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Research Article

Docking, steered molecular dynamics, and QSAR studies as strategies for studying isoflavonoids as 5-, 12-, and 15-lipoxygenase inhibitors

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Pages 1511-1519 | Received 07 Dec 2017, Accepted 23 Mar 2018, Published online: 04 May 2018

References

  • Andreou, A., & Feussner, I. (2009). Lipoxygenases – structure and reaction mechanism. Phytochemistry, 70, 1504–1510. doi:10.1016/j.phytochem.2009.05.008
  • Bartocci, E., & Lió, P. (2016). Computational modeling, formal analysis, and tools for systems biology. PLoS Computational Biology, 12(1), 1–22. doi:10.1371/journal.pcbi.1004591
  • Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81, 3684–3690. doi:10.1063/1.448118
  • Berger, W., De Chandt, M. T. M., & Cairns, C. B. (2007). Zileuton: Clinical implications of 5-lipoxygenase inhibition in severe airway disease. International Journal of Clinical Practice, 61, 663–676. doi:10.1111/j.1742-1241.2007.01320.x
  • Butina, D. (2004). Performance of Kier-Hall E-state descriptors in quantitative structure activity relationship (QSAR) studies of multifunctional molecules. Molecules, 9, 1004–1009. doi:10.3390/91201004
  • Chen, B., Zhang, T., Bond, T., & Gan, Y. (2015). Development of quantitative structure activity relationship (QSAR) model for disinfection byproduct (DBP) research: A review of methods and resources. Journal of Hazardous Materials, 299, 260–279. doi:10.1016/j.jhazmat.2015.06.054
  • Choi, J., Chon, Jae K., Kim, S., & Shin, W. (2008). Conformational flexibility in mammalian 15S-lipoxygenase: Reinterpretation of the crystallographic data. Proteins, 70, 1023–1032. doi:10.1111/j.1600-0625.2009.00894.x
  • Cruciani, G., Crivori, P., Carrupt, P. A., & Testa, B. (2000). Molecular fields in quantitative structure–permeation relationships: The VolSurf approach. Journal of Molecular Structure: THEOCHEM, 503, 17–30. doi:10.1016/S0166-1280(99)00360-7
  • Ferreira, L., dos Santos, R., Oliva, G., & Andricopulo, A. (2015). Molecular docking and structure-based drug design strategies. Molecules, 20, 13384–13421. doi:10.3390/molecules200713384
  • Gelpi, J., Hospital, A., Goñi, R., & Orozco, M. (2015). Molecular dynamics simulations: Advances and applications. Advances and Applications in Bioinformatics and Chemistry, 10, 37–47. doi:10.2147/AABC.S70333
  • Gilbert, N. C., Bartlett, S. G., Waight, M. T., Neau, D. B., Boeglin, W. E., Brash, A. R., & Newcomer, M. E. (2011). The structure of human 5-lipoxygenase. Science, 331, 217–219. doi:10.1126/science.1197203
  • Hirano, T. (1993, January). MOPAC manual (7th ed.). MOPAC Manual.
  • Hofmann, B., & Steinhilber, D. (2013). 5-lipoxygenase inhibitors: A review of recent patents (2010–2012). Expert opinion on therapeutic patents, 23, 895–909. doi:10.1517/13543776.2013.791678
  • Ivanov, I., Heydeck, D., Hofheinz, K., Roffeis, J., O’Donnell, V. B., Kuhn, H., & Walther, M. (2010). Molecular enzymology of lipoxygenases. Archives of Biochemistry and Biophysics, 503, 161–174. doi:10.1016/j.abb.2010.08.016
  • Izrailev, S., Stepaniants, S., Isralewitz, B., Kosztin, D., Lu, H., Molnar, F., & Schulten, K. (1999). Steered molecular dynamics. Computational molecular dynamics: Challenges, methods, ideas SE-2, 4, 39–65. doi:10.1007/978-3-642-58360-5_2
  • Kuhn, H., Banthiya, S., & van Leyen, K. (2015). Mammalian lipoxygenases and their biological relevance. Biochimica et Biophysica Acta (BBA) – Molecular and Cell Biology of Lipids, 1851, 308–330. doi:10.1016/j.bbalip.2014.10.002
  • Mascayano, C., Espinosa, V., Sepúlveda-Boza, S., Hoobler, E. K., Perry, S., Diaz, G., & Holman, T. R. (2014). Enzymatic studies of isoflavonoids as selective and potent inhibitors of human leukocyte 5-lipo-oxygenase. Chemical Biology & Drug Design, 1, n/a–n/a. doi:10.1111/cbdd.12469
