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Abstract
Guanine-rich nucleic acid sequences able to form four-stranded structures (G-quadruplexes, G4) play key cellular regulatory roles and are considered as promising drug targets for anticancer therapy. On the basis of the organization of their structural elements, G4 ligands can be divided into three major families: one, fused heteroaromatic polycyclic systems; two, macrocycles; three, modular aromatic compounds. The design of modular G4 ligands emerged as the answer to achieve not only more drug-like compounds but also more selective ligands by targeting the diversity of the G4 loops and grooves. The rationale behind the design of a very comprehensive set of ligands, with particular focus on the structural features required for binding to G4, is discussed and combined with the corresponding biochemical/biological data to highlight key structure-G4 interaction relationships. Analysis of the data suggests that the shape of the ligand is the major factor behind the G4 stabilizing effect of the ligands. The information here critically reviewed will certainly contribute to the development of new and better G4 ligands with application either as therapeutics or probes.
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Affiliation(s)
- Ana Rita Duarte
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Enrico Cadoni
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Ana S Ressurreição
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Rui Moreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Alexandra Paulo
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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102
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Saintomé C, Alberti P, Guinot N, Lejault P, Chatain J, Mailliet P, Riou JF, Bugaut A. Binding properties of mono- and dimeric pyridine dicarboxamide ligands to human telomeric higher-order G-quadruplex structures. Chem Commun (Camb) 2018; 54:1897-1900. [PMID: 29393312 DOI: 10.1039/c7cc07048a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Here, we report on the in vitro binding properties of the known pyridine dicarboxamide G-quadruplex ligand 360A and a new dimeric analogue (360A)2A to human telomeric DNA higher-order G-quadruplex (G4) structures. This study points to original binding features never reported for G4 ligands, and reveals a greater efficiency for the dimeric ligand to displace RPA (a ssDNA binding protein involved in telomere replication) from telomeric DNA.
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Affiliation(s)
- C Saintomé
- "Structure and Instability of Genomes" laboratory, Sorbonne Universités, Muséum National d'Histoire Naturelle (MNHN), Inserm U1154, CNRS UMR 7196, 75005 Paris, France.
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103
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Cai H, Zhou C, Yang Q, Ai T, Huang Y, Lv Y, Geng J, Xiao D. Single-molecule investigation of human telomeric G-quadruplex interactions with Thioflavin T. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.09.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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104
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Ihmels H, Löhl K, Paululat T, Uebach S. NMR-spectroscopic investigation of the complex between tetraazoniapentapheno[6,7-h]pentaphene and quadruplex DNA Tel26. NEW J CHEM 2018. [DOI: 10.1039/c8nj01931b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The tetraazoniapentapheno[6,7-h]pentaphene binds to the hybrid-1 quadruplex structure of the oligonucleotide Tel26 by terminal π stacking, likely on top of the A3–A9–A21 triplet.
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Affiliation(s)
- Heiko Ihmels
- Department of Chemistry and Biology
- University of Siegen
- Siegen 57068
- Germany
| | - Katharina Löhl
- Department of Chemistry and Biology
- University of Siegen
- Siegen 57068
- Germany
| | - Thomas Paululat
- Department of Chemistry and Biology
- University of Siegen
- Siegen 57068
- Germany
| | - Sandra Uebach
- Department of Chemistry and Biology
- University of Siegen
- Siegen 57068
- Germany
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105
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Kudrev AG. The Evidence of Cooperative Binding of a Ligand to G4 DNA. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2017; 2017:6780521. [PMID: 29181223 PMCID: PMC5664379 DOI: 10.1155/2017/6780521] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/24/2017] [Indexed: 06/07/2023]
Abstract
Intrinsic constants of the ligand binding with G4 DNA (guanine-rich DNA sequence) using quantitative standards can be convenient providing the assessment for elucidating the possibility of such structures participation in biochemical processes. In the present communication, the hard + soft modelling approach to calculate intrinsic constants of a ligand binding with short DNA molecule, particularly such as G4 DNA, has been proposed. The suggested approach has focused upon the quantitative evaluating of a mutual influence between sites and between bound ligands. The cross-validation between a new hard + soft modelling and conventional stepwise complex formation algorithm has been conducted. A number of simulated examples will illustrate the methodology. The experimental mole-ratio titration of TMPyP4 by G4 DNA [(CG3)2CGC(AG3)2G] has been reexamined. The [(CG3)2CGC(AG3)2G] that folds from a G-rich sequence found in the promoter region of c-kit oncogene can be considered as a molecule with two equivalent mutually influence binding sites.
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Affiliation(s)
- A. G. Kudrev
- Saint Petersburg State University, 7/9 Universitetskaya Nab., St. Petersburg 199034, Russia
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106
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Yao X, Song D, Qin T, Yang C, Yu Z, Li X, Liu K, Su H. Interaction between G-Quadruplex and Zinc Cationic Porphyrin: The Role of the Axial Water. Sci Rep 2017; 7:10951. [PMID: 28887497 PMCID: PMC5591184 DOI: 10.1038/s41598-017-11413-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/23/2017] [Indexed: 01/27/2023] Open
Abstract
The interaction of ligands with G-quadruplexes has attracted considerable attention due to its importance in molecular recognition and anticancer drugs design. Here, we utilize triplet excited state as a sensitive reporter to study the binding interaction of zinc cationic porphyrin (ZnTMPyP4) with three G-quadruplexes, AG3(T2AG3)3, (G4T4G4)2, and (TG4T)4. By monitoring the triplet decay dynamics of ZnTMPyP4 with transient absorption spectroscopy, the coexisted binding modes via π-π stacking of porphyrin macrocycle and the G-quartets are allowed to be identified quantitatively, which involve intercalation (25% and 36%) versus end-stacking (75% and 64%) for AG3(T2AG3)3 and (G4T4G4)2, and end-stacking (23%) versus partial intercalation (77%) for (TG4T)4. It is shown that the steric hindrance of the axial water decreases greatly the percentage of intercalation. Further, a rapid assessment of binding stoichiometry is fulfilled by measuring the triplet decay dynamics under various [G-quadruplex]/[ZnTMPyP4] ratios. The binding stoichiometric ratios of G-quadruplex/ZnTMPyP4 are 1:2 for AG3(T2AG3)3, 1:1 for (G4T4G4)2, and 1:2 for (TG4T)4, which agree well with results obtained by the conventional method of continuous variation analysis. These results reveal a clear scenario of G-quadruplex/ZnTMPyP4 interaction and provide mechanistic insights for the application of anticancer drug designs using G-quadruplex as target.
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Affiliation(s)
- Xiangzi Yao
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Di Song
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Tingxiao Qin
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunfan Yang
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Ze Yu
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Xiaohong Li
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Kunhui Liu
- College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Hongmei Su
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.
- College of Chemistry, Beijing Normal University, Beijing, 100875, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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107
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Yu Y, Su G, Zhu H, Zhu Q, Chen Y, Xu B, Li Y, Zhang W. Proximity hybridization-mediated isothermal exponential amplification for ultrasensitive electrochemical protein detection. Int J Nanomedicine 2017; 12:5903-5914. [PMID: 28860756 PMCID: PMC5566414 DOI: 10.2147/ijn.s142015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In this study, we fabricated a novel electrochemical biosensing platform on the basis of target-triggered proximity hybridization-mediated isothermal exponential amplification reaction (EXPAR) for ultrasensitive protein analysis. Through rational design, the aptamers for protein recognition were integrated within two DNA probes. Via proximity hybridization principle, the affinity protein-binding event was converted into DNA assembly process. The recognition of protein by aptamers can trigger the strand displacement through the increase of the local concentrations of the involved probes. As a consequence, the output DNA was displaced, which can hybridize with the duplex probes immobilized on the electrode surface subsequently, leading to the initiation of the EXPAR as well as the cleavage of duplex probes. Each cleavage will release the gold nanoparticles (AuNPs) binding sequence. With the modification of G-quadruplex sequence, electrochemical signals were yielded by the AuNPs through oxidizing 3,3',5,5'-tetramethylbenzidine in the presence of H2O2. The study we proposed exhibited high sensitivity toward platelet-derived growth factor BB (PDGF-BB) with the detection limit of 52 fM. And, this method also showed great selectivity among the PDGF isoforms and performed well in spiked human serum samples.
