1
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Dong Y, Hu MH. Discovery of a minimalistic DIE-based fluorescent probe for detection of parallel G-quadruplex forms. Bioorg Chem 2023; 141:106879. [PMID: 37748327 DOI: 10.1016/j.bioorg.2023.106879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 09/27/2023]
Abstract
G-quadruplexes (G4s) are considered to be involved in some key biological processes, leading to the development of a large number of G4 fluorescent probes, which offer possibilities to study G4 dynamics as well as their biological roles. However, the structures of G4s show high polymorphism, which can be classified into parallel, hybrid and antiparallel forms, and the probes targeting a certain topology are limited. In this study, we have developed a minimalistic fluorescent probe by exploiting the disaggregation-induced emission (DIE) principle. The further studies demonstrated that this probe exhibited promising selectivity toward parallel DNA and RNA G4 forms in vitro. Moreover, it was found that this probe could be applied to map the RNA G4s that always form into parallel topologies in live cells, which distinguished it from other reported DIE-based probes that often targeted the mitochondrial or nuclear DNA G4s. To the best of our knowledge, this was the first DIE-based fluorescent probe for mapping cellular RNA G4s.
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Affiliation(s)
- Yun Dong
- School of Pharmacy and Food Sciences, Zhuhai College of Science and Technology, Zhuhai 519041, China; Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmacy, Shenzhen University Medical School, Shenzhen 518060, China
| | - Ming-Hao Hu
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmacy, Shenzhen University Medical School, Shenzhen 518060, China.
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2
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Li JH, You PD, Lu F, Tang HY, Guo HY, Zhou CQ. NIR C-Myc Pu22 G-quadruplex probe as a photosensitizer for bioimaging and antitumor study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 294:122533. [PMID: 36842212 DOI: 10.1016/j.saa.2023.122533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/05/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
Despite the fact that C-Myc G-quadruplex in the oncogene promoter regions is one of the crucial targets of antitumor drugs, the selectivities and proliferation inhibitions of its probes towards tumor cells remain a big challenge. Until now, no effective C-Myc G-quadruplex probes have been reported as a photosensitizer to increase their antitumor activities. Here, the first NIR C-Myc G-quadruplex probe PDS-SQ has been designed, comprising a G-quadruplex binder PDS and a squaraine dye SQ as a photosensitizer. Conjugate PDS-SQ could selectively NIR image C-Myc Pu22 G-quadruplex in tumor cells, and show stronger antitumor activity in the irradiation by a chemo-photodynamic method than in the dark. The study provides a new way to develop the novel NIR C-Myc G-quadruplex probes with more potent antitumor activities.
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Affiliation(s)
- Jun-Hui Li
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Pei-Dan You
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Fei Lu
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Hao-Yun Tang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Hong-Yan Guo
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Chun-Qiong Zhou
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China.
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3
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Wang XD, Wang JX, Yu BY, Zhang SQ, Hu MH. Non-fused imidazole-biphenyl analogs repress triple-negative breast cancer growth by mainly stabilizing the c-MYC G-quadruplex via a multi-site binding mode. Bioorg Med Chem 2023; 88-89:117336. [PMID: 37209638 DOI: 10.1016/j.bmc.2023.117336] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 05/08/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023]
Abstract
As oncogene c-MYC is abnormally expressed during TNBC pathogenesis, stabilizing its promoter G-quadruplex (G4), which may thus inhibit c-MYC expression and promote DNA damage, may be a potential anti-TNBC strategy. However, large quantities of potential G4-forming sites exist in the human genome, which represents a potential drug selectivity problem. In order to achieve better recognition for c-MYC G4, we herein presented a new approach of designing small-molecule ligands by linking tandem aromatic rings with the c-MYC G4 selective binding motifs. Thus, a series of non-fused, conformation-tunable imidazole-biphenyl analogs were designed and synthesized. Among them, the optimal ligand appeared more effective on stabilizing c-MYC G4 than other types of G4s possibly through an adaptive, multi-site binding mode involved of end-stacking, groove-binding and loop-interacting. Then, the optimal ligand exerted good inhibitory activity on c-MYC expression and induced remarkable DNA damage, leading to the occurrence of G2/M phase arrest, apoptosis and autophagy. Furthermore, the optimal ligand exhibited potent antitumor effects in a TNBC xenograft tumor model. To sum up, this work offers new insights for the development of selective c-MYC G4 ligands against TNBC.
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Affiliation(s)
- Xiao-Dong Wang
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmacy, Shenzhen University Medical School, Shenzhen 518060, China
| | - Jia-Xin Wang
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmacy, Shenzhen University Medical School, Shenzhen 518060, China
| | - Bing-Ying Yu
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmacy, Shenzhen University Medical School, Shenzhen 518060, China
| | - Shu-Quan Zhang
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmacy, Shenzhen University Medical School, Shenzhen 518060, China
| | - Ming-Hao Hu
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmacy, Shenzhen University Medical School, Shenzhen 518060, China.
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4
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Stężycka O, Frańska M, Beszterda-Buszczak M. Exploring Glycosylated Soy Isoflavones Affinities toward G-tetrads as Studied by Survival Yield Method. Chemphyschem 2023; 24:e202300056. [PMID: 36861944 DOI: 10.1002/cphc.202300056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/17/2023] [Indexed: 03/03/2023]
Abstract
Taking soy-based food supplements for menopausal symptoms by women may reduce the risk of cancer. Therefore, the interaction between nucleic acids (or their constituents) and ingredients of the supplements, e. g., isoflavone glucosides, on the molecular level, has been of interest with respect to cancer therapy. In this work, the interaction between isoflavone glucosides and G-tetrads, namely [4G+Na]+ ions (G stands for guanosine or deoxyguanosine), were analyzed by using electrospray ionization-collision induced dissociation-mass spectrometry (ESI-CID-MS) and survival yields method. The strength of isoflavone glucosides-[4G+Na]+ interaction in the gas phase was determined from Ecom50 - the energy required to fragment 50 % of selected precursor ions. Glycitin-[4G+Na]+ interaction was found to be the strongest, and the interaction between isoflavone glucosides and guanosine tetrad was established to be stronger than that between isoflavone glucosides and deoxyguanosine tetrad.
