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Choudhury SD, Kumar P, Choudhury D. Bioactive nutraceuticals as G4 stabilizers: potential cancer prevention and therapy-a critical review. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:3585-3616. [PMID: 38019298 DOI: 10.1007/s00210-023-02857-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023]
Abstract
G-quadruplexes (G4) are non-canonical, four-stranded, nucleic acid secondary structures formed in the guanine-rich sequences, where guanine nucleotides associate with each other via Hoogsteen hydrogen bonding. These structures are widely found near the functional regions of the mammalian genome, such as telomeres, oncogenic promoters, and replication origins, and play crucial regulatory roles in replication and transcription. Destabilization of G4 by various carcinogenic agents allows oncogene overexpression and extension of telomeric ends resulting in dysregulation of cellular growth-promoting oncogenesis. Therefore, targeting and stabilizing these G4 structures with potential ligands could aid cancer prevention and therapy. The field of G-quadruplex targeting is relatively nascent, although many articles have demonstrated the effect of G4 stabilization on oncogenic expressions; however, no previous study has provided a comprehensive analysis about the potency of a wide variety of nutraceuticals and some of their derivatives in targeting G4 and the lattice of oncogenic cell signaling cascade affected by them. In this review, we have discussed bioactive G4-stabilizing nutraceuticals, their sources, mode of action, and their influence on cellular signaling, and we believe our insight would bring new light to the current status of the field and motivate researchers to explore this relatively poorly studied arena.
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Affiliation(s)
- Satabdi Datta Choudhury
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology (IIT), Mandi, Himachal Pradesh, 175005, India
| | - Diptiman Choudhury
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India.
- Centre for Excellence in Emerging Materials, Thapar Institute of Engineering and Technology, Patiala, Punjab, 147004, India.
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2
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Stężycka O, Kasperkowiak M, Frańska M, Nowak D, Hoffmann M. Oxygen Atom from Carbonyl Group as an Important Binding Agent to the G-Quadruplex - Study Case of Flavonoids. Chempluschem 2024:e202400186. [PMID: 38713672 DOI: 10.1002/cplu.202400186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/09/2024]
Abstract
In the field of anticancer therapy study it is of great interest to find effective G-quadruplex ligands which may be of potential use in medical treatment or cancer prevention. Since among the compounds of natural origin, flavonoids have attracted notable attention because of their unique properties and promising therapeutic applications, an interesting question was to identify the flavonoid structural features that could provide effective binding properties toward G-quadruplex. By using electrospray ionization mass spectrometry, followed by the survival yield method, it has been shown that the flavonoid molecules which contain an available C4=O carbonyl group form more stable adducts with G-tetrads than the other ones. Molecular docking has shown that C4=O carbonyl group can be a source of hydrogen bonds and/or π-stacking interactions. Therefore, the flavonoid molecules which contain an available C4=O carbonyl group can be regarded as good binders of G-quadruplexes.
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Affiliation(s)
- Olga Stężycka
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Małgorzata Kasperkowiak
- Centre for Advanced Technologies, Adam Mickiewicz University, Uniwersytetu Poznańskiego 10, 61-614, Poznań, Poland
| | - Magdalena Frańska
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Damian Nowak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
| | - Marcin Hoffmann
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
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3
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Ye H, Zhang H, Xiang J, Shen G, Yang F, Wang F, Wang J, Tang Y. Advances and prospects of natural dietary polyphenols as G-quadruplex stabilizers in biomedical applications. Int J Biol Macromol 2024; 254:127825. [PMID: 37926317 DOI: 10.1016/j.ijbiomac.2023.127825] [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: 07/19/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
G-quadruplexes (G4s) have arrested continuous interest in cancer research, and targeting G4s with small molecules has become an ideal approach for drug development. Plant-based dietary polyphenols have attracted much attention for their remarkable anti-cancer effects. Studies have suggested that polyphenols exhibit interesting scaffolds to bind G4s, which can effectively downregulate the proto-oncogenes by stabilizing those G4 structures. Therefore, this review not only summarizes studies on natural dietary polyphenols (including analogs) as G4 stabilizers, but also reveals their anti-cancer activities. Furthermore, the structural and antioxidant insights of polyphenols with G4s are discussed, and future development is proposed. These insights may pave the way for the development of the next generation of anti-cancer drugs targeting nucleic acids.
