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Malek-Esfandiari Z, Rezvani-Noghani A, Sohrabi T, Mokaberi P, Amiri-Tehranizadeh Z, Chamani J. Molecular Dynamics and Multi-Spectroscopic of the Interaction Behavior between Bladder Cancer Cells and Calf Thymus DNA with Rebeccamycin: Apoptosis through the Down Regulation of PI3K/AKT Signaling Pathway. J Fluoresc 2023; 33:1537-1557. [PMID: 36787038 DOI: 10.1007/s10895-023-03169-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 02/03/2023] [Indexed: 02/15/2023]
Abstract
The interaction of Rebeccamycin with calf thymus (ctDNA) in the absence and presence of H1 was investigated by molecular dynamics, multi-spectroscopic, and cellular techniques. According to fluorescence and circular dichroism spectroscopies, Rebeccamycin interacted with ctDNA in the absence of H1 through intercalator or binding modes, while the presence of H1 resulted in revealing theintercalator, as the dominant role, and groove binding modes of ctDNA-Rebeccamycin complex. The binding constants, which were calculated to be 1.22 × 104 M-1 and 7.92 × 105 M-1 in the absence and presence of H1, respectively, denoted the strong binding of Rebeccamycin with ctDNA. The binding constants of Rebeccamycin with ct DNA in the absence and presence of H1 were calculated at 298, 303 and 308 K. Considering the thermodynamic parameters (ΔH0 and ΔS0), both vander waals forces and hydrogen bonds played predominant roles throughout the binding of Rebeccamycin to ctDNA in the absence and presence of H1. The outcomes of circular dichroism suggested the lack of any major conformational changes in ctDNA upon interacting with Rebeccamycin, except some perturbations in native B-DNA at local level. Additionally, the effect of NaCl and KI on ctDNA-Rebeccamycin complex provided further evidence for the reliance of their interaction modes on substituted groups. The observed increase in the relative viscosity of ctDNA caused by the enhancement of Rebeccamycin confirmed their intercalation and groove binding modes in the absence and presence of H1. Moreover, the assessments of molecular docking simulation corroborated these experimental results and also elucidated the effectiveness of Rebeccamycinin inhibiting and proliferating T24 and 5637 cells. Meanwhile, the ability of Rebeccamycin in inhibiting cell proliferation and tumor growth through the induction of apoptosis by down regulating the PI3K/AKT signaling pathway were provided.
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Affiliation(s)
- Zohreh Malek-Esfandiari
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Azadeh Rezvani-Noghani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Tahmineh Sohrabi
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Parisa Mokaberi
- 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
| | - Jamshidkhan Chamani
- Department of Biology, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran.
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2
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Cheng H, Qin C, Yang B, Hu X, Gatheru Waigi M, Vasilyeva GK, Gao Y. Non-covalent binding interaction between phthalic acid esters and DNA. ENVIRONMENT INTERNATIONAL 2022; 161:107095. [PMID: 35063790 DOI: 10.1016/j.envint.2022.107095] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 01/04/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
The interaction of phthalic acid esters (PAEs) with DNA is known to be responsible for the disruption of endocrine functions and the teratogenic and carcinogenic effects. However, the binding strength and mechanism of this important process has often been neglected. Here, we confirmed the binding interaction between PAEs and DNA via fluorescence titration quenching experiment. The linear fitting curve proved that PAEs could bind to DNA, and the binding constants (KA) were 4.11 × 105, 1.04 × 105, 7.60 × 104, 1.99 × 104, and 1.42 × 103 L/mol for diethyl phthalate (DEP), bis(2-ethylhexyl) phthalate (DEHP), dibutyl phthalate (DBP), dimethyl phthalate (DMP), and benzyl butyl phthalate (BBP), respectively. DNA melting point, UV-vis spectra and Fourier transform infrared spectroscopy (FTIR) analyses revealed that PAEs interact predominantly with thymines in the DNA minor groove. Quantum chemical calculations showed that hydrogen bonding and van der Waals force formation between PAEs and DNA bases dominated the binding interaction. However, PAEs-DNA binding did not induce any DNA conformation change since the circular dichroism and FTIR spectra of B-DNA were not change. The electrostatic surface potential (ESP) might act an important role in PAEs-DNA binding interaction. This work will broaden our understanding of the interaction between PAEs and genetic materials.
