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Kumari N, Chaudhary M, Awasthi P. Sulfonyl-acetohydrazide derivatives as juvenile hormone mimics to be insect growth regulators. Bioorg Chem 2024; 153:107781. [PMID: 39255607 DOI: 10.1016/j.bioorg.2024.107781] [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: 07/11/2024] [Revised: 08/17/2024] [Accepted: 08/29/2024] [Indexed: 09/12/2024]
Abstract
The need for targeted pest control strategies has led to the development of juvenile hormone (JH) mimics that selectively disrupt the life cycles of harmful insect species. Present study focuses on the synthesis, characterization and evaluation of sulfonyl-acetohydrazide derivatives (H1-H8) as novel JH mimics on two different insect species, with an emphasis on their insect-specific action. The yellow fever mosquito, Aedes aegypti and cabbage leaf borer, Spodoptera litura, were selected for this investigation. Our results indicate that while these compounds exhibit negligible effects on the development of Aedes aegypti, they demonstrate a potent and specific action against Spodoptera litura. The sulfonyl-acetohydrazide derivatives induced significant developmental abnormalities and increased mortality rates in Spodoptera litura larvae, leading to a marked disruption in their life cycle. Additionally, Density Functional Theory methods were employed to elucidate the electronic structure and corelate the reactivity of the synthesized compounds with the insect growth regulating activity (IGR). The DNA-binding study of synthesized JH analogs has been carried out using UV-vis spectroscopy for toxicity assessment against biomolecule DNA. All the synthesized JH analogs (H1-H8) show IGR action and exhibit better reactivity and reduced toxicity as compared to the commercial in use IGR, pyriproxyfen.
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Affiliation(s)
- Neetika Kumari
- Department of Chemistry, National Institute of Technology, Hamirpur 177005, Himachal Pradesh, India
| | - Manisha Chaudhary
- Department of Entomology, College of Agriculture, CSKHPKV Palampur, Palampur 176062, Himachal Pradesh, India
| | - Pamita Awasthi
- Department of Chemistry, National Institute of Technology, Hamirpur 177005, Himachal Pradesh, India.
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2
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Dorafshan Tabatabai AS, Dehghanian E, Mansouri-Torshizi H, Feizi-Dehnayebi M. Computational and experimental examinations of new antitumor palladium(II) complex: CT-DNA-/BSA-binding, in-silico prediction, DFT perspective, docking, molecular dynamics simulation and ONIOM. J Biomol Struct Dyn 2024; 42:5447-5469. [PMID: 37349936 DOI: 10.1080/07391102.2023.2226715] [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: 02/12/2023] [Accepted: 06/12/2023] [Indexed: 06/24/2023]
Abstract
Since the design of metal complexes with better biological activities is important, herein a new palladium(II) complex bearing en and acac (en and acac stand for ethylenediamine and acetylacetonato, respectively) as its ligands, [Pd(en)(acac)]NO3 complex, was synthesized and fully characterized. Quantum chemical computations of the palladium(II) complex were done via DFT/B3LYP method. Cytotoxicity activity of the new compound on leukemia cell line (K562) was assessed via MTT method. The findings indicated that the metal complex has remarkable cytotoxic effect than cisplatin. OSIRIS DataWarrior software was employed to calculate in-silico physicochemical and toxicity parameters of the synthesized complex which rendered significant results. To comprehend the interaction type of new metal compound with macromolecules, the in depth investigation of interaction of mentioned complex with CT-DNA and BSA was accomplished by fluorescence, UV-Visible absorption spectroscopy, viscosity measurement, gel electrophoresis, FRET analysis and circular dichroism (CD) spectroscopy. On the other hand, computational molecular docking was carried out and the obtained data demonstrated that H-bond and van der Waals forces are the dominant forces for the binding of the compound to the mentioned biomolecules. Molecular dynamics simulation was also done and confirmed the stability of best docked pose of palladium(II) complex inside DNA or BSA over the time and in presence of water solvent. Also, Our own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM) methodology based on the hybridization of quantum mechanics and molecular mechanics (QM/MM) methodology was accomplished to inquire about binding of Pd(II) complex with DNA or BSA.HIGHLIGHTSNew biologically active Pd(II) complex was synthesized and characterized.The in silico studies of the designed complex and its ligands were accomplished by OSIRIS DataWarrior softwareInteraction with CT-DNA and BSA was assessed by various spectroscopic methods.Molecular docking simulation supported the interaction with both macromolecules.Based on ONIOM analysis, the structures of the complex and biomolecules are altered after binding. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Effat Dehghanian
- Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
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3
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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: 4] [Impact Index Per Article: 4.0] [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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4
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Contreras-Trigo B, Díaz-García V, Oyarzún P. A Novel Preanalytical Strategy Enabling Application of a Colorimetric Nanoaptasensor for On-Site Detection of AFB1 in Cattle Feed. SENSORS (BASEL, SWITZERLAND) 2022; 22:9280. [PMID: 36501982 PMCID: PMC9735511 DOI: 10.3390/s22239280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
Aflatoxin contamination of cattle feed is responsible for serious adverse effects on animal and human health. A number of approaches have been reported to determine aflatoxin B1 (AFB1) in a variety of feed samples using aptasensors. However, rapid analysis of AFB1 in these matrices remains to be addressed in light of the complexity of the preanalytical process. Herein we describe an optimization on the preanalytical stage to minimize the sample processing steps required to perform semi-quantitative colorimetric detection of AFB1 in cattle feed using a gold nanoparticle-based aptasensor (nano-aptasensor). The optical behavior of the nano-aptasensor was characterized in different organics solvents, with acetonitrile showing the least interference on the activity of the nan-aptasensor. This solvent was selected as the extractant agent for AFB1-containing feed, allowing for the first time, direct colorimetric detection from the crude extract (detection limit of 5 µg/kg). Overall, these results lend support to the application of this technology for the on-site detection of AFB1 in the dairy sector.
