458
Views
11
CrossRef citations to date
0
Altmetric
Research Articles

Examining the stability of binding modes of the co-crystallized inhibitors of human HDAC8 by molecular dynamics simulation

, , , & ORCID Icon
Pages 1751-1760 | Received 12 Apr 2019, Accepted 01 May 2019, Published online: 20 May 2019

References

  • Aramsangtienchai, P., He, B., Miller, S. P., Dai, L., Zhao, Y., Lin, H., & Spiegelman, N. A. (2016). HDAC8 catalyzes the hydrolysis of long chain fatty acyl lysine. ACS Chemical Biology, 11(10), 2685–2692. doi: 10.1021/acschembio.6b00396
  • Bradner, J. E., West, N., Grachan, M. L., Greenberg, E. F., Haggarty, S. J., Warnow, T., & Mazitschek, R. (2010). Chemical phylogenetics of histone deacetylases. Nature Chemical Biology, 6(3), 238–243. doi: 10.1038/nchembio.313
  • Chakrabarti, A., Melesina, J., Kolbinger, F. R., Oehme, I., Senger, J., Witt, O., … Jung, M. (2016). Targeting histone deacetylase 8 as a therapeutic approach to cancer and neurodegenerative diseases. Future Medicinal Chemistry, 8(13), 1609–1634. doi: 10.4155/fmc-2016-0117
  • Chakrabarti, A., Oehme, I., Witt, O., Oliveira, G., Sippl, W., Romier, C., … Jung, M. (2015). HDAC8: A multifaceted target for therapeutic interventions. Trends in Pharmacological Sciences, 36(7), 481–492. doi: 10.1016/j.tips.2015.04.013
  • Cole, K. E., Dowling, D. P., Boone, M. A., Phillips, A. J., & Christianson, D. W. (2011). Structural basis of the antiproliferative activity of largazole, a depsipeptide inhibitor of the histone deacetylases. Journal of the American Chemical Society, 133(32), 12474–12477. doi: 10.1021/ja205972n
  • Deardorff, M. A., Bando, M., Nakato, R., Watrin, E., Itoh, T., Minamino, M., … Clark, D. (2012). HDAC8 mutations in Cornelia de Lange syndrome affect the cohesion acetylation cycle. Nature, 489(7415), 313–317. doi: 10.1038/nature11316
  • Decroos, C., Bowman, C. M., Moser, J.-A. S., Christianson, K. E., Deardorff, M. A., & Christianson, D. W. (2014). Compromised structure and function of HDAC8 mutants identified in Cornelia de Lange Syndrome spectrum disorders. ACS Chemical Biology, 9(9), 2157–2164. doi: 10.1021/cb5003762
  • Dewaker, V., Srivastava, P. N., Verma, S., & Prabhakar, Y. S. (2019). Molecular dynamics study of HDAC8-largazole analogues co-crystals for designing potential anticancer compounds. Journal of Biomolecular Structure and Dynamics, 1. doi: 10.1080/07391102.2019.1598497
  • Dowling, D. P., Gantt, S. L., Gattis, S. G., Fierke, C. A., & Christianson, D. W. (2008). Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors. Biochemistry, 47(51), 13554–13563. doi: 10.1021/bi801610c
  • Falkenberg, K. J., & Johnstone, R. W. (2014). Histone deacetylases and their inhibitors in cancer, neurological diseases and immune disorders. Nature Reviews Drug Discovery, 13(9), 673–691. doi: 10.1038/nrd4360
  • Grozinger, C. M., Hassig, C. A., Schreiber, S. L. (1999). Three proteins define a class of human histone deacetylases related to yeast Hda1p. PNAS, 96(9), 4868–4873. doi: 10.1073/pnas.96.9.4868
  • Kaiser, F. J., Ansari, M., Braunholz, D., Gil-Rodríguez, M. C., Decroos, C., Wilde, J. J., … Amor, D. (2014). Loss-of-function HDAC8 mutations cause a phenotypic spectrum of Cornelia de Lange syndrome-like features, ocular hypertelorism, large fontan fontanelle and X-linked inheritance. Human Molecular Genetics, 23(11), 2888–2900.
  • Kim, S., Lee, J., Jo, S., Brooks 3rd , C.L., Lee, H.S., Im, W., (2017). CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. Journal of computational chemistry, 38, 1879–1886. doi: 10.1002/jcc.24829
  • Kijima, M., Yoshida, M., Sugita, K., Horinouchi, S., & Beppu, T. (1993). Trapoxin, an antitumor cyclic tetrapeptide, is an irreversible inhibitor of mammalian histone deacetylase. Journal of Biological Chemistry, 268(30), 22429–22435.
  • Lee, J., Cheng, X., Swails, J. M., Yeom, M. S., Eastman, P. K., Lemkul, J. A., … Im, W. (2016). CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. Journal of Chemical Theory and Computation, 12, 405–413. doi: 10.1021/acs.jctc.5b00935.