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Affiliation(s)
- Huanfeng Ye
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Hong Zhang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; Beijing National Laboratory for Molecular Sciences (BNLMS), PR China.
| | - Junfeng Xiang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Gang Shen
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; Beijing National Laboratory for Molecular Sciences (BNLMS), PR China
| | - Fengmin Yang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; Beijing National Laboratory for Molecular Sciences (BNLMS), PR China
| | - Fangfang Wang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jie Wang
- Department of Cardiology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100053, PR China.
| | - Yalin Tang
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; University of Chinese Academy of Sciences, Beijing 100049, PR China; Beijing National Laboratory for Molecular Sciences (BNLMS), PR China.
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4
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Stężycka O, Frańska M, Beszterda-Buszczak M. Exploring Glycosylated Soy Isoflavones Affinities toward G-tetrads as Studied by Survival Yield Method. Chemphyschem 2023; 24:e202300056. [PMID: 36861944 DOI: 10.1002/cphc.202300056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/17/2023] [Indexed: 03/03/2023]
Abstract
Taking soy-based food supplements for menopausal symptoms by women may reduce the risk of cancer. Therefore, the interaction between nucleic acids (or their constituents) and ingredients of the supplements, e. g., isoflavone glucosides, on the molecular level, has been of interest with respect to cancer therapy. In this work, the interaction between isoflavone glucosides and G-tetrads, namely [4G+Na]+ ions (G stands for guanosine or deoxyguanosine), were analyzed by using electrospray ionization-collision induced dissociation-mass spectrometry (ESI-CID-MS) and survival yields method. The strength of isoflavone glucosides-[4G+Na]+ interaction in the gas phase was determined from Ecom50 - the energy required to fragment 50 % of selected precursor ions. Glycitin-[4G+Na]+ interaction was found to be the strongest, and the interaction between isoflavone glucosides and guanosine tetrad was established to be stronger than that between isoflavone glucosides and deoxyguanosine tetrad.
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Affiliation(s)
- Olga Stężycka
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Magdalena Frańska
- Institute of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965, Poznań, Poland
| | - Monika Beszterda-Buszczak
- Poznań University of Life Sciences, Department of Food Biochemistry and Analysis, Mazowiecka 48, 60-623, Poznań, Poland
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5
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Li ML, Yuan JM, Yuan H, Wu BH, Huang SL, Li QJ, Ou TM, Wang HG, Tan JH, Li D, Chen SB, Huang ZS. Design, Synthesis, and Evaluation of New Sugar-Substituted Imidazole Derivatives as Selective c-MYC Transcription Repressors Targeting the Promoter G-Quadruplex. J Med Chem 2022; 65:12675-12700. [PMID: 36121464 DOI: 10.1021/acs.jmedchem.2c00467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
c-MYC is a key driver of tumorigenesis. Repressing the transcription of c-MYC by stabilizing the G-quadruplex (G4) structure with small molecules is a potential strategy for cancer therapy. Herein, we designed and synthesized 49 new derivatives by introducing carbohydrates to our previously developed c-MYC G4 ligand 1. Among these compounds, 19a coupled with a d-glucose 1,2-orthoester displayed better c-MYC G4 binding, stabilization, and protein binding disruption abilities than 1. Our further evaluation indicated that 19a blocked c-MYC transcription by targeting the promoter G4, leading to c-MYC-dependent cancer cell death in triple-negative breast cancer cell MDA-MB-231. Also, 19a significantly inhibited tumor growth in the MDA-MB-231 mouse xenograft model accompanied by c-MYC downregulation. Notably, the safety of 19a was dramatically improved compared to 1. Our findings indicated that 19a could become a promising anticancer candidate, which suggested that introducing carbohydrates to improve the G4-targeting and antitumor activity is a feasible option.