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Zangeneh monfared F, Shahabadi N, Mahmoudi Hashemi M, Sadat Meibodi F, Mirjafari Z. Zinc oxide nanoparticles coated with food colorant Brilliant black: Synthesis, characterization, and comparative DNA interaction and antibacterial activity studies. J FOOD PROCESS PRES 2021. [DOI: 10.1111/jfpp.15514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
| | - Nahid Shahabadi
- Inorganic Chemistry Department, Faculty of Chemistry Razi University Kermanshah Iran
- Medical Biology Research Center (MBRC) Kermanshah University of Medical Sciences Kermanshah Iran
| | | | - Farhat Sadat Meibodi
- Department of Organic Chemistry, Faculty of Chemistry Razi University Kermanshah Iran
| | - Zohreh Mirjafari
- Department of Chemistry, Science and Research Branch Islamic Azad University Tehran Iran
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6
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Kou SB, Zhou KL, Lin ZY, Lou YY, Shi JH, Liu YX. Insights into the binding properties of calf thymus DNA with lopinavir from spectroscopic and computational studies. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115491] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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7
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Hansda S, Mitra A, Ghosh R. Studies to explore the UVA photosensitizing action of 9-phenylacridine in cells by interaction with DNA. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2021; 40:393-422. [PMID: 33586599 DOI: 10.1080/15257770.2021.1880011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Acridine and its derivatives are well known for their DNA binding properties. In this report, we present our findings on evaluating different binding parameters of the interaction of 9-phenylacridine (ACPH) with DNA. Absorption spectroscopic studies including standard and reverse titration, the effects of ionic strength and temperature on titration, and Job plot analysis were done to calculate the binding constant and determine the different thermodynamic parameters and stoichiometry of the binding. Spectrofluorimetry and circular dichroism (CD) spectral titration were also utilized to confirm these findings. The results indicated that ACPH binds to DNA reversibly through non-electrostatic interactions by hydrogen bonding and van der Waals interactions. The binding constant and the number of binding sites were of the order 103 M-1 and ≈2, respectively with a binding stoichiometry of 1:4. The binding of ACPH with DNA was spontaneous, exothermic and enthalpy-driven. The extent of uptake of ACPH in B16 melanoma cells was estimated. As this compound absorbs in the UVA region, the effect of treatment with ACPH prior to UVA exposure was assessed to evaluate its phototoxicity in these cells. Our results indicated that the binding to DNA enhanced damage to sensitize cells to killing through apoptosis. Our findings indicated its potential to act as a photosensitizer.
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Affiliation(s)
- Surajit Hansda
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, West Bengal, India
| | - Anindita Mitra
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, West Bengal, India
| | - Rita Ghosh
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani, West Bengal, India
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8
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Hu M, Zhu M, Xin L, Zhang G, Wu S, Hu X, Gong D. Change of benzo(a)pyrene during frying and its groove binding to calf thymus DNA. Food Chem 2021; 350:129276. [PMID: 33609937 DOI: 10.1016/j.foodchem.2021.129276] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 09/21/2020] [Accepted: 12/20/2020] [Indexed: 01/07/2023]
Abstract
Benzo[a]pyrene (BaP), a prototype of polycyclic aromatic hydrocarbons (PAHs) with potential mutagenicity, toxicity and carcinogenicity, is ubiquitous in deep-fried foods. Herein, the changes in eight specific PAHs (PAH8) concentration in sunflower oil during frying were investigated by gas chromatography-triple quadrupole-mass spectrometry (GC-QqQ-MS). PAH8 concentrations in sunflower oil were 23.92-27.82 μg kg-1 and increased with increasing frying time. The detected BaP levels were 3.64-4.00 μg kg-1, exceeding the upper limit (2 μg kg-1) set by European Union (EU), though below the limiting value (10 μg kg-1) in China. The interaction between BaP and calf thymus DNA (ctDNA) was explored through various spectroscopic methods and molecular docking. Melting studies, denaturation experiments, ionic strength effects and viscosity measurements indicated that BaP interacted with ctDNA primarily via groove binding as evidenced by circular dichroism analysis and molecular docking. Further gel electrophoresis assays suggested that DNA was damaged at high levels of BaP.
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Affiliation(s)
- Mingming Hu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Miao Zhu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Le Xin
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Bor S. Luh Food Safety Research Centre, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Guowen Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China.
| | - Shimin Wu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China; Bor S. Luh Food Safety Research Centre, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xing Hu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Deming Gong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
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9
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New thiazoldinone substituted 2,6-diarypiperidin-4-one: Synthesis, crystal structure, spectral characterization, binding mode with calf thymus DNA. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.126899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Liu Y, Lu J, Sun J, Lu F, Bie X, Lu Z. Membrane disruption and DNA binding of Fusarium graminearum cell induced by C16-Fengycin A produced by Bacillus amyloliquefaciens. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.03.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Ličen M, Masiero S, Drevenšek-Olenik I. Photoisomerizable Guanosine Derivative as a Probe for DNA Base-Pairing in Langmuir Monolayers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:6550-6561. [PMID: 31030520 PMCID: PMC6727594 DOI: 10.1021/acs.langmuir.9b00429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/26/2019] [Indexed: 06/09/2023]
Abstract
Mixtures of azo-functionalized amphiphilic derivatives of guanosine and of amphiphilic derivatives of other DNA nucleobases were deposited at an air-water interface and repeatedly irradiated with light of 340 and 440 nm wavelengths. The consequent switching between cis and trans configurations of the azobenzene moiety caused changes in the surface pressure of the film, which were analyzed using a model based on the two-dimensional Van der Waals equation of state. For mixed films of guanosine and cytidine derivatives, the analysis revealed a significant modification of the strength of intermolecular interaction caused by the optical irradiation, while no such modifications were identified in mixed films involving other nucleobases. The difference is attributed to light-induced breaking of the hydrogen bonding that is established only between specific nucleobases. The results demonstrate that photosensitive nucleoside derivatives can be used as an efficient probe for base-pairing in Langmuir monolayers.
