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Xiao C, Li Y, Liu Y, Dong R, He X, Lin Q, Zang X, Wang K, Xia Y, Kong L. Overcoming Cancer Persister Cells by Stabilizing the ATF4 Promoter G-quadruplex. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401748. [PMID: 38994891 DOI: 10.1002/advs.202401748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 06/23/2024] [Indexed: 07/13/2024]
Abstract
Persister cells (PS) selected for anticancer therapy have been recognized as a significant contributor to the development of treatment-resistant malignancies. It is found that imposing glutamine restriction induces the generation of PS, which paradoxically bestows heightened resistance to glutamine restriction treatment by activating the integrated stress response and initiating the general control nonderepressible 2-activating transcription factor 4-alanine, serine, cysteine-preferring transporter 2 (GCN2-ATF4-ASCT2) axis. Central to this phenomenon is the stress-induced ATF4 translational reprogramming. Unfortunately, directly targeting ATF4 protein has proven to be a formidable challenge because of its flat surface. Nonetheless, a G-quadruplex structure located within the promoter region of ATF4 (ATF4-G4) is uncovered and resolved, which functions as a transcriptional regulator and can be targeted by small molecules. The investigation identifies the natural compound coptisine (COP) as a potent binder that interacts with and stabilizes ATF4-G4. For the first time, the high-resolution structure of the COP-ATF4-G4 complex is determined. The formation of this stable complex disrupts the interaction between transcription factor AP-2 alpha (TFAP2A) and ATF4-G4, resulting in a substantial reduction in intracellular ATF4 levels and the eventual death of cancer cells. These seminal findings underscore the potential of targeting the ATF4-G4 structure to yield significant therapeutic advantages within the realm of persister cancer cells induced by glutamine-restricted therapy.
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Affiliation(s)
- Chengmei Xiao
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yipu Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yushuang Liu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Ruifang Dong
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xiaoyu He
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qing Lin
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Xin Zang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Kaibo Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yuanzheng Xia
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
- Shenzhen Research Institute of China Pharmaceutical University, Shenzhen, 518057, China
| | - Lingyi Kong
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Bioactive Natural Product Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
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Zhao Z, Wang J, Yu H, Wang X. Guide for phenotype-specific profiling of DNA G-quadruplex-regulated genes. STAR Protoc 2024; 5:102820. [PMID: 38198280 PMCID: PMC10820308 DOI: 10.1016/j.xpro.2023.102820] [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: 09/01/2023] [Revised: 11/06/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
DNA G-quadruplex (G4) is a non-canonical four-stranded secondary structure that has been shown to play a role in epigenetic modulation of gene expression. Here, we present a primer on phenotype-specific profiling of DNA G-quadruplex-regulated genes. We provide guidance on in silico exploration of G4-related genes and phenotypes, and in vitro and in vivo validation of the relationship between G4 and phenotype. We describe commonly utilized techniques and detail critical steps involved in determining the phenotype-specific G4-regulated genes for subsequent investigations.
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Affiliation(s)
- Zhuoyang Zhao
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Institute of Gastroenterology, Guangzhou, Guangdong 510655, China; Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Key Laboratory of Orthopedics and Traumatology, Guangzhou 510080, China
| | - Jianru Wang
- Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Key Laboratory of Orthopedics and Traumatology, Guangzhou 510080, China
| | - Huichuan Yu
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Institute of Gastroenterology, Guangzhou, Guangdong 510655, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong 510655, China.
| | - Xiaolin Wang
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Institute of Gastroenterology, Guangzhou, Guangdong 510655, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong 510655, China.
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Romano F, Di Porzio A, Iaccarino N, Riccardi G, Di Lorenzo R, Laneri S, Pagano B, Amato J, Randazzo A. G-quadruplexes in cancer-related gene promoters: from identification to therapeutic targeting. Expert Opin Ther Pat 2023; 33:745-773. [PMID: 37855085 DOI: 10.1080/13543776.2023.2271168] [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: 06/26/2023] [Accepted: 10/11/2023] [Indexed: 10/20/2023]
Abstract
INTRODUCTION Guanine-rich DNA sequences can fold into four-stranded noncanonical secondary structures called G-quadruplexes (G4s) which are widely distributed in functional regions of the human genome, such as telomeres and gene promoter regions. Compelling evidence suggests their involvement in key genome functions such as gene expression and genome stability. Notably, the abundance of G4-forming sequences near transcription start sites suggests their potential involvement in regulating oncogenes. AREAS COVERED This review provides an overview of current knowledge on G4s in human oncogene promoters. The most representative G4-binding ligands have also been documented. The objective of this work is to present a comprehensive overview of the most promising targets for the development of novel and highly specific anticancer drugs capable of selectively impacting the expression of individual or a limited number of genes. EXPERT OPINION Modulation of G4 formation by specific ligands has been proposed as a powerful new tool to treat cancer through the control of oncogene expression. Actually, most of G4-binding small molecules seem to simultaneously target a range of gene promoter G4s, potentially influencing several critical driver genes in cancer, thus producing significant therapeutic benefits.
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Affiliation(s)
- Francesca Romano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Anna Di Porzio
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | | | | | - Sonia Laneri
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
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Yadav A, Upadhyay S, Kant R, Srivastava AK. Regioselective Synthesis of Phenanthridines via Pd(II)-Catalyzed Annulative C( sp2)-H Activation. J Org Chem 2023; 88:13568-13583. [PMID: 37738300 DOI: 10.1021/acs.joc.3c01234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
A robust synthesis of phenanthridines has been described via Pd(II)-catalyzed domino C(sp2)-H activation/N-arylation using oxime esters with aryl acyl peroxides in a highly regioselective manner. This protocol is compatible with acetophenone as well as benzophenone-derived oxime esters and allows modular construction of functionalized phenanthridines with wide tolerance of electronic functionality. Further transformations were conducted to synthesize key building blocks, and control experiments were performed to understand the plausible reaction mechanism.
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Affiliation(s)
- Anamika Yadav
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Surabhi Upadhyay
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Ruchir Kant
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Ajay Kumar Srivastava
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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5
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Wang X, Wang L, Zhang J, Liu Y, Xie H, Zeng J, Cheng P. Photoredox catalysed reductive aminomethylation of quaternary benzophenanthridine alkaloids. Nat Prod Res 2023; 37:3551-3555. [PMID: 35767365 DOI: 10.1080/14786419.2022.2092732] [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: 03/08/2022] [Revised: 05/12/2022] [Accepted: 06/11/2022] [Indexed: 10/17/2022]
Abstract
Reduction of C = N double bond is the most important phase I metabolism process of quaternary benzophenanthridine alkaloids (QBAs). Inspired by the NADPH mediated reduction in QBAs, a visible-light promoted reductive aminomethylation of QBAs for synthesis of 6-substituted benzophenanthridines was reported using QBAs and N,N-dimethylaniline as coupling partners in this study. An α-amino radical that derived from QBAs was supposed to be the key intermediate in this visible-light promoted reductive aminomethylation reaction.
