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Joshi J, McCauley MJ, Morse M, Muccio MR, Kanlong JG, Rocha MS, Rouzina I, Musier-Forsyth K, Williams MC. Mechanism of DNA Intercalation by Chloroquine Provides Insights into Toxicity. Int J Mol Sci 2024; 25:1410. [PMID: 38338688 PMCID: PMC10855526 DOI: 10.3390/ijms25031410] [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: 01/01/2024] [Revised: 01/18/2024] [Accepted: 01/20/2024] [Indexed: 02/12/2024] Open
Abstract
Chloroquine has been used as a potent antimalarial, anticancer drug, and prophylactic. While chloroquine is known to interact with DNA, the details of DNA-ligand interactions have remained unclear. Here we characterize chloroquine-double-stranded DNA binding with four complementary approaches, including optical tweezers, atomic force microscopy, duplex DNA melting measurements, and isothermal titration calorimetry. We show that chloroquine intercalates into double stranded DNA (dsDNA) with a KD ~ 200 µM, and this binding is entropically driven. We propose that chloroquine-induced dsDNA intercalation, which happens in the same concentration range as its observed toxic effects on cells, is responsible for the drug's cytotoxicity.
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Affiliation(s)
- Joha Joshi
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
| | - Micah J. McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
| | - Michael R. Muccio
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Joseph G. Kanlong
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Márcio S. Rocha
- Department of Physics, Universidade Federal de Viçosa, Viçosa CEP 36570-900, MG, Brazil;
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
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Hao J, Wang Z, Li Y, Deng Y, Fan Y, Huang Y. A novel signal amplification strategy for label-free electrochemical DNA sensor based on the interaction between α-cyclodextrin and ferrocenyl indicator. Bioelectrochemistry 2023; 151:108373. [PMID: 36702078 DOI: 10.1016/j.bioelechem.2023.108373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/22/2023]
Abstract
The synthesized ferrocene appended naphthalimide derivative (FND) exhibited great binding ability toward dsDNA, while its usage as the electrochemical hybridization indicator was restricted by the poor water solubility. Herein, a simple and effective signal amplification strategy for FND based label-free DNA biosensors was developed based on the interaction between FND and cyclodextrin. α-Cyclodextrin (α-CD), β-cyclodextrin (β-CD) and γ-cyclodextrin (γ-CD) were helpful to amplify the signal of the DNA biosensor, while the signal amplification effect of α-CD was better than that of β-CD and γ-CD. Under the optimum conditions, there was a 3-fold increase in the sensitivity of the DNA biosensor after the addition of α-CD. The interaction between FND and α-/β-/γ-CD was investigated by differential pulse voltammetry and fluorescence experiment. Experimental results showed that α-CD not only minimized the impact on the electrochemical activity of FND but also improved the dispersity of FND in aqueous solution. That was why the proposed biosensor showed higher sensitivity in the presence of α-CD. This strategy was universal for other ferrocenyl indicators with similar structures as used in this work.
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Affiliation(s)
- Jie Hao
- Key Laboratory of Ningxia Ethnomedicine Modernization, Ministry of Education, Ningxia Engineering and Technology Research Center of Characteristic Chinese Medicine Modernization, College of Pharmacy, Ningxia Medical University, Yinchuan 750004, PR China
| | - Zhenbo Wang
- Key Laboratory of Ningxia Ethnomedicine Modernization, Ministry of Education, Ningxia Engineering and Technology Research Center of Characteristic Chinese Medicine Modernization, College of Pharmacy, Ningxia Medical University, Yinchuan 750004, PR China
| | - Yafei Li
- Key Laboratory of Ningxia Ethnomedicine Modernization, Ministry of Education, Ningxia Engineering and Technology Research Center of Characteristic Chinese Medicine Modernization, College of Pharmacy, Ningxia Medical University, Yinchuan 750004, PR China
| | - Yaru Deng
- Key Laboratory of Ningxia Ethnomedicine Modernization, Ministry of Education, Ningxia Engineering and Technology Research Center of Characteristic Chinese Medicine Modernization, College of Pharmacy, Ningxia Medical University, Yinchuan 750004, PR China
| | - Yanru Fan
- Key Laboratory of Ningxia Ethnomedicine Modernization, Ministry of Education, Ningxia Engineering and Technology Research Center of Characteristic Chinese Medicine Modernization, College of Pharmacy, Ningxia Medical University, Yinchuan 750004, PR China.
