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Luo Y, Granzhan A, Marquevielle J, Cucchiarini A, Lacroix L, Amrane S, Verga D, Mergny JL. Guidelines for G-quadruplexes: I. In vitro characterization. Biochimie 2023; 214:5-23. [PMID: 36596406 DOI: 10.1016/j.biochi.2022.12.019] [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: 10/29/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/02/2023]
Abstract
Besides the well-known DNA double-helix, non-canonical nucleic acid structures regulate crucial biological activities. Among these oddities, guanine-rich DNA sequences can form unusual four-stranded secondary structures called G-quadruplexes (G4s). G4-prone sequences have been found in the genomes of most species, and G4s play important roles in essential processes such as transcription, replication, genome integrity and epigenetic regulation. Here, we present a short overview of G-quadruplexes followed by a detailed description of the biophysical and biochemical methods used to characterize G4s in vitro. The principles, experimental details and possible shortcomings of each method are discussed to provide a comprehensive view of the techniques used to study these structures. We aim to provide a set of guidelines for standardizing research on G-quadruplexes; these guidelines are not meant to be a dogmatic set of rules, but should rather provide useful information on the methods currently used to study these fascinating motifs.
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Affiliation(s)
- Yu Luo
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France; CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France; CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
| | - Julien Marquevielle
- Université de Bordeaux, ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, 33076, Bordeaux, France
| | - Anne Cucchiarini
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Laurent Lacroix
- Institut de Biologie de L'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Samir Amrane
- Université de Bordeaux, ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, 33076, Bordeaux, France
| | - Daniela Verga
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France; CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France.
| | - Jean-Louis Mergny
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France; Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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Liu L, Jin X, Lu X, Guo L, Lu P, Yu H, Lv B. Mechanisms of Surfactin from Bacillus subtilis SF1 against Fusarium foetens: A Novel Pathogen Inducing Potato Wilt. J Fungi (Basel) 2023; 9:jof9030367. [PMID: 36983535 PMCID: PMC10056554 DOI: 10.3390/jof9030367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/10/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Fusarium wilt is a severe and worldwide disease in potato cultivation. In this study, Fusarium foetens was first identified as the pathogen of potato wilt. Bacillus subtilis SF1 has the potential for controlling potato wilt induced by F. foetens, resulting in a mycelium growth inhibition of 52.50 ± 2.59% in vitro and a significant decrease in incidence rate by 45.56% in vivo. This research highlighted the antifungal activity of surfactin from B. subtilis SF1 and attempted to reveal the unknown antifungal mechanisms. Surfactin inhibited F. foetens mycelium growth beyond the concentration of 20 μg/μL. Surfactin-treated mycelium appeared to have morphological malformation. Surfactin enhanced reduced glutathione production and caused the increase in values of the extracellular fluids in OD260 and OD280. Surfactin induced differential protein expression and changed the genes’ transcription levels. Surfactin binds to fungal DNA via groove-binding mode, with a binding constant of Kb 2.97 × 104 M−1. Moreover, B. subtilis SF1 harbored genes encoding plant-promoting determinants, making potato seedlings grow vigorously. The results will help provide a comprehensive understanding of the mechanisms of surfactin against filamentous fungi and the application of surfactin-producing microbial in the biocontrol of plant pathogenic fungi.
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Affiliation(s)
- Lin Liu
- College of Life Science, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaofan Jin
- College of Life Science, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiuhua Lu
- College of Life Science, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao 266109, China
| | - Lizhong Guo
- College of Life Science, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao 266109, China
| | - Peiwei Lu
- Bayer Crop Science China Co., Ltd., Hangzhou 310018, China
| | - Hao Yu
- College of Life Science, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao 266109, China
- Correspondence: (H.Y.); (B.L.)
| | - Beibei Lv
- Biotechnology Research Institute, Key Laboratory of Agricultural Genetics and Breeding, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
- Correspondence: (H.Y.); (B.L.)
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Spychala J. Antitumor activity of triazine mimic antibiotics for DNA-binding implications (impressive activity in vitro against a variety of tumor types in the NCI-60 screen): NSC 710607 to fight HCT-116 human colon carcinoma cell lines in vivo using the hollow fiber assay and xenograft mouse models. J Cancer Res Clin Oncol 2023:10.1007/s00432-023-04604-6. [PMID: 36780052 DOI: 10.1007/s00432-023-04604-6] [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: 12/05/2022] [Accepted: 01/25/2023] [Indexed: 02/14/2023]
Abstract
PURPOSE Successful clinical applications of DNA-directed selective cytotoxic agents disrupt the vital replication/transcription processes and ultimately lead to cancer cell death. This study aimed to examine the growth screen of two lead triazine compounds in a number of cell lines and xenografts and to develop anticancer agents with noncovalent binding affinity bringing fewer side effects. METHODS The NCI initial hollow fiber test was performed using an established procedure. The cytostatic and cytocidal capacities of the test compounds were assessed by evaluating cytotoxicity by simply performing a standard cellular viability assay. The nude mouse human tumor xenograft system was used as an in vivo model. RESULTS More sensitive drug with sub-micromolar activity met the interdisciplinary criteria for testing and was referred to evaluations in subcutaneous colorectal carcinoma HCT-116 human tumor xenografted into nude mice. Principal findings of the study: total cytostasis, almost nontoxic schedules, specific working hypotheses, strong rationale for the potential use, and important general implications (relevance to human biology). NSC 710607 displayed in vivo better than Cisplatin and 5-fluorouracil abilities to significantly decrease tumor growth. CONCLUSION Cell proliferation can be reduced or stopped in vivo in view of the xenograft results. The mimic molecule behaves as DNA-binding antitumor antibiotics with great potential as general anticancer agents and deserves further trials. NSC 710607 represents the result of a design strategy with outstanding potential. This study also identifies the prognostic significance and is likely to translate to other species or systems.
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Tentellino C, Tipping WJ, McGee LMC, Bain LM, Wetherill C, Laing S, Tyson-Hirst I, Suckling CJ, Beveridge R, Scott FJ, Faulds K, Graham D. Ratiometric imaging of minor groove binders in mammalian cells using Raman microscopy. RSC Chem Biol 2022; 3:1403-1415. [PMID: 36544571 PMCID: PMC9709774 DOI: 10.1039/d2cb00159d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/23/2022] [Indexed: 02/02/2023] Open
Abstract
Quantitative drug imaging in live cells is a major challenge in drug discovery and development. Many drug screening techniques are performed in solution, and therefore do not consider the impact of the complex cellular environment in their result. As such, important features of drug-cell interactions may be overlooked. In this study, Raman microscopy is used as a powerful technique for semi-quantitative imaging of Strathclyde-minor groove binders (S-MGBs) in mammalian cells under biocompatible imaging conditions. Raman imaging determined the influence of the tail group of two novel minor groove binders (S-MGB-528 and S-MGB-529) in mammalian cell models. These novel S-MGBs contained alkyne moieties which enabled analysis in the cell-silent region of the Raman spectrum. The intracellular uptake concentration, distribution and mechanism were evaluated as a function of the pK a of the tail group, morpholine and amidine, for S-MGB-528 and S-MGB-529, respectively. Although S-MGB-529 had a higher binding affinity to the minor groove of DNA in solution-phase measurements, the Raman imaging data indicated that S-MGB-528 showed a greater degree of intracellular accumulation. Furthermore, using high resolution stimulated Raman scattering (SRS) microscopy, the initial localisation of S-MGB-528 was shown to be in the nucleus before accumulation in the lysosome, which was demonstrated using a multimodal imaging approach. This study highlights the potential of Raman spectroscopy for semi-quantitative drug imaging studies and highlights the importance of imaging techniques to investigate drug-cell interactions, to better inform the drug design process.
