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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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Priyadharshini RD, Ponkarpagam S, Vennila KN, Elango KP. Multi-spectroscopic and free energy landscape analysis on the binding of antiviral drug remdesivir with calf thymus DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 278:121363. [PMID: 35580462 DOI: 10.1016/j.saa.2022.121363] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/16/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Remdesivir (REM) is an antiviral drug, which exercises its effect by targeting specifically RNA-dependent RNA polymerase. The interaction of REM with calf thymus DNA (CT-DNA) was investigated by multi-spectroscopic techniques (UV-Vis, fluorescence, circular dichroism and 31P NMR) in combination with different biophysical experiments and metadynamics simulation studies. UV-Vis and fluorescence spectroscopic analysis indicated formation of a complex between REM and CT-DNA, whose binding constant is in the order of 104 M-1. Competitive displacement assays with ethidium bromide (EB) and Hoechst 33258 shown that REM binds to CT-DNA via intercalation mode. Significant alteration in the band due to base stacking pairs at 274 nm in the circular dichroism spectrum, appreciable increase in relative viscosity of the biomolecule upon binding with REM and the results of potassium iodide quenching studies confirmed that REM intercalates into the base pairs of CT-DNA. Thermodynamic parameters revealed that the binding of REM to CT-DNA is a spontaneous process (ΔG0 < 0) and the main force which holds them together in the REM/CT-DNA complex is electrostatic interaction (ΔH0 < 0 and ΔS0 > 0). The up-field shift in the 31P NMR signal of REM on interaction with CT-DNA suggested that phenyl ring adjacent to the phosphate moiety of REM may involve in the intercalation process. This is well supported by the analysis of free energy surface landscape derived from metadynamics simulation studies.
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Affiliation(s)
- R Durga Priyadharshini
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624 302, India
| | - S Ponkarpagam
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624 302, India
| | - K N Vennila
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624 302, India
| | - Kuppanagounder P Elango
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624 302, India.
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Pathak VM, Verma VK, Rawat BS, Kaur B, Babu N, Sharma A, Dewali S, Yadav M, Kumari R, Singh S, Mohapatra A, Pandey V, Rana N, Cunill JM. Current status of pesticide effects on environment, human health and it's eco-friendly management as bioremediation: A comprehensive review. Front Microbiol 2022; 13:962619. [PMID: 36060785 PMCID: PMC9428564 DOI: 10.3389/fmicb.2022.962619] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/07/2022] [Indexed: 11/22/2022] Open
Abstract
Pesticides are either natural or chemically synthesized compounds that are used to control a variety of pests. These chemical compounds are used in a variety of sectors like food, forestry, agriculture and aquaculture. Pesticides shows their toxicity into the living systems. The World Health Organization (WHO) categorizes them based on their detrimental effects, emphasizing the relevance of public health. The usage can be minimized to a least level by using them sparingly with a complete grasp of their categorization, which is beneficial to both human health and the environment. In this review, we have discussed pesticides with respect to their global scenarios, such as worldwide distribution and environmental impacts. Major literature focused on potential uses of pesticides, classification according to their properties and toxicity and their adverse effect on natural system (soil and aquatic), water, plants (growth, metabolism, genotypic and phenotypic changes and impact on plants defense system), human health (genetic alteration, cancer, allergies, and asthma), and preserve food products. We have also described eco-friendly management strategies for pesticides as a green solution, including bacterial degradation, myco-remediation, phytoremediation, and microalgae-based bioremediation. The microbes, using catabolic enzymes for degradation of pesticides and clean-up from the environment. This review shows the importance of finding potent microbes, novel genes, and biotechnological applications for pesticide waste management to create a sustainable environment.