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Affiliation(s)
- Xinhao Wang
- Hunan Agricultural University, Changsha, Hunan, China
| | - Lin Wang
- Hunan Agricultural University, Changsha, Hunan, China
| | | | - Yisong Liu
- Hunan Agricultural University, Changsha, Hunan, China
| | - Hongqi Xie
- Hunan Agricultural University, Changsha, Hunan, China
| | - Jianguo Zeng
- Hunan Agricultural University, Changsha, Hunan, China
| | - Pi Cheng
- Hunan Agricultural University, Changsha, Hunan, China
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6
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Wang L, Li K, Ye T, Huang L, Wu H, Zhang J, Xie H, Liu Y, Zeng J, Cheng P. Visible-Light-Promoted α-Benzylation of N-Phenyl α-Amino Acids to α-Amino Phenylpropanoids. J Org Chem 2023; 88:11924-11934. [PMID: 37560787 DOI: 10.1021/acs.joc.3c01196] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
A new method for the synthesis of α-amino phenylpropanoids under blue light-emitting diode irradiation has been developed through α-C-H benzylation of readily available N-phenyl glycine ester with benzyl oxalates as a coupling partner under mild conditions. A range of N-phenyl glycine esters were successfully converted to α-amino phenylpropanoid products in moderate to good yields. The utility of this methodology is underlined by its application to the late-state modification of natural products.
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Affiliation(s)
- Lin Wang
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Horticulture, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Kang Li
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Horticulture, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Tian Ye
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Lei Huang
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Huilan Wu
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Horticulture, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Jingxuan Zhang
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Horticulture, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Hongqi Xie
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Yisong Liu
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Jianguo Zeng
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Pi Cheng
- Hunan Key Laboratory of Traditional Chinese Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
- College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan 410128, China
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7
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Wu S, Jiang L, Lei L, Fu C, Huang J, Hu Y, Dong Y, Chen J, Zeng Q. Crosstalk between G-quadruplex and ROS. Cell Death Dis 2023; 14:37. [PMID: 36653351 PMCID: PMC9849334 DOI: 10.1038/s41419-023-05562-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 12/25/2022] [Accepted: 01/05/2023] [Indexed: 01/19/2023]
Abstract
The excessive production of reactive oxygen species (ROS) can lead to single nucleic acid base damage, DNA strand breakage, inter- and intra-strand cross-linking of nucleic acids, and protein-DNA cross-linking involved in the pathogenesis of cancer, neurodegenerative diseases, and aging. G-quadruplex (G4) is a stacked nucleic acid structure that is ubiquitous across regulatory regions of multiple genes. Abnormal formation and destruction of G4s due to multiple factors, including cations, helicases, transcription factors (TFs), G4-binding proteins, and epigenetic modifications, affect gene replication, transcription, translation, and epigenetic regulation. Due to the lower redox potential of G-rich sequences and unique structural characteristics, G4s are highly susceptible to oxidative damage. Additionally, the formation, stability, and biological regulatory role of G4s are affected by ROS. G4s are involved in regulating gene transcription, translation, and telomere length maintenance, and are therefore key players in age-related degeneration. Furthermore, G4s also mediate the antioxidant process by forming stress granules and activating Nrf2, which is suggestive of their involvement in developing ROS-related diseases. In this review, we have summarized the crosstalk between ROS and G4s, and the possible regulatory mechanisms through which G4s play roles in aging and age-related diseases.
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Affiliation(s)
- Songjiang Wu
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Ling Jiang
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Li Lei
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Chuhan Fu
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Jinhua Huang
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Yibo Hu
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Yumeng Dong
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China
| | - Jing Chen
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China.
| | - Qinghai Zeng
- Department of Dermatology, Third Xiangya Hospital, Central South University, 138 Tongzipo Road, 410013, Changsha, Hunan, PR China.
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Shu HY, Peng YZ, Hang WJ, Zhang M, Shen L, Wang DW, Zhou N. Trimetazidine enhances myocardial angiogenesis in pressure overload-induced cardiac hypertrophy mice through directly activating Akt and promoting the binding of HSF1 to VEGF-A promoter. Acta Pharmacol Sin 2022; 43:2550-2561. [PMID: 35217815 PMCID: PMC9525722 DOI: 10.1038/s41401-022-00877-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/21/2022] [Indexed: 02/07/2023] Open
Abstract
Latest clinical research shows that trimetazidine therapy during the perioperative period relieves endothelial dysfunction in patients with unstable angina induced by percutaneous coronary intervention. In this study we investigated the effects of TMZ on myocardial angiogenesis in pressure overload-induced cardiac hypertrophy mice. Cardiac hypertrophy was induced in mice by transverse aortic constriction (TAC) surgery. TAC mice were administered trimetazidine (2.8 mg/100 µL, i.g.) for 28 consecutive days. We showed that trimetazidine administration significantly increased blood vessel density in the left ventricular myocardium and abrogated cardiac dysfunction in TAC mice. Co-administration of a specific HSF1 inhibitor KRIBB11 (1.25 mg/100 µL, i.h.) abrogated the angiogenesis-promoting effects of trimetazidine in TAC mice. Using luciferase reporter and electrophoretic mobility shift assays we demonstrated that the transcription factor HSF1 bound to the promoter region of VEGF-A, and the transcriptional activity of HSF1 was enhanced upon trimetazidine treatment. In molecular docking analysis we found that trimetazidine directly bound to Akt via a hydrogen bond with Asp292 and a pi-pi bond with Trp80. In norepinephrine-treated HUVECs, we showed that trimetazidine significantly increased the phosphorylation of Akt and the synergistic nuclear translocation of Akt and HSF1, as well as the binding of Akt and HSF1 in the nucleus. These results suggest that trimetazidine enhances myocardial angiogenesis through a direct interaction with Akt and promotion of nuclear translocation of HSF1, and that trimetazidine may be used for the treatment of myocardial angiogenic disorders in hypertensive patients.
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Affiliation(s)
- Hong-Yang Shu
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yi-Zhong Peng
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wei-Jian Hang
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Min Zhang
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Lan Shen
- Department of Cardiology, Shanghai Chest Hospital Shanghai Jiaotong University, Shanghai, 200030, China
| | - Dao-Wen Wang
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ning Zhou
- Division of Cardiology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Hubei Key Laboratory of Genetics and Molecular Mechanism of Cardiologic Disorders, Huazhong University of Science and Technology, Wuhan, 430030, China.
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9
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Dey A, Pandav K, Nath M, Barthwal R, Prasad R. Molecular rec§ognition of telomere DNA sequence by 2, 6 anthraquinone derivatives leads to thermal stabilization and induces apoptosis in cancer cells. Int J Biol Macromol 2022; 221:355-370. [PMID: 36041576 DOI: 10.1016/j.ijbiomac.2022.08.156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022]
Abstract
According to current research, anti-cancer anthraquinones impact telomere disruption and may interact with G-quadruplex DNA that triggers signaling to apoptosis. The present study represents the biophysical investigation of oxidative stress, late apoptosis, and induced senescence among cancer cells after binding laboratory synthesized piperidine-based anthraquinone derivatives, 2, 6- Bis [(3-piperidino)acetamido)]anthracene-9,10-dione (N1P) and 2, 6-Bis [piperidino)propionamido]anthracene-9,10-dione (N2P), with G-quadruplex DNA. We employed biophysical approaches to explore the interaction of synthetic anthraquinone derivatives with quadruplex DNA sequences to influence biological activities in the presence of K+ and Na+ cations. The binding affinity for N2P and N1P are Kb = 5.8 × 106 M-1 and Kb = 1.0 × 106 M-1, respectively, leading to hypo-/hyper-chromism with 5-7 nm red shift and significant fluorescence quenching and changes in ellipticity resulting in external binding of both the ligands to G-quadruplex DNA. Ligand binding induced enhancement of thermostability of G4 DNA is greater in Na+ environment (ΔTm = 34 °C) as compared to that in K+ environment (ΔTm = 21 °C), thereby restricting telomerase binding access to telomeres. Microscopic images of treated cells indicated cellular shape, nuclear condensation, and fragmentation alterations. The findings pave the path for therapeutic research, given the great potential of modifying anthraquinone substituent groups towards improved efficacy, ROS generation, and G-quadruplex DNA selectivity.
