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Verebová V, Bedlovičová Z, Bednáriková Z, Staničová J. Monitoring of DNA structural changes after incorporation of the phenylpyrazole insecticide fipronil. Arch Biochem Biophys 2024; 756:110001. [PMID: 38636692 DOI: 10.1016/j.abb.2024.110001] [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: 01/22/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
The use of insecticides presents a risk to the environment because they can accumulate in the water, soil, air, and organisms, endangering human and animal health. It is therefore essential to investigate the effects of different groups of insecticides on individual biomacromolecules such as DNA. We studied fipronil, which belongs to the group of phenylpyrazole insecticides. The interaction of fipronil with calf thymus DNA was investigated using spectroscopic methods (absorption and fluorescence spectroscopy) complemented with infrared spectroscopy and viscosity measurement. Fluorescence emission spectroscopy showed the formation of a fipronil/DNA complex with a combined static and dynamic type of quenching. The binding constant was 4.15 × 103 L/mol. Viscosity changes were recorded to confirm/disconfirm the intercalation mode of interaction. A slight change in DNA viscosity in the presence of fipronil was observed. The phenylpyrazole insecticide does not cause significant conformational changes in DNA structure or increase of its chain length. We hypothesize that fipronil is incorporated into the minor groove of the DNA macromolecule via hydrogen interactions as indicated by FT-IR and CD measurements.
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Affiliation(s)
- Valéria Verebová
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine & Pharmacy, Komenského 73, 040 01, Košice, Slovakia
| | - Zdenka Bedlovičová
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine & Pharmacy, Komenského 73, 040 01, Košice, Slovakia
| | - Zuzana Bednáriková
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Science, Watsonova 1935/47, 040 01, Košice, Slovakia
| | - Jana Staničová
- Department of Chemistry, Biochemistry and Biophysics, University of Veterinary Medicine & Pharmacy, Komenského 73, 040 01, Košice, Slovakia; Institute of Biophysics and Informatics, First Faculty of Medicine, Charles University, Kateřinská 1, Prague, Czech Republic.
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2
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Tian Z, Ding T, Niu H, Mu Y, Xu N, Kong M, Zhang Y, Tian Z, Wu Y, Wang C. The substituent group effect: investigation of naphthalimide-spermidine conjugates binding to DNA by spectroscopy, molecular docking and dynamics. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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3
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Shahabadi N, Farhadi R. Multispectroscopic and molecular docking studies on DNA binding of guaifenesin drug. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2021; 40:317-335. [PMID: 33463400 DOI: 10.1080/15257770.2021.1872793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The interaction mechanism of guaifenesin drug; (RS)-3-(2-methoxyphenoxy)propane-1,2-diol; and calf thymus DNA was characterized by multiple spectroscopic and molecular docking approaches. The changes in drug electronic absorption with increasing DNA concentration and also the observed significant quenching of guaifenesin emission in the presence of DNA proved the complex formation between guaifenesin and DNA during the interactions. Both the binding constant and thermodynamic parameters for the interaction have been calculated in 283, 298, and 310 K at pH 7.4. The results Δ H 0 = 17.87 kJ/mol and Δ S 0 = 143.31 J/mol.K confirmed the role of hydrophobic force in the guaifenesin-DNA interaction. Circular dichroism study showed that guaifenesin causes decrease in the negative band of CT-DNA and at the same time the positive band increases which indicated the transition of DNA conformation from B to A. KI quenching experiment specifies that guaifenesin binds to DNA via nonintercalative mode. The competitive studies based on known Hoechst 33258 and methylene blue probes proved the groove binding mode in guaifenesin-DNA adduct. Further, full agreement of molecular docking simulation with the experimental results of binding constant and interaction mode, support high accuracy of the results.
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Affiliation(s)
- Nahid Shahabadi
- Faculty of Chemistry, Department of Inorganic Chemistry, Razi University, Kermanshah, Iran.,Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Reza Farhadi
- Faculty of Chemistry, Department of Inorganic Chemistry, Razi University, Kermanshah, Iran
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Silva MP, Saibert C, Bortolotto T, Bortoluzzi AJ, Schenk G, Peralta RA, Terenzi H, Neves A. Dinuclear copper(II) complexes with derivative triazine ligands as biomimetic models for catechol oxidases and nucleases. J Inorg Biochem 2020; 213:111249. [PMID: 33011624 DOI: 10.1016/j.jinorgbio.2020.111249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/25/2020] [Accepted: 08/30/2020] [Indexed: 11/28/2022]
Abstract
The research reported herein focuses on the synthesis of two new Cu(II) complexes {[Cu2(2-X-4,6-bis(di-2-picolylamino)-1,3,5-triazine], with X = butane-1,4-diamine (2) or N-methylpyrenylbutane-1,4-diamine (3)}, the latter with a pyrene group as a possible DNA intercalating agent. The structure of complex (3) was determined by X-ray crystallography and shows the dinuclear {CuII(μ-OCH3)2CuII} unit in which the CuII···CuII distance of 3.040 Å is similar to that of 2.97 Å previously found for 1, which contains a {CuII(μ-OH)2CuII} structural unit. Complexes (2) and (3) were also characterized in spectroscopic and electrochemical studies, and catecholase-like activity were performed for both complexes. The kinetic parameters obtained for the oxidation of the model substrate 3,5-di-tert-butylcatechol revealed that the insertion of the spacer butane-1,4-diamine and the pyrene group strongly contributes to increasing the catalytic efficiency of these systems. In fact, Kass becomes significantly higher, indicating that these groups influence the interaction between the complex and the substrate. These complexes also show DNA cleavage under mild conditions with moderate reaction times. The rate of cleavage (kcat) indicated that the presence of butane-1,4-diamine and pyrene increased the activity of both complexes. The reaction mechanism seems to have oxidative and hydrolytic features and the effect of DNA groove binding compounds and circular dichroism indicate that all complexes interact with plasmid DNA through the minor groove. High-resolution DNA cleavage assays provide information on the interaction mechanism and for complex (2) a specificity for the unpaired hairpin region containing thymine bases was observed, in contrast to (3).
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Affiliation(s)
- Marcos P Silva
- Laboratório de Bioinorgânica e Cristalografia - LABINC, Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, Santa Catarina, Brazil
| | - Cristine Saibert
- Centro de Biologia Molecular Estrutural - CEBIME, Departamento de Bioquímica, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, Santa Catarina, Brazil
| | - Tiago Bortolotto
- Centro de Biologia Molecular Estrutural - CEBIME, Departamento de Bioquímica, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, Santa Catarina, Brazil
| | - Adailton J Bortoluzzi
- Laboratório de Bioinorgânica e Cristalografia - LABINC, Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, Santa Catarina, Brazil
| | - Gerhard Schenk
- School of Molecular and Microbial Sciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Rosely A Peralta
- Laboratório de Bioinorgânica e Cristalografia - LABINC, Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, Santa Catarina, Brazil.
| | - Hernán Terenzi
- Centro de Biologia Molecular Estrutural - CEBIME, Departamento de Bioquímica, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, Santa Catarina, Brazil.
| | - Ademir Neves
- Laboratório de Bioinorgânica e Cristalografia - LABINC, Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, Santa Catarina, Brazil.
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5
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Galiana-Roselló C, Aceves-Luquero C, González J, Martínez-Camarena Á, Villalonga R, Fernández de Mattos S, Soriano C, Llinares J, García-España E, Villalonga P, González-Rosende ME. Toward a Rational Design of Polyamine-Based Zinc-Chelating Agents for Cancer Therapies. J Med Chem 2020; 63:1199-1215. [PMID: 31935092 DOI: 10.1021/acs.jmedchem.9b01554] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In vitro viability assays against a representative panel of human cancer cell lines revealed that polyamines L1a and L5a displayed remarkable activity with IC50 values in the micromolar range. Preliminary research indicated that both compounds promoted G1 cell cycle arrest followed by cellular senescence and apoptosis. The induction of apoptotic cell death involved loss of mitochondrial outer membrane permeability and activation of caspases 3/7. Interestingly, L1a and L5a failed to activate cellular DNA damage response. The high intracellular zinc-chelating capacity of both compounds, deduced from the metal-specific Zinquin assay and ZnL2+ stability constant values in solution, strongly supports their cytotoxicity. These data along with quantum mechanical studies have enabled to establish a precise structure-activity relationship. Moreover, L1a and L5a showed appropriate drug-likeness by in silico methods. Based on these promising results, L1a and L5a should be considered a new class of zinc-chelating anticancer agents that deserves further development.
