Identification of human tau-tubulin kinase 1 inhibitors: an integrated e-pharmacophore-based virtual screening and molecular dynamics simulation

References

• Alder, B. J., & Wainwright, T. E. (1959). Studies in molecular dynamics. I. General method. Journal of Chemical Physics, 31(2), 459–466. doi:10.1063/1.1730376
   Web of Science ®Google Scholar
• Anantram, A., Kundaikar, H., Degani, M., & Prabhu, A. (2018). Molecular dynamics simulations on an inhibitor of anti-apoptotic Bcl-2 proteins for insights into its interaction mechanism for anti-cancer activity. Journal of Biomolecular Structure and Dynamics, 1–13. doi:10.1080/07391102.2018.1508371
   PubMedGoogle Scholar
• Asai, H., Ikezu, S., Woodbury, M. E., Yonemoto, G. M., Cui, L., & Ikezu, T. (2014). Accelerated neurodegeneration and neuroinflammation in transgenic mice expressing P301L tau mutant and tau-tubulin kinase 1. American Journal of Pathology, 184(3), 808–818.
   PubMed Web of Science ®Google Scholar
• Ayoub, A. T., Craddock, T. J., Klobukowski, M., & Tuszynski, J. (2014). Analysis of the strength of interfacial hydrogen bonds between tubulin dimers using quantum theory of atoms in molecules. Biophysical Journal, 107(3), 740–750. doi:10.1016/j.bpj.2014.05.047
   PubMed Web of Science ®Google Scholar
• Baell, J. B., & Holloway, G. A. (2010). New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. Journal of Medicinal Chemistry, 53(7), 2719–2740. doi:10.1021/jm901137j
   PubMed Web of Science ®Google Scholar
• Barcellos, M. P., Santos, C. B. R., Federico, L. B., Almeida, P. F. D., da Silva, C. H. T. D P., & Taft, C. A. (2018). Pharmacophore and structure-based drug design, molecular dynamics and admet/tox studies to design novel potential pad4 inhibitors. Journal of Biomolecular Structure and Dynamics, 1–16. doi:10.1080/07391102.2018.1444511
   Google Scholar
• Berthold, M. R., Cebron, N., Dill, F., Gabriel, T. R., Kötter, T., Meinl, T., … Wiswedel, B. (2007). KNIME: The Konstanz Information Miner Studies in Classification. In Data Analysis, and Knowledge Organisation (GfKL 2007) (pp. 319–326). Berlin, Heidelberg: Springer.
   Google Scholar
• Clark, D. E. (2003). In silico prediction of blood-brain barrier permeation. Drug Discovery Today, 8(20), 927–933.
   PubMed Web of Science ®Google Scholar
• Dixon, S. L., Smondyrev, A. M., Knoll, E. H., Rao, S. N., Shaw, D. E., & Friesner, R. A. (2006). PHASE: A new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. Journal of Computer-Aided Molecular Design, 20(10-11), 647–671. doi:10.1007/s10822-006-9087-6
   PubMed Web of Science ®Google Scholar
• Duffy, E. M., & Jorgensen, W. L. (2000). Prediction of properties from simulations: Free energies of solvation in hexadecane, octanol, and water. Journal of the American Chemical Society, 122(12), 2878–2888. doi:10.1021/ja993663t
   Web of Science ®Google Scholar
• Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. Journal of Chemical Physics, 103(19), 8577–8593. doi:10.1063/1.470117
   Web of Science ®Google Scholar
• Global Burden of Disease Study. (2015). Global, regional, and national incidence, prevalence, and years lived with disability for 301 acute and chronic diseases and injuries in 188 countries, 1990-2013: A systematic analysis for the Global Burden of Disease Study 2013. Lancet (London, England), 386(9995), 743–800.