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Affiliation(s)
- M. Ličen
- Department
of Complex Matter, Jožef Stefan Institute, Jamova 39, SI 1000 Ljubljana, Slovenia
| | - S. Masiero
- Dipartimento
di Chimica “G. Ciamician”, Alma Mater Studiorum—Università di Bologna, Via San Giacomo 11, I-40126 Bologna, Italy
| | - I. Drevenšek-Olenik
- Department
of Complex Matter, Jožef Stefan Institute, Jamova 39, SI 1000 Ljubljana, Slovenia
- Faculty
of Mathematics and Physics, University of
Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia
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12
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Biçer E, Pehlivan V, Bekiroğlu YG. Synthesis, Characterization, in vitro Antifungal Activities and Calf Thymus DNA Interactions of Two Different Hydroxy Benzaldehyde Derivative Schiff Bases from Sulfamethizole: Electrochemical, Spectroscopic and Biological Study. RUSS J ELECTROCHEM+ 2019. [DOI: 10.1134/s1023193519050045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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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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14
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Jamali T, Kavoosi G, Safavi M, Ardestani SK. In-vitro evaluation of apoptotic effect of OEO and thymol in 2D and 3D cell cultures and the study of their interaction mode with DNA. Sci Rep 2018; 8:15787. [PMID: 30361692 PMCID: PMC6202332 DOI: 10.1038/s41598-018-34055-w] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/10/2018] [Indexed: 12/22/2022] Open
Abstract
Oliveria decumbens is an Iranian endemic plant used extensively in traditional medicine. Recently, some studies have been performed on biological effects of Oliveria essential oil (OEO). However, to our knowledge, the anticancer activity of OEO has not been reported. Based on our GC/MS analysis, the basic ingredients of OEO are thymol, carvacrol, p-cymene and γ-terpinene. Therefore, we used OEO and its main component, thymol, to explore their effects on cell growth inhibition and anticancer activity. Despite having a limited effect on L929 normal cells, OEO/thymol induced cytotoxicity in MDA-MB231 breast cancer monolayers (2D) and to a lesser extent in MDA-MB231 spheroids (3D). Flow cytometry, caspase-3 activity assay in treated monolayers/spheroids and also fluorescence staining and DNA fragmentation in treated monolayers demonstrated apoptotic death mode. Indeed, OEO/thymol increased the Reactive Oxygen Species (ROS) level leading to mitochondrial membrane potential (MMP, ΔΨm) loss, caspase-3 activation and DNA damage caused S-phase cell cycle arrest. Furthermore, immunoblotting studies revealed the activation of intrinsic and maybe extrinsic apoptosis pathways by OEO/thymol. Additionally, in-vitro experiments, indicated that OEO/thymol interacts with DNA via minor grooves confirmed by docking method. Altogether, our reports underlined the potential of OEO to be considered as a new candidate for cancer therapy.
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Affiliation(s)
- Tahereh Jamali
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Maliheh Safavi
- Department of Biotechnology, Iranian Research Organization for Science and Technology, Tehran, Iran
| | - Susan K Ardestani
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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15
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Mitra A, Saikh F, Das J, Ghosh S, Ghosh R. Studies on the interaction of a synthetic nitro-flavone derivative with DNA: A multi-spectroscopic and molecular docking approach. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 203:357-369. [PMID: 29885634 DOI: 10.1016/j.saa.2018.05.073] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 05/09/2018] [Accepted: 05/20/2018] [Indexed: 06/08/2023]
Abstract
Interaction of a ligand with DNA is often the basis of drug action of many molecules. Flavones are important in this regard as their structural features confer them the ability to bind to DNA. 2-(4-Nitrophenyl)-4H-chromen-4-one (4NCO) is an important biologically active synthetic flavone derivative. We are therefore interested in studying its interaction with DNA. Absorption spectroscopy studies included standard and reverse titration, effect of ionic strength on titration, determination of stoichiometry of binding and thermal denaturation. Spectrofluorimetry techniques included fluorimetric titration, quenching studies and fluorescence displacement assay. Assessment of relative viscosity and estimation of thermodynamic parameters from CD spectral studies were also undertaken. Furthermore, molecular docking analyses were also done with different short DNA sequences. The fluorescent flavone 4NCO reversibly interacted with DNA through partial intercalation as well as minor-groove binding. The binding constant and the number of binding sites were of the order 104 M-1 and 1 respectively. The binding stoichiometry with DNA was found to be 1:1. The nature of the interaction of 4NCO with DNA was hydrophobic in nature and the process of binding was spontaneous, endothermic and entropy-driven. The flavone also showed a preference for binding to GC rich sequences. The study presents a profile for structural and thermodynamic parameters, for the binding of 4NCO with DNA. DNA is an important target for ligands that are effective against cell proliferative disorders. In this regard, the molecule 4NCO is important since it can exert its biological activity through its DNA binding ability and can be a potential drug candidate.
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Affiliation(s)
- A Mitra
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India
| | - F Saikh
- Department of Chemistry, Organic Section, Jadavpur University, Kolkata 700032, West Bengal, India
| | - J Das
- Department of Chemistry, Organic Section, Jadavpur University, Kolkata 700032, West Bengal, India
| | - S Ghosh
- Department of Chemistry, Organic Section, Jadavpur University, Kolkata 700032, West Bengal, India
| | - R Ghosh
- Department of Biochemistry & Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India.
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16
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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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17
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Ahmad A, Ahmad M. Deciphering the mechanism of interaction of edifenphos with calf thymus DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 188:244-251. [PMID: 28732283 DOI: 10.1016/j.saa.2017.07.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 07/10/2017] [Accepted: 07/12/2017] [Indexed: 06/07/2023]
Abstract
Edifenphos is an important organophosphate pesticide with many antifungal and anti-insecticidal properties but it may cause potential hazards to human health. In this work, we have tried to explore the binding mode of action and mechanism of edifenphos to calf thymus DNA (CT-DNA). Several experiments such as ultraviolet-visible absorption spectra and emission spectroscopy showed complex formation between edifenphos and CT-DNA and low binding constant values supporting groove binding mode. These results were further confirmed by circular dichroism (CD), CT-DNA melting studies, viscosity measurements, density functional theory and molecular docking. CD study suggests that edifenphos does not alter native structure of CT-DNA. Isothermal calorimetry reveals that binding of edifenphos with CT-DNA is enthalpy driven process. Competitive binding assay and effect of ionic strength showed that edifenphos binds to CT-DNA via groove binding manner. Hence, edifenphos is a minor groove binder preferably interacting with A-T regions with docking score -6.84kJ/mol.
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Affiliation(s)
- Ajaz Ahmad
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India
| | - Masood Ahmad
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh 202002, India.
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Fekri R, Salehi M, Asadi A, Kubicki M. Spectroscopic studies, structural characterization and electrochemical studies of two cobalt (III) complexes with tridentate hydrazone Schiff base ligands: Evaluation of antibacterial activities, DNA‐binding, BSA interaction and molecular docking. Appl Organomet Chem 2017. [DOI: 10.1002/aoc.4019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Roghayeh Fekri
- Department of Chemistry, College of ScienceSemnan University Semnan Iran
| | - Mehdi Salehi
- Department of Chemistry, College of ScienceSemnan University Semnan Iran
| | - Asadollah Asadi
- Department of Biology, Faculty of ScienceUniversity of Mohaghegh Ardabili Ardabil Iran
| | - Maciej Kubicki
- Faculty of ChemistryAdam Mickiewicz University Umultowska 89b 61‐614 Poznan Poland
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19
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Yan XW, Xie YR, Jin ZM, Hu ML, Zhou LP. Three Arene-Ru(II) compounds of 2-halogen-5-aminopyridine: Synthesis, characterization, and cytotoxicity. Appl Organomet Chem 2017. [DOI: 10.1002/aoc.3923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xiao-Wei Yan
- College of Materials and Environmental Engineering, Guangxi Key Laboratory of Calcium Carbonate Resources Comprehensive Utilization; Hezhou University; Hezhou Guangxi 542800 People's Republic of China
| | - Yong-Rong Xie
- Key Laboratory of Jiangxi University for Functional Materials Chemistry, Gannan Normal University; Ganzhou Jiangxi 341000 People's Republic of China
| | - Zhi-Min Jin
- College of Pharmaceutical Sciences; Zhejiang University of Technology; Zhejiang Hangzhou 310014 People's Republic of China
| | - Mao-Lin Hu
- Institute of New Materials & Industrial Technology; Wenzhou University; Wenzhou Zhejiang 325035 People's Republic of China
| | - Liang-Pu Zhou
- College of Pharmaceutical Sciences; Zhejiang University of Technology; Zhejiang Hangzhou 310014 People's Republic of China
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20
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Groove Binding of Vanillin and Ethyl Vanillin to Calf Thymus DNA. J Fluoresc 2017; 27:1815-1828. [DOI: 10.1007/s10895-017-2119-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/14/2017] [Indexed: 10/19/2022]
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21
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Interaction between bioactive compound 11a-N-tosyl-5-deoxi-pterocarpan (LQB-223) and Calf thymus DNA: Spectroscopic approach, electrophoresis and theoretical studies. Int J Biol Macromol 2017; 96:223-233. [DOI: 10.1016/j.ijbiomac.2016.12.044] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/09/2016] [Accepted: 12/09/2016] [Indexed: 12/24/2022]
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22
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Xia K, Zhang G, Gong D. Deciphering the intercalative binding modes of benzoyl peroxide with calf thymus DNA. LUMINESCENCE 2017; 32:988-998. [PMID: 28116811 DOI: 10.1002/bio.3281] [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: 10/09/2016] [Revised: 12/13/2016] [Accepted: 12/19/2016] [Indexed: 12/23/2022]
Abstract
The binding of benzoyl peroxide (BPO), a flour brightener, with calf thymus DNA (ctDNA) was predicted by molecular simulation, and this were confirmed using multi-spectroscopic techniques and a chemometrics algorithm. The molecular docking result showed that BPO could insert into the base pairs of ctDNA, and the adenine bases were the preferential binding sites which were validated by the analysis of Fourier transform infrared spectra. The mode of binding of BPO with ctDNA was an intercalation as supported by the results from ctDNA melting and viscosity measurements, iodide quenching effects and competitive binding investigations. The circular dichroism and DNA cleavage assays indicated that BPO induced a conformational change from B-like DNA structure towards to A-like form, but did not lead to significant damage in the DNA. The complexation was driven mainly by hydrogen bonds and hydrophobic interactions. Moreover, the ultraviolet-visible (UV-vis) spectroscopic data matrix was resolved by a multivariate curve resolution-alternating least-squares algorithm. The equilibrium concentration profiles for the components (BPO, ctDNA and BPO-ctDNA complex) were extracted from the highly overlapping composite response to quantitatively monitor the BPO-ctDNA interaction. This study has provided insights into the mechanism of the interaction of BPO with ctDNA and potential hazards of the food additive.