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Affiliation(s)
- Mao-Lin Li
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jing-Mei Yuan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Hao Yuan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Bi-Han Wu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Shi-Liang Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Qing-Jiang Li
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Hong-Gen Wang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Ding Li
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
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6
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Chen X, He Z, Wu X, Mao D, Feng C, Zhang J, Chen G. Comprehensive study of the interaction between Puerariae Radix flavonoids and DNA: From theoretical simulation to structural analysis to functional analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 231:118109. [PMID: 32062512 DOI: 10.1016/j.saa.2020.118109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
Puerariae Radix (PR) is a natural herb whose active ingredient is mainly flavonoids. To explore the interaction between PR flavonoids and DNA not only has important biological implications for understanding the mechanism of action, but also helps develop PR products for the design of appropriate dietary interventions to aid cancer treatment. In this work, we comprehensively studied the interaction between six kinds of PR flavonoids and DNA from four different and progressive levels, including molecular docking, multi-spectral analysis, and functional analysis in vitro and in cell. Results show that the DNA binding affinity of six flavonoids is in an order of quercetin > formononetin > daidzein > puerarin > 4'-methoxy puerarin > puerarin 6″-O-xyloside (POS), in which quercetin can significantly inhibit DNA amplification owing to its strongest binding affinity. The binding between quercetin and DNA is further revealed to be intercalated binding, which can cause conformational changes in DNA, thereby exhibiting an activity of cell cycle arrest and anti-proliferative. This property of quercetin can be utilized for the further development of flavonoids with anticancer activity. In addition to the potential application, this work also provides a platform for the comprehensive study of the interaction between micromolecules and DNA.
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Affiliation(s)
- Xu Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, PR China; Experimental Center for Life Sciences, Shanghai University, Shanghai, PR China
| | - Ziyu He
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, PR China
| | - Xianyong Wu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, PR China
| | - Dongsheng Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, PR China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, PR China
| | - Juan Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, PR China
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, PR China.
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7
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Chasing Particularities of Guanine- and Cytosine-Rich DNA Strands. Molecules 2020; 25:molecules25030434. [PMID: 31972988 PMCID: PMC7037129 DOI: 10.3390/molecules25030434] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 01/17/2023] Open
Abstract
By substitution of natural nucleotides by their abasic analogs (i.e., 1',2'-dideoxyribose phosphate residue) at critically chosen positions within 27-bp DNA constructs originating from the first intron of N-myc gene, we hindered hybridization within the guanine- and cytosine-rich central region and followed formation of non-canonical structures. The impeded hybridization between the complementary strands leads to time-dependent structural transformations of guanine-rich strand that are herein characterized with the use of solution-state NMR, CD spectroscopy, and native polyacrylamide gel electrophoresis. Moreover, the DNA structural changes involve transformation of intra- into inter-molecular G-quadruplex structures that are thermodynamically favored. Intriguingly, the transition occurs in the presence of complementary cytosine-rich strands highlighting the inability of Watson-Crick base-pairing to preclude the transformation between G-quadruplex structures that occurs via intertwining mechanism and corroborates a role of G-quadruplex structures in DNA recombination processes.