| | - Yu Huang
- Key Laboratory of Ningxia Ethnomedicine Modernization, Ministry of Education, Ningxia Engineering and Technology Research Center of Characteristic Chinese Medicine Modernization, College of Pharmacy, Ningxia Medical University, Yinchuan 750004, PR China.
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3
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Pavithra K, Priyadharshini RD, Vennila KN, Elango KP. Multi-spectroscopic and molecular simulation methods of analysis to explore the mode of binding of Mebendazole drug with calf-thymus DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 300:122938. [PMID: 37269657 DOI: 10.1016/j.saa.2023.122938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/13/2023] [Accepted: 05/27/2023] [Indexed: 06/05/2023]
Abstract
UV-vis, fluorescence, circular dichroism (CD) and 1H NMR spectroscopic techniques have been employed to explore the mode of binding of Mebendazole (MBZ) drug with calf thymus DNA (CT-DNA). UV-vis and fluorescence spectral studies suggested a complex formation between the drug and nucleic acid. The fluorescence of MBZ was found to enhance upon binding with CT-DNA through a ground state complex formation with Kb in the order of 104 M-1. The thermodynamic aspects indicated that the complex formation is a spontaneous process and an entropy-driven one. ΔH0 > 0 and ΔS0 > 0 revealed that hydrophobic interaction plays a dominant role in the stabilization of the complex. Competitive dye displacement assays with ethidium bromide (EB) and Hoechst 33258 dyes and viscosity measurements pointed out that MBZ binds with CT-DNA via intercalation mode, which is confirmed by CD and 1H NMR spectral studies as well as denaturation studies. Molecular docking analysis could not match well with the experimental results. However, molecular simulation studies and the resultant free energy surface (FES) analysis clearly showed that the benzimidazole ring of MBZ intercalated between the base pairs of the nucleic acid, which is in excellent agreement with the results of the various biophysical experiments.
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Affiliation(s)
- K Pavithra
- Department of Chemistry, Gandhigram Rural Institute (Deemed to be University), Gandhigram 624302, India
| | - R Durga Priyadharshini
- 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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Abdel Hakiem AF, El-Sagheir AMK, Draz ME, Mohamed NA, Aboraia AS. Assessment of binding interaction to salmon sperm DNA of two antiviral agents and ecofriendly nanoparticles: comprehensive spectroscopic study. BMC Chem 2023; 17:39. [PMID: 37076904 PMCID: PMC10114480 DOI: 10.1186/s13065-023-00952-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 04/05/2023] [Indexed: 04/21/2023] Open
Abstract
The direct binding of antiviral agents; Daclatasvir and valacyclovir and green synthesized nanoparticles to salmon sperm DNA have been assessed in a comparative study. The nanoparticles were synthesized by the hydrothermal autoclave method and have been fully characterized. The interactive behavior and competitive binding of the analytes to DNA in addition to the thermodynamic properties were deeply investigated by the UV-visible spectroscopy. The binding constants were monitored in the physiological pH conditions to be 1.65 × 106, 4.92 × 105 and 3.12 × 105 for daclatasvir,valacyclovir and quantum dots, respectively. The significant changes in the spectral features of all analytes have proven intercalative binding. The competitive study has confirmed that, daclatasvir, valacyclovir, and the quantum dots have exhibited groove binding. All analytes have shown good entropy and enthalpy values indicating stable interactions. The electrostatic and non-electrostatic kinetic parameters have been determined through studying the binding interactions at different concentrations of KCl solutions. A molecular modelling study has been applied to demonstrate the binding interactions and their mechanisms. The obtained results were complementary and afforded new eras for the therapeutic applications.
