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Kumar D, Gauri, Kaur N. Multispectroscopic and computational techniques to study the interaction of anthraquinone appended sensor with calf thymus DNA. J Biomol Struct Dyn 2024; 42:4370-4378. [PMID: 37227792 DOI: 10.1080/07391102.2023.2216302] [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: 03/14/2023] [Accepted: 05/16/2023] [Indexed: 05/27/2023]
Abstract
An anthraquinone based derivative (AQ) has been designed and synthesized to find its applications for the interactions with calf thymus DNA (ctDNA) involving various spectroscopic techniques, thermodynamic and computational approaches. The UV-vis studies pointed to interaction of AQ with ctDNA via groove binding mode, which has been further supported well by the ionic strength studies, viscosity measurement, circular dichroism and melting temperature (Tm) curves. These findings have been further validated by dye-displacement assay and molecular docking studies. The analysis of thermodynamic parameters supports that the AQ-ctDNA binding is entropy favoured and enthalpy disfavoured and main acting binding interaction is hydrophobic interaction. The outcomes of the molecular modelling suggested that AQ might have entered the A-T abundant area of the ctDNA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Deepak Kumar
- Department of Chemistry, Panjab University, Chandigarh, India
| | - Gauri
- Department of Chemistry, Panjab University, Chandigarh, India
| | - Navneet Kaur
- Department of Chemistry, Panjab University, Chandigarh, India
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2
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Luikham S, Yanthan S, Bhattacharyya J. Mechanistic investigation into the binding property of Yohimbe towards natural polymeric DNAs. Sci Rep 2023; 13:15487. [PMID: 37726357 PMCID: PMC10509242 DOI: 10.1038/s41598-023-40713-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/16/2023] [Indexed: 09/21/2023] Open
Abstract
DNA interactions with multivalent ligand(s) have increasingly become the subject of substantial research. For several small molecules with therapeutic potential, nucleic acids serve as their primary molecular target. Such interaction has been shown to affect transcription or replication, ultimately leading to apoptotic cell death. As a result, researchers are becoming increasingly interested in understanding how small molecules interact with DNA making it possible to develop new, DNA-specific drugs. The bioactive indole alkaloid, Yohimbe (Yohimbine; Yh) has been broadly studied in pharmacological properties while its binding mode to DNA has not been explicated so far. This study adopted molecular modelling and multi-spectroscopic methods to investigate the interaction between Yohimbine and herring testes (HT DNA) in physiological conditions. Minor hypochromic and bathochromic shifts of fluorescence intensity were observed, suggesting the binding of Yh to HT DNA. The Scatchard plot analyses using the McGhee-von Hipple method revealed non-cooperative binding and affinities in the range of 105 M-1. The thermodynamic parameters suggested exothermic binding, which was favoured by negative enthalpy and positive entropy changes from temperature-dependent fluorescence experiments. Salt-dependent fluorescence suggested that the interaction between the ligand and DNA was governed by non-polyelectrolytic forces. The results of iodide quenching, urea denaturation assay, dye displacement, and in silico molecular docking, suggested groove binding of Yh to HT DNA. Thus, the groove binding mechanism of interaction was validated by both biophysical and computational techniques. The structural elucidation and energetic profiling of Yh's interaction with naturally occurring polymeric DNA can be useful to the development of DNA-targeted therapeutics.
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Affiliation(s)
- Soching Luikham
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Nagaland, 797103, India
| | - Senchumbeni Yanthan
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Nagaland, 797103, India
| | - Jhimli Bhattacharyya
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Nagaland, 797103, India.
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Thanoon RD, Ibadi EA, Ahmad I, Alamir HTA, Alwan M, Hashim FS, Khaled DW, Alkhafaji AT, Asiri M, Alsaalamy A. Experimental and theoretical investigations of Erbium complex: DNA/BSA interaction, anticancer and antibacterial studies. Front Chem 2023; 11:1266520. [PMID: 37701051 PMCID: PMC10493310 DOI: 10.3389/fchem.2023.1266520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023] Open
Abstract
To assess the biological potential of an Er complex that contains a 2,2'-bipyridine ligand, various techniques such as multispectral and molecular modeling procedures were utilized to examine its DNA-binding ability, BSA binding affinity, antimicrobial effects, and anticancer properties. By analyzing fluorescent information and employing the vant' Hoff equation, important parameters such as the innate docking coefficient (Kb), Stern-Volmer coefficient (KSV), and thermodynamic properties including modifications in liberated energy (ΔG°), enthalpy (∆H°), and entropy (∆S°) were determined. The trial findings suggest that the compound can bind to DNA, primarily through groove binding. Additionally, the engagement between the Er compound and the protein BSA was examined using emission spectroscopy technique, revealing a powerful binding affinity between the compound and BSA. The Er complex binds to BSA primarily via hydrogen links and van der Waals forces, as indicated by the adverse values of ΔH° and ∆S°. Through a static quenching process, the complex significantly reduces the intrinsic fluorescence of BSA. Molecular binding calculations and rivalrous binding trials confirm that this compound dock to hydrophobic remains found in site III of BSA. Additionally, the Er complex demonstrates promising results in terms of its anticancer and antimicrobial activities based on screening tests.