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Affiliation(s)
- Olga Stężycka
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Magdalena Frańska
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Monika Beszterda-Buszczak
- Poznań University of Life Sciences, Department of Food Biochemistry and Analysis, Mazowiecka 48, 60-623, Poznań, Poland
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5
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Zhao L, Ahmed F, Zeng Y, Xu W, Xiong H. Recent Developments in G-Quadruplex Binding Ligands and Specific Beacons on Smart Fluorescent Sensor for Targeting Metal Ions and Biological Analytes. ACS Sens 2022; 7:2833-2856. [PMID: 36112358 DOI: 10.1021/acssensors.2c00992] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The G-quadruplex structure is crucial in several biological processes, including DNA replication, transcription, and genomic maintenance. G-quadruplex-based fluorescent probes have recently gained popularity because of their ease of use, low cost, excellent selectivity, and sensitivity. This review summarizes the latest applications of G-quadruplex structures as detectors of genome-wide, enantioselective catalysts, disease therapeutics, promising drug targets, and smart fluorescence probes. In every section, sensing of G-quadruplex and employing G4 for the detection of other analytes were introduced, respectively. Since the discovery of the G-quadruplex structure, several studies have been conducted to investigate its conformations, biological potential, stability, reactivity, selectivity for chemical modification, and optical properties. The formation mechanism and advancements for detecting different metal ions (Na+, K+, Ag+, Tl+, Cu+/Cu2+, Hg2+, and Pb2+) and biomolecules (AMP, ATP, DNA/RNA, microRNA, thrombin, T4 PNK, RNase H, ALP, CEA, lipocalin 1, and UDG) using fluorescent sensors based on G-quadruplex modification, such as dye labels, artificial nucleobase moieties, dye complexes, intercalating dyes, and bioconjugated nanomaterials (AgNCs, GO, QDs, CDs, and MOF) is described herein. To investigate these extremely efficient responsive agents for diagnostic and therapeutic applications in medicine, fluorescence sensors based on G-quadruplexes have also been employed as a quantitative visualization technique.
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Affiliation(s)
- Long Zhao
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China.,College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Farid Ahmed
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Yating Zeng
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Weiqing Xu
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Hai Xiong
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, P. R. China
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6
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Zhao H, Wong HY, Ji D, Lyu K, Kwok CK. Novel L-RNA Aptamer Controls APP Gene Expression in Cells by Targeting RNA G-Quadruplex Structure. ACS APPLIED MATERIALS & INTERFACES 2022; 14:30582-30594. [PMID: 35762921 DOI: 10.1021/acsami.2c06390] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Guanine quadruplex (G4) structure is a four-stranded nucleic acid secondary structure motif with unique chemical properties and important biological roles. Amyloid precursor protein (APP) is an Alzheimer's disease (AD)-related gene, and recently, we reported the formation of RNA G4 (rG4) at the 3'UTR of APP mRNA and demonstrated its repressive role in translation. Herein, we apply rG4-SELEX to develop a novel L-RNA aptamer, L-Apt.8f, which binds to APP 3'UTR D-rG4 strongly with subnanomolar affinity. We structurally characterize the aptamer and find that it contains a thermostable and parallel G4 motif, and mutagenesis analysis identifies the key nucleotides that are involved in the target recognition. We also reveal that the L-Apt.8f-APP D-rG4 interaction is enantiomeric-, magnesium ion-, and potassium ion-dependent. Notably, L-Apt.8f preferentially recognizes APP rG4 over other structural motifs, and it can control the APP reporter gene and native transcript translation in cells. Our work introduces a novel strategy and reports a new L-aptamer candidate to target APP 3'UTR rG4 structure, which laid the foundation for further applying L-RNA as an important class of biomolecule for practical L-aptamer-based targeting and controlling of gene expression in cells.
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Affiliation(s)
- Haizhou Zhao
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR 999077, China
| | - Hei Yuen Wong
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR 999077, China
| | - Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR 999077, China
| | - Kaixin Lyu
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR 999077, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR 999077, China
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
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7
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Umar MI, Chan CY, Kwok CK. Development of RNA G-quadruplex (rG4)-targeting L-RNA aptamers by rG4-SELEX. Nat Protoc 2022; 17:1385-1414. [PMID: 35444329 DOI: 10.1038/s41596-022-00679-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 12/15/2021] [Indexed: 11/09/2022]
Abstract
RNA G-quadruplex (rG4)-SELEX is a method that generates L-RNA aptamers to target an rG4 structure of interest, which can be applied to inhibit G-quadruplex-mediated interactions that have important roles in gene regulation and function. Here we present a Protocol Extension substantially modifying an existing SELEX protocol to describe in detail the procedures involved in performing rG4-SELEX to identify rG4-specific binders that can effectively suppress rG4-peptide and rG4-protein associations. This Protocol Extension improves the speed of aptamer discovery and identification, offering a suite of techniques to characterize the aptamer secondary structure and monitor binding affinity and specificity, and demonstrating the utility of the L-RNA aptamer. The previous protocol mainly describes the identification of RNA aptamers against proteins of interest, whereas in this Protocol Extension we present the development of an unnatural RNA aptamer against an RNA structure of interest, with the potential to be applicable to other nucleic acid motifs or biomolecules. rG4-SELEX starts with a random D-RNA library incubated with the L-rG4 target of interest, followed by binding, washing and elution of the library. Enriched D-aptamer candidates are sequenced and structurally characterized. Then, the L-aptamer is synthesized and used for different applications. rG4-SELEX can be carried out by an experienced molecular biologist with a basic understanding of nucleic acids. The development of rG4-targeting L-RNA aptamers expands the current rG4 toolkit to explore innovative rG4-related applications, and opens new doors to discovering novel rG4 biology in the near future. The duration of each selection cycle as outlined in the protocol is ~2 d.