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Affiliation(s)
- Christian Tentellino
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - William J. Tipping
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of StrathclydeGlasgow G1 1RDUK
| | - Leah M. C. McGee
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of StrathclydeGlasgowG1 1XLUK
| | - Laura M. Bain
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of StrathclydeGlasgowG1 1XLUK
| | - Corinna Wetherill
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - Stacey Laing
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - Izaak Tyson-Hirst
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde Glasgow G1 1XL UK
| | - Colin J. Suckling
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of StrathclydeGlasgowG1 1XLUK
| | - Rebecca Beveridge
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde Glasgow G1 1XL UK
| | - Fraser J. Scott
- Department of Pure and Applied Chemistry, Thomas Graham Building, University of StrathclydeGlasgowG1 1XLUK
| | - Karen Faulds
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
| | - Duncan Graham
- Centre for Molecular Nanometrology, WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde Glasgow G1 1RD UK
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Ma X, Shi L, Zhang B, Liu L, Fu Y, Zhang X. Recent advances in bioprobes and biolabels based on cyanine dyes. Anal Bioanal Chem 2022; 414:4551-4573. [PMID: 35359180 DOI: 10.1007/s00216-022-03995-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/19/2022] [Accepted: 02/28/2022] [Indexed: 11/30/2022]
Abstract
As a functional dye, cyanine dye promotes the widespread application of bioprobes in the fields of medicine, genetics and environment, owing to its advantages of good photophysical properties, excellent biocompatibility and low toxicity to biological systems. Nowadays, it is mainly used in the fields of life sciences such as fluorescent labeling of biological macromolecules, disease diagnosis, immunoassay and DNA detection, all of which lie at the core of this review. First, we briefly introduced the characteristics and principles of the cyanine dye bioprobe. Afterward, we paid attention to the recent progress of cyanine dye bioprobes widely used in the 10 years from 2010 to 2020. The application of cyanine dyes as bioprobes with different identification elements, including enzymes, organelles, immunity and DNAs, was mainly summarized. Finally, this review gave an outlook on the future development trend of cyanine dye bioprobes. This facilitates the construction of a new type of multifunctional fluorescent probe and promotes its clinical application.
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Affiliation(s)
- Xiaoying Ma
- College of Chemical Engineering, Hebei and Tangshan Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology, 063210, Tangshan, China
| | - Lei Shi
- College of Chemical Engineering, Hebei and Tangshan Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology, 063210, Tangshan, China.
| | - Buyue Zhang
- College of Chemical Engineering, Hebei and Tangshan Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology, 063210, Tangshan, China
| | - Lu Liu
- College of Chemical Engineering, Hebei and Tangshan Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology, 063210, Tangshan, China
| | - Yao Fu
- College of Chemical Engineering, Hebei and Tangshan Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology, 063210, Tangshan, China
| | - Xiufeng Zhang
- College of Chemical Engineering, Hebei and Tangshan Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology, 063210, Tangshan, China.
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Murade CU, Shubeita GT. A fluorescent reporter on electrostatic DNA-ligand interactions. BIOMEDICAL OPTICS EXPRESS 2022; 13:159-167. [PMID: 35154861 PMCID: PMC8803044 DOI: 10.1364/boe.439791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/22/2021] [Accepted: 11/28/2021] [Indexed: 06/14/2023]
Abstract
Among the various types of interactions between biomolecules, electrostatic interactions dominate as these are long-range interactions and are often a generic first step in the recruitment of specific ligands. DNA, being a highly charged molecule, attracts a plethora of molecules. Interactions between DNA and proteins or small molecules shape the overall function of the cell. Various processes such as DNA replication, DNA repair, synthesis of mRNA, and packaging of DNA are mediated by interactions between protein molecules and DNA that are predominantly electrostatic. Here, we present a fluorescence resonance energy transfer (FRET)-based probe which can report on the electrostatic interactions between the negatively-charged DNA and positively-charged metal ions, oligopeptides, as well as DNA groove-binding drug molecules. The simplicity, sensitivity, and versatility of the DNA-based probe makes it suited for applications where specific protein-DNA interactions can be probed, and DNA-binding drugs can be discovered in high-throughput screens of compound libraries. This is particularly relevant given that some of the most potent antitumor and antimicrobial drugs associate with DNA electrostatically.
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Ortiz de Luzuriaga I, Elleuchi S, Jarraya K, Artacho E, Lopez X, Gil A. Semi-empirical and Linear-Scaling DFT Methods to Characterize duplex DNA and G-quadruplexes in Presence of Interacting Small Molecules. Phys Chem Chem Phys 2022; 24:11510-11519. [DOI: 10.1039/d2cp00214k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The computational study of DNA and its interaction with ligands is a highly relevant area of research, with significant consequences for developing new therapeutic strategies. However, the computational description of...
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3-Methyl-imidazo[2,1-b]thiazole derivatives as a new class of antifolates: Synthesis, in vitro/in vivo bio-evaluation and molecular modeling simulations. Bioorg Chem 2021; 115:105205. [PMID: 34329992 DOI: 10.1016/j.bioorg.2021.105205] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/07/2021] [Accepted: 07/20/2021] [Indexed: 11/24/2022]
Abstract
Inhibiting the Dihydrofolate reductase (DHFR) enzyme has been validated in multiple clinical manifestations related to bacterial infection, malaria, and multiple types of cancer. Herein, novel series of 3-methyl-imidazo[2,1-b] thiazole-based analogs were synthesized and biologically evaluated for their in vitro inhibitory profile towards DHFR. Compounds 22 and 23 exhibited potent inhibitory profile targeting DHFR (IC50 0.079 and 0.085 µM, respectively comparable to MTX IC50 0.087 µM). Compounds 22 and 23 showed promising cytotoxicity against MCF7 breast cancer cell lines inducing cell cycle arrest and apoptosis. Furthermore, Compound 23 showed its potential to reduce body weight and tumor volume significantly, using Ehrlich ascites carcinoma (EAC) solid tumor animal model of breast cancer, compared to control-treated groups. Further, molecular modeling simulations validated the potential of 22 and 23 to have high affinity binding towards Arg22 and Phe31 residues via π-π interaction and hydrogen bonding within DHFR binding pocket. Computer-assisted ADMET study suggested that the newly synthesized analogs could have high penetration to the blood brain barrier (BBB), better intestinal absorption, non-inhibitors of CYP2D6, adequate plasma protein binding and good passive oral absorption. The obtained model and pattern of substitution could be used for further development of DHFR inhibitors.
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Wróbel A, Drozdowska D. Recent Design and Structure-Activity Relationship Studies on the Modifications of DHFR Inhibitors as Anticancer Agents. Curr Med Chem 2021; 28:910-939. [PMID: 31622199 DOI: 10.2174/0929867326666191016151018] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Dihydrofolate reductase (DHFR) has been known for decades as a molecular target for antibacterial, antifungal and anti-malarial treatments. This enzyme is becoming increasingly important in the design of new anticancer drugs, which is confirmed by numerous studies including modelling, synthesis and in vitro biological research. This review aims to present and discuss some remarkable recent advances in the research of new DHFR inhibitors with potential anticancer activity. METHODS The scientific literature of the last decade on the different types of DHFR inhibitors has been searched. The studies on design, synthesis and investigation structure-activity relationships were summarized and divided into several subsections depending on the leading molecule and its structural modification. Various methods of synthesis, potential anticancer activity and possible practical applications as DHFR inhibitors of new chemical compounds were described and discussed. RESULTS This review presents the current state of knowledge on the modification of known DHFR inhibitors and the structures and searches for about eighty new molecules, designed as potential anticancer drugs. In addition, DHFR inhibitors acting on thymidylate synthase (TS), carbon anhydrase (CA) and even DNA-binding are presented in this paper. CONCLUSION Thorough physicochemical characterization and biological investigations highlight the structure-activity relationship of DHFR inhibitors. This will enable even better design and synthesis of active compounds, which would have the expected mechanism of action and the desired activity.
