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Arévalo-Ruiz M, Amrane S, Rosu F, Belmonte-Reche E, Peñalver P, Mergny JL, Morales JC. Symmetric and dissymmetric carbohydrate-phenyl ditriazole derivatives as DNA G-quadruplex ligands: Synthesis, biophysical studies and antiproliferative activity. Bioorg Chem 2020; 99:103786. [DOI: 10.1016/j.bioorg.2020.103786] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 02/27/2020] [Accepted: 03/20/2020] [Indexed: 02/04/2023]
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Pitorri M, Franceschin M, Serafini I, Ciccòla A, Frezza C, Bianco A. New Developments in the Synthesis of EMICORON. High Throughput 2018; 7:ht7030022. [PMID: 30158479 PMCID: PMC6165106 DOI: 10.3390/ht7030022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/14/2018] [Accepted: 08/21/2018] [Indexed: 11/18/2022] Open
Abstract
This paper reports on the modification of two synthetic steps in the usual protocol used for obtaining EMICORON. EMICORON is a benzo[ghi]perylen-diimide, which was synthesized for the first time in our laboratory in 2012, and has shown to have in vivo antitumor activities that interferes with the tumor growth and development using a multi-target mechanism of action. The provided modifications, which involved the reaction times, the reaction conditions, and the work-up procedures, allowed the global yield of the process to be increased from 28% to about 40%. Thus, this new procedure may be more suitable for recovering higher amounts of EMICORON to be used in further preclinical studies.
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Affiliation(s)
- Massimo Pitorri
- Dipartimento di Chimica: Università di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Marco Franceschin
- Dipartimento di Chimica: Università di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Ilaria Serafini
- Dipartimento di Chimica: Università di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Alessandro Ciccòla
- Dipartimento di Chimica: Università di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Claudio Frezza
- Dipartimento di Biologia Ambientale: Università di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy.
| | - Armandodoriano Bianco
- Dipartimento di Chimica: Università di Roma "La Sapienza", Piazzale Aldo Moro 5, 00185 Rome, Italy.
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Rivera-Sánchez MC, García-Arriaga M, Hobley G, Morales-de-Echegaray AV, Rivera JM. Small-Molecule-Based Self-Assembled Ligands for G-Quadruplex DNA Surface Recognition. ACS OMEGA 2017; 2:6619-6627. [PMID: 29104952 PMCID: PMC5664172 DOI: 10.1021/acsomega.7b01255] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 09/27/2017] [Indexed: 05/08/2023]
Abstract
Most drugs are small molecules because of their attractive pharmacokinetics, manageable development and manufacturing, and effective binding into the concave crevices of bio-macromolecules. Despite these features, they often fall short when it comes to effectively recognizing the surfaces of bio-macromolecules. One way to overcome the challenge of biomolecular surface recognition is to develop small molecules that become self-assembled ligands (SALs) prior to binding. Herein, we report SALs made from 8-aryl-2'-deoxyguanosine derivatives forming precise hydrophilic supramolecular G-quadruplexes (SGQs) with excellent size, shape, and charge complementarity to G-quadruplex DNA (QDNA). We show that only those compounds forming SGQs act as SALs, which in turn differentially stabilize QDNAs from selected oncogene promoters and the human telomeric regions. Fluorescence resonance energy-transfer melting assays are consistent with spectroscopic, calorimetric, and light scattering studies, showing the formation of a "sandwichlike" complex QDNA·SGQ·QDNA. These results open the door for the advent of SALs that recognize QDNAs and potentially the surfaces of other bio-macromolecules such as proteins.
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Affiliation(s)
- María
del C. Rivera-Sánchez
- Department of Chemistry and
Molecular Sciences Research Center, University
of Puerto Rico at Río Piedras, San Juan, Puerto Rico 00926, United States
| | - Marilyn García-Arriaga
- Department of Chemistry and
Molecular Sciences Research Center, University
of Puerto Rico at Río Piedras, San Juan, Puerto Rico 00926, United States
| | - Gerard Hobley
- Department of Chemistry and
Molecular Sciences Research Center, University
of Puerto Rico at Río Piedras, San Juan, Puerto Rico 00926, United States
| | - Ana V. Morales-de-Echegaray
- Department of Chemistry and
Molecular Sciences Research Center, University
of Puerto Rico at Río Piedras, San Juan, Puerto Rico 00926, United States
| | - José M. Rivera
- Department of Chemistry and
Molecular Sciences Research Center, University
of Puerto Rico at Río Piedras, San Juan, Puerto Rico 00926, United States
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Takada T, Umakoshi Y, Nakamura M, Yamana K. A Luminescent Perylenediimide as a Binding Ligand for Pyrimidine/Pyrimidine Mismatches Within a DNA Duplex. ChemistrySelect 2017. [DOI: 10.1002/slct.201701310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Tadao Takada
- Department of Applied Chemistry, Graduate School of Engineering; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Yu Umakoshi
- Department of Applied Chemistry, Graduate School of Engineering; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Mitsunobu Nakamura
- Department of Applied Chemistry, Graduate School of Engineering; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Kazushige Yamana
- Department of Applied Chemistry, Graduate School of Engineering; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
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D'Urso A, Randazzo R, Rizzo V, Gangemi CMA, Romanucci V, Zarrelli A, Tomaselli G, Milardi D, Borbone N, Purrello R, Piccialli G, Di Fabio G, Oliviero G. Stabilization vs. destabilization of G-quadruplex superstructures: the role of the porphyrin derivative having spermine arms. Phys Chem Chem Phys 2017. [PMID: 28650039 DOI: 10.1039/c7cp02816d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction of the porphyrin derivative H2TCPPSpm4, having spermine pendants in the four meso positions, with the G-quadruplex (GQ) structure formed by the DNA aptamer TGGGAG has been investigated by means of UV, electronic circular dichroism and PAGE studies. The results reported here demonstrate that the porphyrin derivative is capable of stabilizing or destabilizing the higher-ordered structures of parallel GQs, depending on the method used to reach their relative stoichiometry (titration vs. single addition). Noteworthily, when two equivalents of H2TCPPSpm4 were mixed directly with one equivalent of the (TGGGAG)4 GQ to reach a 2 : 1 H2TCPPSpm4 : GQ ratio T1/2 higher than 80 °C was also observed confirming the presence of higher-ordered GQ structures.
