101
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DNA nanostructures based biosensor for the determination of aromatic compounds. Biosens Bioelectron 2015; 72:191-6. [DOI: 10.1016/j.bios.2015.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 04/30/2015] [Accepted: 05/03/2015] [Indexed: 11/17/2022]
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102
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Tomar JS. In-silico modeling studies of G-quadruplex with soy isoflavones having anticancerous activity. J Mol Model 2015; 21:193. [PMID: 26164556 DOI: 10.1007/s00894-015-2723-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/08/2015] [Indexed: 12/12/2022]
Abstract
Telomere forms t-loop and G-quadruplex as the protective structure and the formation of these structures hinder the telomerase enzyme action. The binding affinities of ligand which stabilize the G-quadruplex represent good correlation with telomerase inhibition depicted in the anti-cancerous action. Most of the potent G-quadruplex stabilizing compounds suffer from the poor drug like properties. Herein, natural dietary compounds isoflavones were taken for the theoretical study to examine their stabilizing effect on G-quadruplex structure. The experimental G-quadruplex complexes were reproduced to obtain and validate the theoretical parameters. The obtained theoretical binding energies are in significant correlation with the experimental data. Analysis of binding shows isoflavones to be groove binders, and differential nature of quadruplex grooves might be beneficial in the selectivity aspects. Among all, derrubone was found to have better selectivity as well as affinity for the G-quadruplex comparable to well known ligand TMPyP4. The GBSA rescoring result enlightens the various interaction terms involved in the binding process. Cumulative stabilizing effects coming from VDW, ES, and GB energy terms attest to optimal binding of derrubone molecule which can be considered as a lead for the higher phases of drug designing. These findings are of great value in terms of unexplored groove binding modes and the studied natural compounds might be helpful to direct the focus of synthetic chemists in designing of new generation of antitumor agents.
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Affiliation(s)
- Jyoti Singh Tomar
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, 247667, Uttarakhand, India,
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103
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Li ZX, Li J, Li Y, You K, Xu H, Wang J. Novel insights into the apoptosis mechanism of DNA topoisomerase I inhibitor isoliquiritigenin on HCC tumor cell. Biochem Biophys Res Commun 2015; 464:548-53. [PMID: 26159926 DOI: 10.1016/j.bbrc.2015.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 07/01/2015] [Indexed: 01/20/2023]
Abstract
The inhibitory effect of DNA topoisomerase (Top I) by isoliquiritigenin(ISO) were investigated and their interaction mechanism was evaluated using methods including UV-vis absorption, fluorescence, coupled with molecular simulation, and using the MTT method of inhibition rate of HCC tumor cell SNU475 proliferation assay, finally, the interaction of ISO with calf thymus DNA was investigated by melting measurements and molecular docking studies. It was found that isoliquiritigenin reversibly inhibited DNA Top I in a competitive manner with the concentrations of ISO resulting in 50% activity lost (IC50) were estimated to be 0.178 ± 0.12 mM. Isoliquiritigenin exhibited a strong ability to quench the intrinsic fluorescence of Top I through a static quenching procedure. The positive values of enthalpy change and entropy change suggested that the binding of isoliquiritigenin to Top I was driven mainly by hydrophobic interactions. The molecular docking results revealed isoliquiritigenin actually interacted with the primary amino acid residues on the active site of Top I, and the detection results of fluorescence staining and the inhibitory effect on the growth of HCC SUN475 showed that isoliquiritigenin induced the apoptosis cells increased gradually. The interaction of ISO with DNA can cause the denaturation temperature to be increased, which indicated that the stabilization of the DNA helix was increased in the presence of ISO, which indicated that the results provide strong evidence for intercalative binding of ISO with DNA.
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Affiliation(s)
- Ze-Xin Li
- Department of General Surgery, The First Affiliated Hospital of Xinxiang Medical University, 453100, China
| | - Jian Li
- Department of General Surgery, The First Affiliated Hospital of Xinxiang Medical University, 453100, China
| | - Yan Li
- Department of General Surgery, The First Affiliated Hospital of Xinxiang Medical University, 453100, China
| | - Kun You
- Department of General Surgery, The First Affiliated Hospital of Xinxiang Medical University, 453100, China
| | - Hongwei Xu
- Department of General Surgery, The First Affiliated Hospital of Xinxiang Medical University, 453100, China
| | - Jianguo Wang
- Department of General Surgery, The First Affiliated Hospital of Xinxiang Medical University, 453100, China.