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Affiliation(s)
- Cristina Galiana-Roselló
- Instituto de Ciencia Molecular (ICMol), Departamento de Química Inorgánica , Universidad de Valencia , Paterna, 46980 Valencia , Spain.,Departamento de Farmacia, Facultad de Ciencias de la Salud , Universidad CEU Cardenal Herrera, C/ Ramón y Cajal, s/n , Alfara del Patriarca, 46115 Valencia , Spain
| | - Clara Aceves-Luquero
- Cancer Cell Biology Laboratory, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS) , Universitat de les Illes Balears, and Institut d'Investigació Sanitària Illes Balears (IdISBa) , Palma, 07122 Illes Balears , Spain
| | - Jorge González
- Instituto de Ciencia Molecular (ICMol), Departamento de Química Inorgánica , Universidad de Valencia , Paterna, 46980 Valencia , Spain
| | - Álvaro Martínez-Camarena
- Instituto de Ciencia Molecular (ICMol), Departamento de Química Inorgánica , Universidad de Valencia , Paterna, 46980 Valencia , Spain
| | - Ruth Villalonga
- Departament de Química , Universitat de les llles Balears , Palma, 07122 Illes Balears , Spain
| | - Silvia Fernández de Mattos
- Cancer Cell Biology Laboratory, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS) , Universitat de les Illes Balears, and Institut d'Investigació Sanitària Illes Balears (IdISBa) , Palma, 07122 Illes Balears , Spain.,Departament de Biologia Fonamental , Universitat de les Illes Balears , Palma, 07122 Illes Balears , Spain
| | - Concepción Soriano
- Departamento de Química Orgánica , Universidad de Valencia , C/Dr. Moliner s/n , Burjassot, 46100 Valencia , Spain
| | - José Llinares
- Departamento de Química Orgánica , Universidad de Valencia , C/Dr. Moliner s/n , Burjassot, 46100 Valencia , Spain
| | - Enrique García-España
- Instituto de Ciencia Molecular (ICMol), Departamento de Química Inorgánica , Universidad de Valencia , Paterna, 46980 Valencia , Spain
| | - Priam Villalonga
- Cancer Cell Biology Laboratory, Institut Universitari d'Investigació en Ciències de la Salut (IUNICS) , Universitat de les Illes Balears, and Institut d'Investigació Sanitària Illes Balears (IdISBa) , Palma, 07122 Illes Balears , Spain
| | - María Eugenia González-Rosende
- Departamento de Farmacia, Facultad de Ciencias de la Salud , Universidad CEU Cardenal Herrera, C/ Ramón y Cajal, s/n , Alfara del Patriarca, 46115 Valencia , Spain
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6
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Thomas TJ, Tajmir-Riahi HA, Pillai CKS. Biodegradable Polymers for Gene Delivery. Molecules 2019; 24:molecules24203744. [PMID: 31627389 PMCID: PMC6832905 DOI: 10.3390/molecules24203744] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 12/13/2022] Open
Abstract
The cellular transport process of DNA is hampered by cell membrane barriers, and hence, a delivery vehicle is essential for realizing the potential benefits of gene therapy to combat a variety of genetic diseases. Virus-based vehicles are effective, although immunogenicity, toxicity and cancer formation are among the major limitations of this approach. Cationic polymers, such as polyethyleneimine are capable of condensing DNA to nanoparticles and facilitate gene delivery. Lack of biodegradation of polymeric gene delivery vehicles poses significant toxicity because of the accumulation of polymers in the tissue. Many attempts have been made to develop biodegradable polymers for gene delivery by modifying existing polymers and/or using natural biodegradable polymers. This review summarizes mechanistic aspects of gene delivery and the development of biodegradable polymers for gene delivery.
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Affiliation(s)
- T J Thomas
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, KTL N102, 675 Hoes Lane, Piscataway, NJ 08854, USA.
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA.
| | | | - C K S Pillai
- Department of Chemistry-Biochemistry-Physics, University of Québec in Trois-Rivières, C. P. 500, Trois-Rivières, QC G9A 5H7, Canada.
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7
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Ahmadi F, Shabrandi N, Hosseinzadeh L, Azizian H. Two DNA binding modes of a zinc-metronidazole and biological evaluation as a potent anti-cancer agent. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:449-480. [PMID: 30689502 DOI: 10.1080/15257770.2018.1562073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A complex of metronidazole (MTZ) with zinc ion was synthesized and characterized by UV-Vis, Fourier transform infrared (FT-IR), 1H-NMR, X-ray crystallography and thermal gravimetric-differential thermal analysis (TG-DTA). The cytotoxicity effect of the synthesized complex investigated over SKNMC, A549, MCF-7, and MCDK cell lines and the results have shown that it has high cytotoxic potential over cancer cell lines. In order to clarify the mechanism of cell cytotoxicity, the oxidative stress and binding of the complex to the calf thymus-DNA studied by evaluating the intrinsic binding constant and defining thermodynamic parameters of complex over the DNA accompanying with in silico molecular modeling method. For this purpose, the complex optimized at the B3LYP/LANL2DZ level and docked over the DNA structure. The results revealed that the metronidazole-zinc complex interacted with DNA via hydrogen binding and electrostatic interaction to the minor groove region and phosphate backbone of DNA, respectively.
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Affiliation(s)
- Farhad Ahmadi
- a Department of Medicinal Chemistry Faculty of Pharmacy , Kermanshah University of Medical Sciences , Kermanshah , Iran.,b Physiology Research Center Iran University of Medical Sciences , Tehran , Iran.,c Department of Medicinal Chemistry Faculty of Pharmacy-International Campus , Iran University of Medical Sciences , Tehran , Iran
| | - Nosaibeh Shabrandi
- a Department of Medicinal Chemistry Faculty of Pharmacy , Kermanshah University of Medical Sciences , Kermanshah , Iran
| | - Leilah Hosseinzadeh
- d Student Research Committee, Faculty of Pharmacy , Kermanshah University of Medical Sciences , Kermanshah , Iran
| | - Homa Azizian
- c Department of Medicinal Chemistry Faculty of Pharmacy-International Campus , Iran University of Medical Sciences , Tehran , Iran
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8
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Shabana AA, Butler IS, Castonguay A, Mostafa M, Jean-Claude BJ, Mostafa SI. DNA interaction and anticancer evaluation of new palladium(II), platinum(II) and silver(I) complexes based on (Δ)- and (Λ)-1,2–bis-(1H-benzimidazol-2-yl)-1,2-ethanediol enantiomers. Polyhedron 2018. [DOI: 10.1016/j.poly.2018.07.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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9
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Baltazar C, Mun R, Tajmir-Riahi H, Bariyanga J. Spectroscopic studies on the interaction of mimosine with BSA and DNA. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.01.039] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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10
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Terui Y, Yoshida T, Sakamoto A, Saito D, Oshima T, Kawazoe M, Yokoyama S, Igarashi K, Kashiwagi K. Polyamines protect nucleic acids against depurination. Int J Biochem Cell Biol 2018; 99:147-153. [PMID: 29649565 DOI: 10.1016/j.biocel.2018.04.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 03/21/2018] [Accepted: 04/06/2018] [Indexed: 11/20/2022]
Abstract
Depurination is accelerated by heat and reactive oxygen species under physiological conditions. We previously reported that polyamines are involved in mitigation of heat shock and oxidative stresses through stimulation of the synthesis of heat shock and antioxidant proteins. This time, we investigated whether polyamines are directly involved in protecting nucleic acids from thermal depurination induced by high temperature. The suppressing efficiencies of depurination of DNA by spermine, caldopentamine and caldohexamine in the presence of 1 mM Mg2+, were approximately 50%, 60% and 80%, respectively. Mg2+ also protected nucleic acids against depurination but to a lesser degree than polyamines. Longer unusual polyamines were more effective at protecting DNA against depurination compared to standard polyamines. The tRNA depurination suppressing efficiencies of spermine, caldopentamine and caldohexamine in the presence of 1 mM Mg2+, were approximately 60%, 70% and 80%, respectively. Standard polyamines protected tRNA and ribosomes more effectively than DNA against thermal depurination. Branched polyamines such as mitsubishine and tetrakis(3-aminopropyl)ammonium also protected RNA more effectively than DNA against depurination. These results suggest that the suppressing effect of depurination of nucleic acids (DNA and RNA) depends on the types of polyamines: i.e. to maintain functional conformation of nucleic acids at high temperature, longer and branched polyamines play important roles in protecting nucleic acids from depurination compared to standard polyamines and Mg2+.