  • Lehmann, M., Hoffmann, M. J., Koch, A., Ulrich, S. M., Schulz, W. A., & Niegisch, G. (2014). Histone deacetylase 8 is deregulated in urothelial cancer but not a target for efficient treatment. Journal of Experimental Clinical Cancer Research, 33, 59.doi: 10.1186/s13046-014-0059-8
  • Lombardi, P. M., Angell, H. D., Whittington, D. A., Flynn, E. F., Rajashankar, K. R., & Christianson, D. W. (2011). Structure of prokaryotic polyamine deacetylase reveals evolutionary functional relationships with eukaryotic histone deacetylases. Biochemistry, 50(11), 1808–1817. doi: 10.1021/bi101859k.
  • Micelli, C., & Rastelli, G. (2015). Histone deacetylases: Structural determinants of inhibitor selectivity. Drug Discovery Today, 20(6), 718–735. doi: 10.1016/j.drudis.2015.01.007
  • Morris, G., & Huey, R. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30, 2785–2791. doi: 10.1002/jcc.21256.AutoDock4
  • Noor, Z., Afzal, N., & Rashid, S. (2015). Exploration of novelinhibitors for class I histone deacetylase isoforms by QSAR modeling and molecular dynamics simulation assays. PLoS One, 10(10), e0139588. doi: 10.1371/journal.pone.0139588
  • Olson, D. E., Udeshi, N. D., Wolfson, N. A., Pitcairn, C. A., Sullivan, E. D., Jaffe, J. D., … Holson, E. B. (2014). An Unbiased approach to identify endogenous substrates of “histone” deacetylase 8. ACS Chemical Biology, 9(10), 2210–2216. doi: 10.1021/cb500492r
  • Park, S. Y., Jun, J. A., Jeong, K. J., Heo, H. J., Sohn, J. S., Lee, H. Y., … Kang, J. (2011). Histone deacetylases 1, 6 and 8 are critical for invasion in breast cancer. Oncology Reports, 25(6), 1677–1681. doi: 10.3892/or.2011.1236
  • 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
  • Porter, N. J., & Christianson, D. W. (2017). Binding of the Microbial Cyclic Tetrapeptide Trapoxin A to the Class I Histone Deacetylase HDAC8. ACS Chemical Biology, 12(9), 2281–2286. doi: 10.1021/acschembio.7b00330
  • Rettig, E., Koeneke, F., Trippel, W. C., Mueller, J., Burhenne, A., Kopp-Schneider, J., … Oehme, I. (2015). Selective inhibition of HDAC8 decreases neuroblastoma growth in vitro and in vivo and enhances retinoic acid-mediated differentiation. Cell Death & Disease, 6(2), e1657. doi: 10.1038/cddis.2015.24
  • Sixto-López, Y., Bello, M., & Correa-Basurto, J. (2019). Insights into structural features of HDAC1 and its selectivity inhibition elucidated by Molecular dynamic simulation and Molecular Docking. Journal of Biomolecular Structure and Dynamics, 37(3), 584–610. doi: 10.1080/07391102.2018.1441072
  • Sixto-López, Y., Gómez-Vidal, J. A., & Correa-Basurto, J. (2014). Exploring the Potential binding Sites of Some Known HDAC Inhibitors on Some HDAC8 Conformers by Docking Studies. Applied Biochemistry and Biotechnology, 173(7), 1907–1926. doi: 10.1007/s12010-014-0976-1
  • Somoza, J. R., Skene, R. J., Katz, B. A., Mol, C., Ho, J. D., Jennings, A. J., … Tari, L. W. (2004). Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases. Structure, 12(7), 1325–1334. doi: 10.1016/j.str.2004.04.012
  • Tabackman, A. A., Frankson, R., Marsan, E. S., Perry, K., & Cole, K. E. (2016). Structure of 'linkerless' hydroxamic acid inhibitor-HDAC8 complex confirms the formation of an isoform-specific subpocket. Journal of Structural Biology, 195(3), 373–378.
  • Tambunan, U. S. F., Bakri, R., Prasetia, T., Parikesit, A. A., & Kerami, D. (2013). Molecular dynamics simulation of complex histones deacetylase (HDAC) class II Homo Sapiens with suberoylanilide hydroxamic acid (SAHA) and its derivatives as inhibitors of cervical cancer. Bioinformation, 9(13), 696–700. doi: 10.6026/97320630009696
  • Thangapandian, S., John, S., & Lee, K. W. (2012). Molecular dynamics simulation study explaining inhibitor selectivity in different class of histone deacetylases. Journal of Biomolecular Structure and Dynamics, 29(4), 677–698. doi: 10.1080/07391102.2012.10507409