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Affiliation(s)
- Yanyan Yu
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Gaoxing Su
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Hongyan Zhu
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Qing Zhu
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Yong Chen
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Bohui Xu
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Yuqin Li
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
| | - Wei Zhang
- School of Pharmacy, Nantong University, Nantong, People's Republic of China
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108
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Piraux G, Bar L, Abraham M, Lavergne T, Jamet H, Dejeu J, Marcélis L, Defrancq E, Elias B. New Ruthenium-Based Probes for Selective G-Quadruplex Targeting. Chemistry 2017; 23:11872-11880. [PMID: 28609545 DOI: 10.1002/chem.201702076] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Indexed: 01/13/2023]
Abstract
Telomeric regions containing G-quadruplex (G4) structures play a pivotal role in the development of cancers. The development of specific binders for G4s is thus of great interest in order to gain a deeper understanding of the role of these structures, and to ultimately develop new anticancer drug candidates. For several years, RuII complexes have been studied as efficient probes for DNA. Interest in these complexes stems mainly from the tunability of their structures and properties, and the possibility of using light excitation as a tool to probe their environment or to selectively trigger their reaction with a biological target. Herein, we report on the synthesis and thorough study of new RuII complexes based on a novel dipyrazino[2,3-a:2',3'-h]phenazine ligand (dph), obtained through a Chichibabin-like reaction. Luminescence experiments, surface plasmon resonance (SPR), and computational studies have demonstrated that these complexes behave as selective probes for G-quadruplex structures.
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Affiliation(s)
- Guillaume Piraux
- Institut de la Matière Condensée et des Nanosciences (IMCN)-Molécules, Solides et Réactivité (MOST), Université catholique de Louvain, Place Louis Pasteur 1, bte L4.01.02, 1348, Louvain-la-Neuve, Belgium
| | - Laure Bar
- Université Grenoble-Alpes, UMR CNRS 5250, 38000, Grenoble, France
| | - Michaël Abraham
- Institut de la Matière Condensée et des Nanosciences (IMCN)-Molécules, Solides et Réactivité (MOST), Université catholique de Louvain, Place Louis Pasteur 1, bte L4.01.02, 1348, Louvain-la-Neuve, Belgium
| | - Thomas Lavergne
- Université Grenoble-Alpes, UMR CNRS 5250, 38000, Grenoble, France
| | - Hélène Jamet
- Université Grenoble-Alpes, UMR CNRS 5250, 38000, Grenoble, France
| | - Jérôme Dejeu
- Université Grenoble-Alpes, UMR CNRS 5250, 38000, Grenoble, France
| | - Lionel Marcélis
- Institut de la Matière Condensée et des Nanosciences (IMCN)-Molécules, Solides et Réactivité (MOST), Université catholique de Louvain, Place Louis Pasteur 1, bte L4.01.02, 1348, Louvain-la-Neuve, Belgium
| | - Eric Defrancq
- Université Grenoble-Alpes, UMR CNRS 5250, 38000, Grenoble, France
| | - Benjamin Elias
- Institut de la Matière Condensée et des Nanosciences (IMCN)-Molécules, Solides et Réactivité (MOST), Université catholique de Louvain, Place Louis Pasteur 1, bte L4.01.02, 1348, Louvain-la-Neuve, Belgium
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109
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Li X, Zhang H, Tang Y, Wu P, Xu S, Zhang X. A Both-End Blocked Peroxidase-Mimicking DNAzyme for Low-Background Chemiluminescent Sensing of miRNA. ACS Sens 2017; 2:810-816. [PMID: 28723123 DOI: 10.1021/acssensors.7b00178] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
G-quadruplex DNAzymes that exhibited peroxidase-like activity have been shown to be appealing reporters for amplified readout of biosensing events simply by their formation or dissociation in the presence of analytes. For low background signaling, the efficient preblock of DNAzymes is critically important. Herein, we report a both-end blocked DNAzyme beacon strategy for chemiluminescent biosensing. The catalytic activity of peroxidase-mimicking DNAzyme can be inactivated fully by fixing both ends of the DNAzyme sequence, and easily recovered via a strand displace reaction between the miRNA and the block DNA. The efficient block and recovery of DNAzymes provide the both-end blocked beacon the highest signal-to-background ratio (over 25) among the reported DNAzymes for amplification-free detection of miRNA. As a result, the beacon allowed detection of subpicomolar miRNA without any labeling and amplification procedures, which is about 40-fold more sensitive than the traditional hairpin fluorescence beacon. Also, it exhibited excellent discrimination ability that can distinguish single-base mismatch miRNA. The simplicity, high sensitivity, and selectivity provided by the beacon make it a promising alternative tool for nucleic acid detection.
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Affiliation(s)
- Xianming Li
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Houchun Zhang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Yurong Tang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Peng Wu
- Analytical & Testing Center, Sichuan University, Chengdu 610064, China
| | - Shuxia Xu
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Xinfeng Zhang
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
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110
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Qin T, Liu K, Song D, Yang C, Su H. Porphyrin Bound to i-Motifs: Intercalation versus External Groove Binding. Chem Asian J 2017; 12:1578-1586. [DOI: 10.1002/asia.201700398] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/05/2017] [Indexed: 01/21/2023]
Affiliation(s)
- Tingxiao Qin
- Beijing National Laboratory for Molecular Sciences (BNLMS); Institute of Chemistry, Chinese Academy of Sciences; Beijing 100190 P.R. China
- University of Chinese Academy of Sciences; Beijing 100049 P.R. China
| | - Kunhui Liu
- College of Chemistry; Beijing Normal University; Beijing 100875 P.R. China
| | - Di Song
- Beijing National Laboratory for Molecular Sciences (BNLMS); Institute of Chemistry, Chinese Academy of Sciences; Beijing 100190 P.R. China
| | - Chunfan Yang
- College of Chemistry; Beijing Normal University; Beijing 100875 P.R. China
| | - Hongmei Su
- College of Chemistry; Beijing Normal University; Beijing 100875 P.R. China
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111
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Endoh T, Sugimoto N. Conformational Dynamics of mRNA in Gene Expression as New Pharmaceutical Target. CHEM REC 2017; 17:817-832. [DOI: 10.1002/tcr.201700016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER); Konan University; 7-1-20 Minatojima-minamimachi Chuo-ku, Kobe 650-0047 Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER); Konan University; 7-1-20 Minatojima-minamimachi Chuo-ku, Kobe 650-0047 Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST); Konan University; 7-1-20 Minatojima-minamimachi Chuo-ku, Kobe 650-0047 Japan
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112
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Xie H, Ding M, Liu M, Hu T, Zhang F. Synthesis of Functionalized Biaryls and Poly(hetero)aryl Containing Medium-Sized Lactones with Cyclic Diaryliodonium Salts. Org Lett 2017; 19:2600-2603. [PMID: 28481117 DOI: 10.1021/acs.orglett.7b00933] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A novel one-pot procedure is described for the transition-metal catalyzed sequential difunctionalization of diaryliodonium reagents. Reaction of commercially available anthranilic acid derivatives with readily available cyclic diaryliodonium salts followed by a Sonogashira coupling afforded various alkyne substituted biaryls in good to excellent yields. The functionalized biaryls were then utilized for the rapid and efficient one-pot synthesis of novel poly(hetero)aryl containing 10-membered lactones which are potential G-quadruplex binders and telomerase inhibitors.