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Affiliation(s)
- Arpita Dey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Kumud Pandav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Mala Nath
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Ritu Barthwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India.
| | - Ramasare Prasad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India.
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10
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Biver T. Discriminating between Parallel, Anti-Parallel and Hybrid G-Quadruplexes: Mechanistic Details on Their Binding to Small Molecules. Molecules 2022; 27:molecules27134165. [PMID: 35807410 PMCID: PMC9268745 DOI: 10.3390/molecules27134165] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 12/04/2022] Open
Abstract
G-quadruplexes (G4) are now extensively recognised as a peculiar non-canonical DNA geometry that plays a prime importance role in processes of biological relevance whose number is increasing continuously. The same is true for the less-studied RNA G4 counterpart. G4s are stable structures; however, their geometrical parameters may be finely tuned not only by the presence of particular sequences of nucleotides but also by the salt content of the medium or by a small molecule that may act as a peculiar topology inducer. As far as the interest in G4s increases and our knowledge of these species deepens, researchers do not only verify the G4s binding by small molecules and the subsequent G4 stabilisation. The most innovative studies now aim to elucidate the mechanistic details of the interaction and the ability of a target species (drug) to bind only to a peculiar G4 geometry. In this focused review, we survey the advances in the studies of the binding of small molecules of medical interest to G4s, with particular attention to the ability of these species to bind differently (intercalation, lateral binding or sitting atop) to different G4 topologies (parallel, anti-parallel or hybrid structures). Some species, given the very high affinity with some peculiar G4 topology, can first bind to a less favourable geometry and then induce its conversion. This aspect is also considered.
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Affiliation(s)
- Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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11
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Kretzmann JA, Irving KL, Smith NM, Evans CW. Modulating gene expression in breast cancer via DNA secondary structure and the CRISPR toolbox. NAR Cancer 2022; 3:zcab048. [PMID: 34988459 PMCID: PMC8693572 DOI: 10.1093/narcan/zcab048] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 12/11/2022] Open
Abstract
Breast cancer is the most commonly diagnosed malignancy in women, and while the survival prognosis of patients with early-stage, non-metastatic disease is ∼75%, recurrence poses a significant risk and advanced and/or metastatic breast cancer is incurable. A distinctive feature of advanced breast cancer is an unstable genome and altered gene expression patterns that result in disease heterogeneity. Transcription factors represent a unique therapeutic opportunity in breast cancer, since they are known regulators of gene expression, including gene expression involved in differentiation and cell death, which are themselves often mutated or dysregulated in cancer. While transcription factors have traditionally been viewed as 'undruggable', progress has been made in the development of small-molecule therapeutics to target relevant protein-protein, protein-DNA and enzymatic active sites, with varying levels of success. However, non-traditional approaches such as epigenetic editing, transcriptional control via CRISPR/dCas9 systems, and gene regulation through non-canonical nucleic acid secondary structures represent new directions yet to be fully explored. Here, we discuss these new approaches and current limitations in light of new therapeutic opportunities for breast cancers.
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Affiliation(s)
- Jessica A Kretzmann
- Laboratory for Biomolecular Nanotechnology, Department of Physics, Technical University of Munich, Am Coulombwall 4a, 85748 Garching, Germany
| | - Kelly L Irving
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Nicole M Smith
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
| | - Cameron W Evans
- School of Molecular Sciences, The University of Western Australia, 35 Stirling Hwy, Crawley, WA 6009, Australia
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12
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Chen JN, He YD, Liang HT, Cai TT, Chen Q, Zheng KW. Regulation of PDGFR-β gene expression by targeting the G-vacancy bearing G-quadruplex in promoter. Nucleic Acids Res 2021; 49:12634-12643. [PMID: 34850916 PMCID: PMC8682790 DOI: 10.1093/nar/gkab1154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/14/2021] [Accepted: 11/09/2021] [Indexed: 12/31/2022] Open
Abstract
G-quadruplex is an essential element in gene transcription that serves as a promising drug target. Guanine-vacancy-bearing G-quadruplex (GVBQ) is a newly identified G-quadruplex that has distinct structural features from the canonical G-quadruplex. Potential GVBQ-forming motifs are widely distributed in gene promoter regions. However, whether GVBQ can form in genomic DNA and be an effective target for manipulating gene expression is unknown. Using photo-crosslinking, dimethyl sulfate footprinting, exonuclease digestion and in vitro transcription, we demonstrated the formation of a GVBQ in the G-rich nuclease hypersensitivity element within the human PDGFR-β gene promoter region in both single-stranded and double-stranded DNA. The formation of GVBQ in dsDNA could be induced by negative supercoiling created by downstream transcription. We also found that the PDGFR-β GVBQ was specifically recognized and stabilized by a new synthetic porphyrin guanine conjugate (mPG). Targeting the PDGFR-β GVBQ in human cancer cells using the mPG could specifically alter PDGFR-β gene expression. Our work illustrates that targeting GVBQ with mPG in human cells can regulate the expression level of a specific gene, thus indicating a novel strategy for drug development.
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Affiliation(s)
- Juan-Nan Chen
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Yi-de He
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China.,School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, P.R. China
| | - Hui-Ting Liang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Ting-Ting Cai
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Qi Chen
- School of Public Health (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
| | - Ke-Wei Zheng
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-Sen University, Guangzhou 510006, P.R. China
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13
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Exploration of the Hsa-miR-1587-Protein Interaction and the Inhibition to CASK. Int J Mol Sci 2021; 22:ijms221910716. [PMID: 34639058 PMCID: PMC8509502 DOI: 10.3390/ijms221910716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/18/2021] [Accepted: 09/27/2021] [Indexed: 11/23/2022] Open
Abstract
Hsa-miR-1587 has been found to be capable of forming G-quadruplex structures and is overexpressed in multiple cancer cell lines. Here, we explored the interactions between miR-1587 and proteins. HuProt™ human proteome microarray was utilized to screen the binding proteins, and it was discovered that CASK could bind to miR-1587 on the base of the G-quadruplex structure. Moreover, reelin and p21, which are downstream of CASK, were downregulated both transcriptionally and translationally by miR-1587, uncovered by q-RT-PCR and Western blot assays. Bioinformatic analysis was performed on STRING and Panther platforms, leading to the discovery that miR-1587 may be involved in intracellular metabolic and transcriptional physiological processes. This study explores the interaction of hsa-miR-1587 with proteins and provides a new strategy for the regulation of G-rich microRNA’s function.
