201
Views
5
CrossRef citations to date
0
Altmetric
Articles

In silico 3D structure modeling and inhibitor binding studies of human male germ cell-associated kinase

, &
Pages 1710-1719 | Received 14 Apr 2014, Accepted 18 Sep 2014, Published online: 27 Oct 2014

References

  • Aleksandrov, A., & Simonson, T. (2010). Molecular dynamics simulations show that conformational selection governs the binding preferences of imatinib for several tyrosine kinases. Journal of Biological Chemistry, 285, 13807–13815.10.1074/jbc.M110.109660
  • Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215, 403–410.10.1016/S0022-2836(05)80360-2
  • Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., … Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28, 235–242.10.1093/nar/28.1.235
  • Bladt, F., & Birchmeier, C. (1993). Characterization and expression analysis of the murine rck gene: A protein kinase with a potential function in sensory cells. Differentiation, 53, 115–122.10.1111/dif.1993.53.issue-2
  • Bussi, G., Donadio, D., & Parrinello, M. (2007). Canonical sampling through velocity rescaling. The Journal of Chemical Physics, 126, 014101.10.1063/1.2408420
  • Carbain, B., Paterson, D. J., Anscombe, E., Campbell, A. J., Cano, C., Echalier, A., … Griffin, R. J. (2014). 8-Substituted O(6)-cyclohexylmethylguanine CDK2 inhibitors: Using structure-based inhibitor design to optimize an alternative binding mode. Journal of Medicinal Chemistry, 57, 56–70.
  • Chen, W., Chang, C. E., & Gilson, M. K. (2004). Calculation of cyclodextrin binding affinities: Energy, entropy, and implications for drug design. Biophysical Journal, 87, 3035–3049.10.1529/biophysj.104.049494
  • Chu, X. J., DePinto, W., Bartkovitz, D., So, S. S., Vu, B. T., Packman, K., … Fotouhi, N. (2006). Discovery of [4-Amino-2-(1-methanesulfonyl piperidin-4-ylamino)pyrimidin-5-yl](2,3-difluoro-6-methoxyphenyl) methanone (R547), a potent and selective cyclin-dependent kinase inhibitor with significant in vivo antitumor activity. Journal of Medicinal Chemistry, 49, 6549–6560.10.1021/jm0606138
  • Cui, Q., Sulea, T., Schrag, J. D., Munger, C., Hung, M. N., Naïm, M., … Purisima, E. O. (2008). Molecular dynamics—Solvated interaction energy studies of protein–protein interactions: The MP1–p14 scaffolding complex. Journal of Molecular Biology, 379, 787–802.10.1016/j.jmb.2008.04.035
  • Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98, 10089–10092.10.1063/1.464397
  • Davis, M. I., Hunt, J. P., Herrgard, S., Ciceri, P., Wodicka, L. M., Pallares, G., … Zarrinkar, P. P. (2011). Comprehensive analysis of kinase inhibitor selectivity. Nature Biotechnology, 29, 1046–1051.10.1038/nbt.1990
  • Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103, 8577–8593.10.1063/1.470117
  • Eswar, N., Marti-Renom, M. A., Webb, B., Madhusudhan, M. S., Eramian, D., Shen, M., … Sali, A. (2006). Comparative protein structure modeling using MODELLER. In Ann Boyle (Ed.), Current protocols in bioinformatics (pp. 5.6.1–5.6.30). Wiley Online Library.
  • Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18, 1463–1472.10.1002/(ISSN)1096-987X
  • Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4, 435–447.10.1021/ct700301q
  • Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A., & Simmerling, C. (2006). Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins: Structure, Function, and Bioinformatics, 65, 712–725.10.1002/prot.v65:3
  • Jones, G., Willett, P., & Glen, R. C. (1995). Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. Journal of Molecular Biology, 245, 43–53.10.1016/S0022-2836(95)80037-9
  • Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. J. (1997). Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology, 267, 727–748.10.1006/jmbi.1996.0897
  • Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., … Higgins, D. G. (2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947–2948.10.1093/bioinformatics/btm404
  • Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26, 283–291.10.1107/S0021889892009944
  • Lee, D. K., Duan, H. O., & Chang, C. (2000). From androgen receptor to the general transcription factor TFIIH. Identification of cdk activating kinase (CAK) as an androgen receptor NH(2)-terminal associated coactivator. Journal of Biological Chemistry, 275, 9308–9313.10.1074/jbc.275.13.9308
  • Levinson, N. M., Kuchment, O., Shen, K., Young, M. A., Koldobskiy, M., Karplus, M., … Kuriyan, J. (2006). A Src-like inactive conformation in the Abl tyrosine kinase domain. PLoS Biology, 4, e144.10.1371/journal.pbio.0040144
  • Lill, M. A., & Thompson, J. J. (2011). Solvent interaction energy calculations on molecular dynamics trajectories: Increasing the efficiency using systematic frame selection. Journal of Chemical Information and Modeling, 51, 2680–2689.10.1021/ci200191m
  • Lim, J. T., Mansukhani, M., & Weinstein, I. B. (2005). Cyclin-dependent kinase 6 associates with the androgen receptor and enhances its transcriptional activity in prostate cancer cells. Proceedings of the National Academy of Sciences, 102, 5156–5161.10.1073/pnas.0501203102
  • Lüthy, R., Bowie, J. U., & Eisenberg, D. (1992). Assessment of protein models with three-dimensional profiles. Nature, 356, 83–85.
  • Ma, A. H., Xia, L., Desai, S. J., Boucher, D. L., Guan, Y., Shih, H. M., … Kung, H. J. (2006). Male germ cell-associated kinase, a male-specific kinase regulated by androgen, is a coactivator of androgen receptor in prostate cancer cells. Cancer Research, 66, 8439–8447.
  • Matsushime, H., Jinno, A., Takagi, N., & Shibuya, M. (1990). A novel mammalian protein kinase gene (mak) is highly expressed in testicular germ cells at and after meiosis. Molecular and Cellular Biology, 10, 2261–2268.
  • Moilanen, A. M., Karvonen, U., Poukka, H., Janne, O. A., & Palvimo, J. J. (1998). Activation of androgen receptor function by a novel nuclear protein kinase. Molecular Biology of the Cell, 9, 2527–2543.10.1091/mbc.9.9.2527
  • Naïm, M., Bhat, S., Rankin, K. N., Dennis, S., Chowdhury, S. F., Siddiqi, I., Drabik, P., Sulea, T., Bayly, C. I., Jakalian, A., & Purisima, E. O. (2007). Solvated interaction energy (SIE) for scoring protein−ligand binding affinities. 1. Exploring the parameter space. Journal of Chemical Information and Modeling, 47, 122–133.10.1021/ci600406v
  • Omura, S., Iwai, Y., Hirano, A., Nakagawa, A., Awaya, J., Tsuchiya, H., Takahashi, Y., & Masuma, R. (1977). A new alkaloid AM-2282 of Streptomyces origin taxonomy, fermentation, isolation and preliminary characterization. The Journal of Antibiotics, 30, 275–282.10.7164/antibiotics.30.275
  • Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52, 7182–7190.10.1063/1.328693
  • Penas, C., Ramachandran, V., & Ayad, N. G. (2012). The APC/C Ubiquitin Ligase: From cell biology to tumorigenesis. Frontiers in Oncology, 1, 60.
  • Pilat, M. J., Kamradt, J. M., & Pienta, K. J. (1998). Hormone resistance in prostate cancer. Cancer and Metastasis Reviews, 17, 373–381.10.1023/A:1006166511344
  • Purisima, E. O. (1998). Fast summation boundary element method for calculating solvation free energies of macromolecules. Journal of Computational Chemistry, 19, 1494–1504.10.1002/(ISSN)1096-987X
  • Purisima, E. O., & Nilar, S. H. (1995). A simple yet accurate boundary-element method for continuum dielectric calculations. Journal of Computational Chemistry, 16, 681–689.10.1002/(ISSN)1096-987X
  • Qi, H., Labrie, Y., Grenier, J., Fournier, A., Fillion, C., & Labrie, C. (2001). Androgens induce expression of SPAK, a STE20/SPS1-related kinase, in LNCaP human prostate cancer cells. Molecular and Cellular Endocrinology, 182, 181–192.10.1016/S0303-7207(01)00560-3