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Affiliation(s)
- Hao Xie
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology , Hangzhou, 310014, P. R. China
| | - Mingruo Ding
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology , Hangzhou, 310014, P. R. China
| | - Min Liu
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology , Hangzhou, 310014, P. R. China
| | - Tao Hu
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology , Hangzhou, 310014, P. R. China
| | - Fengzhi Zhang
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Delta Region, Zhejiang University of Technology , Hangzhou, 310014, P. R. China
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113
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Padmapriya K, Barthwal R. NMR based structural studies decipher stacking of the alkaloid coralyne to terminal guanines at two different sites in parallel G-quadruplex DNA, [d(TTGGGGT)]4 and [d(TTAGGGT)]4. Biochim Biophys Acta Gen Subj 2017; 1861:37-48. [DOI: 10.1016/j.bbagen.2016.11.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/13/2016] [Accepted: 11/08/2016] [Indexed: 01/15/2023]
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114
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Musumeci D, Amato J, Zizza P, Platella C, Cosconati S, Cingolani C, Biroccio A, Novellino E, Randazzo A, Giancola C, Pagano B, Montesarchio D. Tandem application of ligand-based virtual screening and G4-OAS assay to identify novel G-quadruplex-targeting chemotypes. Biochim Biophys Acta Gen Subj 2017; 1861:1341-1352. [PMID: 28130159 DOI: 10.1016/j.bbagen.2017.01.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/16/2017] [Accepted: 01/23/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND G-quadruplex (G4) structures are key elements in the regulation of cancer cell proliferation and their targeting is deemed to be a promising strategy in anticancer therapy. METHODS A tandem application of ligand-based virtual screening (VS) calculations together with the experimental G-quadruplex on Oligo Affinity Support (G4-OAS) assay was employed to discover novel G4-targeting compounds. The interaction of the selected compounds with the investigated G4 in solution was analysed through a series of biophysical techniques and their biological activity investigated by immunofluorescence and MTT assays. RESULTS A focused library of 60 small molecules, designed as putative G4 groove binders, was identified through the VS. The G4-OAS experimental screening led to the selection of 7 ligands effectively interacting with the G4-forming human telomeric DNA. Evaluation of the biological activity of the selected compounds showed that 3 ligands of this sub-library induced a marked telomere-localized DNA damage response in human tumour cells. CONCLUSIONS The combined application of virtual and experimental screening tools proved to be a successful strategy to identify new bioactive chemotypes able to target the telomeric G4 DNA. These compounds may represent useful leads for the development of more potent and selective G4 ligands. GENERAL SIGNIFICANCE Expanding the repertoire of the available G4-targeting chemotypes with improved physico-chemical features, in particular aiming at the discovery of novel, selective G4 telomeric ligands, can help in developing effective anti-cancer drugs with fewer side effects. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Pasquale Zizza
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | | | - Chiara Cingolani
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy.
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115
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Jana J, Mondal S, Bhattacharjee P, Sengupta P, Roychowdhury T, Saha P, Kundu P, Chatterjee S. Chelerythrine down regulates expression of VEGFA, BCL2 and KRAS by arresting G-Quadruplex structures at their promoter regions. Sci Rep 2017; 7:40706. [PMID: 28102286 PMCID: PMC5244364 DOI: 10.1038/srep40706] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 12/12/2016] [Indexed: 12/22/2022] Open
Abstract
A putative anticancer plant alkaloid, Chelerythrine binds to G-quadruplexes at promoters of VEGFA, BCL2 and KRAS genes and down regulates their expression. The association of Chelerythrine to G-quadruplex at the promoters of these oncogenes were monitored using UV absorption spectroscopy, fluorescence anisotropy, circular dichroism spectroscopy, CD melting, isothermal titration calorimetry, molecular dynamics simulation and quantitative RT-PCR technique. The pronounced hypochromism accompanied by red shifts in UV absorption spectroscopy in conjunction with ethidium bromide displacement assay indicates end stacking mode of interaction of Chelerythrine with the corresponding G-quadruplex structures. An increase in fluorescence anisotropy and CD melting temperature of Chelerythrine-quadruplex complex revealed the formation of stable Chelerythrine-quadruplex complex. Isothermal titration calorimetry data confirmed that Chelerythrine-quadruplex complex formation is thermodynamically favourable. Results of quantative RT-PCR experiment in combination with luciferase assay showed that Chelerythrine treatment to MCF7 breast cancer cells effectively down regulated transcript level of all three genes, suggesting that Chelerythrine efficiently binds to in cellulo quadruplex motifs. MD simulation provides the molecular picture showing interaction between Chelerythrine and G-quadruplex. Binding of Chelerythrine with BCL2, VEGFA and KRAS genes involved in evasion, angiogenesis and self sufficiency of cancer cells provides a new insight for the development of future therapeutics against cancer.
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Affiliation(s)
- Jagannath Jana
- Department of Biophysics, Bose Institute, Kolkata, WB, India
| | - Soma Mondal
- Department of Biophysics, Bose Institute, Kolkata, WB, India
| | | | | | | | - Pranay Saha
- Department of Biophysics, Bose Institute, Kolkata, WB, India
| | - Pallob Kundu
- Division of Plant Biology, Bose Institute, Kolkata, WB, India
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116
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Azargun M, Jami-Alahmadi Y, Fridgen TD. The intrinsic stabilities and structures of alkali metal cationized guanine quadruplexes. Phys Chem Chem Phys 2017; 19:1281-1287. [DOI: 10.1039/c6cp07301h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structures and stabilities of self-assembled guanine quadruplexes, M(9eG)8+ (M = Na, K, Rb, Cs; 9eG = 9-ethylguanine), have been studied in the gas phase by blackbody infrared radiative dissociation kinetics to determine the effect the metal cations have on the decomposition energies and reactions of the quadruplex.
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Affiliation(s)
- M. Azargun
- Department of Chemistry
- Memorial University
- St John's
- Canada
| | | | - T. D. Fridgen
- Department of Chemistry
- Memorial University
- St John's
- Canada
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117
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Islam MM, Sato S, Shinozaki S, Takenaka S. Cyclic ferrocenylnaphthalene diimide derivative as a new class of G-quadruplex DNA binding ligand. Bioorg Med Chem Lett 2017; 27:329-335. [DOI: 10.1016/j.bmcl.2016.11.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 10/19/2016] [Accepted: 11/11/2016] [Indexed: 01/01/2023]
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118
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Gao Y, Guang T, Ye X. Sedimentation velocity analysis of TMPyP4-induced dimer formation of human telomeric G-quadruplex. RSC Adv 2017. [DOI: 10.1039/c7ra07758k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Analytical ultracentrifugation sedimentation velocity (AUC-SV) was used to study the interactions between TMPyP4 and AGGG(TTAGGG)3 (Tel22) and the TMPyP4-induced dimer formation of G-quadruplex.
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Affiliation(s)
- Yating Gao
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei
- China
| | - Tianlei Guang
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei
- China
| | - Xiaodong Ye
- Hefei National Laboratory for Physical Sciences at the Microscale
- Department of Chemical Physics
- University of Science and Technology of China
- Hefei
- China
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119
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Pithan PM, Decker D, Druzhinin SI, Ihmels H, Schönherr H, Voß Y. 8-Styryl-substituted coralyne derivatives as DNA binding fluorescent probes. RSC Adv 2017; 7:10660-10667. [PMID: 28496973 PMCID: PMC5361113 DOI: 10.1039/c6ra27684a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/30/2017] [Indexed: 12/16/2022] Open
Abstract
8-Styryl-substituted coralyne derivatives bind to duplex and quadruplex DNA and may be used for fluorimetric staining of nucleoli in cells.
Six new 8-styryl-substituted coralyne derivatives 4a–f were synthesized from coralyne (2) by a base catalysed Knoevenagel type reaction. It was shown by photometric and fluorimetric titrations of double stranded and quadruplex DNA to 4b–d as well as by fluorimetric DNA denaturation experiments that these ligands bind to DNA with different binding modes at varying ligand-DNA ratios (LDR). Specifically, the addition of DNA caused initially a hypochromic effect in absorbance and, at a particular LDR, the development of a new red shifted absorption band with a hyperchromic effect. Furthermore, 4b–d induced a significant and selective stabilization of quadruplex DNA towards unfolding (ΔTm = 31.6–32.9 °C at LDR = 5), which is even more pronounced as compared to the parent compound coralyne (2). Most notably, the addition of DNA to the dimethylamino-substituted derivative 4b leads to a new, strongly red-shifted emission band at 695 nm. Hence, this derivative is a fluorescent probe that changes its fluorescence colour from green to red in the presence of DNA and even allows the fluorimetric analysis of living cells by staining of the nucleoli.