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Affiliation(s)
- Raid D. Thanoon
- Department of Medical Biochemical Analysis, Cihan University-Erbil, Kurdistan Region, Iraq
| | - Emam Atiyah Ibadi
- Department of Pharmacy, Al-Mustaqbal University College, Babylon, Iraq
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | | | - Marim Alwan
- Medical Lab Techniques, College of Medical Technology, Al-Farahidi University, Baghdad, Iraq
| | - Furqan S. Hashim
- Department of Medical Laboratories Technology, Al-Nisour University College, Baghdad, Iraq
| | | | | | - Mohammed Asiri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Ali Alsaalamy
- College of Technical Engineering, Imam Ja’afar Al‐Sadiq University, Baghdad, Iraq
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Zhang X, Li X, Wang D, Weng T, Wang L, Yuan L, Wang Q, Liu J, Wu Y, Liu M. Spectroscopic, calorimetric and cytotoxicity studies on the combined binding of daunorubicin and acridine orange to a DNA tetrahedron. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 295:122583. [PMID: 36905740 DOI: 10.1016/j.saa.2023.122583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Chemotherapy-phototherapy (CTPT) combination drugs co-loaded by targeted DNA nanostructures can achieve controlled drug delivery, reduce toxic side effects and overcome multidrug resistance. Herein, we constructed and characterized a DNA tetrahedral nanostructure (MUC1-TD) linked with the targeting aptamer MUC1. The interaction of daunorubicin (DAU)/acridine orange (AO) alone and in combination with MUC1-TD and the influence of the interaction on the cytotoxicity of the drugs were evaluated. Potassium ferrocyanide quenching analysis and DNA melting temperature assays were used to demonstrate the intercalative binding of DAU/AO to MUC1-TD. The interactions of DAU and/or AO with MUC1-TD were analyzed by fluorescence spectroscopy and differential scanning calorimetry. The number of binding sites, binding constant, entropy and enthalpy changes of the binding process were obtained. The binding strength and binding sites of DAU were higher than those of AO. The presence of AO in the ternary system weakened the binding of DAU to MUC1-TD. In vitro cytotoxicity studies demonstrated that the loading of MUC1-TD augmented the inhibitory effects of DAU and AO and the synergistic cytotoxic effects of DAU + AO on MCF-7 cells and MCF-7/ADR cells. Cell uptake studies showed that the loading of MUC1-TD was beneficial in promoting the apoptosis of MCF-7/ADR cells due to its enhanced targeting to the nucleus. This study has important guiding significance for the combined application of DAU and AO co-loaded by DNA nanostructures to overcome multidrug resistance.
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Affiliation(s)
- Xinpeng Zhang
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China.
| | - Xinyu Li
- School of Chemistry and Chemical Engineering, Liaocheng University, Hunan Road, Liaocheng 252059, China.
| | - Danfeng Wang
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China.
| | - Tianxin Weng
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China.
| | - Lu Wang
- School of Chemistry and Chemical Engineering, Liaocheng University, Hunan Road, Liaocheng 252059, China.
| | - Lixia Yuan
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China.
| | - Qingpeng Wang
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China.
| | - Jie Liu
- School of Chemistry and Chemical Engineering, Liaocheng University, Hunan Road, Liaocheng 252059, China.
| | - Yushu Wu
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China.
| | - Min Liu
- Institute of Biopharmaceutical Research, Liaocheng University, Hunan Road, Liaocheng 252059, China; School of Chemistry and Chemical Engineering, Liaocheng University, Hunan Road, Liaocheng 252059, China.