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Affiliation(s)
- Yusuke Terui
- Faculty of Pharmacy, Chiba Institute of Science, Choshi, Chiba, Japan.
| | - Taketo Yoshida
- Faculty of Pharmacy, Chiba Institute of Science, Choshi, Chiba, Japan
| | - Akihiko Sakamoto
- Faculty of Pharmacy, Chiba Institute of Science, Choshi, Chiba, Japan
| | | | - Tairo Oshima
- Institute of Environmental Biology, Kyowa-Kako, Machida, Tokyo, Japan
| | | | | | - Kazuei Igarashi
- Amine Pharma Research Institute, Innovation Plaza at Chiba University, Chiba, Japan; Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Keiko Kashiwagi
- Faculty of Pharmacy, Chiba Institute of Science, Choshi, Chiba, Japan.
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Moradi SZ, Nowroozi A, Sadrjavadi K, Moradi S, Mansouri K, Hosseinzadeh L, Shahlaei M. Direct evidences for the groove binding of the Clomifene to double stranded DNA. Int J Biol Macromol 2018; 114:40-53. [PMID: 29555513 DOI: 10.1016/j.ijbiomac.2018.03.040] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 02/10/2018] [Accepted: 03/09/2018] [Indexed: 12/25/2022]
Abstract
It has been reported that the antiestrogen Tamoxifen induces liver tumors in rats and genotoxic effects in vitro through DNA interaction. So, it can be proposed that its structural analogue, Clomifene, also can bind to DNA. To test this hypothesis, the DNA binding properties of Clomifene have been studied by absorption spectroscopy, fluorescence spectroscopy, cellular uptake, cell viability, cell proliferation and molecular modeling techniques. Evidences are provided that Clomifene could interact with DNA via minor groove interaction mode. The negative ΔG value implied that the interaction occurred between DNA and Clomifene spontaneously. Also, the positive ΔH and positive ΔS values indicated that the binding of Clomifene with DNA is mainly entropy driven and the enthalpy is unfavorable parameter. This also suggests that the hydrophobic interaction plays a major role in the binding with overall binding constant of K=5.645×107M-1 at 298K. From the results of docking, it can be concluded that Hydrogen bonds is also one of the most important interactions. The increase in entropy of system after binding might be due to the destruction of the DNA structure.
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Affiliation(s)
| | - Amin Nowroozi
- Pharmaceutical Sciences Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Komail Sadrjavadi
- Pharmaceutical Sciences Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sajad Moradi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Kamran Mansouri
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Leila Hosseinzadeh
- Pharmaceutical Sciences Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohsen Shahlaei
- Nano Drug Delivery Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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12
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Rong RX, Wang SS, Liu X, Li RF, Wang KR, Cao ZR, Li XL. Lysosomes-targeting imaging and anticancer properties of novel bis-naphthalimide derivatives. Bioorg Med Chem Lett 2018; 28:742-747. [DOI: 10.1016/j.bmcl.2018.01.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/05/2018] [Accepted: 01/07/2018] [Indexed: 12/27/2022]
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13
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Ahmadi F, Vahedpour T, Alizadeh AA. The evaluation of Cr-curcumin-DNA complexation by experimental and theoretical approaches. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2018; 37:35-52. [PMID: 29336691 DOI: 10.1080/15257770.2017.1414241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Chromium(III) chloride mediates DNA-DNA cross-linking. Some chromium complexes promote programmed cell death in specific ligand environment through binding to DNA. One strategy that can be supposed for reduction of Cr3+ binding affinity to DNA is using curcumin as a chelator. In the current study, the [Cr(Curcumin)(EtOH)2](NO3)2 (CCC) was synthesized and characterized by UV/Vis, FT-IR, CHN and spectrophotometric titration techniques. The mole ratio plot revealed a 1:1 complex between Cr3+ and curcumin in solution. Binding interaction of this complex with calf thymus-DNA (CT-DNA) was investigated using UV/Vis, circular dichroism (CD), FT-IR and cyclic voltammetry. The intrinsic binding constants of CCC with DNA, measured by UV/Vis and cyclic voltammetry, were 1.60 × 105 and 1.13 × 105, respectively. The thermodynamic studies showed that the reaction is enthalpy and entropy favoured. CD analysis revealed that only Λ-CCC interacts with DNA and Δ-CCC form has no tendency towards DNA. Based on FT-IR studies, it was understood that CCC interacts with DNA via minor groove binding. The docking simulation was carried out for finding the binding mode of CCC to DNA, too. All of data demonstrated that the curcumin significantly reduced the affinity of Cr3+ to the DNA and the form of Δ-CCC has no interaction with DNA.
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Affiliation(s)
- Farhad Ahmadi
- a Medicinal Chemistry Department , Faculty of Pharmacy-International Campous, Iran University of Medical Sciences
| | - Teymour Vahedpour
- b Biotechnology Research Center, Tabriz University of Medical Sciences , Tabriz , Iran.,c Faculty of pharmacy, Tabriz University of Medical Sciences , Tabriz , Iran
| | - Ali Akbar Alizadeh
- b Biotechnology Research Center, Tabriz University of Medical Sciences , Tabriz , Iran
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Collapse of DNA in packaging and cellular transport. Int J Biol Macromol 2017; 109:36-48. [PMID: 29247730 DOI: 10.1016/j.ijbiomac.2017.12.076] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 01/02/2023]
Abstract
The dawn of molecular biology and recombinant DNA technology arose from our ability to manipulate DNA, including the process of collapse of long extended DNA molecules into nanoparticles of approximately 100 nm diameter. This condensation process is important for the packaging of DNA in the cell and for transporting DNA through the cell membrane for gene therapy. Multivalent cations, such as natural polyamines (spermidine and spermine), were initially recognized for their ability to provoke DNA condensation. Current research is targeted on molecules such as linear and branched polymers, oligopeptides, polypeptides and dendrimers that promote collapse of DNA to nanometric particles for gene therapy and on the energetics of DNA packaging.
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Serre D, Erbek S, Berthet N, Ronot X, Martel-Frachet V, Thomas F. Copper(II) complexes of N 3O tripodal ligands appended with pyrene and polyamine groups: Anti-proliferative and nuclease activities. J Inorg Biochem 2017; 179:121-134. [PMID: 29222969 DOI: 10.1016/j.jinorgbio.2017.11.006] [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] [Received: 08/17/2017] [Revised: 10/28/2017] [Accepted: 11/04/2017] [Indexed: 10/18/2022]
Abstract
A series of tripodal ligands based on the 2-tert-butyl-4-R-6-phenol was synthesized, where R=aldehyde (HL1), R=putrescine-pyrene (HL2) and R=putrescine (HL3). A dinucleating ligand wherein a putrescine group connects two tripodal moieties was also prepared (H2L4). The corresponding copper complexes (1, 2, 3, and 4, respectively) were prepared and characterized. We determined the phenol's pKas in the range 2.47-3.93. The DNA binding constants were determined at 6×106, 5.5×105 and 2.7×106 for 2, 3 and 4, respectively. The complexes display a metal-centered reduction wave at Epc,red=-0.45 to -0.5V vs. saturated calomel electrode, as well as a ligand-centered oxidation wave above 0.57V at pH7. In the presence of ascorbate they promote an efficient cleavage of DNA, with for example a concentration required to cleave 50% of supercoiled DNA of 1.7μM for 2. The nuclease activity is affected by the nature of the R group: putrescine-pyrene≈bis-ligating>putrescine>aldehyde. The species responsible for strand scission is the hydroxyl radical. The cytotoxicity of the complexes was evaluated on bladder cancer cell lines sensitive or resistant to cis-platin. The IC50 of complexes 2 and 4 span over a short range (1.3-2μM) for the two cell lines. They are lower than those of the other complexes (3.1-9.7μM) and cis-platin. The most active compounds block the cell cycle at the G0/1 phase and promote apoptosis.