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104
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Fu XB, Liu DD, Lin Y, Hu W, Mao ZW, Le XY. Water-soluble DNA minor groove binders as potential chemotherapeutic agents: synthesis, characterization, DNA binding and cleavage, antioxidation, cytotoxicity and HSA interactions. Dalton Trans 2015; 43:8721-37. [PMID: 24770345 DOI: 10.1039/c3dt53577k] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Two new water-soluble copper(ii)-dipeptide complexes: [Cu(glygly)(PyTA)]ClO4·1.5H2O (1) and [Cu(glygly)(PzTA)]ClO4·1.5H2O (2) (glygly = glycylglycine anion, PyTA = 2,4-diamino-6-(2'-pyridyl)-1,3,5-triazine and PzTA = 2,4-diamino-6-(2'-pyrazino)-1,3,5-triazine), utilizing two interrelated DNA base-like ligands (PyTA and PzTA), have been synthesized and characterized. The structure elucidation for 1 performed by single crystal X-ray diffraction showed a one dimensional chain conformation in which the central copper ions arrange in a five-coordinate distorted square-pyramidal geometry. Spectroscopic titration, viscosity and electrophoresis measurements revealed that the complexes bound to DNA via an outside groove binding mode, and cleaved pBR322 DNA efficiently in the presence of ascorbate, probably via an oxidative mechanism with the involvement of ˙OH and ˙O2(-). Notably, the complexes exhibited considerable in vitro cytotoxicity against four human carcinoma cell lines (HepG2, HeLa, A549 and U87) with IC50 values ranging from 41.68 to 159.17 μM, in addition to their excellent SOD mimics (IC50 ~ 0.091 and 0.114 μM). Besides, multispectroscopic evidence suggested their HSA-binding at the cavity containing Trp-214 in subdomain IIA with moderate affinity, mainly via hydrophobic interaction. Further, the molecular docking technique utilized for ascertaining the mechanism and mode of action towards DNA and HSA theoretically verified the experimental results.
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Affiliation(s)
- Xia-Bing Fu
- Department of Applied Chemistry, South China Agricultural University, Guangzhou 510642, PR China.
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105
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Computational docking simulations of a DNA-aptamer for argininamide and related ligands. J Comput Aided Mol Des 2015; 29:643-54. [PMID: 25877490 DOI: 10.1007/s10822-015-9844-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/09/2015] [Indexed: 10/23/2022]
Abstract
The binding properties of sequence-specific nucleic acids (aptamers) to low-molecular-weight ligands, macromolecules and even cells attract substantial scientific interest. These ligand-DNA complexes found different applications for sensing, nanomedicine, and DNA nanotechnology. Structural information on the aptamer-ligand complexes is, however, scarce, even though it would open-up the possibilities to design novel features in the complexes. In the present study we apply molecular docking simulations to probe the features of an experimentally documented L-argininamide aptamer complex. The docking simulations were performed using AutoDock 4.0 and YASARA Structure software, a well-suited program for following intermolecular interactions and structures of biomolecules, including DNA. We explored the binding features of a DNA aptamer to L-argininamide and to a series of arginine derivatives or arginine-like ligands. We find that the best docking results are obtained after an energy-minimization of the parent ligand-aptamer complexes. The calculated binding energies of all mono-substituted guanidine-containing ligands show a good correlation with the experimentally determined binding constants. The results provide valuable guidelines for the application of docking simulations for the prediction of aptamer-ligand structures, and for the design of novel features of ligand-aptamer complexes.
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106
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Scalese G, Benítez J, Rostán S, Correia I, Bradford L, Vieites M, Minini L, Merlino A, Coitiño EL, Birriel E, Varela J, Cerecetto H, González M, Pessoa JC, Gambino D. Expanding the family of heteroleptic oxidovanadium(IV) compounds with salicylaldehyde semicarbazones and polypyridyl ligands showing anti-Trypanosoma cruzi activity. J Inorg Biochem 2015; 147:116-25. [PMID: 25824466 DOI: 10.1016/j.jinorgbio.2015.03.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/01/2015] [Accepted: 03/04/2015] [Indexed: 01/01/2023]
Abstract
Searching for prospective vanadium-based drugs for the treatment of Chagas disease, a new series of heteroleptic [V(IV)O(L-2H)(NN)] compounds was developed by including the lipophilic 3,4,7,8-tetramethyl-1,10-phenanthroline (tmp) NN ligand and seven tridentate salicylaldehyde semicarbazone derivatives (L1-L7). The compounds were characterized in the solid state and in solution. EPR spectroscopy suggests that the NN ligand is bidentate bound through both nitrogen donor atoms in an axial-equatorial mode. The EPR and (51)V-NMR spectra of aerated solutions at room temperature indicate that the compounds are stable to hydrolysis and that no significant oxidation of V(IV) to V(V) takes place at least in 24h. The complexes are more active in vitro against Trypanosoma cruzi, the parasite responsible for Chagas disease, than the reference drug Nifurtimox and most of them are more active than previously reported [V(IV)O(L-2H)(NN)] complexes of other NN co-ligands. Selectivity towards the parasite was analyzed using J-774 murine macrophages as mammalian cell model. Due to both, high activity and high selectivity, L2, L4, L5 and L7 complexes could be considered new hits for further drug development. Lipophilicity probably plays a relevant role in the bioactivity of the new compounds. The [V(IV)O(L-2H)(NN)] compounds were designed aiming DNA as potential molecular target. Therefore, the novel L1-L7 tmp complexes were screened by computational modeling, comparing their DNA-binding features with those of previously reported [V(IV)O(L-2H)(NN)] compounds with different NN co-ligands. Whereas all the complexes interact well with DNA, with binding modes and strength tuned in different extents by the NN and semicarbazone co-ligands, molecular docking suggests that the observed anti-T. cruzi activity cannot be explained upon DNA intercalation as the sole mechanism of action.
