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Tomczyk MD, Kuźnik N, Walczak K. Cyclen-based artificial nucleases: Three decades of development (1989–2022). Part a – Hydrolysis of phosphate esters. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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2
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Tosolini M, Gianferrara T, Mion G, Dovigo L, Mancin F, Sissi C, Tecilla P. Interaction with plasmid DNA of Hoechst-TACN conjugates. Supramol Chem 2019. [DOI: 10.1080/10610278.2019.1699657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Massimo Tosolini
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Teresa Gianferrara
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Giuliana Mion
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Luca Dovigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Fabrizio Mancin
- Department of Chemical Sciences, University of Padova, Padova, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Paolo Tecilla
- Department of Mathematic and Geosciences, University of Trieste, Trieste, Italy
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3
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Kawamoto Y, Bando T, Sugiyama H. Sequence-specific DNA binding Pyrrole-imidazole polyamides and their applications. Bioorg Med Chem 2018; 26:1393-1411. [PMID: 29439914 DOI: 10.1016/j.bmc.2018.01.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/25/2018] [Accepted: 01/28/2018] [Indexed: 12/25/2022]
Abstract
Pyrrole-imidazole polyamides (Py-Im polyamides) are cell-permeable compounds that bind to the minor groove of double-stranded DNA in a sequence-specific manner without causing denaturation of the DNA. These compounds can be used to control gene expression and to stain specific sequences in cells. Here, we review the history, structural variations, and functional investigations of Py-Im polyamides.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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4
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Zhou H, Gao J, Chen Z, Duan S, Li C, Qiao R. Double-strand cleavage of DNA by a polyamide-phenazine-di-N-oxide conjugate. Bioorg Med Chem Lett 2017; 28:284-288. [PMID: 29292228 DOI: 10.1016/j.bmcl.2017.12.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/09/2017] [Accepted: 12/23/2017] [Indexed: 11/15/2022]
Abstract
Phenazine and its derivatives have been widely applied as nucleic acid cleavage agents due to active oxygen activating the C-H bond of the substrate. However, diffusion of oxygen radicals limits their potential applications in the DNA-targeted metal-free drug. Introduction of groove binder moiety such as polyamide enhanced the regional stability of radical molecules and reduced cytotoxicity of the drugs. In this work, we described the design and synthesis of a polyamide-modified phenazine-di-N-oxide as a DNA double-strand cleavage agent. The gel assays showed the hybrid conjugates can effectively break DNA double strands in a non-random manner under physiological conditions. The probable binding mode to DNA was investigated by sufficient spectral experiments, revealing weak interaction between hybrid ligand and nucleic acid molecules. The results of our study have implications on the design of groove-binding hybrid molecules as new artificial nucleases and may provide a strategy for developing efficient and safe DNA cleavage reagents.
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Affiliation(s)
- Hang Zhou
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Juanhong Gao
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Zhaohang Chen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Shan Duan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Chao Li
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China.
| | - Renzhong Qiao
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China; State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences, Peking University Health Sciences Center, Beijing 100083, PR China.
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5
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Conjugates between minor groove binders and Zn(II)-tach complexes: Synthesis, characterization, and interaction with plasmid DNA. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.04.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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6
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Zhou H, Chen D, Bai JK, Sun XL, Li C, Qiao RZ. Effect of ligand sequence-specific modification on DNA hybrid catalysis. Org Biomol Chem 2017; 15:6738-6745. [DOI: 10.1039/c7ob01249g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a sequence-specific catalytic ligand as a chemical modification strategy to achieve DNA-based asymmetric reactions with sequence-dependent enantioselectivity.
