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Smarzewska S, Ignaczak A, Koszelska K. Electrochemical and theoretical studies of the interaction between anticancer drug ponatinib and dsDNA. Sci Rep 2024; 14:2278. [PMID: 38280929 PMCID: PMC10821894 DOI: 10.1038/s41598-024-52609-z] [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: 10/30/2023] [Accepted: 01/21/2024] [Indexed: 01/29/2024] Open
Abstract
In this study, electrochemical and theoretical studies were performed to explain the interaction mechanism between ponatinib (PNT), a third generation tyrosine kinase inhibitor, and dsDNA. The electrochemical part was conducted in phosphate-buffered saline (PBS) at physiological pH of 7.4 and in acetate buffer with a pH of 4.7, using square wave voltammetry. A boron-doped diamond electrode was used in a bulk-incubated solution. The theoretical part was investigated using computational methods, such as the semiempirical method PM7 and density functional theory (DFT). Significant differences in the electrochemical behavior of PNT in the presence of DNA confirmed the occurrence of interactions. The results obtained in the acetate buffer strongly suggested the preferential interaction of PNT with guanine residues. However, at physiological pH, it can be concluded that PNT interacts with dGua and dAdo in the dsDNA molecule. These results are consistent with outcomes from the theoretical studies, where quantum-chemical calculations showed that both electrochemically detectable nucleobases form hydrogen bonds with the drug. These bonds appeared to be stronger with guanine than with adenine. According to the computational studies, the dsDNA major groove is the energetically preferred site for the complexation of PNT.
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Affiliation(s)
- Sylwia Smarzewska
- Department of Inorganic and Analytical Chemistry, University of Lodz, 12 Tamka Str, 91-403, Lodz, Poland
| | - Anna Ignaczak
- Department of Physical Chemistry, University of Lodz, 163/165 Pomorska Str, 90-236, Lodz, Poland.
| | - Kamila Koszelska
- Department of Inorganic and Analytical Chemistry, University of Lodz, 12 Tamka Str, 91-403, Lodz, Poland.
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Arsenault-Escobar S, Fuentes-Galvez JF, Orellana C, Bollo S, Sierra-Rosales P, Miranda-Rojas S. Unveiling the tartrazine binding mode with ds-DNA by UV-visible spectroscopy, electrochemical, and QM/MM methods. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 292:122400. [PMID: 36739665 DOI: 10.1016/j.saa.2023.122400] [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: 09/30/2022] [Revised: 12/31/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Here, we studied the interaction between the food colorant tartrazine (TZ) and double stranded DNA (dsDNA), using spectroscopic, electrochemical, and computational methods such as QM/MM combined with TD-DFT. Despite the UV-vis spectroscopy is widely used to study the interaction between molecules, for the case of TZ there are discrepancies in the analyses presented in the literature available, presenting both hyperchromic and hypochromic effects and consequently different rationalizations for their results. Herein we propose the combination of UV-vis experiments with the design of high-level computational models capable of reproducing the experimental behavior to finally define the proper binding mode at the molecular scale together with the rationalization of the experimental optical response due to the complex formation. To complement the UV-vis experiments, we propose the use of electrochemical measurements, to support the results obtained through UV-vis spectroscopy, as it has been successfully used for the determination of interaction modes between small molecules and biomolecules in any condition. Our UV-vis spectroscopy experiments showed only a hypochromic effect of the absorption spectra of TZ after interaction with DNA, indicative of TZ being deeply buried in the DNA structure. The effect of ionic strength in the experimental procedures led to the dissociation of TZ, thus indicating that the interaction mode was groove binding. On the other hand, the electrochemical studies showed an irreversible reduction peak of TZ, which after the interaction with DNA exhibited a positive shift in potential that can be attributed to groove binding. The binding constant for TZ-DNA was calculated as 4.45x104M-1 (UV-vis) and 5.75x104M-1 (electrochemistry), in line with other groove binder azo dyes. Finally, through the QM/MM calculations we found that the minor-groove binding mode interacting in zones rich in adenine and thymine was the model best suited to reproduce the experimental UV-vis response.