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Affiliation(s)
- Gonzalo Scalese
- Cátedra de Química Inorgánica, Facultad de Química, Universidad de la República, Gral. Flores 2124, 11800 Montevideo, Uruguay
| | - Julio Benítez
- Cátedra de Química Inorgánica, Facultad de Química, Universidad de la República, Gral. Flores 2124, 11800 Montevideo, Uruguay
| | - Santiago Rostán
- Cátedra de Química Inorgánica, Facultad de Química, Universidad de la República, Gral. Flores 2124, 11800 Montevideo, Uruguay
| | - Isabel Correia
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Lara Bradford
- Cátedra de Química Inorgánica, Facultad de Química, Universidad de la República, Gral. Flores 2124, 11800 Montevideo, Uruguay
| | - Marisol Vieites
- Cátedra de Química Inorgánica, Facultad de Química, Universidad de la República, Gral. Flores 2124, 11800 Montevideo, Uruguay
| | - Lucía Minini
- Laboratorio de Química Teórica y Computacional, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Uruguay
| | - Alicia Merlino
- Laboratorio de Química Teórica y Computacional, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Uruguay
| | - E Laura Coitiño
- Laboratorio de Química Teórica y Computacional, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400, Uruguay
| | - Estefania Birriel
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias-Facultad de Química, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Javier Varela
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias-Facultad de Química, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Hugo Cerecetto
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias-Facultad de Química, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Mercedes González
- Grupo de Química Medicinal, Laboratorio de Química Orgánica, Facultad de Ciencias-Facultad de Química, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - João Costa Pessoa
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Dinorah Gambino
- Cátedra de Química Inorgánica, Facultad de Química, Universidad de la República, Gral. Flores 2124, 11800 Montevideo, Uruguay.
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107
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Deligkaris C, Ascone AT, Sweeney KJ, Greene AJQ. Validation of a computational docking methodology to identify the non-covalent binding site of ligands to DNA. MOLECULAR BIOSYSTEMS 2015; 10:2106-25. [PMID: 24853173 DOI: 10.1039/c4mb00239c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Despite the biomedical consequences of carcinogen-DNA interactions and the potential of DNA as a drug target in medicinal chemistry, only a small number of studies have validated or used docking methods for the prediction of the physical binding of small molecules to DNA. Knowledge of the DNA-physically-bound ligand geometry can lead to the elucidation of the molecular-level mechanism of drugs as well as predicting the subsequent chemical interactions that lead to DNA damage from carcinogens. We sought to validate AutoDock 4.2, a docking method that includes a physics-based free energy function and a Lamarckian Genetic Algorithm, for the prediction of ligand geometries upon physical binding to DNA. We performed simulations by systematically changing the length of the search process for a comprehensive set of 32 ligand-DNA molecular systems with different physico-chemical properties, and we used a free-energy-based convergence criterion to terminate our simulations. For 11 out of 28 molecular systems for which convergence was achieved, the lowest binding free energy geometries were within 2 Å of the experimentally determined geometry. Considering all predicted sites with free energy changes within 20% of the lowest binding free energy site, we found a site within 2 Å of the experimentally determined geometry for 24 out of the 28 systems. However, the predicted hydrogen bonding interactions were different for most molecular systems compared to the same interactions in the experimentally determined geometry. We discuss reasons for the successes and failures, implications, and the importance of ensuring an adequate search in docking calculations. Overall, we concluded that AutoDock 4.2 can be used to predict the non-covalent binding geometry of a small molecule to DNA with some limitations.