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8
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Paul S, Hossain SS, M BD, Samanta A. Interactions between a Bioflavonoid and c-MYC Promoter G-Quadruplex DNA: Ensemble and Single-Molecule Investigations. J Phys Chem B 2019; 123:2022-2031. [DOI: 10.1021/acs.jpcb.9b00335] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Sneha Paul
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Sk Saddam Hossain
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Bala Divya M
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Anunay Samanta
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
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9
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Saha P, Panda D, Dash J. The application of click chemistry for targeting quadruplex nucleic acids. Chem Commun (Camb) 2019; 55:731-750. [PMID: 30489575 DOI: 10.1039/c8cc07107a] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Cu(i)-catalyzed azide and alkyne 1,3-dipolar cycloaddition (CuAAC), commonly known as the "click reaction", has emerged as a powerful and versatile synthetic tool that finds a broad spectrum of applications in chemistry, biology and materials science. The efficiency, selectivity and versatility of the CuAAC reactions have enabled the preparation of vast arrays of triazole compounds with biological and pharmaceutical applications. In this feature article, we outline the applications and future prospects of click chemistry in the synthesis and development of small molecules that target G-quadruplex nucleic acids and show promising biological activities. Furthermore, this article highlights the template-assisted in situ click chemistry for developing G-quadruplex specific ligands and the use of click chemistry for enhancing drug specificity as well as designing imaging and sensor systems to elucidate the biological functions of G-quadruplex nucleic acids in live cells.
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Affiliation(s)
- Puja Saha
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India.
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Zhou Y, Yu Y, Gao L, Fei Y, Ye T, Li Q, Zhou X, Gan N, Shao Y. Structuring polarity-inverted TBA to G-quadruplex for selective recognition of planarity of natural isoquinoline alkaloids. Analyst 2018; 143:4907-4914. [PMID: 30238092 DOI: 10.1039/c8an01561a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Efficient structuring of DNA by small molecules is very crucial in developing DNA-based novel switches with an ideal performance. In this work, we found that inverting only the polarity of the 3' terminal guanine of the thrombin-binding aptamer (3iTBA) totally eradicates the original TBA G-quadruplex (G4) structure in K+. The unstructured 3iTBA can be further refolded upon specifically interacting with small molecules of natural isoquinoline alkaloids (IAs) due to their fruitful binding patterns with variant nucleic acid structures. We identified that 3iTBA can serve as a topology selector for planar IAs. Nitidine (NIT), owing to the planar aromatic ring and coplanar substituents, is the most efficient to restructure the 3iTBA random coil toward the anti-parallel G4 conformation. However, common metal ions can't realize this structuring. The topology selector competency of 3iTBA toward IAs' planarity can be visualized using gold nanoparticles (AuNPs) as the chromogenic readout. Our work expands the G4 repertoire by exploring the polarity inversion regulation and provides a new approach to switch nucleic acid structures toward a small molecule structure-sensitive sensor.
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Affiliation(s)
- Yufeng Zhou
- Institute of Physical Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China.
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11
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Ganesan K, Xu B. Telomerase Inhibitors from Natural Products and Their Anticancer Potential. Int J Mol Sci 2017; 19:ijms19010013. [PMID: 29267203 PMCID: PMC5795965 DOI: 10.3390/ijms19010013] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 12/10/2017] [Accepted: 12/19/2017] [Indexed: 12/25/2022] Open
Abstract
Telomeres and telomerase are nowadays exploring traits on targets for anticancer therapy. Telomerase is a unique reverse transcriptase enzyme, considered as a primary factor in almost all cancer cells, which is mainly responsible to regulate the telomere length. Hence, telomerase ensures the indefinite cell proliferation during malignancy—a hallmark of cancer—and this distinctive feature has provided telomerase as the preferred target for drug development in cancer therapy. Deactivation of telomerase and telomere destabilization by natural products provides an opening to succeed new targets for cancer therapy. This review aims to provide a fundamental knowledge for research on telomere, working regulation of telomerase and its various binding proteins to inhibit the telomere/telomerase complex. In addition, the review summarizes the inhibitors of the enzyme catalytic subunit and RNA component, natural products that target telomeres, and suppression of transcriptional and post-transcriptional levels. This extensive understanding of telomerase biology will provide indispensable information for enhancing the efficiency of rational anti-cancer drug design.
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Affiliation(s)
- Kumar Ganesan
- Food Science and Technology Program, Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai 519087, China.
| | - Baojun Xu
- Food Science and Technology Program, Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai 519087, China.