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Affiliation(s)
- Doti Serre
- Département de Chimie Moléculaire, Université Grenoble Alpes, UMR-5250 CNRS UGA, CS 40700, 38058 Grenoble Cedex 9, France
| | - Sule Erbek
- EPHE, PSL Research University, IAB, INSERM UGA U1209 - CNRS UMR 5309, 38700 La Tronche, France
| | - Nathalie Berthet
- Département de Chimie Moléculaire, Université Grenoble Alpes, UMR-5250 CNRS UGA, CS 40700, 38058 Grenoble Cedex 9, France
| | - Xavier Ronot
- EPHE, PSL Research University, IAB, INSERM UGA U1209 - CNRS UMR 5309, 38700 La Tronche, France
| | | | - Fabrice Thomas
- Département de Chimie Moléculaire, Université Grenoble Alpes, UMR-5250 CNRS UGA, CS 40700, 38058 Grenoble Cedex 9, France.
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Tian Z, Cui H, Liu H, Dong J, Dong H, Zhao L, Li X, Zhang Y, Huang Y, Song L, Bian L, Wang Y, Xu X, Wang C. Study on the interaction between the 1,4,5,8-naphthalene diimide-spermine conjugate (NDIS) and DNA using a spectroscopic approach and molecular docking. MEDCHEMCOMM 2017; 8:2079-2092. [PMID: 30108725 PMCID: PMC6072523 DOI: 10.1039/c7md00389g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/26/2017] [Indexed: 01/23/2023]
Abstract
The interaction of herring sperm DNA with the 1,4,5,8-naphthalene diimide-spermine conjugate (NDIS) was studied by UV/vis absorption, fluorescence and CD spectroscopic methods. Compared with the 1,8-naphthalimide-spermidine conjugate (NIS), the values of KSV (quenching constant) and Kb (binding constant) of NDIS were larger, and the hypochromic effect in the UV/vis spectra and the quenching effect in the fluorescence of NDIS were more significant. The interaction mode between NDIS and DNA was mainly groove binding. The fluorescence experiments at varying temperatures showed that the binding process of NDIS and DNA was static, as both hydrogen bonds and hydrophobic forces played a major role in the binding of NDIS and DNA. The CD spectrum indicated that NDIS caused a conformational change, like the B to A-DNA transition, and the tests using KI and NaCl and 1H NMR spectroscopy indicated that NDIS was not a classical DNA inserter. All the results demonstrated that both the polyamine side chain and the aromatic rings affect the process of NDIS binding to DNA, which is thus obviously different from that of NIS. The conclusion was confirmed by the in silico molecular docking experiments.
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Affiliation(s)
- Zhiyong Tian
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Hailong Cui
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - He Liu
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Jun Dong
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Huanyang Dong
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Luyao Zhao
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Xueting Li
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Yan Zhang
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Yingying Huang
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Lina Song
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Longxiang Bian
- The Key Laboratory of Natural Medicine and Immuno-Engineering , Henan University , Kaifeng 475004 , China . ; ; Tel: +86 18621534352 ; Tel: +86 13619810550
| | - Yuxia Wang
- Institute of Chemical Biology , Henan University , Kaifeng 475004 , China . ; Tel: +86 18739998722
| | - Xuejun Xu
- The Key Laboratory of Natural Medicine and Immuno-Engineering , Henan University , Kaifeng 475004 , China . ; ; Tel: +86 18621534352 ; Tel: +86 13619810550
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering , Henan University , Kaifeng 475004 , China . ; ; Tel: +86 18621534352 ; Tel: +86 13619810550
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17
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Tian Z, Zhao L, Dong H, Zhang Y, Zhang Y, Ren Q, Shao S, Huang Y, Song L, Guo T, Xu X, Wang C. Study on the interaction of anthracenyl-methyl homospermidine conjugate (ANTMHspd) with DNA by spectroscopic methods. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 169:27-34. [DOI: 10.1016/j.jphotobiol.2017.02.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/21/2017] [Indexed: 11/16/2022]
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18
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Jafari F, Moradi S, Nowroozi A, Sadrjavadi K, Hosseinzadeh L, Shahlaei M. Exploring the binding mechanism of paraquat to DNA by a combination of spectroscopic, cellular uptake, molecular docking and molecular dynamics simulation methods. NEW J CHEM 2017. [DOI: 10.1039/c7nj01645j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The possibility that paraquat may exert its toxicity also by interaction with DNA is studied using a combination of different computational and experimental techniques.
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Affiliation(s)
- Fataneh Jafari
- Pharmaceuticas Sciences Research Center, School of Pharmacy, Kermanshah University of Medical Sciences
- Kermanshah
- Iran
| | - Sajad Moradi
- Nano Drug Delivery Research Center, School of Pharmacy, Kermanshah University of Medical Sciences
- Kermanshah
- Iran
| | - Amin Nowroozi
- Pharmaceuticas Sciences Research Center, School of Pharmacy, Kermanshah University of Medical Sciences
- Kermanshah
- Iran
| | - Komail Sadrjavadi
- Pharmaceuticas Sciences Research Center, School of Pharmacy, Kermanshah University of Medical Sciences
- Kermanshah
- Iran
| | - Leila Hosseinzadeh
- Pharmaceuticas Sciences Research Center, School of Pharmacy, Kermanshah University of Medical Sciences
- Kermanshah
- Iran
| | - Mohsen Shahlaei
- Medical Biology Research Center, Kermanshah University of Medical Sciences
- Kermanshah
- Iran
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Proposed binding mechanism of galbanic acid extracted from Ferula assa-foetida to DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 166:63-73. [PMID: 27886594 DOI: 10.1016/j.jphotobiol.2016.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 11/05/2016] [Accepted: 11/08/2016] [Indexed: 12/31/2022]
Abstract
Recently, galbanic acid (GA), a sesquiterpenoid coumarin, has been introduced as an apoptotic and geno/cytotoxicity agent. In the present study, GA has been extracted from Ferula assa-foetida, a native medicinal plant in Iran, and characterized by 1H NMR, mass spectroscopy. Additionally, spectroscopic studies have been performed in order to investigate its DNA-interaction mode. The electrochemical behavior of GA has been studied by cyclic voltammetry (CV) in various scan rates. In neutral media (pH=7.3) one irreversible cathodic peak was obtained at -1.46 V, while in higher scan rates an irreversible one was determined at -1.67 V. According to the voltametric data GA can be easily reduced by 2e-/2H+ mechanism at hanging mercury drop electrode (HMDE). The interaction of GA with ct-DNA was evaluated by CV, differential pulse voltammetry (DPV), enhancement fluorescence, UV-Vis, FT-IR spectroscopy and molecular docking. The molecular docking study shows that the GA interacts to DNA on partial intercalation mode via DNA groove binding and forms a complex by van der Waals and electroastatic interactions. In addition, the thermodynamic parameters of GA-DNA complex were investigated with ΔH°, ΔS° and ΔG° values of 15.81KJmol-1, 133.95Jmol-1 and -23.10KJmol-1, respectively. All data revealed that the GA is binding to DNA by van der Waals and electrostatic interactions through the partial intercalations from the DNA's grooves.
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20
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Kabir A, Dutta D, Mandal C, Suresh Kumar G. Molecular Recognition of tRNA with 1-Naphthyl Acetyl Spermine, Spermine, and Spermidine: A Thermodynamic, Biophysical, and Molecular Docking Investigative Approach. J Phys Chem B 2016; 120:10871-10884. [PMID: 27690446 DOI: 10.1021/acs.jpcb.6b05391] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The role of tRNA in protein translational machinery and the influence of polyamines on the interaction of acylated and deacylated tRNA with ribosomes make polyamine-tRNA interaction conspicuous. We studied the interaction of two biogenic polyamines, spermine (SPM) and spermidine (SPD), with tRNAPhe and compared the results to those of the analogue 1-naphthyl acetyl spermine (NASPM). The binding affinity of SPM was comparable to that of NASPM; both were higher than that of SPD. The interactions led to significant thermal stabilization of tRNAPhe and an increase in the enthalpy of transition. All the interactions were exothermic in nature and displayed prominent enthalpy-entropy compensation behavior. The entropy-driven nature of the interaction, the structural perturbations observed, and docking results proved that the polyamines were bound in the groove of the anticodon arm of tRNAPhe. The amine groups of polyamines were involved in extensive electrostatic, H-bonding, and van der Waals interactions with tRNAPhe. The naphthyl group of NASPM showed an additional stacking interaction with G24 and G26 of tRNAPhe, which was absent in others. The results demonstrate that 1-naphthyl acetyl spermine can target the same binding sites as the biogenic polyamines without substituting for the functions played by them, which may lead to exhibition of selective anticancer cytotoxicity.