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108
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al-Rashida M, Ahsen S. In search of a docking protocol to distinguish between DNA intercalators and groove binders: genetic algorithm vs. shape-complementarity based docking methods. RSC Adv 2015. [DOI: 10.1039/c5ra09929c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A comparison of docking of DNA groove binders and intercalators using genetic algorithm and shape-complementarity based methods is presented.
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Affiliation(s)
- Mariya al-Rashida
- Department of Chemistry
- Forman Christian College (A Chartered University)
- Lahore 54600
- Pakistan
| | - Sana Ahsen
- Department of Chemistry
- Forman Christian College (A Chartered University)
- Lahore 54600
- Pakistan
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109
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Hassan Khan NU, Zaib S, Sultana K, Khan I, Mougang-Soume B, Nadeem H, Hassan M, Iqbal J. Metal complexes of tosyl sulfonamides: design, X-ray structure, biological activities and molecular docking studies. RSC Adv 2015. [DOI: 10.1039/c4ra16124f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
CompoundNA3bound inside the active site of the enzyme.
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Affiliation(s)
- Najm Ul Hassan Khan
- Riphah Institute of Pharmaceutical Sciences
- Riphah International University
- Islamabad-44000
- Pakistan
| | - Sumera Zaib
- Department of Biochemistry
- Hazara University
- Garden Campus
- Mansehra
- Pakistan
| | | | - Imtiaz Khan
- School of Chemistry
- University of Nottingham
- University Park
- Nottingham
- UK
| | | | - Humaira Nadeem
- Riphah Institute of Pharmaceutical Sciences
- Riphah International University
- Islamabad-44000
- Pakistan
| | - Mukhtiar Hassan
- Department of Biochemistry
- Hazara University
- Garden Campus
- Mansehra
- Pakistan
| | - Jamshed Iqbal
- Centre for Advanced Drug Research
- COMSATS Institute of Information Technology
- Abbottabad-22060
- Pakistan
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110
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Icsel C, Yilmaz VT, Kaya Y, Samli H, Harrison WTA, Buyukgungor O. New palladium(ii) and platinum(ii) 5,5-diethylbarbiturate complexes with 2-phenylpyridine, 2,2′-bipyridine and 2,2′-dipyridylamine: synthesis, structures, DNA binding, molecular docking, cellular uptake, antioxidant activity and cytotoxicity. Dalton Trans 2015; 44:6880-95. [DOI: 10.1039/c5dt00728c] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DNA interaction, antioxidant and cytotoxic activities of Pd(ii)/Pt(ii) 5,5-diethylbarbiturate complexes were evaluated.
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Affiliation(s)
- Ceyda Icsel
- Department of Chemistry
- Faculty of Arts and Sciences
- Uludag University
- 16059 Bursa
- Turkey
| | - Veysel T. Yilmaz
- Department of Chemistry
- Faculty of Arts and Sciences
- Uludag University
- 16059 Bursa
- Turkey
| | - Yunus Kaya
- Department of Chemistry
- Faculty of Arts and Sciences
- Uludag University
- 16059 Bursa
- Turkey
| | - Hale Samli
- Department of Genetics
- Faculty of Veterinary Medicine
- Uludag University
- 16059 Bursa
- Turkey
| | | | - Orhan Buyukgungor
- Department of Physics
- Faculty of Arts and Sciences
- Ondokuz Mayis University
- 55159 Samsun
- Turkey
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111
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Kundu P, Ghosh S, Chattopadhyay N. Exploration of the binding interaction of a potential nervous system stimulant with calf-thymus DNA and dissociation of the drug–DNA complex by detergent sequestration. Phys Chem Chem Phys 2015; 17:17699-709. [DOI: 10.1039/c5cp02101d] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The binding interaction of a potential nervous system stimulant with calf-thymus DNA has been divulged and dissociation of the drug–DNA complex has been achieved by the detergent sequestration method.