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Affiliation(s)
- Kaixin Xia
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Guowen Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Deming Gong
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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23
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Wang LH, Zhang ZH, Zeng XA, Gong DM, Wang MS. Combination of microbiological, spectroscopic and molecular docking techniques to study the antibacterial mechanism of thymol against Staphylococcus aureus: membrane damage and genomic DNA binding. Anal Bioanal Chem 2016; 409:1615-1625. [PMID: 27900434 DOI: 10.1007/s00216-016-0102-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/07/2016] [Accepted: 11/15/2016] [Indexed: 12/13/2022]
Abstract
Thymol (2-isopropyl-5-methylphenol) is a natural ingredient used as flavor or preservative agent in food products. The antibacterial mechanism of thymol against Gram-positive, Staphylococcus aureus was investigated in this work. A total of 15 membrane fatty acids were identified in S. aureus cells by gas chromatography-mass spectrometry. Exposure to thymol at low concentrations induced obvious alterations in membrane fatty acid composition, such as decreasing the proportion of branched 12-methyltetradecanoic acid and 14-methylhexadecanoic acid (from 22.4 and 17.3% to 7.9 and 10.3%, respectively). Membrane permeability assay and morphological image showed that thymol at higher concentrations disrupted S. aureus cell membrane integrity, which may decrease cell viability. Moreover, the interaction of thymol with genomic DNA was also investigated using multi-spectroscopic techniques, docking and atomic force microscopy. The results indicated that thymol bound to the minor groove of DNA with binding constant (K a) value of (1.22 ± 0.14) × 104 M-1, and this binding interaction induced a mild destabilization in the DNA secondary structure, and made DNA molecules to be aggregated. Graphical Abstract Thymol exerts its antibacterial effect throught destruction of bacterial cell membrane and binding directly to genomic DNA.
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Affiliation(s)
- Lang-Hong Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, 510641, China.,Food Green Processing and Nutrition Regulation Research Center of Guangdong Province, South China University of Technology, Guangzhou, Guangdong, 510641, China
| | - Zhi-Hong Zhang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, 510641, China.,Food Green Processing and Nutrition Regulation Research Center of Guangdong Province, South China University of Technology, Guangzhou, Guangdong, 510641, China
| | - Xin-An Zeng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, 510641, China. .,Food Green Processing and Nutrition Regulation Research Center of Guangdong Province, South China University of Technology, Guangzhou, Guangdong, 510641, China.
| | - De-Ming Gong
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand.
| | - Man-Sheng Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, No. 348 West Xianjiahu Road, Changsha, Hunan, 410205, China
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Tao M, Zhang G, Pan J, Xiong C. Deciphering the groove binding modes of tau-fluvalinate and flumethrin with calf thymus DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 155:28-37. [PMID: 26571092 DOI: 10.1016/j.saa.2015.11.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 10/30/2015] [Accepted: 11/03/2015] [Indexed: 06/05/2023]
Abstract
Tau-fluvalinate (TFL) and flumethrin (FL), widely used in agriculture and a class of synthetic pyrethroid pesticides with a similar structure, may cause a potential security risk. Herein, the modes of binding in vitro of TFL and FL with calf thymus DNA (ctDNA) were characterized by fluorescence, UV-vis absorption, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy with the aid of viscosity measurements, melting analyses and molecular docking studies. The fluorescence titration indicated that both TFL and FL bound to ctDNA forming complexes through hydrogen bonding and van der Waals forces. The binding constants of TFL and FL with ctDNA were in the range of 10(4)Lmol(-1), and FL exhibited a higher binding propensity than TFL. The iodide quenching effect, single/double-stranded DNA effects, and ctDNA melting and viscosity measurements demonstrated that the binding of both TFL and FL to ctDNA was groove mode. The FT-IR analyses suggested the A-T region of the minor groove of ctDNA as the preferential binding for TFL and FL, which was confirmed by the displacement assays with Hoechst 33258 probe, and the molecular docking visualized the specific binding. The changes in CD spectra indicated that both FL and TFL induced the perturbation on the base stacking and helicity of B-DNA, but the disturbance caused by FL was more obvious. Gel electrophoresis analyses indicated that both TFL and FL did not cause significant DNA cleavage. This study provides novel insights into the binding properties of TFL/FL with ctDNA and its toxic mechanisms.
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Affiliation(s)
- Mo Tao
- State Key Laboratory of Food Science and Technology, Nanchang University, 235, Nanjing East Road, Nanchang 330047, China
| | - Guowen Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, 235, Nanjing East Road, Nanchang 330047, China.
| | - Junhui Pan
- State Key Laboratory of Food Science and Technology, Nanchang University, 235, Nanjing East Road, Nanchang 330047, China
| | - Chunhong Xiong
- State Key Laboratory of Food Science and Technology, Nanchang University, 235, Nanjing East Road, Nanchang 330047, China
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25
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Singla P, Luxami V, Paul K. Triazine–benzimidazole conjugates: synthesis, spectroscopic and molecular modelling studies for interaction with calf thymus DNA. RSC Adv 2016. [DOI: 10.1039/c5ra24001h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Triazine–benzimidazole analogues with different substitutions of primary and secondary amines as well as aryl groups were synthesized and studied their interactions with calf thymus DNA.
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Affiliation(s)
- Prinka Singla
- School of Chemistry and Biochemistry
- Thapar University
- Patiala-147004
- India
| | - Vijay Luxami
- School of Chemistry and Biochemistry
- Thapar University
- Patiala-147004
- India
| | - Kamaldeep Paul
- School of Chemistry and Biochemistry
- Thapar University
- Patiala-147004
- India
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26
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Cifuentes T, Cayupi J, Celis-Barros C, Zapata-Torres G, Ballesteros R, Ballesteros-Garrido R, Abarca B, Jullian C. Spectroscopic studies of the interaction of 3-(2-thienyl)-[1,2,3]triazolo[1,5-a]pyridine with 2,6-dimethyl-β-cyclodextrin and ctDNA. Org Biomol Chem 2016; 14:9760-9767. [DOI: 10.1039/c6ob01573e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The studied effect of the inclusion complex on the ctDNA interaction indicates that the TTP-DMβCD complex binds similarly to ctDNA compared to free TTP.