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Affiliation(s)
- P M Pithan
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - D Decker
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - S I Druzhinin
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - H Ihmels
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - H Schönherr
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - Y Voß
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
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120
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Cao Q, Li Y, Freisinger E, Qin PZ, Sigel RKO, Mao ZW. G-quadruplex DNA targeted metal complexes acting as potential anticancer drugs. Inorg Chem Front 2017. [DOI: 10.1039/c6qi00300a] [Citation(s) in RCA: 174] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
This review summarizes the recent development of G4 DNA targeted metal complexes and discusses their potential as anticancer drugs.
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Affiliation(s)
- Qian Cao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- China
| | - Yi Li
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- China
| | - Eva Freisinger
- University of Zurich
- Department of Chemistry
- CH-8057 Zurich
- Switzerland
| | - Peter Z. Qin
- Department of Chemistry
- University of Southern California
- Los Angeles
- USA
| | | | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry
- School of Chemistry and Chemical Engineering
- Sun Yat-Sen University
- Guangzhou 510275
- China
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121
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Kumar V, kashav T, Islam A, Ahmad F, Hassan MI. Structural insight into C9orf72 hexanucleotide repeat expansions: Towards new therapeutic targets in FTD-ALS. Neurochem Int 2016; 100:11-20. [DOI: 10.1016/j.neuint.2016.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 08/12/2016] [Accepted: 08/12/2016] [Indexed: 12/12/2022]
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122
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Jin H, Liu Y, Xu T, Qu X, Bian F, Sun Q. Quantum Dots–Ligand Complex as Ratiometric Fluorescent Nanoprobe for Visual and Specific Detection of G-Quadruplex. Anal Chem 2016; 88:10411-10418. [DOI: 10.1021/acs.analchem.6b01967] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Haojun Jin
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yuqian Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Tianshu Xu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xiaojun Qu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Feika Bian
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qingjiang Sun
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
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123
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Zhao A, Zhao C, Ren J, Qu X. Enantioselective targeting left-handed Z-G-quadruplex. Chem Commun (Camb) 2016; 52:1365-8. [PMID: 26616287 DOI: 10.1039/c5cc08401f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Herein, we report the first example where an M-enantiomer of a chiral metal complex can selectively stabilize a left-handed G-quadruplex, but its P-enantiomer cannot. The interactions between the chiral metal complexes and the left-handed G-quadruplex were evaluated by UV melting, circular dichroism, isothermal titration calorimetry, gel electrophoresis and NMR titrations.
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Affiliation(s)
- Andong Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Graduate School of the Chinese Academy of Sciences, Changchun, Jilin 130022, China.
| | - Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Graduate School of the Chinese Academy of Sciences, Changchun, Jilin 130022, China.
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Graduate School of the Chinese Academy of Sciences, Changchun, Jilin 130022, China.
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Graduate School of the Chinese Academy of Sciences, Changchun, Jilin 130022, China.
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124
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Zhang X, Huang Z, Wu S, Lin R, Liu J, Su N. Investigation of antitumor mechanism of the chiral ruthenium complex Λ-[Ru(phen) 2 p-MOPIP] 2+ in human gastric cancer MGC-803 cells. INORG CHEM COMMUN 2016. [DOI: 10.1016/j.inoche.2016.07.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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125
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Padmapriya K, Barthwal R. Nuclear magnetic resonance studies reveal stabilization of parallel G-quadruplex DNA [d(T 2 G 4 T)] 4 upon binding to protoberberine alkaloid coralyne. Bioorg Med Chem Lett 2016; 26:4915-4918. [DOI: 10.1016/j.bmcl.2016.09.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Revised: 09/02/2016] [Accepted: 09/06/2016] [Indexed: 12/17/2022]
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126
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Panich S, Haj Sleiman M, Steer I, Ladame S, Edel JB. Real-Time Monitoring of Ligand Binding to G-Quadruplex and Duplex DNA by Whispering Gallery Mode Sensing. ACS Sens 2016. [DOI: 10.1021/acssensors.6b00301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sirirat Panich
- Department of Chemistry and ‡Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Mazen Haj Sleiman
- Department of Chemistry and ‡Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Isobel Steer
- Department of Chemistry and ‡Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Sylvain Ladame
- Department of Chemistry and ‡Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
| | - Joshua B. Edel
- Department of Chemistry and ‡Department of Bioengineering, Imperial College London, South Kensington Campus, London, SW7 2AZ, United Kingdom
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127
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Ali A, Kamra M, Roy S, Muniyappa K, Bhattacharya S. Novel Oligopyrrole Carboxamide based Nickel(II) and Palladium(II) Salens, Their Targeting of Human G-Quadruplex DNA, and Selective Cancer Cell Toxicity. Chem Asian J 2016; 11:2542-54. [DOI: 10.1002/asia.201600655] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/16/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Asfa Ali
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560 012 India
| | - Mohini Kamra
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560 012 India
| | - Soma Roy
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560 012 India
| | - K. Muniyappa
- Department of Biochemistry; Indian Institute of Science; Bangalore 560 012 India
| | - Santanu Bhattacharya
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560 012 India
- Director's Research Unit; Indian Association for the Cultivation of Science; Kolkata 700 032 India
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128
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Pradeep TP, Barthwal R. NMR structure of dual site binding of mitoxantrone dimer to opposite grooves of parallel stranded G-quadruplex [d-(TTGGGGT)]4. Biochimie 2016; 128-129:59-69. [DOI: 10.1016/j.biochi.2016.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 07/11/2016] [Indexed: 12/27/2022]
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129
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Ju HP, Wang YZ, You J, Hou XM, Xi XG, Dou SX, Li W, Wang PY. Folding Kinetics of Single Human Telomeric G-Quadruplex Affected by Cisplatin. ACS OMEGA 2016; 1:244-250. [PMID: 30023477 PMCID: PMC6044606 DOI: 10.1021/acsomega.6b00044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/22/2016] [Indexed: 05/27/2023]
Abstract
G-Quadruplex DNA structure has been proven to be a binding target for small molecular organic compounds and hence regarded as a promising pharmacological target. Cisplatin is a widely used chemotherapy drug that targets duplex DNA and was recently shown to react also with G-quadruplex, implying that cisplatin actually may also target G-quadruplex. In this work, we employed magnetic tweezers to investigate the influence of cisplatin on the folding kinetics of single human telomeric G-quadruplex. It was revealed that cisplatin and G-quadruplex interact in two different and competitive ways that depend on cisplatin concentration.