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Affiliation(s)
- Pronab Kundu
- Department of Chemistry
- Jadavpur University
- Kolkata – 700 032
- India
| | - Saptarshi Ghosh
- Department of Chemistry
- Jadavpur University
- Kolkata – 700 032
- India
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112
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Rodrigues ARO, Carvalho MSD, Cardoso JAV, Calhelha RC, Queiroz MJR, Coutinho PJ, Castanheira EM. Benzothienoquinolines: New one-pot synthesis and fluorescence studies of their interaction with DNA and polynucleotides. J Photochem Photobiol A Chem 2014. [DOI: 10.1016/j.jphotochem.2014.08.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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113
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Khairutdinov B, Ermakova E, Sitnitsky A, Stoikov I, Zuev Y. Supramolecular complex formed by DNA oligonucleotide and thiacalix[4]arene. NMR-spectroscopy and molecular docking. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.05.073] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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114
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Qin Z, Li X, Zhou M. A Theoretical Study on Hydrogen-Bonded Complex of Proflavine Cation and Water: The Site-dependent Feature of Hydrogen Bond Strengthening and Weakening. J CHIN CHEM SOC-TAIP 2014. [DOI: 10.1002/jccs.201400089] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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115
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Snyder RD, Holt PA, Maguire JM, Trent JO. Evidence for the contribution of non-covalent steroid interactions between DNA and topoisomerase in the genotoxicity of steroids. Drug Chem Toxicol 2014; 38:212-9. [PMID: 24975547 DOI: 10.3109/01480545.2014.928725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Fifty two steroids and 9 Vitamin D analogs were docked into ten crystallographically-defined DNA dinucleotide sites and two human topoisomerase II ATP binding sites using two computational programs, Autodock and Surflex. It is shown that both steroids and Vitamin D analogs exhibit a propensity for non-covalent intercalative binding to DNA. A higher predicted binding affinity was found, however, for steroids and the ATP binding site of topoisomerase; in fact these drugs exhibited among the highest topo II binding observed in over 1370 docked drugs. These findings along with genotoxicity data from 26 additional steroids not subjected to docking analysis, support a mechanism wherein the long known, but poorly understood, clastogenicity of steroids may be attributable to inhibition of topoisomerase. A "proof of principle" experiment with dexamethasone demonstrated this to be the likely mechanism of clastogenicity of, at least, this steroid. The generality of this proposed mechanism of genotoxicity across the steroids and vitamin-D analogs is discussed.
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Affiliation(s)
- Ronald D Snyder
- RDS Consulting Services , 3335 Grand Falls Blvd, Maineville, OH , United States and
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116
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Zhou X, Zhang G, Wang L. Probing the binding mode of psoralen to calf thymus DNA. Int J Biol Macromol 2014; 67:228-37. [DOI: 10.1016/j.ijbiomac.2014.03.038] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/13/2014] [Accepted: 03/14/2014] [Indexed: 01/31/2023]
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117
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Saeed A, al-Rashida M, Hamayoun M, Mumtaz A, Iqbal J. Carbonic anhydrase inhibition by 1-aroyl-3-(4-aminosulfonylphenyl)thioureas. J Enzyme Inhib Med Chem 2014; 29:901-5. [DOI: 10.3109/14756366.2013.866660] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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118
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Rescifina A, Zagni C, Varrica MG, Pistarà V, Corsaro A. Recent advances in small organic molecules as DNA intercalating agents: synthesis, activity, and modeling. Eur J Med Chem 2014; 74:95-115. [PMID: 24448420 DOI: 10.1016/j.ejmech.2013.11.029] [Citation(s) in RCA: 178] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/26/2013] [Accepted: 11/28/2013] [Indexed: 11/28/2022]
Abstract
The interaction of small molecules with DNA plays an essential role in many biological processes. As DNA is often the target for majority of anticancer and antibiotic drugs, study about the interaction of drug and DNA has a key role in pharmacology. Moreover, understanding the interactions of small molecules with DNA is of prime significance in the rational design of more powerful and selective anticancer agents. Two of the most important and promising targets in cancer chemotherapy include DNA alkylating agents and DNA intercalators. For these last the DNA recognition is a critical step in their anti-tumor action and the intercalation is not only one kind of the interactions in DNA recognition but also a pivotal step of several clinically used anti-tumor drugs such as anthracyclines, acridines and anthraquinones. To push clinical cancer therapy, the discovery of new DNA intercalators has been considered a practical approach and a number of intercalators have been recently reported. The intercalative binding properties of such molecules can also be harnessed as diagnostic probes for DNA structure in addition to DNA-directed therapeutics. Moreover, the problem of intercalation site formation in the undistorted B-DNA of different length and sequence is matter of tremendous importance in molecular modeling studies and, nowadays, three models of DNA intercalation targets have been proposed that account for the binding features of intercalators. Finally, despite DNA being an important target for several drugs, most of the docking programs are validated only for proteins and their ligands. Therefore, a default protocol to identify DNA binding modes which uses a modified canonical DNA as receptor is needed.
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Affiliation(s)
- Antonio Rescifina
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy.
| | - Chiara Zagni
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Maria Giulia Varrica
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Venerando Pistarà
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
| | - Antonino Corsaro
- Dipartimento di Scienze del Farmaco, Università di Catania, Viale Andrea Doria 6, 95125 Catania, Italy
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119
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Ghosh S, Kundu P, Paul BK, Chattopadhyay N. Binding of an anionic fluorescent probe with calf thymus DNA and effect of salt on the probe–DNA binding: a spectroscopic and molecular docking investigation. RSC Adv 2014. [DOI: 10.1039/c4ra14298e] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Binding mode of biologically relevant anionic probe, ANS, with ctDNA is divulged from spectroscopic and molecular docking studies.