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Affiliation(s)
- Mubarak I Umar
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,RNA Molecular Biology Group, National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD, USA
| | - Chun-Yin Chan
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.,Institut für Chemische Epigenetik München (ICEM), Ludwig-Maximilians-Universtität München, Munich, Germany
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China. .,Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
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8
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Hu MH, Lin JH, Huang Q. Discovery of a fluorescent, long chain-bridged bispurine that selectively targets the c-MYC G-quadruplex. Bioorg Chem 2022; 122:105750. [PMID: 35325695 DOI: 10.1016/j.bioorg.2022.105750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/14/2022] [Accepted: 03/17/2022] [Indexed: 11/30/2022]
Abstract
G-quadruplexes (G4s) are special nucleic acid structures which are involved in the regulation of some key biological events like transcription and translation, which are now treated as promising therapeutic targets for cancers. Stabilizing the promoter G4 by small-molecule ligands can suppress the c-MYC oncogene transcription, thus inhibiting cancer cell proliferation. So far, targeting the very structure, a number of ligands have been reported. However, most of them showed unsatisfactory specificity to the c-MYC G4 over other G4s, resulting in uncertain side effects. In this contribution, we discovered a new class of bispurines bridged with flexible hydrocarbon chains, which presented somewhat selectivity to the c-MYC G4 possibly by adaptive binding, which then showed clear inhibition on the c-MYC expression rather than other G4-driven oncogenes. Moreover, these novel molecules had the potential to fluorescently label G4s. We believed that this study may shed light on the discovery of new functional small molecules targeting a specific G4 structure.
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Affiliation(s)
- Ming-Hao Hu
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen 518060, China; Shenzhen Key Laboratory for Nano-Biosensing Technology (ZDSYS20210112161400001), Shenzhen University Health Science Center, Shenzhen 518060, China.
| | - Jia-Hong Lin
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen 518060, China
| | - Qiong Huang
- Nation-Regional Engineering Lab for Synthetic Biology of Medicine, International Cancer Center, School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen 518060, China
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9
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Yu Z, Huang W, Shi L, Ke S, Xu S. Selective probes targeting c-MYC Pu22 G-quadruplex and their application in live mice imaging. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.09.087] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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Long W, Zheng BX, Li Y, Huang XH, Lin DM, Chen CC, Hou JQ, Ou TM, Wong WL, Zhang K, Lu YJ. Rational design of small-molecules to recognize G-quadruplexes of c-MYC promoter and telomere and the evaluation of their in vivo antitumor activity against breast cancer. Nucleic Acids Res 2022; 50:1829-1848. [PMID: 35166828 PMCID: PMC8887543 DOI: 10.1093/nar/gkac090] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 01/20/2022] [Accepted: 01/27/2022] [Indexed: 12/31/2022] Open
Abstract
DNA G4-structures from human c-MYC promoter and telomere are considered as important drug targets; however, the developing of small-molecule-based fluorescent binding ligands that are highly selective in targeting these G4-structures over other types of nucleic acids is challenging. We herein report a new approach of designing small molecules based on a non-selective thiazole orange scaffold to provide two-directional and multi-site interactions with flanking residues and loops of the G4-motif for better selectivity. The ligands are designed to establish multi-site interactions in the G4-binding pocket. This structural feature may render the molecules higher selectivity toward c-MYC G4s than other structures. The ligand–G4 interaction studied with 1H NMR may suggest a stacking interaction with the terminal G-tetrad. Moreover, the intracellular co-localization study with BG4 and cellular competition experiments with BRACO-19 may suggest that the binding targets of the ligands in cells are most probably G4-structures. Furthermore, the ligands that either preferentially bind to c-MYC promoter or telomeric G4s are able to downregulate markedly the c-MYC and hTERT gene expression in MCF-7 cells, and induce senescence and DNA damage to cancer cells. The in vivo antitumor activity of the ligands in MCF-7 tumor-bearing mice is also demonstrated.
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Affiliation(s)
- Wei Long
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, PR China
| | - Bo-Xin Zheng
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, PR China
| | - Ying Li
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, PR China
| | - Xuan-He Huang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, PR China
| | - Dan-Min Lin
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, PR China
| | - Cui-Cui Chen
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, PR China
| | - Jin-Qiang Hou
- Department of Chemistry, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario P7B 5E1, Canada.,Thunder Bay Regional Health Research Institute, 980 Oliver Road, Thunder Bay, Ontario P7B 6V4, Canada
| | - Tian-Miao Ou
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Wing-Leung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China
| | - Kun Zhang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, PR China.,School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P.R. China; International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, PR China
| | - Yu-Jing Lu
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, PR China
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11
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I. V. Ramos C, A. S. Almodôvar V, Candeias N, Santos T, Cruz C, Graça P. M. S. Neves M, Tomé AC. Diketopyrrolo[3,4–c]pyrrole derivative as a promising ligand for the stabilization of G-quadruplex DNA structures. Bioorg Chem 2022; 122:105703. [DOI: 10.1016/j.bioorg.2022.105703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 12/11/2022]
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12
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Takahashi S, Kotar A, Tateishi-Karimata H, Bhowmik S, Wang ZF, Chang TC, Sato S, Takenaka S, Plavec J, Sugimoto N. Chemical Modulation of DNA Replication along G-Quadruplex Based on Topology-Dependent Ligand Binding. J Am Chem Soc 2021; 143:16458-16469. [PMID: 34554731 DOI: 10.1021/jacs.1c05468] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Ligands that bind to and stabilize guanine-quadruplex (G4) structures to regulate DNA replication have therapeutic potential for cancer and neurodegenerative diseases. Because there are several G4 topologies, ligands that bind to their specific types may have the ability to preferentially regulate the replication of only certain genes. Here, we demonstrated that binding ligands stalled the replication of template DNA at G4, depending on different topologies. For example, naphthalene diimide derivatives bound to the G-quartet of G4 with an additional interaction between the ligand and the loop region of a hybrid G4 type from human telomeres, which efficiently repressed the replication of the G4. Thus, these inhibitory effects were not only stability-dependent but also topology-selective based on the manner in which G4 structures interacted with G4 ligands. Our original method, referred to as a quantitative study of topology-dependent replication (QSTR), was developed to evaluate correlations between replication rate and G4 stability. QSTR enabled the systematic categorization of ligands based on topology-dependent binding. It also demonstrated accuracy in determining quantitatively how G4 ligands control the intermediate state of replication and the kinetics of G4 unwinding. Hence, the QSTR index would facilitate the design of new drugs capable of controlling the topology-dependent regulation of gene expression.