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Affiliation(s)
- Agnieszka Wróbel
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University, Białystok, Poland
| | - Danuta Drozdowska
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University, Białystok, Poland
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Singu PS, Chilakamarthi U, Mahadik NS, Keerti B, Valipenta N, Mokale SN, Nagesh N, Kumbhare RM. Benzimidazole-1,2,3-triazole hybrid molecules: synthesis and study of their interaction with G-quadruplex DNA. RSC Med Chem 2021; 12:416-429. [PMID: 34046624 DOI: 10.1039/d0md00414f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/12/2021] [Indexed: 12/18/2022] Open
Abstract
A series of new benzimidazole-1,2,3-triazole hybrid derivatives have been synthesized via 'click' reaction and evaluated for their in vitro cytotoxicity as well as DNA binding affinity. MTT assay showed that all the six compounds are cytotoxic to PC3 and B16-F10 cancer cell lines. Though all the compounds showed moderate interaction with G4, c-Myc promoter DNA and dsDNA, 4f exhibited selective interaction with G-quadruplex DNA over duplex DNA as demonstrated by spectroscopic experiments like UV-vis spectroscopy, fluorescence spectroscopy, CD spectroscopy, thermal melting and fluorescence lifetime experiments. They also confirm the G-quadruplex DNA stabilizing potential of 4f. Viscosity measurements also confirm that 4f exhibits high G-quadruplex DNA selectivity over duplex DNA. Docking studies supported the spectroscopic observations. Cell cycle analysis showed that 4f induces G2/M phase arrest and induces apoptosis. Hence, from these experimental results it is evident that compound 4f may be a G-quadruplex DNA groove binding molecule with anticancer activity.
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Affiliation(s)
- Padma S Singu
- Department of Fluoro-Agrochemicals, CSIR-Indian Institute of Chemical Technology Tarnaka Hyderabad 500007 India .,Academy of Scientific and Innovative Research (AcSIR) Ghaziabad India
| | - Ushasri Chilakamarthi
- Polymers and Functional Materials Division, CSIR-Indian Institute of Chemical Technology Hyderabad-500007 India
| | - Namita S Mahadik
- Applied Biology Division, CSIR-Indian Institute of Chemical Technology Hyderabad-500007 India
| | - Bhamidipati Keerti
- Applied Biology Division, CSIR-Indian Institute of Chemical Technology Hyderabad-500007 India
| | - Narasimhulu Valipenta
- Department of Fluoro-Agrochemicals, CSIR-Indian Institute of Chemical Technology Tarnaka Hyderabad 500007 India .,Academy of Scientific and Innovative Research (AcSIR) Ghaziabad India
| | - Santosh N Mokale
- Y. B. Chavan College of Pharmacy Dr. Rafiq Zakaria Campus Aurangabad-431001 India
| | - Narayana Nagesh
- Medical Biotechnology Complex, CSIR-Centre for Cellular and Molecular Biology ANNEXE II, Uppal Road Hyderabad 500007 India
| | - Ravindra M Kumbhare
- Department of Fluoro-Agrochemicals, CSIR-Indian Institute of Chemical Technology Tarnaka Hyderabad 500007 India .,Academy of Scientific and Innovative Research (AcSIR) Ghaziabad India
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A novel insight into the cytotoxic effects of Tephrosin with calf thymus DNA: Experimental and in silico approaches. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114728] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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12
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Iqbal Farooqi S, Arshad N, Perveen F, Ali Channar P, Saeed A, Javed A, Hökelek T, Flörke U. Structure and surface analysis of ibuprofen-organotin conjugate: Potential anti-cancer drug candidacy of the compound is proven by in-vitro DNA binding and cytotoxicity studies. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114845] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Wang Z, Li J, Liu J, Wang L, Lu Y, Liu JP. Molecular insight into the selective binding between human telomere G-quadruplex and a negatively charged stabilizer. Clin Exp Pharmacol Physiol 2020; 47:892-902. [PMID: 31894867 DOI: 10.1111/1440-1681.13249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 12/30/2019] [Indexed: 12/13/2022]
Abstract
The single-strand human telomere overhang forms intramolecular high-order structures named G-quadruplex (G4) under physiological conditions. Telomere G4 stabilization prevents telomere lengthening by telomerase in cancer cells representing a promising strategy in cancer therapy. Using molecular docking and molecular dynamics (MD) simulations, specific binding of the anionic phthalocyanine 3,4',4'',4'''-tetrasulfonic acid (APC) to the human hybrid (3 + 1) G4s was investigated at the atomic level. We found that APC preferred the end-stacking binding with the telomere hybrid type II (hybrid-II) G4 as compared to the groove binding with the hybrid type I (hybrid-I) G4 remarkable stabilizing effect and more favourable binding free energies. Analysis of non-covalent interaction and decomposition of the binding free energy revealed that van der Waals interaction played a leading role in the binding of APC and telomere hybrid G4s. These findings provide evidence for the first time to shed light on the designs of selective telomere G4 stabilizers.
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Affiliation(s)
- Zhiguo Wang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Jianfeng Li
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Jun Liu
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Lihui Wang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Yanhua Lu
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Jun-Ping Liu
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University, Hangzhou, China.,Department of Immunology, Central Eastern Clinical School, Monash University, Melbourne, Australia.,Hudson Institute of Medical Research, Clayton, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, Australia
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Khosravifar F, Dehghan G, Bidoki SK, Mahdavi M. DNA‐binding activity and cytotoxic and cell‐cycle arrest properties of some new coumarin derivatives: a multispectral and computational investigation. LUMINESCENCE 2019; 35:98-106. [DOI: 10.1002/bio.3702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 07/17/2019] [Accepted: 08/03/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Fariba Khosravifar
- Department of Biology, Faculty of SciencePayame Noor University (PNU) P. O. Box 19395‐3697 Tehran Iran
| | - Gholamreza Dehghan
- Department of Biology, Faculty of Natural SciencesUniversity of Tabriz Tabriz Iran
| | - Seyed Kazem Bidoki
- Department of Biology, Faculty of SciencePayame Noor University (PNU) P. O. Box 19395‐3697 Tehran Iran
| | - Majid Mahdavi
- Department of Biology, Faculty of Natural SciencesUniversity of Tabriz Tabriz Iran
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Kinyanyi D, Amwayi P, Wamalwa M, Obiero G. Comparative in silico study of congocidine congeners as potential inhibitors of African swine fever virus. PLoS One 2019; 14:e0221175. [PMID: 31461446 PMCID: PMC6713398 DOI: 10.1371/journal.pone.0221175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/31/2019] [Indexed: 01/08/2023] Open
Abstract
African swine fever virus (ASFV) infection is fatal in domesticated pigs, with a mortality rate approaching 100%. This may result in economic losses and threats to food security. Currently, there are no approved vaccines or antiviral therapies for ASFV. Therefore, in this study, we evaluated congocidine congeners and a tris-benzimidazole as potential inhibitors of ASFV transcription using an in silico approach. We applied redocking of congocidine and docking of its congeners and a tris-benzimidazole to a receptor containing B-DNA with AT-motifs as a target to mimic conserved ASFV late gene promoters. Subsequently, the binding scores of DNA-ligand docked complexes were evaluated and their binding affinity was estimated. Molecular dynamics (MD) simulation was then used to assess ligand behavior within the minor groove. From our results, it is evident the less toxic congocidine congeners and tris-benzimidazole could dock to AT-rich regions significantly. Additionally, the predicted binding affinities had suitable values comparable to other experimentally determined minor groove binders, MD simulation of the docked DNA-ligand complexes and subsequent molecular trajectory visualization further showed that the ligands remained embedded in the minor groove during the time course of simulation, indicating that these ligands may have potential applications in abrogating ASFV transcription.