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Affiliation(s)
| | - Vijay K. Verma
- Department of Microbiology, University of Delhi, New Delhi, India
| | - Balwant Singh Rawat
- Department of Pharmaceutical Sciences, Gurukul Kangri Deemed to be University, Haridwar, India
| | - Baljinder Kaur
- Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Neelesh Babu
- Department of Microbiology, Baba Farid Institute of Technology, Sudhowala, India
| | - Akansha Sharma
- Allergy and Immunology Section, CSIR-IGIB, New Delhi, India
| | - Seeta Dewali
- Laboratory of Alternative Protocols in Zoology and Biotechnology Research Laboratory, Department of Zoology, Kumaun University, Nainital, India
| | - Monika Yadav
- Cancer Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Reshma Kumari
- Department of Botany & Microbiology, Gurukul Kangri Deemed to be University, Haridwar, India
| | - Sevaram Singh
- Multidisciplinary Clinical Translational Research, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Asutosh Mohapatra
- Food Process Engineering, National Institute of Food Technology, Entrepreneurship and Management, Thanjavur, India
| | - Varsha Pandey
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Newai Tonk, India
| | - Nitika Rana
- Department of Environmental Science, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, India
| | - Jose Maria Cunill
- Biotechnology Engineering, Universidad Politécnica Metropolitana de Puebla, Mexico, Mexico
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Ameen F, Siddiqui S, Jahan I, Nayeem SM, Rehman SU, Tabish M. Studying the interaction of scopolamine with calf-thymus DNA: An in-vitro and in-silico approach and genotoxicity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 265:120391. [PMID: 34571375 DOI: 10.1016/j.saa.2021.120391] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
Scopolamine is used to treat various CNS disorder like urinary incontinence, motion sickness, spasmic movements. Despite its pharmaceutical properties, its interaction with DNA is not yet reported. In this article, the interaction between scopolamine and ct-DNA is reported using a combination of biophysical techniques. UV-visible and steady-state fluorescence spectroscopy were used to study interaction and complex formation. Competitive displacement assays and potassium iodide quenching confirmed the mode of binding between scopolamine and DNA. Structural changes induced in the ct-DNA in the presence of scopolamine were evaluated by CD spectroscopy. The plasmid nicking and NBT assay confirmed the genotoxic effect of scopolamine. In-silico study by molecular docking and molecular dynamics simulation revealed the mode of interaction, major stabilizing forces as well as the nucleotide sequences to which the scopolamine binds.
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Affiliation(s)
- Faisal Ameen
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
| | - Sharmin Siddiqui
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
| | - Ishrat Jahan
- Department of Chemistry, Faculty of Science, A.M. University, Aligarh, U.P. 202002, India
| | - Shahid M Nayeem
- Department of Chemistry, Faculty of Science, A.M. University, Aligarh, U.P. 202002, India
| | - Sayeed Ur Rehman
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India.
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Zeng G, Chen F, Lei Y, Zhou L, Yang X, Guo H, Tuo X, Guo Y. Revealing the binding properties between resorcinol and DNA. LUMINESCENCE 2021; 37:4-13. [PMID: 34499419 DOI: 10.1002/bio.4140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/12/2021] [Accepted: 09/06/2021] [Indexed: 01/08/2023]
Abstract
Resorcinol (1,3-dihydroxybenzene) is a common coupling agent in permanent hair dyes, and has arrested people's attention for its potential hazard to human health. However, the action mechanism of resorcinol and human DNA has not been elucidated. In this research, the binding properties between resorcinol and calf thymus DNA (ct-DNA) were studied for the first time through various spectral and molecular docking techniques. Spectral studies showed that the initial fluorescence quenching of resorcinol against DNA was a static one. The result of ΔH < 0 and ΔS > 0 was produced from thermodynamic experimental data, therefore it could be concluded that electrostatic force was the major driving force, while binding constant Kb was 1.56 × 104 M-1 at 298 K. The electrostatic binding network between resorcinol and ct-DNA was established explicitly through competitive substitution analysis and other spectral approaches. The results of FT-IR absorption spectra indicated that resorcinol had bound to the DNA phosphate skeleton. Molecular docking clearly revealed that binding occurred between hydroxyl groups of resorcinol and phosphorus oxygen bonds (P-O) of the DNA skeleton. These findings may deepen our understanding of the action mechanism between resorcinol and ct-DNA and provide some useful data on the effect of resorcinol on human diseases.
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Affiliation(s)
- Guofang Zeng
- College of Chemistry, Nanchang University, Nanchang, Jiangxi, China
| | - Fengping Chen
- School of Pharmacy, Nanchang University, Nanchang, Jiangxi, China
| | - Yating Lei
- School of Pharmacy, Nanchang University, Nanchang, Jiangxi, China
| | - Like Zhou
- College of Chemistry, Nanchang University, Nanchang, Jiangxi, China
| | - Xi Yang
- School of Pharmacy, Nanchang University, Nanchang, Jiangxi, China
| | - Hui Guo
- College of Chemistry, Nanchang University, Nanchang, Jiangxi, China
| | - Xun Tuo
- College of Chemistry, Nanchang University, Nanchang, Jiangxi, China
| | - Ying Guo
- College of Chemistry, Nanchang University, Nanchang, Jiangxi, China
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Ramotowska S, Ciesielska A, Makowski M. What Can Electrochemical Methods Offer in Determining DNA-Drug Interactions? Molecules 2021; 26:3478. [PMID: 34200473 PMCID: PMC8201389 DOI: 10.3390/molecules26113478] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 11/16/2022] Open
Abstract
The interactions of compounds with DNA have been studied since the recognition of the role of nucleic acid in organisms. The design of molecules which specifically interact with DNA sequences allows for the control of the gene expression. Determining the type and strength of such interaction is an indispensable element of pharmaceutical studies. Cognition of the therapeutic action mechanisms is particularly important for designing new drugs. Owing to their sensitivity, simplicity, and low costs, electrochemical methods are increasingly used for this type of research. Compared to other techniques, they require a small number of samples and are characterized by a high reliability. These methods can provide information about the type of interaction and the binding strength, as well as the damage caused by biologically active molecules targeting the cellular DNA. This review paper summarizes the various electrochemical approaches used for the study of the interactions between pharmaceuticals and DNA. The main focus is on the papers from the last decade, with particular attention on the voltammetric techniques. The most preferred experimental approaches, the electrode materials and the new methods of modification are presented. The data on the detection ranges, the binding modes and the binding constant values of pharmaceuticals are summarized. Both the importance of the presented research and the importance of future prospects are discussed.