   PubMed Web of Science ®Google Scholar
• Goedert, M., Spillantini, M., Jakes, R., Rutherford, D., & Crowther, R. (1989). Multiple isoforms of human microtubule-associated protein tau: Sequences and localization in neurofibrillary tangles of Alzheimer's disease. Neuron, 3(4), 519–526. doi:10.1016/0896-6273(89)90210-9
   PubMed Web of Science ®Google Scholar
• Hoover, W. G. (1985). Canonical dynamics: Equilibrium phase-space distributions. Physical Review A, 31(3), 1695. doi:10.1103/PhysRevA.31.1695
   PubMed Web of Science ®Google Scholar
• Humphreys, D. D., Friesner, R. A., & Berne, B. J. (1994). A multiple-time-step molecular dynamics algorithm for macromolecules. The Journal of Physical Chemistry, 98(27), 6885–6892. doi:10.1021/j100078a035
   Web of Science ®Google Scholar
• Iqbal, K., Liu, F., & Gong, C.-X. (2016). Tau and neurodegenerative disease: The story so far. Nature Reviews Neurology, 12(1), 15.doi:10.1038/nrneurol.2015.225
   PubMed Web of Science ®Google Scholar
• Iqbal, K., Liu, F., & Gong, C.-X. (2018). Recent developments with tau-based drug discovery. Expert Opinion on Drug Discovery, 13(5), 399–410. doi:10.1080/17460441.2018.1445084
   PubMed Web of Science ®Google Scholar
• 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(7), 1757–1768. doi:10.1021/ci3001277
   PubMed Web of Science ®Google Scholar
• Jasial, S., Hu, Y., & Bajorath, J. R. (2017). How frequently are pan-assay interference compounds active? Large-scale analysis of screening data reveals diverse activity profiles, low global hit frequency, and many consistently inactive compounds. Journal of Medicinal Chemistry, 60(9), 3879–3886. doi:10.1021/acs.jmedchem.7b00154
   PubMed Web of Science ®Google Scholar
• Jayaraj, J. M., Krishnasamy, G., Lee, J.-K., & Muthusamy, K. (2018). In silico identification and screening of CYP24A1 inhibitors: 3D QSAR pharmacophore mapping and molecular dynamics analysis. Journal of Biomolecular Structure and Dynamics, 1–15. doi:10.1080/07391102.2018.1464958
   Google Scholar
• Jorgensen, W. L., Maxwell, D. S., & Tirado-Rives, J. (1996). Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society, 118(45), 11225–11236. doi:10.1021/ja9621760
   Web of Science ®Google Scholar
• Kaminski, G. A., Friesner, R. A., Tirado-Rives, J., & Jorgensen, W. L. (2001). Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. The Journal of Physical Chemistry B, 105(28), 6474–6487. doi:10.1021/jp003919d
   Web of Science ®Google Scholar
• Kiefer, S. E., Chang, C., Kimura, S. R., Gao, M., Xie, D., Zhang, Y., … Sheriff, S. (2014). The structure of human tau-tubulin kinase 1 both in the apo form and in complex with an inhibitor. Acta Crystallographica Section F Structural Biology Communications, 70(Pt 2), 173–181. doi:10.1107/S2053230X14000144
   PubMedGoogle Scholar
• Lagorce, D., Bouslama, L., Becot, J., Miteva, M. A., & Villoutreix, B. O. (2017). FAF-Drugs4: Free ADME-tox filtering computations for chemical biology and early stages drug discovery. Bioinformatics, 33(22), 3658–3660. doi:10.1093/bioinformatics/btx491
   PubMed Web of Science ®Google Scholar
• Landrum, G. (2013). RDKit: Cheminformatics and machine learning software. RDKIT. ORG.
   Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23(1-3), 3–25. doi:10.1016/S0169-409X(96)00423-1
   Web of Science ®Google Scholar
• Lund, H., Cowburn, R. F., Gustafsson, E., Strömberg, K., Svensson, A., Dahllund, L., … Sunnemark, D. (2013). Tau‐tubulin kinase 1 expression, phosphorylation and co‐localization with phospho‐Ser422 Tau in the Alzheimer's disease brain. Brain Pathology, 23(4), 378–389. doi:10.1111/bpa.12001
   PubMed Web of Science ®Google Scholar
• Martyna, G. J., Tobias, D. J., & Klein, M. L. (1994). Constant pressure molecular dynamics algorithms. Journal of Chemical Physics., 101(5), 4177–4189. doi:10.1063/1.467468
   Web of Science ®Google Scholar
• Ntie-Kang, F. (2013). An in silico evaluation of the ADMET profile of the StreptomeDB database. SpringerPlus, 2(1), 353.