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Affiliation(s)
| | | | - Chhabinath Mandal
- National Institute of Pharmaceutical and Educational Research , Kolkata 700032, India
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21
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Szumilak M, Merecz A, Strek M, Stanczak A, Inglot TW, Karwowski BT. DNA Interaction Studies of Selected Polyamine Conjugates. Int J Mol Sci 2016; 17:E1560. [PMID: 27657041 PMCID: PMC5037830 DOI: 10.3390/ijms17091560] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 09/09/2016] [Accepted: 09/09/2016] [Indexed: 01/26/2023] Open
Abstract
The interaction of polyamine conjugates with DNA double helix has been studied. Binding properties were examined by ethidium bromide (EtBr) displacement and DNA unwinding/topoisomerase I/II (Topo I/II) activity assays, as well as dsDNA thermal stability studies and circular dichroism spectroscopy. Genotoxicity of the compounds was estimated by a comet assay. It has been shown that only compound 2a can interact with dsDNA via an intercalative binding mode as it displaced EtBr from the dsDNA-dye complex, with Kapp = 4.26 × 10⁶ M-1; caused an increase in melting temperature; changed the circular dichroism spectrum of dsDNA; converted relaxed plasmid DNA into a supercoiled molecule in the presence of Topo I and reduced the amount of short oligonucleotide fragments in the comet tail. Furthermore, preliminary theoretical study has shown that interaction of the discussed compounds with dsDNA depends on molecule linker length and charge distribution over terminal aromatic chromophores.
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Affiliation(s)
- Marta Szumilak
- Department of Hospital Pharmacy, Faculty of Pharmacy, Medical University of Lodz, 1 Muszynskiego Street, 90-151 Lodz, Poland.
| | - Anna Merecz
- Food Science Department, Faculty of Pharmacy, Medical University of Lodz, 1 Muszynskiego Street, 90-151 Lodz, Poland.
| | - Malgorzata Strek
- Department of Nucleic Acids Biochemistry, Medical University of Lodz, 251 Pomorska Street, 92-213 Lodz, Poland.
| | - Andrzej Stanczak
- Department of Hospital Pharmacy, Faculty of Pharmacy, Medical University of Lodz, 1 Muszynskiego Street, 90-151 Lodz, Poland.
| | - Tadeusz W Inglot
- Department of Medicinal Chemistry, Medical University of Lublin, 4 Jaczewskiego Street, 20-090 Lublin, Poland.
| | - Boleslaw T Karwowski
- Food Science Department, Faculty of Pharmacy, Medical University of Lodz, 1 Muszynskiego Street, 90-151 Lodz, Poland.
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22
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Ahmadi F, Valadbeigi S, Sajjadi SE, Shokoohinia Y, Azizian H, Taheripak G. Grandivittin as a natural minor groove binder extracted from Ferulago macrocarpa to ct-DNA, experimental and in silico analysis. Chem Biol Interact 2016; 258:89-101. [PMID: 27569860 DOI: 10.1016/j.cbi.2016.08.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 08/06/2016] [Accepted: 08/24/2016] [Indexed: 12/13/2022]
Abstract
Ferulago macrocarpa (Fenzl) Boiss., is an endemic medicinal herb of Iran. In this study a dihydrofuranocoumarin called grandivittin (GRA) was separate and purified from Ferulago macrocarpa (Fenzl) Boiss, and characterized by (1)H NMR and Mass spectroscopic methods. The electrochemical behavior of GRA was evaluated by cyclic voltammetry (CV). The interaction of GRA with calf thymus double strand deoxyribonucleic acid (ct-DNA), was evaluated by CV, differential pulse voltammetry (DPV), fluorescence, UV-Vis, FT-IR and molecular modeling methods. The thermodynamic parameters of GRA-DNA complex were measured and reported as: ΔH = 15.04 kJ mol(-1), ΔS = 105.54 J mol(-1) and ΔG = -15.62 kJ mol(-1). Docking simulation was performed to investigate the probable binding mode of GRA to various DNA, too. The polymerase extension study was performed using real-time PCR to confirm the inhibitory effect of GRA on polymerase extension activity as a mirror of binding to ct-DNA. However, all data showed that the grooves binding especially minor groove between GRA and ct-DNA is more predominant rather than other binding modes.
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Affiliation(s)
- F Ahmadi
- Department of Medicinal Chemistry, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran; Department of Medicinal Chemistry, Faculty of Pharmacy - International Campus, Iran University of Medical Sciences, Tehran, Iran.
| | - S Valadbeigi
- Department of Medicinal Chemistry, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - S E Sajjadi
- Department of Pharmacognosy, School of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Y Shokoohinia
- Department of Pharmacognosy, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - H Azizian
- Department of Medicinal Chemistry, Faculty of Pharmacy - International Campus, Iran University of Medical Sciences, Tehran, Iran
| | - G Taheripak
- Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
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23
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Interactions of diamines with adenosine-5'-triphosphate (ATP) in the systems including copper(II) ions. J Inorg Biochem 2016; 162:73-82. [PMID: 27289347 DOI: 10.1016/j.jinorgbio.2016.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 04/25/2016] [Accepted: 06/03/2016] [Indexed: 11/23/2022]
Abstract
Interactions were studied in the systems ATP/tn and ATP/Put (tn=1,3-diaminopropane, Put=putrescine) whereas the complexation reactions in ternary systems Cu(II)/ATP/tn and Cu(II)/ATP/Put. Results of the potentiometric and spectroscopic studies evidenced the formation of adducts of the type (ATP)Hx(PA), where PA=diamine. The thermodynamic stability of the complexes and the mode of interactions were determined. On the basis of analysis of changes in the positions of NMR signals, in the pH range of (ATP)H3(Put) formation, the preferred centres of the interaction between ATP and Put are the endocyclic nitrogen atoms from the nucleotide. On the other hand, the shorter diamine tn in the entire pH range reacts with the phosphate groups from ATP. The positive centres of noncovalent interactions are the protonated NHx+ groups from amines. In both complexes Cu(ATP)H2(tn) and Cu(ATP)H3(Put) formed in ternary systems at pH<6.5, the amines are in the outer sphere of coordination with the noncovalent interaction with anchoring Cu(ATP). Only the phosphate groups from the nucleotide take part in metalation. At higher pH in the range of Cu(ATP)(PA) complex formation, significant differences in the reactions of the two amines appear. The shorter one (tn) binds Cu(II) ions with two nitrogen atoms, while putrescine coordinates in the monofunctional mode, which is undoubtedly related to the differences in lengths of methylene chain. This explains the considerable differences in the stability of Cu(ATP)(tn) and Cu(ATP)(Put). In both complexes the nucleotide is coordinated through phosphate groups. SYNOPSIS As a result of noncovalent interactions ATP forms molecular complexes with 1,3-diaminopropane and 1,4-diaminobutane (putrescine). Significant differences in the mode of interactions between the two diamines were observed in ATP/diamine binary systems and in ternary systems Cu(II)/ATP/diamine, at high pH.