  • Ramachandran, G. N., Ramakrishnan, C., & Sasisekharan, V. (1963). Stereochemistry of polypeptide chain configurations. Journal of Molecular Biology, 7, 95–99.
  • Revill, P., Serradell, N., Bolós, J., & Rosa, E. (2007). Lestaurtinib. Drugs of the Future, 32, 215–222.10.1358/dof.2007.032.03.1084137
  • Richards, F. M. (1977). Areas, volumes, packing, and protein structure. Annual Review of Biophysics and Bioengineering, 6, 151–176.10.1146/annurev.bb.06.060177.001055
  • Sadar, M. D., Hussain, M., & Bruchovsky, N. (1999). Prostate cancer: Molecular biology of early progression to androgen independence. Endocrine Related Cancer, 6, 487–502.10.1677/erc.0.0060487
  • Šali, A., & Blundell, T. L. (1993). Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology, 234, 779–815.10.1006/jmbi.1993.1626
  • Santo, L., Vallet, S., Hideshima, T., Cirstea, D., Ikeda, H., Pozzi, S., … Raje, N. (2010). AT7519, A novel small molecule multi-cyclin-dependent kinase inhibitor, induces apoptosis in multiple myeloma via GSK-3beta activation and RNA polymerase II inhibition. Oncogene, 29, 2325–2336.10.1038/onc.2009.510
  • Schrantz, N., Correia, J., Fowler, B., Ge, Q., Sun, Z., & Bokoch, G. M. (2004). Mechanism of p21-activated kinase 6-mediated inhibition of androgen receptor signaling. Journal of Biological Chemistry, 279, 1922–1931.10.1074/jbc.M311145200
  • Sekine, C., Sugihara, T., Miyake, S., Hirai, H., Yoshida, M., Miyasaka, N., & Kohsaka, H. (2008). Successful treatment of animal models of rheumatoid arthritis with small-molecule cyclin-dependent kinase inhibitors. The Journal of Immunology, 180, 1954–1961.10.4049/jimmunol.180.3.1954
  • Sousa da Silva, A. W., & Vranken, W. F. (2012). ACPYPE – AnteChamber PYthon parser interfacE. BMC Research Notes, 5, 367.10.1186/1756-0500-5-367
  • Tanneeru, K., & Guruprasad, L. (2012). Ligand-based 3-D pharmacophore generation and molecular docking of mTOR kinase inhibitors. Journal of Molecular Modeling, 18, 1611–1624.10.1007/s00894-011-1184-3
  • Tanneeru, K., & Guruprasad, L. (2013). Ponatinib is a Pan-BCR-ABL kinase inhibitor: MD simulations and SIE study. PLoS One, 8, e78556.10.1371/journal.pone.0078556
  • Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 4673–4680.10.1093/nar/22.22.4673
  • Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26, 1701–1718.10.1002/(ISSN)1096-987X
  • Wang, L. Y., & Kung, H. J. (2012). Male germ cell-associated kinase is overexpressed in prostate cancer cells and causes mitotic defects via deregulation of APC/CCDH1. Oncogene, 31, 2907–2918.10.1038/onc.2011.464
  • Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25, 1157–1174.10.1002/(ISSN)1096-987X
  • Wang, J. M., Wang, W., Kollman, P. A., & Case, D. A. (2006). Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling, 25, 247–260.10.1016/j.jmgm.2005.12.005
  • Willard, L., Ranjan, A., Zhang, H., Monzavi, H., Boyko, R. F., Sykes, B. D., & Wishart, D. S. (2003). VADAR: A web server for quantitative evaluation of protein structure quality. Nucleic Acids Research, 31, 3316–3319.10.1093/nar/gkg565
  • Xia, L., Robinson, D., Ma, A. H., Chen, H. C., Wu, F., Qiu, Y., & Kung, H. J. (2002). Identification of human male germ cell-associated kinase, a kinase transcriptionally activated by androgen in prostate cancer cells. Journal of Biological Chemistry, 277, 35422–35433.10.1074/jbc.M203940200
  • Xu, M., Yu, L., Wan, B., Yu, L., & Huang, Q. (2011). Predicting inactive conformations of protein kinases using active structures: Conformational selection of type-II inhibitors. PLoS One, 6, e22644.10.1371/journal.pone.0022644
  • Yang, F., Li, X., Sharma, M., Zarnegar, M., Lim, B., & Sun, Z. (2001). Androgen receptor specifically interacts with a novel p21-activated kinase, PAK6. Journal of Biological Chemistry, 276, 15345–15353.10.1074/jbc.M010311200

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.