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Affiliation(s)
- A D'Urso
- Department of Chemical Science, University of Catania, V.le A Doria 6, 95125, Catania, Italy.
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7
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Micheli E, Altieri A, Cianni L, Cingolani C, Iachettini S, Bianco A, Leonetti C, Cacchione S, Biroccio A, Franceschin M, Rizzo A. Perylene and coronene derivatives binding to G-rich promoter oncogene sequences efficiently reduce their expression in cancer cells. Biochimie 2016; 125:223-31. [DOI: 10.1016/j.biochi.2016.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/08/2016] [Indexed: 11/28/2022]
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8
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Rocca R, Costa G, Artese A, Parrotta L, Ortuso F, Maccioni E, Pinato O, Greco ML, Sissi C, Alcaro S, Distinto S, Moraca F. Hit Identification of a Novel Dual Binder for h-telo/c-myc G-Quadruplex by a Combination of Pharmacophore Structure-Based Virtual Screening and Docking Refinement. ChemMedChem 2016; 11:1721-33. [PMID: 27008476 DOI: 10.1002/cmdc.201600053] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 02/29/2016] [Indexed: 12/28/2022]
Abstract
It is well known that G-quadruplexes are targets of great interest for their roles in crucial biological processes, such as aging and cancer. Hence, a promising strategy for anticancer drug therapy is the stabilization of these structures by small molecules. We report a high-throughput in silico screening of commercial libraries from several different vendors by means of a combined structure-based pharmacophore model approach followed by docking simulations. The compounds selected by the virtual screening procedure were then tested for their ability to interact with human telomeric G-quadruplex folding by circular dichroism, fluorescence spectroscopy, and fluorescence intercalator displacement. Our approach resulted in the identification of a 13-[(dimethylamino)methyl]-12-hydroxy-8H-benzo[c]indolo[3,2,1-ij][1,5]naphthyridin-8-one derivative as a novel promising stabilizer of G-quadruplex structures within the human telomeric and the c-myc promoter sequences.
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Affiliation(s)
- Roberta Rocca
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy.
| | - Anna Artese
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Lucia Parrotta
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Elias Maccioni
- Department of Life and Environment Sciences, University of Cagliari, Via Ospedale 72, 09124, Cagliari, Italy
| | - Odra Pinato
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Maria Laura Greco
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
| | - Simona Distinto
- Department of Life and Environment Sciences, University of Cagliari, Via Ospedale 72, 09124, Cagliari, Italy
| | - Federica Moraca
- Dipartimento di Scienze della Salute, Università degli Studi "Magna Graecia" di Catanzaro, Campus "Salvatore Venuta", Viale Europa, 88100, Catanzaro, Italy
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Pagoaga B, Mongin O, Caselli M, Vanossi D, Momicchioli F, Blanchard-Desce M, Lemercier G, Hoffmann N, Ponterini G. Optical and photophysical properties of anisole- and cyanobenzene-substituted perylene diimides. Phys Chem Chem Phys 2016; 18:4924-41. [DOI: 10.1039/c5cp07758c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Substituent and solvent effects on the one- and two-photon absorption and the photophysical properties of eight bay-substituted perylene-diimides are reported and analyzed.
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Affiliation(s)
- Bernard Pagoaga
- Université de Reims Champagne-Ardenne
- ICMR UMR no. 7312
- 51687 Reims Cedex 2
- France
| | - Olivier Mongin
- Université Rennes 1
- UMR CNRS 6510
- Chimie et Photonique Moléculaires
- 35042 Rennes cedex
- France
| | - Monica Caselli
- Dipartimento di Scienze Chimiche e Geologiche
- Università di Modena e Reggio Emilia
- 41125 Modena
- Italy
| | - Davide Vanossi
- Dipartimento di Scienze Chimiche e Geologiche
- Università di Modena e Reggio Emilia
- 41125 Modena
- Italy
| | - Fabio Momicchioli
- Dipartimento di Scienze Chimiche e Geologiche
- Università di Modena e Reggio Emilia
- 41125 Modena
- Italy
| | | | - Gilles Lemercier
- Université de Reims Champagne-Ardenne
- ICMR UMR no. 7312
- 51687 Reims Cedex 2
- France
| | - Norbert Hoffmann
- Université de Reims Champagne-Ardenne
- ICMR UMR no. 7312
- 51687 Reims Cedex 2
- France
| | - Glauco Ponterini
- Dipartimento di Scienze della Vita
- Università di Modena e Reggio Emilia
- 41125 Modena
- Italy
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10
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Yamamoto Y, Kinoshita M, Katahira Y, Shimizu H, Di Y, Shibata T, Tai H, Suzuki A, Neya S. Characterization of Heme–DNA Complexes Composed of Some Chemically Modified Hemes and Parallel G-Quadruplex DNAs. Biochemistry 2015; 54:7168-77. [DOI: 10.1021/acs.biochem.5b00989] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Yasuhiko Yamamoto
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Masashi Kinoshita
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Yuya Katahira
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Haruna Shimizu
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Yue Di
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Tomokazu Shibata
- Department
of Chemistry, University of Tsukuba, Tsukuba 305-8571, Japan
| | - Hulin Tai
- Graduate
School of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Akihiro Suzuki
- Department
of Materials Engineering, National Institute of Technology, Nagaoka College, Nagaoka 940-8532, Japan
| | - Saburo Neya
- Department
of Physical Chemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chuoh-Inohana, Chiba 260-8675, Japan
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11
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Yaku H, Murashima T, Miyoshi D, Sugimoto N. A mRNA-Responsive G-Quadruplex-Based Drug Release System. SENSORS 2015; 15:9388-403. [PMID: 25905703 PMCID: PMC4431183 DOI: 10.3390/s150409388] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 04/08/2015] [Accepted: 04/08/2015] [Indexed: 11/16/2022]
Abstract
G-quadruplex-based drug delivery carriers (GDDCs) were designed to capture and release a telomerase inhibitor in response to a target mRNA. Hybridization between a loop on the GDDC structure and the mRNA should cause the G-quadruplex structure of the GDDC to unfold and release the bound inhibitor, anionic copper(II) phthalocyanine (CuAPC). As a proof of concept, GDDCs were designed with a 10-30-mer loop, which can hybridize with a target sequence in epidermal growth factor receptor (EGFR) mRNA. Structural analysis using circular dichroism (CD) spectroscopy showed that the GDDCs form a (3 + 1) type G-quadruplex structure in 100 mM KCl and 10 mM MgCl2 in the absence of the target RNA. Visible absorbance titration experiments showed that the GDDCs bind to CuAPC with Ka values of 1.5 × 105 to 5.9 × 105 M−1 (Kd values of 6.7 to 1.7 μM) at 25 °C, depending on the loop length. Fluorescence titration further showed that the G-quadruplex structure unfolds upon binding to the target RNA with Ka values above 1.0 × 108 M−1 (Kd values below 0.01 μM) at 25 °C. These results suggest the carrier can sense and bind to the target RNA, which should result in release of the bound drug. Finally, visible absorbance titration experiments demonstrated that the GDDC release CuAPC in response to the target RNA.