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Affiliation(s)
- Saptarshi Ghosh
- Department of Chemistry
- Jadavpur University
- Kolkata – 700032, India
| | - Pronab Kundu
- Department of Chemistry
- Jadavpur University
- Kolkata – 700032, India
| | - Bijan Kumar Paul
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462066, India
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120
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Affiliation(s)
- Yocheved Gilad
- Department of Chemistry, Bar Ilan University, Ramat-Gan 52900, Israel
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121
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Hu W, Deng S, Huang J, Lu Y, Le X, Zheng W. Intercalative interaction of asymmetric copper(II) complex with DNA: Experimental, molecular docking, molecular dynamics and TDDFT studies. J Inorg Biochem 2013; 127:90-8. [DOI: 10.1016/j.jinorgbio.2013.07.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2013] [Revised: 07/23/2013] [Accepted: 07/23/2013] [Indexed: 10/26/2022]
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122
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Samanta SK, Dutta D, Roy S, Bhattacharya K, Sarkar S, Dasgupta AK, Pal BC, Mandal C, Mandal C. Mahanine, A DNA Minor Groove Binding Agent Exerts Cellular Cytotoxicity with Involvement of C-7-OH and −NH Functional Groups. J Med Chem 2013; 56:5709-21. [DOI: 10.1021/jm400290q] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Suman K. Samanta
- Cancer Biology and Inflammatory
Disorder Division, Council of Scientific and Industrial Research—Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Devawati Dutta
- Cancer Biology and Inflammatory
Disorder Division, Council of Scientific and Industrial Research—Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Sarita Roy
- Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road,
Kolkata 700019, India
| | - Kaushik Bhattacharya
- Cancer Biology and Inflammatory
Disorder Division, Council of Scientific and Industrial Research—Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Sayantani Sarkar
- Cancer Biology and Inflammatory
Disorder Division, Council of Scientific and Industrial Research—Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
| | - Anjan K. Dasgupta
- Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road,
Kolkata 700019, India
| | - Bikas C. Pal
- National Institute of Pharmaceutical Education and Research, Kolkata, 4
Raja S. C. Mullick Road, Kolkata 700032, India
| | - Chhabinath Mandal
- National Institute of Pharmaceutical Education and Research, Kolkata, 4
Raja S. C. Mullick Road, Kolkata 700032, India
| | - Chitra Mandal
- Cancer Biology and Inflammatory
Disorder Division, Council of Scientific and Industrial Research—Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, India
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123
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Ueberschaar N, Dahse HM, Bretschneider T, Hertweck C. Rational Design of an Apoptosis-Inducing Photoreactive DNA Intercalator. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302439] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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124
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Ueberschaar N, Dahse HM, Bretschneider T, Hertweck C. Rational Design of an Apoptosis-Inducing Photoreactive DNA Intercalator. Angew Chem Int Ed Engl 2013; 52:6185-9. [DOI: 10.1002/anie.201302439] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2013] [Indexed: 01/22/2023]
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125
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Zhang Y, Zhang G, Li Y, Hu Y. Probing the binding of insecticide permethrin to calf thymus DNA by spectroscopic techniques merging with chemometrics method. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:2638-2647. [PMID: 23448177 DOI: 10.1021/jf400017f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The binding of permethrin (PE) with calf thymus DNA (ctDNA) in physiological buffer (pH 7.4) was investigated by ultraviolet-visible (UV-vis) absorption, fluorescence, circular dichroism (CD), and Fourier transform infrared (FT-IR) spectroscopy merging with multivariate curve resolution-alternating least-squares (MCR-ALS) chemometrics approach. The MCR-ALS was applied to resolve the combined spectroscopic data matrix, which was obtained by UV-vis and fluorescence methods. The concentration profiles of PE, ctDNA, and PE-ctDNA complex and their pure spectra were then successfully obtained. The PE molecular was found to be able to intercalate into the base pairs of ctDNA as evidenced by decreases in resonance light-scattering signal and iodide-quenching effect and increase in ctDNA viscosity. The results of FT-IR spectra indicated that PE was prone to bind to G-C base pairs of ctDNA, and the molecular docking studies were used to validate and clarify the specific binding. The observed changes in CD signals revealed that the DNA turned into a more highly wound form of B-conformation. The calculated thermodynamic parameters, enthalpy change (ΔH°) and entropy change (ΔS°), suggested that hydrogen bonds and van der Waals forces played a predominant role in the binding of PE to ctDNA.