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Affiliation(s)
- Hao Cheng
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Chao Qin
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China; Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials, College of Life Science and Technology, Jinan University, Guangzhou 510632, PR China
| | - Bing Yang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Michael Gatheru Waigi
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Galina K Vasilyeva
- Institute of Physicochemical and Biological Problems in Soil Science, RAS, Pushchino, Moscow region 1422290, Russia
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China.
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Ji C, Yin X, Duan H, Liang L. Molecular complexes of calf thymus DNA with various bioactive compounds: Formation and characterization. Int J Biol Macromol 2020; 168:775-783. [PMID: 33227330 DOI: 10.1016/j.ijbiomac.2020.11.135] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 10/22/2022]
Abstract
The interaction between biomacromolecules and ligands has attracted great interest because of their biological properties. Calf thymus DNA (ctDNA) can interact with bioactive compounds to form complexes. Here, ctDNA-ligand complexes were studied using fluorescence, absorption, and infrared spectroscopy, circular dichroism, ABTS assay and competitive displacement. The binding constants of bioactive compounds at the intercalative site of ctDNA ranked in order kaempferol > apigenin > quercetin > curcumin > riboflavin, while the binding constants at minor groove sites ranked quercetin > kaempferol > naringenin ~ apigenin > hesperetin > curcumin ~ resveratrol ~ riboflavin > caffeic acid. CtDNA maintained stable B-form with an enhancement of base stacking and a decrease of right-handed helicity in the presence of these bioactive compounds, except for hesperetin and caffeic acid. Bioactive compounds preferentially bound to guanine bases and tended to transfer into a more hydrophobic environment upon complexation with ctDNA. The DNA complexation did not affect the ABTS·+ scavenging capacity of quercetin, kaempferol, resveratrol and apigenin but increased the ones of naringenin, caffeic acid, curcumin, hesperetin and riboflavin. The data gathered here should be useful to understand the binding modes of DNA with ligands for their potential application in pharmaceutical and food industries.
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Affiliation(s)
- Chuye Ji
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
| | - Xin Yin
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province 214122, China
| | - Hongwei Duan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 70 Nanyang Drive, Singapore 637457, Singapore
| | - Li Liang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu Province 214122, China.
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Li S, Pan J, Zhang G, Xu J, Gong D. Characterization of the groove binding between di-(2-ethylhexyl) phthalate and calf thymus DNA. Int J Biol Macromol 2017; 101:736-746. [DOI: 10.1016/j.ijbiomac.2017.03.136] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 01/03/2023]
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Zhou X, Zhang C, Zhang G, Liao Y. Intercalation of the daphnetin–Cu(ii) complex with calf thymus DNA. RSC Adv 2016. [DOI: 10.1039/c5ra22274e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The daphnetin–Cu(ii) complex binds to the A–T bases region of ctDNA and causes cleavage of plasmid DNA.
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Affiliation(s)
- Xiaoyue Zhou
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Cen Zhang
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Guowen Zhang
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Yijing Liao
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
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Liu BM, Zhang J, Liu Y, Zhang LP, Ma P, Wang X, Liu B. Multi-spectroscopic methods investigation on the interaction of tenoxicam with DNA. LUMINESCENCE 2015; 30:1313-7. [DOI: 10.1002/bio.2899] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 11/13/2014] [Accepted: 02/12/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Bing-Mi Liu
- Department of Pharmacy; Liaoning University; Shenyang People's Republic of China
| | - Jun Zhang
- Department of Pharmacy; Liaoning University; Shenyang People's Republic of China
| | - Yang Liu
- Department of Pharmacy; Liaoning University; Shenyang People's Republic of China
| | - Li-Ping Zhang
- Department of Pharmacy; Liaoning University; Shenyang People's Republic of China
| | - Ping Ma
- General Hospital of the Rocket Force; Department of Clinical Pharmacology; Beijing People's Republic of China
| | - Xin Wang
- Department of Pharmacy; Liaoning University; Shenyang People's Republic of China
| | - Bin Liu
- Department of Pharmacy; Liaoning University; Shenyang People's Republic of China
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Zhou X, Zhang G, Pan J. Groove binding interaction between daphnetin and calf thymus DNA. Int J Biol Macromol 2014; 74:185-94. [PMID: 25541356 DOI: 10.1016/j.ijbiomac.2014.12.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 12/25/2022]
Abstract
The binding characteristics of daphnetin with calf thymus DNA (ctDNA) were investigated by multispectroscopic and chemometric approaches coupled with DNA viscosity measurements, melting studies and molecular docking technique. The expanded UV-vis spectral data matrix was processed by multivariate curve resolution-alternating least-squares method to obtain the concentration profiles of the components (daphnetin, ctDNA and daphnetin-ctDNA complex) to quantitatively monitor the daphnetin-ctDNA interaction. The groove mode of daphnetin binding to ctDNA was concluded by little change in melting temperature, viscosity of ctDNA and iodide quenching effect as well as increase in single-stranded DNA quenching effect. Moreover, the quantitative data for the competitive binding between daphnetin and Hoechst 33258 for ctDNA obtained by resolving the three-way synchronous fluorescence spectra data using parallel factor analysis modeling further supported the groove binding. The molecular docking visualized the results of the Fourier transform infrared analysis that the adenine and thymine bases in the minor groove of ctDNA were the main binding sites for daphnetin, and the circular dichroism spectra showed that the groove binding of daphnetin to ctDNA led to the conformational change in ctDNA from B-form to A-form. This study revealed the interaction mechanism of daphnetin with ctDNA.
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Affiliation(s)
- Xiaoyue Zhou
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Guowen Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China.
| | - Junhui Pan
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
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Zhao T, Bi S, Wang Y, Wang T, Pang B, Gu T. In vitro studies on the behavior of salmeterol xinafoate and its interaction with calf thymus DNA by multi-spectroscopic techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 132:198-204. [PMID: 24866086 DOI: 10.1016/j.saa.2014.04.158] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 04/18/2014] [Accepted: 04/28/2014] [Indexed: 06/03/2023]
Abstract
The salmeterol xinafoate (SX) binding to calf thymus DNA in vitro was explored by fluorescence, resonance light scattering (RLS), UV-vis absorption, as well as viscometry, ionic strength effect and DNA melting techniques. It was found that SX could bind to DNA weakly, and the binding constants (Ka) were determined as 8.52×10(3), 8.31×10(3) and 6.14×10(3) L mol(-1) at 18, 28 and 38°C respectively. When bound to DNA, SX showed fluorescence quenching in the fluorescence spectra and hyperchromic effect in the absorption spectra. Stern-Volmer plots revealed that the quenching of fluorescence of SX by DNA was a static quenching. Furthermore, the relative viscosity and melting temperature of DNA solution were hardly influenced by SX, while the fluorescence intensity of SX-DNA was observed to decrease with the increasing ionic strength of system. Also, the binding constant between SX and double stranded DNA (dsDNA) was much weaker than that between SX and single stranded DNA (ssDNA). All these results suggested that the binding mode of SX to DNA should be groove binding. The obtained thermodynamic parameters indicated that electrostatic force might play a predominant role in SX binding to DNA. The quantum yield (φ) of SX was measured as 0.13 using comparative method. Based on the Förster resonance energy transfer theory (FRET), the binding distance (r0) between the acceptor and donor was calculated as 4.10 nm.
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Affiliation(s)
- Tingting Zhao
- College of Chemistry, Changchun Normal University, Changchun 130032, China
| | - Shuyun Bi
- College of Chemistry, Changchun Normal University, Changchun 130032, China.
| | - Yu Wang
- College of Chemistry, Changchun Normal University, Changchun 130032, China
| | - Tianjiao Wang
- College of Chemistry, Changchun Normal University, Changchun 130032, China
| | - Bo Pang
- TechnologyCenterofInspectionandQuarantine, Jilin Entry-Exit Inspection and Quarantine Bureau, Changchun 130062, China
| | - Tingting Gu
- TechnologyCenterofInspectionandQuarantine, Jilin Entry-Exit Inspection and Quarantine Bureau, Changchun 130062, China
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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: 25] [Impact Index Per Article: 2.5] [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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N'soukpoé-Kossi C, Bourassa P, Mandeville J, Tajmir-Riahi H. Modelling of vitamin A binding to tRNA. J Pharm Biomed Anal 2014; 99:28-34. [DOI: 10.1016/j.jpba.2014.06.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/25/2014] [Accepted: 06/13/2014] [Indexed: 10/25/2022]
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Agudelo D, Bourassa P, Bérubé G, Tajmir-Riahi HA. Intercalation of antitumor drug doxorubicin and its analogue by DNA duplex: Structural features and biological implications. Int J Biol Macromol 2014; 66:144-50. [DOI: 10.1016/j.ijbiomac.2014.02.028] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 02/10/2014] [Accepted: 02/13/2014] [Indexed: 11/15/2022]
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12
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Tajmir-Riahi HA, Nafisi S, Sanyakamdhorn S, Agudelo D, Chanphai P. Applications of chitosan nanoparticles in drug delivery. Methods Mol Biol 2014; 1141:165-84. [PMID: 24567139 DOI: 10.1007/978-1-4939-0363-4_11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have reviewed the binding affinities of several antitumor drugs doxorubicin (Dox), N-(trifluoroacetyl) doxorubicin (FDox), tamoxifen (Tam), 4-hydroxytamoxifen (4-Hydroxytam), and endoxifen (Endox) with chitosan nanoparticles of different sizes (chitosan-15, chitosan-100, and chitosan-200 KD) in order to evaluate the efficacy of chitosan nanocarriers in drug delivery systems. Spectroscopic and molecular modeling studies showed the binding sites and the stability of drug-polymer complexes. Drug-chitosan complexation occurred via hydrophobic and hydrophilic contacts as well as H-bonding network. Chitosan-100 KD was the more effective drug carrier than the chitosan-15 and chitosan-200 KD.
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Affiliation(s)
- H A Tajmir-Riahi
- Department of Chemistry-Physics, University of Québec at Trois-Rivières, Trois-Rivières, QC, Canada
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Ma Y, Pan J, Zhang G, Zhang Y. Binding properties of butylated hydroxytoluene with calf thymus DNA in vitro. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 126:112-8. [DOI: 10.1016/j.jphotobiol.2013.07.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 07/07/2013] [Accepted: 07/09/2013] [Indexed: 11/17/2022]
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Zhu P, Zhang G, Ma Y, Zhang Y, Miao H, Wu Y. Study of DNA interactions with bifenthrin by spectroscopic techniques and molecular modeling. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2013; 112:7-14. [PMID: 23651773 DOI: 10.1016/j.saa.2013.04.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Revised: 03/17/2013] [Accepted: 04/02/2013] [Indexed: 06/02/2023]
Abstract
The interaction between bifenthrin (BF) and calf thymus DNA (ctDNA) in physiological buffer (pH 7.4) was investigated by UV-vis absorption, fluorescence, circular dichroism (CD), and Fourier transform infrared (FT-IR) spectroscopy, coupled with viscosity measurements and molecular docking techniques. It was found that BF molecular could intercalate into the base pairs of ctDNA as evidenced by significant increases in absorption intensity, fluorescence polarization and relative viscosity of ctDNA, decrease in iodide quenching effect, and induced CD spectral changes. The association constant of BF with ctDNA was evaluated to be in the order of 10(4) L mol(-1). Thermodynamic analysis of the binding data obtained at different temperatures suggested that the binding process was primarily driven by hydrogen bonds and van der Waals forces, as the values of the enthalpy change (ΔH) and the entropy change (ΔS) were calculated to be -31.13±1.89 kJ mol(-1) and -22.79±1.21 J mol(-1) K(-1), respectively. The results of FT-IR spectra and molecular docking showed that a specific binding mainly existed between BF and adenine and guanine bases.
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Affiliation(s)
- Pan Zhu
- State Key Laboratory of Food Science and Technology, Nanchang University, No. 235, Nanjing East Road, Nanchang 330047, Jiangxi, China
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15
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Agudelo D, Bourassa P, Beauregard M, Bérubé G, Tajmir-Riahi HA. tRNA binding to antitumor drug doxorubicin and its analogue. PLoS One 2013; 8:e69248. [PMID: 23922696 PMCID: PMC3726733 DOI: 10.1371/journal.pone.0069248] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/06/2013] [Indexed: 12/16/2022] Open
Abstract
The binding sites of antitumor drug doxorubicin (DOX) and its analogue N-(trifluoroacetyl) doxorubicin (FDOX) with tRNA were located, using FTIR, CD, fluorescence spectroscopic methods and molecular modeling. Different binding sites are involved in drug-tRNA adducts with DOX located in the vicinity of A-29, A-31, A-38, C-25, C-27, C-28, G-30 and U-41, while FDOX bindings involved A-23, A-44, C-25, C-27, G-24, G-42, G-53, G-45 and U-41 with similar free binding energy (-4.44 for DOX and -4.41 kcal/mol for FDOX adducts). Spectroscopic results showed that both hydrophilic and hydrophobic contacts are involved in drug-tRNA complexation and FDOX forms more stable complexes than DOX with K DOX-tRNA=4.7 (± 0.5)× 10(4) M(-1) and K FDOX-tRNA=6.3 (± 0.7)× 10(4) M(-1). The number of drug molecules bound per tRNA (n) was 0.6 for DOX and 0.4 for FDOX. No major alterations of tRNA structure were observed and tRNA remained in A-family conformation, while biopolymer aggregation and particle formation occurred at high drug concentrations.
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Affiliation(s)
- Daniel Agudelo
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Philippe Bourassa
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Marc Beauregard
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Gervais Bérubé
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Heidar-Ali Tajmir-Riahi
- Department of Chemistry and Physics, University of Québec at Trois-Rivières, Trois-Rivières, Québec, Canada
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Ghosh D, Saha C, Hossain M, Dey SK, Kumar GS. Biophysical studies of mutated K562 DNA (erythroleukemic cells) binding to adriamycin and daunomycin reveal that mutations induce structural changes influencing binding behavior. J Biomol Struct Dyn 2013; 31:331-41. [DOI: 10.1080/07391102.2012.698190] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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17
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Zhang Y, Zhang G, Fu P, Ma Y, Zhou J. Study on the interaction of triadimenol with calf thymus DNA by multispectroscopic methods and molecular modeling. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 96:1012-1019. [PMID: 22944149 DOI: 10.1016/j.saa.2012.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 08/03/2012] [Accepted: 08/07/2012] [Indexed: 06/01/2023]
Abstract
The binding mechanism of triadimenol (NOL) to calf thymus DNA (ctDNA) in physiological buffer (pH 7.4) was investigated by multispectroscopic methods including UV-vis absorption, fluorescence, circular dichroism (CD), Fourier transform infrared (FT-IR), and nuclear magnetic resonance ((1)H NMR) spectroscopy, coupled with viscosity measurements and atomic force microscopy (AFM) technique. The results suggested that NOL interacted with ctDNA by intercalation mode. CD and AFM assays showed that NOL can damage the base stacking of ctDNA and result in regional cleavage of the two DNA strands. FT-IR and (1)H NMR spectra coupled with molecular docking revealed that a specific binding mainly exists between NOL and G-C base pairs of the ctDNA where two hydrogen bonds form. Moreover, the association constants of NOL with DNA at three different temperatures were determined to be in the 10(3) L mol(-1) range. The calculated thermodynamic parameters suggested that the binding of NOL to ctDNA was driven mainly by hydrogen bond and van der Waals.