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Affiliation(s)
- Hidenobu Yaku
- Advanced Research Division, Panasonic Corporation, 3-4 Hikaridai, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan.
| | - Takashi Murashima
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Naoki Sugimoto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
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12
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Gershberg J, Radić Stojković M, Škugor M, Tomić S, Rehm TH, Rehm S, Saha-Möller CR, Piantanida I, Würthner F. Sensing of Double-Stranded DNA/RNA Secondary Structures by Water Soluble Homochiral Perylene Bisimide Dyes. Chemistry 2015; 21:7886-95. [DOI: 10.1002/chem.201500184] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Indexed: 12/12/2022]
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Xu L, Chen X, Wu J, Wang J, Ji L, Chao H. Dinuclear Ruthenium(II) Complexes That Induce and Stabilise G-Quadruplex DNA. Chemistry 2015; 21:4008-20. [DOI: 10.1002/chem.201405991] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Indexed: 11/08/2022]
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Structure-based virtual screening of novel natural alkaloid derivatives as potential binders of h-telo and c-myc DNA G-quadruplex conformations. Molecules 2014; 20:206-23. [PMID: 25547724 PMCID: PMC6272608 DOI: 10.3390/molecules20010206] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/15/2014] [Indexed: 01/08/2023] Open
Abstract
Several ligands can bind to the non-canonical G-quadruplex DNA structures thereby stabilizing them. These molecules can act as effective anticancer agents by stabilizing the telomeric regions of DNA or by regulating oncogene expression. In order to better interact with the quartets of G-quadruplex structures, G-binders are generally characterized by a large aromatic core involved in π-π stacking. Some natural flexible cyclic molecules from Traditional Chinese Medicine have shown high binding affinity with G-quadruplex, such as berbamine and many other alkaloids. Using the structural information available on G-quadruplex structures, we performed a high throughput in silico screening of commercially available alkaloid derivative databases by means of a structure-based approach based on docking and molecular dynamics simulations against the human telomeric sequence d[AG3(T2AG3)3] and the c-myc promoter structure. We identified 69 best hits reporting an improved theoretical binding affinity with respect to the active set. Among them, a berberine derivative, already known to remarkably inhibit telomerase activity, was related to a better theoretical affinity versusc-myc.
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Dhayan H, Baydoun AR, Kukol A. G-quadruplex formation of FXYD1 pre-mRNA indicates the possibility of regulating expression of its protein product. Arch Biochem Biophys 2014; 560:52-8. [DOI: 10.1016/j.abb.2014.07.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/25/2014] [Accepted: 07/10/2014] [Indexed: 11/25/2022]
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16
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Schulze-Adams M, Bernet B, Touboul D, Egli D, Herdeis L, Vasella A. Oligonucleotide Analogues with Integrated Bases and Backbone. Part 32. Helv Chim Acta 2014. [DOI: 10.1002/hlca.201400175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Pontinha ADR, Lombardo CM, Neidle S, Oliveira-Brett AM. Triazole-linked phenyl derivatives: redox mechanisms and in situ electrochemical evaluation of interaction with dsDNA. Bioelectrochemistry 2014; 101:97-105. [PMID: 25194950 DOI: 10.1016/j.bioelechem.2014.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 07/08/2014] [Accepted: 08/13/2014] [Indexed: 11/28/2022]
Abstract
The redox mechanism of two trisubstituted triazole-linked phenyl derivatives (CL41 and CL42) and a disubstituted triazole-linked phenyl derivative (CL2r50) were studied using cyclic, differential pulse and square wave voltammetry at a glassy carbon electrode. The CL41, CL42 and CL2r50 oxidation is a complex, pH-dependent irreversible process involving the formation of electroactive products that undergo two consecutive reversible oxidation reactions. The DNA interaction with CL41, CL42 and CL2r50 was investigated by differential pulse voltammetry using the dsDNA-electrochemical biosensor and in DNA/trisubstituted triazole incubated solutions. All three trisubstituted triazole-linked phenyl derivatives interacted with dsDNA causing morphological and oxidative damage to the dsDNA structure in a time-dependent manner. The DNA-electrochemical biosensor enabled the detection of oxidative damage to DNA following the occurrence of the 8-oxoGua and/or 2,8-oxoAde oxidation peaks.
