| | - Elena Butovskaya
- Department of Molecular Medicine , University of Padua , via A. Gabelli 63 , 35121 Padua , Italy
| | - Marta Recagni
- Department of Applied Research and Technological Development , Fondazione IRCCS Istituto Nazionale dei Tumori di Milano , Via G. A. Amadeo 42 , 20133 Milan , Italy
| | - Mauro Freccero
- Department of Chemistry , University of Pavia , v. le Taramelli 10 , 27100 , Pavia , Italy
| | - Nadia Zaffaroni
- Department of Applied Research and Technological Development , Fondazione IRCCS Istituto Nazionale dei Tumori di Milano , Via G. A. Amadeo 42 , 20133 Milan , Italy
| | - Sara N Richter
- Department of Molecular Medicine , University of Padua , via A. Gabelli 63 , 35121 Padua , Italy
| | - Marco Folini
- Department of Applied Research and Technological Development , Fondazione IRCCS Istituto Nazionale dei Tumori di Milano , Via G. A. Amadeo 42 , 20133 Milan , Italy
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20
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Marchetti C, Zyner KG, Ohnmacht SA, Robson M, Haider SM, Morton JP, Marsico G, Vo T, Laughlin-Toth S, Ahmed AA, Di Vita G, Pazitna I, Gunaratnam M, Besser RJ, Andrade ACG, Diocou S, Pike JA, Tannahill D, Pedley RB, Evans TRJ, Wilson WD, Balasubramanian S, Neidle S. Targeting Multiple Effector Pathways in Pancreatic Ductal Adenocarcinoma with a G-Quadruplex-Binding Small Molecule. J Med Chem 2018; 61:2500-2517. [PMID: 29356532 PMCID: PMC5867665 DOI: 10.1021/acs.jmedchem.7b01781] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Indexed: 12/11/2022]
Abstract
Human pancreatic ductal adenocarcinoma (PDAC) involves the dysregulation of multiple signaling pathways. A novel approach to the treatment of PDAC is described, involving the targeting of cancer genes in PDAC pathways having over-representation of G-quadruplexes, using the trisubstituted naphthalene diimide quadruplex-binding compound 2,7-bis(3-morpholinopropyl)-4-((2-(pyrrolidin-1-yl)ethyl)amino)benzo[ lmn][3,8]phenanthroline-1,3,6,8(2 H,7 H)-tetraone (CM03). This compound has been designed by computer modeling, is a potent inhibitor of cell growth in PDAC cell lines, and has anticancer activity in PDAC models, with a superior profile compared to gemcitabine, a commonly used therapy. Whole-transcriptome RNA-seq methodology has been used to analyze the effects of this quadruplex-binding small molecule on global gene expression. This has revealed the down-regulation of a large number of genes, rich in putative quadruplex elements and involved in essential pathways of PDAC survival, metastasis, and drug resistance. The changes produced by CM03 represent a global response to the complexity of human PDAC and may be applicable to other currently hard-to-treat cancers.
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Affiliation(s)
- Chiara Marchetti
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Katherine G. Zyner
- Cancer
Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, U.K.
| | - Stephan A. Ohnmacht
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Mathew Robson
- Cancer
Research UK Cancer Centre, UCL Cancer Institute, University College London, London WC1E 6BT, U.K.
| | - Shozeb M. Haider
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Jennifer P. Morton
- Cancer
Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD U.K.
- Institute
of Cancer Sciences. University of Glasgow, Glasgow G12 8QQ, U.K.
| | - Giovanni Marsico
- Cancer
Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, U.K.
| | - Tam Vo
- Department
of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Sarah Laughlin-Toth
- Department
of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Ahmed A. Ahmed
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Gloria Di Vita
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Ingrida Pazitna
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Mekala Gunaratnam
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Rachael J. Besser
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Ana C. G. Andrade
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
| | - Seckou Diocou
- UCL
Cancer Institute, University College London, London WC1E 6BT, U.K.
| | - Jeremy A. Pike
- Cancer
Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, U.K.
| | - David Tannahill
- Cancer
Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, U.K.
| | - R. Barbara Pedley
- UCL
Cancer Institute, University College London, London WC1E 6BT, U.K.
| | - T. R. Jeffry Evans
- Cancer
Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD U.K.
- Institute
of Cancer Sciences. University of Glasgow, Glasgow G12 8QQ, U.K.
| | - W. David Wilson
- Department
of Chemistry and Center for Biotechnology and Drug Design, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Shankar Balasubramanian
- Cancer
Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, U.K.
- Department
of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K.
- The
School of Clinical Medicine, University
of Cambridge, Cambridge CB2 0SP, U.K.
| | - Stephen Neidle
- UCL
School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, U.K.