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Affiliation(s)
- Shuntaro Takahashi
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Anita Kotar
- Slovenian NMR Center, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
| | - Hisae Tateishi-Karimata
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Sudipta Bhowmik
- Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
| | - Zi-Fu Wang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
| | - Ta-Chau Chang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan
| | - Shinobu Sato
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka 804-8550, Japan
| | - Shigeori Takenaka
- Department of Applied Chemistry, Kyushu Institute of Technology, Fukuoka 804-8550, Japan
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
| | - Naoki Sugimoto
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.,FIRST (Graduate School of Frontiers of Innovative Research in Science and Technology), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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13
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Oshchepkov AS, Reznichenko O, Xu D, Morozov BS, Granzhan A, Kataev EA. Dye-functionalized phosphate-binding macrocycles: from nucleotide to G-quadruplex recognition and "turn-on" fluorescence sensing. Chem Commun (Camb) 2021; 57:10632-10635. [PMID: 34581337 DOI: 10.1039/d1cc04096k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A novel strategy to design "turn-on" fluorescent receptors for G-quadruplexes of DNA is presented, which relies on the connection of phosphate binding macrocycles (PBM) with naphthalimide dyes. A new PBM-dye family was synthesized and evaluated in terms of binding and detection of nucleotides and DNA G-quadruplexes of different topologies.
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Affiliation(s)
- Aleksandr S Oshchepkov
- Department of Chemistry and Pharmacy, University Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany. .,Institute of Chemistry, Technische Universität Chemnitz, 09107 Chemnitz, Germany
| | - Oksana Reznichenko
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, Bât. 110, Centre Universitaire Paris Sud, F-91405 Orsay, France
| | - Dan Xu
- Institute of Chemistry, Technische Universität Chemnitz, 09107 Chemnitz, Germany
| | - Boris S Morozov
- Department of Chemistry and Pharmacy, University Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany. .,Institute of Chemistry, Technische Universität Chemnitz, 09107 Chemnitz, Germany
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, Bât. 110, Centre Universitaire Paris Sud, F-91405 Orsay, France
| | - Evgeny A Kataev
- Department of Chemistry and Pharmacy, University Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany. .,CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, Bât. 110, Centre Universitaire Paris Sud, F-91405 Orsay, France
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14
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Santos T, Salgado GF, Cabrita EJ, Cruz C. G-Quadruplexes and Their Ligands: Biophysical Methods to Unravel G-Quadruplex/Ligand Interactions. Pharmaceuticals (Basel) 2021; 14:769. [PMID: 34451866 PMCID: PMC8401999 DOI: 10.3390/ph14080769] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022] Open
Abstract
Progress in the design of G-quadruplex (G4) binding ligands relies on the availability of approaches that assess the binding mode and nature of the interactions between G4 forming sequences and their putative ligands. The experimental approaches used to characterize G4/ligand interactions can be categorized into structure-based methods (circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography), affinity and apparent affinity-based methods (surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and mass spectrometry (MS)), and high-throughput methods (fluorescence resonance energy transfer (FRET)-melting, G4-fluorescent intercalator displacement assay (G4-FID), affinity chromatography and microarrays. Each method has unique advantages and drawbacks, which makes it essential to select the ideal strategies for the biological question being addressed. The structural- and affinity and apparent affinity-based methods are in several cases complex and/or time-consuming and can be combined with fast and cheap high-throughput approaches to improve the design and development of new potential G4 ligands. In recent years, the joint use of these techniques permitted the discovery of a huge number of G4 ligands investigated for diagnostic and therapeutic purposes. Overall, this review article highlights in detail the most commonly used approaches to characterize the G4/ligand interactions, as well as the applications and types of information that can be obtained from the use of each technique.
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Affiliation(s)
- Tiago Santos
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal;
| | - Gilmar F. Salgado
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR 5320, IECB, 33607 Pessac, France;
| | - Eurico J. Cabrita
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal;
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Carla Cruz
- CICS-UBI—Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal;
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15
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Molecular engineering of a near-infrared fluorescent ligand for tracking mitochondrial DNA G-quadruplexes. Anal Chim Acta 2021; 1169:338600. [PMID: 34088367 DOI: 10.1016/j.aca.2021.338600] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/28/2021] [Accepted: 04/29/2021] [Indexed: 11/22/2022]
Abstract
G-quadruplexes are supposed to exist in mitochondrial DNA, which may participate in the regulation of mitochondrial metabolism. However, their formation dynamics and cellular roles are still unknown, calling for the development of promising small-molecule fluorescent probes for detecting mitochondrial DNA (mtDNA) G4s in live cells. In this study, we engineered a NIR fluorescent probe termed IZIN-1 by conjugating a typical G4 ligand and a mitochondrion-targeting AIE luminogen, which was then found to be able to emit NIR fluorescence by binding to mtDNA G4s via a distinctive mode. Cell-based experiments demonstrated that IZIN-1 may track mtDNA G4 formation in live cells. Collectively, this work provides a promising example about how to design a fluorescent probe targeting mtDNA G4s, and also offers a feasible chemical tool for investigating mtDNA G4s in live cells.