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Affiliation(s)
- A Dora R Pontinha
- Department of Chemistry, University of Coimbra, Coimbra 3004-535, Portugal
| | | | - Stephen Neidle
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
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Parrotta L, Ortuso F, Moraca F, Rocca R, Costa G, Alcaro S, Artese A. Targeting unimolecular G-quadruplex nucleic acids: a new paradigm for the drug discovery? Expert Opin Drug Discov 2014; 9:1167-87. [PMID: 25109710 DOI: 10.1517/17460441.2014.941353] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
INTRODUCTION G-quadruplexes (G4s) are targets of great interest because of their roles in crucial biological processes, such as aging and cancer. G4s are based on the formation of G-quartets, stabilised by Hoogsteen-type hydrogen bonds and by interaction with cations between the tetrads. These biologically relevant conformations were first discovered in eukaryotic chromosomal telomeric DNA, but have also been found in the proximal location of promoters in a number of human genes. Therefore, the extensive analysis of an intriguing target could move towards the rational drug design of new selective anticancer agents. AREAS COVERED The authors review G4 structural characterisation, with detailed insight related to the polymorphism issue. The authors describe the topologically distinct G4 structural forms and the factors involved in their interconversion mechanisms, such as the sequence of the oligonucleotides, the strand stoichiometry and orientation, the syn-anti conformation of the guanine glycosidic bonds and the G4 loop types and the environmental factors. Furthermore, the authors report several studies related to folding and unfolding kinetic profiles in order to understand the conformational view of monomolecular G4 formations. EXPERT OPINION G4 unimolecular nucleic acids can be considered as valid targets for the rational drug development of novel anticancer agents. Structural biology represents an essential link between the biology and medicinal chemistry knowledge in this field. In silico methods have already been demonstrated to be useful, especially if well integrated with biophysical tests. If this proves successful, the G4-targeting paradigm could also be extended to drug discovery beyond neoplastic pathologies.
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Affiliation(s)
- Lucia Parrotta
- Università degli Studi "Magna Græcia", Dipartimento di Scienze della Salute , Campus "S. Venuta", Viale Europa, Germaneto, 88100, Catanzaro , Italy
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Pagoaga B, Giraudet L, Hoffmann N. Synthesis and Characterisation of 1,7-Di- and Inherently Chiral 1,12-Di- and 1,6,7,12-Tetraarylperylenetetracarbox-3,4:9,10-diimides. European J Org Chem 2014. [DOI: 10.1002/ejoc.201402625] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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20
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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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21
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Franceschin M, Nocioni D, Biroccio A, Micheli E, Cacchione S, Cingolani C, Venditti A, Zizza P, Bianco A, Altieri A. Design and synthesis of a new dimeric xanthone derivative: enhancement of G-quadruplex selectivity and telomere damage. Org Biomol Chem 2014; 12:9572-82. [DOI: 10.1039/c4ob01658k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dimerization of the xanthone core greatly enhances G-quadruplex binding and biological activity.
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Affiliation(s)
- Marco Franceschin
- University of Rome “Sapienza”
- Department of Chemistry
- Roma 00185, Italy
| | - Daniele Nocioni
- University of Rome “Sapienza”
- Department of Chemistry
- Roma 00185, Italy
| | - Annamaria Biroccio
- Experimental Chemotherapy Laboratory
- Regina Elena National Cancer Institute
- Italy
| | - Emanuela Micheli
- University of Rome “Sapienza”
- Department of Biology and Biotechnology “Charles Darwin”
- Roma 00185, Italy
- Istituto Pasteur-Fondazione Cenci-Bolognetti
- Roma 00185, Italy
| | - Stefano Cacchione
- University of Rome “Sapienza”
- Department of Biology and Biotechnology “Charles Darwin”
- Roma 00185, Italy
- Istituto Pasteur-Fondazione Cenci-Bolognetti
- Roma 00185, Italy
| | - Chiara Cingolani
- Experimental Chemotherapy Laboratory
- Regina Elena National Cancer Institute
- Italy
| | | | - Pasquale Zizza
- Experimental Chemotherapy Laboratory
- Regina Elena National Cancer Institute
- Italy
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Liao G, Chen X, Wu J, Qian C, Wang H, Ji L, Chao H. Novel ruthenium(ii) polypyridyl complexes as G-quadruplex stabilisers and telomerase inhibitors. Dalton Trans 2014; 43:7811-9. [DOI: 10.1039/c3dt53547a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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23
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Abstract
Guanosine (G) and isoguanosine (isoG) derivatives can self-assemble, yielding supramolecules that have found broad applications in diverse fields.
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Affiliation(s)
| | - Raphaël Rodriguez
- Institut de Chimie des Subtances Naturelles
- Centre National de la Recherche Scientifique
- Avenue de la Terrasse
- Gif-sur-Yvette, France
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24
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Wei D, Todd AK, Zloh M, Gunaratnam M, Parkinson GN, Neidle S. Crystal structure of a promoter sequence in the B-raf gene reveals an intertwined dimer quadruplex. J Am Chem Soc 2013; 135:19319-29. [PMID: 24295054 DOI: 10.1021/ja4101358] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sequence d(GGGCGGGGAGGGGGAAGGGA) occurs in the promoter region of the B-raf gene. An X-ray crystallographic study has found that this forms an unprecedented dimeric quadruplex arrangement, with a core of seven consecutive G-quartets and an uninterrupted run of six potassium ions in the central channel of the quadruplex. Analogy with previously reported promoter quadruplexes had initially suggested that in common with these a monomeric quadruplex was to be expected. The structure has a distorted G·C·G·C base quartet at one end and four flipped-out adenosine nucleosides at the other. The only loops in the structure are formed by the cytosine and by the three adenosines within the sequence, with all of the guanosines participating in G-quartet formation. Solution UV and circular dichroism data are in accord with a stable quadruple arrangement being formed. 1D NMR data, together with gel electrophoresis measurements, are consistent with a dimer being the dominant species in potassium solution. A single-chain intramolecular quadruplex has been straightforwardly constructed using molecular modeling, by means of a six-nucleotide sequence joining 3' and 5' ends of each strand in the dimer. A human genomic database search has revealed a number of sequences containing eight or more consecutive short G-tracts, suggesting that such intramolecular quadruplexes could be formed within the human genome.