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14
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Luo Z, Li R, Zhu T, Liu C, Feng H, Aboagye Nartey K, Liu Q, Xu X. Iron‐Catalyzed Oxidative Decabonylation/Radical Cyclization of Aliphatic Aldehydes with Biphenyl Isocyanides: A New Pathway For the Synthesis of 6‐Alkylphenanthridines. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202100112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Zaigang Luo
- State Key Laboratory of Mining Response and Disaster Prevention and Control in Deep Coal Mines College of Chemical Engineering AnHui University of Science and Technology Huainan 232001 P. R. China
| | - Rui Li
- State Key Laboratory of Mining Response and Disaster Prevention and Control in Deep Coal Mines College of Chemical Engineering AnHui University of Science and Technology Huainan 232001 P. R. China
| | - Tao Zhu
- State Key Laboratory of Mining Response and Disaster Prevention and Control in Deep Coal Mines College of Chemical Engineering AnHui University of Science and Technology Huainan 232001 P. R. China
| | - Chen‐Fu Liu
- School of Pharmaceutical Science Gannan Medical University Ganzhou 341000 P. R. China
| | - Haoran Feng
- State Key Laboratory of Mining Response and Disaster Prevention and Control in Deep Coal Mines College of Chemical Engineering AnHui University of Science and Technology Huainan 232001 P. R. China
| | - Kojo Aboagye Nartey
- State Key Laboratory of Mining Response and Disaster Prevention and Control in Deep Coal Mines College of Chemical Engineering AnHui University of Science and Technology Huainan 232001 P. R. China
| | - Qiannan Liu
- State Key Laboratory of Mining Response and Disaster Prevention and Control in Deep Coal Mines College of Chemical Engineering AnHui University of Science and Technology Huainan 232001 P. R. China
| | - Xuemei Xu
- State Key Laboratory of Mining Response and Disaster Prevention and Control in Deep Coal Mines College of Chemical Engineering AnHui University of Science and Technology Huainan 232001 P. R. China
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15
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Cheng P, Wang W, Wang X, Wang L, Liu W, Zeng J. Biomimetic synthesis of 6-substituted dihydrobenzophenanthridine alkaloids based on visible-light promoted radical addition reaction. Nat Prod Res 2020; 36:341-347. [PMID: 32597223 DOI: 10.1080/14786419.2020.1784171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Oxidative C-H functionalization of dihydrobenzophenanthridines catalyzed by dihydrobenzophenanthridine oxidase (DBOX) is believed to be the key step involved in the biosynthetic pathway of some novel 6-substituted benzophenanthridine alkaloids. In this study, a visible-light promoted biomimetic synthesis of 6-substituted benzophenanthridines was reported under photoredox-neutral conditions. α-Amino radical that derived from dihydrobenzophenanthridines was supposed to be the key intermediate in this visible-light promoted radical-type Michael addition reaction.
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Affiliation(s)
- Pi Cheng
- Key Laboratory of Traditional Chinese Veterinary Medicine of Hunan Province, Hunan Agricultural University, Changsha, China
| | - Wei Wang
- Key Laboratory of Traditional Chinese Veterinary Medicine of Hunan Province, Hunan Agricultural University, Changsha, China
| | - Xinhao Wang
- Key Laboratory of Traditional Chinese Veterinary Medicine of Hunan Province, Hunan Agricultural University, Changsha, China
| | - Lin Wang
- Key Laboratory of Traditional Chinese Veterinary Medicine of Hunan Province, Hunan Agricultural University, Changsha, China
| | - Wei Liu
- Key Laboratory of Traditional Chinese Veterinary Medicine of Hunan Province, Hunan Agricultural University, Changsha, China
| | - Jianguo Zeng
- Key Laboratory of Traditional Chinese Veterinary Medicine of Hunan Province, Hunan Agricultural University, Changsha, China
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16
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Roy S, Ali A, Kamra M, Muniyappa K, Bhattacharya S. Specific stabilization of promoter G-Quadruplex DNA by 2,6-disubstituted amidoanthracene-9,10-dione based dimeric distamycin analogues and their selective cancer cell cytotoxicity. Eur J Med Chem 2020; 195:112202. [PMID: 32302880 DOI: 10.1016/j.ejmech.2020.112202] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/19/2020] [Accepted: 03/01/2020] [Indexed: 10/24/2022]
Abstract
We have designed and synthesized anthraquinone containing compounds which have oligopyrrole side chains of varying lengths. These compounds stabilized the G-quadruplex DNA formed in the promoter regions of c-MYC oncogenes selectively over the duplex DNA. These observations were recorded using UV-vis spectroscopic titrations, fluorescence measurements and circular dichroism (CD) spectral titrations. The potency of the compounds to stabilize the G4 DNA has been shown from the thermal denaturation experiments. The compound interacts with c-MYC G-quadruplex DNA through stacking mode as obtained from ethidium bromide displacement assay, cyclic voltammetric titration, and docking experiments. Molecular modeling studies suggested that the stacking of the anthraquinone moiety over the G-tetrad of the G4 structures are responsible for the stability of such quadruplex secondary structure. Furthermore, polymerase stop assay also supported the formation of stable G4 structures in the presence of the above-mentioned compounds. The compounds have shown selective cancer cell (HeLa and HEK293T) cytotoxicity over normal cells (NIH3T3 and HDFa) under in vitro conditions as determined from MTT based cell viability assay. Apoptosis was found to be the mechanistic pathway underlying the cancer cell cytotoxicity as obtained from Annexin V-FITC and PI dual staining assay which was further substantiated by nuclear morphological changes as observed by AO/EB dual staining assay. Cellular morphological changes, as well as nuclear condensation and fragmentation upon treatment with these compounds, were observed under bright field and confocal microscopy.
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Affiliation(s)
- Soma Roy
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Asfa Ali
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Mohini Kamra
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India; School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, 700032, India.
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17
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Cui X, Chen H, Zhang Q, Xu M, Yuan G, Zhou J. Exploration of the Structure and Recognition of a G-quadruplex in the her2 Proto-oncogene Promoter and Its Transcriptional Regulation. Sci Rep 2019; 9:3966. [PMID: 30850693 PMCID: PMC6408435 DOI: 10.1038/s41598-019-39941-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/23/2019] [Indexed: 12/02/2022] Open
Abstract
G-quadruplexes in oncogene promoters provide putative targets for transcriptional regulation. The structure of a putative G-quadruplex sequence (S1: GGAGAAGGAGGAGGTGGAGGAGGAGGG) in potassium solution in the her2 promoter has been resolved mainly through nuclear magnetic resonance (NMR) spectroscopy. By application of various NMR spectra, we proved the formation of a four-layer G-quadruplex composing of two G-tetrads and two G/A-mixed planes with a four-residues loop (A3-G4-A5-A6). Further evidence from a luciferase reporter assay, Q-RT-PCR and Western blotting indicates that S1 G-quadruplex formation can repress her2 promoter activity, and a selected G-quadruplex ligand cβ can enhance the repression by down regulating her2 transcription and expression. These findings provide a G-quadruplex target and perspective implications in her2 transcriptional regulation.
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Affiliation(s)
- Xiaojie Cui
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China. .,College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China.
| | - Han Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Qiang Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Ming Xu
- Department of Cardiology, Institute of Vascular Medicine, Department of Cardiology, Peking University Third Hospital, Beijing, 100191, China
| | - Gu Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Jiang Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
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18
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Shah P, Choi SW, Nagda R, Geczy R, Cho SK, Bhang YJ, Kim TH, Song TY, Lee PH, Kang JH, Thulstrup PW, Bjerrum MJ, Jung IL, Yang SW. The structural shift of a DNA template between a hairpin and a dimer tunes the emission color of DNA-templated AgNCs. NANOSCALE 2018; 10:20717-20722. [PMID: 30398269 DOI: 10.1039/c8nr06186f] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The scaffolding DNA sequence and the size of silver nanoclusters (AgNCs), confined in a DNA template are the key parameters in determining the fluorescent properties of DNA-stabilized silver nanoclusters (DNA/AgNCs). In addition, we suggest here that the structural shift of a DNA hairpin-dimer is as important as the DNA sequence in determining the emission wavelength of DNA/AgNCs. Furthermore, we show that the structural shift post AgNC formation can be triggered by incubation time and pre-AgNC formation under salt conditions. As an important factor in predicting the emission properties of DNA/AgNCs, the modulation of DNA secondary structures with either sequence changes or ionic conditions can be applied for the dual-color detection system of a target molecule. Particularly, the dual-color detection method may increase the reliability of DNA/AgNC sensors for miRNAs.