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Affiliation(s)
- T. Cifuentes
- Departamento Química Orgánica y Fisicoquímica
- Facultad de Ciencias Químicas y Farmacéuticas
- Universidad de Chile
- Chile
| | - J. Cayupi
- Departamento Química Orgánica y Fisicoquímica
- Facultad de Ciencias Químicas y Farmacéuticas
- Universidad de Chile
- Chile
| | - C. Celis-Barros
- Departamento Química Inorgánica y Analítica
- Facultad de Ciencias Químicas y Farmacéuticas
- Universidad de Chile
- Chile
| | - G. Zapata-Torres
- Departamento Química Inorgánica y Analítica
- Facultad de Ciencias Químicas y Farmacéuticas
- Universidad de Chile
- Chile
| | - Rafael Ballesteros
- Departamento de Química Orgánica
- Facultad de Farmacia
- Universidad de Valencia
- Spain
| | | | - B. Abarca
- Departamento de Química Orgánica
- Facultad de Farmacia
- Universidad de Valencia
- Spain
| | - C. Jullian
- Departamento Química Orgánica y Fisicoquímica
- Facultad de Ciencias Químicas y Farmacéuticas
- Universidad de Chile
- Chile
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Farajzadeh Dehkordi M, Dehghan G, Mahdavi M, Hosseinpour Feizi MA. Investigation on the Binding Mode of 3, 4-Dihydropyrano[c]Chromene Derivative with Double Strand DNA. Adv Pharm Bull 2015; 5:477-81. [PMID: 26819919 DOI: 10.15171/apb.2015.065] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/14/2015] [Accepted: 06/27/2015] [Indexed: 11/09/2022] Open
Abstract
PURPOSE The study on the interaction between small molecules and DNA has been very useful for investigating the structure and physical properties of DNA, elucidating the damage mechanism of DNA and significant in the design of new drugs targeted to DNA. This article describes an interaction of native calf thymus DNA (ctDNA) with a new 3, 4-dihydropyrano[c]chromene derivative, 2-amino-4-(4- chlorophenyl)-5-oxo-4H, 5H-pyrano-[3, 2-c] chromene-3-carbonitrile (4-CC) by using spectroscopic and viscometric techniques. METHODS The interaction between 4-CC and ctDNA is realized from the UV absorption spectrophotometry, viscosimetry, circular dichroism and fluorescence spectroscopic techniques which shows that the successive interaction of 4-CC with ctDNA occurs. RESULTS The experimental results revealed that 4-CC can interact with DNA through non- intercalative mode and the intrinsic binding constant (Kb) for 4-CC with DNA was estimated to 2.37 (±0.001) ×103 M-1. Methylene blue (MB) displacement studies revealed that 4-CC did not have any effect on MB bound DNA which is indicative of groove binding mode. Furthermore, 4-CC induces detectable changes in the CD spectrum of ctDNA as well as changes in its viscosity study corroborate the above experimental results. CONCLUSION These results further advance our knowledge on the molecular aspects on the interaction of 4-CC to nucleic acids.
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Affiliation(s)
| | - Gholamreza Dehghan
- Department of Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
| | - Majid Mahdavi
- Department of Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
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28
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Shahabadi N, Moradi Fili S, Shahlaei M. Synthesis, characterization and comparative DNA interaction studies of new copper(II) and nickel(II) complexes containing mesalamine drug using molecular modeling and multispectroscopic methods. J COORD CHEM 2015. [DOI: 10.1080/00958972.2015.1078897] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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
| | - Soraya Moradi Fili
- Faculty of Chemistry, Department of Inorganic Chemistry, Razi University, Kermanshah, Iran
| | - Mohsen Shahlaei
- Faculty of Pharmacy, Department of Medicinal Chemistry, Medical Sciences University, Kermanshah, Iran
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29
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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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30
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Zhou X, Zhang G, Pan J. Groove binding interaction between daphnetin and calf thymus DNA. Int J Biol Macromol 2014; 74:185-94. [PMID: 25541356 DOI: 10.1016/j.ijbiomac.2014.12.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 12/25/2022]
Abstract
The binding characteristics of daphnetin with calf thymus DNA (ctDNA) were investigated by multispectroscopic and chemometric approaches coupled with DNA viscosity measurements, melting studies and molecular docking technique. The expanded UV-vis spectral data matrix was processed by multivariate curve resolution-alternating least-squares method to obtain the concentration profiles of the components (daphnetin, ctDNA and daphnetin-ctDNA complex) to quantitatively monitor the daphnetin-ctDNA interaction. The groove mode of daphnetin binding to ctDNA was concluded by little change in melting temperature, viscosity of ctDNA and iodide quenching effect as well as increase in single-stranded DNA quenching effect. Moreover, the quantitative data for the competitive binding between daphnetin and Hoechst 33258 for ctDNA obtained by resolving the three-way synchronous fluorescence spectra data using parallel factor analysis modeling further supported the groove binding. The molecular docking visualized the results of the Fourier transform infrared analysis that the adenine and thymine bases in the minor groove of ctDNA were the main binding sites for daphnetin, and the circular dichroism spectra showed that the groove binding of daphnetin to ctDNA led to the conformational change in ctDNA from B-form to A-form. This study revealed the interaction mechanism of daphnetin with ctDNA.
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Affiliation(s)
- Xiaoyue Zhou
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Guowen Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China.
| | - Junhui Pan
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
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31
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Zhang G, Wang L, Zhou X, Li Y, Gong D. Binding characteristics of sodium saccharin with calf thymus DNA in vitro. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:991-1000. [PMID: 24437661 DOI: 10.1021/jf405085g] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The binding characteristics of sodium saccharin (SSA), an artificial sweetener, with calf thymus DNA (ctDNA) were investigated by multispectroscopic techniques, chemometrics, and molecular simulation. A combined fluorescence and UV-vis spectroscopic data matrix was resolved by the multivariate curve resolution-alternating least-squares (MCR-ALS) chemometrics algorithm. The MCR-ALS analysis extracted simultaneously the concentration profiles and spectra for the three components (SSA, ctDNA, and SSA-ctDNA complex) to quantitatively monitor the SSA-ctDNA interaction, which is difficult to perform by conventional spectroscopic approach. The binding mode of SSA to ctDNA was principally through groove binding as revealed by ctDNA melting temperature studies, viscosity measurements, and iodide and salt quenching effects. Analysis of the Fourier transform infrared and circular dichroism spectra as well as molecular docking indicated that SSA preferentially bound to the guanine base of ctDNA and led to a transformation from B-like DNA structure to A-like conformation. Moreover, gel electrophoresis results suggested that SSA did not induce any significant cleavage in plasmid DNA.