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Affiliation(s)
- Dengguo Wei
- UCL School of Pharmacy, University College London , London WC1N 1AX, United Kingdom
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25
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Altieri A, Alvino A, Ohnmacht S, Ortaggi G, Neidle S, Nocioni D, Franceschin M, Bianco A. Xanthene and xanthone derivatives as G-quadruplex stabilizing ligands. Molecules 2013; 18:13446-70. [PMID: 24177701 PMCID: PMC6269716 DOI: 10.3390/molecules181113446] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 10/21/2013] [Accepted: 10/23/2013] [Indexed: 12/14/2022] Open
Abstract
Following previous studies on anthraquinone and acridine-based G-quadruplex ligands, here we present a study of similar aromatic cores, with the specific aim of increasing G-quadruplex binding and selectivity with respect to duplex DNA. Synthesized compounds include two and three-side chain xanthone and xanthene derivatives, as well as a dimeric “bridged” form. ESI and FRET measurements suggest that all the studied molecules are good G-quadruplex ligands, both at telomeres and on G-quadruplex forming sequences of oncogene promoters. The dimeric compound and the three-side chain xanthone derivative have been shown to represent the best compounds emerging from the different series of ligands presented here, having also high selectivity for G-quadruplex structures with respect to duplex DNA. Molecular modeling simulations are in broad agreement with the experimental data.
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Affiliation(s)
- Alessandro Altieri
- Dipartimento di Chimica, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, Roma 00185, Italy; E-Mails: (A.A.); (G.O.); (D.N.); (M.F.)
- Authors to whom correspondence should be addressed; E-Mails: (A.A.); (A.B.); Tel.: +39-064-991-3229/3622 (A.A. & A.B.) Fax: +39-064-991-3841 (A.A. & A.B.)
| | - Antonello Alvino
- Dipartimento di Chimica, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, Roma 00185, Italy; E-Mails: (A.A.); (G.O.); (D.N.); (M.F.)
| | - Stephan Ohnmacht
- The UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; E-Mails: (S.O.); (S.N.)
| | - Giancarlo Ortaggi
- Dipartimento di Chimica, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, Roma 00185, Italy; E-Mails: (A.A.); (G.O.); (D.N.); (M.F.)
| | - Stephen Neidle
- The UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK; E-Mails: (S.O.); (S.N.)
| | - Daniele Nocioni
- Dipartimento di Chimica, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, Roma 00185, Italy; E-Mails: (A.A.); (G.O.); (D.N.); (M.F.)
| | - Marco Franceschin
- Dipartimento di Chimica, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, Roma 00185, Italy; E-Mails: (A.A.); (G.O.); (D.N.); (M.F.)
| | - Armandodoriano Bianco
- Dipartimento di Chimica, Università di Roma “La Sapienza”, Piazzale Aldo Moro 5, Roma 00185, Italy; E-Mails: (A.A.); (G.O.); (D.N.); (M.F.)
- Authors to whom correspondence should be addressed; E-Mails: (A.A.); (A.B.); Tel.: +39-064-991-3229/3622 (A.A. & A.B.) Fax: +39-064-991-3841 (A.A. & A.B.)
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26
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Ohnmacht SA, Ciancimino C, Vignaroli G, Gunaratnam M, Neidle S. Optimization of anti-proliferative activity using a screening approach with a series of bis-heterocyclic G-quadruplex ligands. Bioorg Med Chem Lett 2013; 23:5351-5. [DOI: 10.1016/j.bmcl.2013.07.057] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 07/18/2013] [Accepted: 07/24/2013] [Indexed: 12/20/2022]
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27
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Bare GA, Sherman JC. Multiple phosphate-linked nucleotide couplings via 5′ silyl ether protection in the phosphite triester and phosphoramidite approaches. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2013.04.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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28
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Shibata T, Dohno C, Nakatani K. G-quadruplex formation of entirely hydrophobic DNA in organic solvents. Chem Commun (Camb) 2013; 49:5501-3. [PMID: 23660830 DOI: 10.1039/c3cc42221f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We report herein a novel hydrophobic G-quadruplex DNA consisting of dodecyl phosphotriester linkages. The 6-mer hydrophobic DNA having a TG4T sequence binds to monovalent cations to form a tetramolecular G-quadruplex in low polarity organic solvents.
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Affiliation(s)
- Tomonori Shibata
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki 567-0047, Japan
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29
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Ishihara Y, Kimura S. Four-peptide-nanotube bundle formation by self-assembling of cyclic tetra-β-peptide using g-quartet motif. Biopolymers 2013; 100:141-7. [DOI: 10.1002/bip.22177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 10/10/2012] [Indexed: 12/22/2022]
Affiliation(s)
- Yusuke Ishihara
- Department of Material Chemistry; Graduate School of Engineering; Kyoto University; Nishikyo-Ku; Kyoto; 615-8510; Japan
| | - Shunsaku Kimura
- Department of Material Chemistry; Graduate School of Engineering; Kyoto University; Nishikyo-Ku; Kyoto; 615-8510; Japan
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30
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Micco M, Collie GW, Dale AG, Ohnmacht SA, Pazitna I, Gunaratnam M, Reszka AP, Neidle S. Structure-based design and evaluation of naphthalene diimide G-quadruplex ligands as telomere targeting agents in pancreatic cancer cells. J Med Chem 2013; 56:2959-74. [PMID: 23514618 DOI: 10.1021/jm301899y] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Tetra-substituted naphthalene diimide (ND) derivatives with positively charged termini are potent stabilizers of human telomeric and gene promoter DNA quadruplexes and inhibit the growth of human cancer cells in vitro and in vivo. The present study reports the enhancement of the pharmacological properties of earlier ND compounds using structure-based design. Crystal structures of three complexes with human telomeric intramolecular quadruplexes demonstrate that two of the four strongly basic N-methyl-piperazine groups can be replaced by less basic morpholine groups with no loss of intermolecular interactions in the grooves of the quadruplex. The new compounds retain high affinity to human telomeric quadruplex DNA but are 10-fold more potent against the MIA PaCa-2 pancreatic cancer cell line, with IC50 values of ~10 nM. The lead compound induces cellular senescence but does not inhibit telomerase activity at the nanomolar dosage levels required for inhibition of cellular proliferation. Gene array qPCR analysis of MIA PaCa-2 cells treated with the lead compound revealed significant dose-dependent modulation of a distinct subset of genes, including strong induction of DNA damage responsive genes CDKN1A, DDIT3, GADD45A/G, and PPM1D, and repression of genes involved in telomere maintenance, including hPOT1 and PARP1.