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Affiliation(s)
- Dickson Kinyanyi
- Department of Biochemistry and Biotechnology, Technical University of Kenya, Nairobi, Kenya
- * E-mail:
| | - Peris Amwayi
- Department of Biochemistry and Biotechnology, Technical University of Kenya, Nairobi, Kenya
| | - Mark Wamalwa
- Department of Biochemistry and Biotechnology, Kenyatta University, Nairobi, Kenya
| | - George Obiero
- Center for Biotechnology and Bioinformatics, University of Nairobi, Nairobi, Kenya
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Shahabadi N, Akhtarshenas S, Hadidi S. Synthesis, characterization and DNA interaction studies of new copper complex containing pseudoephedrine hydrochloride drug. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:680-699. [PMID: 30942140 DOI: 10.1080/15257770.2019.1599909] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A new copper(II) complex, [Cu(pse)(phen)Cl2]; in which phen = 1,10-phenanthroline and pse = pseudoephedrine hydrochloride drug; was synthesized and characterized by FT-IR, Mass and UV-Vis spectroscopy in combination with computational methods. Binding interaction of this complex with calf thymus DNA (ct-DNA) has been investigated by absorption, emission, circular dichroism, molecular docking and viscosity measurements. The complex displays significant binding properties of ct-DNA. The results of fluorescence and UV-Vis absorption spectroscopy indicated that, this complex interacted with ct-DNA in a groove-binding mode, and the binding constant was 8 × 104 L mol-1. Competitive fluorimetric studies with Hoechst 33258 have shown that Cu(II) complex exhibit the ability to displace the DNA-bound Hoechst 33258 indicating that it binds to DNA in strong competition with Hoechst 33258 for the groove binding. Furthermore, the complex induces detectable changes in the CD spectrum of ct-DNA and does not induce any changes in DNA viscosity which verified the groove-binding mode. The molecular modeling results illustrated that the complex strongly binds to groove of DNA by relative binding energy of docked structure (-27.61 kJ mol-1).
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Affiliation(s)
- Nahid Shahabadi
- a Department of Inorganic chemistry Faculty of Chemistry , Razi University , Kermanshah , Iran.,b Medical Biology Research Center (MBRC) Kermanshah University of Medical Sciences , Kermanshah , Iran
| | - Shirin Akhtarshenas
- a Department of Inorganic chemistry Faculty of Chemistry , Razi University , Kermanshah , Iran
| | - Saba Hadidi
- a Department of Inorganic chemistry Faculty of Chemistry , Razi University , Kermanshah , Iran.,b Medical Biology Research Center (MBRC) Kermanshah University of Medical Sciences , Kermanshah , Iran
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17
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Sabir F, Farooq RK, Asim.ur.Rehman, Ahmed N. Monocyte as an Emerging Tool for Targeted Drug Delivery: A Review. Curr Pharm Des 2019; 24:5296-5312. [DOI: 10.2174/1381612825666190102104642] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 12/21/2018] [Indexed: 12/30/2022]
Abstract
Monocytes are leading component of the mononuclear phagocytic system that play a key role in phagocytosis and removal of several kinds of microbes from the body. Monocytes are bone marrow precursor cells that stay in the blood for a few days and migrate towards tissues where they differentiate into macrophages. Monocytes can be used as a carrier for delivery of active agents into tissues, where other carriers have no significant access. Targeting monocytes is possible both through passive and active targeting, the former one is simply achieved by enhanced permeation and retention effect while the later one by attachment of ligands on the surface of the lipid-based particulate system. Monocytes have many receptors e.g., mannose, scavenger, integrins, cluster of differentiation 14 (CD14) and cluster of differentiation 36 (CD36). The ligands used against these receptors are peptides, lectins, antibodies, glycolipids, and glycoproteins. This review encloses extensive introduction of monocytes as a suitable carrier system for drug delivery, the design of lipid-based carrier system, possible ways for delivery of therapeutics to monocytes, and the role of monocytes in the treatment of life compromising diseases such as cancer, inflammation, stroke, etc.
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Affiliation(s)
- Fakhara Sabir
- Department of Pharmacy, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Rai K. Farooq
- Department of Neuroscience Research, Institute of Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, P.O Box 1982, Dammam 31441, Saudi Arabia
| | - Asim.ur.Rehman
- Department of Pharmacy, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Naveed Ahmed
- Department of Pharmacy, Quaid-i-Azam University, Islamabad 45320, Pakistan
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18
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Shi WJ, Ren FD. Cooperativity effect of the ππ interaction between drug and DNA on intercalative binding induced by H-bonds: a QM/QTAIM investigation of the curcuminadenineH 2O model system. Phys Chem Chem Phys 2019; 21:11871-11882. [PMID: 31119251 DOI: 10.1039/c9cp01667h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In order to reveal the nature of intercalative binding of drug to DNA, the cooperativity effect of the ππ interaction was investigated in the curcuminadenineH2O model system by applying a combined QM and QTAIM computational approach. The H-bonds between the electron-donating group of curcumin and adenine induce the formation of the ππ stacking. The introduction of H2O weakens the H-bonding and ππ interactions, leading to an anti-cooperativity effect, as is confirmed by the AIM (atoms in molecules) and RDG (reduced density gradient) analysis. Thus, it can be inferred that the anti-cooperative effect is the main driving force for the intercalative binding of drug to DNA bases, which is in agreement with many experimental phenomena. Therefore, the designed DNA-targeted intercalating drugs should possess not only hydrophobic moieties, but also strong electron-donating groups bound to the DNA bases with H-bonds, which can slow the variation rates of the strengths of the H-bonding and ππ interactions between drug and DNA bases in the anti-cooperative process, leading to the intercalation formation. The enthalpy change is the major factor driving the positive thermodynamic cooperativity.
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Affiliation(s)
- Wen-Jing Shi
- The Second Hospital of Shanxi Medical University, Taiyuan 030053, China.
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19
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Prusov AN, Smirnova TA, Kolomijtseva GY. Thermodynamic Study of Interactions of Distamycin A with Chromatin in Rat Liver Nuclei in the Presence of Polyamines. BIOCHEMISTRY (MOSCOW) 2018; 83:1231-1244. [PMID: 30472960 DOI: 10.1134/s0006297918100085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We studied the thermodynamics of melting of isolated rat liver nuclei with different degrees of chromatin condensation determined by the concentration of polyamines (PA) and the solution ionic strength, as well as the effect of the antibiotic distamycin A (DM) on melting. Differential scanning calorimetry (DSC) profiles of nuclear preparations contained three peaks that reflected melting of three main chromatin domains. The number of peaks did not depend on the degree of condensation; however, nuclei with more condensed chromatin had a higher total enthalpy. DM stabilized peaks II and III corresponding to the melting of relaxed and topologically strained DNA, respectively, but destabilized peak I corresponding to the melting of nucleosome core histones. At the saturating concentration (DM/DNA molar ratio = 0.1), DM increased Tm of peaks II and III by ~5°C and decreased Tm of peak I by ~2.5°C. Based on the dependence of ΔH on DM concentration, we established that at low DM/DNA ratio (≤0.03), when DM interacted predominantly with AT-rich DNA regions, the enthalpy of peak II decreased in parallel with the increase in the enthalpy of peak III, which indicated that DM induces structural transitions in the nuclear chromatin associated with the increase in torsional stress in DNA. An increase in free energy under saturation conditions was equal to the change in the free energy of DM interaction with DNA. However, the increase in the enthalpy of melting of the nuclei in the presence of DM was much greater than the enthalpy of titration of nuclei with DM. This indicates a significant increase in the strength of interaction between the two DNA strands apparently due, among other things, to changes in the torsional stress of DNA in the nuclei. Titration of the nuclei with increasing PA concentrations resulted in the decrease in the number of DM-binding sites and the non-monotonous dependence of the enthalpy and entropy contribution to the binding free energy on the PA content. We suggested that the observed differences in the thermodynamic parameters were due to the different width of the minor groove in the nuclear chromatin DNA, which depends on PA concentration.