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21
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Doria F, Nadai M, Zuffo M, Perrone R, Freccero M, Richter SN. A red-NIR fluorescent dye detecting nuclear DNA G-quadruplexes: in vitro analysis and cell imaging. Chem Commun (Camb) 2018; 53:2268-2271. [PMID: 28149992 PMCID: PMC5471928 DOI: 10.1039/c6cc08492c] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Light-up of nuclear G-quadruplex DNA in cells by an aggregating and red/NIR emitting dye.
Aggregation, red-NIR emission and light-up upon nucleic acid G-quadruplex binding have been investigated for a prototype core-extended naphthalene diimide, which is capable of fast cellular entry and nucleolar localization. Both high-level colocalization with an anti-G-quadruplex antibody and nucleolin displacement reveal that the compound targets and thus makes visible nuclear DNA G-quadruplexes.
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Affiliation(s)
- F Doria
- Dept. of Chemistry, University of Pavia, V.le Taramelli 10, 27100 Pavia, Italy.
| | - M Nadai
- Dept. of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy.
| | - M Zuffo
- Dept. of Chemistry, University of Pavia, V.le Taramelli 10, 27100 Pavia, Italy.
| | - R Perrone
- Dept. of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy.
| | - M Freccero
- Dept. of Chemistry, University of Pavia, V.le Taramelli 10, 27100 Pavia, Italy.
| | - S N Richter
- Dept. of Molecular Medicine, University of Padua, via Gabelli 63, 35121 Padua, Italy.
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22
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Kremer M, Kersten M, Höger S. Efficient catalytic vicinal diamination of arylene diimides. Org Chem Front 2018. [DOI: 10.1039/c8qo00222c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
New substitution patterns for rylene diimides by catalytic diamination.
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Affiliation(s)
- Michael Kremer
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
| | - Maximilian Kersten
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
| | - Sigurd Höger
- Kekulé-Institut für Organische Chemie und Biochemie
- Rheinische Friedrich-Wilhelms-Universität Bonn
- 53121 Bonn
- Germany
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23
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Weißenstein A, Grande V, Saha-Möller CR, Würthner F. Water-soluble naphthalene diimides: synthesis, optical properties, and colorimetric detection of biogenic amines. Org Chem Front 2018. [DOI: 10.1039/c8qo00611c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Biocompatible water-soluble naphthalene diimides (NDIs) were synthesized and a core-dichlorinated NDI was shown to detect primary amines and biogenic diamines.
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Affiliation(s)
| | - Vincenzo Grande
- Center for Nanosystems Chemistry (CNC)
- Universität Würzburg
- 97074 Würzburg
- Germany
| | | | - Frank Würthner
- Institut für Organische Chemie
- Universität Würzburg
- 97074 Würzburg
- Germany
- Center for Nanosystems Chemistry (CNC)
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24
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Hangarge RV, La DD, Boguslavsky M, Jones LA, Kim YS, Bhosale SV. An Aza‐12‐crown‐4 Ether‐Substituted Naphthalene Diimide Chemosensor for the Detection of Lithium Ion. ChemistrySelect 2017. [DOI: 10.1002/slct.201702085] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Rahul V. Hangarge
- School of Science RMIT University GPO Box 2476 Melbourne VIC 3001 Australia
| | - Duong Duc La
- School of Science RMIT University GPO Box 2476 Melbourne VIC 3001 Australia
| | - Miron Boguslavsky
- School of Science RMIT University GPO Box 2476 Melbourne VIC 3001 Australia
| | - Lathe A. Jones
- School of Science RMIT University GPO Box 2476 Melbourne VIC 3001 Australia
- Centre for Advanced Materials and Industrial Chemistry (CAMIC), School of Science RMIT University GPO Box 2476 Melbourne 3001 Victoria Australia
| | - Yong Shin Kim
- Department of Applied Chemistry Hanyang University Ansan 15588, Republic of Korea
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25
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Perrone R, Lavezzo E, Riello E, Manganelli R, Palù G, Toppo S, Provvedi R, Richter SN. Mapping and characterization of G-quadruplexes in Mycobacterium tuberculosis gene promoter regions. Sci Rep 2017; 7:5743. [PMID: 28720801 PMCID: PMC5515968 DOI: 10.1038/s41598-017-05867-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/02/2017] [Indexed: 12/04/2022] Open
Abstract
Mycobacterium tuberculosis is the causative agent of tuberculosis (TB), one of the top 10 causes of death worldwide in 2015. The recent emergence of strains resistant to all current drugs urges the development of compounds with new mechanisms of action. G-quadruplexes are nucleic acids secondary structures that may form in G-rich regions to epigenetically regulate cellular functions. Here we implemented a computational tool to scan the presence of putative G-quadruplex forming sequences in the genome of Mycobacterium tuberculosis and analyse their association to transcription start sites. We found that the most stable G-quadruplexes were in the promoter region of genes belonging to definite functional categories. Actual G-quadruplex folding of four selected sequences was assessed by biophysical and biomolecular techniques: all molecules formed stable G-quadruplexes, which were further stabilized by two G-quadruplex ligands. These compounds inhibited Mycobacterium tuberculosis growth with minimal inhibitory concentrations in the low micromolar range. These data support formation of Mycobacterium tuberculosis G-quadruplexes in vivo and their potential regulation of gene transcription, and prompt the use of G4 ligands to develop original antitubercular agents.