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Affiliation(s)
- S Arsenault-Escobar
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, P.O Box 8940577, San Joaquín, Santiago, Chile
| | - J F Fuentes-Galvez
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, P.O Box 8940577, San Joaquín, Santiago, Chile
| | - C Orellana
- Departamento de Química, Facultad de Ciencias, Universidad de Chile, P.O. Box 653, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - S Bollo
- Centro de Investigación de Procesos Redox (CiPRex), Universidad de Chile. Sergio Livingstone Polhammer 1007, Independencia, Santiago, Chile; Advanced Center for Chronic Diseases (ACCDiS), Universidad de Chile. Sergio Livingstone Polhammer 1007, Independencia, Santiago, Chile
| | - P Sierra-Rosales
- Programa Institucional de Fomento a la Investigación, Desarrollo e Innovación, Universidad Tecnológica Metropolitana, Ignacio Valdivieso 2409, P.O Box 8940577, San Joaquín, Santiago, Chile.
| | - S Miranda-Rojas
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, República 275, Santiago, Chile.
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Kinetic and thermodynamic studies on the interaction between calf thymus DNA and food additive vanillin - electrochemical methods. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Chen D, Yu X, Qin Y, Liao ZY, Li T, Guo FF, Song KX, Yu RL, Xia YM, Gao WW. Electrochemical detection of DNA damage caused by novel potential 2-nitroimidazole naphthalimide-based hypoxia tumor-targeting agent with mimimum side effects. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Meena VK, Ghatak HR. Electrochemical Advanced Oxidation of Lamotrigine at Ti/DSA (Ta2O5-Ir2O5) and Stainless Steel Anodes. J ELECTROCHEM SCI TE 2022. [DOI: 10.33961/jecst.2021.01074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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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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Dindar ÇK, Erkmen C, Yıldırım S, Bozal-Palabiyik B, Uslu B. Interaction of citalopram and escitalopram with calf Thymus DNA: A spectrofluorometric, voltammetric, and liquid chromatographic approach. J Pharm Biomed Anal 2021; 195:113891. [PMID: 33422834 DOI: 10.1016/j.jpba.2021.113891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 12/17/2022]
Abstract
Citalopram (CIT) and its S-enantiomer, escitalopram (ESC), are antidepressants belonging to the class called selective serotonin reuptake inhibitors and have many different pharmacological and biological properties. Understanding the interaction mechanism of small drug molecules with DNA both helps in the development of new DNA-targeted drugs and provides more in-depth knowledge for controlling gene expression. In this study, the interaction of CIT and ESC with double-stranded calf thymus DNA (ct-dsDNA) was investigated for the first time. Spectrofluorometric, liquid chromatographic, and voltammetric response profiles of drugs and ct-dsDNA at different concentrations showed DNA-drug complex formation. Calculated binding constants were greater with all three techniques for ESC compared to CIT and were of the order of 103-104, which is in accordance with those of well-known groove binders. The results also showed the significant effect of chirality on complex formation. The thermodynamic parameters, including free energy change (ΔG < 0) and enthalpy change (ΔH < 0) obtained at different temperatures, indicated that complex formation was mainly driven by hydrogen bonding and van der Waals forces for both drugs. The results of this study may enhance the understanding of the interaction between CIT or ESC and ct-dsDNA and can be considered as the pioneer for future studies to uncover possible hidden phenotypes of these compounds.
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Affiliation(s)
- Çiğdem Kanbeş Dindar
- Ankara University, Faculty of Pharmacy, Department of Analytical Chemistry, 06560, Ankara, Turkey
| | - Cem Erkmen
- Ankara University, Faculty of Pharmacy, Department of Analytical Chemistry, 06560, Ankara, Turkey
| | - Sercan Yıldırım
- Karadeniz Technical University, Faculty of Pharmacy, Department of Analytical Chemistry, 61080, Trabzon, Turkey
| | - Burcin Bozal-Palabiyik
- Ankara University, Faculty of Pharmacy, Department of Analytical Chemistry, 06560, Ankara, Turkey
| | - Bengi Uslu
- Ankara University, Faculty of Pharmacy, Department of Analytical Chemistry, 06560, Ankara, Turkey.
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