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Affiliation(s)
- Pratik Shah
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Korea.
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19
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Nadai M, Doria F, Scalabrin M, Pirota V, Grande V, Bergamaschi G, Amendola V, Winnerdy FR, Phan AT, Richter SN, Freccero M. A Catalytic and Selective Scissoring Molecular Tool for Quadruplex Nucleic Acids. J Am Chem Soc 2018; 140:14528-14532. [PMID: 30351011 PMCID: PMC6242190 DOI: 10.1021/jacs.8b05337] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A copper complex embedded in the structure of a water-soluble naphthalene diimide has been designed to bind and cleave G-quadruplex DNA. We describe the properties of this ligand, including its catalytic activity in the generation of ROS. FRET melting, CD, NMR, gel sequencing, and mass spectrometry experiments highlight a unique and unexpected selectivity in cleaving G-quadruplex sequences. This selectivity relies both on the binding affinity and structural features of the targeted G-quadruplexes.
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Affiliation(s)
- Matteo Nadai
- Department of Molecular Medicine , University of Padua , via Gabelli 63 , 35121 Padua , Italy
| | - Filippo Doria
- Department of Chemistry , University of Pavia , V. le Taramelli 10 , 27100 Pavia , Italy
| | - Matteo Scalabrin
- Department of Molecular Medicine , University of Padua , via Gabelli 63 , 35121 Padua , Italy
| | - Valentina Pirota
- Department of Chemistry , University of Pavia , V. le Taramelli 10 , 27100 Pavia , Italy
| | - Vincenzo Grande
- Department of Chemistry , University of Pavia , V. le Taramelli 10 , 27100 Pavia , Italy
| | - Greta Bergamaschi
- Department of Chemistry , University of Pavia , V. le Taramelli 10 , 27100 Pavia , Italy
| | - Valeria Amendola
- Department of Chemistry , University of Pavia , V. le Taramelli 10 , 27100 Pavia , Italy
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Sara N Richter
- Department of Molecular Medicine , University of Padua , via Gabelli 63 , 35121 Padua , Italy
| | - Mauro Freccero
- Department of Chemistry , University of Pavia , V. le Taramelli 10 , 27100 Pavia , Italy
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20
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Hu X, Yang D, Yao T, Gao R, Wumaier M, Shi S. Regulation of multi-factors (tail/loop/link/ions) for G-quadruplex enantioselectivity of Δ- and Λ- [Ru(bpy) 2(dppz-idzo)] 2. Dalton Trans 2018; 47:5422-5430. [PMID: 29594288 DOI: 10.1039/c8dt00501j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chiral recognition of DNA molecules is important because much evidence has indicated that transformations of chirality and diverse conformations of DNA are involved in a series of key biological events. Among these, enrichment of G-quadruplexes (GQs) in the genome, and the exploration of their multiple structures, has aroused great interest. Herein, we compared nearly 100 different sequences with 3'-tail sequences of variable length or different linkers or diverse loops and mutative ionic concentrations. All sequences were capable of forming stable GQs, with fluorescence signal enhancement upon binding with Δ- and Λ- [Ru(bpy)2(dppz-idzo)]2+ (Δ/Λ-1). Our results show that multiple factors, including the 3'-tail length, linkers, loop length and ionic concentration, regulate the enantioselectivity of GQs. Furthermore, molecular docking simulations revealed that chiral recognition of GQs depends on the binding site. To the best of our knowledge, this is the first systematic study regarding the regulation of multi-factors for GQ selectivity of chiral Ru-complexes. These results will serve as a useful reference for enantioselective recognition of genomic GQs and may facilitate the development of chiral anticancer agents for targeting GQs.
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Affiliation(s)
- Xiaochun Hu
- Shanghai Key Lab of Chemical Assessment and Sustainability, Department of Chemistry, Tongji University, 1239 Siping Road, 200092 Shanghai, PR China.
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21
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Kumari B, Kumari R, Das P. Visual detection of G-quadruplex with mushroom derived highly fluorescent carbon quantum dots. J Pharm Biomed Anal 2018; 157:137-144. [DOI: 10.1016/j.jpba.2018.05.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/23/2018] [Accepted: 05/11/2018] [Indexed: 01/04/2023]
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22
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Ding S, Zhao Y, Ma Q, Tian S, Ren H, Zhu M, Li K, Miao Z. Silver(I)-mediated Reaction of 2-Isocyanobiaryl with Alkyl Trifluoroborates: Efficient Synthesis of 6-Alkylated Phenanthridines. CHEM LETT 2018. [DOI: 10.1246/cl.180009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Siyi Ding
- Key Laboratory of Organic Polymer Photoelectric Materials, School of Science, Xijing University, Xi’an Shaanxi 710123, P. R. China
| | - Yuzhen Zhao
- Key Laboratory of Organic Polymer Photoelectric Materials, School of Science, Xijing University, Xi’an Shaanxi 710123, P. R. China
| | - Qiang Ma
- Key Laboratory of Organic Polymer Photoelectric Materials, School of Science, Xijing University, Xi’an Shaanxi 710123, P. R. China
| | - Shaopeng Tian
- Key Laboratory of Organic Polymer Photoelectric Materials, School of Science, Xijing University, Xi’an Shaanxi 710123, P. R. China
| | - Huaping Ren
- Key Laboratory of Organic Polymer Photoelectric Materials, School of Science, Xijing University, Xi’an Shaanxi 710123, P. R. China
| | - Min Zhu
- Key Laboratory of Organic Polymer Photoelectric Materials, School of Science, Xijing University, Xi’an Shaanxi 710123, P. R. China
| | - Kexuan Li
- Key Laboratory of Organic Polymer Photoelectric Materials, School of Science, Xijing University, Xi’an Shaanxi 710123, P. R. China
| | - Zongcheng Miao
- Key Laboratory of Organic Polymer Photoelectric Materials, School of Science, Xijing University, Xi’an Shaanxi 710123, P. R. China
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Wei ZZ, Qin QP, Meng T, Deng CX, Liang H, Chen ZF. 5-Bromo-oxoisoaporphine platinum(II) complexes exhibit tumor cell cytotoxcicity via inhibition of telomerase activity and disruption of c-myc G-quadruplex DNA and mitochondrial functions. Eur J Med Chem 2018; 145:360-369. [DOI: 10.1016/j.ejmech.2017.12.092] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 11/20/2017] [Accepted: 12/29/2017] [Indexed: 01/01/2023]
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24
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Topological impact of noncanonical DNA structures on Klenow fragment of DNA polymerase. Proc Natl Acad Sci U S A 2017; 114:9605-9610. [PMID: 28827350 DOI: 10.1073/pnas.1704258114] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Noncanonical DNA structures that stall DNA replication can cause errors in genomic DNA. Here, we investigated how the noncanonical structures formed by sequences in genes associated with a number of diseases impacted DNA polymerization by the Klenow fragment of DNA polymerase. Replication of a DNA sequence forming an i-motif from a telomere, hypoxia-induced transcription factor, and an insulin-linked polymorphic region was effectively inhibited. On the other hand, replication of a mixed-type G-quadruplex (G4) from a telomere was less inhibited than that of the antiparallel type or parallel type. Interestingly, the i-motif was a better inhibitor of replication than were mixed-type G4s or hairpin structures, even though all had similar thermodynamic stabilities. These results indicate that both the stability and topology of structures formed in DNA templates impact the processivity of a DNA polymerase. This suggests that i-motif formation may trigger genomic instability by stalling the replication of DNA, causing intractable diseases.