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Affiliation(s)
- Hai-Peng Ju
- Beijing
National Laboratory for Condensed Matter Physics and Key Laboratory
of Soft Matter Physics, Institute of Physics,
Chinese Academy of Sciences, No. 8 3rd South Street, Zhongguancun, Beijing 100190, China
| | - Yi-Zhou Wang
- Beijing
National Laboratory for Condensed Matter Physics and Key Laboratory
of Soft Matter Physics, Institute of Physics,
Chinese Academy of Sciences, No. 8 3rd South Street, Zhongguancun, Beijing 100190, China
| | - Jing You
- Beijing
National Laboratory for Condensed Matter Physics and Key Laboratory
of Soft Matter Physics, Institute of Physics,
Chinese Academy of Sciences, No. 8 3rd South Street, Zhongguancun, Beijing 100190, China
| | - Xi-Miao Hou
- School
of Life Sciences, Northwest A&F University, No. 3 Taicheng Road, Yangling 712100, China
| | - Xu-Guang Xi
- School
of Life Sciences, Northwest A&F University, No. 3 Taicheng Road, Yangling 712100, China
| | - Shuo-Xing Dou
- Beijing
National Laboratory for Condensed Matter Physics and Key Laboratory
of Soft Matter Physics, Institute of Physics,
Chinese Academy of Sciences, No. 8 3rd South Street, Zhongguancun, Beijing 100190, China
| | - Wei Li
- Beijing
National Laboratory for Condensed Matter Physics and Key Laboratory
of Soft Matter Physics, Institute of Physics,
Chinese Academy of Sciences, No. 8 3rd South Street, Zhongguancun, Beijing 100190, China
| | - Peng-Ye Wang
- Beijing
National Laboratory for Condensed Matter Physics and Key Laboratory
of Soft Matter Physics, Institute of Physics,
Chinese Academy of Sciences, No. 8 3rd South Street, Zhongguancun, Beijing 100190, China
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130
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Gribas AV, Zatsepin TS, Korolev SP, Gottikh MB, Sakharov IY. Suicide inactivation of covalent peroxidase-mimicking DNAzyme with hydrogen peroxide and its protection by a reductant substrate. Talanta 2016; 155:212-5. [DOI: 10.1016/j.talanta.2016.04.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 04/12/2016] [Accepted: 04/16/2016] [Indexed: 12/29/2022]
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131
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132
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Wu Q, Mei W, Zheng K, Ding Y. Self-assembly of c-myc DNA promoted by a single enantiomer ruthenium complex as a potential nuclear targeting gene carrier. Sci Rep 2016; 6:28582. [PMID: 27381008 PMCID: PMC4933878 DOI: 10.1038/srep28582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 06/07/2016] [Indexed: 12/26/2022] Open
Abstract
Gene therapy has long been limited in the clinic, due in part to the lack of safety and efficacy of the gene carrier. Herein, a single enantiomer ruthenium(II) complex, Λ-[Ru(bpy)2(p-BEPIP)](ClO4)2 (Λ-RM0627, bpy = 4,4'-bipyridine, p-BEPIP = 2-(4-phenylacetylenephenyl)imidazole [4,5f][1, 10] phenanthroline), has been synthesized and investigated as a potential gene carrier that targets the nucleus. In this report, it is shown that Λ-RM0627 promotes self-assembly of c-myc DNA to form a nanowire structure. Further studies showed that the nano-assembly of c-myc DNA that induced Λ-RM0627 could be efficiently taken up and enriched in the nuclei of HepG2 cells. After treatment of the nano-assembly of c-myc DNA with Λ-RM0627, over-expression of c-myc in HepG2 cells was observed. In summary, Λ-RM0627 played a key role in the transfer and release of c-myc into cells, which strongly indicates Λ-RM0627 as a potent carrier of c-myc DNA that targets the nucleus of tumor cells.
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Affiliation(s)
- Qiong Wu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Wenjie Mei
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Kangdi Zheng
- Traditional Chinese Medicine College, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yang Ding
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
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133
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Stevens AJ, Kennedy HL, Kennedy MA. Fluorescence Methods for Probing G-Quadruplex Structure in Single- and Double-Stranded DNA. Biochemistry 2016; 55:3714-25. [PMID: 27253207 DOI: 10.1021/acs.biochem.6b00327] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Interest in exploring G-quadruplex (G4) structures in nucleic acids is growing as it becomes more widely recognized that these structures have many interesting biological roles and chemical properties. Probing the G4-forming potential of DNA with dimethyl sulfate, polymerase stop assays, or nuclease digestion are three commonly used techniques that usually employ radio-isotopic labels for visualization. However, as fluorescent labeling methods have grown in popularity and versatility, many laboratories have moved away from the routine use of radio-isotopic methods. We have adapted traditional procedures for structural analysis of G4-forming DNA sequences by using fluorescent labels and capillary electrophoresis and demonstrate their application to well-studied G4 structures, including c-MYC PU27 G4. The three fluorescent assays described here allow interrogation of G4 structures in double- and single-stranded DNA substrates, using either chemical or enzymatic cleavage. When combined, these techniques can provide valuable information for the investigation of G4 topology and structure, as well as visualizing any structural effects caused by interaction of quadruplexes with the complementary C-rich DNA strand.
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Affiliation(s)
- Aaron J Stevens
- Department of Pathology, University of Otago , Christchurch, New Zealand
| | - Hannah L Kennedy
- Department of Pathology, University of Otago , Christchurch, New Zealand.,Molecular Pathology Laboratory, Canterbury Health Laboratories, Canterbury District Health Board , Christchurch, New Zealand
| | - Martin A Kennedy
- Department of Pathology, University of Otago , Christchurch, New Zealand
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134
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Kang BH, Gao ZF, Li N, Shi Y, Li NB, Luo HQ. Thiazole orange as a fluorescent probe: Label-free and selective detection of silver ions based on the structural change of i-motif DNA at neutral pH. Talanta 2016; 156-157:141-146. [PMID: 27260446 DOI: 10.1016/j.talanta.2016.05.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/27/2016] [Accepted: 05/01/2016] [Indexed: 02/05/2023]
Abstract
Silver ions have been widely applied to many fields and have harmful effects on environments and human health. Herein, a label-free optical sensor for Ag(+) detection is constructed based on thiazole orange (TO) as a fluorescent probe for the recognition of i-motif DNA structure change at neutral pH. Ag(+) can fold a C-rich single stranded DNA sequence into i-motif DNA structure at neutral pH and that folding is reversible by chelation with cysteine (Cys). The DNA folding process can be indicated by the fluorescence change of TO, which is non-fluorescent in free molecule state and emits strong fluorescence after the incorporation with i-motif DNA. Thus, a rapid, sensitive, and selective method for the detection of Ag(+) and Cys is developed with a detection limit of 17 and 280nM, respectively. It is worth noting that the mechanism underlying the increase of the fluorescence of thiazole orange in the presence of i-motif structure is explained. Moreover, a fluorescent DNA logic gate is successfully designed based on the Ag(+)/Cys-mediated reversible fluorescence changes. The proposed detection strategy is label-free and economical. In addition, this system shows a great promise for i-motif/TO complex to analyze Ag(+) in the real samples.
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Affiliation(s)
- Bei Hua Kang
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Zhong Feng Gao
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Na Li
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yan Shi
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Nian Bing Li
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Hong Qun Luo
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
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135
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Fung SK, Zou T, Cao B, Chen T, To WP, Yang C, Lok CN, Che CM. Luminescent platinum(II) complexes with functionalized N-heterocyclic carbene or diphosphine selectively probe mismatched and abasic DNA. Nat Commun 2016; 7:10655. [PMID: 26883164 PMCID: PMC4757794 DOI: 10.1038/ncomms10655] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 01/06/2016] [Indexed: 01/09/2023] Open
Abstract
The selective targeting of mismatched DNA overexpressed in cancer cells is an appealing strategy in designing cancer diagnosis and therapy protocols. Few luminescent probes that specifically detect intracellular mismatched DNA have been reported. Here we used Pt(II) complexes with luminescence sensitive to subtle changes in the local environment and report several Pt(II) complexes that selectively bind to and identify DNA mismatches. We evaluated the complexes' DNA-binding characteristics by ultraviolet/visible absorption titration, isothermal titration calorimetry, nuclear magnetic resonance and quantum mechanics/molecular mechanics calculations. These Pt(II) complexes show up to 15-fold higher emission intensities upon binding to mismatched DNA over matched DNA and can be utilized for both detecting DNA abasic sites and identifying cancer cells and human tissue samples with different levels of mismatch repair. Our work highlights the potential of luminescent Pt(II) complexes to differentiate between normal cells and cancer cells which generally possess more aberrant DNA structures. DNA pairing defects such as mismatched and abasic DNA are prevalent in cancer cells. Here, the authors present luminescent platinum based probes capable of preferentially binding to mismatched and abasic DNA, and reporting this by a significant luminescence enhancement
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Affiliation(s)
- Sin Ki Fung
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Taotao Zou
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.,HKU Shenzhen Institute of Research and Innovation Shenzhen, Shenzhen 518053, China
| | - Bei Cao
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Tianfeng Chen
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Wai-Pong To
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chen Yang
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.,HKU Shenzhen Institute of Research and Innovation Shenzhen, Shenzhen 518053, China
| | - Chun-Nam Lok
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Chi-Ming Che
- State Key Laboratory of Synthetic Chemistry, Institute of Molecular Functional Materials, Chemical Biology Centre, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong, China.,HKU Shenzhen Institute of Research and Innovation Shenzhen, Shenzhen 518053, China
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136
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Changenet-Barret P, Gustavsson T, Markovitsi D, Manet I. Ultrafast Electron Transfer in Complexes of Doxorubicin with Human Telomeric G-Quadruplexes and GC Duplexes Probed by Femtosecond Fluorescence Spectroscopy. Chemphyschem 2016; 17:1264-72. [PMID: 26790038 DOI: 10.1002/cphc.201501091] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 01/23/2023]
Abstract
Doxorubicin (DOX) is a natural anthracycline widely used in chemotherapy; its combined application as a chemotherapeutic and photodynamic agent has been recently proposed. In this context, understanding the photoinduced properties of DOX complexes with nucleic acids is crucial. Herein, the study of photoinduced electron transfer in DOX-DNA complexes by femtosecond fluorescence spectroscopy is reported. The behaviour of complexes with two model DNA structures, a G-quadruplex (G4) formed by the human telomeric sequence (Tel21) and a d(GC) duplex, is compared. The DOX affinity for these two sequences is similar. Although both 1:1 and 2:1 stoichiometries have been reported for DOX-G4 complexes, only 1:1 complexes form with the duplex. The steady-state absorption indicates a strong binding interaction with the duplex due to drug intercalation between the GC base pairs. In contrast, the interaction of DOX with Tel21 is much weaker and arises from drug binding on the G4 external faces at two independent binding sites. As observed for DOX-d(GC) complexes, fluorescence of the drug in the first binding site of Tel21 exhibits decays within a few picoseconds following a biphasic pattern; this is attributed to the existence of two drug conformations. The fluorescence of the drug in the second binding site of Tel21 shows slower decays within 150 ps. These timescales are consistent with electron transfer from the guanines to the excited drug, as favoured by the lower oxidation potential of the stacked guanines of G4 with respect to those in the duplex.