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Affiliation(s)
- Marialuisa Micco
- The School of Pharmacy, University College London, London WC1N 1AX, UK
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31
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Franceschin M, Bombelli C, Borioni S, Bozzuto G, Eleuteri S, Mancini G, Molinari A, Bianco A. A new perylene bisimide bola amphiphile: synthesis, characterization, fluorescent properties and applications as a potential probe. NEW J CHEM 2013. [DOI: 10.1039/c3nj00116d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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32
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Altieri A, Franceschin M, Nocioni D, Alvino A, Casagrande V, Scarpati ML, Bianco A. Total Synthesis of Taspine and a Symmetrical Analogue: Study of Binding to G-Quadruplex DNA by ESI-MS. European J Org Chem 2012. [DOI: 10.1002/ejoc.201201034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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33
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Czerwinska I, Juskowiak B. Photoisomerizable arylstilbazolium ligands recognize parallel and antiparallel structures of G-quadruplexes. Int J Biol Macromol 2012; 51:576-82. [DOI: 10.1016/j.ijbiomac.2012.06.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 06/20/2012] [Accepted: 06/21/2012] [Indexed: 11/26/2022]
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34
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Franceschin M, Rizzo A, Casagrande V, Salvati E, Alvino A, Altieri A, Ciammaichella A, Iachettini S, Leonetti C, Ortaggi G, Porru M, Bianco A, Biroccio A. Aromatic core extension in the series of N-cyclic bay-substituted perylene G-quadruplex ligands: increased telomere damage, antitumor activity, and strong selectivity for neoplastic over healthy cells. ChemMedChem 2012; 7:2144-54. [PMID: 23097341 DOI: 10.1002/cmdc.201200348] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Indexed: 11/08/2022]
Abstract
Based on previous work on both perylene and coronene derivatives as G-quadruplex binders, a novel chimeric compound was designed: N,N'-bis[2-(1-piperidino)-ethyl]-1-(1-piperidinyl)-6-[2-(1-piperidino)-ethyl]-benzo[ghi]perylene-3,4:9,10-tetracarboxylic diimide (EMICORON), having one piperidinyl group bound to the perylene bay area (positions 1, 12 and 6, 7 of the aromatic core), sufficient to guarantee good selectivity, and an extended aromatic core able to increase the stacking interactions with the terminal tetrad of the G-quadruplex. The obtained "chimera" molecule, EMICORON, rapidly triggers extensive DNA damage of telomeres, associated with the delocalization of telomeric protein protection of telomeres 1 (POT1), and efficiently limits the growth of both telomerase-positive and -negative tumor cells. Notably, the biological effects of EMICORON are more potent than those of the previously described perylene derivative (PPL3C), and more interestingly, EMICORON appears to be detrimental to transformed and tumor cells, while normal fibroblasts expressing telomerase remain unaffected. These results identify a new promising G-quadruplex ligand, structurally and biologically similar on one side to coronene and on the other side to a bay-monosubstituted perylene, that warrants further studies.
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Affiliation(s)
- Marco Franceschin
- Dipartimento di Chimica, Sapienza Università di Roma, P.le.A. Moro 5, 00185 Roma, Italy
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Paul A, Maji B, Misra SK, Jain AK, Muniyappa K, Bhattacharya S. Stabilization and structural alteration of the G-quadruplex DNA made from the human telomeric repeat mediated by Tröger's base based novel benzimidazole derivatives. J Med Chem 2012; 55:7460-71. [PMID: 22827615 DOI: 10.1021/jm300442r] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Ligand-induced stabilization of the G-quadruplex DNA structure derived from the single-stranded 3'-overhang of the telomeric DNA is an attractive strategy for the inhibition of the telomerase activity. The agents that can induce/stabilize a DNA sequence into a G-quadruplex structure are therefore potential anticancer drugs. Herein we present the first report of the interactions of two novel bisbenzimidazoles (TBBz1 and TBBz2) based on Tröger's base skeleton with the G-quadruplex DNA (G4DNA). These Tröger's base molecules stabilize the G4DNA derived from a human telomeric sequence. Evidence of their strong interaction with the G4DNA has been obtained from CD spectroscopy, thermal denaturation, and UV-vis titration studies. These ligands also possess significantly higher affinity toward the G4DNA over the duplex DNA. The above results obtained are in excellent agreement with the biological activity, measured in vitro using a modified TRAP assay. Furthermore, the ligands are selectively more cytotoxic toward the cancerous cells than the corresponding noncancerous cells. Computational studies suggested that the adaptive scaffold might allow these ligands to occupy not only the G-quartet planes but also the grooves of the G4DNA.
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Affiliation(s)
- Ananya Paul
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
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36
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Marcélis L, Ghesquière J, Garnir K, Kirsch-De Mesmaeker A, Moucheron C. Photo-oxidizing RuII complexes and light: Targeting biomolecules via photoadditions. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2012.02.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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37
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Ji X, Sun H, Zhou H, Xiang J, Tang Y, Zhao C. The interaction of telomeric DNA and C-myc22 G-quadruplex with 11 natural alkaloids. Nucleic Acid Ther 2012; 22:127-36. [PMID: 22480315 DOI: 10.1089/nat.2012.0342] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Telomeric DNA and C-myc22 are DNA G-quadruplex (G4)-forming sequences associated with tumorigenesis. Ligands that can facilitate the formation and increase the stabilization of G4 can halt tumor cell proliferation and have been regarded as potential anti-cancer drugs. In the present study, we have investigated the interaction of 11 natural alkaloids with G4 formed by telomeric DNA and C-myc22 sequences. Our results indicated that sanguinarine (San), palmatine (Pal), and berberine (Beb) of the first series (S1) can induce the formation of G4 as well as increase the stabilization ability. Daurisoline (S2-1), O-methyldauricine (S2-2), O-diacetyldaurisoline (S2-3), daurinoline (S2-4), dauricinoline (S2-5), N,N'-dimethyldauricine iodide (S2-6), and N,N'-dimethyldaurisoline iodide (S2-7) of the second series (S2) showed similar stabilization ability. We found that unsaturated ring C, N(+) positively charged centers, and conjugated aromatic rings are key factors to increase the stabilization ability of S1, and we gave some advice on structure modification to S2 through structure-activity study. Besides, we found San and Pal to be cell cycle blocker in G(1). San was speculated to bind to G4 through intercalation or end stacking.