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25
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Targeting glioma stem cells in vivo by a G-quadruplex-stabilizing synthetic macrocyclic hexaoxazole. Sci Rep 2017; 7:3605. [PMID: 28620243 PMCID: PMC5472576 DOI: 10.1038/s41598-017-03785-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/03/2017] [Indexed: 11/15/2022] Open
Abstract
G-quadruplex (G4) is a higher-order nucleic acid structure that is formed by guanine-rich sequences. G4 stabilization by small-molecule compounds called G4 ligands often causes cytotoxicity, although the potential medicinal impact of this effect has not been fully established. Here we demonstrate that a synthetic G4 ligand, Y2H2-6M(4)-oxazole telomestatin derivative (6OTD), limits the growth of intractable glioblastoma (grade IV glioma) and glioma stem cells (GSCs). Experiments involving a human cancer cell line panel and mouse xenografts revealed that 6OTD exhibits antitumor activity against glioblastoma. 6OTD inhibited the growth of GSCs more potently than it did the growth of differentiated non-stem glioma cells (NSGCs). 6OTD caused DNA damage, G1 cell cycle arrest, and apoptosis in GSCs but not in NSGCs. These DNA damage foci tended to colocalize with telomeres, which contain repetitive G4-forming sequences. Compared with temozolomide, a clinical DNA-alkylating agent against glioma, 6OTD required lower concentrations to exert anti-cancer effects and preferentially affected GSCs and telomeres. 6OTD suppressed the intracranial growth of GSC-derived tumors in a mouse xenograft model. These observations indicate that 6OTD targets GSCs through G4 stabilization and promotion of DNA damage responses. Therefore, G4s are promising therapeutic targets for glioblastoma.
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Zhang L, Tan W, Zhou J, Xu M, Yuan G. Investigation of G-quadruplex formation in the FGFR2 promoter region and its transcriptional regulation by liensinine. Biochim Biophys Acta Gen Subj 2017; 1861:884-891. [PMID: 28132898 DOI: 10.1016/j.bbagen.2017.01.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/21/2017] [Accepted: 01/25/2017] [Indexed: 01/09/2023]
Abstract
BACKGROUND Fibroblast growth factor receptor 2 (FGFR2) is overexpressed in breast cancer tissues and cells, and has been shown to be a susceptibility factor for breast cancer. In this study, we found that the G-rich sequences in the FGFR2 promoter region can form G-quadruplexes, which could be the target and inhibitor of the FGFR2 gene. METHODS Initially, the formation of G-quadruplexes was confirmed by ESI-MS and CD, and DMS footprinting experiments gave the folding pattern of the G-quadruplexes. After luciferase reporter assays revealed that the G-quadruplex could inhibit the activity of the FGFR2 promoter, MS and SPR showed binding affinity and selectivity of the ligand. Then cell culture experiments and ChIP assay showed the bioactivity of the ligand. RESULTS We found that three G-rich sequences (S1-S3) in the FGFR2 promoter region can form G-quadruplex structures. And a natural alkaloid, liensinine, was found to bind to the S1 G-quadruplex with relative high affinity and selectivity. Cell culture experiments showed that liensinine inhibits FGFR2 activity at both the transcriptional and translational levels. Moreover, chromatin immunoprecipitation assay (ChIP) results showed that liensinine blocks the binding of E2F1 at the transcription factor binding site (TFBS) in the S1 sequence, which is the mechanism through which liensinine inhibits the FGFR2 gene. CONCLUSIONS A natural alkaloid was discovered to selectively bind to the S1 G-quadruplex with relative high affinity, and therefore inhibited FGFR2 transcription and translation. GENERAL SIGNIFICANCE Our discovery offers a useful strategy to inhibit FGFR2 transcription, i.e., targeting the G-quadruplex with a natural alkaloid.
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Affiliation(s)
- Lulu Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wei Tan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiang Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Analytical Instrumentation Center, Peking University, Beijing 100871, China.
| | - Ming Xu
- Institute of Vascular Medicine, Department of Cardiology, Peking University Third Hospital, Key Laboratory of Molecular Cardiovascular Sciences of Ministry of Education, Beijing 100191, China.
| | - Gu Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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27
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Qi X, Li L, Wu Y, Yu L, Qi Z, Xue F. Synthesis of Highly Substituted 5,6-Dihydrobenzo[j]phenanthridine Derivatives via Domino Reaction. HETEROCYCLES 2017. [DOI: 10.3987/com-17-13754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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28
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Nie Z, Ding Q, Peng Y. Synthesis of 6-aroyl phenanthridines by Fe-catalyzed oxidative radical cyclization of 2-isocyanobiphenyls with benzylic alcohols. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.11.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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G-quadruplex formation in the Oct4 promoter positively regulates Oct4 expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:175-183. [PMID: 27863263 DOI: 10.1016/j.bbagrm.2016.11.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 11/11/2016] [Accepted: 11/14/2016] [Indexed: 11/21/2022]
Abstract
The Oct4 gene codes for a transcription factor that plays a critical role in the maintenance of pluripotency in embryonic and cancer stem cells. Its expression thus has to be tightly regulated. We performed biophysical characterization of the promoter region using a combination of UV absorption, CD, and NMR spectroscopies, native PAGE and chemical probing, which was followed by functional studies involving luciferase reporter assays performed in osteosarcoma and human embryonic stem cell lines. We have shown that the evolutionarily conserved G-rich region close to the Oct4 transcription start site in the non-template strand forms a parallel G-quadruplex structure. We characterized its structure and stability upon point mutations in its primary structure. Functional studies then revealed that whereas the wild type quadruplex sequence ensures high reporter gene expression, the expression of mutated variants is significantly decreased proportionally to the destabilizing effect of the mutations on the quadruplex. A ligand, N-methyl mesoporphyrin IX that increases the stability of formed quadruplex rescued the reporter expression of single-mutated variants to the level of wild-type, but it has no effect on a mutated variant that cannot form quadruplex. These data indicate that the quadruplex acts as a strong, positive regulator of Oct4 expression and as such it might serve as a potential target for therapeutic intervention.
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Li J, Matsumoto J, Bai LP, Murata A, Dohno C, Nakatani K. A Ligand That Targets CUG Trinucleotide Repeats. Chemistry 2016; 22:14881-14889. [PMID: 27573860 DOI: 10.1002/chem.201602741] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Indexed: 11/06/2022]
Abstract
The development of small molecules that can recognize specific RNA secondary and tertiary structures is currently an important research topic for developing tools to modulate gene expression and therapeutic drugs. Expanded CUG trinucleotide repeats, known as toxic RNA, capture the splicing factor MBNL1 and are causative of neurological disorder myotonic dystrophy type 1 (DM1). Herein, the rational molecular design, synthesis, and binding analysis of 2,9-diaminoalkyl-substituted 1,10-phenanthroline (DAP), which bound to CUG trinucleotide repeats, is described. The results of melting temperature (Tm ) analyses, surface plasmon resonance (SPR) assay, and electrospray spray ionization time-of-flight (ESI-TOF) mass spectrometry showed that DAP bound to r(CUG)9 but not to r(CAG)9 and r(CGG)9 . The dual luciferase assay clearly indicated DAP bound to the r(CUG)n repeat by affecting the translation in vitro.
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Affiliation(s)
- Jinxing Li
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, 567-0047, Japan
| | - Jun Matsumoto
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, 567-0047, Japan
| | - Li-Ping Bai
- State Key Laboratory of Quality Research in Chinese Medicine and, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau, China
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, 567-0047, Japan
| | - Chikara Dohno
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, 567-0047, Japan.