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24
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Jastrząb R, Łomozik L, Tylkowski B. Complexes of biogenic amines in their role in living systems. PHYSICAL SCIENCES REVIEWS 2016. [DOI: 10.1515/psr-2016-0003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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25
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26
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Thomas TJ, Tajmir-Riahi HA, Thomas T. Polyamine–DNA interactions and development of gene delivery vehicles. Amino Acids 2016; 48:2423-31. [DOI: 10.1007/s00726-016-2246-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 04/27/2016] [Indexed: 12/11/2022]
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Moosa BA, Sagar S, Li S, Esau L, Kaur M, Khashab NM. Synthesis and anticancer evaluation of spermatinamine analogues. Bioorg Med Chem Lett 2016; 26:1629-1632. [DOI: 10.1016/j.bmcl.2016.01.083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 01/25/2016] [Accepted: 01/29/2016] [Indexed: 12/31/2022]
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28
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Tian Z, Huang Y, Zhang Y, Song L, Qiao Y, Xu X, Wang C. Spectroscopic and molecular modeling methods to study the interaction between naphthalimide-polyamine conjugates and DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 158:1-15. [PMID: 26926663 DOI: 10.1016/j.jphotobiol.2016.01.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/29/2016] [Indexed: 11/28/2022]
Abstract
The effect of polyamine side chains on the interaction between naphthalimide-polyamine conjugates (1-7) and herring sperm DNA was studied by UV/vis absorption and fluorescent spectra under physiological conditions (pH=7.4). The diverse spectral data and further molecular docking simulation in silico indicated that the aromatic moiety of these compounds could intercalate into the DNA base pairs while the polyamine motif might simultaneously locate in the minor groove. The triamine compound 7 can interact more potently with DNA than the corresponding diamine compounds (1-6). The presence of the bulky terminal group in the diamine side chain reduced the binding strength of compound 1 with DNA, compared to other diamine compounds (2-6). In addition, the increasing methylene number in the diamine backbone generally results in the elevated binding constant of compounds-DNA complex. The fluorescent tests at different temperature revealed that the quenching mechanism was a static type. The binding constant and thermodynamic parameter showed that the binding strength and the type of interaction force, associated with the side chains, were mainly hydrogen bonding and hydrophobic force. And the calculated free binding energies of molecular docking are generally consistent with the stability of polyamine-DNA complexes. The circular dichroism assay about the impact of compounds 1-7 on DNA conformation testified the B to A-like conformational change.
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Affiliation(s)
- Zhiyong Tian
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Yingying Huang
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Yan Zhang
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Lina Song
- Institute of Chemical Biology, Henan University, Kaifeng 475004, China
| | - Yan Qiao
- Basic Medical College, Zhengzhou University, Zhengzhou, 475008, China; State Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xuejun Xu
- Basic Medical College, Zhengzhou University, Zhengzhou, 475008, China; The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, china.
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, china.
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29
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El-Asmy HA, Butler IS, Mouhri ZS, Jean-Claude BJ, Emmam M, Mostafa SI. Synthesis, characterization and DNA interaction studies of new complexes containing 2-mercaptobenzothiazole and different dinitrogen or phosphorous aromatic donors. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2015.10.041] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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30
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Torres-Nuñez A, Faulds K, Graham D, Alvarez-Puebla RA, Guerrini L. Silver colloids as plasmonic substrates for direct label-free surface-enhanced Raman scattering analysis of DNA. Analyst 2016; 141:5170-80. [DOI: 10.1039/c6an00911e] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Unraveling the role played by the surface chemistry of silver colloids in the direct SERS analysis of DNA.
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Affiliation(s)
- A. Torres-Nuñez
- Medcom Advance
- 08840 Viladecans
- Spain
- Centro Tecnológico de la Química de Catalunya
- 43007 Tarragona
| | - K. Faulds
- Department of Pure and Applied Chemistry
- Technology and Innovation Centre
- University of Strathclyde
- Glasgow G1 1RD
- UK
| | - D. Graham
- Department of Pure and Applied Chemistry
- Technology and Innovation Centre
- University of Strathclyde
- Glasgow G1 1RD
- UK
| | - R. A. Alvarez-Puebla
- Medcom Advance
- 08840 Viladecans
- Spain
- Centro Tecnológico de la Química de Catalunya
- 43007 Tarragona
| | - L. Guerrini
- Medcom Advance
- 08840 Viladecans
- Spain
- Department of Pure and Applied Chemistry
- Technology and Innovation Centre
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31
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Wang YQ, Zhang HM. Exploration of binding of bisphenol A and its analogues with calf thymus DNA by optical spectroscopic and molecular docking methods. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2015; 149:9-20. [DOI: 10.1016/j.jphotobiol.2015.04.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 03/17/2015] [Accepted: 04/20/2015] [Indexed: 01/18/2023]
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32
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Daneshmehr MA, Ahmadi F, Ahmadi B, Shakiba E. Deciphering the binding mode of dinitramine herbicide to ct-DNA, a thermodynamic discussion. FOOD AGR IMMUNOL 2015. [DOI: 10.1080/09540105.2015.1055555] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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33
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Mi R, Tu B, Bai XT, Chen J, Ouyang Y, Hu YJ. Binding properties of palmatine to DNA: spectroscopic and molecular modeling investigations. LUMINESCENCE 2015; 30:1344-51. [PMID: 25829078 DOI: 10.1002/bio.2904] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 02/21/2015] [Accepted: 02/22/2015] [Indexed: 12/20/2022]
Abstract
Palmatine, an isoquinoline alkaloid, is an important medicinal herbal extract with diverse pharmacological and biological properties. In this work, spectroscopic and molecular modeling approaches were employed to reveal the interaction between palmatine and DNA isolated from herring sperm. The absorption spectra and iodide quenching results indicated that groove binding was the main binding mode of palmatine to DNA. Fluorescence studies indicated that the binding constant (K) of palmatine and DNA was ~ 10(4)L·mol(-1). The associated thermodynamic parameters, ΔG, ΔH, and ΔS, indicated that hydrogen bonds and van der Waals forces played major roles in the interaction. The effects of chemical denaturant, thermal denaturation and pH on the interaction were investigated and provided further support for the groove binding mode. In addition to experimental approaches, molecular modeling was conducted to verify binding pattern of palmatine-DNA.
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Affiliation(s)
- Ran Mi
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi, 435002, People's Republic of China
| | - Bao Tu
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi, 435002, People's Republic of China
| | - Xiao-Ting Bai
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi, 435002, People's Republic of China
| | - Jun Chen
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi, 435002, People's Republic of China
| | - Yu Ouyang
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi, 435002, People's Republic of China
| | - Yan-Jun Hu
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi, 435002, People's Republic of China
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Preedia Babu E, Subastri A, Suyavaran A, Lokeshwara Rao P, Suresh Kumar M, Jeevaratnam K, Thirunavukkarasu C. Extracellularly synthesized ZnO nanoparticles interact with DNA and augment gamma radiation induced DNA damage through reactive oxygen species. RSC Adv 2015. [DOI: 10.1039/c5ra09935h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
ZnONPs were synthesized using ferulic acid as the reductant and the intricate twofold role as DNA binders and radio sensitizers was revealed, which can pave the way for anticancer therapy.
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Affiliation(s)
- E. Preedia Babu
- Department of Biochemistry and Molecular Biology
- Pondicherry University
- India
| | - A. Subastri
- Department of Biochemistry and Molecular Biology
- Pondicherry University
- India
| | - A. Suyavaran
- Department of Biochemistry and Molecular Biology
- Pondicherry University
- India
| | - P. Lokeshwara Rao
- Department of Biochemistry and Molecular Biology
- Pondicherry University
- India
| | | | - K. Jeevaratnam
- Department of Biochemistry and Molecular Biology
- Pondicherry University
- India
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35
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Husain MA, Rehman SU, Ishqi HM, Sarwar T, Tabish M. Spectroscopic and molecular docking evidence of aspirin and diflunisal binding to DNA: a comparative study. RSC Adv 2015. [DOI: 10.1039/c5ra09181k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Deciphering the binding mode between aspirin/diflunisal with Ct-DNA.
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Affiliation(s)
| | - Sayeed Ur Rehman
- Department of Biochemistry
- Faculty of Life Sciences
- A.M. University
- Aligarh
- India
| | | | - Tarique Sarwar
- Department of Biochemistry
- Faculty of Life Sciences
- A.M. University
- Aligarh
- India
| | - Mohammad Tabish
- Department of Biochemistry
- Faculty of Life Sciences
- A.M. University
- Aligarh
- India
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36
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Arjmand F, Yousuf I, Zaidi Y, Toupet L. Crystal structure determination, spectroscopic characterization and biological profile of a tailored ionic molecular entity, Sn(iv) iminodiacetic acid–piperazinediium conjugate: in vitro DNA/RNA binding studies, Topo I inhibition activity, cytotoxic and systemic toxicity studies. RSC Adv 2015. [DOI: 10.1039/c4ra13718c] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In vitro DNA/RNA binding studies and cytotoxic activity of complex 1 along with its in vivo systemic toxicity assay.