  • Mascayano, C., Espinosa, V., Sepúlveda-Boza, S., Hoobler, E. K., & Perry, S. (2013). In vitro study of isoflavones and isoflavans as potent inhibitors of human 12- and 15-lipoxygenases. Chemical Biology and Drug Design, 82, 317–325. doi:10.1111/cbdd.12157
  • Meirer, K., Steinhilber, D., & Proschak, E. (2014). Inhibitors of the arachidonic acid cascade: Interfering with multiple pathways. Basic and Clinical Pharmacology and Toxicology, 114, 83–91. doi:10.1111/bcpt.12134
  • Miura, M. (2015). Therapeutic drug monitoring of imatinib, nilotinib, and dasatinib for patients with chronic myeloid leukemia. Biological & Pharmaceutical Bulletin, 38, 645–654. doi:10.1248/bpb.b15-00103
  • Moin, S. T., Hofer, T. S., Sattar, R., & Ul-Haq, Z. (2011). Molecular dynamics simulation of mammalian 15S-lipoxygenase with AMBER force field. European Biophysics Journal, 40, 715–726. doi:10.1007/s00249-011-0684-5
  • 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. doi:10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B
  • Nategholeslam, M., Gray, C. G., & Tomberli, B. (2014). Implementation of the forward−reverse method for calculating the potential of mean force using a dynamic restraining protocol. Journal of Physical Chemistry B, 118, 14203–14214.
  • Oliva, R., Chermak, E., & Cavallo, L. (2015). Analysis and ranking of protein–protein docking models using inter-residue contacts and inter-molecular contact maps. Molecules, 20, 12045–12060. doi:10.3390/molecules200712045
  • Park, S., & Schulten, K. (2004). Calculating potentials of mean force from steered molecular dynamics simulations. The Journal of Chemical Physics, 120, 5946–5961. doi:10.1063/1.1651473
  • Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., … Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26, 1781–1802. doi:10.1002/jcc.20289
  • Pontiki, E., & Hadjipavlou-Litina, D. (2008). Lipoxygenase inhibitors: A comparative QSAR study review and evaluation of new QSARs. Medicinal Research Reviews, 28, 39–117. doi:10.1002/med.20099
  • Prigge, S. T., Boyington, J. C., Faig, M., Doctor, K. S., & Gaffney, B. J. (1997). Structure and mechanism of lipoxygenases. Biochimie, 79, 629–636. doi:10.1016/S0300-9084(97)83495-5
  • Schröder, M., Häfner, A. K., Hofmann, B., Rådmark, O., Tumulka, F., Abele, R., … Dötsch, Volker (2014). Stabilisation and characterisation of the isolated regulatory domain of human 5-lipoxygenase. Biochimica et Biophysica Acta (BBA) – Molecular and Cell Biology of Lipids, 1841, 1538–1547. doi:10.1016/j.bbalip.2014.07.022
  • Sousa da Silva, A. W., & Vranken, W. F. (2012). ACPYPE – AnteChamber PYthon Parser interfacE. BMC Research Notes, 5, 367. doi:10.1186/1756-0500-5-367
  • Uciechowska, U., Schemies, J., Scharfe, M., Lawson, M., Wichapong, K., Jung, M., & Sippl, W. (2012). Binding free energy calculations and biological testing of novel thiobarbiturates as inhibitors of the human NAD+ dependent histone deacetylase Sirt2. MedChemComm, 3, 167. doi:10.1039/c1md00214g
  • Vilar, S., Cozza, G., & Moro, S. (2008). Medicinal Chemistry and the molecular operating environment (MOE): Application of QSAR and molecular docking to drug discovery. Current Topics in Medicinal Chemistry, 8, 1555–1572. doi:10.2174/156802608786786624
  • Wermuth, C. G., Ganellin, C. R., Lindberg, P., & Mitscher, L. (1998). Glossary of terms used in medicinal chemistry (IUPAC Recommendations 1998). Pure and Applied Chemistry, 70, 1129–1143. doi:10.1351/pac197951081725
  • Werz, O. (2007). Inhibition of 5-lipoxygenase product synthesis by natural compounds of plant origin. Planta Medica, 73, 1331–1357. doi:10.1055/s-2007-990242
  • Xu, S., Mueser, T. C., Marnett, L. J., & Funk, M. O. (2012). Crystal structure of 12-lipoxygenase catalytic-domain-inhibitor complex identifies a substrate-binding channel for catalysis. Structure, 20, 1490–1497. doi:10.1016/j.str.2012.06.003

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