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31
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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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32
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Zhou Y, Wu C, Dong X, Qu J. Synthesis of 6-Trichloromethylphenanthridines by Transition Metal-Free Radical Cyclization of 2-Isocyanobiphenyls. J Org Chem 2016; 81:5202-8. [DOI: 10.1021/acs.joc.6b00885] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yuhan Zhou
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical Science and Technology, Dalian University of Technology, Dalian 116024, P.R. China
| | - Changpeng Wu
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical Science and Technology, Dalian University of Technology, Dalian 116024, P.R. China
| | - Xiaoliang Dong
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical Science and Technology, Dalian University of Technology, Dalian 116024, P.R. China
| | - Jingping Qu
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical Science and Technology, Dalian University of Technology, Dalian 116024, P.R. China
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Investigation on the formation, conversion and bioactivity of a G-quadruplex structure in the PALB2 gene. Int J Biol Macromol 2016; 83:242-8. [DOI: 10.1016/j.ijbiomac.2015.11.069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 10/22/2022]
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34
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Liu Z, Huang Y, Xie H, Liu W, Zeng J, Cheng P. A novel C–C radical–radical coupling reaction promoted by visible light: facile synthesis of 6-substituted N-methyl 5,6-dihydrobenzophenanthridine alkaloids. RSC Adv 2016. [DOI: 10.1039/c6ra05927a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A photoredox mediated radical–radical coupling ofN-methyl 5,6-dihydrobenzophenanthridine alkaloids with α-electron withdrawing group substituted bromoalkane has been developed.
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Affiliation(s)
- Zhaoying Liu
- National and Provincial Union Engineering Research Center for the Veterinary Herbal Medicine Resources and Initiative
- Hunan Agricultural University
- Changsha
- China
| | - Yajun Huang
- National and Provincial Union Engineering Research Center for the Veterinary Herbal Medicine Resources and Initiative
- Hunan Agricultural University
- Changsha
- China
| | - Hongqi Xie
- National and Provincial Union Engineering Research Center for the Veterinary Herbal Medicine Resources and Initiative
- Hunan Agricultural University
- Changsha
- China
- Hunan Co-Innovation Center for Utilization of Botanicals Functional Ingredients
| | - Wei Liu
- National and Provincial Union Engineering Research Center for the Veterinary Herbal Medicine Resources and Initiative
- Hunan Agricultural University
- Changsha
- China
| | - Jianguo Zeng
- National and Provincial Union Engineering Research Center for the Veterinary Herbal Medicine Resources and Initiative
- Hunan Agricultural University
- Changsha
- China
- Hunan Co-Innovation Center for Utilization of Botanicals Functional Ingredients
| | - Pi Cheng
- National and Provincial Union Engineering Research Center for the Veterinary Herbal Medicine Resources and Initiative
- Hunan Agricultural University
- Changsha
- China
- Hunan Co-Innovation Center for Utilization of Botanicals Functional Ingredients
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35
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Wang W, Sui Y, Zhang L, Tan W, He X, Xie X. Recognition of an important G-quadruplex in the HIV-1 promoter with natural small molecules. CAN J CHEM 2016. [DOI: 10.1139/cjc-2015-0215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Targeting a G-quadruplex with chemical small molecules is a useful strategy for gene therapy for disease. The guanine-rich sequence d(5′-TG1G2CCTG3G4G5CG6G7G8ACTG9G10G11-3′) in the HIV-1 promoter can form a G-quadruplex structure. In this study, circular dichroism was performed to study the conformation and thermal stability of the HIV-1 G-quadruplex before and after adding small molecules. A DMS footprinting assay was used to identify which guanosine can be integrated into the G-quadruplex structure. Electrospray ionization mass spectrometry was used to evaluate the binding affinities of the small molecules with the G-quadruplex. Our results showed that G1, G2, G3, G4, G7, G8, G9, and G10 of the above oligonucleotides formed a two G-tetrad antiparallel G-quadrulex, and nitidine chloride was found to have the highest binding affinity toward the HIV-1 G-quadruplex among the eight studied small molecules. The Tm value of the G-quadruplex was enhanced from 56.6 to 63.2 °C when fourfold nitidine chloride was added. This is potentially a novel approach for anti-HIV-1 drug development.
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Affiliation(s)
- Weixuan Wang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yang Sui
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Lulu Zhang
- Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wei Tan
- Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiangwei He
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xiangming Xie
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
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36
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Cytotoxicities, telomerase and topoisomerases I inhibitory activities and interactions of terpyridine derivatives with DNAs. Chem Res Chin Univ 2015. [DOI: 10.1007/s40242-015-5256-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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37
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Qi Y, Chen H, Tan W, Li Y, Yuan G, Xu M. The genomic sequences near the mir-23b-27b-24-1 cluster form G-quadruplexes and are selectively bound by the natural alkaloid tetrandrine. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1611-1616. [PMID: 28339154 DOI: 10.1002/rcm.7251] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/02/2015] [Accepted: 06/11/2015] [Indexed: 06/06/2023]
Abstract
RATIONALE Although the microRNAs miR-23b, miR-27b and miR-24 are located in the same cluster, their expressions in various pathological states are not always comparable. By searching the genomic sequence around mir23b-27b-24-1 in rat, we identified three potential G-quadruplex sequences (PQS) which can fold into different types of G-quadruplexes, including parallel or antiparallel. Natural alkaloids, tetrandrine (TET), displayed different binding affinity with the three G-quadruplexes which may potentially regulate the expression of mir23b-27b-24-1 cluster members. METHODS Both electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy were utilized to detect the formation of G-quadruplexes. Six small molecules were screened by ESI-MS for their binding affinity with three G-quadruplexes, which were evaluated by their IRa values. RESULTS The results of ESI-MS and CD experiments confirmed the formation of three G-quadruplexes neighboring the mir23b-27b-24-1 cluster; two of them adopted antiparallel G-quadruplexes, another adopted a parallel G-quadruplex. Screening of small molecules by ESI-MS showed tetrandrine had selective binding affinity for the parallel G-quadruplex. G-quadruplex stabilization by tetrandrine was verified by CD variable temperature measurements. CONCLUSIONS The gene of the mir23b-27b-24-1 cluster harbors three G-quadruplexes with typical sequences and structures. Tetrandrine had a selective binding affinity to the parallel G-quadruplex and stabilized it significantly. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Yanchao Qi
- Department of Cardiology, Institute of Vascular Medicine, Peking University Third Hospital, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Ministry of Health and Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
| | - Han Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University
| | - Wei Tan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University
| | - Yanyan Li
- Department of Cardiology, Institute of Vascular Medicine, Peking University Third Hospital, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Ministry of Health and Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
| | - Gu Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University
| | - Ming Xu
- Department of Cardiology, Institute of Vascular Medicine, Peking University Third Hospital, Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Key Laboratory of Cardiovascular Molecular Biology and Regulatory Peptides, Ministry of Health and Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing, China
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38
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Guo W, Li S, Tang L, Li M, Wen L, Chen C. Synthesis of 6-(Arylthio)phenanthridines by Copper-Catalyzed Tandem Reactions of 2-Biaryl Isothiocyanates with Diaryliodonium Salts. Org Lett 2015; 17:1232-5. [DOI: 10.1021/acs.orglett.5b00197] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Weisi Guo
- State
Key Laboratory Base of Eco-Chemical Engineering, College of Chemistry
and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Shoulei Li
- State
Key Laboratory Base of Eco-Chemical Engineering, College of Chemistry
and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Lin Tang
- State
Key Laboratory Base of Eco-Chemical Engineering, College of Chemistry
and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Ming Li
- State
Key Laboratory Base of Eco-Chemical Engineering, College of Chemistry
and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Lirong Wen
- State
Key Laboratory Base of Eco-Chemical Engineering, College of Chemistry
and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Chao Chen
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
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39
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Qin M, Chen Z, Luo Q, Wen Y, Zhang N, Jiang H, Yang H. Two-quartet G-quadruplexes formed by DNA sequences containing four contiguous GG runs. J Phys Chem B 2015; 119:3706-13. [PMID: 25689673 DOI: 10.1021/jp512914t] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The DNA sequence containing four contiguous GG runs (G2NxG2NyG2NzG2, G2 sequence) has the potential to form a two-quartet G-quadruplex. However, the prevalence, structure, and function of G2 sequences have not been well-studied. Here, bioinformatics analysis reveals the abundance of G2 sequences in the human genome and their enrichment in promoter regions. The density of G2 sequences in the genome and promoters is much higher than that of the G3 sequence (G3NxG3NyG3NzG3). Experiments show that the conformations and thermal stabilities of the two-quartet G-quadruplexes of G2 sequences are highly sensitive to the length and composition of the loops. Among the two-quartet G-quadruplexes, the parallel G-quadruplex with a loop length of 1 and the antiparallel G-quadruplex with a loop length of 3 show high thermal stabilities. Additionally, the stable parallel G-quadruplexes are stacked into intermolecular higher-order structures. This work determines the prevalence of G2 sequences in the human genome and demonstrates that the G-quadruplex structures for certain loop lengths and compositions may be stable in vivo. Thus, more attention should be paid to the structure and function of the two-quartet G-quadruplex.