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Affiliation(s)
- Rosalba Perrone
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Enrico Lavezzo
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Erika Riello
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Riccardo Manganelli
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy.
| | - Roberta Provvedi
- Department of Biology, University of Padua, via Ugo Bassi 58/b, 35121, Padua, Italy.
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua, via Gabelli 63, 35121, Padua, Italy.
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26
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Choudhury P, Das K, Das PK. l-Phenylalanine-Tethered, Naphthalene Diimide-Based, Aggregation-Induced, Green-Emitting Organic Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:4500-4510. [PMID: 28438019 DOI: 10.1021/acs.langmuir.7b00452] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The present article delineates the formation of green fluorescent organic nanoparticle through supramolecular aggregation of naphthalene diimide (NDI)-based, carboxybenzyl-protected, l-phenylalanine-appended bola-amphiphile, NDI-1. The amphiphilic molecule is soluble in DMSO, and, with gradual addition of water within the DMSO solution, the amphiphile starts to self-assemble via H-type aggregation to form spherical nanoparticles. These self-assembly of NDI-1 in the presence of a high amount of water exhibited aggregation-induced emission (AIE) through excimer formation. Notably, in the presence of 99% water content, the amphiphile forms spherical aggregated nanoparticles as confirmed from microscopic investigations and dynamic light scattering study. Interestingly, the emission maxima of molecularly dissolved NDI-1 (weak blue fluorescence) red-shifted upon aggregation with increase in water concentration and led to the formation of green-emitting fluorescent organic nanoparticles (FONPs) at 99% water content. These green-emitting FONPs were utilized in cell imaging as well as for efficient transportation of anticancer drug curcumin inside mammalian cells.
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Affiliation(s)
- Pritam Choudhury
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur , Kolkata - 700032, India
| | - Krishnendu Das
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur , Kolkata - 700032, India
| | - Prasanta Kumar Das
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur , Kolkata - 700032, India
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27
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Sur S, Tiwari V, Sinha D, Kamran MZ, Dubey KD, Suresh Kumar G, Tandon V. Naphthalenediimide-Linked Bisbenzimidazole Derivatives as Telomeric G-Quadruplex-Stabilizing Ligands with Improved Anticancer Activity. ACS OMEGA 2017; 2:966-980. [PMID: 30023623 PMCID: PMC6044781 DOI: 10.1021/acsomega.6b00523] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/28/2017] [Indexed: 05/22/2023]
Abstract
Human telomeric G-quadruplex DNA stabilization has emerged as an exciting novel approach for anticancer drug development. In the present study, we have designed and synthesized three C2-symmetric bisubstituted bisbenzimidazole naphthalenediimide (NDI) ligands, ALI-C3 , BBZ-ARO, and BBZ-AROCH2 , which stabilize human telomeric G-quadruplex DNA with high affinity. Herein, we have studied the binding affinities and thermodynamic contributions of each of these molecules with G-quadruplex DNA and compared the same to those of the parent NDI analogue, BMSG-SH-3. Results of fluorescence resonance energy transfer and surface plasmon resonance demonstrate that these ligands have a higher affinity for G4-DNA over duplex DNA and induce the formation of a G-quadruplex. The binding equilibrium constants obtained from the microcalorimetry studies of BBZ-ARO, ALI-C3 , and BBZ-AROCH2 were 8.47, 6.35, and 3.41 μM, respectively, with h-telo 22-mer quadruplex. These showed 10 and 100 times lower binding affinity with h-telo 12-mer and duplex DNA quadruplexes, respectively. Analysis of the thermodynamic parameters obtained from the microcalorimetry study suggests that interactions were most favorable for BBZ-ARO among all of the synthesized compounds. The ΔGfree obtained from molecular mechanics Poisson-Boltzmann surface area calculations of molecular dynamics (MD) simulation studies suggest that BBZ-ARO interacted strongly with G4-DNA. MD simulation results showed the highest hydrogen bond occupancy and van der Waals interactions were between the side chains of BBZ-ARO and the DNA grooves. A significant inhibition of telomerase activity (IC50 = 4.56 μM) and induced apoptosis in cancer cell lines by BBZ-ARO suggest that this molecule has the potential to be developed as an anticancer agent.