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16
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Paul R, Dutta D, Das T, Debnath M, Dash J. G4 Sensing Pyridyl-Thiazole Polyamide Represses c-KIT Expression in Leukemia Cells. Chemistry 2021; 27:8590-8599. [PMID: 33851760 DOI: 10.1002/chem.202100907] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Indexed: 12/27/2022]
Abstract
Specific sensing and functional tuning of nucleic acid secondary structures remain less explored to date. Herein, we report a thiazole polyamide TPW that binds specifically to c-KIT1 G-quadruplex (G4) with sub-micromolar affinity and ∼1 : 1 stoichiometry and represses c-KIT proto-oncogene expression. TPW shows up to 10-fold increase in fluorescence upon binding with c-KIT1 G4, but shows weak or no quantifiable binding to other G4s and ds26 DNA. TPW can increase the number of G4-specific antibody (BG4) foci and mark G4 structures in cancer cells. Cell-based assays reveal that TPW can efficiently repress c-KIT expression in leukemia cells via a G4-dependent process. Thus, the polyamide can serve as a promising probe for G-quadruplex recognition with the ability to specifically alter c-KIT oncogene expression.
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Affiliation(s)
- Raj Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Debasish Dutta
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Tania Das
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Manish Debnath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India
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17
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Sun R, Guo X, Yang D, Tang Y, Lu J, Sun H. c-Myc G-quadruplex is sensitively and specifically recognized by a fluorescent probe. Talanta 2021; 226:122125. [PMID: 33676679 DOI: 10.1016/j.talanta.2021.122125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 10/22/2022]
Abstract
The G-quadruplex structure formed by the c-myc gene sequence has attracted much attention due to its important physiological function in biology and wide application in nanotechnology. So far, probes capable of recognition of c-myc G-quadruplex with both high specificity and sensitivity are still scarce. This work presented a cyanine dye fluorescent probe named Cy-1, which has almost no fluorescence in aqueous solution, but showing more than 1000-fold fluorescence enhancement for recognizing c-myc G-quadruplex. Cy-1 also has good specificity and can selectively recognize c-myc G-quadruplex from other a variety of G-quadruplex and non-G-quadruplex structures. These properties make Cy-1 a promising probe for c-myc G-quadruplex recognition in nanotechnology or biology.
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Affiliation(s)
- Ranran Sun
- School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, 201620, PR China; Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Xiaomeng Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Dawei Yang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Jie Lu
- School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, 201620, PR China.
| | - Hongxia Sun
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, PR China.
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18
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Liu X, Liu N, Deng Y, Wang S, Liu T, Tang Y, Chen Y, Lu J. A luminescence probe for c‐myc G‐quadruplex by a triphenylamine‐appended ruthenium complex. Appl Organomet Chem 2021. [DOI: 10.1002/aoc.6143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xue‐Wen Liu
- Hunan Province Cooperative Innovation Centre for the Construction & Development of Dongting Lake Ecological Economic Zone, Hunan Provincial Key Laboratory of Water Treatment Functional Materials, Hunan Province Engineering Research Centre of Electroplating Wastewater Reuse Technology, College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde China
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering Nanjing University Nanjing China
| | - Ning‐Yi Liu
- Hunan Province Cooperative Innovation Centre for the Construction & Development of Dongting Lake Ecological Economic Zone, Hunan Provincial Key Laboratory of Water Treatment Functional Materials, Hunan Province Engineering Research Centre of Electroplating Wastewater Reuse Technology, College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde China
| | - Yuan‐Qing Deng
- Hunan Province Cooperative Innovation Centre for the Construction & Development of Dongting Lake Ecological Economic Zone, Hunan Provincial Key Laboratory of Water Treatment Functional Materials, Hunan Province Engineering Research Centre of Electroplating Wastewater Reuse Technology, College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde China
| | - Shan Wang
- Hunan Province Cooperative Innovation Centre for the Construction & Development of Dongting Lake Ecological Economic Zone, Hunan Provincial Key Laboratory of Water Treatment Functional Materials, Hunan Province Engineering Research Centre of Electroplating Wastewater Reuse Technology, College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde China
| | - Ting Liu
- Hunan Province Cooperative Innovation Centre for the Construction & Development of Dongting Lake Ecological Economic Zone, Hunan Provincial Key Laboratory of Water Treatment Functional Materials, Hunan Province Engineering Research Centre of Electroplating Wastewater Reuse Technology, College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde China
| | - Yu‐Cai Tang
- Hunan Province Cooperative Innovation Centre for the Construction & Development of Dongting Lake Ecological Economic Zone, Hunan Provincial Key Laboratory of Water Treatment Functional Materials, Hunan Province Engineering Research Centre of Electroplating Wastewater Reuse Technology, College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde China
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering Nanjing University Nanjing China
| | - Yuan‐Dao Chen
- Hunan Province Cooperative Innovation Centre for the Construction & Development of Dongting Lake Ecological Economic Zone, Hunan Provincial Key Laboratory of Water Treatment Functional Materials, Hunan Province Engineering Research Centre of Electroplating Wastewater Reuse Technology, College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde China
| | - Ji‐Lin Lu
- Hunan Province Cooperative Innovation Centre for the Construction & Development of Dongting Lake Ecological Economic Zone, Hunan Provincial Key Laboratory of Water Treatment Functional Materials, Hunan Province Engineering Research Centre of Electroplating Wastewater Reuse Technology, College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde China
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering Nanjing University Nanjing China
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19
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Yu QQ, Gao JJ, Lang XX, Li HY, Wang MQ. Microenvironment-Sensitive Fluorescent Ligand Binds Ascaris Telomere Antiparallel G-Quadruplex DNA with Blue-Shift and Enhanced Emission. Chembiochem 2020; 22:1042-1048. [PMID: 33140570 DOI: 10.1002/cbic.202000671] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/02/2020] [Indexed: 11/10/2022]
Abstract
The development of small molecules that can selectively target G-quadruplex (G4) DNAs has drawn considerable attention due to their unique physiological and pathological functions. However, only a few molecules have been found to selectively bind a particular G4 DNA structure. We have developed a fluorescence ligand Q1, a molecular scaffold with a carbazole-pyridine core bridged by a phenylboronic acid side chain, that acts as a selective ascaris telomere antiparallel G4 DNA ASC20 ligand with about 18 nm blue-shifted and enhanced fluorescence intensity. Photophysical properties revealed that Q1 was sensitive to the microenvironment and gave the best selectivity to ASC20 with an equilibrium binding constant Ka =6.04×105 M-1 . Time-resolved fluorescence studies also demonstrated that Q1 showed a longer fluorescence lifetime in the presence of ASC20. The binding characteristics of Q1 with ASC20 were shown in detail in a fluorescent intercalator displacement (FID) assay, a 2-Ap titration experiment and by molecular docking. Ligand Q1 could adopt an appropriate pose at terminal G-quartets of ASC20 through multiple interactions including π-π stacking between aromatic rings; this led to strong fluorescence enhancement. In addition, a co-staining image showed that Q1 is mainly distributed in the cytoplasm. Accordingly, this work provides insights for the development of ligands that selectively targeting a specific G4 DNA structure.