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Affiliation(s)
- Mingyan Qin
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China
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40
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Chen ZF, Qin QP, Qin JL, Liu YC, Huang KB, Li YL, Meng T, Zhang GH, Peng Y, Luo XJ, Liang H. Stabilization of G-quadruplex DNA, inhibition of telomerase activity, and tumor cell apoptosis by organoplatinum(II) complexes with oxoisoaporphine. J Med Chem 2015; 58:2159-79. [PMID: 25650792 DOI: 10.1021/jm5012484] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Two G-quadruplex ligands [Pt(L(a))(DMSO)Cl] (Pt1) and [Pt(L(b))(DMSO)Cl] (Pt2) have been synthesized and fully characterized. The two complexes are more selective for SK-OV-3/DDP tumor cells versus normal cells (HL-7702). It was found that both Pt1 and Pt2 could be a telomerase inhibitor targeting G-quadruplex DNA. This is the first report demonstrating that telomeric, c-myc, and bcl-2 G-quadruplexes and caspase-3/9 preferred to bind with Pt2 rather than Pt1, which also can induce senescence and apoptosis. The different biological behavior of Pt1 and Pt2 may correlate with the presence of a 6-hydroxyl group in L(b). Importantly, Pt1 and Pt2 exhibited higher safety in vivo and more effective inhibitory effects on tumor growth in the HCT-8 and NCI-H460 xenograft mouse model, compared with cisplatin. Taken together, these mechanistic insights indicate that both Pt1 and Pt2 display low toxicity and could be novel anticancer drug candidates.
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Affiliation(s)
- Zhen-Feng Chen
- State Key Laboratory Cultivation Base for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmacy, Guangxi Normal University , Yucai Road 15, Guilin 541004, P. R. China
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Recognition of chelerythrine to human telomeric DNA and RNA G-quadruplexes. Sci Rep 2014; 4:6767. [PMID: 25341562 PMCID: PMC4208030 DOI: 10.1038/srep06767] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 09/29/2014] [Indexed: 01/25/2023] Open
Abstract
A study on binding of antitumor chelerythrine to human telomeric DNA/RNA G-quadruplexes was performed by using DNA polymerase stop assay, UV-melting, ESI-TOF-MS, UV-Vis absorption spectrophotometry and fluorescent triazole orange displacement assay. Chelerythrine selectively binds to and stabilizes the K(+)-form hybrid-type human telomeric DNA G-quadruplex of biological significance, compared with the Na(+)-form antiparallel-type DNA G-quadruplex. ESI-TOF-MS study showed that chelerythrine possesses a binding strength for DNA G-quadruplex comparable to that of TMPyP4 tetrachloride. Both 1:1 and 2:1 stoichiometries were observed for chelerythrine's binding with DNA and RNA G-quadruplexes. The binding strength of chelerythrine with RNA G-quadruplex is stronger than that with DNA G-quadruplex. Fluorescent triazole orange displacement assay revealed that chelerythrine interacts with human telomeric RNA/DNA G-quadruplexes by the mode of end- stacking. The relative binding strength of chelerythrine for human telomeric RNA and DNA G-quadruplexes obtained from ESI-TOF-MS experiments are respectively 6.0- and 2.5-fold tighter than that with human telomeric double-stranded hairpin DNA. The binding selectivity of chelerythrine for the biologically significant K(+)-form human telomeric DNA G-quadruplex over the Na(+)-form analogue, and binding specificity for human telomeric RNA G-quadruplex established it as a promising candidate in the structure-based design and development of G-quadruplex specific ligands.
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Dai Q, Yu JT, Feng X, Jiang Y, Yang H, Cheng J. Di-tertButyl Peroxide-Promoted Sequential Methylation and Intramolecular Aromatization of Isonitriles. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201400660] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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43
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Feng X, Zhu H, Wang L, Jiang Y, Cheng J, Yu JT. TBHP-promoted sequential carboxamidation and aromatisation of aryl isonitriles with formamides. Org Biomol Chem 2014; 12:9257-63. [DOI: 10.1039/c4ob01850h] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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44
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Small-molecule quadruplex-targeted drug discovery. Bioorg Med Chem Lett 2014; 24:2602-12. [DOI: 10.1016/j.bmcl.2014.04.029] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/06/2014] [Accepted: 04/08/2014] [Indexed: 01/24/2023]
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45
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Wang L, Zhu H, Guo S, Cheng J, Yu JT. TBHP-promoted sequential radical silylation and aromatisation of aryl isonitriles with silanes. Chem Commun (Camb) 2014; 50:10864-7. [DOI: 10.1039/c4cc04773g] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
TBHP-promoted sequential silylation and aromatisation of isonitriles was developed, where the silyl group was regioselectively installed at the 6-position of phenanthridines. The addition of a silyl radical to the isonitrile followed by an intramolecular aromatic cyclization was involved in this transformation.
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Affiliation(s)
- Lei Wang
- School of Petrochemical Engineering
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology
- Jiangsu Province Key Laboratory of Fine Petrochemical Engineering
- Changzhou University
- Changzhou 213164, P. R. China
| | - Hui Zhu
- School of Petrochemical Engineering
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology
- Jiangsu Province Key Laboratory of Fine Petrochemical Engineering
- Changzhou University
- Changzhou 213164, P. R. China
| | - Songjin Guo
- School of Petrochemical Engineering
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology
- Jiangsu Province Key Laboratory of Fine Petrochemical Engineering
- Changzhou University
- Changzhou 213164, P. R. China
| | - Jiang Cheng
- School of Petrochemical Engineering
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology
- Jiangsu Province Key Laboratory of Fine Petrochemical Engineering
- Changzhou University
- Changzhou 213164, P. R. China
| | - Jin-Tao Yu
- School of Petrochemical Engineering
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology
- Jiangsu Province Key Laboratory of Fine Petrochemical Engineering
- Changzhou University
- Changzhou 213164, P. R. China
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