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Articles

Molecular modeling and spectroscopic studies of semustine binding with DNA and its comparison with lomustine–DNA adduct formation

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Pages 1653-1668 | Received 12 Jul 2014, Accepted 21 Sep 2014, Published online: 28 Oct 2014

References

  • Agarwal, S., Jangir, D. K., & Mehrotra, R. (2013). Spectroscopic studies of the effects of anticancer drug mitoxantrone interaction with calf-thymus DNA. Journal of Photochemistry and Photobiology B: Biology, 120, 177–182.10.1016/j.jphotobiol.2012.11.001
  • Agarwal, S., Jangir, D. K., Mehrotra, R., Lohani, N., & Rajeswari, M. (2014). A structural insight into major groove directed binding of nitrosourea derivative nimustine with DNA: A spectroscopic study. PLoS ONE, 9, e104115.10.1371/journal.pone.0104115
  • Agarwal, S., Jangir, D. K., Singh, P., & Mehrotra, R. (2014). Spectroscopic analysis of the interaction of lomustine with calf thymus DNA. Journal of Photochemistry and Photobiology B: Biology, 130, 281–286.10.1016/j.jphotobiol.2013.11.017
  • Ahmad, R., Arakawa, H., & Tajmir-Riahi, H. (2003). A comparative study of DNA complexation with Mg(II) and Ca(II) in aqueous solution: Major and minor grooves bindings. Biophysical Journal, 84, 2460–2466.10.1016/S0006-3495(03)75050-4
  • Aksel, T., Majumdar, A., & Barrick, D. (2011). The contribution of entropy, enthalpy, and hydrophobic desolvation to cooperativity in repeat-protein folding. Structure, 19, 349–360.10.1016/j.str.2010.12.018
  • Alex, S., & Dupuis, P. (1989). FT-IR and Raman investigation of cadmium binding by DNA. Inorganica Chimica Acta, 157, 271–281.10.1016/S0020-1693(00)80552-6
  • Bai, B.-Q., Zhao, L.-J., & Zhong, R.-G. (2010). Analysis of deoxyribonucleic acid interstrand cross-links induced by nitrosourea with high performance liquid chromatographyelectrospray ionization tandem mass spectrometry. Chinese Journal of Analytical Chemistry, 4, 532–536.
  • Bai, B., Zhao, L., & Zhong, R. (2011). Quantification of meCCNU-induced dG-dC crosslinks in oligonucleotide duplexes by liquid chromatography/electrospray ionization tandem mass spectrometry. Rapid Communications in Mass Spectrometry, 25, 2027–2034.10.1002/rcm.5064
  • Banerjee, S., Bright, S. A., Smith, J. A., Burgeat, J., Martínez-Calvo, M., Williams, D. C., Kelly, J. M., & Gunnlaugsson, T. (2014). A supramolecular approach to enantioselective DNA recognition using enantiomerically resolved cationic 4-Amino-1, 8-naphthalimide based Tröger’s bases. The Journal of Organic Chemistry, 79, 9272–9283.
  • Banyay, M., Sarkar, M., & Gräslund, A. (2003). A library of IR bands of nucleic acids in solution. Biophysical Chemistry, 104, 477–488.10.1016/S0301-4622(03)00035-8
  • Berman, H. M. & Schneider, B. (1999). Nucleic acid hydration. Handbook of nucleic acid structure. S. Neidle, ed. London: Oxford University.
  • Boice, J. D., Jr, Greene, M. H., Killen, J. Y., Jr, Ellenberg, S. S., Keehn, R. J., McFadden, E., … Fraumeni, J. F., Jr (1983). Leukemia and preleukemia after adjuvant treatment of gastrointestinal cancer with semustine (Methyl-CCNU). New England Journal of Medicine, 309, 1079–1084.10.1056/NEJM198311033091802
  • Bokma, J. T., Curtis, W. J., & Blok, J. (1987). CD of the li-salt of DNA in ethanol/water mixtures: Evidence for the B-to C-form transition in solution. Biopolymers, 26, 893–909.10.1002/(ISSN)1097-0282
  • Brahms, S., Brahms, J., & Van Holde, K. (1976). Nature of conformational changes in poly[d(A-T)-d(A-T)] in the premelting region. Proceedings of the National Academy of Sciences, 73, 3453–3457.10.1073/pnas.73.10.3453
  • Brahms, J., Pilet, J., Lan, T.-T. P., & Hill, L. (1973). Direct evidence of the C-like form of sodium deoxyribonucleate. Proceedings of the National Academy of Sciences, 70, 3352–3355.10.1073/pnas.70.12.3352
  • Braun, C. S., Jas, G. S., Choosakoonkriang, S., Koe, G. S., Smith, J. G., & Middaugh, C. R. (2003). The structure of DNA within cationic lipid/DNA complexes. Biophysical Journal, 84, 1114–1123.10.1016/S0006-3495(03)74927-3
  • Chaires, J. B. (1998). Drug – DNA interactions. Current Opinion in Structural Biology, 8, 314–320.10.1016/S0959-440X(98)80064-X
  • Chan, A., Kilkuskie, R., & Hanlon, S. (1979). Correlations between the duplex winding angle and the circular dichroism spectrum of calf thymus DNA. Biochemistry, 18, 84–91.10.1021/bi00568a013
  • Connors, K. (1991). Binding constants: The measurement of molecular complex stability 1987 (Chap 4, pp. 141–188). Ann Arbor, MI: University of Michigan.