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Affiliation(s)
- Pascale Changenet-Barret
- LIDYL, CEA, CNRS, Université Paris Saclay, F-91191, Gif-sur-Yvette, France. .,LOB, CNRS, INSERM, Université Paris Saclay, 91128, Palaiseau, France.
| | - Thomas Gustavsson
- LIDYL, CEA, CNRS, Université Paris Saclay, F-91191, Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris Saclay, F-91191, Gif-sur-Yvette, France
| | - Ilse Manet
- Istituto per la Sintesi Organica e la Fotoreattività, CNR, via P. Gobetti 101, 40129, Bologna, Italy.
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137
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Debnath M, Ghosh S, Panda D, Bessi I, Schwalbe H, Bhattacharyya K, Dash J. Small molecule regulated dynamic structural changes of human G-quadruplexes. Chem Sci 2016; 7:3279-3285. [PMID: 29997820 PMCID: PMC6006475 DOI: 10.1039/c6sc00057f] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/02/2016] [Indexed: 01/26/2023] Open
Abstract
A carbazole derivative (BTC) regulates the dynamics of unstructured human c-MYC and h-TELO sequences by folding them into compact quadruplex structures.
The changes in structure and dynamics of oncogenic (c-MYC) and telomeric (h-TELO) G-rich DNA sequences due to the binding of a novel carbazole derivative (BTC) are elucidated using single-molecule Förster resonance energy transfer (sm-FRET), fluorescence correlation spectroscopy (FCS) and NMR spectroscopy. In contrast to the previous reports on the binding of ligands to pre-folded G-quadruplexes, this work illustrates how ligand binding changes the conformational equilibria of both unstructured G-rich DNA sequences and K+-folded G-quadruplexes. The results demonstrate that K+ free c-MYC and h-TELO exist as unfolded and partially folded conformations. The binding of BTC shifts the equilibria of both investigated DNA sequences towards the folded G-quadruplex structure, increases the diffusion coefficients and induces faster end-to-end contact formation. BTC recognizes a minor conformation of the c-MYC quadruplex and the two-tetrad basket conformations of the h-TELO quadruplex.
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Affiliation(s)
- Manish Debnath
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Shirsendu Ghosh
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India
| | - Deepanjan Panda
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
| | - Irene Bessi
- Institute of Organic Chemistry and Chemical Biology , Goethe University Frankfurt and Center for Biomolecular Magnetic Resonance (BMRZ) , Max-von-Laue Strasse 7 , 60438 , Frankfurt am Main , Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology , Goethe University Frankfurt and Center for Biomolecular Magnetic Resonance (BMRZ) , Max-von-Laue Strasse 7 , 60438 , Frankfurt am Main , Germany
| | - Kankan Bhattacharyya
- Department of Physical Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India
| | - Jyotirmayee Dash
- Department of Organic Chemistry , Indian Association for the Cultivation of Science , Jadavpur , Kolkata-700032 , India .
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138
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Felsenstein KM, Saunders LB, Simmons JK, Leon E, Calabrese DR, Zhang S, Michalowski A, Gareiss P, Mock BA, Schneekloth JS. Small Molecule Microarrays Enable the Identification of a Selective, Quadruplex-Binding Inhibitor of MYC Expression. ACS Chem Biol 2016; 11:139-48. [PMID: 26462961 PMCID: PMC4719142 DOI: 10.1021/acschembio.5b00577] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
![]()
The
transcription factor MYC plays a pivotal role in cancer initiation,
progression, and maintenance. However, it has proven difficult to
develop small molecule inhibitors of MYC. One attractive route to
pharmacological inhibition of MYC has been the prevention of its expression
through small molecule-mediated stabilization of the G-quadruplex
(G4) present in its promoter. Although molecules that bind globally
to quadruplex DNA and influence gene expression are well-known, the
identification of new chemical scaffolds that selectively modulate
G4-driven genes remains a challenge. Here, we report an approach for
the identification of G4-binding small molecules using small molecule
microarrays (SMMs). We use the SMM screening platform to identify
a novel G4-binding small molecule that inhibits MYC expression in
cell models, with minimal impact on the expression of other G4-associated
genes. Surface plasmon resonance (SPR) and thermal melt assays demonstrated
that this molecule binds reversibly to the MYC G4 with single digit
micromolar affinity, and with weaker or no measurable binding to other
G4s. Biochemical and cell-based assays demonstrated that the compound
effectively silenced MYC transcription and translation via a G4-dependent
mechanism of action. The compound induced G1 arrest and was selectively
toxic to MYC-driven cancer cell lines containing the G4 in the promoter
but had minimal effects in peripheral blood mononucleocytes or a cell
line lacking the G4 in its MYC promoter. As a measure of selectivity,
gene expression analysis and qPCR experiments demonstrated that MYC
and several MYC target genes were downregulated upon treatment with
this compound, while the expression of several other G4-driven genes
was not affected. In addition to providing a novel chemical scaffold
that modulates MYC expression through G4 binding, this work suggests
that the SMM screening approach may be broadly useful as an approach
for the identification of new G4-binding small molecules.