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Affiliation(s)
- Guowen Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang 330047, China
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32
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Shahabadi N, Fili SM, Kheirdoosh F. Study on the interaction of the drug mesalamine with calf thymus DNA using molecular docking and spectroscopic techniques. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 128:20-6. [DOI: 10.1016/j.jphotobiol.2013.08.005] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 07/31/2013] [Accepted: 08/04/2013] [Indexed: 01/14/2023]
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Shaghaghi M, Dehghan G, Jouyban A, Sistani P, Arvin M. Studies of interaction between terbium(III)-deferasirox and double helix DNA by spectral and electrochemical methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 120:467-472. [PMID: 24211806 DOI: 10.1016/j.saa.2013.09.073] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 09/11/2013] [Accepted: 09/26/2013] [Indexed: 06/02/2023]
Abstract
DNA binding studies of terbium(III)-deferasirox (Tb3+-DFX) complex were monitored to understand the reaction mechanism and introduce a new probe for the assay of DNA. In the present work, UV absorption spectrophotometry, fluorescence spectroscopy, circular dichroism (CD), cyclic voltammetry (CV) and viscosity measurement were employed to study the interactions of Tb3+-DFX with calf thymus DNA (ctDNA). The binding of Tb3+-DFX complex to ctDNA showed a hyperchromic effect in the absorption spectra and the increase in fluorescence quenching effect (amount) of Tb3+-DFX complex in the presence of ctDNA. The binding constants (Kb) for the complex with ctDNA were estimated to be 1.8×10(4) M(-1) through UV absorption spectrophotometry and fluorescence spectroscopy. Upon addition of the complex, clear decreases were observed in the viscosity of ctDNA. The CD spectra indicated that there are certain detectable conformational changes in the DNA double helix when the complex was added. The CV method showed that both anodic and cathodic peak potentials of Tb3+-DFX complex showed negative shifts on the addition of the ctDNA. Further, competitive methylene blue binding studies with fluorescence spectroscopy have shown that the complex can bind to ctDNA through nonintercalative mode. The experimental results suggest that Tb3+-DFX complex binds to DNA via groove binding and/or electrostatic binding mode.
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Affiliation(s)
- Masoomeh Shaghaghi
- Department of Chemistry, University of Payame Noor, P.O. Box. 19395-3697, Tehran, Iran
| | - Gholamreza Dehghan
- Department of Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran.
| | - Abolghasem Jouyban
- Drug Applied Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parisa Sistani
- Department of Biochemistry, University of Payame Noor, P.O. Box. 19395-3697, Tehran, Iran
| | - Mitra Arvin
- Department of Biology, Faculty of Natural Science, University of Tabriz, Tabriz, Iran
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In Vitro Evaluation of Zn–Norfloxacin Complex as a Potent Cytotoxic and Antibacterial Agent, Proposed Model for DNA Binding. Appl Biochem Biotechnol 2013; 170:988-1009. [DOI: 10.1007/s12010-013-0255-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 04/21/2013] [Indexed: 10/26/2022]
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35
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Ahmadi F, Jafari B, Rahimi-Nasrabadi M, Ghasemi S, Ghanbari K. Proposed model for in vitro interaction between fenitrothion and DNA, by using competitive fluorescence, (31)P NMR, (1)H NMR, FT-IR, CD and molecular modeling. Toxicol In Vitro 2012; 27:641-50. [PMID: 23153512 DOI: 10.1016/j.tiv.2012.11.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 10/24/2012] [Accepted: 11/03/2012] [Indexed: 10/27/2022]
Abstract
In this work we proposed a model for in vitro interaction of fenitrothion (FEN) with calf thymus-DNA by combination of multispectroscopic and two dimensional molecular modeling (ONIOM) methods. The circular dichroism results showed that FEN changes the conformation of B-DNA and caused some changes to C-DNA form. The FT-IR results confirmed a partial intercalation between FEN and edges of all base pairs. The competitive fluorescence, using methylene blue as fluorescence probe, in the presence of increasing amounts of FEN, revealed that FEN is able to release the non-intercalated methylene blue from the DNA. The weak chemical shift and peak broadening of (1)H NMR spectrum of FEN in the presence of DNA confirmed a non-intercalation mode. The (31)P NMR showed that FEN interacts more with DNA via its -NO2 moiety. The ONIOM, based on the hybridization of QM/MM (DFT, 6.31++G (d,p)/UFF) methodology, was also performed by Gaussian 2003 package. The results revealed that the interaction is base sequence dependent, and FEN interacts more with AT base sequences.