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Affiliation(s)
- Ahmed Faried Abdel Hakiem
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, South Valley University, Qena, 83523, Egypt.
| | | | - Mohammed E Draz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, 11152, Egypt
| | - Niveen A Mohamed
- Department of Pharmaceutical Chemistry, Unaizah College of Pharmacy, Qassim University, Unaizah, 5888, Saudi Arabia
| | - Ahmed Safwat Aboraia
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut, 71516, Egypt
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Wang L, Wu Y, Weng T, Li X, Zhang X, Zhang Y, Yuan L, Zhang Y, Liu M. Binding of combined irinotecan and epicatechin to a pH-responsive DNA tetrahedron for controlled release and enhanced cytotoxicity. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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Rupar J, Dobričić V, Brborić J, Čudina O, Aleksić MM. Square wave voltammetric study of interaction between 9-acridinyl amino acid derivatives and DNA. Bioelectrochemistry 2022; 149:108323. [DOI: 10.1016/j.bioelechem.2022.108323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/27/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
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7
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Nimal R, Nur Unal D, Erkmen C, Bozal-Palabiyik B, Siddiq M, Eren G, Shah A, Uslu B. Development of the electrochemical, spectroscopic and molecular docking approaches toward the investigation of interaction between DNA and anti-leukemic drug azacytidine. Bioelectrochemistry 2022; 146:108135. [DOI: 10.1016/j.bioelechem.2022.108135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 12/16/2022]
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Elshafey R, Abo-Sobehy GF, Radi AE. Graphene oxide/graphene quantum dots: A platform for probing ds-DNA-dimethoate interaction and dimethoate sensing. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Alipour E, Norouzi S, Moradi S. The development of an electrochemical DNA biosensor based on quercetin as a new electroactive indicator for DNA hybridization detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:719-729. [PMID: 33491010 DOI: 10.1039/d0ay01993c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
An electrochemical DNA biosensor was designed for the detection of a specific target DNA after hybridization with a complementary DNA probe immobilized onto a glassy carbon electrode surface. Quercetin was successfully used as a new electroactive indicator for the hybridization detection. Different interactions of quercetin with single-stranded DNA (ss-DNA) and double-stranded DNA (ds-DNA) led to different electrochemical signals, which were recorded as cyclic and differential pulse voltammograms enabling hybridization detection. Various parameters influencing the biosensor performance were evaluated, and optimized conditions were obtained. Also, the detection limit of 83 pM with a relative standard deviation of 4.6% was obtained for the determination of complementary oligonucleotides. Then, the developed biosensor was applied successively for the detection of short sequences of hepatitis C virus (HCV1). The hybridization between the probe (PHCV1) and its complementary sequence (HCV1a) as the target was studied. Some hybridization experiments with noncomplementary oligonucleotides also showed that the suggested DNA sensor responds selectively to the target.
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Affiliation(s)
- Esmaeel Alipour
- Electroanalytical Chemistry Laboratory, Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran.