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Affiliation(s)
- Farukh Arjmand
- Department of Chemistry
- Aligarh Muslim University
- Aligarh 202002
- India
| | - Imtiyaz Yousuf
- Department of Chemistry
- Aligarh Muslim University
- Aligarh 202002
- India
| | - Yusra Zaidi
- Department of Zoology
- Aligarh Muslim University
- Aligarh 202002
- India
| | - Loic Toupet
- Institut de Physique de Rennes
- UMR 625
- Université de Rennes 1
- 35042 Rennes, Cedex
- France
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37
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Husain MA, Sarwar T, Rehman SU, Ishqi HM, Tabish M. Ibuprofen causes photocleavage through ROS generation and intercalates with DNA: a combined biophysical and molecular docking approach. Phys Chem Chem Phys 2015; 17:13837-50. [DOI: 10.1039/c5cp00272a] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Ibuprofen is an important nonsteroidal anti inflammatory drug which intercalates with DNA and causes phototoxicity through ROS generation.
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Affiliation(s)
| | - Tarique Sarwar
- Department of Biochemistry
- Faculty of Life Sciences
- A.M. University
- Aligarh
- India
| | - Sayeed Ur Rehman
- Department of Biochemistry
- Faculty of Life Sciences
- A.M. University
- Aligarh
- India
| | | | - Mohammad Tabish
- Department of Biochemistry
- Faculty of Life Sciences
- A.M. University
- Aligarh
- India
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38
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Kabir A, Kumar GS. Probing the interaction of spermine and 1-naphthyl acetyl spermine with DNA polynucleotides: a comparative biophysical and thermodynamic investigation. MOLECULAR BIOSYSTEMS 2014; 10:1172-83. [PMID: 24643290 DOI: 10.1039/c3mb70616h] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The interaction of spermine and its analogue, 1-naphthyl acetyl spermine with four double stranded DNA polynucleotides has been studied to understand the structural and thermodynamic basis of the binding. The efficacy and specificity of DNA binding of this analogue has not yet been revealed. The energetics of the interaction was studied by isothermal titration calorimetry and differential scanning calorimetry. Circular dichroism spectroscopy, UV-thermal melting and ethidium bromide displacement assay have been employed to characterize the association. Circular dichroism studies showed that 1-naphthyl acetyl spermine caused a stronger structural perturbation in the polynucleotides. Among the adenine-thymine polynucleotides the alternating polynucleotide was more preferred by naphthyl acetyl spermine compared to the preference of spermine for the homo sequence. The higher melting stabilization revealed by the optical melting and differential scanning calorimetry results suggested that the binding of 1-naphthyl acetyl spermine increased the melting temperature and the total standard molar enthalpy of the transition of adenine-thymine polynucleotides. Microcalorimetry results revealed that unlike spermine the binding of 1-naphthyl acetyl spermine was endothermic. The interaction was characterized by total enthalpy-entropy compensation and high standard molar heat capacity values. There are differences in the mode of association of 1-naphthyl acetyl spermine and spermine. 1-naphthyl acetyl spermine binds with an enhanced affinity with the adenine-thymine hetero polynucleotide. Thus, the result suggests the importance of polyamine analogues and their ability to interfere with normal polyamine interactions.
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Affiliation(s)
- Ayesha Kabir
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700 032, India.
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Abstract
Recent progress with techniques for monitoring RNA structure in cells such as ‘DMS-Seq’ and ‘Structure-Seq’ suggests that a new era of RNA structure-function exploration is on the horizon. This will also include systematic investigation of the factors required for the structural integrity of RNA. In this context, much evidence accumulated over 50 years suggests that polyamines play important roles as modulators of RNA structure. Here, we summarize and discuss recent literature relating to the roles of these small endogenous molecules in RNA function. We have included studies directed at understanding the binding interactions of polyamines with polynucleotides, tRNA, rRNA, mRNA and ribozymes using chemical, biochemical and spectroscopic tools. In brief, polyamines bind RNA in a sequence-selective fashion and induce changes in RNA structure in context-dependent manners. In some cases the functional consequences of these interactions have been observed in cells. Most notably, polyamine-mediated effects on RNA are frequently distinct from those of divalent cations (i.e. Mg2+) confirming their roles as independent molecular entities which help drive RNA-mediated processes.
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Affiliation(s)
- Helen L Lightfoot
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Jonathan Hall
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, CH-8093, Zürich, Switzerland
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Kabir A, Suresh Kumar G. Targeting double-stranded RNA with spermine, 1-naphthylacetyl spermine and spermidine: a comparative biophysical investigation. J Phys Chem B 2014; 118:11050-64. [PMID: 25184857 DOI: 10.1021/jp5035294] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
RNA targeting is an evolving new approach to anticancer therapeutics that requires identification of small molecules to selectively target specific RNA structures. In this report, the interaction of biogenic polyamines spermine, spermidine and the synthetic analogue 1-naphthylacetyl spermine with three double-stranded RNA polynucleotides--poly(I)·poly(C), poly(C)·poly(G), and poly(A)·poly(U)--has been described to understand the structural and thermodynamic basis of the binding and the comparative efficacy of the analogue over the natural polyamines. Circular dichroism spectroscopy, thermal melting experiments, and ethidium bromide displacement assay were used to characterize the interaction. Microcalorimetry studies were performed to deduce the energetics of the interaction and atomic force microscopy experiments done to gain insight into the interaction at the molecular level. The experiments demonstrated structural perturbations in the polynucleotides on binding of the polyamines. Thermal melting studies showed enhanced stabilization of RNA-polyamine complexes with increase in the total standard molar enthalpy of transition. The binding affinity was strongest for poly(I)·poly(C) as revealed by microcalorimetry results and varied as poly(I)·poly(C) > poly(C)·poly(G) > poly(A)·poly(U). The order of affinity for the polyamines was spermine >1-naphthylacetyl spermine > spermidine. Total enthalpy-entropy compensation and high standard molar heat capacity values characterized the interactions. The results of the study on the binding of polyamines to dsRNAs presented here have been compared to those reported earlier with dsDNAs. The present findings advance our knowledge on the mechanism of interaction of polyamines with RNA and may help in the search for analogues that can interfere with biogenic polyamine metabolism and function.
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Affiliation(s)
- Ayesha Kabir
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR - Indian Institute of Chemical Biology , Kolkata 700 032, India
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41
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Jangir DK, Mehrotra R. Raman spectroscopic evaluation of DNA adducts of a platinum containing anticancer drug. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 130:386-389. [PMID: 24810023 DOI: 10.1016/j.saa.2014.04.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 03/30/2014] [Accepted: 04/04/2014] [Indexed: 06/03/2023]
Abstract
Mechanistic understanding of the interaction of drugs with their target molecules is important for better understanding of their mode of action and to improve their efficacy. Carboplatin is a platinum containing anticancer drug, used to treat different type of tumors. In the present work, we applied Raman spectroscopy to study the interaction of carboplatin with DNA at molecular level using different carboplatin-DNA molar ratios. These Raman spectroscopic results provide comprehensive understanding on the carboplatin-DNA interactions and indicate that DNA cross-linked adducts formed by carboplatin are similar to cisplatin adducts. The results indicate that guanine N7 and adenine N7 are the putative sites for carboplatin interaction. It is observed that carboplatin has some affinity toward cytosine in DNA. Phosphate sugar backbone of DNA showed conformation perturbation in DNA which were easily sensible at higher concentrations of carboplatin. Most importantly, carboplatin interaction induces intermediate A- and B-DNA conformations at the cross-linking sites.
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Affiliation(s)
- Deepak K Jangir
- Quantum Optics and Photon Physics, CSIR-National Physical Laboratory, Dr. K.S. Krishnan Road, New Delhi 110012, India
| | - Ranjana Mehrotra
- Quantum Optics and Photon Physics, CSIR-National Physical Laboratory, Dr. K.S. Krishnan Road, New Delhi 110012, India.