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Affiliation(s)
- Souvik Sur
- Chemical
Biology Laboratory, Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Vinod Tiwari
- Chemical
Biology Laboratory, Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Devapriya Sinha
- Chemical
Biology Laboratory, Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Mohammad Zahid Kamran
- Special
Center for Molecular Medicine, Jawaharlal
Nehru University, New Delhi 110067, India
| | | | - Gopinatha Suresh Kumar
- Biophysical
Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Vibha Tandon
- Chemical
Biology Laboratory, Department of Chemistry, University of Delhi, Delhi 110007, India
- Special
Center for Molecular Medicine, Jawaharlal
Nehru University, New Delhi 110067, India
- E-mail: , . Phone: 91-11-26741640; 91-11-26708783
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Doria F, Nadai M, Costa G, Sattin G, Gallati C, Bergamaschi G, Moraca F, Alcaro S, Freccero M, Richter SN. Extended Naphthalene Diimides with Donor/Acceptor Hydrogen-Bonding Properties Targeting G-Quadruplex Nucleic Acids. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600757] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Filippo Doria
- Department of Chemistry; University of Pavia; v.le Taramelli 10 27100 Pavia Italy
| | - Matteo Nadai
- Department of Molecular Medicine; University of Padua; via Gabelli 63 35121 Padua Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute Università degli Studi “Magna Graecia” di Catanzaro Campus “Salvatore Venuta”; Viale Europa 88100 Catanzaro Italy
| | - Giovanna Sattin
- Department of Molecular Medicine; University of Padua; via Gabelli 63 35121 Padua Italy
| | - Caroline Gallati
- Department of Chemistry; University of Pavia; v.le Taramelli 10 27100 Pavia Italy
| | - Greta Bergamaschi
- Department of Chemistry; University of Pavia; v.le Taramelli 10 27100 Pavia Italy
| | - Federica Moraca
- Dipartimento di Scienze della Salute Università degli Studi “Magna Graecia” di Catanzaro Campus “Salvatore Venuta”; Viale Europa 88100 Catanzaro Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute Università degli Studi “Magna Graecia” di Catanzaro Campus “Salvatore Venuta”; Viale Europa 88100 Catanzaro Italy
| | - Mauro Freccero
- Department of Chemistry; University of Pavia; v.le Taramelli 10 27100 Pavia Italy
| | - Sara N. Richter
- Department of Molecular Medicine; University of Padua; via Gabelli 63 35121 Padua Italy
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Al Kobaisi M, Bhosale SV, Latham K, Raynor AM, Bhosale SV. Functional Naphthalene Diimides: Synthesis, Properties, and Applications. Chem Rev 2016; 116:11685-11796. [DOI: 10.1021/acs.chemrev.6b00160] [Citation(s) in RCA: 557] [Impact Index Per Article: 69.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Mohammad Al Kobaisi
- School
of Applied Sciences, RMIT University
, GPO Box 2476, Melbourne, Victoria
3001, Australia
| | - Sidhanath V. Bhosale
- Polymers
and Functional Materials Division, CSIR-Indian Institute of Chemical Technology
, Hyderabad, Telangana-500007, India
| | - Kay Latham
- School
of Applied Sciences, RMIT University
, GPO Box 2476, Melbourne, Victoria
3001, Australia
| | - Aaron M. Raynor
- School
of Applied Sciences, RMIT University
, GPO Box 2476, Melbourne, Victoria
3001, Australia
| | - Sheshanath V. Bhosale
- School
of Applied Sciences, RMIT University
, GPO Box 2476, Melbourne, Victoria
3001, Australia
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31
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Maniam S, Sandanayake S, Izgorodina EI, Langford SJ. Unusual Products from Oxidation of Naphthalene Diimides. ASIAN J ORG CHEM 2016. [DOI: 10.1002/ajoc.201600048] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Subashani Maniam
- School of Chemistry Monash University Wellington Road Clayton 3800 Victoria Australia
| | - Saman Sandanayake
- School of Chemistry Monash University Wellington Road Clayton 3800 Victoria Australia
| | | | - Steven J. Langford
- School of Chemistry Monash University Wellington Road Clayton 3800 Victoria Australia
- School of Science Monash University Malaysia, Jalan Lagoon Selatan 46150 Bandar Sunway Petaling Jaya Selangor Malaysia
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Salvati E, Doria F, Manoli F, D'Angelo C, Biroccio A, Freccero M, Manet I. A bimodal fluorescent and photocytotoxic naphthalene diimide for theranostic applications. Org Biomol Chem 2016; 14:7238-49. [DOI: 10.1039/c6ob00987e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe the bimodal activity of a water-soluble tetracationic naphthalene diimide as red light emitter for fluorescence imaging, including fluorescence-lifetime imaging, and singlet oxygen photosensitizer, inducing photocytotoxicity in cancer cells.