   PubMedGoogle Scholar
• Sato, S., Cerny, R. L., Buescher, J. L., & Ikezu, T. (2006). Tau-tubulin kinase 1 (TTBK1), a neuron-specific tau kinase candidate, is involved in tau phosphorylation and aggregation. Journal of Neurochemistry, 98(5), 1573–1584. doi:10.1111/j.1471-4159.2006.04059.x
   PubMed Web of Science ®Google Scholar
• Sato, S., Xu, J., Okuyama, S., Martinez, L. B., Walsh, S. M., Jacobsen, M. T., … Ikezu, T. (2008). Spatial learning impairment, enhanced CDK5/p35 activity, and downregulation of NMDA receptor expression in transgenic mice expressing tau-tubulin kinase 1. Journal of Neuroscience, 28(53), 14511–14521. doi:10.1523/JNEUROSCI.3417-08.2008
   PubMed Web of Science ®Google Scholar
• Saubern, S., Guha, R., & Baell, J. B. (2011). KNIME workflow to assess PAINS filters in SMARTS format. Comparison of RDKit and Indigo cheminformatics libraries. Molecular Informatics, 30(10), 847–850. doi:10.1002/minf.201100076
   PubMed Web of Science ®Google Scholar
• Sterling, T., & Irwin, J. J. (2015). ZINC 15-ligand discovery for everyone. Journal of Chemical Information and Modeling, 55(11), 2324–2337. doi:10.1021/acs.jcim.5b00559
   PubMed Web of Science ®Google Scholar
• Sulaiman, K. O., Kolapo, T. U., Onawole, A. T., Islam, M. A., Adegoke, R. O., & Badmus, S. O. (2018). Molecular dynamics and combined docking studies for the identification of Zaire ebola virus inhibitors. Journal of Biomolecular Structure and Dynamics, 1–12. doi:10.1080/07391102.2018.1506362
   PubMedGoogle Scholar
• Takahashi, M., Tomizawa, K., Sato, K., Ohtake, A., & Omori, A. (1995). A novel tau-tubulin kinase from bovine brain . FEBS Letters, 372(1), 59–64.
   PubMed Web of Science ®Google Scholar
• Toxvaerd, S., & Dyre, J. C. (2011). Communication: Shifted forces in molecular dynamics. The Journal of Chemical Physics, 134(8), 0811021-4. doi:10.1063/1.3558787
   PubMed Web of Science ®Google Scholar
• Wang, H., Aslanian, R., & Madison, V. S. (2008). Induced-fit docking of mometasone furoate and further evidence for glucocorticoid receptor 17α pocket flexibility. Journal of Molecular Graphics and Modelling, 27(4), 512–521. doi:10.1016/j.jmgm.2008.09.002
   PubMed Web of Science ®Google Scholar
• Wu, P., Nielsen, T. E., & Clausen, M. H. (2016). Small-molecule kinase inhibitors: An analysis of FDA-approved drugs. Drug Discovery Today, 21(1), 5–10. doi:10.1016/j.drudis.2015.07.008
   PubMed Web of Science ®Google Scholar
• Xu, J., Sato, S., Okuyama, S., Swan, R. J., Jacobsen, M. T., Strunk, E., & Ikezu, T. (2010). Tau-tubulin kinase 1 enhances prefibrillar tau aggregation and motor neuron degeneration in P301L FTDP-17 tau-mutant mice. Faseb Journal, 24(8), 2904–2915. doi:10.1096/fj.09-150144
   PubMed Web of Science ®Google Scholar
• Xue, Y., Wan, P. T., Hillertz, P., Schweikart, F., Zhao, Y., Wissler, L., & Dekker, N. (2013). X‐ray structural analysis of Tau‐Tubulin kinase 1 and its interactions with small molecular inhibitors. ChemMedChem, 8(11), 1846–1854. doi:10.1002/cmdc.201300274
   PubMed Web of Science ®Google Scholar