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42
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Ahmadi F, Ghanbari K. Proposed model for binding of permethrin and deltamethrin insecticides with ct-DNA, a structural comparative study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2014; 106:136-145. [PMID: 24836888 DOI: 10.1016/j.ecoenv.2014.02.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 02/13/2014] [Accepted: 02/19/2014] [Indexed: 06/03/2023]
Abstract
In this work, the interaction of two synthetic pyrethroid insecticides, permethrin (PER) and deltamethrin (DEL), with ct-DNA has been studied by cyclic voltammetry (CV), circular dichroism (CD), competitive fluorescence, atomic force microscopy (AFM), UV-vis spectroscopy, thermodynamic measurements, Fourier-transform infra-red (FT-IR), high performance liquid chromatography (HPLC) and two-layered ONIOM (our N-layered integrated molecular orbital+molecular mechanics) (DFT B3LYP, 6-31++G(d, p):UFF) molecular modeling methods. The last four methods were also utilized to study the binding of DEL with DNA. The results revealed that the PER may interact through partial intercalation and groove binding process while the PER only interacts through groove binding. Finally, the insecticides structure effect on interaction is discussed.
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Affiliation(s)
- F Ahmadi
- Novel Drug Delivery Research Center, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah 67145-1673, Islamic Republic of Iran; Department of Medicinal Chemistry, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah 67145-1673, Islamic Republic of Iran
| | - K Ghanbari
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Azad University of Tehran, Islamic Republic of Iran; Department of Medicinal Chemistry, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah 67145-1673, Islamic Republic of Iran.
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Spectroscopic study on the interaction between naphthalimide-polyamine conjugates and DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 138:202-10. [PMID: 24976624 DOI: 10.1016/j.jphotobiol.2014.06.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 05/30/2014] [Accepted: 06/03/2014] [Indexed: 01/06/2023]
Abstract
The interaction of naphthalimide-polyamine conjugates with herring sperm DNA was studied by UV/vis absorption and fluorescent spectra under physiological conditions (pH=7.4). The observed spectral quenching of compounds by DNA and the displacement of EB from DNA-EB complex by compounds indicated that these naphthalimide-polyamine conjugates could intercalate into the DNA base pairs. The UV test also showed that these compounds caused the conformational alteration of DNA. Further caloric fluorescent tests revealed that the quenching mechanism was a static type, which Ksv of 1-DNA, 2-DNA and 1-DNA-EB, 2-DNA-EB 3-DNA-EB was 1.208×10(4), 7.792×10(3) and 1.712×10(4), 1.287×10(4), 2.874×10(4), respectively, at room temperature. The obtained quenching constant, binding constant and thermodynamic parameters suggested that binding strength was associated with substituted groups on naphthalene backbone, and the type of interaction force included mainly hydrogen bonding and weak van der Waals. The binding process was mainly driven by hydrogen bond and van der Waals. Additionally, the effect of NaCl on compounds-DNA interaction provided further evidence that their interaction modes were dependent on substituted groups.
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44
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Kakuchi R, Theato P. Preparation of Functional Polyamine Scaffolds via Mitsunobu Post-Polymerization Modification Reactions. Macromol Rapid Commun 2014. [DOI: 10.1002/marc.201300849] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ryohei Kakuchi
- Institute for Technical and Macromolecular Chemistry; University of Hamburg; Bundesstr. 45 D-20146 Hamburg Germany
| | - Patrick Theato
- Institute for Technical and Macromolecular Chemistry; University of Hamburg; Bundesstr. 45 D-20146 Hamburg Germany
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45
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Encapsulation of biogenic and synthetic polyamines by nanoparticles PEG and mPEG-anthracene. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 130:30-9. [DOI: 10.1016/j.jphotobiol.2013.10.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 10/20/2013] [Accepted: 10/22/2013] [Indexed: 11/19/2022]
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46
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Ma Y, Pan J, Zhang G, Zhang Y. Binding properties of butylated hydroxytoluene with calf thymus DNA in vitro. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 126:112-8. [DOI: 10.1016/j.jphotobiol.2013.07.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 07/07/2013] [Accepted: 07/09/2013] [Indexed: 11/17/2022]
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47
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Charak S, Mehrotra R. Structural investigation of idarubicin–DNA interaction: Spectroscopic and molecular docking study. Int J Biol Macromol 2013; 60:213-8. [DOI: 10.1016/j.ijbiomac.2013.05.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Revised: 05/05/2013] [Accepted: 05/25/2013] [Indexed: 10/26/2022]
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48
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Determination of acetamiprid partial-intercalative binding to DNA by use of spectroscopic, chemometrics, and molecular docking techniques. Anal Bioanal Chem 2013; 405:8871-83. [DOI: 10.1007/s00216-013-7294-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/05/2013] [Accepted: 08/06/2013] [Indexed: 01/07/2023]
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49
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Sen A, Sahu D, Ganguly B. In silico studies toward understanding the interactions of DNA base pairs with protonated linear/cyclic diamines. J Phys Chem B 2013; 117:9840-50. [PMID: 23909683 DOI: 10.1021/jp402847u] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protonated amino groups are ubiquitous in nature and important in the fields of chemistry and biology. In search of efficient polyamine analogues, we have performed DFT calculations on the interactions of some simple cyclic and constrained protonated diamines with the DNA base pairs and compared the results with those obtained for the corresponding interactions involving linear diamines, which mimic biogenic polyamines such as spermine. The interactions are mainly governed by the strong hydrogen bonding between the ligand and the DNA base pairs. The DFT calculations suggest that the major-groove N7 interaction (GC base pair) with linear diamine is energetically more favored than other possible interactions, as reported with spermine. The cyclic diamines exhibited better interactions with the N7 site of the AT and GC base pairs of DNA than the linear diamines. The net atomic charges calculated for the protonated amine hydrogens were higher for the cyclic systems than for the linear diamines, inducing better binding affinity with the DNA base pairs. The stable conformers of cyclic diamines were predicted using the MP2/aug-cc-pVDZ level of theory. The positions of the protonated diamine groups in these cyclic systems are crucial for effective binding with the DNA base pairs. The DFT-calculated results show that diequatorial (ee) 1,2-cyclohexadiamine (CHDA) is a promising candidate as a polyamine analogue for biogenic polyamines. Molecular dynamics simulations were performed using explicit water molecules for the interaction of representative ligands with the DNA base pairs to examine the influence of solvent molecules on such interactions.
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Affiliation(s)
- Anik Sen
- Computation and Simulation Unit, Analytical Discipline & Centralized Instrument Facility, CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar, Gujarat 364002, India
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50
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Kabir A, Suresh Kumar G. Binding of the biogenic polyamines to deoxyribonucleic acids of varying base composition: base specificity and the associated energetics of the interaction. PLoS One 2013; 8:e70510. [PMID: 23894663 PMCID: PMC3722294 DOI: 10.1371/journal.pone.0070510] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 06/24/2013] [Indexed: 11/18/2022] Open
Abstract
Background The thermodynamics of the base pair specificity of the binding of the polyamines spermine, spermidine, putrescine, and cadaverine with three genomic DNAs Clostridium perfringens, 27% GC, Escherichia coli, 50% GC and Micrococcus lysodeikticus, 72% GC have been studied using titration calorimetry and the data supplemented with melting studies, ethidium displacement and circular dichroism spectroscopy results. Methodology/Principal Findings Isothermal titration calorimetry, differential scanning calorimetry, optical melting studies, ethidium displacement, circular dichroism spectroscopy are the various techniques employed to characterize the interaction of four polyamines, spermine, spermidine, putersine and cadaverine with the DNAs. Polyamines bound stronger with AT rich DNA compared to the GC rich DNA and the binding varied depending on the charge on the polyamine as spermine>spermidine >putrescine>cadaverine. Thermodynamics of the interaction revealed that the binding was entropy driven with small enthalpy contribution. The binding was influenced by salt concentration suggesting the contribution from electrostatic forces to the Gibbs energy of binding to be the dominant contributor. Each system studied exhibited enthalpy-entropy compensation. The negative heat capacity changes suggested a role for hydrophobic interactions which may arise due to the non polar interactions between DNA and polyamines. Conclusion/Significance From a thermodynamic analysis, the AT base specificity of polyamines to DNAs has been elucidated for the first time and supplemented by structural studies.
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Affiliation(s)
- Ayesha Kabir
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- * E-mail:
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