  • Degtyareva, N. N., Wallace, B. D., Bryant, A. R., Loo, K. M., & Petty, J. T. (2007). Hydration changes accompanying the binding of Minor groove ligands with DNA. Biophysical Journal, 92, 959–965.10.1529/biophysj.106.097451
  • Glasel, J. (1995). Validity of nucleic acid purities monitored by 260 nm/280 nm absorbance ratios. BioTechniques, 18, 62–63.
  • Gombar, C. T., Tong, W. P., & Ludlum, D. B. (1980). Mechanism of action of the nitrosoureas—IV. Biochemical Pharmacology, 29, 2639–2643.10.1016/0006-2952(80)90079-9
  • González-Ruiz, V., Olives, A. I., Martín, M. A., Ribelles, P., Ramos, M. T., & Menéndez, J. C. (2011). An overview of analytical techniques employed to evidence drug-DNA interactions. Applications to the design of genosensors. Biomedical Engineering, Trends, Research and Technologies (Chap. 3, pp. 65–90). Rijeka: InTech.
  • Goodsell, D. S., Morris, G. M., & Olson, A. J. (1996). Automated docking of flexible ligands: Applications of autodock. Journal of Molecular Recognition, 9, 1–5.10.1002/(ISSN)1099-1352
  • Haq, I., & Ladbury, J. (2000). Drug–DNA recognition: energetics and implications for design. Journal of Molecular Recognition, 13, 188–197.10.1002/(ISSN)1099-1352
  • Hayes, M. T., Bartley, J., Parsons, P. G., Eaglesham, G. K., & Prakash, A. S. (1997). Mechanism of Action of Fotemustine, a New Chloroethylnitrosourea Anticancer Agent: Evidence for the Formation of Two DNA-Reactive Intermediates Contributing to Cytotoxicity. Biochemistry, 36, 10646–10654.10.1021/bi970791q
  • Huang, C. C., Couch, G. S., Pettersen, E. F., & Ferrin, T. E. (1996). Chimera: An extensible molecular modeling application constructed using standard components. Pacific Symposium on Biocomputing, San Francisco, 1, 1519–1523.
  • Huang, S.-Y., & Zou, X. (2010). Inclusion of solvation and entropy in the knowledge-based scoring function for protein−ligand interactions. Journal of Chemical Information and Modeling, 50, 262–273.10.1021/ci9002987
  • Huey, R., & Morris, G. M. (2008). Using AutoDock 4 with AutoDockTools: A Tutorial (pp. 54–56). La Jolla, CA: The Scripps Research Institute.
  • Irwin, J. J., Sterling, T., Mysinger, M. M., Bolstad, E. S., & Coleman, R. G. (2012). ZINC: A free tool to discover chemistry for biology. Journal of Chemical Information and Modeling, 52, 1757–1768.10.1021/ci3001277
  • Jangir, D. K., Charak, S., Mehrotra, R., & Kundu, S. (2011). FTIR and circular dichroism spectroscopic study of interaction of 5-fluorouracil with DNA. Journal of Photochemistry and Photobiology B: Biology, 105, 143–148.10.1016/j.jphotobiol.2011.08.003
  • Jangir, D. K., Kundu, S., & Mehrotra, R. (2013). Role of minor groove width and hydration pattern on amsacrine interaction with DNA. PLoS ONE, 8, e69933.10.1371/journal.pone.0069933
  • Johnson, W. (1994). CD of nucleic acids. Circular Dichroism: Principles and Applications (pp. 523–540). New York: Wiley & Sons.
  • Kankia, B. I., Barany, G., & Musier-Forsyth, K. (2005). Unfolding of DNA quadruplexes induced by HIV-1 nucleocapsid protein. Nucleic Acids Research, 33, 4395–4403.10.1093/nar/gki741
  • Kennard, O. (1993). DNA-drug interactions. Pure and Applied Chemistry, 65, 1213–1222.
