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Nguyễn Cường Quốc(1), Trần Quang Đệ(2), Nguyễn Trọng Tuân, Bùi Thị Bửu Huê

Nghiên cứu tương tác của vorinostat với enzyme HDAC8 (1T67) bằng Autodock

Interactive study of vorinostat with enzyme HDAC8 (1T67) by Autodock

Khoa học (ĐH Cần Thơ)

2020

6A

77-88

1859-2333

Autodock, Molecular docking, HDAC, Ung thư, Vorinostat

Autodock, Docking, Enzyme HDAC, Tumor cells, Vorinostat

Vorinostat là thuốc có khả năng ức chế enzyme HDAC, được FDA Hoa Kỳ phê duyệt năm 2006 điều trị u lympho tế bào T ở da. Trong số 18 loại enzyme HDAC, vorinostat ức chế mạnh hoạt động của enzyme HDAC1, HDAC2, HDAC3 và HDAC6. Tuy nhiên, vẫn chưa có nhiều tài liệu công bố về khả năng ức chế của vorinostat về HDAC8 (1T67). Trong nghiên cứu này, các tương tác của vorinostat với enzyme HDAC8 (1T67) được thực hiện và mô tả bằng việc docking vorinostat vào vùng hoạt động của enzyme HDAC8 thông qua Autodock. HDAC8 là HDAC loại I được coi là mục tiêu điều trị trong các bệnh khác nhau bao gồm ung thư, nhiễm ký sinh trùng và hội chứng Cornelia de Lange. Trong các tế bào khối u vú xâm lấn, HDAC8 là một trong ba thành viên nhóm các HDAC được điều hòa và điều trị xâm lấn. Phân tích kết quả docking cho thấy vorinostat tương tác mạnh với ion Zn+2, Gly151, Gly304, Asp178, Tyr306, Phe207, Met274 và các amino acid khác. Do đó, kết quả là tiền đề giúp thiết kế các chất ức chế chọn lọc HDAC8 mới.

Vorinostat is a histone deacetylase inhibitor which was approved by the US FDA in 2006 for the treatment of cutaneous manifestations in patients with cutaneous T-cell lymphoma. Among 18 HDAC enzymes, vorinostat is a potent inhibitor of the activity of HDAC1, HDAC2, HDAC3 and HDAC6. However, there have not been many published papers on the inhibitory capacity against HDAC8 (1T67) of vorinostat. In this study, the interactions of vorinostat with the enzyme HDAC8 (1T67) were performed and described by docking vorinostat into the active zone of the HDAC8 enzyme using Autodock. HDAC8 is a class I histone deacetylase implicated as a therapeutic target in various diseases, including cancer, parasitic infections and Cornelia de Lange syndrome. In invasive breast tumor cells, HDAC8 is among the three HDAC family members that are upregulated and driving invasiveness. The docking analysis shows vorinostat’s interactions with Zn+2 ion, Gly151, Gly304, Asp178, Tyr306, Phe207, Met274 and other less interacting residues. Therefore, the results could act as a momentum for further studies on the design of new isozyme-selective HDAC8 inhibitors.