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Morawska K, Ciesielski W, Smarzewska S. First electroanalytical studies of methoxyfenozide and its interactions with dsDNA. J Electroanal Chem (Lausanne) 2021. [DOI: 10.1016/j.jelechem.2021.115030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Bolat G. Investigation of poly(CTAB-MWCNTs) composite based electrochemical DNA biosensor and interaction study with anticancer drug Irinotecan. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105426] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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12
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Morawska K, Popławski T, Ciesielski W, Smarzewska S. Interactions of lamotrigine with single- and double-stranded DNA under physiological conditions. Bioelectrochemistry 2020; 136:107630. [DOI: 10.1016/j.bioelechem.2020.107630] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/03/2020] [Accepted: 08/03/2020] [Indexed: 12/18/2022]
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13
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Gold nanoparticles anchored graphitized carbon nanofibers ionic liquid electrode for ultrasensitive and selective electrochemical sensing of anticancer drug irinotecan. Mikrochim Acta 2020; 187:579. [DOI: 10.1007/s00604-020-04560-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/13/2020] [Indexed: 02/06/2023]
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14
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Ibrahim M, Ibrahim H, Almandil NB, Sayed MA, Kawde AN. A new hybrid nanocomposite electrode based on Au/CeO 2-decorated functionalized glassy carbon microspheres for the voltammetric sensing of quercetin and its interaction with DNA. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:2846-2857. [PMID: 32930208 DOI: 10.1039/d0ay00507j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A new hybrid composite containing cerium oxide nanoparticle (CeO2NP) and gold nanoparticle (AuNP)-decorated functionalized glassy carbon microspheres (FGCM) was synthesized (Au/CeO2@FGCM). As a result, an Au/CeO2@FGCM-paraffin oil paste electrode (PE) (Au/CeO2@FGCM-PE) was fabricated and employed for the voltammetric sensing of quercetin (QRT). The structure and surface morphology of Au/CeO2@FGCM were studied by X-ray diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Cyclic voltammetry (CV), square wave voltammetry (SWV) and electrochemical impedance spectroscopy (EIS) were employed for the investigation of the electrochemical behavior of Au/CeO2@FGCM-PE. Under the optimum conditions, the SWV oxidation peak current showed linear dependence on the QRT concentration in the range from 48 nM to 1.09 μM. The achieved limits of detection and quantitation were 0.37 nM and 1.22 nM, respectively. Au/CeO2@FGCM-PE was reproducible, sensitive and stable and displayed anti-interference ability for various common interferents. The proposed method was also successfully applied for real sample analysis. The QRT content extracted from natural sources was determined, and satisfactory results were achieved. Furthermore, the interaction of QRT with salmon testes and calf thymus dsDNA (st-DNA and ct-DNA) on Au/CeO2@FGCM-PE was studied by CV and SWV. The corresponding binding constant (K), surface concentration (Γ), and Gibbs free energy (ΔG°) were computed for the free QRT and the bound QRT-dsDNA complex. The calculated K values for the QRT-ct-DNA and QRT-st-DNA complexes were found to be 6.24 × 105 M-1 and 3.63 × 105 M-1, respectively, which revealed that QRT strongly interacted with ct-DNA compared to that with st-DNA. The decreased intensity of the QRT oxidation peak resulting from its interaction with dsDNA provides a chance to use QRT as a new indicator to analyze ct-DNA and st-DNA.
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Affiliation(s)
- Mohamed Ibrahim
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia.
| | - Hossieny Ibrahim
- Chemistry Department, Faculty of Science, Assiut University, Assiut, Egypt.
| | - Noor B Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia.
| | - Marwa A Sayed
- Department of Industrial Pharmacy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Abdel-Nasser Kawde
- Chemistry Department, College of Sciences, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
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A fast method for the detection of irinotecan in plasma samples by combining solid phase extraction and differential pulse voltammetry. Anal Bioanal Chem 2020; 412:1585-1595. [DOI: 10.1007/s00216-020-02386-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/10/2019] [Accepted: 01/03/2020] [Indexed: 12/27/2022]
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16
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Machini WBS, Marques NV, Oliveira‐Brett AM. In Situ
Evaluation of Anticancer Monoclonal Antibody Nivolumab‐DNA Interaction Using a DNA‐Electrochemical Biosensor. ChemElectroChem 2019. [DOI: 10.1002/celc.201901005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Wesley B. S. Machini
- Department of Chemistry, Faculty of Science and Technology University of Coimbra 3004-535 Coimbra Portugal
| | - Nuno V. Marques
- Serviços Farmacêuticos Centro Hospitalar e Universitário de Coimbra, EPE 3000-075 Coimbra Portugal
| | - Ana Maria Oliveira‐Brett
- Department of Chemistry, Faculty of Science and Technology University of Coimbra 3004-535 Coimbra Portugal
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Oliveira R, Amaro F, Azevedo M, Vale N, Gonçalves H, Antunes C, Rego R. New voltammetric and spectroscopic studies to quinacrine-DNA-Cdots interaction. Electrochim Acta 2019. [DOI: 10.1016/j.electacta.2019.03.068] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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