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Affiliation(s)
- Erica Salvati
- Oncogenomic and Epigenetic Unit
- Regina Elena National Cancer Institute
- 53 Rome
- Italy
| | - Filippo Doria
- Dipartimento di Chimica
- Università di Pavia
- 27100 Pavia
- Italy
| | - Francesco Manoli
- Istituto per la Sintesi Organica e la Fotoreattività
- Consiglio Nazionale delle Ricerche
- 40129 Bologna
- Italy
| | - Carmen D'Angelo
- Oncogenomic and Epigenetic Unit
- Regina Elena National Cancer Institute
- 53 Rome
- Italy
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit
- Regina Elena National Cancer Institute
- 53 Rome
- Italy
| | - Mauro Freccero
- Dipartimento di Chimica
- Università di Pavia
- 27100 Pavia
- Italy
| | - Ilse Manet
- Istituto per la Sintesi Organica e la Fotoreattività
- Consiglio Nazionale delle Ricerche
- 40129 Bologna
- Italy
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33
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Yue Y, Huo F, Lee S, Yin C, Yoon J, Chao J, Zhang Y, Cheng F. A Dual Colorimetric/Fluorescence System for Determining pH Based on the Nucleophilic Addition Reaction of an o
-Hydroxymerocyanine Dye. Chemistry 2015; 22:1239-43. [DOI: 10.1002/chem.201504395] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Yongkang Yue
- Institute of Molecular Science; Shanxi University; Taiyuan 030-006 P. R. China
| | - Fangjun Huo
- Research Institute of Applied Chemistry; Shanxi University; Taiyuan 030-006 P. R. China
- Department of Chemistry; University of Missouri; 601 South college Avenue Columbia Missouri 65211 USA
| | - Songyi Lee
- Department of Chemistry and Nano Science; Ewha Womans University; Seoul 120-750 Korea
| | - Caixia Yin
- Institute of Molecular Science; Shanxi University; Taiyuan 030-006 P. R. China
- Department of Chemistry; University of Missouri; 601 South college Avenue Columbia Missouri 65211 USA
| | - Juyoung Yoon
- Department of Chemistry and Nano Science; Ewha Womans University; Seoul 120-750 Korea
| | - Jianbin Chao
- Research Institute of Applied Chemistry; Shanxi University; Taiyuan 030-006 P. R. China
| | - Yongbin Zhang
- Research Institute of Applied Chemistry; Shanxi University; Taiyuan 030-006 P. R. China
| | - Fangqin Cheng
- Institute of Molecular Science; Shanxi University; Taiyuan 030-006 P. R. China
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Perrone R, Doria F, Butovskaya E, Frasson I, Botti S, Scalabrin M, Lago S, Grande V, Nadai M, Freccero M, Richter SN. Synthesis, Binding and Antiviral Properties of Potent Core-Extended Naphthalene Diimides Targeting the HIV-1 Long Terminal Repeat Promoter G-Quadruplexes. J Med Chem 2015; 58:9639-52. [PMID: 26599611 PMCID: PMC4690987 DOI: 10.1021/acs.jmedchem.5b01283] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
We have previously reported that
stabilization of the G-quadruplex
structures in the HIV-1 long terminal repeat (LTR) promoter suppresses
viral transcription. Here we sought to develop new G-quadruplex ligands
to be exploited as antiviral compounds by enhancing binding toward
the viral G-quadruplex structures. We synthesized naphthalene diimide
derivatives with a lateral expansion of the aromatic core. The new
compounds were able to bind/stabilize the G-quadruplex to a high extent,
and some of them displayed clear-cut selectivity toward the viral
G-quadruplexes with respect to the human telomeric G-quadruplexes.
This feature translated into low nanomolar anti-HIV-1 activity toward
two viral strains and encouraging selectivity indexes. The selectivity
depended on specific recognition of LTR loop residues; the mechanism
of action was ascribed to inhibition of LTR promoter activity in cells.
This is the first example of G-quadruplex ligands that show increased
selectivity toward the viral G-quadruplexes and display remarkable
antiviral activity.