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Affiliation(s)
- Yue Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University , No. 235, Nanjing East Road, Nanchang 330047, Jiangxi, China
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126
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O'Sullivan EC, Miller CM, Deane FM, McCarthy FO. Emerging Targets in the Bioactivity of Ellipticines and Derivatives. STUDIES IN NATURAL PRODUCTS CHEMISTRY 2013. [DOI: 10.1016/b978-0-444-62615-8.00006-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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127
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Huang JP, Mojib N, Goli RR, Watkins S, Waites KB, Ravindra R, Andersen DT, Bej AK. Antimicrobial activity of PVP from an Antarctic bacterium, Janthinobacterium sp. Ant5-2, on multi-drug and methicillin resistant Staphylococcus aureus. NATURAL PRODUCTS AND BIOPROSPECTING 2012; 2. [PMCID: PMC4131597 DOI: 10.1007/s13659-012-0021-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Multiple drug resistant (MDR) and methicillin-resistant Staphylococcus aureus (MRSA) have become increasingly prevalent as a community acquired infection. As a result limited treatment options are available with conventional synthetic antibiotics. Bioprospecting natural products with potent antimicrobial activity show promise for developing new drugs against this pathogen. In this study, we have investigated the antimicrobial activity of a purple violet pigment (PVP) from an Antarctic bacterium, Janthinobacterium sp. Ant5-2 on 15 clinical MDR and MRSA strains. The colorimetric resazurin assay was employed to determine the minimum inhibitory concentration (MIC90) of PVP against MDR and MRSA. The MIC90 ranged between 1.57 µg/mL and 3.13 µg/mL, which are significantly lower than many antimicrobials tested from natural sources against this pathogen. The spectrophotometrically determined growth analysis and total microscopic counts using Live/dead® BacLight™ fluorescent stain exhibited a steady decrease in viability of both MDR and MRSA cultures following treatment with PVP at the MIC levels. In silico predictive molecular docking study revealed that PVP could be a DNA-targeting minor groove binding antimicrobial compound. The continued development of novel antimicrobials derived from natural sources with the combination of a suite of conventional antibiotics could stem the rising pandemic of MDR and MRSA along with other deadly microbial pathogens. ![]()
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Affiliation(s)
- Jonathan P. Huang
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294-1170 USA
| | - Nazia Mojib
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294-1170 USA
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900 Saudi Arabia
| | - Rakesh R. Goli
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294-1170 USA
| | - Samantha Watkins
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294-1170 USA
| | - Ken B. Waites
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294-1170 USA
| | - Rasik Ravindra
- Head Land Sada, National Centre for Antarctic & Ocean Research, Vasco-da-Gama Goa, 403804 India
| | - Dale T. Andersen
- Carl Sagan Center for the Study of Life in the Universe, SETI Institute, Mountain View, CA 94043 USA
| | - Asim K. Bej
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL 35294-1170 USA
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128
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Riccardi Sirtori F, Aldini G, Colombo M, Colombo N, Malyszko J, Vistoli G, D'Alessio R. Molecular Recognition of T:G Mismatched Base Pairs in DNA as Studied by Electrospray Ionization Mass Spectrometry. ChemMedChem 2012; 7:1112-22. [DOI: 10.1002/cmdc.201100526] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 03/09/2012] [Indexed: 01/04/2023]
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129
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Kumar KS, Selvaraju C, Malar EJP, Natarajan P. Existence of a new emitting singlet state of proflavine: femtosecond dynamics of the excited state processes and quantum chemical studies in different solvents. J Phys Chem A 2011; 116:37-45. [PMID: 22145576 DOI: 10.1021/jp207495r] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proflavine (3,6-diaminoacridine) shows fluorescence emission with lifetime, 4.6 ± 0.2 ns, in all the solvents irrespective of the solvent polarity. To understand this unusual photophysical property, investigations were carried out using steady state and time-resolved fluorescence spectroscopy in the pico- and femtosecond time domain. Molecular geometries in the ground and low-lying excited states of proflavine were examined by complete structural optimization using ab initio quantum chemical computations at HF/6-311++G** and CIS/6-311++G** levels. Time dependent density functional theory (TDDFT) calculations were performed to study the excitation energies in the low-lying excited states. The steady state absorption and emission spectral details of proflavine are found to be influenced by solvents. The femtosecond fluorescence decay of the proflavine in all the solvents follows triexponential function with two ultrafast decay components (τ(1) and τ(2)) in addition to the nanosecond component. The ultrafast decay component, τ(1), is attributed to the solvation dynamics of the particular solvent used. The second ultrafast decay component, τ(2), is found to vary from 50 to 215 ps depending upon the solvent. The amplitudes of the ultrafast decay components vary with the wavelength and show time dependent spectral shift in the emission maximum. The observation is interpreted that the time dependent spectral shift is not only due to solvation dynamics but also due to the existence of more than one emitting state of proflavine in the solvent used. Time resolved area normalized emission spectral (TRANES) analysis shows an isoemissive point, indicating the presence of two emitting states in homogeneous solution. Detailed femtosecond fluorescence decay analysis allows us to isolate the two independent emitting components of the close lying singlet states. The CIS and TDDFT calculations also support the existence of the close lying emitting states. The near constant lifetime observed for proflavine in different solvents is suggested to be due to the similar dipole moments of the ground and the evolved emitting singlet state of the dye from the Franck-Condon excited state.