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Ponkarpagam S, Vennila KN, Elango KP. Molecular spectroscopic and molecular simulation studies on the interaction of oral contraceptive drug Ormeloxifene with CT-DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 278:121351. [PMID: 35567820 DOI: 10.1016/j.saa.2022.121351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 06/15/2023]
Abstract
The interaction between oral contraceptive drug Ormeloxifene (ORM) and calf thymus DNA (CT-DNA) was studied using UV-Vis, fluorescence, circular dichroism (CD) and 1H NMR spectral techniques under physiological buffer (pH 7.4). Competitive binding assays with ethidium bromide (EB) and Hoechst 33258, viscosity measurements, KI quenching studies, molecular docking and metadynamics simulation studies were also substantiated the spectroscopic results. ORM is found to binds in the minor groove of CT-DNA as evidenced by: (1) non-displacement of EB from EB/CT-DNA complex; (2) appreciable displacement of Hoechst 33258 from its CT-DNA complex; (3) slight alteration in the CD signal; (4) small shifts (Δδ < 0.033 ppm) without broadening in 1H NMR signals and (5) the nearly equal extent of quenching of fluorescence of ORM by KI in the absence and presence of CT-DNA. Negative values of both enthalpy and entropy changes pointed out that the interaction between ORM and CT-DNA is governed mainly by H-bonding and van der Waals forces. Negative free energy change suggested a spontaneous interaction between ORM and CT-DNA. The free energy landscape of the binding process was computed using metadynamics simulation. The simulation study results disclosed that ORM binds to the minor groove of DNA through H-bonding and π-π stacking interactions. The results of molecular docking and simulation studies corroborate the available experimental data.
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Affiliation(s)
- 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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Akram M, Lal H, Kabir-Ud-Din. Exploring the binding mode of ester-based cationic gemini surfactants with calf thymus DNA: A detailed physicochemical, spectroscopic and theoretical study. Bioorg Chem 2021; 119:105555. [PMID: 34923244 DOI: 10.1016/j.bioorg.2021.105555] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 11/29/2021] [Accepted: 12/09/2021] [Indexed: 12/21/2022]
Abstract
Gene therapy is a transfectant method for the treatment of hereditary disease, which transfers the gene mutation into the cells. In the view of the high prospects of utilization of cationic gemini surfactants as a non-viral vector for the gene transfection, we have made a comprehensive study on the interactions between a recently synthesized series of ester-functionalized cationic Cm-E2O-Cm gemini surfactants (m = 12, 14 and 16) with calf thymus deoxyribonucleic acid (ctDNA) utilizing various techniques. The micellization behavior of gemini surfactants has been altered in the presence of ctDNA. A series of measurements (fluorescence, UV-vis and time-resolved fluorescence) show that the quenching of ctDNA proceeds by a static mechanism. The competitive displacement studies (EB, AO and HO), KI quenching analysis, CD studies and viscosity measurements suggested intercalative binding mode in a stoichiometry ratio of 1:1 with the Kb (binding constant) order being: C16-E2O-C16 > C14-E2O-C14 > C12-E2O-C12. The thermodynamic parameters show that the geminis interacted with ctDNA spontaneously through ionic/electrostatic interactions. Furthermore, the theoretical approaches offer accurate insights about the binding of gemini surfactants with DNA, and are in consistence with the experimental results.
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Affiliation(s)
- Mohd Akram
- Department of Chemistry, Aligarh Muslim University, Aligarh-202002, India.
| | - Hira Lal
- Department of Chemistry, Aligarh Muslim University, Aligarh-202002, India
| | - Kabir-Ud-Din
- Department of Chemistry, College of Natural and Computational Sciences, Arba Minch University, Arba Minch, Ethiopia
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Hussain I, Fatima S, Siddiqui S, Ahmed S, Tabish M. Exploring the binding mechanism of β-resorcylic acid with calf thymus DNA: Insights from multi-spectroscopic, thermodynamic and bioinformatics approaches. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119952. [PMID: 34052761 DOI: 10.1016/j.saa.2021.119952] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 06/12/2023]
Abstract
β-resorcylic acid (BR) is a phytochemical which is widely used in the food industry as a flavouring agent and preservative. It has also been found to exhibit antibacterial action against several types of food-borne bacteria. DNA is the main molecular target for many small molecules of therapeutic importance. Hence, the interest is rapidly growing among the researchers to elucidate the interaction between small molecules and DNA. Thus, paving the way to design novel DNA-specific drugs. In this study, an attempt was made to examine the mechanism of binding of BR with calf thymus DNA (ctDNA) with the help of various experiments based on spectroscopy and in silico studies. The spectroscopic studies like UV absorption and fluorescence affirmed the complex formation between BR and ctDNA. The observed binding constant was in the order of 103 M-1 which is indicative of the groove binding mechanism. These findings were further verified by dye-displacement assay, potassium iodide quenching, urea denaturation assay, the study of the effect of ssDNA, circular dichroism and DNA thermal denaturing studies. Different temperature-based fluorescence and isothermal titration calorimetry (ITC) experiments were employed to evaluate thermodynamic parameters. The analysis of thermodynamic parameters supports the enthalpically driven, exothermic and spontaneous nature of the reaction between BR and ctDNA. The forces involved in the binding process were mainly found to be hydrogen bonding, van der Waals and hydrophobic interactions. The results obtained from the molecular docking and molecular dynamics (MD) simulation were consistent with the in vitro experiments, which support the groove binding mode of BR with ctDNA.