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12
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Arévalo-Ruiz M, Doria F, Belmonte-Reche E, De Rache A, Campos-Salinas J, Lucas R, Falomir E, Carda M, Pérez-Victoria JM, Mergny JL, Freccero M, Morales JC. Synthesis, Binding Properties, and Differences in Cell Uptake of G-Quadruplex Ligands Based on Carbohydrate Naphthalene Diimide Conjugates. Chemistry 2017; 23:2157-2164. [PMID: 27925323 DOI: 10.1002/chem.201604886] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Indexed: 11/06/2022]
Abstract
The G-quadruplexes (G4s) are currently being explored as therapeutic targets in cancer and other pathologies. Six carbohydrate naphthalene diimide conjugates (carb-NDIs) have been synthesized as G4 ligands to investigate their potential selectivity in G4 binding and cell penetration. Carb-NDIs have shown certain selectivity for G4 structures against DNA duplexes, but different sugar moieties do not induce a preference for a specific G4 topology. Interestingly, when monosaccharides were attached through a short ethylene linker to the NDI scaffold, their cellular uptake was two- to threefold more efficient than that when the sugar was directly attached through its anomeric position. Moreover, a correlation between more efficient cell uptake of these carb-NDIs and their higher toxicity in cancerous cell lines has been observed. Carb-NDIs seem to be mainly translocated into cancer cells through glucose transporters (GLUT), of which GLUT4 plays a major role.
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Affiliation(s)
- Matilde Arévalo-Ruiz
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
| | - Filippo Doria
- Department of Chemistry, University of Pavia, V.le Taramelli 10, 27100, Pavia, Italy
| | - Efres Belmonte-Reche
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
| | - Aurore De Rache
- Institut Européen de Chimie Biologie (IECB), ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, 2, rue Robert Escarpit, Pessac, France
| | - Jenny Campos-Salinas
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
| | - Ricardo Lucas
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
| | - Eva Falomir
- Department of Inorganic and Organic Chemistry, University Jaume I, 12071, Castellón, Spain
| | - Miguel Carda
- Department of Inorganic and Organic Chemistry, University Jaume I, 12071, Castellón, Spain
| | - José María Pérez-Victoria
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
| | - Jean-Louis Mergny
- Institut Européen de Chimie Biologie (IECB), ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, 2, rue Robert Escarpit, Pessac, France
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, V.le Taramelli 10, 27100, Pavia, Italy
| | - Juan Carlos Morales
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC, Parque Tecnológico Ciencias de la Salud, Avenida del Conocimiento, s/n, 18016, Armilla, Granada, Spain
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13
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Mondal S, Jana J, Sengupta P, Jana S, Chatterjee S. Myricetin arrests human telomeric G-quadruplex structure: a new mechanistic approach as an anticancer agent. MOLECULAR BIOSYSTEMS 2016; 12:2506-18. [DOI: 10.1039/c6mb00218h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The use of small molecules to arrest G-quadruplex structure has become a potential strategy for the development and design of a new class of anticancer therapeutics.