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Affiliation(s)
- Kenneth M. Felsenstein
- Laboratory
of Cancer Biology and Genetics, National Cancer Institute, Building
37, Room 3146, Bethesda, Maryland 20892-4258, United States
- NCI/JHU Molecular Targets and Drug Discovery Program, Baltimore, Maryland, United States
| | - Lindsey B. Saunders
- Chemical
Biology Laboratory, National Cancer Institute, Building 376, Room 225C, P.O. Box B, Frederick, Maryland 21702-1201, United States
| | - John K. Simmons
- Laboratory
of Cancer Biology and Genetics, National Cancer Institute, Building
37, Room 3146, Bethesda, Maryland 20892-4258, United States
| | - Elena Leon
- Laboratory
of Cancer Biology and Genetics, National Cancer Institute, Building
37, Room 3146, Bethesda, Maryland 20892-4258, United States
- NCI/JHU Molecular Targets and Drug Discovery Program, Baltimore, Maryland, United States
| | - David R. Calabrese
- Chemical
Biology Laboratory, National Cancer Institute, Building 376, Room 225C, P.O. Box B, Frederick, Maryland 21702-1201, United States
| | - Shuling Zhang
- Laboratory
of Cancer Biology and Genetics, National Cancer Institute, Building
37, Room 3146, Bethesda, Maryland 20892-4258, United States
| | - Aleksandra Michalowski
- Laboratory
of Cancer Biology and Genetics, National Cancer Institute, Building
37, Room 3146, Bethesda, Maryland 20892-4258, United States
| | - Peter Gareiss
- Yale Center for Molecular Discovery, West Haven, Connecticut, United States
| | - Beverly A. Mock
- Laboratory
of Cancer Biology and Genetics, National Cancer Institute, Building
37, Room 3146, Bethesda, Maryland 20892-4258, United States
| | - John S. Schneekloth
- Chemical
Biology Laboratory, National Cancer Institute, Building 376, Room 225C, P.O. Box B, Frederick, Maryland 21702-1201, United States
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139
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Cheng M, Li Y, Zhou J, Jia G, Lu SM, Yang Y, Li C. Enantioselective sulfoxidation reaction catalyzed by a G-quadruplex DNA metalloenzyme. Chem Commun (Camb) 2016; 52:9644-7. [DOI: 10.1039/c6cc03016e] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Enantioselective sulfoxidation reaction is achieved for the first time by a human telomeric G-quadruplex DNA based biocatalyst.
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Affiliation(s)
- Mingpan Cheng
- State Key Laboratory of Catalysis
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Yinghao Li
- State Key Laboratory of Catalysis
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Jun Zhou
- State Key Laboratory of Catalysis
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Guoqing Jia
- State Key Laboratory of Catalysis
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Sheng-Mei Lu
- State Key Laboratory of Catalysis
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Yan Yang
- State Key Laboratory of Catalysis
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
| | - Can Li
- State Key Laboratory of Catalysis
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences
- Dalian 116023
- China
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140
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141
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Zhang Z, Wen JY, Lv BB, Li X, Ying X, Wang YJ, Zhang HT, Wang H, Liu HY, Chang CK. Photocytotoxicity and G-quadruplex DNA interaction of water-soluble gallium(III) tris(N
-methyl-4-pyridyl)corrole complex. Appl Organomet Chem 2015. [DOI: 10.1002/aoc.3408] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Zhao Zhang
- Department of Chemistry; South China University of Technology; Guangzhou 510640 PR China
| | - Jin-Yan Wen
- Department of Chemistry; South China University of Technology; Guangzhou 510640 PR China
| | - Biao-Biao Lv
- Department of Applied Physics; South China University of Technology; Guangzhou 510640 PR China
| | - Xu Li
- Department of Biochemistry and Molecular Biology; Guang Dong Medical University; Zhanjiang 524023 PR China
| | - Xiao Ying
- Department of Applied Physics; South China University of Technology; Guangzhou 510640 PR China
| | - Ya-Jun Wang
- Department of Biochemistry and Molecular Biology; Guang Dong Medical University; Zhanjiang 524023 PR China
| | - Hai-Tao Zhang
- Department of Biochemistry and Molecular Biology; Guang Dong Medical University; Zhanjiang 524023 PR China
| | - Hui Wang
- State Key Laboratory of Optoelectronics Materials and Technologies; Sun-Yat Sen University; Guangzhou 510275 China
| | - Hai-Yang Liu
- Department of Chemistry; South China University of Technology; Guangzhou 510640 PR China
- State Key Laboratory of Optoelectronics Materials and Technologies; Sun-Yat Sen University; Guangzhou 510275 China
| | - C.-K. Chang
- Department of Chemistry; Michigan State University; E. Lansing MI 48824 USA
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142
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Zhu J, Zhang L, Dong S, Wang E. How to split a G-quadruplex for DNA detection: new insight into the formation of DNA split G-quadruplex. Chem Sci 2015; 6:4822-4827. [PMID: 29142717 PMCID: PMC5667574 DOI: 10.1039/c5sc01287b] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 05/31/2015] [Indexed: 01/30/2023] Open
Abstract
Here, we get a new insight into the formation of a split G-quadruplex from the viewpoints of the split mode and guanine base number. An unusual result is that the split mode 4 : 8 performed best in six split modes, including the frequently used mode 1 : 3 and 2 : 2 in the split G-quadruplex enhanced fluorescence assay. Circular dichroism spectra verified the conclusion. The application of the split G-quadruplex based assay in DNA detection was performed on the point mutations of the JAK2 V617F and HBB genes. A multi-target analysis method based on a pool of G-segments split from T30695 (GGGTGGGTGGGTGGGT) by the magic "law of 4 : 8" was established.
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Affiliation(s)
- Jinbo Zhu
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun 130022 , P. R. China .
- University of Chinese Academy of Sciences , Beijing , 100049 , P. R. China
| | - Libing Zhang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun 130022 , P. R. China .
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun 130022 , P. R. China .
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun 130022 , P. R. China .
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143
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Zhang Q, Liu YC, Kong DM, Guo DS. Tetraphenylethene Derivatives with Different Numbers of Positively Charged Side Arms have Different Multimeric G-Quadruplex Recognition Specificity. Chemistry 2015; 21:13253-60. [DOI: 10.1002/chem.201501847] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Indexed: 01/10/2023]
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144
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Pyridostatins selectively recognize two different forms of the human telomeric G-quadruplex structures and their anti-tumor activities in vitro. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.05.081] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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145
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Human telomerase inhibitors from microbial source. World J Microbiol Biotechnol 2015; 31:1329-41. [DOI: 10.1007/s11274-015-1893-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/18/2015] [Indexed: 12/31/2022]
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146
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Shi S, Xu JH, Gao X, Huang HL, Yao TM. Binding Behaviors for Different Types of DNA G-Quadruplexes: Enantiomers of [Ru(bpy)2(L)](2+) (L=dppz, dppz-idzo). Chemistry 2015; 21:11435-45. [PMID: 26118412 DOI: 10.1002/chem.201501093] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Indexed: 11/11/2022]
Abstract
Polymorphic DNA G-quadruplex recognition has attracted great interest in recent years. The strong binding affinity and potential enantioselectivity of chiral [Ru(bpy)2 (L)](2+) (L=dipyrido[3,2-a:2',3'-c]phenazine, dppz-10,11-imidazolone; bpy=2,2'-bipyridine) prompted this investigation as to whether the two enantiomers, Δ and Λ, can show different effects on diverse structures with a range of parallel, antiparallel and mixed parallel/antiparallel G-quadruplexes. These studies provide a striking example of chiral-selective recognition of DNA G-quadruplexes. As for antiparallel (tel-Na(+)) basket G-quadruplex, the Λ enantiomers bind stronger than the Δ enantiomers. Moreover, the behavior reported here for both enantiomers stands in sharp contrast to B-DNA binding. The chiral selectivity toward mixed parallel/antiparallel (tel-K(+)) G-quadruplex of both compounds is weak. Different loop arrangements can change chiral complex selectivity for both antiparallel and mixed parallel/antiparallel G-quadruplex. Whereas both Δ and Λ isomers bind to parallel G-quadruplexes with comparable affinity, no appreciable stereoselective G-quadruplex binding of the isomers was observed. In addition, different binding stoichiometries and binding modes for Δ and Λ enantiomers were confirmed. The results presented here indicate that chiral selective G-quadruplex binding is not only related to G-quadruplex topology, but also to the sequence and the loop constitution.
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Affiliation(s)
- Shuo Shi
- Shanghai Key Laboratory of Chemical Assessment and Sustainability, Department of Chemistry, Tongji University, Shanghai, 200092 (P.R. China).
| | - Jin-Hong Xu
- Shanghai Key Laboratory of Chemical Assessment and Sustainability, Department of Chemistry, Tongji University, Shanghai, 200092 (P.R. China)
| | - Xing Gao
- Shanghai Key Laboratory of Chemical Assessment and Sustainability, Department of Chemistry, Tongji University, Shanghai, 200092 (P.R. China)
| | - Hai-Liang Huang
- Shanghai Key Laboratory of Chemical Assessment and Sustainability, Department of Chemistry, Tongji University, Shanghai, 200092 (P.R. China)
| | - Tian-Ming Yao
- Shanghai Key Laboratory of Chemical Assessment and Sustainability, Department of Chemistry, Tongji University, Shanghai, 200092 (P.R. China).