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Affiliation(s)
- Rosalba Perrone
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia , V.le Taramelli 10, 27100 Pavia, Italy
| | - Elena Butovskaya
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Silvia Botti
- Department of Chemistry, University of Pavia , V.le Taramelli 10, 27100 Pavia, Italy
| | - Matteo Scalabrin
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Sara Lago
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Vincenzo Grande
- Department of Chemistry, University of Pavia , V.le Taramelli 10, 27100 Pavia, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Mauro Freccero
- Department of Chemistry, University of Pavia , V.le Taramelli 10, 27100 Pavia, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
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Zuffo M, Doria F, Spalluto V, Ladame S, Freccero M. Red/NIR G-Quadruplex Sensing, Harvesting Blue Light by a Coumarin-Naphthalene Diimide Dyad. Chemistry 2015; 21:17596-600. [DOI: 10.1002/chem.201503020] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/09/2015] [Indexed: 12/22/2022]
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Ghule NV, Bhosale RS, Kharat K, Puyad AL, Bhosale SV, Bhosale SV. A Naphthalenediimide-Based Fluorescent Sensor for Detecting the pH within the Rough Endoplasmic Reticulum of Living Cells. Chempluschem 2015; 80:485-489. [PMID: 31973408 DOI: 10.1002/cplu.201402307] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 11/05/2014] [Indexed: 11/08/2022]
Abstract
An amino-core-substituted naphthalenediimide (NDI) derivative has been synthesized in good yield in two steps. The NDI bearing a diamine moiety undergoes a reversible protonation-deprotonation process, which results in intensity changes in the absorption and emission spectra. This derivative exhibits good photostability, good selectivity, high sensitivity, and is employed to exhibit the pH within the rough endoplasmic reticulum of living cells.
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Affiliation(s)
- Namdev V Ghule
- Polymers and Functional Materials Division, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad, Telangana 500007 (India)
| | - Rajesh S Bhosale
- RMIT-IICT Research Centre, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad, Telangana 500007 (India)
| | - Kiran Kharat
- Department of Biotechnology, Deogiri College, Station Road, Auranagabad, Maharashtra 431005 (India)
| | - Avinash L Puyad
- School of Chemical Sciences, Swami RamanandTeerthMarathwada University, Nanded, Maharashtra 431606 (India)
| | - Sheshanath V Bhosale
- School of Applied Sciences, RMIT University, GPO Box 2476V, Melbourne, VIC 3001 (Australia)
| | - Sidhanath V Bhosale
- Polymers and Functional Materials Division, CSIR-Indian Institute of Chemical Technology, Uppal Road, Hyderabad, Telangana 500007 (India)
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37
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Prato G, Silvent S, Saka S, Lamberto M, Kosenkov D. Thermodynamics of binding of di- and tetrasubstituted naphthalene diimide ligands to DNA G-quadruplex. J Phys Chem B 2015; 119:3335-47. [PMID: 25635929 DOI: 10.1021/jp509637y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Naphthalene diimide ligands have the potential to stabilize human telomeric G-quadruplex DNA via noncovalent interactions. Stabilization of G-quadruplex high order structures has become an important strategy to develop novel anticancer therapeutics. In this study four naphthalene diimide based ligands were analyzed in order to elucidate the principal factors determining contributions to G-quadruplex-ligand binding. Three possible modes of binding and their respective Gibbs free energies for two naphthalene diimide based di-N-alkylpyridinium substituted ligands have been determined using a molecular docking technique and compared to experimental results. The structures obtained from the molecular docking calculations, were analyzed using the ab initio based fragment molecular orbital (FMO) method in order to determine the major enthalpic contributions to the binding and types of interactions between the ligand and specific residues of the G-quadruplex. A computational methodology for the efficient and inexpensive ligand optimization as compared to fully ab initio methods based on the estimation of binding affinities of the naphthalene diimide derived ligands to G-quadruplex is proposed.
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Affiliation(s)
- Gary Prato
- Department of Chemistry and Physics, Monmouth University , 400 Cedar Avenue, West Long Branch, New Jersey 07764, United States
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38
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Doria F, Folini M, Grande V, Cimino-Reale G, Zaffaroni N, Freccero M. Naphthalene diimides as red fluorescent pH sensors for functional cell imaging. Org Biomol Chem 2015; 13:570-6. [DOI: 10.1039/c4ob02054e] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Water-soluble naphthalene diimides have been designed and synthesized as cell permeable pH “turned-on” fluorescent sensors for cellular applications.
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Affiliation(s)
- Filippo Doria
- Dipartimento di Chimica
- Università di Pavia
- 27100 Pavia
- Italy
| | - Marco Folini
- Molecular Pharmacology Unit
- Department of Experimental Oncology and Molecular Medicine
- Fondazione IRCCS Istituto Nazionale dei Tumori
- Milano
- Italy
| | | | - Graziella Cimino-Reale
- Molecular Pharmacology Unit
- Department of Experimental Oncology and Molecular Medicine
- Fondazione IRCCS Istituto Nazionale dei Tumori
- Milano
- Italy
| | - Nadia Zaffaroni
- Molecular Pharmacology Unit
- Department of Experimental Oncology and Molecular Medicine
- Fondazione IRCCS Istituto Nazionale dei Tumori
- Milano
- Italy
| | - Mauro Freccero
- Dipartimento di Chimica
- Università di Pavia
- 27100 Pavia
- Italy
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39
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Leng B, Lu D, Jia X, Yang X, Gao X. Synthesis of monolateral and bilateral sulfur-heterocycle fused naphthalene diimides (NDIs) from monobromo and dibromo NDIs. Org Chem Front 2015. [DOI: 10.1039/c4qo00252k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Monolateral and bilateral sulfur-heterocycle fused naphthalene diimides (NDIs) are successfully synthesized from monobromo and dibromo NDIs via nucleophilic aromatic substitution reactions and the subsequent oxidative aromatization processes.