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Affiliation(s)
- Soma Mondal
- Department of Biophysics
- Bose Institute
- Kolkata-700054
- India
| | - Jagannath Jana
- Department of Biophysics
- Bose Institute
- Kolkata-700054
- India
| | | | - Samarjit Jana
- Department of Zoology
- West Bengal State University
- Kolkata-126
- India
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14
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Tomar JS. In-silico modeling studies of G-quadruplex with soy isoflavones having anticancerous activity. J Mol Model 2015; 21:193. [PMID: 26164556 DOI: 10.1007/s00894-015-2723-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/08/2015] [Indexed: 12/12/2022]
Abstract
Telomere forms t-loop and G-quadruplex as the protective structure and the formation of these structures hinder the telomerase enzyme action. The binding affinities of ligand which stabilize the G-quadruplex represent good correlation with telomerase inhibition depicted in the anti-cancerous action. Most of the potent G-quadruplex stabilizing compounds suffer from the poor drug like properties. Herein, natural dietary compounds isoflavones were taken for the theoretical study to examine their stabilizing effect on G-quadruplex structure. The experimental G-quadruplex complexes were reproduced to obtain and validate the theoretical parameters. The obtained theoretical binding energies are in significant correlation with the experimental data. Analysis of binding shows isoflavones to be groove binders, and differential nature of quadruplex grooves might be beneficial in the selectivity aspects. Among all, derrubone was found to have better selectivity as well as affinity for the G-quadruplex comparable to well known ligand TMPyP4. The GBSA rescoring result enlightens the various interaction terms involved in the binding process. Cumulative stabilizing effects coming from VDW, ES, and GB energy terms attest to optimal binding of derrubone molecule which can be considered as a lead for the higher phases of drug designing. These findings are of great value in terms of unexplored groove binding modes and the studied natural compounds might be helpful to direct the focus of synthetic chemists in designing of new generation of antitumor agents.
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Affiliation(s)
- Jyoti Singh Tomar
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India,
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15
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Liu X, Chen Y, Fierke CA. A real-time fluorescence polarization activity assay to screen for inhibitors of bacterial ribonuclease P. Nucleic Acids Res 2014; 42:e159. [PMID: 25249623 PMCID: PMC4227764 DOI: 10.1093/nar/gku850] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribonuclease P (RNase P) is an essential endonuclease that catalyzes the 5′ end maturation of precursor tRNA (pre-tRNA). Bacterial RNase P is an attractive potential antibacterial target because it is essential for cell survival and has a distinct subunit composition compared to the eukaryal counterparts. To accelerate both structure-function studies and discovery of inhibitors of RNase P, we developed the first real-time RNase P activity assay using fluorescence polarization/anisotropy (FP/FA) with a 5′ end fluorescein-labeled pre-tRNAAsp substrate. This FP/FA assay also detects binding of small molecules to pre-tRNA. Neomycin B and kanamycin B bind to pre-tRNAAsp with a Kd value that is comparable to their IC50 value for inhibition of RNase P, suggesting that binding of these antibiotics to the pre-tRNA substrate contributes to the inhibitory activity. This assay was optimized for high-throughput screening (HTS) to identify specific inhibitors of RNase P from a 2880 compound library. A natural product derivative, iriginol hexaacetate, was identified as a new inhibitor of Bacillus subtilis RNase P. The FP/FA methodology and inhibitors reported here will further our understanding of RNase P molecular recognition and facilitate discovery of antibacterial compounds that target RNase P.
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Affiliation(s)
- Xin Liu
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yu Chen
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carol A Fierke
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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16
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Fu Y, Duan X, Chen X, Zhang J, Li W. Enantioselective separation of chiral ofloxacin using functional Cu(ii)-coordinated G-rich oligonucleotides. RSC Adv 2014. [DOI: 10.1039/c3ra43251c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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17
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Hänsel R, Foldynová-Trantírková S, Dötsch V, Trantírek L. Investigation of quadruplex structure under physiological conditions using in-cell NMR. Top Curr Chem (Cham) 2013; 330:47-65. [PMID: 22760824 DOI: 10.1007/128_2012_332] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
In this chapter we describe the application of in-cell NMR spectroscopy to the investigation of G-quadruplex structures inside living Xenopus laevis oocytes and in X. laevis egg extract. First, in-cell NMR spectroscopy of nucleic acids (NA) is introduced and applications and limitations of the approach are discussed. In the following text the application of in-cell NMR spectroscopy to investigation of G-quadruplexes are reviewed. Special emphasis is given to the discussion of the influence of the intracellular environmental factors such as low molecular weight compounds, molecular crowding, and hydration on structural behavior of G-quadruplexes. Finally, future perspectives of in-cell NMR spectroscopy for quantitative characterization of G-quadruplexes and NA are discussed.