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Affiliation(s)
| | | | - Mariusz Makowski
- Department of Bioinorganic Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (S.R.); (A.C.)
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Macii F, Salvadori G, Bonini R, Giannarelli S, Mennucci B, Biver T. Binding of model polycyclic aromatic hydrocarbons and carbamate-pesticides to DNA, BSA, micelles and liposomes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 223:117313. [PMID: 31277031 DOI: 10.1016/j.saa.2019.117313] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 06/19/2019] [Accepted: 06/23/2019] [Indexed: 06/09/2023]
Abstract
The binding to biosubstrates and micellar systems of pollutants as the polycyclic aromatic hydrocarbon (PAH) derivatives 1-aminopyrene (1-PyNH2) and 1-hydroxymethylpyrene (1-PyMeOH) and the carbamate-pesticides 1-naphthyl-N-methylcarbamate (carbaryl, CA) and methyl benzimidazol-2-ylcarbamate (carbendazim, CBZ) was analysed through an integrated strategy combining spectroscopy and quantum chemistry. As biosubstrates, natural DNA and bovine serum albumin (BSA) were taken into account for a thermodynamic analysis of the binding features through spectrophotometric and spectrofluorometric techniques. In all cases, a strong DNA interaction is present and intercalation is supposed as the major binding mode. For the PAH derivatives, DNA binding is found to be favoured under high salt conditions and BSA static quenching and binding with 1:1 stoichiometry occurs. The molecular structure and optical properties of 1-PyNH2, CA and CBZ together with their intercalated adducts in DNA were studied also by means of quantum chemical approach. The (TD)DFT calculations on intercalated dye/DNA adducts quantitatively reproduce the experimentally observed spectroscopic changes, thus confirming the intercalation hypothesis. The theoretical approach also provides information on the adducts' geometries and on the amount of charge transfer with DNA. Moreover, ultrafiltration tests in the presence of anionic (SDS), cationic (DTAC) and neutral (Triton X) micellar aggregates and liposomes provided insights into lipophilicity and cellular membrane affinity. PAH derivatives show high retention coefficient in all cases, whereas in the case of carbamate-pesticides micellar retention might be significantly reduced and is very limited in the case of liposomes.
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Affiliation(s)
- Francesca Macii
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Rachele Bonini
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Stefania Giannarelli
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Tarita Biver
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy; Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
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8
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Shiri F, Hadidi S, Rahimi-Nasrabadi M, Ahmadi F, Ganjali MR, Ehrlich H. Synthesis, characterization and DNA binding studies of a new ibuprofen-platinum(II) complex. J Biomol Struct Dyn 2019; 38:1119-1129. [PMID: 31012380 DOI: 10.1080/07391102.2019.1597769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The study is focused on the synthesis of a novel complex of ibuprofen and Platinum(II). The formation of the product was characterized through analytical tools including Fourier-transform infrared spectroscopy, proton nuclear magnetic resonance, ultraviolet-visible spectroscopy, mass spectrometry as well as density functional theory. Using the continuous variation method, the stoichiometry of Pt(HIb)2(Cl)2 binding on DNA (ct-DNA) determines as a single class of binding. Based on the results of Stern-Volmer analysis on the fluorescence quenching data, the quenching mechanism was determined to be static in nature. The studies indicated that the complex could bind DNA molecules via groove binding for four major reasons. Initially, the complex-DNA binding constant determined based on spectrophotometric data were found to be comparable to those of groove-binding drugs. In addition, the competitive fluorimetric based on the applications of Hoechst 33258 proved the ability of Pt(HIb)2(Cl)2 to displace with Hoechst in its DNA-bounded form, reflecting the competition between Pt(HIb)2(Cl)2 and Hoechst for groove binding. Further, no considerable changes were observed in the intensity of the methylene blue (MB)-DNA system after adding the Pt(HIb)2(Cl)2 complex, reflecting the stability of MB molecules in the DNA helix and a non-intercalative bonds of Pt(HIb)2(Cl)2 interaction on DNA. Finally, minor changes in the viscosity of DNA in the presence of Pt(HIb)2(Cl)2, indicated that changes in the length of DNA in the presence of the complex are negligible, supporting the assumption of DNA groove-binding. Also induced CD spectral changes and docking simulations were in favor of the groove mechanism for the Pt(HIb)2(Cl)2-DNA binding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Farshad Shiri
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Faculty of Pharmacy, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Saba Hadidi
- Inorganic Chemistry Department, Faculty of Chemistry, Razi University, Kermanshah, Iran.,Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mehdi Rahimi-Nasrabadi
- Chemical Injuries Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.,Faculty of Pharmacy, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Farhad Ahmadi
- Physiology Research Center, Iran University of Medical Sciences, Tehran, Iran.,Department of Medicinal Chemistry, School of Pharmacy-International Campus, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Ganjali