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Affiliation(s)
- Irfan Hussain
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, U.P. 202002, India
| | - Sana Fatima
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, U.P. 202002, India
| | - Sharmin Siddiqui
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, U.P. 202002, India
| | - Shahbaz Ahmed
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, U.P. 202002, India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences, A.M.U, Aligarh, U.P. 202002, India.
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9
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Nengroo ZR, Ahmad A, Tantary A, Ganie AS, Shah ZU. Design and synthesis of fatty acid derived 4-methoxybenzylamides as antimicrobial agents. Heliyon 2021; 7:e06842. [PMID: 33981896 PMCID: PMC8082265 DOI: 10.1016/j.heliyon.2021.e06842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/27/2021] [Accepted: 04/13/2021] [Indexed: 11/30/2022] Open
Abstract
A new series of fatty acid amides viz. N-(4-methoxybenzyl)undec-10-enamide (5), (9Z, 12R)-12-Hydroxy-N-(4-methoxybenzyl)octadec-9-enamide (6) and N-(4-methoxy benzyl)oleamide (7) were synthesized by using a suitable synthetic route involving DCC and DMAP as catalysts. The synthesized compounds were characterized through FTIR, NMR spectroscopy, and mass spectrometry. DNA binding studies through spectroscopy and molecular docking were performed to evaluate the binding mechanism of molecules (5-7) with (ctDNA). The inhibition zone with reference to standards, Minimum Inhibitory Concentration (MIC) and Minimum Killing Concentration (MKC) values were determined to study the in vitro antimicrobial activity for tested compounds. Among all the tested compounds, the compound 6 containing hydroxy group at the fatty acid chain showed most powerful antifungal as well as antibacterial activity.
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Affiliation(s)
| | - Aijaz Ahmad
- Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Adil Tantary
- Department of Botany, Aligarh Muslim University, Aligarh 202002, India
| | - Adil Shafi Ganie
- Environmental Chemistry Section, Department of Chemistry Aligarh Muslim University, Aligarh 202002, India
| | - Zeshan Umar Shah
- Department of Zoology, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India
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Li Y, Qian C, Li Y, Yang Y, Lin D, Liu X, Chen C. Syntheses, crystal structures of two Fe(III) Schiff base complexes with chelating o-vanillin aroylhydrazone and exploration of their bio-relevant activities. J Inorg Biochem 2021; 218:111405. [PMID: 33689963 DOI: 10.1016/j.jinorgbio.2021.111405] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 11/28/2022]
Abstract
Two novel Fe(III) complexes, Fe(HL1)2Cl·1.25H2O (1) and Fe(HL2)2·Et3NH·H2O (2) (H2L1 = o-vanillin benzoylhydrazone, H3L2 = o-vanillin salicylhydrazone) are prepared. X-ray single crystal diffraction confirms that the hydrazone ligands can be chelated to iron centre resulting in a six-coordinate octahedral configuration. Both complexes show major intercalation effect to the herring sperm deoxyribonucleic acid (HS-DNA) with high binding constants of 2.01 × 104 M-1 and 2.24 × 104 M-1, respectively. Molecular docking studies reveal both complexes can intercalate at the gap of DC5-DG2 and DG6-DC1 base pairs of DNA hexamer (1Z3F). The interaction of the complex 1 with plasmid pBR322 DNA induces distinguishable alterations of the DNA morphology. Further, the structure of plasmid pBR322 DNA treated with complex 1 in the presence of ascorbic acid has been damaged probably due to the reactive oxygen species (ROS) generation. What's more, both complexes show high affinity with bovine serum albumin (BSA), the binding constants measured by fluorescence techniques are 5.75 × 106 M-1 and 4.39 × 107 M-1, respectively. Molecular docking demonstrates that the complexes prefer the binding pocket of site III (subdomain IIB) of BSA (PDB ID: 4F5S). Similarly, dynamic light scattering (DLS) reveals that the complexes not only bind to BSA but also induce bigger size aggregates as the concentration increases.