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Affiliation(s)
- Farhad Ahmadi
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Zhang X, Li M, Cui Y, Zhao J, Cui Z, Li Q, Qu K. Electrochemical Behavior of Calcein and the Interaction Between Calcein and DNA. ELECTROANAL 2012. [DOI: 10.1002/elan.201200192] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Ahmadi F, Jamali N, Moradian R, Astinchap B. Binding Studies of Pyriproxyfen to DNA by Multispectroscopic Atomic Force Microscopy and Molecular Modeling Methods. DNA Cell Biol 2012; 31:259-68. [DOI: 10.1089/dna.2011.1303] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Farhad Ahmadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Nasibeh Jamali
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Rostam Moradian
- Department of Physics, Faculty of Science, Razi University, Kermanshah, Iran
- Nano Technology Research Laboratory, Razi University, Kermanshah, Iran
| | - Bandar Astinchap
- Department of Physics, Faculty of Science, Razi University, Kermanshah, Iran
- Nano Technology Research Laboratory, Razi University, Kermanshah, Iran
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Ahmadi F, Jamali N, Jahangard-Yekta S, Jafari B, Nouri S, Najafi F, Rahimi-Nasrabadi M. The experimental and theoretical QM/MM study of interaction of chloridazon herbicide with ds-DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 79:1004-12. [PMID: 21600841 DOI: 10.1016/j.saa.2011.04.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 03/20/2011] [Accepted: 04/10/2011] [Indexed: 05/06/2023]
Abstract
We report a multispectroscopic, voltammetric and theoretical hybrid of QM/MM study of the interaction between double-stranded DNA containing both adenine-thymine and guanine-cytosine alternating sequences and chloridazon (CHL) herbicide. The electrochemical behavior of CHL was studied by cyclic voltammetry on HMDE, and the interaction of ds-DNA with CHL was investigated by both cathodic differential pulse voltammetry (CDPV) at a hanging mercury drop electrode (HMDE) and anodic differential pulse voltammetry (ADPV) at a glassy carbon electrode (GCE). The constant bonding of CHL-DNA complex that was obtained by UV/vis, CDPV and ADPV was 2.1×10(4), 5.1×10(4) and 2.6×10(4), respectively. The competition fluorescence studies revealed that the CHL quenches the fluorescence of DNA-ethidium bromide complex significantly and the apparent Stern-Volmer quenching constant has been estimated to be 1.71×10(4). Thermal denaturation study of DNA with CHL revealed the ΔTm of 8.0±0.2°C. Thermodynamic parameters, i.e., enthalpy (ΔH), entropy (ΔS°), and Gibbs free energy (ΔG) were 98.45 kJ mol(-1), 406.3 J mol(-1) and -22.627 kJ mol(-1), respectively. The ONIOM, based on the hybridization of QM/MM (DFT, 6.31++G(d,p)/UFF) methodology, was also performed using Gaussian 2003 package. The results revealed that the interaction is base sequence dependent, and the CHL has more interaction with ds-DNA via the GC base sequence. The results revealed that CHL may have an interaction with ds-DNA via the intercalation mode.
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Affiliation(s)
- F Ahmadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Islamic Republic of Iran.
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Ahmadi F, Alizadeh AA, Shahabadi N, Rahimi-Nasrabadi M. Study binding of Al-curcumin complex to ds-DNA, monitoring by multispectroscopic and voltammetric techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 79:1466-1474. [PMID: 21704553 DOI: 10.1016/j.saa.2011.05.002] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Revised: 04/23/2011] [Accepted: 05/01/2011] [Indexed: 05/31/2023]
Abstract
In this work a complex of Al3+ with curcumin ([Al(curcumin) (EtOH)2](NO3)2) was synthesized and characterized by UV-vis, FT-IR, elemental analysis and spectrophotometric titration techniques. The mole ratio plot revealed a 1:1 complex between Al3+ and curcumin in solution. For binding studies of this complex to calf thymus-DNA various methods such as: UV-vis, fluorescence, circular dichroism (CD), FT-IR spectroscopy and cyclic voltammetry were used. The intrinsic binding constant of ACC with DNA at 25°C was calculated by UV-vis and cyclic voltammetry as 2.1×10(4) and 2.6×10(4), respectively. The thermodynamic studies showed that the reaction is enthalpy and entropy favored. The CD results showed that only the Δ-ACC interacts with DNA and the Δ-ACC form has not any tendency to interact with DNA, also the pure curcumin has not any stereoselective interaction with CT-DNA. Fluorimetric studies showed that fluorescence enhancement was initiated by a static process in the ground state. The cyclic voltammetry showed that ACC interact with DNA with a binding site size of 2. From the FT-IR we concluded that the Δ-ACC interacts with DNA via partial electrostatic and minor groove binding. In comparison with previous works it was concluded that curcumin significantly reduced the affinity of Al3+ to the DNA.
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Affiliation(s)
- F Ahmadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah 67145-1673, Islamic Republic of Iran.
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Ahmadi F, Ghasemi S, Rahimi-Nasrabadi M. Adsorptive cathodic stripping determination of minoxidil in pharmaceutical, cream and shampoo products. ACTA ACUST UNITED AC 2011. [DOI: 10.1135/cccc2011001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The cyclic voltammetric behavior of minoxidil was studied in a buffer with pH 3. Contradictory to that mentioned in a previously published work, the cyclic voltammogram of minoxidil exhibited a single 2-electron irreversible reduction wave in a buffer with pH 3. This wave was attributed to the reduction of the N→O bond. The cathodic differential pulse wave height decreased on the increase of pH till it disappeared in solution with pH 7.2. The quantitative trace determination of minoxidil was studied at a hanging mercury drop electrode by adsorptive cathodic stripping voltammetry. A fully validated sensitive procedure based on controlled adsorptive accumulation of the drug onto a HMDE was developed for its direct determination. Accumulation of minoxidil was found to be optimized in 0.1 M Britton–Robinson buffer with pH 2.0 as supporting electrolyte under the following conditions: accumulation potential –0.2 V, accumulation time 40 s, scan rate 40 mV s–1 and pulse height 50 mV. The proposed procedure was applied successfully for determination of minoxidil in its topical solution and illegal shampoo and cream. The mean recoveries of the minoxidil were 99.8, 97.8 and 96.7% and with RSD of 0.86, 1.24 and 1.89% in pharmaceutical topical solution, shampoo and cream, respectively.
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Ahmadi F, Jafari B. Voltammetry and Spectroscopy Study of In Vitro Interaction of Fenitrothion with DNA. ELECTROANAL 2010. [DOI: 10.1002/elan.201000516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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