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Affiliation(s)
- Robert Hänsel
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University, Frankfurt/Main, Germany
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18
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Zhang J, Wang X, Fu Y, Han Y, Cheng J, Zhang Y, Li W. Highly active subnano palladium clusters embedded in i-motif DNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:14345-50. [PMID: 23944161 DOI: 10.1021/la402153b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Highly active subnano Pd clusters were synthesized using i-motif DNA as the template through characterization via ESI MS, DLS, XPS, UV-vis, and FTIR. It is indicated that Pd1-Pd5 clusters are generated at a [Pd]/[base] ratio of 0.2, Pd8 to Pd9 clusters are generated at a [Pd]/[base] ratio of 0.5, and large nanoparticles with the size about 2.6 nm are formed at a [Pd]/[base] ratio of 2.0. The i-motif-stabilized Pd8-Pd9 clusters show high catalytic activity toward the reduction of 4-nitrophenol with a relative rate constant value of 2034 min(-1) (mM Pd)(-1). DFT calculations disclose that the unique structure of the i-motif with consecutive hemiprotonated CH(+)·C pairs can efficiently ligate Pd ions at the N3 sites of cytosines and that the synthesized Pd clusters consist of metallic Pd atoms as well as positively charged Pd that is ligated by nucleobases, which is capable of facilitating the activation of the nitryl group of 4-nitrophenol. This work suggests a promising pathway to preparing subnano metal catalysts with enhanced catalytic activity using programmable DNA scaffolds.
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Affiliation(s)
- Jinli Zhang
- Key Laboratory of Systems Bioengineering MOE and ‡Key Laboratory for Green Chemical Technology MOE, School of Chemical Engineering & Technology, Tianjin University , Tianjin 300072, People's Republic of China
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19
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Fu Y, Wang X, Zhang J, Li W. Nanomaterials and nanoclusters based on DNA modulation. Curr Opin Biotechnol 2013; 28:33-8. [PMID: 24832072 DOI: 10.1016/j.copbio.2013.10.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 10/25/2013] [Accepted: 10/31/2013] [Indexed: 12/27/2022]
Abstract
Besides the inherent chirality, DNA is enriched by nitrogen and oxygen functional groups that are preferential to coordinate with transition metal ions, and its self-assembled structures, including the G-quadruplex, the i-motif, and the conventional Watson-Crick duplex, etc., can be adjusted via different base pairings. Recently biotemplating on the basis of DNA self-assembly has been considered as an attractive method to construct switchable nanomaterials, to direct crystal growth and to design enantioselective selectors/catalysts. This review briefly covers the recent progress relevant to DNA modulated nano/subnano materials. The long-term goal of this area of research is to explore novel promisingly environmental-benign approaches to construct switchable nanomachines, nano/subnano clusters and enantioselective recognition platforms respectively, through DNA-based modulation.
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Affiliation(s)
- Yan Fu
- Key Laboratory of Systems Bioengineering MOE, Key Laboratory for Green Chemical Technology MOE, Tianjin University, Tianjin 300072, People's Republic of China
| | - Xian Wang
- Key Laboratory of Systems Bioengineering MOE, Key Laboratory for Green Chemical Technology MOE, Tianjin University, Tianjin 300072, People's Republic of China
| | - Jinli Zhang
- Key Laboratory of Systems Bioengineering MOE, Key Laboratory for Green Chemical Technology MOE, Tianjin University, Tianjin 300072, People's Republic of China
| | - Wei Li
- Key Laboratory of Systems Bioengineering MOE, Key Laboratory for Green Chemical Technology MOE, Tianjin University, Tianjin 300072, People's Republic of China.