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Affiliation(s)
- A N Prusov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - T A Smirnova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.,Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - G Ya Kolomijtseva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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20
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Pan J, Cao DL, Ren FD, Wang JL, Yang L. Theoretical investigation into the cooperativity effect between the intermolecular π∙π and H-bonding interactions in the curcumin∙cytosine∙H2O system. J Mol Model 2018; 24:298. [DOI: 10.1007/s00894-018-3836-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/14/2018] [Indexed: 12/25/2022]
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21
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Duchemin N, Skiredj A, Mansot J, Leblanc K, Vasseur J, Beniddir MA, Evanno L, Poupon E, Smietana M, Arseniyadis S. DNA‐Templated [2+2] Photocycloaddition: A Straightforward Entry into the Aplysinopsin Family of Natural Products. Angew Chem Int Ed Engl 2018; 57:11786-11791. [DOI: 10.1002/anie.201806357] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Nicolas Duchemin
- Queen Mary University of LondonSchool of Biological and Chemical Sciences Mile End Road London E1 4NS UK
| | - Adam Skiredj
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCISUniversité Paris-SudUniversité Paris-Saclay 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Justine Mansot
- Institut des Biomolécules Max MousseronCNRS, UMR 5247 Université de MontpellierENSCM Place Eugène Bataillon 34095 Montpellier France
| | - Karine Leblanc
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCISUniversité Paris-SudUniversité Paris-Saclay 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Jean‐Jacques Vasseur
- Institut des Biomolécules Max MousseronCNRS, UMR 5247 Université de MontpellierENSCM Place Eugène Bataillon 34095 Montpellier France
| | - Mehdi A. Beniddir
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCISUniversité Paris-SudUniversité Paris-Saclay 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Laurent Evanno
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCISUniversité Paris-SudUniversité Paris-Saclay 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Erwan Poupon
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCISUniversité Paris-SudUniversité Paris-Saclay 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Michael Smietana
- Institut des Biomolécules Max MousseronCNRS, UMR 5247 Université de MontpellierENSCM Place Eugène Bataillon 34095 Montpellier France
| | - Stellios Arseniyadis
- Queen Mary University of LondonSchool of Biological and Chemical Sciences Mile End Road London E1 4NS UK
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Duchemin N, Skiredj A, Mansot J, Leblanc K, Vasseur JJ, Beniddir MA, Evanno L, Poupon E, Smietana M, Arseniyadis S. DNA-Templated [2+2] Photocycloaddition: A Straightforward Entry into the Aplysinopsin Family of Natural Products. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806357] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Nicolas Duchemin
- Queen Mary University of London; School of Biological and Chemical Sciences; Mile End Road London E1 4NS UK
| | - Adam Skiredj
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCIS; Université Paris-Sud; Université Paris-Saclay; 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Justine Mansot
- Institut des Biomolécules Max Mousseron; CNRS, UMR 5247 Université de Montpellier; ENSCM; Place Eugène Bataillon 34095 Montpellier France
| | - Karine Leblanc
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCIS; Université Paris-Sud; Université Paris-Saclay; 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron; CNRS, UMR 5247 Université de Montpellier; ENSCM; Place Eugène Bataillon 34095 Montpellier France
| | - Mehdi A. Beniddir
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCIS; Université Paris-Sud; Université Paris-Saclay; 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Laurent Evanno
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCIS; Université Paris-Sud; Université Paris-Saclay; 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Erwan Poupon
- Laboratoire de Pharmacognosie associé au CNRS, UMR 8076 BioCIS; Université Paris-Sud; Université Paris-Saclay; 5 rue Jean-Baptiste Clément 92296 Châtenay-Malabry France
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron; CNRS, UMR 5247 Université de Montpellier; ENSCM; Place Eugène Bataillon 34095 Montpellier France
| | - Stellios Arseniyadis
- Queen Mary University of London; School of Biological and Chemical Sciences; Mile End Road London E1 4NS UK
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23
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Hadwiger LA, Tanaka K. DNA Damage and Chromatin Conformation Changes Confer Nonhost Resistance: A Hypothesis Based on Effects of Anti-cancer Agents on Plant Defense Responses. FRONTIERS IN PLANT SCIENCE 2018; 9:1056. [PMID: 30087685 PMCID: PMC6066612 DOI: 10.3389/fpls.2018.01056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 06/28/2018] [Indexed: 05/06/2023]
Abstract
Over the last decades, medical research has utilized DNA altering procedures in cancer treatments with the objective of killing cells or suppressing cell proliferation. Simultaneous research related to enhancing disease resistance in plants reported that alterations in DNA can enhance defense responses. These two opposite perspectives have in common their effects on the center for gene transcription, the nuclear chromatin. A review of selected research from both anticancer- and plant defense-related research provides examples of some specific DNA altering actions: DNA helical distortion, DNA intercalation, DNA base substitution, DNA single cleavage by DNases, DNA alkylation/methylation, and DNA binding/exclusion. The actions of the pertinent agents are compared, and their proposed modes of action are described in this study. Many of the DNA specific agents affecting resistance responses in plants, e.g., the model system using pea endocarp tissue, are indeed anticancer agents. The tumor cell death or growth suppression in cancer cells following high level treatments may be accompanied with chromatin distortions. Likewise, in plants, DNA-specific agents activate enhanced expression of many genes including defense genes, probably due to the chromatin alterations resulting from the agents. Here, we propose a hypothesis that DNA damage and chromatin structural changes are central mechanisms in initiating defense gene transcription during the nonhost resistance response in plants.
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Affiliation(s)
- Lee A. Hadwiger
- Department of Plant Pathology, Washington State University, Pullman, WA, United States
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24
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A novel calix[4]pyrrole derivative as a potential anticancer agent that forms genotoxic adducts with DNA. Sci Rep 2018; 8:11075. [PMID: 30038406 PMCID: PMC6056420 DOI: 10.1038/s41598-018-29314-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/09/2018] [Indexed: 01/03/2023] Open
Abstract
meso-(p-acetamidophenyl)-calix[4]pyrrole 3 was found to exhibit remarkable cytotoxicity towards A549 cancer cells. A comparative study including the isomer of 3 meso-(m-acetamidophenyl)-calix[4]pyrrole 5, as well as molecules containing 'fragments' of these structures, demonstrated that both the calix[4]pyrrole and the acetamidophenyl units are essential for high cytotoxicity. Although calix[4]pyrroles and other anion-complexing ionophores have recently been reported to induce apoptosis by perturbing cellular chloride concentrations, in our study an alternative mechanism has emerged, as proven by the isolation of covalent DNA adducts revealed by the 32P postlabelling technique. Preliminary pharmacokinetic studies indicate that 3 is able to cross the Blood-Brain-Barrier, therefore being a potential drug that could kill primary and brain metastatic cancer cells simultaneously.
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25
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Portugal J. Challenging transcription by DNA-binding antitumor drugs. Biochem Pharmacol 2018; 155:336-345. [PMID: 30040927 DOI: 10.1016/j.bcp.2018.07.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/20/2018] [Indexed: 12/15/2022]
Abstract
Cancer has been associated with altered gene expression. Therefore, transcription and its regulation by transcription factors are considered key points to be explored in the pursuit of more efficient antitumor agents. This paper reviews the effects of DNA-binding drugs on the interaction between transcription factors and DNA, and it discusses recent advances in the understanding of the mechanisms by which small compounds interfere with the activity of transcription factors and gene expression. Many DNA-binding drugs, some of them in clinical use, can compete with a variety of transcription factors for their preferred binding sites in gene promoters, or they can covalently modify DNA, thus preventing transcription factors from recognizing their binding sites. On the other hand, transcription factor activity can be impaired through modification of the protein factors or their complexes. Several "omic" tools have been developed to explore the genome-wide changes in gene expression induced by DNA-binding drugs, which reveal details of the mechanisms of action. Transcriptomic profiles obtained from drug-treated cells and of samples collected from patients upon treatment provide insights into the in vivo mechanisms of drug action related to the inhibition of gene transcription. The information available about the molecular structure and mechanisms of action of both transcription factors and DNA-binding drugs, together with the new opportunities provided by functional genomics, should encourage the development of new more-selective DNA-binding antitumor drugs to target a single gene with little effect on others.
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Affiliation(s)
- José Portugal
- Instituto de Diagnóstico Ambiental y Estudios del Agua, CSIC, E-08034 Barcelona, Spain.
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26
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Bhaduri S, Ranjan N, Arya DP. An overview of recent advances in duplex DNA recognition by small molecules. Beilstein J Org Chem 2018; 14:1051-1086. [PMID: 29977379 PMCID: PMC6009268 DOI: 10.3762/bjoc.14.93] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 04/06/2018] [Indexed: 12/13/2022] Open
Abstract
As the carrier of genetic information, the DNA double helix interacts with many natural ligands during the cell cycle, and is amenable to such intervention in diseases such as cancer biogenesis. Proteins bind DNA in a site-specific manner, not only distinguishing between the geometry of the major and minor grooves, but also by making close contacts with individual bases within the local helix architecture. Over the last four decades, much research has been reported on the development of small non-natural ligands as therapeutics to either block, or in some cases, mimic a DNA–protein interaction of interest. This review presents the latest findings in the pursuit of novel synthetic DNA binders. This article provides recent coverage of major strategies (such as groove recognition, intercalation and cross-linking) adopted in the duplex DNA recognition by small molecules, with an emphasis on major works of the past few years.