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Affiliation(s)
- Quan-Qi Yu
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, P. R. China
| | - Juan-Juan Gao
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, P. R. China
| | - Xue-Xian Lang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, P. R. China
| | - Hong-Yao Li
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, P. R. China
| | - Ming-Qi Wang
- School of Pharmacy, Jiangsu University, Zhenjiang, 212013, P. R. China
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20
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Suseela YV, Satha P, Murugan NA, Govindaraju T. Recognition of G-quadruplex topology through hybrid binding with implications in cancer theranostics. Theranostics 2020; 10:10394-10414. [PMID: 32929356 PMCID: PMC7482797 DOI: 10.7150/thno.48675] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 07/09/2020] [Indexed: 12/19/2022] Open
Abstract
The selective recognition and imaging of oncogene specific G-quadruplex (GQ) structures holds great promise in the development of diagnostic therapy (theranostics) for cancer and has been challenging due to their structural dynamics and diversity. We report selective recognition of GQ by a small molecule through unique hybrid loop stacking and groove binding mode with turn on far-red fluorescence response and anticancer activity demonstrating the potential implications for GQ-targeted cancer theranostics. Methods: Biophysical investigation reveal the turn on far-red emission property of TGP18 for selective recognition of GQ. In cellulo studies including DNA damage and oxidative stress evaluation guided us to perform in vitro (3D spheroid) and in vivo (xenograft mice model) anti-cancer activity, and tumor tissue imaging to assess the theranostic potential of TGP18. Results: Neocuproine-based far-red turn on fluorescence probe TGP18 shows GQ-to-duplex selectivity and specifically recognizes BCL-2 GQ with high affinity through a unique hybrid binding mode involving loop-stacking and groove interactions. Our study reveals that the selective recognition originating from the distinct loop structure of GQ that alters the overall probe interaction and binding affinity. TGP18 binding to anti-apoptotic BCL-2 GQ ablates the pro-survival function and elicit anti-cancer activity by inducing apoptosis in cancer cells. We deciphered that inhibition of BCL-2 transcription synergized with signaling cascade of nucleolar stress, DNA damage and oxidative stress in triggering apoptosis signaling pathway. Conclusion: Intervention of GQ mediated lethality by TGP18 has translated into anti-cancer activity in both in vitro 3D spheroid culture and in vivo xenograft models of lung and breast cancer with superior efficacy for the former. In vivo therapeutic efficacy supplemented with tumor 3D spheroid and tissue imaging potential define the role of TGP18 in GQ-targeted cancer theranostics.
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21
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Human MYC G-quadruplex: From discovery to a cancer therapeutic target. Biochim Biophys Acta Rev Cancer 2020; 1874:188410. [PMID: 32827579 DOI: 10.1016/j.bbcan.2020.188410] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023]
Abstract
Overexpression of the MYC oncogene is a molecular hallmark of both cancer initiation and progression. Targeting MYC is a logical and effective cancer therapeutic strategy. A special DNA secondary structure, the G-quadruplex (G4), is formed within the nuclease hypersensitivity element III1 (NHE III1) region, located upstream of the MYC gene's P1 promoter that drives the majority of its transcription. Targeting such G4 structures has been a focus of anticancer therapies in recent decades. Thus, a comprehensive review of the MYC G4 structure and its role as a potential therapeutic target is timely. In this review, we first outline the discovery of the MYC G4 structure and evidence of its formation in vitro and in cells. Then, we describe the functional role of G4 in regulating MYC gene expression. We also summarize three types of MYC G4-interacting proteins that can promote, stabilize and unwind G4 structures. Finally, we discuss G4-binding molecules and the anticancer activities of G4-stabilizing ligands, including small molecular compounds and peptides, and assess their potential as novel anticancer therapeutics.