  • Kypr, J., Kejnovská, I., Renčiuk, D., & Vorlíčková, M. (2009). Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Research, 37, 1713–1725.10.1093/nar/gkp026
  • Lenglet, G., & David-Cordonnier, M.-H. (2010). DNA-destabilizing agents as an alternative approach for targeting DNA: Mechanisms of action and cellular consequences. Journal of Nucleic Acids, 2010, 1–17.
  • Li, Z. (2012). The kinetics and mechanisms of some fundamental organic reactions of nitro compounds. All Graduate Theses and Dissertations: Paper 1407. Utah State University Libraries, Logan, UT.
  • Loprete, D., & Hartman, K. (1993). Conditions for the stability of the B, C, and Z structural forms of poly(dG-dC) in the presence of lithium, potassium, magnesium, calcium, and zinc cations. Biochemistry, 32, 4077–4082.10.1021/bi00066a032
  • Mayer, R. G., & Drago, R. S. (1976). Interpretation of isosbestic points. Inorganic Chemistry, 15, 2010–2011.10.1021/ic50162a064
  • McCann, J. J., Lo, T. M., & Webster, D. (1971). Cross-linking of DNA by alkylating agents and effects on DNA function in the chick embryo. Cancer Research, 31, 1573–1579.
  • McCormick, J. E., & Stanley McElhinney, R. (1990). Nitrosoureas from chemist to physician: Classification and recent approaches to drug design. European Journal of Cancer and Clinical Oncology, 26, 207–221.10.1016/0277-5379(90)90214-E
  • Mehrotra, R., Jangir, D., Agarwal, S., Ray, B., Singh, P., & Srivastava, A. K. (2013). Interaction studies of anticancer drug lomustine with calf thymus DNA using surface enhanced Raman spectroscopy. MAPAN, 28, 273–277.10.1007/s12647-013-0086-5
  • Miyagami, M., Tsubokawa, T., Tazoe, M., & Kagawa, Y. (1990). Intra-arterial ACNU chemotherapy employing 20% mannitol osmotic blood-brain barrier disruption for malignant brain tumors. Neurologia Medico-Chirurgica, 30, 582–590.10.2176/nmc.30.582
  • Miyahara, T., Nakatsuji, H., & Sugiyama, H. (2012). Helical structure and circular dichroism spectra of DNA: A theoretical study. The Journal of Physical Chemistry A, 117, 42–55.
  • Morris, G., Goodsell, D., Halliday, R., Huey, R., Hart, W., Belew, R., & Olson, A. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19, 1639–1662.10.1002/(ISSN)1096-987X
  • Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., & Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19, 1639–1662.10.1002/(ISSN)1096-987X
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30, 2785–2791.10.1002/jcc.v30:16
  • Naghipur, A., Ikonomou, M. G., Kebarle, P., & Lown, J. W. (1990). Mechanism of action of (2-haloethyl)nitrosoureas on DNA: discrimination between alternative pathways of DNA base modification by 1,3-bis(2-fluoroethyl)-1-nitrosourea by using specific deuterium labeling and identification of reaction products by HPLC/tandem mass spectrometry. Journal of the American Chemical Society, 112, 3178–3187.10.1021/ja00164a046
  • Nandy, A., & Basak, S. C. (2010). New approaches to drug–DNA interactions based on graphical representation and numerical characterization of DNA sequences. Current Computer-Aided Drug Design, 6, 283–289.10.2174/1573409911006040283
  • Neidle, S., Rayner, E. L., Simpson, I. J., Smith, N. J., Mann, J., Baron, A., … Kelland, L. R. (1999). Symmetric bis-benzimidazoles: new sequence-selective DNA-binding molecules. Chemical Communications, 10, 929–930.10.1039/a901074b
  • O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of cheminformatics, 3, 1–14.
  • Patil, S. D., & Rhodes, D. G. (2000). Conformation of oligodeoxynucleotides associated with anionic liposomes. Nucleic Acids Research, 28, 4125–4129.10.1093/nar/28.21.4125
  • Pohle, W., Selle, C., Gauger, D. R., Zantl, R., Artzner, F., & Rädler, J. O. (2000). FTIR spectroscopic characterization of a cationic lipid–DNA complex and its components. Physical Chemistry Chemical Physics, 2, 4642–4650.10.1039/b003898i
  • Portugal, J., & Subirana, J. (1985). Counterions which favour the C form of DNA. The EMBO journal, 4, 2403–2408.
  • Puyo, S., Montaudon, D., & Pourquier, P. (2013). From old alkylating agents to new minor groove binders. Critical Reviews in Oncology/Hematology, 89, 43–61.