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Affiliation(s)
- Bing Leng
- Key Laboratory of Synthetic and Self-Assembly Chemistry for Organic Functional Molecules
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Dong Lu
- Key Laboratory of Synthetic and Self-Assembly Chemistry for Organic Functional Molecules
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
| | - Xueshun Jia
- Department of Chemistry
- Shanghai University
- Shanghai 200444
- China
| | - Xiaodi Yang
- Laboratory of Advanced Materials
- Fudan University
- Shanghai 200433
- China
| | - Xike Gao
- Key Laboratory of Synthetic and Self-Assembly Chemistry for Organic Functional Molecules
- Shanghai Institute of Organic Chemistry
- Chinese Academy of Sciences
- Shanghai 200032
- China
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40
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Doria F, Oppi A, Manoli F, Botti S, Kandoth N, Grande V, Manet I, Freccero M. A naphthalene diimide dyad for fluorescence switch-on detection of G-quadruplexes. Chem Commun (Camb) 2015; 51:9105-8. [DOI: 10.1039/c5cc01536g] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A non-fluorescent dimeric naphthalene diimide dye becomes red emitting upon G-quadruplex binding.
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Affiliation(s)
- F. Doria
- Dipartimento di Chimica
- Università di Pavia
- 27100 Pavia
- Italy
| | - A. Oppi
- Dipartimento di Chimica
- Università di Pavia
- 27100 Pavia
- Italy
| | - F. Manoli
- Istituto per la sintesi organica e la fotoreattività (ISOF)
- CNR
- 40129 Bologna
- Italy
| | - S. Botti
- Dipartimento di Chimica
- Università di Pavia
- 27100 Pavia
- Italy
| | - N. Kandoth
- Dipartimento di Chimica
- Università di Pavia
- 27100 Pavia
- Italy
| | - V. Grande
- Dipartimento di Chimica
- Università di Pavia
- 27100 Pavia
- Italy
| | - I. Manet
- Istituto per la sintesi organica e la fotoreattività (ISOF)
- CNR
- 40129 Bologna
- Italy
| | - M. Freccero
- Dipartimento di Chimica
- Università di Pavia
- 27100 Pavia
- Italy
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41
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Nadai M, Doria F, Germani L, Richter SN, Freccero M. A Photoreactive G-Quadruplex Ligand Triggered by Green Light. Chemistry 2014; 21:2330-4. [DOI: 10.1002/chem.201405215] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 01/17/2023]
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42
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Nandre KP, Al Kobaisi M, Bhosale RS, Latham K, Bhosale SV, Bhosale SV. pH triggered self-assembly induced enhanced emission of phosphonic acid appended naphthalenediimide amphiphile. RSC Adv 2014. [DOI: 10.1039/c4ra07925f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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43
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Suraru SL, Würthner F. Strategies for the synthesis of functional naphthalene diimides. Angew Chem Int Ed Engl 2014; 53:7428-48. [PMID: 24961807 DOI: 10.1002/anie.201309746] [Citation(s) in RCA: 236] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Indexed: 12/21/2022]
Abstract
Naphthalene diimides, which have for a long time been in the shadow of their higher homologues the perylene diimides, currently belong to the most investigated classes of organic compounds. This is primarily due to the initial synthetic studies on core functionalization that were carried out at the beginning of the last decade, which facilitated diverse structural modifications of the naphthalene scaffold. Compounds with greatly modified optical and electronic properties that can be easily and effectively modulated by appropriate functionalization were made accessible through relatively little synthetic effort. This resulted in diverse interesting applications. The electron-deficient character of these compounds makes them highly valuable, particularly in the field of organic electronics as air-stable n-type semiconductors, while absorption bands over the whole visible spectral range through the introduction of core substituents enabled interesting photosystems and photovoltaic applications. This Review provides an overview on different approaches towards core functionalization as well as on synthetic strategies for the core expansion of naphthalene diimides that have been developed mainly in the last five years.