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Affiliation(s)
- Yueqin Li
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, People's Republic of China; College of Chemical Engineering, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, Nanjing Forestry University, Nanjing 210037, People's Republic of China.
| | - Changhao Qian
- College of Chemical Engineering, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Yun Li
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Yong Yang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Dong Lin
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Xiaohui Liu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Chen Chen
- College of Chemical Engineering, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, Nanjing Forestry University, Nanjing 210037, People's Republic of China
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Alves JEF, de Oliveira JF, de Lima Souza TRC, de Moura RO, de Carvalho Júnior LB, Alves de Lima MDC, de Almeida SMV. Novel indole-thiazole and indole-thiazolidinone derivatives as DNA groove binders. Int J Biol Macromol 2021; 170:622-635. [PMID: 33359805 DOI: 10.1016/j.ijbiomac.2020.12.153] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 10/22/2022]
Abstract
In this study, we report the synthesis of eight novel indole-thiazole and indole-thiazolidinone derivatives, as well as their ability to interact with DNA, analysed through the UV-vis absorption, fluorescence, circular dichroism (CD), viscosity techniques and molecular docking. The ctDNA interaction analysis demonstrated different spectroscopic effects and the affinity constants (Kb) calculated by the UV-vis absorption method were between 2.08 × 105 and 6.99 × 106 M-1, whereas in the fluorescence suppression constants (Ksv) ranged between 0.38 and 0.77 × 104 M-1 and 0.60-7.59 × 104 M-1 using Ethidium Bromide (EB) and 4',6-Diamidino-2-phenylindole (DAPI) as fluorescent probes, respectively. Most derivatives did not alter significantly the secondary structure of the ctDNA according to the CD results. None of the compounds was able to change the relative viscosity of the ctDNA. These results prove that compounds interact with ctDNA via groove binding, which was confirmed by A-T rich oligonucleotide sequence assay with compound JF-252, suggesting the importance of both the phenyl ring coupled to C-4 thiazole ring and the bromo-unsubstituted indole nucleus.
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Affiliation(s)
| | | | | | - Ricardo Olímpio de Moura
- Departamento de Ciências Farmacêuticas, Centro de Ciências Biológicas e da Saúde, Universidade Estadual da Paraíba e Bodocongo, Campina Grande, PB 58429-500, Brazil
| | | | - Maria do Carmo Alves de Lima
- Laboratório de Química e Inovação Terapêutica (LQIT) - Departamento de Antibióticos, Universidade Federal de Pernambuco, 50670-901, Brazil
| | - Sinara Mônica Vitalino de Almeida
- Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco, 50670-901, Brazil; Laboratório de Biologia Molecular, Universidade de Pernambuco (UPE), Multicampi Garanhuns, Garanhuns, PE 55290-000, Brazil.
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12
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13
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Hirashima S, Sugiyama H, Park S. Construction of a FRET System in a Double-Stranded DNA Using Fluorescent Thymidine and Cytidine Analogs. J Phys Chem B 2020; 124:8794-8800. [DOI: 10.1021/acs.jpcb.0c06879] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Shingo Hirashima
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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14
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Recent development of nucleic acid nanosensors to detect sequence-specific binding interactions: From metal ions, small molecules to proteins and pathogens. SENSORS INTERNATIONAL 2020; 1:100034. [PMID: 34766041 PMCID: PMC7434487 DOI: 10.1016/j.sintl.2020.100034] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023] Open
Abstract
DNA carries important genetic instructions and plays vital roles in regulating biological activities in living cells. Proteins such as transcription factors binds to DNA to regulate the biological functions of DNA, and similarly many drug molecules also bind to DNA to modulate its functions. Due to the importance of protein-DNA and drug-DNA binding, there has been intense effort in developing novel nanosensors in the same length scale as DNA, to effectively study these binding interactions in details. In addition, aptamers can be artificially selected to detect metal ions and pathogens such as bacteria and viruses, making nucleic acid nanosensors more versatile in detecting a large variety of analytes. In this minireview, we first explained the different types and binding modes of protein-DNA and drug-DNA interactions in the biological systems, as well as aptamer-target binding. This was followed by the review of five types of nucleic acid nanosensors based on optical or electrochemical detection. The five types of nucleic acid nanosensors utilizing colorimetric, dynamic light scattering (DLS), surface-enhanced Raman spectroscopy (SERS), fluorescence and electrochemical detections have been recently developed to tackle some of the challenges in high-throughput screening technology for large scale analysis, which is especially useful for drug development and mass screening for pandemic outbreak such as SARS or COVID-19.