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Affiliation(s)
| | - Nihar Ranjan
- National Institute of Pharmaceutical Education and Research (NIPER), Raebareli 122003, India
| | - Dev P Arya
- NUBAD, LLC, 900B West Faris Rd., Greenville 29605, SC, USA.,Clemson University, Hunter Laboratory, Clemson 29634, SC, USA
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27
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Wu Y, Bai J, Liu X, Liu L, Zhong K, Huang Y, Gao H. Antibacterial effect of 3-p-trans-coumaroyl-2-hydroxyquinic acid, a phenolic compound from needles ofCedrus deodara, on cellular functions ofStaphylococcus aureus. RSC Adv 2018; 8:4969-4975. [PMID: 35539522 PMCID: PMC9077780 DOI: 10.1039/c7ra13457f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 01/22/2018] [Indexed: 11/21/2022] Open
Abstract
Structure–activity relationship of 3-p-trans-coumaroyl-2-hydroxyquinic acid, a phenolic compound from needles ofCedrus deodara, againstStaphylococcus aureusand its effect on the cellular functions.
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Affiliation(s)
- Yanping Wu
- Healthy Food Evaluation Research Center
- Sichuan University
- Chengdu 610065
- China
- Department of Food Science and Technology
| | - Jinrong Bai
- Department of Food Science and Technology
- College of Light Industry, Textile and Food Engineering
- Sichuan University
- Chengdu 610065
- China
| | - Xiaoyan Liu
- Department of Food Science and Technology
- College of Light Industry, Textile and Food Engineering
- Sichuan University
- Chengdu 610065
- China
| | - Lijin Liu
- Department of Public Health
- West China Medical School
- Sichuan University
- Chengdu 610041
- China
| | - Kai Zhong
- Healthy Food Evaluation Research Center
- Sichuan University
- Chengdu 610065
- China
- Department of Food Science and Technology
| | - Yina Huang
- Department of Public Health
- West China Medical School
- Sichuan University
- Chengdu 610041
- China
| | - Hong Gao
- Healthy Food Evaluation Research Center
- Sichuan University
- Chengdu 610065
- China
- Department of Food Science and Technology
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28
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Zhen JP, Wei XC, Shi WJ, Huang ZY, Jin B, Zhou YK. Cooperativity effect involving drug-DNA/RNA intermolecular interaction: A B3LYP-D3 and MP2 theoretical investigation on ketoprofen⋯cytosine⋯H 2O system. J Biomol Struct Dyn 2017; 36:3587-3606. [PMID: 29092677 DOI: 10.1080/07391102.2017.1400469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In order to examine the origin of the drug action and design new DNA/RNA-targeted drugs, the cooperativity effect involving drug-DNA/RNA intermolecular interaction in ketoprofen⋯cytosine⋯H2O ternary system were investigated by the B3LYP, B3LYP-D3, and MP2 methods with the 6-311++G(2d,p) basis set. The thermodynamic cooperativity was also evaluated at 310.15 K. The N-H⋯O, O-H⋯O, O-H⋯N, C-H⋯N, and C-H⋯O H bonds coexist in ternary complexes. The intermolecular interactions obtained by B3LYP-D3 are close to those calculated by MP2. The steric effects and van der Waals interactions have little influence on the cooperativity effects. The anti-cooperativity effect in ket⋯cyt⋯H2O is far more notable than the cooperativity effect, and the stability of the cyclic structure with anti-cooperativity effect is higher than that of the linear structure with cooperativity effect, as is confirmed by the AIM (atoms in molecules) and RDG (reduced density gradient) analysis. Thus, it can be inferred that, in the presence of H2O, the anti-cooperativity effect plays a dominant role in the drug-DNA/RNA interaction, and the nature of the hydration in the binding of drugs to DNA/RNA bases is the H-bonding anti-cooperativity effect. Furthermore, the drug always links simultaneously with DNA/RNA base and H2O, and only in this way can the biological activity of drugs play a role. In most cases, the enthalpy change is the major factor driving the cooperativity, as is different from most of biomacromolecule complexes.
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Affiliation(s)
- Jun-Ping Zhen
- a Molecular Imaging Laboratory, Department of Radiology , The Second Hospital of Shanxi Medical University , Taiyuan 030053 , China
| | - Xiao-Chun Wei
- a Molecular Imaging Laboratory, Department of Radiology , The Second Hospital of Shanxi Medical University , Taiyuan 030053 , China
| | - Wen-Jing Shi
- a Molecular Imaging Laboratory, Department of Radiology , The Second Hospital of Shanxi Medical University , Taiyuan 030053 , China
| | - Zhu-Yuan Huang
- a Molecular Imaging Laboratory, Department of Radiology , The Second Hospital of Shanxi Medical University , Taiyuan 030053 , China
| | - Bo Jin
- a Molecular Imaging Laboratory, Department of Radiology , The Second Hospital of Shanxi Medical University , Taiyuan 030053 , China
| | - Yu-Kun Zhou
- a Molecular Imaging Laboratory, Department of Radiology , The Second Hospital of Shanxi Medical University , Taiyuan 030053 , China
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29
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Rajebhosale BS, Dongre SN, Deshpande SS, Kate AN, Kumbhar AA. Aryl-1H-imidazole[4,5 f ][1,10]phenanthroline Cu(II) complexes: Electrochemical and DNA interaction studies. J Inorg Biochem 2017; 175:129-137. [DOI: 10.1016/j.jinorgbio.2017.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 07/05/2017] [Accepted: 07/09/2017] [Indexed: 10/19/2022]
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30
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Ewida MA, Abou El Ella DA, Lasheen DS, Ewida HA, El-Gazzar YI, El-Subbagh HI. Thiazolo[4,5-d]pyridazine analogues as a new class of dihydrofolate reductase (DHFR) inhibitors: Synthesis, biological evaluation and molecular modeling study. Bioorg Chem 2017; 74:228-237. [PMID: 28865294 DOI: 10.1016/j.bioorg.2017.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 08/12/2017] [Accepted: 08/22/2017] [Indexed: 01/08/2023]
Abstract
A new series of 1,3-thiazoles and thiazolo[4,5-d]pyridazine both bearing the 2-thioureido function were designed, synthesized and evaluated for their invitro DHFR inhibition and antitumor activities. Compound 26 proved to be the most active DHFR inhibitor (IC50 of 0.06μM). Compound 4, 20 and 21 showed in vitro antitumor activity against a collection of cancer cell lines. Compound 26 proved lethal to HS 578T breast cancer cell line with IC50 value of 0.8μM, inducing cell cycle arrest and apoptosis. Molecular modeling studies concluded that recognition with key amino acids Phe 31 and Arg 22 is essential for DHFR binding. The obtained model could be useful for the development of new class of DHFR inhibitors.
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Affiliation(s)
- Menna A Ewida
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences & Pharmaceutical Industries, Future University in Egypt, 12311 Cairo, Egypt
| | - Dalal A Abou El Ella
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Deena S Lasheen
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Heba A Ewida
- Department of Pharmacology and Biochemistry, Faculty of Pharmaceutical Sciences & Pharmaceutical Industries, Future University in Egypt, 12311 Cairo, Egypt
| | - Yomna I El-Gazzar
- Department of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences & Pharmaceutical Industries, Future University in Egypt, 12311 Cairo, Egypt
| | - Hussein I El-Subbagh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, 35516 Mansoura, Egypt.
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31
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Aikawa H, Yano A, Nakatani K. A 2,7-diamino-1,4,8-triazanaphthalene derivative selectively binds to cytosine bulge DNA only at a weakly acidic pH. Org Biomol Chem 2017; 15:1313-1316. [PMID: 27847943 DOI: 10.1039/c6ob02273a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis and properties of 2,7-diamino-1,4,8-triazanaphthalene (azaDANP) are described. AzaDANP is protonated only at a weakly acidic pH to bind to the cytosine bulge DNA duplex selectively. Upon binding of azaDANP to the cytosine bulge DNA, a new absorption band at 407 nm appears, and the absorption change of azaDANP on binding to the target is very sensitive to environmental pH with a bell-shaped pH-absorption profile.