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Affiliation(s)
- Sabin-Lucian Suraru
- Universität Würzburg, Institut für Organische Chemie and Center for Nanosystems Chemistry, Am Hubland, 97074 Würzburg (Germany)
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44
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Suraru SL, Würthner F. Strategien für die Synthese funktioneller Naphthalindiimide. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309746] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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45
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Small-molecule quadruplex-targeted drug discovery. Bioorg Med Chem Lett 2014; 24:2602-12. [DOI: 10.1016/j.bmcl.2014.04.029] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/06/2014] [Accepted: 04/08/2014] [Indexed: 01/24/2023]
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46
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Maniam S, Higginbotham HF, Guo SX, Bell TDM, Izgorodina EI, Langford SJ. A Redox Switchable Dihydrobenzo[b]pyrazine Push-Pull System. ASIAN J ORG CHEM 2014. [DOI: 10.1002/ajoc.201402015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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47
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Miao JT, Fan C, Shi XY, Sun R, Xu YJ, Ge JF. Colorimetric and ratiometric pH responses by the protonation of phenolate within hemicyanine. Analyst 2014; 139:6290-7. [DOI: 10.1039/c4an01505c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The indolium–phenol based tetramethylene hemicyanine has colorimetric and ratiometric optical responses under acidic and basic conditions.
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Affiliation(s)
- Jia-Tao Miao
- College of Chemistry
- Chemical Engineering and Material Science
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Soochow University
- Suzhou 215123, China
| | - Chen Fan
- School of Radiation Medicine and Protection
- Medicinal College of Soochow University
- Suzhou 215123, China
| | - Xiao-Yu Shi
- College of Chemistry
- Chemical Engineering and Material Science
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Soochow University
- Suzhou 215123, China
| | - Ru Sun
- College of Chemistry
- Chemical Engineering and Material Science
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Soochow University
- Suzhou 215123, China
| | - Yu-Jie Xu
- School of Radiation Medicine and Protection
- Medicinal College of Soochow University
- Suzhou 215123, China
| | - Jian-Feng Ge
- College of Chemistry
- Chemical Engineering and Material Science
- Collaborative Innovation Center of Suzhou Nano Science and Technology
- Soochow University
- Suzhou 215123, China
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48
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Yang Z, Cao J, He Y, Yang JH, Kim T, Peng X, Kim JS. Macro-/micro-environment-sensitive chemosensing and biological imaging. Chem Soc Rev 2014; 43:4563-601. [DOI: 10.1039/c4cs00051j] [Citation(s) in RCA: 604] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We have summarized the research progress on fluorescent sensors responsive to environmental factors, including local viscosity, polarity, temperature, hypoxia and pH.
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Affiliation(s)
- Zhigang Yang
- Department of Chemistry
- Korea University
- Seoul 136-701, Korea
- Key Laboratory of Sensor Analysis of Tumor Marker Ministry of Education
- College of Chemistry and Molecular Engineering
| | - Jianfang Cao
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian 116024, China
| | - Yanxia He
- Department of Chemistry
- Korea University
- Seoul 136-701, Korea
- Key Laboratory of Sensor Analysis of Tumor Marker Ministry of Education
- College of Chemistry and Molecular Engineering
| | - Jung Ho Yang
- Department of Chemistry
- Korea University
- Seoul 136-701, Korea
| | - Taeyoung Kim
- Department of Chemistry
- Korea University
- Seoul 136-701, Korea
| | - Xiaojun Peng
- State Key Laboratory of Fine Chemicals
- Dalian University of Technology
- Dalian 116024, China
| | - Jong Seung Kim
- Department of Chemistry
- Korea University
- Seoul 136-701, Korea
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Cytotoxicity and DNA-binding property of water-soluble naphthalene diimide derivatives bearing 2-oligoethoxy ethanamine side chain end-labeled with tertiary amino groups. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0823-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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50
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Doria F, Manet I, Grande V, Monti S, Freccero M. Water-Soluble Naphthalene Diimides as Singlet Oxygen Sensitizers. J Org Chem 2013; 78:8065-73. [DOI: 10.1021/jo401347z] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Filippo Doria
- Dipartimento di Chimica, Università
di Pavia, V. le Taramelli 10, 27100 Pavia, Italy
| | - Ilse Manet
- Istituto per la Sintesi Organica
e la Fotoreattività, Consiglio Nazionale delle Ricerche, via Gobetti 101, 40129 Bologna, Italy
| | - Vincenzo Grande
- Dipartimento di Chimica, Università
di Pavia, V. le Taramelli 10, 27100 Pavia, Italy
| | - Sandra Monti
- Istituto per la Sintesi Organica
e la Fotoreattività, Consiglio Nazionale delle Ricerche, via Gobetti 101, 40129 Bologna, Italy
| | - Mauro Freccero
- Dipartimento di Chimica, Università
di Pavia, V. le Taramelli 10, 27100 Pavia, Italy
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