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Affiliation(s)
- H. Zhou
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - D. Chen
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - J. K. Bai
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - X. L. Sun
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - C. Li
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
| | - R. Z. Qiao
- State Key Laboratory of Chemical Resource Engineering
- Beijing University of Chemical Technology
- Beijing 100029
- P. R. China
- State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences
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7
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Qiao H, Ma C, Zhang X, Jing X, Li C, Zhao Y. Insight into DNA Minor Groove Unspecific Binding of Pyrrole Polyamide. Bioconjug Chem 2015; 26:2054-61. [PMID: 26301419 DOI: 10.1021/acs.bioconjchem.5b00309] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemistry-based approaches have exploited base-pairing for sequence-specific recognition of DNA. A variety of sequence-specific Py-Im hairpin polyamides to target sequences of biological interest have been widely developed. Here we reported that an eight-ring N-methylpyrrole polyamide can induce a strong negative signal when it interacted with ct-DNA in the minor groove, which differs from the typical CD signal induced by hairpin polyamide reported previously. Our current efforts mainly focused on investigating possible reasons and binding mode by CD spectroscopy, singular value decomposition, and atomic force microscopy. The results suggested that partly compacted DNA may form due to the unfolded binding mode that made DNA shrink along the axis of duplex. In addition, this unfolded binding was remarkably restrained in high ionic strength medium where the neutralized phosphate groups in the DNA backbone narrowed the minor groove. The present work might help to understand deeply how the Py-Im polyamides bind to duplex DNA under different conditions and, in particular, be applied to gene manipulation and expression.
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Affiliation(s)
- Hongwei Qiao
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry of Tsinghua University, Beijing 100084, P. R. China
| | - Chunying Ma
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 100029 Beijing, P. R. China
| | - Xiao Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 100029 Beijing, P. R. China
| | - Xi Jing
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 100029 Beijing, P. R. China
| | - Chao Li
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, 100029 Beijing, P. R. China
| | - Yufen Zhao
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry of Tsinghua University, Beijing 100084, P. R. China
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8
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Li C, Ma C, Zhang J, Qian N, Ding J, Qiao R, Zhao Y. Design and synthesis of novel distamycin-modified nucleoside analogues as HIV-1 reverse transcriptase inhibitors. Antiviral Res 2013; 102:54-60. [PMID: 24342709 DOI: 10.1016/j.antiviral.2013.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 11/09/2013] [Accepted: 12/08/2013] [Indexed: 11/17/2022]
Abstract
Design and synthesis of nucleoside analogues have persistently attracted extensive interest because of their potential application in the field of antiviral therapy, and its study also receives additional impetus for improvement in the ProTide technology. Previous studies have made great strides in the design and discovery of monophosphorylated nucleoside analogues as potential kinase-independent antiretrovirals. In this work, a series of nucleoside phosphoramidates modified by distamycin analogues was synthesized and evaluated as nucleoside reverse transcriptase inhibitors (NRTIs) in HIV-1-infected MT-4 and CEM cells, including variations in nucleoside, alkyl moiety, and the structure of distamycin analogues. These compounds exhibited modest potency with the EC50 value in the range of 1.3- to 6.5-fold lower than their corresponding parent drugs in MT-4 cells, which may be attributed to increasing intracellular availability due to the existence of distamycin analogue with favorable hydrophilic-lipophilic equilibrium. Meanwhile, the length of distamycin analogue was considered and assessed as an important factor that could affect antiviral activity and cytotoxicity. Enzymatic and metabolic stability studies have been performed in order to better understand the antiviral behavior of these compounds. The present work revealed the compounds to have a favorable and selective anti-HIV-1 activity in MT-4 and CEM cells, and helped to develop strategies for design and synthesis of effective monophosphorylated nucleoside analogues, which may be applied to antiretroviral research as NRTIs.
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Affiliation(s)
- Chao Li
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China.
| | - Chunying Ma
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Jin Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Ning Qian
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Jingjing Ding
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Renzhong Qiao
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China; State Key Laboratory of Natural and Biomimetic Drugs School of Pharmaceutical Sciences, Peking University Health Science Center, Beijing 100191, PR China.
| | - Yufen Zhao
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
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Feng FM, Cai S, Liu FA, Xie JQ. Studies of DNA-Binding and DNA-Cutting Mechanism of an Azamacrocyclic Cerium Complex with Carboxyl Branch. PROGRESS IN REACTION KINETICS AND MECHANISM 2013. [DOI: 10.3184/146867813x13738207456695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
An azamacrocyclic compound with a carboxyl branch, 5,5,7,12,12,14-hexamethyl-1,4,8,11-tetraazacyclo-tetradecane- N/-acetic acid (L), and its cerium complex were synthesised and characterised. The mode of combination of the cerium complex with DNA was investigated by fluorescence and UV-Vis absorption spectroscopy. The cutting function of the cerium complex towards supercoiled DNA was studied by the gel electrophoresis method. The results show that metal complex can bind to the phosphate group of DNA double helix and promote the hydrolysis of the phosphodiester bond of supercoiled DNA (Form I); under certain conditions, supercoiled form DNA (Form I) was transformed into the nicked form DNA (Form II) under the strong cutting effect of the macrocyclic cerium complex; the cutting is completed by a hydrolysis mechanism.