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Affiliation(s)
- Karuppannan Senthil Kumar
- National Centre for Ultrafast Processes, Taramani Campus, University of Madras, Chennai 600 113, India
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130
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Li F, Li X, Liu X, Zhang L, You L, Zhao J, Wu H. Noncovalent interactions between hydroxylated polycyclic aromatic hydrocarbon and DNA: molecular docking and QSAR study. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2011; 32:373-81. [PMID: 22004956 DOI: 10.1016/j.etap.2011.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 07/21/2011] [Accepted: 08/02/2011] [Indexed: 05/08/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) can be hydroxylated by CYP450-oxidases (1A1 and 1B1 mainly) and may cause DNA damage and cancer. However, the mechanism of such interactions has not been fully understood. In this study, an integrated molecular docking and QSAR approach was employed to further investigate the binding interactions between hydroxylated PAHs (HO-PAHs) and calf thymus DNA (CT-DNA). Molecular docking, hydrogen-bonding, hydrophobic and π-π interactions were observed to be characteristic interactions between HO-PAHs and DNA. An optimum QSAR model with good robustness and predictability was developed based on the molecular structural parameters calculated by the density function theory and partial least squares. Additionally, the developed QSAR model indicated that the molecular size, polarizability and electrostatic potential of HO-PAHs were related to the binding affinities to DNA.
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Affiliation(s)
- Fei Li
- Key Laboratory of Coastal Zone Environment Processes, CAS, Shandong Provincial Key Laboratory of Coastal Zone Environment Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
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131
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Yamuna E, Zeller M, Rajendra Prasad KJ. Syntheses of indolo[3,2,1-d,e]phenanthridines and isochromeno[3,4-a] carbazoles: palladium catalyzed intramolecular arylation via C–H functionalization. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.09.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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132
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Guo Y, Yue Q, Gao B. Molecular docking study investigating the possible mode of binding of C.I. Acid Red 73 with DNA. Int J Biol Macromol 2011; 49:55-61. [DOI: 10.1016/j.ijbiomac.2011.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 03/10/2011] [Accepted: 03/18/2011] [Indexed: 10/18/2022]
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133
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Zhai Q, Xu L, Ge Y, Tian T, Wu W, Yan S, Zhou Y, Deng M, Liu Y, Zhou X. Site-Specific Recognition of Guanosine by Manganese(III) Corroles in DNA Non-Duplex Regions through Active Oxygen Transfer. Chemistry 2011; 17:8890-5. [DOI: 10.1002/chem.201101128] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Indexed: 01/17/2023]
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134
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Dubois MA, Grandbois A, Collins SK, Schmitzer AR. Introduction of axial chirality in a planar aromatic ligand results in chiral recognition with DNA. J Mol Recognit 2011; 24:288-94. [DOI: 10.1002/jmr.1055] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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135
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Jones JE, Amoroso AJ, Dorin IM, Parigi G, Ward BD, Buurma NJ, Pope SJA. Bimodal, dimetallic lanthanide complexes that bind to DNA: the nature of binding and its influence on water relaxivity. Chem Commun (Camb) 2011; 47:3374-6. [DOI: 10.1039/c1cc00111f] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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136
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Sreenivas DK, Nagarajan R. Palladium-mediated intramolecular O-arylation: a simple route for the synthesis of quino[2,3-c] and quino[3,2-b]carbazoles. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.10.073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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137
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Yuriev E, Agostino M, Ramsland PA. Challenges and advances in computational docking: 2009 in review. J Mol Recognit 2010; 24:149-64. [DOI: 10.1002/jmr.1077] [Citation(s) in RCA: 223] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 07/20/2010] [Accepted: 07/21/2010] [Indexed: 12/12/2022]
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