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22
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Deiana M, Chand K, Jamroskovic J, Das RN, Obi I, Chorell E, Sabouri N. A site-specific self-assembled light-up rotor probe for selective recognition and stabilization of c-MYC G-quadruplex DNA. NANOSCALE 2020; 12:12950-12957. [PMID: 32525170 DOI: 10.1039/d0nr03404e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Direct and unambiguous evidence of the formation of G-quadruplexes (G4s) in human cells have shown their implication in several key biological events and has emphasized their role as important targets for small-molecule cancer therapeutics. Here, we report on the first example of a self-assembled molecular-rotor G4-binder able to discriminate between an extensive panel of G4 and non-G4 structures and to selectively light-up (up to 64-fold), bind (nanomolar range), and stabilize the c-MYC promoter G4 DNA. In particular, association with the c-MYC G4 triggers the disassembly of its supramolecular state (disaggregation-induced emission, DIE) and induces geometrical restrictions (motion-induced change in emission, MICE) leading to a significant enhancement of its emission yield. Moreover, this optical reporter is able to selectively stabilize the c-MYC G4 and inhibit DNA synthesis. Finally, by using confocal laser-scanning microscopy (CLSM) we show the ability of this compound to localize primarily in the subnuclear G4-rich compartments of cancer cells. This work provides a benchmark for the future design and development of a new generation of smart sequence-selective supramolecular G4-binders that combine outstanding sensing and stability properties, to be utilized in anti-cancer therapy.
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Affiliation(s)
- Marco Deiana
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden.
| | - Karam Chand
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden.
| | - Jan Jamroskovic
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden.
| | | | - Ikenna Obi
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden.
| | - Erik Chorell
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden.
| | - Nasim Sabouri
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden.
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23
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Liu X, Liu N, Deng Y, Wang S, Liu T, Tang Y, Chen Y, Lu J. An unexpected fluorescent probe for G‐quadruplex DNA based on a nitro‐substituted ruthenium (II) complex. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.5703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Xue‐Wen Liu
- Hunan Province Cooperative Innovation Center for the Construction & Development of Dongting Lake Ecological Economic Zone, Hunan Provincial Key Laboratory of Water Treatment Functional Materials, Hunan Province Engineering Research Center of Electroplating Wastewater Reuse Technology, College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde 415000 China
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 P. R. China
| | - Ning‐Yi Liu
- Hunan Province Cooperative Innovation Center for the Construction & Development of Dongting Lake Ecological Economic Zone, Hunan Provincial Key Laboratory of Water Treatment Functional Materials, Hunan Province Engineering Research Center of Electroplating Wastewater Reuse Technology, College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde 415000 China
| | - Yuan‐Qing Deng
- Hunan Province Cooperative Innovation Center for the Construction & Development of Dongting Lake Ecological Economic Zone, Hunan Provincial Key Laboratory of Water Treatment Functional Materials, Hunan Province Engineering Research Center of Electroplating Wastewater Reuse Technology, College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde 415000 China
| | - Shan Wang
- Hunan Province Cooperative Innovation Center for the Construction & Development of Dongting Lake Ecological Economic Zone, Hunan Provincial Key Laboratory of Water Treatment Functional Materials, Hunan Province Engineering Research Center of Electroplating Wastewater Reuse Technology, College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde 415000 China
| | - Ting Liu
- Hunan Province Cooperative Innovation Center for the Construction & Development of Dongting Lake Ecological Economic Zone, Hunan Provincial Key Laboratory of Water Treatment Functional Materials, Hunan Province Engineering Research Center of Electroplating Wastewater Reuse Technology, College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde 415000 China
| | - Yu‐Cai Tang
- Hunan Province Cooperative Innovation Center for the Construction & Development of Dongting Lake Ecological Economic Zone, Hunan Provincial Key Laboratory of Water Treatment Functional Materials, Hunan Province Engineering Research Center of Electroplating Wastewater Reuse Technology, College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde 415000 China
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 P. R. China
| | - Yuan‐Dao Chen
- Hunan Province Cooperative Innovation Center for the Construction & Development of Dongting Lake Ecological Economic Zone, Hunan Provincial Key Laboratory of Water Treatment Functional Materials, Hunan Province Engineering Research Center of Electroplating Wastewater Reuse Technology, College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde 415000 China
| | - Ji‐Lin Lu
- Hunan Province Cooperative Innovation Center for the Construction & Development of Dongting Lake Ecological Economic Zone, Hunan Provincial Key Laboratory of Water Treatment Functional Materials, Hunan Province Engineering Research Center of Electroplating Wastewater Reuse Technology, College of Chemistry and Materials Engineering Hunan University of Arts and Science Changde 415000 China
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering Nanjing University Nanjing 210023 P. R. China
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24
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25
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Zheng BX, She MT, Long W, Xu YY, Zhang YH, Huang XH, Liu W, Hou JQ, Wong WL, Lu YJ. A small-sized benzothiazole–indolium fluorescent probe: the study of interaction specificity targeting c-MYC promoter G-quadruplex structures and live cell imaging. Chem Commun (Camb) 2020; 56:15016-15019. [DOI: 10.1039/d0cc06525k] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A small-sized and target-specific fluorescent probe reveals the presence of c-MYC DNA G4-structures in cells and shows anticancer activity.