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15
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Aramesh-Boroujeni Z, Jahani S, Khorasani-Motlagh M, Kerman K, Aramesh N, Asadpour S, Noroozifar M. Experimental and theoretical investigations of Dy(III) complex with 2,2'-bipyridine ligand: DNA and BSA interactions and antimicrobial activity study. J Biomol Struct Dyn 2019; 38:4746-4763. [PMID: 31684852 DOI: 10.1080/07391102.2019.1689170] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
In this study, the interactions of a novel metal complex [Dy(bpy)2Cl3.OH2] (bpy is 2,2'-bipyridine) with fish salmon DNA (FS-DNA) and bovine serum albumin (BSA) were investigated by experimental and theoretical methods. All results suggested significant binding between the Dy(III) complex with FS-DNA and BSA. The binding constants (Kb), Stern-Volmer quenching constants (KSV) of Dy(III)-complex with FS-DNA and BSA at various temperatures as well as thermodynamic parameters using Van't Hoff equation were obtained. The experimental results from absorption, ionic strength, iodide ion quenching, ethidium bromide (EtBr) quenching studies and positive ΔH˚ and ΔS˚ suggested that hydrophobic groove-binding mode played a predominant role in the binding of Dy(III)-complex with FS-DNA. Indeed, the molecular docking results for DNA-binding were in agreement with experimental data. Besides, the results found from experimental and molecular modeling indicated that the Dy(III)-complex bound to BSA via Van der Waals interactions. Moreover, the results of competitive tests by phenylbutazone, ibuprofen, and hemin (as a site-I, site-II and site-III markers, respectively) considered that the site-III of BSA is the most possible binding site for Dy(III)-complex. In addition, Dy(III) complex was concurrently screened for its antimicrobial activities. The presented data provide a promising platform for the development of novel metal complexes that target nucleic acids and proteins with antimicrobial activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zahra Aramesh-Boroujeni
- Department of Clinical Laboratory, AlZahra Hospital, Isfahan University of Medical Sciences, Isfahan, Iran.,Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
| | - Shohreh Jahani
- Nano Bioeletrochemistry Research Center, Bam University of Medical Sciences, Bam, Iran
| | | | - Kagan Kerman
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Nahal Aramesh
- Department of Chemistry, Faculty of Sciences, Yasouj University, Yasouj, Iran
| | - Saeid Asadpour
- Department of Chemistry, Faculty of Sciences, Shahrekord University, Shahrekord, Iran
| | - Meissam Noroozifar
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
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16
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Kılıç H. Experiment-based physicochemical aspects for the coulombic hydration kinetics and thermodynamics of a pyrimidine and thiopyrimidine. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.06.090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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17
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Xu F, Lu C, Wu Q, Chen J, Gu W, Du W, You M. Study on antitumor molecular mechanism of Alisols based on p53DNA. Int J Biol Macromol 2018; 116:1163-1174. [PMID: 29800662 DOI: 10.1016/j.ijbiomac.2018.05.158] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/22/2018] [Accepted: 05/22/2018] [Indexed: 11/17/2022]
Abstract
Methyl thiazolyl tetrazolium (MTT) assay, UV-vis absorption spectroscopy, fluorescence spectroscopy and molecular simulation were used to investigate the antitumor activity of alisol A, alisol B and an 1:1 mixture of both compounds, the mechanism of its interaction with anti-cancer target p53DNA and explored the antitumor mechanism of alisols. MTT assay showed that the order of antitumor activity was:alisol B > alisol A > alisol A-alisol B(1:1). Spectroscopic experiments and molecular simulation suggested that alisol A, alisol B and their mixture interact with p53DNA in by partial insertion and the strength of binding affinity was consistent with the MTT assay. The Ksv of alisol A was 9.35 × 104 L·mol-1, Kq was 9.35 × 1012 L·mol-1·s-1 and the Ksv and Kq of alisol B were 11.61 × 104 L·mol-1 and 11.61 × 1012 L·mol-1·s-1. The molecular simulation revealed that competitive antagonism was observed in the interaction between the alisol mixture and p53DNA. The critical groups and significant binding sites for the interaction between alisol monomers and p53DNA include C19-OH and C22-OH of the alisols; N2 and H21 of the guanine deoxynucleotide (DG8), N2-H21 of the DG7, O4' of the DG9 in the f-chain of p53DNA; and C2-O2 of the cytosine deoxynucleotide (DC16) in the e-chain of p53DNA. Also, the C-22 and C23- of the alisols and the DA18-DT5 base pairs of p53DNA were key factors in the interaction of the mixture with p53DNA.