- Center of Excellence in Electrochemistry, University of Tehran, Tehran, Iran.,Biosensor Research Centre, Endocrinology & Metabolism Molecular and Cellular Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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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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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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11
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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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12
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Hemalatha K, Madhumitha G, Al-Dhabi NA, Arasu MV. Importance of fluorine in 2,3-dihydroquinazolinone and its interaction study with lysozyme. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 162:176-188. [DOI: 10.1016/j.jphotobiol.2016.06.036] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 06/11/2016] [Accepted: 06/22/2016] [Indexed: 01/25/2023]
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13
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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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Neaga I, Bodoki E, Hambye S, Blankert B, Oprean R. Study of nucleic acid–ligand interactions by capillary electrophoretic techniques: A review. Talanta 2016; 148:247-56. [DOI: 10.1016/j.talanta.2015.10.077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/21/2015] [Accepted: 10/25/2015] [Indexed: 10/22/2022]
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15
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Huang YM, Zheng SJ, Yan J, Yang HQ, Wu D, Wang Q, Li H. Investigation on the interaction of letrozole with herring sperm DNA through spectroscopic and modeling methods. LUMINESCENCE 2015; 31:1077-84. [DOI: 10.1002/bio.3074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 11/11/2015] [Accepted: 11/12/2015] [Indexed: 01/18/2023]
Affiliation(s)
- Yan-Mei Huang
- College of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
| | - Shou-Jun Zheng
- College of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
| | - Jin Yan
- College of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
| | - Hong-Qin Yang
- College of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
| | - Di Wu
- College of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
| | - Qing Wang
- College of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
| | - Hui Li
- College of Chemical Engineering; Sichuan University; Chengdu People's Republic of China
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16
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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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17
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Rehman SU, Sarwar T, Husain MA, Ishqi HM, Tabish M. Studying non-covalent drug-DNA interactions. Arch Biochem Biophys 2015; 576:49-60. [PMID: 25951786 DOI: 10.1016/j.abb.2015.03.024] [Citation(s) in RCA: 238] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 03/09/2015] [Accepted: 03/28/2015] [Indexed: 12/14/2022]
Abstract
Drug-DNA interactions have been extensively studied in the recent past. Various techniques have been employed to decipher these interactions. DNA is a major target for a wide range of drugs that may specifically or non-specifically interact with DNA and affect its functions. Interaction between small molecules and DNA are of two types, covalent interactions and non-covalent interactions. Three major modes of non-covalent interactions are electrostatic interactions, groove binding and intercalative binding. This review primarily focuses on discussing various techniques used to study non-covalent interactions that occur between drugs and DNA. Additionally, we report several techniques that may be employed to analyse the binding mode of a drug with DNA. These techniques provide data that are reliable and simple to interpret.
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Affiliation(s)
- Sayeed Ur Rehman
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
| | - Tarique Sarwar
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
| | - Mohammed Amir Husain
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
| | - Hassan Mubarak Ishqi
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences, A.M. University, Aligarh, U.P. 202002, India.
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18
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Spectroscopic and Chemometrics Analysis of the Hydrolytic Process of Folpet and Its Interaction with DNA. J SOLUTION CHEM 2014. [DOI: 10.1007/s10953-014-0211-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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19
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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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Zhou X, Zhang G, Wang L. Probing the binding mode of psoralen to calf thymus DNA. Int J Biol Macromol 2014; 67:228-37. [DOI: 10.1016/j.ijbiomac.2014.03.038] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/13/2014] [Accepted: 03/14/2014] [Indexed: 01/31/2023]
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21
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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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