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Affiliation(s)
- Fa-mei Feng
- College of Chemistry and Pharmaceutical Engineering, Sichuan University of Science and Engineering, Zigong, Sichuan 643000, P.R. China
| | - Shulan Cai
- College of Chemistry and Pharmaceutical Engineering, Sichuan University of Science and Engineering, Zigong, Sichuan 643000, P.R. China
| | - Fu-an Liu
- College of Chemistry and Pharmaceutical Engineering, Sichuan University of Science and Engineering, Zigong, Sichuan 643000, P.R. China
| | - Jia-qing Xie
- College of Chemistry and Chemical Engineering, Chongqing University of Technology, Chongqing 400054, P.R. China
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Zhang Y, Wang Q, Wen J, Wang X, Mahmood MHR, Ji L, Liu H. DNA Binding and Oxidative Cleavage by a Water-soluble Carboxyl Manganese(III) Corrole. CHINESE J CHEM 2013. [DOI: 10.1002/cjoc.201300488] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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11
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Verzele D, Madder A. Synthetic Progress in cMyc-Max Oncoprotein Miniaturization: Semi-Online Monitoring Gives Solid-Phase Access to Hydrophobic b(-HLH-)ZIP Peptidosteroid Tweezers. European J Org Chem 2012. [DOI: 10.1002/ejoc.201201235] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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12
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Desbouis D, Troitsky IP, Belousoff MJ, Spiccia L, Graham B. Copper(II), zinc(II) and nickel(II) complexes as nuclease mimetics. Coord Chem Rev 2012. [DOI: 10.1016/j.ccr.2011.12.005] [Citation(s) in RCA: 127] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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13
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Abstract
The development of synthetic agents able to hydrolytically cleave DNA with high efficiency and selectivity is still a fascinating challenge. Over the years, many examples have been reported reproducing part of the behaviour of the corresponding natural enzymes. Eventually, even the possibility to apply such systems to the manipulation of DNA of higher organisms has been demonstrated. However, efficiency of enzymes is still unrivalled. This feature article discusses the progress reported toward the realization of synthetic nucleases with particular attention to the comprehension of the reaction mechanisms and to the strategies that need to be addressed to obtain more efficient systems.
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Affiliation(s)
- Fabrizio Mancin
- Dipartimento di Scienze Chimiche, Università di Padova, via Marzolo 1, I -35131 Padova, Italy.
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14
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Ullrich S, Nazir Z, Büsing A, Scheffer U, Wirth D, Bats JW, Dürner G, Göbel MW. Cleavage of phosphodiesters and of DNA by a bis(guanidinium)naphthol acting as a metal-free anion receptor. Chembiochem 2011; 12:1223-9. [PMID: 21500334 DOI: 10.1002/cbic.201100022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Indexed: 11/07/2022]
Abstract
Phosphoric acid diesters form anions at neutral pH. As a result of charge repulsion they are notoriously resistant to hydrolysis. Nucleophilic attack, however, can be promoted by different types of electrophilic catalysts that bind to the anions and reduce their negative charge density. Although in most cases phosphodiester-cleaving enzymes and synthetic catalysts rely on Lewis acidic metal ions, some exploit the guanidinium residues of arginine as metal-free electrophiles. Here we report that a combination of two guanidines and a hydroxy group yields highly reactive receptor molecules that can attack a broad range of phosphodiester substrates by nucleophilic displacement at phosphorus in a single-turnover mode. Some stable O-phosphates were isolated and characterized further by NMR spectroscopy. The bis(guanidinium)naphthols also cleave plasmid DNA, presumably by a transphosphorylation mechanism.
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Affiliation(s)
- Stefan Ullrich
- Institut für Organische Chemie und Chemische Biologie, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main, Germany
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