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20
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Shan C, Tan JH, Ou TM, Huang ZS. Natural products and their derivatives as G-quadruplex binding ligands. Sci China Chem 2013. [DOI: 10.1007/s11426-013-4920-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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Yang H, Zhong HJ, Leung KH, Chan DSH, Ma VPY, Fu WC, Nanjunda R, Wilson WD, Ma DL, Leung CH. Structure-based design of flavone derivatives as c-myc oncogene down-regulators. Eur J Pharm Sci 2013; 48:130-41. [DOI: 10.1016/j.ejps.2012.10.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Revised: 09/19/2012] [Accepted: 10/02/2012] [Indexed: 12/21/2022]
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22
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Xu N, Yang H, Cui M, Song F, Liu Z, Liu S. A Study of Interaction between Flavonoids and the Parallel Quadruplex Structure [d(TGGGGT)]
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by Electrospray Ionization Mass Spectrometry. CHINESE J CHEM 2012. [DOI: 10.1002/cjoc.201100641] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Niusheng Xu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Hongmei Yang
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Meng Cui
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Fengrui Song
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Zhiqiang Liu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Shuying Liu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- Changchun University of Chinese Medicine, Changchun, Jilin 130117, China
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23
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Nakamura T, Iida K, Tera M, Shin-ya K, Seimiya H, Nagasawa K. A caged ligand for a telomeric G-quadruplex. Chembiochem 2012; 13:774-7. [PMID: 22438312 DOI: 10.1002/cbic.201200013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Indexed: 12/31/2022]
Affiliation(s)
- Takahiro Nakamura
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho Koganei, Tokyo 184-8588, Japan
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24
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He X, Zhang Z, Zhang Q, Yuan G. Selective recognition of G-quadruplex in the vascular endothelial growth factor gene with small-molecule natural products by electrospray ionization (ESI) mass spectrometry and circular dichroism (CD) spectrometry. CAN J CHEM 2012. [DOI: 10.1139/v11-104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD) spectroscopy were used to investigate selective recognition of G-quadruplex in the vascular endothelial growth factor (VEGF) gene with 12 small-molecule natural products. We found that kaempferol, a natural flavonol, shows the highest binding affinity among the 12 natural molecules. The results from ESI-MS and CD spectra indicated that kaempferol could enhance the thermal stability of the VEGF–G-quadruplex and showed selective recognition for the G-quadruplex in a solution consisting of the G-quadruplex and the corresponding duplex DNA.
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Affiliation(s)
- Xiangwei He
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Department of Chemical Biology, College of Chemistry, Peking University, Beijing 100871, P. R. China
| | - Zhenjiang Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Department of Chemical Biology, College of Chemistry, Peking University, Beijing 100871, P. R. China
| | - Qiang Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Department of Chemical Biology, College of Chemistry, Peking University, Beijing 100871, P. R. China
| | - Gu Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Department of Chemical Biology, College of Chemistry, Peking University, Beijing 100871, P. R. China
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25
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Fu Y, Wang X, Zhang J, Xiao Y, Li W, Wang J. Orderly microaggregates of G-/C-rich oligonucleotides associated with spermine. Biomacromolecules 2011; 12:747-56. [PMID: 21235226 DOI: 10.1021/bm101372h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Spermine-induced orderly assembling properties of G-/C-rich oligonucleotides are investigated in dilute and crowding conditions. The first time we report that the parallel G-quadruplexes is preferential to condense into anisotropic microaggregates in the presence of spermine, whereas the hybrid-type and the antiparallel G-quadruplexes have no significant interactions with spermine; and spermine can induce the condensation of i-motif C-rich oligonucleotides other than the random coiled C-rich strands. Moreover, the condensation of C-rich oligonucleotides can be reversibly regulated by pH and temperature. G-/C-rich oligonucleotides exhibit the cholesteric liquid crystalline phase at low strand concentration in the presence of spermine under crowding conditions. The results illuminate that the parallel G-quadruplex and i-motifs are probably necessity conformations for G-/C-rich oligonucleotides that involved in the regulation of chromosome organization in living cells.
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Affiliation(s)
- Yan Fu
- Key Laboratory for Green Chemical Technology MOE, Tianjin University, Tianjin 300072, People's Republic of China
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