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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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Ebadi A, Najafi Z, Pakdel-yeganeh H, Dastan D, Chehardoli G. Design, synthesis, molecular modeling and DNA-binding studies of new barbituric acid derivatives. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [PMCID: PMC9092333 DOI: 10.1007/s13738-022-02576-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cancer disease is developing all over the world mainly in developing countries. We should learn more about DNA–ligand interactions to design new drugs that target biological activities like transcription, replication and translation of particular genes. To understand the mechanism of action and design-specific DNA binders, the evaluation of DNA–ligand interactions is critical. Novel barbituric acid derivatives based on (benzyloxy)benzaldehydes were synthesized and evaluated as DNA-binding agents. Among products, molecular docking studies revealed that 4j and 4m have the best interactions with the ctDNA via the minor groove binding. These results were approved by the quantum mechanics calculations. The interaction profiles of the selected compound (4j and 4m) with DNA were evaluated by UV–Visible titration. UV–Visible titration data confirm this interaction. According to the molecular modeling results, the Structure–Activity relationships for all synthesized barbituric acid derivatives were proposed. It was observed that N,N-dimethyl barbituric acid/4-hydroxybenzaldehyde derivatives have better DNA interactions than barbituric acid/vanillin and barbituric acid/3-hydroxybenzaldehyde derivatives.
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3
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Single-step functionalization of silicon nanoparticles providing efficient DNA binding. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.129217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Durga Priyadharshini R, Ponkarpagam S, Vennila KN, Elango KP. Spectroscopic and theoretical evidences for the surface binding of voglibose drug with DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 271:120888. [PMID: 35063822 DOI: 10.1016/j.saa.2022.120888] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/06/2022] [Accepted: 01/09/2022] [Indexed: 06/14/2023]
Abstract
Binding of voglibose (VOG), an alpha glucosidase inhibitor, with CT-DNA has been investigated using various spectroscopic techniques including UV-Vis, fluorescence and circular dichroism (CD) coupled with relative viscosity. Isothermal titration calorimetric studies have been used to calculate the thermodynamic parameters such as ΔH (0.0188 cal/mol), ΔS (63.3 cal/mol/K) and ΔG (-18.8 kcal/mol), which reveal that the binding is a spontaneous process and hydrophobic and H-bonding interactions play major roles in the binding process. Effect of ionic strength confirms the existence of hydrophobic interaction between VOG and CT-DNA. Competitive displacement assays with ethidium bromide (EB) and Hoechst 33258 suggest that VOG possibly binds on the surface of CT-DNA. Viscosity measurements also disclose that the binding could be mainly surface binding. Corroborating the experimental observations, metadynamics molecular simulation studies confirm that VOG binding on the surface of the DNA molecule through hydrophobic interactions and direct and water molecule mediated H-bonding.
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Affiliation(s)
- R Durga Priyadharshini
- Department of Chemistry, Gandhigram Rural Institute - Deemed to be University, Gandhigram 624302, India
| | - S Ponkarpagam
- Department of Chemistry, Gandhigram Rural Institute - Deemed to be University, Gandhigram 624302, India
| | - K N Vennila
- Department of Chemistry, Gandhigram Rural Institute - Deemed to be University, Gandhigram 624302, India
| | - Kuppanagounder P Elango
- Department of Chemistry, Gandhigram Rural Institute - Deemed to be University, Gandhigram 624302, India.
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Sohrabi T, Asadzadeh-Lotfabad M, Shafie Z, Amiri Tehranizadeh Z, Saberi MR, Chamani J. Description of the calf thymus DNA-malathion complex behavior by multi-spectroscopic and molecular modeling techniques: EMF at low and high frequency approaches. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2021; 24:1346-1357. [PMID: 35096292 PMCID: PMC8769509 DOI: 10.22038/ijbms.2021.58083.12907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/07/2021] [Indexed: 11/06/2022]
Abstract
OBJECTIVES Small molecules can bind to DNA via covalent or non-covalent interactions, which results in altering or inhibiting the function of DNA. Thus, understanding the interaction patterns of medicines or other small molecules can be very crucial. In this study, the interaction between malathion and calf thymus DNA (ctDNA), in the absence and presence of electromagnetic field (EMF) at low and high frequencies, was investigated through various spectroscopies and viscosity measurements. MATERIALS AND METHODS The interaction studies were performed by means of absorbance, circular dichroism, fluorescence spectroscopy, viscosity, thermal melting, and molecular modeling techniques. RESULTS The fluorescence intensity of the ctDNA-malathion complex in the presence of EMF, has revealed quenching of fluorescence emission curves. The dynamic interaction and RLS studies have implied the changes in ctDNA-malathion complex throughout the presence of EMF which suggested that hydrophobic forces play the main role in the binding. Studies have revealed that malathion does not have any effect on binding ethidium bromide to ctDNA, which signifies the groove binding. The viscosity of ctDNA increased as the malathion concentration was enlarged. The circular dichroism technique suggested that the ellipticity values of the ctDNA-malathion complex have not increased with enhancing the malathion concentration. Molecular docking and dynamics studies have indicated a potent electrostatic interaction between ctDNA and malathion in the groove binding site. CONCLUSION The results of spectroscopic studies reinforced a potent interaction between malathion and ctDNA in the absence and presence of EMF which can help us for further pharmaceutical drug discoveries.
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Affiliation(s)
- Tahmineh Sohrabi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | | | - Zahra Shafie
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Zeinab Amiri Tehranizadeh
- Medical Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Saberi
- Medical Chemistry Department, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
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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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Xu F, Chen J, Wu Q, Gu W, Shen Y, Lu C, Zhang Y, Liu S, Liao H. The antitumor molecular mechanism of Alisma orientalis with c-myc DNA: multi-spectroscopic analysis and molecular simulation. J Biomol Struct Dyn 2019; 38:4189-4209. [DOI: 10.1080/07391102.2019.1688687] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Fei Xu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jun Chen
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
| | - Qinan Wu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China
- National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing, China
| | - Wei Gu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuqing Shen
- Department of Neurology, Taizhou Second People’s Hospital, Taizhou, China
| | - Cai Lu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yun Zhang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shengjin Liu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Haiying Liao
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
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Shahabadi N, Momeni BZ, Zendehcheshm S. Studies on the Interaction of [SnMe 2Cl 2(bu 2bpy)] Complex with ct-DNA Using Multispectroscopic, Atomic Force Microscopy (AFM) and Molecular Docking. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2019; 38:157-182. [PMID: 31044667 DOI: 10.1080/15257770.2018.1506885] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The interaction of SnMe2Cl2(bu2bpy)complex with calf thymus DNA (ct-DNA) has been explored following, using spectroscopic methods, viscosity measurements, Atomic force microscopy, Thermal denaturation and Molecular docking. It was found that Sn(IV) complex could bind with DNA via intercalation mode as evidenced by hyperchromism and bathochromic in UV-Vis spectrum; these spectral characteristics suggest that the Sn(IV) complex interacts with DNA most likely through a mode that involves a stacking interaction between the aromatic chromophore and the base pairs of DNA. In addition, the fluorescence emission spectra of intercalated methylene blue (MB) with increasing concentrations of SnMe2Cl2(bu2bpy) represented a significant increase of MB intensity as to release MB from MB-DNA system. Positive values of ΔH and ΔS imply that the complex is bound to ct-DNA mainly via the hydrophobic attraction. Large complexes contain the DNA chains with an average size of 859 nm were observed by using AFM for Sn(IV) Complex-DNA. The Fourier transform infrared study showed a major interaction of Sn(IV) complex with G-C and A-T base pairs and a minor perturbation of the backbone PO2 group. Addition of the Sn(IV)complex results in a noticeable rise in the Tm of DNA. In addition, the results of viscosity measurements suggest that SnMe2Cl2(bu2bpy) complex may bind with the classical intercalative mode. From spectroscopic and hydrodynamic studies, it has been found that Sn(IV)complex interacts with DNA by intercalation mode. Optimized docked model of DNA-complex mixture confirmed the experimental results.
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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
| | - Badri Z Momeni
- c Department of Chemistry , K. N. Toosi University of Technology , Tehran , Iran
| | - Saba Zendehcheshm
- a Department of Inorganic Chemistry, Faculty of Chemistry , Razi University , Kermanshah , Iran
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Ramos RDS, Costa JDS, Silva RC, da Costa GV, Rodrigues ABL, Rabelo ÉDM, Souto RNP, Taft CA, Silva CHTDPD, Rosa JMC, Santos CBRD, Macêdo WJDC. Identification of Potential Inhibitors from Pyriproxyfen with Insecticidal Activity by Virtual Screening. Pharmaceuticals (Basel) 2019; 12:E20. [PMID: 30691028 PMCID: PMC6469432 DOI: 10.3390/ph12010020] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 01/17/2019] [Accepted: 01/19/2019] [Indexed: 01/15/2023] Open
Abstract
Aedes aegypti is the main vector of dengue fever transmission, yellow fever, Zika, and chikungunya in tropical and subtropical regions and it is considered to cause health risks to millions of people in the world. In this study, we search to obtain new molecules with insecticidal potential against Ae. aegypti via virtual screening. Pyriproxyfen was chosen as a template compound to search molecules in the database Zinc_Natural_Stock (ZNSt) with structural similarity using ROCS (rapid overlay of chemical structures) and EON (electrostatic similarity) software, and in the final search, the top 100 were selected. Subsequently, in silico pharmacokinetic and toxicological properties were determined resulting in a total of 14 molecules, and these were submitted to the PASS online server for the prediction of biological insecticide and acetylcholinesterase activities, and only two selected molecules followed for the molecular docking study to evaluate the binding free energy and interaction mode. After these procedures were performed, toxicity risk assessment such as LD50 values in mg/kg and toxicity class using the PROTOX online server, were undertaken. Molecule ZINC00001624 presented potential for inhibition for the acetylcholinesterase enzyme (insect and human) with a binding affinity value of -10.5 and -10.3 kcal/mol, respectively. The interaction with the juvenile hormone was -11.4 kcal/mol for the molecule ZINC00001021. Molecules ZINC00001021 and ZINC00001624 had excellent predictions in all the steps of the study and may be indicated as the most promising molecules resulting from the virtual screening of new insecticidal agents.
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Affiliation(s)
- Ryan da Silva Ramos
- Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Amapá 68903-419, Brazil.
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.
- Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Capanema, Pará 68700-030, Brazil.
| | - Josivan da Silva Costa
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.
- Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Capanema, Pará 68700-030, Brazil.
| | - Rai Campos Silva
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.
- Computational Laboratory of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences of Ribeirão Preto, São Paulo 14040-903, Brazil;.
| | - Glauber Vilhena da Costa
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.
| | - Alex Bruno Lobato Rodrigues
- Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Amapá 68903-419, Brazil.
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.
| | - Érica de Menezes Rabelo
- Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Amapá 68903-419, Brazil.
| | | | | | - Carlos Henrique Tomich de Paula da Silva
- Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Capanema, Pará 68700-030, Brazil.
- Computational Laboratory of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences of Ribeirão Preto, São Paulo 14040-903, Brazil;.
| | | | - Cleydson Breno Rodrigues Dos Santos
- Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Amapá 68903-419, Brazil.
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.
- Computational Laboratory of Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences of Ribeirão Preto, São Paulo 14040-903, Brazil;.
| | - Williams Jorge da Cruz Macêdo
- Postgraduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá, Amapá 68903-419, Brazil.
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil.
- Laboratory of Molecular Modeling and Simulation System, Federal Rural University of Amazônia, Capanema, Pará 68700-030, Brazil.
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Probing the binding of lomefloxacin to a calf thymus DNA-histone H1 complex by multi-spectroscopic and molecular modeling techniques. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.02.031] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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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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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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Kesama MR, Dugasani SR, Yoo S, Chopade P, Gnapareddy B, Park SH. Morphological and Optoelectronic Characteristics of Double and Triple Lanthanide Ion-Doped DNA Thin Films. ACS APPLIED MATERIALS & INTERFACES 2016; 8:14109-17. [PMID: 27166922 DOI: 10.1021/acsami.6b02880] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Double and triple lanthanide ion (Ln(3+))-doped synthetic double crossover (DX) DNA lattices and natural salmon DNA (SDNA) thin films are fabricated by the substrate assisted growth and drop-casting methods on given substrates. We employed three combinations of double Ln(3+)-dopant pairs (Tb(3+)-Tm(3+), Tb(3+)-Eu(3+), and Tm(3+)-Eu(3+)) and a triple Ln(3+)-dopant pair (Tb(3+)-Tm(3+)-Eu(3+)) with different types of Ln(3+), (i.e., Tb(3+) chosen for green emission, Tm(3+) for blue, and Eu(3+) for red), as well as various concentrations of Ln(3+) for enhancement of specific functionalities. We estimate the optimum concentration of Ln(3+) ([Ln(3+)]O) wherein the phase transition of Ln(3+)-doped DX DNA lattices occurs from crystalline to amorphous. The phase change of DX DNA lattices at [Ln(3+)]O and a phase diagram controlled by combinations of [Ln(3+)] were verified by atomic force microscope measurement. We also developed a theoretical method to obtain a phase diagram by identifying a simple relationship between [Ln(3+)] and [Ln(3+)]O that in practice was found to be in agreement with experimental results. Finally, we address significance of physical characteristics-current for evaluating [Ln(3+)]O, absorption for understanding the modes of Ln(3+) binding, and photoluminescence for studying energy transfer mechanisms-of double and triple Ln(3+)-doped SDNA thin films. Current and photoluminescence in the visible region increased as the varying [Ln(3+)] increased up to a certain [Ln(3+)]O, then decreased with further increases in [Ln(3+)]. In contrast, the absorbance peak intensity at 260 nm showed the opposite trend, as compared with current and photoluminescence behaviors as a function of varying [Ln(3+)]. A DNA thin film with varying combinations of [Ln(3+)] might provide immense potential for the development of efficient devices or sensors with increasingly complex functionality.
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Affiliation(s)
- Mallikarjuna Reddy Kesama
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University , Suwon 16419, Korea
| | - Sreekantha Reddy Dugasani
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University , Suwon 16419, Korea
| | - Sanghyun Yoo
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University , Suwon 16419, Korea
| | - Prathamesh Chopade
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University , Suwon 16419, Korea
| | - Bramaramba Gnapareddy
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University , Suwon 16419, Korea
| | - Sung Ha Park
- Department of Physics and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University , Suwon 16419, Korea
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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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15
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Das D, Mondal P. Interaction of ruthenium(ii) antitumor complexes with d(ATATAT)2 and d(GCGCGC)2: a theoretical study. NEW J CHEM 2015. [DOI: 10.1039/c4nj02118e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have investigated the interaction of three ruthenium(ii) complexes with d(ATATAT)2 and d(GCGCGC)2 sequences by using the molecular docking and quantum mechanics/molecular mechanics (QM/MM) hybrid method.
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Affiliation(s)
- Dharitri Das
- Department of Chemistry
- Assam University
- Silchar 788011
- India
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16
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Ghasemi S, Ahmadi F. The study of binding of methyl tert-butyl ether to human telomeric G-quadruplex and calf thymus DNA by gas chromatography, a thermodynamic discussion. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 971:112-9. [DOI: 10.1016/j.jchromb.2014.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Revised: 08/30/2014] [Accepted: 09/09/2014] [Indexed: 12/27/2022]
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17
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Intercalation binding of food antioxidant butylated hydroxyanisole to calf thymus DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 141:253-61. [PMID: 25463675 DOI: 10.1016/j.jphotobiol.2014.10.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 09/26/2014] [Accepted: 10/22/2014] [Indexed: 12/28/2022]
Abstract
The binding properties of food antioxidant butylated hydroxyanisole (BHA) associated with calf thymus DNA (ctDNA) in physiological buffer (pH 7.4) were investigated. Experimental results based on fluorescence, UV-vis absorption, circular dichroism (CD), viscosity measurements and autodocking techniques confirmed the intercalation binding between BHA and ctDNA. The changes in Fourier transform infrared spectra of ctDNA induced by BHA suggested that BHA was more prone to bind to G-C rich region of ctDNA, which was further ascertained with the molecular docking studies. Analysis of the CD spectra indicated that this binding interaction led to a transformation from B-like DNA structure toward A-like conformation. The complexation of BHA with ctDNA was driven mainly by hydrogen bonds and hydrophobic forces. The binding constants of the BHA-ctDNA complex were calculated to be 2.03 × 10(4), 1.92 × 10(4) and 1.59 × 10(4)L mol(-1) at 298, 304 and 310 K, respectively. Gel electrophoresis results suggested that intercalated BHA molecules did not significantly affect plasmid DNA. Moreover, the concentration profiles and the spectra for the three reaction components (BHA, ctDNA, and BHA-ctDNA complex) of the system by resolving the augmented UV-vis spectral data matrix with the use of multivariate curve resolution-alternating least squares approach provided quantitative data to estimate the progress of BHA-ctDNA interaction. This study is expected to provide new insights into the mechanism of interaction between BHA and ctDNA.
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18
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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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19
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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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20
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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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21
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Application of two-layer ONIOM for studying the interaction of N-substituted piperazinylfluoroquinolones with ds-DNA. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2012.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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22
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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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Ahmadi F, Jamali N. Study of DNA-Deltamethrin Binding by Voltammetry, Competitive Fluorescence, Thermal Denaturation, Circular Dichroism, and Atomic Force Microscopy Techniques. DNA Cell Biol 2012; 31:811-9. [DOI: 10.1089/dna.2011.1442] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [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, Islamic Republic of Iran
| | - Nasibeh Jamali
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Islamic Republic of Iran
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