  • Thangapandian, S., John, S., Lee, Y., Kim, S., & Lee, K. W. (2011). Dynamic structure-based pharmacophore model development: A new and effective addition in the histone deacetylase 8 (HDAC8) inhibitor discovery. International Journal of Molecular Sciences, 12(12), 9440–9462. doi: 10.3390/ijms12129440
  • Thangapandian, S., John, S., Sakkiah, S., & Lee, K. W. (2010). Ligand and structure based pharmacophore modeling to facilitate novel histone deacetylase 8 inhibitor design. European Journal of Medicinal Chemistry, 45(10), 4409–4417. doi: 10.1016/j.ejmech.2010.06.024
  • Tang, J., Yan, H., & Zhuang, S. (2013). Histone deacetylases as targets for treatment of multiple diseases. Clinical Science, 124(11), 651–662. doi: 10.1042/CS20120504
  • Uba, A. I., & Yelekçi, K. (2018a). Identification of potential isoform-selective histone deacetylase inhibitors for cancer therapy: A combined approach of structure-based virtual screening, ADMET prediction and molecular dynamics simulation assay. Journal of Biomolecular Structure and Dynamics, 36(12), 3231–3245. doi: 10.1080/07391102.2017.1384402
  • Uba, A. I., & Yelekçi, K. (2018b). Carboxylic acid derivatives display potential selectivity for human histone deacetylase 6: Structure-based virtual screening, molecular docking and dynamics simulation studies. Computational Biology and Chemistry, 75, 131–142. doi: 10.1016/j.compbiolchem.2018.05.004
  • Uba, A. I., & Yelekçi, K. (2019). Homology modeling of human histone deacetylase 10 and design of potential selective inhibitors. Journal of Biomolecular Structure and Dynamics. doi: 10.1080/07391102.2018.1521747
  • Vannini, A., Volpari, C., Filocamo, G., Casavola, E. C., Brunetti, M., Renzoni, D., … Di Marco, S. (2004). Crystal structure of a eukaryotic zinc-dependent histone deacetylase, human HDAC8, complexed with a hydroxamic acid inhibitor. Proceedings of the National Academy of Sciences of the United States of America, 101(42), 15064–15069. doi: 10.1073/pnas.0404603101
  • Whitehead, L., Dobler, M. R., Radetich, B., Zhu, Y., Atadja, P. W., Claiborne, T., … Stams, T. (2011). Human HDAC isoform selectivity achieved via exploitation of the acetate release channel with structurally unique small molecule inhibitors. Bioorganics & Medicinal Chemistry, 19(15), 4626–4634. doi: 10.1016/j.bmc.2011.06.030
  • Wolfson, N. A., Pitcairn, C. A., & Fierke, C. A. (2013). HDAC8 substrates: Histones and beyond. Biopolymers, 99(2), 112–126. doi: 10.1002/bip.22135
  • Wu R, Wang R, Zhou N, Cao Z, and Zhang Y. (2010). A Proton-Shuttle Reaction Mechanism for Histone Deacetylase 8 and the Catalytic Role of Metal Ions. Journal of the American Chemical Society, 132(27), 9471–9479.
  • Yan, W., Liu, S., Xu, E., Zhang, J., Zhang, Y., Chen, X., & Chen, X. (2013). Histone deacetylase inhibitors suppress mutant p53 transcription via histone deacetylase 8. Oncogene, 32(5), 599–609. doi: 10.1038/onc.2012.81
  • Ying, Y., Taori, K., Kim, H., Hong, J., & Luesch, H. (2008). Total synthesis and molecular target of largazole, a histone deacetylase inhibitor. Journal of the American Chemical Society, 130(26), 8455–8459. doi: 10.1021/ja8013727
  • Yoshida, M., Nomura, S., & Beppu, T. (1987). Effects of trichostatins on differentiation of murine erythroleukemia cells. Cancer Research, 47, 3688–3691.
  • Yuan, Y., Hu, Z., Bao, M., Sun, R., Long, X., Long, L., … Bao, J. (2019). Screening of novel histone deacetylase 7 inhibitors through molecular docking followed by a combination of molecular dynamics simulations and ligand-based approach. Journal of Biomolecular Structure and Dynamics, 2018 Nov 10, 1–30. doi: 10.1080/07391102.2018.1541141
  • Zhou, H., Wang, C., Deng, T., Tao, R., & Li, W. (2018). Novel urushiol derivatives as HDAC8 inhibitors: Rational design, virtual screening, molecular docking and molecular dynamics studies. Journal of Biomolecular Structure and Dynamics, 2018 Jun36(8), 1966–1978. doi: 10.1080/07391102.2017.1344568

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.