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Affiliation(s)
- Xiaohui Ji
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Beijing Key Laboratory of Gene Engineering Drugs and Biological Technology College of Life Science, Beijing Normal University, Beijing, People's Republic of China
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Görl D, Zhang X, Würthner F. Molecular assemblies of perylene bisimide dyes in water. Angew Chem Int Ed Engl 2012; 51:6328-48. [PMID: 22573415 DOI: 10.1002/anie.201108690] [Citation(s) in RCA: 395] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Indexed: 01/28/2023]
Abstract
Perylene bisimides are among the most valuable functional dyes and have numerous potential applications. As a result of their chemical robustness, photostability, and outstanding optical and electronic properties, these dyes have been applied as pigments, fluorescence sensors, and n-semiconductors in organic electronics and photovoltaics. Moreover, the extended quadrupolar π system of this class of dyes has facilitated the construction of numerous supramolecular architectures with fascinating photophysical properties. However, the supramolecular approach to the formation of perylene bisimide aggregates has been restricted mostly to organic media. Pleasingly, considerable progress has been made in the last few years in developing water-soluble perylene bisimides and their application in aqueous media. This Review provides an up-to-date overview on the self-assembly of perylene bisimides through π-π interactions in aqueous media. Synthetic strategies for the preparation of water-soluble perylene bisimides and the influence of water on the π-π stacking of perylene bisimides as well as the resulting applications are discussed.
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Affiliation(s)
- Daniel Görl
- Universität Würzburg, Institut für Organische Chemie and Center for Nanosystems Chemistry, Am Hubland, 97074 Würzburg, Germany
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39
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Görl D, Zhang X, Würthner F. Molekülverbände von Perylenbisimid-Farbstoffen in Wasser. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108690] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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40
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Jain AK, Paul A, Maji B, Muniyappa K, Bhattacharya S. Dimeric 1,3-Phenylene-bis(piperazinyl benzimidazole)s: Synthesis and Structure–Activity Investigations on their Binding with Human Telomeric G-Quadruplex DNA and Telomerase Inhibition Properties. J Med Chem 2012; 55:2981-93. [DOI: 10.1021/jm200860b] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Akash K Jain
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Ananya Paul
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Basudeb Maji
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - K. Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Santanu Bhattacharya
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
- Chemical Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560012, India
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Nakamura T, Iida K, Tera M, Shin-ya K, Seimiya H, Nagasawa K. A caged ligand for a telomeric G-quadruplex. Chembiochem 2012; 13:774-7. [PMID: 22438312 DOI: 10.1002/cbic.201200013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Indexed: 12/31/2022]
Affiliation(s)
- Takahiro Nakamura
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho Koganei, Tokyo 184-8588, Japan
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Golub E, Freeman R, Willner I. A hemin/G-quadruplex acts as an NADH oxidase and NADH peroxidase mimicking DNAzyme. Angew Chem Int Ed Engl 2012; 50:11710-4. [PMID: 22229160 DOI: 10.1002/anie.201103853] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Eyal Golub
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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43
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Methods of studying telomere damage induced by quadruplex-ligand complexes. Methods 2012; 57:93-9. [PMID: 22410593 DOI: 10.1016/j.ymeth.2012.02.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 02/16/2012] [Accepted: 02/20/2012] [Indexed: 01/08/2023] Open
Abstract
The burgeoning knowledge about the structure of telomeres and the roles of various factors involved in telomere maintenance provides several possible targets for pharmacological intervention. To date the area that has received major attention regarding drug discovery is the targeting the telomeric G-quadruplex (G4) structure. G4 ligands were initially designed to counteract telomerase action at telomeres. Surprisingly, their antiproliferative effects can occur in telomerase negative cells and follow kinetics, which cannot be merely explained by telomere shortening, suggesting that these compounds affect other pathways, not necessarily related to telomere biology. Impressively, it has been shown that polyaromatic compounds featuring end-stacking binding properties trigger a strong DNA damage response at telomeres. This is typical of the telomere deprotection occurring during cellular senescence or upon telomere injury. It emerged that the G4-interacting agents are more than simple telomerase inhibitors and that their direct target is rather telomere than telomerase. This review summarizes the most valid experimental approaches for studying the pharmacological telomere damage induced by G4-ligand complexes.
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Rahman KM, Tizkova K, Reszka AP, Neidle S, Thurston DE. Identification of novel telomeric G-quadruplex-targeting chemical scaffolds through screening of three NCI libraries. Bioorg Med Chem Lett 2012; 22:3006-10. [PMID: 22421021 DOI: 10.1016/j.bmcl.2012.02.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 02/06/2012] [Accepted: 02/07/2012] [Indexed: 11/26/2022]
Abstract
Thirteen compounds with diverse chemical structures have been identified as selective telomeric G-quadruplex-binding ligands through screening the NCI Diversity Set II, the NCI Natural Products Set II and the NCI Mechanistic Diversity Set libraries containing a total of 2307 members against a human telomeric G-quadruplex using a FRET-based DNA melting assay. These compounds show significant selectivity towards a telomeric G-quadruplex compared to duplex DNA, fall within a molecular weight range of 327-533, and are generally consistent with the Lipinski Rule of Five for drug-likeness. Thus they provide new chemical scaffolds for the development of novel classes of G-quadruplex-targeting agents.