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Affiliation(s)
- Fei Xu
- College of pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Cai Lu
- College of pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Qinan Wu
- College of pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China; Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing 210023, China; National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing 210023, China
| | - Jun Chen
- College of pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China; Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing 210023, China
| | - Wei Gu
- College of pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wenjia Du
- College of pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Min You
- College of pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
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18
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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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19
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Chlorinated emodin as a natural antibacterial agent against drug-resistant bacteria through dual influence on bacterial cell membranes and DNA. Sci Rep 2017; 7:12721. [PMID: 28983096 PMCID: PMC5629251 DOI: 10.1038/s41598-017-12905-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 09/12/2017] [Indexed: 02/05/2023] Open
Abstract
The rise in infections caused by drug-resistant pathogens and a lack of effective medicines requires the discovery of new antibacterial agents. Naturally chlorinated emodin 1,3,8-trihydroxy-4-chloro-6-methyl-anthraquinone (CE) from fungi and lichens was found to markedly inhibit the growth of Gram-positive bacteria, especially common drug-resistant bacterial strains, including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VRE). CE was confirmed to cause significant potassium leakage, cell membrane depolarization and damage to the selective permeability of cell membranes in bacterial cells, resulting in bacterial cell death. In addition, CE was shown to have a strong electrostatic interaction with bacterial DNA and induce DNA condensation. Thus, CE is a promising natural antibacterial pharmacophore against Gram-positive bacteria, especially common drug-resistant MRSA and VRE isolates, with a dual antibacterial mechanism that damages bacterial cell membranes and DNA.
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20
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Study of the Binding between Camptothecin Analogs and FTO by Spectroscopy and Molecular Docking. J Fluoresc 2017; 27:1467-1477. [DOI: 10.1007/s10895-017-2086-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/04/2017] [Indexed: 10/19/2022]
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21
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Ren T, Zhang L, Wang J, Song C, Wang R, Chang J. Study on the interaction of taiwaniaquinoids with FTO by spectroscopy and molecular modeling. J Biomol Struct Dyn 2016; 35:3182-3193. [DOI: 10.1080/07391102.2016.1249957] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | - Lijiao Zhang
- College of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, China
| | - Jinqian Wang
- College of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, China
| | - Chuanjun Song
- College of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, China
| | - Ruiyong Wang
- College of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, China
| | - Junbiao Chang
- College of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, China
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22
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de Silva Rodrigues JH, Stein J, Strauss M, Rivarola HW, Ueda-Nakamura T, Nakamura CV, Duszenko M. Clomipramine kills Trypanosoma brucei by apoptosis. Int J Med Microbiol 2016; 306:196-205. [DOI: 10.1016/j.ijmm.2016.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 03/07/2016] [Accepted: 03/28/2016] [Indexed: 12/31/2022] Open
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23
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Parveen M, Ahmad F, Malla AM, Khan MS, Rehman SU, Tabish M, Silva MR, Silva PP. Structure elucidation and DNA binding specificity of natural compounds from Cassia siamea leaves: A biophysical approach. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 159:218-28. [DOI: 10.1016/j.jphotobiol.2016.03.060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 03/23/2016] [Accepted: 03/31/2016] [Indexed: 12/30/2022]
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24
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Interaction of a green ester-bonded gemini surfactant with xanthine oxidase: Biophysical perspective. Int J Biol Macromol 2015; 78:62-71. [DOI: 10.1016/j.ijbiomac.2015.03.050] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 03/20/2015] [Accepted: 03/22/2015] [Indexed: 11/22/2022]
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25
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Aramesh-Boroujeni Z, Khorasani-Motlagh M, Noroozifar M. Multispectroscopic DNA-binding studies of a terbium(III) complex containing 2,2′-bipyridine ligand. J Biomol Struct Dyn 2015; 34:414-26. [DOI: 10.1080/07391102.2015.1038585] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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26
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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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27
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Wang B, Wang Q, Ma M, Cai Z. The inhibition of fluorescence resonance energy transfer between multicolor quantum dots for rapid and sensitive detection of Staphylococcus aureus. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 135:428-434. [PMID: 25105265 DOI: 10.1016/j.saa.2014.07.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Revised: 07/07/2014] [Accepted: 07/15/2014] [Indexed: 06/03/2023]
Abstract
In this paper, we constructed the fluorescence resonance energy transfer (FRET) system between two multi-color quantum dots (QDs) of two sizes for rapid and sensitive detection of Staphylococcus aureus. In this system, green-emitting QDs conjugated with rabbit anti-S. aureus antibodies were used as energy donors while orange-emitting QDs conjugated with goat-anti-rabbit IgG were used as energy acceptors to form FRET system. Pre-binding of Staphylococcus aureus (S. aureus) on the donor occupied the binding sites and thus blocked resonance energy transfer between two colors QDs, leading to the quenching fluorescence of the acceptor. The fluorescence of acceptor has a linear calibration graph with the concentrations of S. aureus from 52 to 2.6×10(5) CFU mL(-1). The low detection limit was 10 CFU/mL. It was worth mentioning that the detection method of S. aureus had been applied to the analysis of apple juice and milk samples, which could potentially be developed into a sensor in the further study.