  • Rueda, L., Banerjee, S., Aziz, M. M., & Raza, M. (2010). Protein–protein interaction prediction using desolvation energies and interface properties. IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 17, 18–21.
  • Sanner, M. F. (1999). Python: A programming language for software integration and development. Journal of Molecular Graphics and Modelling, 17, 57–61.
  • Schabel, F., Jr (1976). Nitrosoureas: A review of experimental antitumor activity. Cancer Treatment Reports, 60, 665–698.
  • Schallreuter, K. U., Gleason, F. K., & Wood, J. M. (1990). The mechanism of action of the nitrosourea anti-tumor drugs on thioredoxin reductase, glutathione reductase and ribonucleotide reductase. Biochimica et Biophysica Acta (BBA)-Molecular Cell Research, 1054, 14–20.
  • Snyder, R. D., Holt, P. A., Maguire, J. M., & Trent, J. O. (2013). Prediction of noncovalent Drug/DNA interaction using computational docking models: Studies with over 1350 launched drugs. Environmental and Molecular Mutagenesis, 54, 668–681.10.1002/em.v54.8
  • Strange, P. G. (1996). The energetics of ligand binding at catecholamine receptors. Trends in Pharmacological Sciences, 17, 238–244.10.1016/0165-6147(96)10025-0
  • Tang, W., Zhao, L.-J., & Zhong, R.-G. (2008). Agarose gel electrophoresis and fluorometric assays for the determination of DNA cross-linking induced by semustine. The 2nd IEEE International Conference on Bioinformatics and Biomedical Engineering (ICBBE), 322, 16–18.
  • Tong, W. P., Kirk, M. C., & Ludlum, D. B. (1983). Mechanism of action of the nitrosoureas – V: Formation of O6-(2-fluoroethyl) guanine and its probable role in the crosslinking of deoxyribonucleic acid. Biochemical Pharmacology, 32, 2011–2015.10.1016/0006-2952(83)90420-3
  • Tyagi, G., Charak, S., & Mehrotra, R. (2012). Binding of an indole alkaloid, vinblastine to double stranded DNA: A spectroscopic insight in to nature and strength of interaction. Journal of Photochemistry and Photobiology B: Biology, 108, 48–52.10.1016/j.jphotobiol.2011.12.009
  • Tyagi, G., Jangir, D. K., Singh, P., & Mehrotra, R. (2010). DNA Interaction Studies of an anticancer plant alkaloid, vincristine, using Fourier transform infrared spectroscopy. DNA and Cell Biology, 29, 693–699.10.1089/dna.2010.1035
  • Vijayalakshmi, R., Kanthimathi, M., Subramanian, V., & Nair, B. U. (2000). DNA Cleavage by a Chromium(III) Complex. Biochemical and Biophysical Research Communications, 271, 731–734.10.1006/bbrc.2000.2707
  • Woods, K. K., Lan, T., McLaughlin, L. W., & Williams, L. D. (2003). The role of minor groove functional groups in DNA hydration. Nucleic Acids Research, 31, 1536–1540.10.1093/nar/gkg240
  • Zhang, Z., Huang, W., Tang, J., Wang, E., & Dong, S. (2002). Conformational transition of DNA induced by cationic lipid vesicle in acidic solution: spectroscopy investigation. Biophysical Chemistry, 97, 7–16.10.1016/S0301-4622(02)00006-6
  • Zhao, L., Li, L., Xu, J., & Zhong, R. (2014). Comparative investigation of the DNA inter-strand crosslinks induced by ACNU, BCNU, CCNU and FTMS using high-performance liquid chromatography–electrospray ionization tandem mass spectrometry. International Journal of Mass Spectrometry, 368, 30–36.10.1016/j.ijms.2014.04.018
  • Zhao, L.-J., Ren, T., Bai, B.-Q., Zhang, R., & Zhong, R.-G. (2011). Comparative investigations of deoxyribonucleic acid interstrand crosslinks induced by semustine using fluorescence and high performance liquid chromatography–mass spectrometry. Chinese Journal of Analytical Chemistry, 4, 476–480.
  • Zhao, L., Zhong, R., & Zhen, Y. (2007). An ONIOM study on the crosslinked base pairs in DNA reacted with chloroethylnitrosoureas. Journal of Theoretical & Computational Chemistry, 6, 631–639.
  • Zheng, K., Liu, F., Xu, X.-M., Li, Y.-T., Wu, Z.-Y., & Yan, C.-W. (2014). Synthesis, structure and molecular docking studies of dicopper (ii) complexes bridged by N-phenolato-N′-[2-(dimethylamino) ethyl] oxamide: The influence of terminal ligands on cytotoxicity and reactivity towards DNA and protein BSA. New Journal of Chemistry, 38, 2964–2978.

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