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147
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O'Day E, Le MTN, Imai S, Tan SM, Kirchner R, Arthanari H, Hofmann O, Wagner G, Lieberman J. An RNA-binding Protein, Lin28, Recognizes and Remodels G-quartets in the MicroRNAs (miRNAs) and mRNAs It Regulates. J Biol Chem 2015; 290:17909-17922. [PMID: 26045559 DOI: 10.1074/jbc.m115.665521] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Indexed: 01/01/2023] Open
Abstract
Lin28 is an evolutionarily conserved RNA-binding protein that inhibits processing of pre-let-7 microRNAs (miRNAs) and regulates translation of mRNAs that control developmental timing, pluripotency, metabolism, and tumorigenesis. The RNA features that mediate Lin28 binding to the terminal loops of let-7 pre-miRNAs and to Lin28-responsive elements (LREs) in mRNAs are not well defined. Here we show that Lin28 target datasets are enriched for RNA sequences predicted to contain stable planar structures of 4 guanines known as G-quartets (G4s). The imino NMR spectra of pre-let-7 loops and LREs contain resonances characteristic of G4 hydrogen bonds. These sequences bind to a G4-binding fluorescent dye, N-methyl-mesoporphyrin IX (NMM). Mutations and truncations in the RNA sequence that prevent G4 formation also prevent Lin28 binding. The addition of Lin28 to a pre-let-7 loop or an LRE reduces G4 resonance intensity and NMM binding, suggesting that Lin28 may function to remodel G4s. Further, we show that NMM inhibits Lin28 binding. Incubation of a human embryonal carcinoma cell line with NMM reduces its stem cell traits. In particular it increases mature let-7 levels, decreases OCT4, HMGA1, CCNB1, CDK4, and Lin28A protein, decreases sphere formation, and inhibits colony formation. Our results suggest a previously unknown structural feature of Lin28 targets and a new strategy for manipulating Lin28 function.
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Affiliation(s)
- Elizabeth O'Day
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115; Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, Massachusetts 02115
| | - Minh T N Le
- Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, Massachusetts 02115
| | - Shunsuke Imai
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Shen Mynn Tan
- Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, Massachusetts 02115
| | - Rory Kirchner
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115
| | - Haribabu Arthanari
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115
| | - Oliver Hofmann
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115
| | - Gerhard Wagner
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115.
| | - Judy Lieberman
- Cellular and Molecular Medicine Program, Boston Children's Hospital, Boston, Massachusetts 02115.
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148
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Richardson BG, Jain AD, Speltz TE, Moore TW. Non-electrophilic modulators of the canonical Keap1/Nrf2 pathway. Bioorg Med Chem Lett 2015; 25:2261-8. [PMID: 25937010 PMCID: PMC4643947 DOI: 10.1016/j.bmcl.2015.04.019] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 04/07/2015] [Accepted: 04/08/2015] [Indexed: 12/30/2022]
Abstract
Nrf2 is the major transcription factor that regulates many of the cytoprotective enzymes involved in the adaptive stress response. Modulation of Nrf2 could be therapeutically useful in a number of disease states. Activation can occur through either an electrophilic or non-electrophilic mechanism. To date, most of the research has focused on electrophilic Nrf2 activators, but there is increasing interest in non-electrophilic modulators of Nrf2. This Digest examines the current selection of small molecules that modulate Nrf2 through non-electrophilic mechanisms, and it highlights new opportunities for this important therapeutic target.
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Affiliation(s)
- B G Richardson
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, 833 S. Wood St., Chicago, IL 60612, United States
| | - A D Jain
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, 833 S. Wood St., Chicago, IL 60612, United States
| | - T E Speltz
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, 833 S. Wood St., Chicago, IL 60612, United States
| | - T W Moore
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, 833 S. Wood St., Chicago, IL 60612, United States; University of Illinois Cancer Center, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL 60612, United States.
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149
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Sun D, Liu Y, Yu Q, Liu D, Zhou Y, Liu J. Selective nuclei accumulation of ruthenium(II) complex enantiomers that target G-quadruplex DNA. J Inorg Biochem 2015; 150:90-9. [PMID: 25911217 DOI: 10.1016/j.jinorgbio.2015.04.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/02/2015] [Accepted: 04/02/2015] [Indexed: 12/26/2022]
Abstract
Different enantiomers exhibit large differences in their biological activity and/or toxicity, but they rarely involve the relationship of the agents for molecular and cellular imaging with the chiral structure of ruthenium complexes. Here, we report that an enantiomer of a polypyridyl ruthenium complex can selectively accumulate in the nucleus of HepG2 cells. Confocal laser scanning microscopy studies show that this phenomenon occurs via a non-endocytotic, but temperature-dependent, mechanism of cellular uptake in HepG2 cells. DNA oligonucleotides with repetitive tracts of guanine bases that can form G-quadruplex structures have aroused interest as therapeutic agents and as targets for anticancer drug design. Various biophysical techniques show that the Λ-enantiomer of ruthenium complexes can selectively stabilize human telomeric G-quadruplex DNA and has a strong preference for G-quadruplex over duplex DNA. Judged from the NMR results, we speculate that at higher 4:1 ligand/G-quadruplex stoichiometry, complex Λ-Ru is likely to bind with each groove of the tetraplex in a dimeric form or intercalate with the G-tetrad in the 3' terminal face and coexist with other modes. The molecular modeling analysis is in agreement with the NMR titrations performed in this investigation indicating that ruthenium complexes are actually characterized by a mixed binding mode. The results provide many opportunities for the development of novel agents for living cell-related studies.
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Affiliation(s)
- Dongdong Sun
- School of life sciences, Anhui Agricultural University, Hefei 230036, China
| | - Yanan Liu
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Qianqian Yu
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Du Liu
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Yanhui Zhou
- Department of Chemistry, Jinan University, Guangzhou 510632, China
| | - Jie Liu
- Department of Chemistry, Jinan University, Guangzhou 510632, China.
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150
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Lavrado J, Ohnmacht SA, Correia I, Leitão C, Pisco S, Gunaratnam M, Moreira R, Neidle S, Santos DJVAD, Paulo A. Indolo[3,2-c]quinoline G-quadruplex stabilizers: a structural analysis of binding to the human telomeric G-quadruplex. ChemMedChem 2015; 10:836-49. [PMID: 25820698 DOI: 10.1002/cmdc.201500067] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/04/2015] [Indexed: 12/22/2022]
Abstract
A library of 5-methylindolo[3,2-c]quinolones (IQc) with various substitution patterns of alkyldiamine side chains were evaluated for G-quadruplex (G4) binding mode and efficiency. Fluorescence resonance energy transfer melting assays showed that IQcs with a positive charge in the heteroaromatic nucleus and two weakly basic side chains are potent and selective human telomeric (HT) and gene promoter G4 stabilizers. Spectroscopic studies with HT G4 as a model showed that an IQc stabilizing complex involves the binding of two IQc molecules (2,9-bis{[3-(diethylamino)propyl]amino}-5-methyl-11H-indolo[3,2-c]quinolin-5-ium chloride, 3 d) per G4 unit, in two non-independent but equivalent binding sites. Molecular dynamics studies suggest that end-stacking of 3 d induces a conformational rearrangement in the G4 structure, driving the binding of a second 3 d ligand to a G4 groove. Modeling studies also suggest that 3 d, with two three-carbon side chains, has the appropriate geometry to participate in direct or water-mediated hydrogen bonding to the phosphate backbone and/or G4 loops, assisted by the terminal nitrogen atoms of the side chains. Additionally, antiproliferative studies showed that IQc compounds 2 d (2-{[3-(diethylamino)propyl]amino}-5-methyl-11H-indolo[3,2-c]quinolin-5-ium chloride) and 3 d are 7- to 12-fold more selective for human malignant cell lines than for nonmalignant fibroblasts.
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Affiliation(s)
- João Lavrado
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisbon (Portugal).
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