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Affiliation(s)
- H Aikawa
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
| | - A Yano
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
| | - K 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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32
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Liu CH, Tsao MH, Sahoo SL, Wu WC. Magnetic nanoparticles with fluorescence and affinity for DNA sensing and nucleus staining. RSC Adv 2017. [DOI: 10.1039/c6ra25610d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The fluorescence magnetic nanoparticles offer versatile platforms for nucleus imaging and DNA adsorption.
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Affiliation(s)
- Chi-Hsien Liu
- Graduate Institute of Biochemical and Biomedical Engineering
- Chang Gung University
- Tao-Yuan 333
- Taiwan
- Graduate Institute of Health Industry Technology
| | - Min-Han Tsao
- Graduate Institute of Biochemical and Biomedical Engineering
- Chang Gung University
- Tao-Yuan 333
- Taiwan
| | - Soubhagya Laxmi Sahoo
- Graduate Institute of Biochemical and Biomedical Engineering
- Chang Gung University
- Tao-Yuan 333
- Taiwan
| | - Wei-Chi Wu
- Department of Ophthalmology
- Chang Gung Memorial Hospital
- Taoyuan
- Taiwan
- College of Medicine
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33
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Shahabadi N, Falsafi M, Maghsudi M. DNA-binding study of anticancer drug cytarabine by spectroscopic and molecular docking techniques. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2016; 36:49-65. [PMID: 27759491 DOI: 10.1080/15257770.2016.1218021] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The interaction of anticancer drug cytarabine with calf thymus DNA (CT-DNA) was investigated in vitro under simulated physiological conditions by multispectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated drug interacted with CT-DNA in a groove-binding mode, while the binding constant of UV-vis and the number of binding sites were 4.0 ± 0.2 × 104 L mol-1 and 1.39, respectively. The fluorimetric studies showed that the reaction between the drugs with CT-DNA is exothermic. Circular dichroism spectroscopy was employed to measure the conformational change of DNA in the presence of cytarabine. Furthermore, the drug induces detectable changes in its viscosity for DNA interaction. The molecular modeling results illustrated that cytarabine strongly binds to groove of DNA by relative binding energy of docked structure -20.61 KJ mol-1. This combination of multiple spectroscopic techniques and molecular modeling methods can be widely used in the investigation on the interaction of small molecular pollutants and drugs with biomacromolecules for clarifying the molecular mechanism of toxicity or side effect in vivo.
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Affiliation(s)
- Nahid Shahabadi
- a Department of Inorganic Chemistry, Faculty of Chemistry , Razi University , Kermanshah , Iran.,b Medical Biology Research Center (MBRC) , Kermanshah University of Medical Sciences , Kermanshah , Iran
| | - Monireh Falsafi
- a Department of Inorganic Chemistry, Faculty of Chemistry , Razi University , Kermanshah , Iran
| | - Maryam Maghsudi
- a Department of Inorganic Chemistry, Faculty of Chemistry , Razi University , Kermanshah , Iran
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34
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Study on interaction between the 2-(2-phenylethyl)-5-methylbenzimidazole and dsDNA using glassy carbon electrode modified with poly-3-amino-1,2,4-triazole-5-thiol. J Electroanal Chem (Lausanne) 2016. [DOI: 10.1016/j.jelechem.2016.06.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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35
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Ivanov AA, Salyanov VI, Zhuze AL. DNA sequence-specific ligands: XV. Synthesis and spectral characteristics of a new series of dimeric bisbenzimidazoles DB(1, 2, 6, 8, 9, 10, 12). RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1068162016020059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Synthesis of Diphenyl Pyridazinone-based flexible system for conformational studies through weak noncovalent interactions: Application in DNA binding. J CHEM SCI 2016. [DOI: 10.1007/s12039-016-1059-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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37
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Jana S, Santra RC, Frontera A, Drew MGB, Ortega-Castro J, Fernández D, Das S, Chattopadhyay S. Copper(II) pseudohalide complexes with isomeric N2O donor Schiff base ligands: Synthesis, characterization and molecular dynamics simulations of interactions with DNA. ChemistrySelect 2016. [DOI: 10.1002/slct.201500018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Subrata Jana
- Department of Chemistry; Inorganic Section; Jadavpur University; Kolkata - 700 032 India
| | - Ramesh Chandra Santra
- Department of Chemistry; Inorganic Section; Jadavpur University; Kolkata - 700 032 India
| | - Antonio Frontera
- Departament de Química; Universitat de les Illes Balears; Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares SPAIN
| | - Michael G. B. Drew
- School of Chemistry; The University of Reading; P.O. Box 224 Whiteknights Reading RG6 6AD UK
| | - Joaquín Ortega-Castro
- Departament de Química; Universitat de les Illes Balears; Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares SPAIN
| | - David Fernández
- Departament de Química; Universitat de les Illes Balears; Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares SPAIN
| | - Saurabh Das
- Department of Chemistry; Inorganic Section; Jadavpur University; Kolkata - 700 032 India
| | - Shouvik Chattopadhyay
- Department of Chemistry; Inorganic Section; Jadavpur University; Kolkata - 700 032 India
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38
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Synthesis and antiproliferative activity evaluation of new thiazole–benzimidazole derivatives using real-time cell analysis (RTCA DP). Med Chem Res 2016. [DOI: 10.1007/s00044-016-1507-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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39
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Unexpected regiospecific formation and DNA binding of new 3-(acridin-9-yl)methyl-2-iminothiazolidin-4-ones. J CHEM SCI 2016. [DOI: 10.1007/s12039-015-1023-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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40
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K. V. D, V. V, C. R. Rational design and interaction studies of combilexins towards duplex DNA. MOLECULAR BIOSYSTEMS 2016; 12:860-7. [DOI: 10.1039/c5mb00808e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Combilexins interact more strongly with DNA than any other class of DNA binders.
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Affiliation(s)
- Dileep K. V.
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram
- Trivandrum-695016
- India
| | - Vijeesh V.
- Department of Biotechnology and Microbiology and Inter-University Centre for Bioscience
- Kannur University
- Palayad P O
- India
| | - Remya C.
- Department of Biotechnology and Microbiology and Inter-University Centre for Bioscience
- Kannur University
- Palayad P O
- India
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41
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Rombouts K, Braeckmans K, Remaut K. Fluorescent Labeling of Plasmid DNA and mRNA: Gains and Losses of Current Labeling Strategies. Bioconjug Chem 2015; 27:280-97. [PMID: 26670733 DOI: 10.1021/acs.bioconjchem.5b00579] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Live-cell imaging has provided the life sciences with insights into the cell biology and dynamics. Fluorescent labeling of target molecules proves to be indispensable in this regard. In this Review, we focus on the current fluorescent labeling strategies for nucleic acids, and in particular mRNA (mRNA) and plasmid DNA (pDNA), which are of interest to a broad range of scientific fields. By giving a background of the available techniques and an evaluation of the pros and cons, we try to supply scientists with all the information needed to come to an informed choice of nucleic acid labeling strategy aimed at their particular needs.
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Affiliation(s)
- K Rombouts
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Braeckmans
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Remaut
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
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42
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Gattuso H, Duchanois T, Besancenot V, Barbieux C, Assfeld X, Becuwe P, Gros PC, Grandemange S, Monari A. Interaction of Iron II Complexes with B-DNA. Insights from Molecular Modeling, Spectroscopy, and Cellular Biology. Front Chem 2015; 3:67. [PMID: 26734600 PMCID: PMC4683171 DOI: 10.3389/fchem.2015.00067] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 11/25/2015] [Indexed: 11/13/2022] Open
Abstract
We report the characterization of the interaction between B-DNA and three terpyridin iron II complexes. Relatively long time-scale molecular dynamics (MD) is used in order to characterize the stable interaction modes. By means of molecular modeling and UV-vis spectroscopy, we prove that they may lead to stable interactions with the DNA duplex. Furthermore, the presence of larger π-conjugated moieties also leads to the appearance of intercalation binding mode. Non-covalent stabilizing interactions between the iron complexes and the DNA are also characterized and evidenced by the analysis of the gradient of the electronic density. Finally, the structural deformations induced on the DNA in the different binding modes are also evidenced. The synthesis and chemical characterization of the three complexes is reported, as well as their absorption spectra in presence of DNA duplexes to prove the interaction with DNA. Finally, their effects on human cell cultures have also been evidenced to further enlighten their biological effects.