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Affiliation(s)
- Beibei Wang
- National R&D Center for Egg Processing, Food Science and Technology College, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, China
| | - Qi Wang
- National R&D Center for Egg Processing, Food Science and Technology College, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, China
| | - Meihu Ma
- National R&D Center for Egg Processing, Food Science and Technology College, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, China
| | - Zhaoxia Cai
- National R&D Center for Egg Processing, Food Science and Technology College, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, China.
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28
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Akram M, Bhat IA, Bhat WF. Conformational alterations induced by novel green 16-E2-16 gemini surfactant in xanthine oxidase: Biophysical insights from tensiometry, spectroscopy, microscopy and molecular modeling. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 150:440-50. [PMID: 26057098 DOI: 10.1016/j.saa.2015.05.056] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 05/07/2015] [Accepted: 05/12/2015] [Indexed: 05/07/2023]
Abstract
Herein we report the interaction of a biodegradable gemini surfactant, ethane-1,2-diyl bis(N,N-dimethyl-N-hexadecylammoniumacetoxy) dichloride (16-E2-16) with bovine milk xanthine oxidase (XO), employing tensiometry, fluorescence spectroscopy, UV spectroscopy, far-UV circular dichroism spectroscopy (CD), Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM), transmission electron microscopy (TEM), and computational molecular modeling. Surface tension results depict substantial changes in the micellar as well as interfacial parameters (CMC, ΠCMC, γCMC, Γmax, Amin, ΔGmic° and ΔGads°) of 16-E2-16 gemini surfactant upon XO combination, deciphering the interaction of XO with the gemini surfactant. Fluorescence measurements reveal that 16-E2-16 gemini surfactant causes quenching in the xanthine oxidase (XO) fluorescence spectra via static procedure and the values of various evaluated binding parameters (KSV, Kb, kq, ΔGb° and n) describe that 16-E2-16 effectively binds to XO. Three dimensional fluorescence, 8-anilino-1-naphthalene sulfonic acid (ANS) binding, F1F3 ratio, UV, CD, FTIR, SEM and TEM results delineate changes in the secondary structure of xanthine oxidase. Molecular docking results provide complement to the steady-state fluorescence findings and support the view that quenching occurs due to non-polar environment experienced by aromatic residues of the enzyme. The results of this study can help scientists to tune the conformation of an enzyme (XO) with biocompatible amphiphilic microstructures, which will help to unfold further understanding in the treatment modes of various diseases like gout, hyperuricemia, liver and brain necrosis.
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Affiliation(s)
- Mohd Akram
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India.
| | - Imtiyaz Ahmad Bhat
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Waseem Feeroze Bhat
- Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, India
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29
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Mi R, Bai XT, Tu B, Hu YJ. Unraveling the coptisine–ctDNA binding mechanism by multispectroscopic, electrochemical and molecular docking methods. RSC Adv 2015. [DOI: 10.1039/c5ra08790b] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This study provides evidences of coptisine–DNA intercalation, which may help to develop new efficient, safe probes for the fluorometric detection of DNA instead of traditional toxic and carcinogenic probes.
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Affiliation(s)
- Ran Mi
- Hubei Collaborative Innovation Center for Rare Metal Chemistry
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology
- Department of Chemistry
- Hubei Normal University
- Huangshi 435002
| | - Xiao-Ting Bai
- Hubei Collaborative Innovation Center for Rare Metal Chemistry
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology
- Department of Chemistry
- Hubei Normal University
- Huangshi 435002
| | - Bao Tu
- Hubei Collaborative Innovation Center for Rare Metal Chemistry
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology
- Department of Chemistry
- Hubei Normal University
- Huangshi 435002
| | - Yan-Jun Hu
- Hubei Collaborative Innovation Center for Rare Metal Chemistry
- Hubei Key Laboratory of Pollutant Analysis & Reuse Technology
- Department of Chemistry
- Hubei Normal University
- Huangshi 435002
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