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Selective isolation of G-quadruplexes by affinity chromatography. J Chromatogr A 2012; 1246:62-8. [PMID: 22398385 DOI: 10.1016/j.chroma.2012.02.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 02/06/2012] [Accepted: 02/09/2012] [Indexed: 01/13/2023]
Abstract
G-quadruplex (G4) is a characteristic secondary structure of nucleic acids containing repetitive tandem guanines. G4-forming sequences are found prevalent in the human genome by bioinformatics analysis. Accumulating evidence has suggested that G4s are involved in many biological processes. Selective isolation of G4s would be an effective tool in the study of G4s. In this paper, we prepared four affinity matrixes using hemin or a perylene derivative (N,N'-Bis-(2-(amino)ethyl)-3,4,9,10-perylenetetracarboxylic acid diimide, Pery01) as ligand, and investigated the retention behaviors of different G4s on these matrixes. Our experimental results suggest that the π-π stacking interaction between ligand and G-tetrad plays a key role in the selective isolation of G4s, whereas the electrostatic interaction between DNA and matrix causes the nonspecific binding. One matrix prepared by immobilizing Pery01 on polyglycidylmethacrylate (PGMA) beads through an aminocaproic acid spacer exhibits good selectivity for parallel structure G4s and has been successfully used to directly isolate a spiked parallel G4 from plasma.
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Rehm TH, Stojković MR, Rehm S, Škugor M, Piantanida I, Würthner F. Interaction of spermine-alanine functionalized perylene bisimide dye aggregates with ds-DNA/RNA secondary structure. Chem Sci 2012. [DOI: 10.1039/c2sc20825c] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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47
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Chakrabarty R, Mukherjee PS, Stang PJ. Supramolecular coordination: self-assembly of finite two- and three-dimensional ensembles. Chem Rev 2011; 111:6810-918. [PMID: 21863792 PMCID: PMC3212633 DOI: 10.1021/cr200077m] [Citation(s) in RCA: 2289] [Impact Index Per Article: 176.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Rajesh Chakrabarty
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Partha Sarathi Mukherjee
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Peter J Stang
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
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Yuan G, Zhang Q, Zhou J, Li H. Mass spectrometry of G-quadruplex DNA: formation, recognition, property, conversion, and conformation. MASS SPECTROMETRY REVIEWS 2011; 30:1121-1142. [PMID: 21520218 DOI: 10.1002/mas.20315] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2010] [Revised: 06/09/2010] [Accepted: 06/09/2010] [Indexed: 05/30/2023]
Abstract
G-quadruplexes are special secondary structures formed from G-rich sequences of DNA, and have proven to play important roles in a number of biological systems, including the regulation of gene transcription and translation. The highly distinctive nature of G-quadruplex structures and their functions suggest that G-quadruplexes can act as novel targets for drug development. As a highly sensitive analytical tool, mass spectrometry has been widely used for the analysis of G-quadruplex structures. Electrospray-ionization mass spectrometry, in particular, has found captivating applications to probe interactions between small molecules and G-quadruplex DNA. In this review, we will discuss: (1) mass spectrometry probing of the formation, binding affinity, and stoichiometry between G-quadruplexes and small molecules; (2) stabilization and collision-dissociation behavior of G-quadruplex DNA; (3) the exploration of the equilibrium transfer between a G-quadruplex and duplex DNA; and (4) the ESI-MS analysis of the conversion of intramolecular and intermolecular G-quadruplexes. Finally, we will also introduce the application of new techniques in the analysis of G-quadruplex conformation, such as ion-mobility and infrared multiphoton-dissociation mass spectrometry. We believe that, with the new technical developments, mass spectrometry will play an unparalleled role in the analysis of the G-quadruplex structures.
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Affiliation(s)
- Gu Yuan
- Beijing National Laboratory for Molecular Sciences, Key Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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Golub E, Freeman R, Willner I. A Hemin/G-Quadruplex Acts as an NADH Oxidase and NADH Peroxidase Mimicking DNAzyme. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103853] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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50
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Franceschin M, Borbone N, Oliviero G, Casagrande V, Scuotto M, Coppola T, Borioni S, Mayol L, Ortaggi G, Bianco A, Amato J, Varra M. Synthesis of a dibromoperylene phosphoramidite building block and its incorporation at the 5' end of a G-quadruplex forming oligonucleotide: spectroscopic properties and structural studies of the resulting dibromoperylene conjugate. Bioconjug Chem 2011; 22:1309-19. [PMID: 21688831 DOI: 10.1021/bc100526q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Previous studies indicate that some perylene bisimide derivatives can drive the assembly of DNA G-quadruplexes, thus suggesting the possible advantage in the adoption of perylene-conjugated G-rich oligonucleotides in biological and biotechnological applications. Nevertheless, the typical poor solubility of perylene bisimides strongly limits the number of suitable chemical strategies to prepare perylene-conjugated oligonucleotides. In order to overcome these difficulties, we employed the earlier described core twisted perylene derivatives possessing unique optical and electronic properties, besides good solubility in common solvents. As a first result, the large-scale synthesis of a new dibromoperylene derivative (PEOEBr) phosphoramidite building block is herein reported. Furthermore, the structural behavior of the conjugated PEOEBr-GGGTTAGGG (HTRp2) human telomeric repeat was investigated by using CD, UV, fluorescence, and gel electrophoresis techniques in desalted water and in K(+)- and Na(+)-containing buffers. We observed that the peculiar property of PEOEBr moieties to form dimers instead of extended aggregates drives the HTRp2 strands toward dimerization and mainly promotes the formation of quadruplex species having both the 5'-ends located at the same side of the structures. However, the counterions present in solutions (K(+) or Na(+)) as well as the strand concentration, also contribute to influence the topology and the stoichiometry of formed structures. Furthermore, unlike the unmodified sequence GGGTTAGGG (HTR2), HTRp2 strands quickly associate into G-quadruplexes even in desalted water, as assessed by CD experiments.
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Affiliation(s)
- Marco Franceschin
- Dipartimento di Chimica, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Roma, Italy
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