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Affiliation(s)
- Hugo Gattuso
- Université de Lorraine – Nancy and Centre National de la Recherche Scientifique, Theory-Simulation-Modeling, SRSMCNancy, France
| | - Thibaut Duchanois
- Université de Lorraine – Nancy and Centre National de la Recherche Scientifique, Hécrin, SRSMCNancy, France
| | - Vanessa Besancenot
- Université de Lorraine – Nancy and Centre National de la Recherche Scientifique, CRANNancy, France
| | - Claire Barbieux
- Université de Lorraine – Nancy and Centre National de la Recherche Scientifique, CRANNancy, France
| | - Xavier Assfeld
- Université de Lorraine – Nancy and Centre National de la Recherche Scientifique, Theory-Simulation-Modeling, SRSMCNancy, France
| | - Philippe Becuwe
- Université de Lorraine – Nancy and Centre National de la Recherche Scientifique, CRANNancy, France
| | - Philippe C. Gros
- Université de Lorraine – Nancy and Centre National de la Recherche Scientifique, Hécrin, SRSMCNancy, France
| | - Stephanie Grandemange
- Université de Lorraine – Nancy and Centre National de la Recherche Scientifique, CRANNancy, France
| | - Antonio Monari
- Université de Lorraine – Nancy and Centre National de la Recherche Scientifique, Theory-Simulation-Modeling, SRSMCNancy, France
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43
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Rubinson M, Parkinson J, Evstigneev M. Entropic binding mode preference in cooperative homo-dimeric drug–DNA recognition. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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44
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Karapetian AT, Grigoryan ZA, Mamasakhlisov YS, Minasyants MV, Vardevanyan PO. Theoretical treatment of helix–coil transition of complexes DNA with two different ligands having different binding parameters. J Biomol Struct Dyn 2015; 34:201-5. [DOI: 10.1080/07391102.2015.1010584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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45
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Chen C, Zhang J, Zhang Y, Yang Z, Wu H, Pan G, Bai Y. Gadolinium(III) and dysprosium(III) complexes with a Schiff base bis(N-salicylidene)-3-oxapentane-1,5-diamine: synthesis, characterization, antioxidation, and DNA-binding studies. J COORD CHEM 2015. [DOI: 10.1080/00958972.2015.1007965] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Chengyong Chen
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, PR China
| | - Jiawen Zhang
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, PR China
| | - Yanhui Zhang
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, PR China
| | - Zaihui Yang
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, PR China
| | - Huilu Wu
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, PR China
| | - Guolong Pan
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, PR China
| | - Yuchen Bai
- School of Chemical and Biological Engineering, Lanzhou Jiaotong University, Lanzhou, PR China
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46
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Zhang C, Ren B, Lin Z, Tong L, Wang H, Chen S. An analysis method for simultaneous screening of deoxyribonucleic acid-binding active compounds and investigating their mechanisms by ultra-fast liquid chromatography tandem mass spectrometry coupled with fluorescence detection technology. J Chromatogr A 2015; 1381:160-72. [DOI: 10.1016/j.chroma.2015.01.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 12/24/2014] [Accepted: 01/08/2015] [Indexed: 12/30/2022]
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47
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Zhang L, McHale CM, Greene N, Snyder RD, Rich IN, Aardema MJ, Roy S, Pfuhler S, Venkatactahalam S. Emerging approaches in predictive toxicology. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2014; 55:679-688. [PMID: 25044351 PMCID: PMC4749138 DOI: 10.1002/em.21885] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 06/19/2014] [Indexed: 05/29/2023]
Abstract
Predictive toxicology plays an important role in the assessment of toxicity of chemicals and the drug development process. While there are several well-established in vitro and in vivo assays that are suitable for predictive toxicology, recent advances in high-throughput analytical technologies and model systems are expected to have a major impact on the field of predictive toxicology. This commentary provides an overview of the state of the current science and a brief discussion on future perspectives for the field of predictive toxicology for human toxicity. Computational models for predictive toxicology, needs for further refinement and obstacles to expand computational models to include additional classes of chemical compounds are highlighted. Functional and comparative genomics approaches in predictive toxicology are discussed with an emphasis on successful utilization of recently developed model systems for high-throughput analysis. The advantages of three-dimensional model systems and stem cells and their use in predictive toxicology testing are also described.
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Affiliation(s)
- Luoping Zhang
- Genes and Environment Laboratory, Division of Environmental Health and Sciences, School of Public Health, University of California, Berkeley, California
| | - Cliona M. McHale
- Genes and Environment Laboratory, Division of Environmental Health and Sciences, School of Public Health, University of California, Berkeley, California
| | - Nigel Greene
- Compound Safety Prediction, Worldwide Medicinal Chemistry, Pfizer World-wide R&D, Groton, Connecticut
| | | | | | - Marilyn J. Aardema
- Marilyn Aardema Consulting, LLC, Fairfield Ohio
- Toxicology Division, BioReliance Corporation, Rockville, Maryland
| | - Shambhu Roy
- Toxicology Division, BioReliance Corporation, Rockville, Maryland
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48
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Kuhn H, Sahu B, Rapireddy S, Ly DH, Frank-Kamenetskii MD. Sequence specificity at targeting double-stranded DNA with a γ-PNA oligomer modified with guanidinium G-clamp nucleobases. ARTIFICIAL DNA, PNA & XNA 2014; 1:45-53. [PMID: 21687526 DOI: 10.4161/adna.1.1.12444] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Revised: 05/19/2010] [Accepted: 05/24/2010] [Indexed: 11/19/2022]
Abstract
γ-PNA, a new class of peptide nucleic acids, promises to overcome previous sequence limitations of double-stranded DNA (dsDNA) targeting with PNA. To check the potential of γ-PNA, we have synthesized a biotinylated, pentadecameric γ-PNA of mixed sequence carrying three guanidinium G-clamp nucleobases. We have found that strand invasion reactions of the γ-PNA oligomer to its fully complementary target within dsDNA occurs with significantly higher binding rates than to targets containing single mismatches. Association of the PNA oligomer to mismatched targets does not go to completion but instead reaches a stationary level at or below 60%, even at conditions of very low ionic strength. Initial binding rates to both matched and mismatched targets experience a steep decrease with increasing salt concentration. We demonstrate that a linear DNA target fragment with the correct target sequence can be purified from DNA mixtures containing mismatched target or unrelated genomic DNA by affinity capture with streptavidin-coated magnetic beads. Similarly, supercoiled plasmid DNA is obtained with high purity from an initial sample mixture that included a linear DNA fragment with the fully complementary sequence. Based on the results obtained in this study we believe that γ-PNA has a great potential for specific targeting of chosen duplex DNA sites in a sequence-unrestricted fashion.
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Affiliation(s)
- Heiko Kuhn
- Center for Advanced Biotechnology; Department of Biomedical Engineering; Boston University; Boston, MA USA
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49
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Hammarson M, Nilsson JR, Li S, Lincoln P, Andréasson J. DNA-Binding Properties of Amidine-Substituted Spiropyran Photoswitches. Chemistry 2014; 20:15855-62. [DOI: 10.1002/chem.201405113] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Indexed: 12/25/2022]
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50
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Vargiu AV, Magistrato A. Atomistic-Level Portrayal of Drug-DNA Interplay: A History of Courtships and Meetings Revealed by Molecular Simulations. ChemMedChem 2014; 9:1966-81. [DOI: 10.1002/cmdc.201402203] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Indexed: 12/19/2022]
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