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Affiliation(s)
- Bo-Xin Zheng
- School of Biomedical and Pharmaceutical Sciences
- Guangdong University of Technology
- Guangzhou 510006
- P. R. China
| | - Meng-Ting She
- School of Biomedical and Pharmaceutical Sciences
- Guangdong University of Technology
- Guangzhou 510006
- P. R. China
| | - Wei Long
- School of Biomedical and Pharmaceutical Sciences
- Guangdong University of Technology
- Guangzhou 510006
- P. R. China
| | - Yong-Yu Xu
- School of Biomedical and Pharmaceutical Sciences
- Guangdong University of Technology
- Guangzhou 510006
- P. R. China
| | - Yi-Han Zhang
- School of Biomedical and Pharmaceutical Sciences
- Guangdong University of Technology
- Guangzhou 510006
- P. R. China
| | - Xuan-He Huang
- School of Biomedical and Pharmaceutical Sciences
- Guangdong University of Technology
- Guangzhou 510006
- P. R. China
| | - Wenjie Liu
- Department of Chemistry
- Lakehead University and Thunder Bay Regional Health Research Institute
- Thunder Bay
- Canada
| | - Jin-Qiang Hou
- Department of Chemistry
- Lakehead University and Thunder Bay Regional Health Research Institute
- Thunder Bay
- Canada
| | - Wing-Leung Wong
- State Key Laboratory of Chemical Biology and Drug Discovery
- Department of Applied Biology Chemical Technology
- The Hong Kong Polytechnic University
- Kowloon
- China
| | - Yu-Jing Lu
- School of Biomedical and Pharmaceutical Sciences
- Guangdong University of Technology
- Guangzhou 510006
- P. R. China
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26
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Paul R, Das T, Debnath M, Chauhan A, Dash J. G-Quadruplex-Binding Small Molecule Induces Synthetic Lethality in Breast Cancer Cells by Inhibiting c-MYC and BCL2 Expression. Chembiochem 2019; 21:963-970. [PMID: 31621996 DOI: 10.1002/cbic.201900534] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Indexed: 12/21/2022]
Abstract
Herein, a prolinamide-derived peptidomimetic that preferentially binds to c-MYC and BCL2 G-quadruplexes present in the promoter regions of apoptosis-related genes (c-MYC and BCL2) over other DNA quadruplexes are described. Biological assays, such as real-time quantitative reverse transcription, western blot, dual luciferase, and small interfering RNA knockdown assays, indicate that the ligand triggers a synthetic lethal interaction by simultaneously inhibiting the expression of c-MYC and BCL2 genes through their promoter G-quadruplexes. The ligand shows antiproliferative activity in MCF-7 cells that overexpress both MYC and BCL2 genes, in comparison to cells that overexpress either of the two. Moreover, the ligand induces S-phase cell-cycle arrest, DNA damage, and apoptosis in MCF-7 cells.
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Affiliation(s)
- Rakesh Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Tania Das
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Manish Debnath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Ajay Chauhan
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
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27
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Dhamodharan V, Pradeepkumar PI. Specific Recognition of Promoter G-Quadruplex DNAs by Small Molecule Ligands and Light-up Probes. ACS Chem Biol 2019; 14:2102-2114. [PMID: 31532996 DOI: 10.1021/acschembio.9b00475] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
G-Quadruplexes (G4s) are four-stranded nucleic acid structures whose underlying G-rich sequences are present across the chromosome and transcriptome. These highly structured elements are known to regulate many key biological functions such as replication, transcription, translation, and genomic stability, thereby providing an additional layer of gene regulation. G4s are structurally dynamic and diverse, and they can fold into numerous topologies. They are potential targets for small molecules, which can modulate their functions. To this end, myriad classes of small molecules have been developed and studied for their ability to bind and stabilize these unique structures. Though many of them can selectively target G4s over duplex DNA, only a few of them can distinguish one G4 topology from others. Design and development of G4-specific ligands are challenging owing to the subtle structural variations among G4 structures. However, screening assays and computational methods have identified a few classes of ligands that preferentially or specifically target the G4 topology of interest over others. This review focuses on the small molecules and fluorescent probes that specifically target human promoter G4s associated with oncogenes. Targeting promoter G4s could circumvent the issues such as undruggability and development of drug resistance associated with the protein targets. The ligands discussed here highlight that development of G4-specific ligands is an achievable goal in spite of the limited structural data available. The future goal is to pursue the development of G4-specific ligands endowed with drug-like properties for G4-based therapeutics and diagnostics.
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Affiliation(s)
- V. Dhamodharan
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
- Okinawa Institute of Science and Technology Graduate University, Okinawa 9040495, Japan
| | - P. I. Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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Umar MI, Ji D, Chan CY, Kwok CK. G-Quadruplex-Based Fluorescent Turn-On Ligands and Aptamers: From Development to Applications. Molecules 2019; 24:E2416. [PMID: 31262059 PMCID: PMC6650947 DOI: 10.3390/molecules24132416] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 06/17/2019] [Accepted: 06/24/2019] [Indexed: 02/08/2023] Open
Abstract
Guanine (G)-quadruplexes (G4s) are unique nucleic acid structures that are formed by stacked G-tetrads in G-rich DNA or RNA sequences. G4s have been reported to play significant roles in various cellular events in both macro- and micro-organisms. The identification and characterization of G4s can help to understand their different biological roles and potential applications in diagnosis and therapy. In addition to biophysical and biochemical methods to interrogate G4 formation, G4 fluorescent turn-on ligands can be used to target and visualize G4 formation both in vitro and in cells. Here, we review several representative classes of G4 fluorescent turn-on ligands in terms of their interaction mechanism and application perspectives. Interestingly, G4 structures are commonly identified in DNA and RNA aptamers against targets that include proteins and small molecules, which can be utilized as G4 tools for diverse applications. We therefore also summarize the recent development of G4-containing aptamers and highlight their applications in biosensing, bioimaging, and therapy. Moreover, we discuss the current challenges and future perspectives of G4 fluorescent turn-on ligands and G4-containing aptamers.
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Affiliation(s)
- Mubarak I Umar
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Danyang Ji
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun-Yin Chan
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China.
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Gangopadhyay A, Mahapatra AK. Phosgene invites selective switch-on fluorescence at ppm concentrations in a Betti base by hindering 2-way PET. NEW J CHEM 2019. [DOI: 10.1039/c9nj02541c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phosgene ignites a decisive and immediate fluorescence response in a simple Betti base.
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Affiliation(s)
- Ankita Gangopadhyay
- Department of Chemistry
- Indian Institute of Engineering Science and Technology (formerly Bengal Engineering and Science University) Shibpur
- Howrah
- India
| | - Ajit Kumar Mahapatra
- Department of Chemistry
- Indian Institute of Engineering Science and Technology (formerly Bengal Engineering and Science University) Shibpur
- Howrah
- India
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