TTKHCNQG, CVv 403

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  • [1] Yamauchi, Y., Boukari, H., Banerjee, I., et al. (2011), Histone deacetylase 8 is required for centrosome cohesion and influenza A virus entry,PLoS Pathogens. 7(10): e1002316
  • [2] Whitehead, L., Dobler, M. R., Radetich, B., et al. (2011), Human HDAC isoform se-lectivity achieved via exploitation of the acetate release channel with structurally unique small molecule inhibitors,Bioorganic & Medicinal Chemistry. 19(15): 4626-4634
  • [3] Wang, Y., Zheng, Q., Zhang, J., et al. (2015), How mutations affecting the ligand-receptor interactions: a combined MD and QM/MM calculation on CYP2E1 and its two mutants,Chemical Research in Chinese Universities. 31(6): 1029-1038
  • [4] Wagner, T., Godmann, M. and Heinzel, T. (2017), Analysis of histone deacetylases sumoylation by immunoprecipitation techniques,In. HDAC/HAT Function Assessment and Inhibitor Development. Springer, 339-351
  • [5] Vannini, A., Volpari, C., Filocamo, G., et al. (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. 101(42): 15064-15069
  • [6] Van den Wyngaert, I., de Vries, W., Kremer, A., et al. (2000), Cloning and c-haracterization of human histone deacetylase 8,FEBS Letters. 478(1-2): 77-83
  • [7] Trott, O. and Olson, A. J. (2010), AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading,Journal of Computational Chemistry. 31(2): 455-461
  • [8] 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 isoformspecific subpocket,Journal of Structural Biology. 195(3): 373-37
  • [9] Son, C. H., Keum, J. H., Yang, K., et al. (2014), Synergistic enhancement of NK cell-mediated cytotoxicity by combination of histone deacetylase inhibitor and ionizing radiation,Radiation Oncology. 9(1): 49-59
  • [10] Somoza, J. R., Skene, R. J., Katz, B. A., et al. (2004), Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases,Structure. 12(7): 1325-1334
  • [11] Siegel, D., Hussein, M., Belani, C., et al. (2009), Vorinostat in solid and hematologic malignancies,Journal of Hematology & Oncology. 2(1): 31-42
  • [12] Rizvi, S. M. D., Shakil, S., Haneef, M. (2013), A simple click by click protocol to perform docking: AutoDock 4.2 made easy for nonbioinformaticians,EXCLI Journal. 12: 831-857
  • [13] Porter, N. J., Christianson, N. H., Decroos, C., Christianson, D. W. (2016), Structural and functional influence of the glycine-rich loop G302GGGY on the catalytic tyrosine of histone deacetylase 8,Biochemistry. 55(48): 6718-6729
  • [14] 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
  • [15] Parbin, S., Kar, S., Shilpi, A., et al. (2014), Histone deacetylases: a saga of perturbed acetylation homeostasis in cancer,Journal of Histochemistry & Cytochemistry. 62(1): 11-33
  • [16] Ortore, G., Colo, F. D. and Martinelli, A. (2009), Docking of hydroxamic acids into HDAC1 and HDAC8: a rationalization of activity trends and se-lectivities,Journal of Chemical information and Modeling. 49(12): 2774-2785
  • [17] Oehme, I., Deubzer, H. E., Lodrini, M., Milde, T., Witt, O. (2009), Targeting of HDAC8 and investigational inhibitors in neuroblastoma,Expert Opinion on Investigational Drugs. 18(11): 1605-1617
  • [18] Mottamal, M., Zheng, S., Huang, T. L., Wang, G. (2015), Histone deacetylase inhibitors in clinical studies as templates for new anticancer agents,Molecules. 20(3): 3898-3941
  • [19] Marek, M., Shaik, T. B., Heimburg, T., et al. (2018), C-haracterization of histone deacetylase 8 (HDAC8) se-lective inhibition reveals specific active site structural and functional determinants,Journal of Medicinal Chemistry. 61(22): 10000- 10016
  • [20] Marek, M., Kannan, S., Hauser, A. T., et al. (2013), Structural basis for the inhibition of histone deacetylase 8 (HDAC8), a key epigenetic player in the blood fluke Schistosoma mansoni,PLoS Pathogens. 9(9): e1003645
  • [21] Li, Y., Seto, E. (2016), HDACs and HDAC inhibitors in cancer development and therapy,Cold Spring Harbor Perspectives in Medicine. 6(10): a026831
  • [22] Lee, H., Sengupta, N., Villagra, A., Rezai-Zadeh, N. and Seto, E. (2006), Histone deacetylase 8 safeguards the human ever-shorter telomeres 1B (hEST1B) protein f-rom ubiquitin-mediated degradation,Molecular and Cellular Biology. 26(14): 5259-5269
  • [23] KrennHrubec, K., Marshall, B. L., Hedglin, M., Verdin, E. and Ulrich, S. M. (2007), Design and evaluation of ‘Linkerless’ hydroxamic acids as se-lective HDAC8 inhibitors,Bioorganic & Medicinal Chemistry Letters. 17(10): 2874-2878
  • [24] Kaiser, F. J., Ansari, M., Braunholz, D., et al. (2014), Loss-of-function HDAC8 mutations cause a phenotypic spectrum of Cornelia de Lange syndrome-like features, ocular hypertelorism, large fontanelle and X-linked inheritance,Human Molecular Genetics. 23(11): 2888-2900
  • [25] Johnstone, R. W. (2002), Histone-deacetylase inhibitors: novel drugs for the treatment of cancer,Nature Reviews Drug Discovery. 1(4): 287-299
  • [26] Huang, Y.x., Zhao, J., Song, Q.h., et al. (2016), Virtual screening and experimental validation of novel histone deacetylase inhibitors,BMC Pharmacology and Toxicology. 17(1): 32-46
  • [27] Hu, E., Chen, Z., Fredrickson, T., et al. (2000), Cloning and c-haracterization of a novel human class I histone deacetylase that functions as a transcription repressor,Journal of Biological Chemistry. 275(20): 15254-15264
  • [28] He, B., Velaparthi, S., Pieffet, G., et al. (2009), Binding ensemble profiling with photoaffinity labeling (BEProFL) approach: mapping the binding poses of HDAC8 inhibitors,Journal of Medicinal Chemistry. 52(22): 7003-7013
  • [29] Grant, S., Easley, C., Kirkpatrick, P. (2007), Vorinostat,Nature Reviews Drug Discovery. 6(1): 21-22
  • [30] Gohlke, H., Hendlich, M., Klebe, G. (2000), Knowledge-based scoring function to predict protein-ligand interactions,Journal of Molecular Biology. 295(2): 337-356
  • [31] Gantt, S. M. L., Decroos, C., Lee, M. S., et al. (2016), General base–general acid catalysis in human histone deacetylase 8,Biochemistry. 55(5): 820-832
  • [32] Falkenberg, K. J. and Johnstone, R. W. (2014), Histone deacetylases and their inhibitors in cancer, neurological diseases and immune disorders,Nature Reviews Drug Discovery. 13(9): 673-691
  • [33] Estiu, G., West, N., Mazitschek, R., et al. (2010), On the inhibition of histone deacetylase 8,Bioorganic & Medicinal Chemistry. 18(11): 4103-4110
  • [34] Decroos, C., Christianson, N. H., Gullett, L. E., et al. (2015), Biochemical and structural c-haracterization of HDAC8 mutants associated with Cornelia de Lange syndrome spectrum disorders,Biochemistry. 54(42): 6501-6513
  • [35] Debnath, S., Debnath, T., Bhaumik, S., et al. (2019), