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Lu XY, Lou YY, Zhou KL, Jiang SL, Shi JH. Exploring the binding characteristics of febuxostat, an inhibitor of xanthine oxidase with calf thymus DNA: Multi-spectroscopic methodologies and molecular docking. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:605-624. [PMID: 35410587 DOI: 10.1080/15257770.2022.2057534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 03/01/2022] [Accepted: 03/19/2022] [Indexed: 06/14/2023]
Abstract
In this paper, the interacting characteristics of febuxostat (FBST), an inhibitor of xanthine oxidase for treating gout patients with hyperuricemia with calf thymus DNA (ctDNA) was investigated through multi-spectroscopic methodologies combined with theoretical calculation for understanding the interacting mode on ctDNA, affinity with ctDNA, interacting forces, as well as the alteration in the conformation of ctDNA after interacting FBST The experimental results demonstrated that interacting FBST with ctDNA formed 1:1 complex, the association constant was 913 M-1 at 298 K, suggesting the affinity of FBST on ctDNA was very weak, the interacting mode of FBST on ctDNA was groove binding, and it inserted into the minor groove with rich A-T region of ctDNA. Based on the results of the thermodynamic analysis and theoretical calculation, it can be inferred that the dominated interacting forces between FBST and ctDNA were van der Waals forces and hydrogen bond. And, interacting FBST with ctDNA was a spontaneous, enthalpy-driven, and exothermic process because of ΔG0 < 0, ΔH0 < 0, and |ΔH0| > T|ΔS0|. The results of the circular dichroism (CD) measurements indicated the conformation of ctDNA was weakly disturbed after interacting with FBST but still maintained B-conform. The studied results offer significant insight into further clarifying whether it has genotoxicity.
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Affiliation(s)
- Xin-Yan Lu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Yan-Yue Lou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Kai-Li Zhou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Shao-Liang Jiang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Jie-Hua Shi
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
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Luo YJ, Wang BL, Kou SB, Lin ZY, Zhou KL, Lou YY, Shi JH. Assessment on the binding characteristics of dasatinib, a tyrosine kinase inhibitor to calf thymus DNA: insights from multi-spectroscopic methodologies and molecular docking as well as DFT calculation. J Biomol Struct Dyn 2019; 38:4210-4220. [PMID: 31581883 DOI: 10.1080/07391102.2019.1676824] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The binding characteristics of calf thymus DNA (ct-DNA) with dasatinib (DSTN), a tyrosine kinase inhibitor was assessed through multi-spectroscopic methodologies and viscosity measurement combined with molecular docking as well as DFT calculation to understand the binding mechanism, affinity of DSTN onto ct-DNA, effect of DSTN on ct-DNA conformation, and among others. The results confirmed DSTN bound onto ct-DNA, leading to forming the DSTN-ct-DNA complex with the binding constant of 4.82 × 103 M-1 at 310 K. DSTN preferentially inserted to the minor groove of ct-DNA with rich A-T region, that was the binding mode of DSTN onto ct-DNA was groove binding. The enthalpic change (ΔH0) and entropic change (ΔS0) during the binding process of DSTN with ct-DNA were 128.9 kJ mol-1 and 489.2 J mol-1 K-1, respectively, confirming clearly that the association of DSTN with ct-DNA was an endothermic process and the dominative driven-force was hydrophobic interaction. Meanwhile, the results also indicated that there was a certain extent of electrostatic force and hydrogen bonding, but they maybe play an auxiliary role. The CD measurement results confirmed the alteration in the helical configuration of ct-DNA but almost no change in the base stacking after binding DSTN. The results revealed that there was the obvious change in the conformation, the dipole moment, and the atomic charge distribution of DSTN in the B-DNA complexes, compared with free DSTN, to satisfy the conformational adaptation. From the obtained fronitier molecular orbitals of DSTN, it can be inferred that the nature of DSTN alters with the change of the environment around DSTN. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yu-Jie Luo
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Bao-Li Wang
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Song-Bo Kou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Zhen-Yi Lin
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Kai-Li Zhou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Yan-Yue Lou
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Jie-Hua Shi
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
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Chen X, Wang B, Zhou K, Lou Y, Kou S, Lin Z, Shi J. Characterizing the Binding Interaction between Erlotinib and Calf Thymus DNA In Vitro Using Multi‐Spectroscopic Methodologies and Viscosity Measurement Combined with Molecular Docking and DFT Calculation. ChemistrySelect 2019. [DOI: 10.1002/slct.201900089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Xue‐Jun Chen
- College of Pharmaceutical ScienceZhejiang University of Technology 18, Chaowang Road, Hangzhou P.R.China
| | - Bao‐Li Wang
- College of Pharmaceutical ScienceZhejiang University of Technology 18, Chaowang Road, Hangzhou P.R.China
| | - Kai‐Li Zhou
- College of Pharmaceutical ScienceZhejiang University of Technology 18, Chaowang Road, Hangzhou P.R.China
| | - Yan‐Yue Lou
- College of Pharmaceutical ScienceZhejiang University of Technology 18, Chaowang Road, Hangzhou P.R.China
| | - Song‐Bo Kou
- College of Pharmaceutical ScienceZhejiang University of Technology 18, Chaowang Road, Hangzhou P.R.China
| | - Zhen‐Yi Lin
- College of Pharmaceutical ScienceZhejiang University of Technology 18, Chaowang Road, Hangzhou P.R.China
| | - Jie‐Hua Shi
- College of Pharmaceutical ScienceZhejiang University of Technology 18, Chaowang Road, Hangzhou P.R.China
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Banerjee A, Majumder P, Sanyal S, Singh J, Jana K, Das C, Dasgupta D. The DNA intercalators ethidium bromide and propidium iodide also bind to core histones. FEBS Open Bio 2014; 4:251-9. [PMID: 24649406 PMCID: PMC3958746 DOI: 10.1016/j.fob.2014.02.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 02/11/2014] [Accepted: 02/11/2014] [Indexed: 01/17/2023] Open
Abstract
Eukaryotic DNA is compacted in the form of chromatin, in a complex with histones and other non-histone proteins. The intimate association of DNA and histones in chromatin raises the possibility that DNA-interactive small molecules may bind to chromatin-associated proteins such as histones. Employing biophysical and biochemical techniques we have characterized the interaction of a classical intercalator, ethidium bromide (EB) and its structural analogue propidium iodide (PI) with hierarchical genomic components: long chromatin, chromatosome, core octamer and chromosomal DNA. Our studies show that EB and PI affect both chromatin structure and function, inducing chromatin compaction and disruption of the integrity of the chromatosome. Calorimetric studies and fluorescence measurements of the ligands demonstrated and characterized the association of these ligands with core histones and the intact octamer in absence of DNA. The ligands affect acetylation of histone H3 at lysine 9 and acetylation of histone H4 at lysine 5 and lysine 8 ex vivo. PI alters the post-translational modifications to a greater extent than EB. This is the first report showing the dual binding (chromosomal DNA and core histones) property of a classical intercalator, EB, and its longer analogue, PI, in the context of chromatin.
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Affiliation(s)
- Amrita Banerjee
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Parijat Majumder
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Sulagna Sanyal
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Jasdeep Singh
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Kuladip Jana
- Division of Molecular Medicine, Centre for Translational Animal Research, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, West Bengal, India
| | - Chandrima Das
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Dipak Dasgupta
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
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Kuzin FE, Shilova IE, Lezzi M, Gruzdev AD. DNA in the centromeric heterochromatin of polytene chromosomes is topologically open. Chromosome Res 2002; 10:201-8. [PMID: 12067209 DOI: 10.1023/a:1015239904723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Heterochromatin differs from euchromatin by a set of specific features. We suggested earlier that specific features of heterochromatin result from differences in DNA topology of these two chromatin types and provided explanations for the majority of them (Gruzdev 2000). We proposed that, unlike topologically closed euchromatic DNA, the DNA of heterochromatin is topologically open, i.e. it likely contains single- or doublestrand breaks. In this work, we studied the topological state of DNA in a block of centromeric heterochromatin and in a euchromatic banded region of Chironomus melanotus polytene chromosomes by microfluorimetric methods using the fluorescent intercalating dye ethidium bromide (EB). It was demonstrated that the fraction of topologically closed DNA in heterochromatin blocks is five-fold smaller than in the banded region. The data obtained support the hypothesis proposed.
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Affiliation(s)
- Fedor E Kuzin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk
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Albert P, Toublan B, Lacorre-Arescaldino I. Change in chromatin organization related to in vivo transcriptional activity and histone synthesis independent of DNA replication during differentiation (germination) of Physarum spherules. Dev Genes Evol 1992; 201:149-156. [PMID: 28305581 DOI: 10.1007/bf00188713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/1991] [Accepted: 02/05/1992] [Indexed: 10/26/2022]
Abstract
During the germination of Physarum spherules, increases have been observed, at the same moment, in the level of in vivo transcriptional activity as measured by [3H] uridine incorporation, and the accessibility of DNA for ethidium bromide staining as shown by flow cytometric measurements. We suppose that the changes observed in these two processes are due to a difference in chromatin organization between the first and the second period of the premitotic germination stage. In the second period, the four nucleosome core histories are synthesized in the absence of DNA replication and may correspond to a replacement of spherulation histone variants by plasmodial histone types in nucleosomes. The synthesis of historic H4 clearly distinguishes the second period of the premitotic germination stage from a growing plasmodium G2 phase, though nuclei exhibit a G2 phase DNA content. The same pattern of histone synthesis has been found during the cell cycle following the first mitosis after germination and the growing plasmodium cell cycle, with a synthesis of two histories H2B and H2A and the high mobility group (HMG)-like protein AS3 during the G2 phase, i.e. in the absence of DNA synthesis.
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Affiliation(s)
- Philippe Albert
- Laboratoire de Biologie Cellulaire, Université de Reims Champagne-Ardenne, B.P. 347, F-51062, Reims Cédex, France
| | - Barbara Toublan
- Laboratoire de Biologie Cellulaire, Université de Reims Champagne-Ardenne, B.P. 347, F-51062, Reims Cédex, France
| | - Isabelle Lacorre-Arescaldino
- Laboratoire de Biologie Cellulaire, Université de Reims Champagne-Ardenne, B.P. 347, F-51062, Reims Cédex, France
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Czupryn M, Toczko K. Lack of nucleosomal structure in a DNase-I-solubilized transcriptionally active chromatin fraction of Physarum polycephalum. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 147:575-80. [PMID: 3979388 DOI: 10.1111/j.0014-2956.1985.00575.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Light treatment of nuclei of Physarum polycephalum microplasmodia with DNase I, at low MgCl2 concentration (less than or equal to 3% DNA acid solubility, 0.1 mM MgCl2) selectively solubilizes a defined fraction of chromatin, in the form of a macromolecular complex. This fraction (up to 15% of the total chromatin) contains a full complement of the core histones and a reduced amount of histone H1, and is enriched in the high-mobility-group type of proteins. It is preferentially associated with nascent RNA and RNA polymerase B actively engaged in transcription. Digestion of DNAase-I-solubilized chromatin by micrococcal nuclease releases a size-heterogeneous population of cleavage products, indicative of lack of a typical nucleosomal packaging. It is concluded that the procedure used allows the isolation of structurally and functionally distinct regions of Physarum chromatin.
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Coffman GL, Yielding LW, Yielding L. Monoazido analog of ethidium as a chromatin probe: binding to DNA. Biopolymers 1984; 23:1067-84. [PMID: 6733248 DOI: 10.1002/bip.360230608] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Grimmond HE, Beerman T. Alteration of chromatin structure induced by the binding of adriamycin, daunorubicin and ethidium bromide. Biochem Pharmacol 1982; 31:3379-86. [PMID: 7150361 DOI: 10.1016/0006-2952(82)90615-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The results reported in this paper show the changes in chromatin structure caused by the binding of adriamycin (ADR), daunorubicin (DR) and ethidium bromide (EtdBr) to DNA in chromatin, either isolated or in nuclei or whole cells. Micrococcal nuclease was used as the structural probe of chromatin. The binding of the drugs to chromatin DNA induced two structural changes. First, it produced an unfolding of the overall chromatin structure as evidenced by the increased production of acid-soluble oligonucleotides for the drug-treated samples above the level of the control sample. Second, it caused a disruption of the core particle structure with increased production of DNA of subnucleosomal size and smearing of the nucleosome pattern. The effects were greatest for duanorubicin, followed by adriamycin and ethidium bromide.
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Edelman IS, Marver D. Mediating events in the action of aldosterone. JOURNAL OF STEROID BIOCHEMISTRY 1980; 12:219-24. [PMID: 6158626 DOI: 10.1016/0022-4731(80)90271-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Paoletti J. Relaxation of chromatin structure induced by ethidium binding. Involvement of the intercalation process. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 100:531-9. [PMID: 510297 DOI: 10.1111/j.1432-1033.1979.tb04199.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this paper we study the effects of the binding of ethidium on the structure of chromatin, using micrococcal nuclease as a structural probe. This binding induces two structural changes of chromatin either isolated or in the nuclei. (a) An unfolding of the overall structure which results in an activation of the rate of degradation by the nuclease. (b) A disorganisation of the core particle structure which has the effect of unwrapping the DNA from the histone core, this disruption can go on so far as to leave only 90 base pairs. By comparing the bindings of ethidium and tetramethylethidium, we conclude that the first type of structural change is due to an electrostatic effect and does not depend upon intercalation. On the other hand, the second one is due to the intercalation process and to the change of topological constraints on the DNA that such a process involves.
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Doenecke D. Modification of DNA in chromatin with methyltransferase from Haemophilus influenzae Rd. EUROPEAN JOURNAL OF BIOCHEMISTRY 1979; 93:481-6. [PMID: 311284 DOI: 10.1111/j.1432-1033.1979.tb12846.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The accessibility of DNA in nucleosome dimers (as a model of the chromosomal chain of nucleosomes) was determined by means of modification methylases from Haemophilus influenzae Rd. Using these enzymes, the rate of modification of nucleosome dimers is about one fifth the rate observed with protein-free DNA from chromatin subunit dimers. Methylated DNA sites in nucleosome dimers are readily accessible to micrococcal nuclease. The analysis of the fragment pattern of nucleosomes after methylation and mild nuclease treatment reveals that the methylated sites are predominantly located in the internucleosomal linker DNA. Polylysine binding experiments further support this interpretation. This compound preferentially interacts with the nucleosomal core DNA and protects it against internal cleavage. It neither affects the degradation of methylated sites drastically nor does it inhibit the methylation of nucleosome dimers. Thus, a combination of protection, cleavage and modification is proposed as a useful tool for the analysis of the structure of chromatin.
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Jerzmanowski A, Staroń K, Tyniec B, Toczko K. Effect of ethidium bromide on the digestion of chromatin DNA with micrococcal nuclease. BIOCHIMICA ET BIOPHYSICA ACTA 1978; 521:493-501. [PMID: 737179 DOI: 10.1016/0005-2787(78)90291-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Intercalation of ethidium bromide into DNA influences the rate of its digestion with micrococcal nuclease in opposite directions depending on whether it is free DNA or DNA in chromatin. In the case of free DNA the binding of ethidium bromide, starting from a very low concentration, results in the inhibition of the rate of digestion (increasing constantly with the increase of the ethidium bromide/nucleotide ratio). In contrast to free DNA the digestion rate as well as the overall amount of nuclease susceptible DNA is increased upon ethidium bromide binding to chromatin, with maximum enhancement around the saturation of intercalation sites. The saturation of intercalation sites in chromatin leads also to the disappearance of the typical micrococcal nuclease digestion pattern of DNA upon gel electrophoresis. Instead, a random cleavage pattern is observed. These data indicate that partial unwinding of chromatin DNA by ethidium bromide results in unmasking new sites for nuclease action. Interpretation of this finding in terms of the nucleosomal structure of chromatin and the mode of ethidium bromide binding to chromatin DNA indicates that newly unmasked sites are localized within the core particle DNA.
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