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Affiliation(s)
- Yepeng Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
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Nafisi S, Montazeri M, Manouchehri F. The effect of Se salts on DNA structure. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2012; 113:36-41. [DOI: 10.1016/j.jphotobiol.2012.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 04/13/2012] [Accepted: 04/18/2012] [Indexed: 11/29/2022]
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Froehlich E, Mandeville JS, Arnold D, Kreplak L, Tajmir-Riahi HA. Effect of PEG and mPEG-Anthracene on tRNA Aggregation and Particle Formation. Biomacromolecules 2011; 13:282-7. [DOI: 10.1021/bm2016515] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E. Froehlich
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières (Québec), Canada G9A 5H7
| | - J. S. Mandeville
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières (Québec), Canada G9A 5H7
| | - D. Arnold
- Department of Physics, Sir James
Dunn Building, Dalhousie University, Lord
Dalhousie Drive, Halifax, Canada NS B3H 3J5
| | - L. Kreplak
- Department of Physics, Sir James
Dunn Building, Dalhousie University, Lord
Dalhousie Drive, Halifax, Canada NS B3H 3J5
| | - H. A. Tajmir-Riahi
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières (Québec), Canada G9A 5H7
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Froehlich E, Mandeville JS, Arnold D, Kreplak L, Tajmir-Riahi HA. PEG and mPEG–Anthracene Induce DNA Condensation and Particle Formation. J Phys Chem B 2011; 115:9873-9. [DOI: 10.1021/jp205079u] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- E. Froehlich
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières (Québec), Canada G9A 5H7
| | - J. S. Mandeville
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières (Québec), Canada G9A 5H7
| | - D. Arnold
- Department of Physics, Sir James Dunn Building, Dalhousie University, Lord Dalhousie Drive, Halifax, Canada NS B3H 3J5
| | - L. Kreplak
- Department of Physics, Sir James Dunn Building, Dalhousie University, Lord Dalhousie Drive, Halifax, Canada NS B3H 3J5
| | - H. A. Tajmir-Riahi
- Department of Chemistry-Biology, University of Québec at Trois-Rivières, C.P. 500, Trois-Rivières (Québec), Canada G9A 5H7
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Rajabi M, Khalilzadeh MA, Mehrzad J. Antiproliferative activity of novel derivative of thiopyran on breast and colon cancer lines and DNA binding. DNA Cell Biol 2011; 31:128-34. [PMID: 21711159 DOI: 10.1089/dna.2011.1291] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Dimethyl-5-acetyl-4-methyl-6-(4-methylphenylimino)-6H-thiopyran-2,3-dicarboxylate (4) has been synthesized and its antiproliferative activity is reported here. Compound 4 inhibited the growth of human colon cancer cell line HCT-15 with an IC(50) value of 3.5 μM and of breast cancer cell line MCF-7 with an IC(50) value of 1.5 μM in a dose/time-dependent manner using a sulforhodamine B assay. Moreover, suppression of clonogenic activity occurred after exposure to 4 at a concentration of 4 μM for HCT-15 and 1.7 μM for MCF-7. The results also showed tumor cell invasion through matrigel and cell adhesion. The effect of ligand complexation on DNA structure led to overall affinity constant of K(4-DNA)=9.8×10(4) M(-1).
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Affiliation(s)
- Mehdi Rajabi
- Department of Chemistry and Biochemistry, Islamic Azad University, Neyshabur Branch, Neyshabur, Iran.
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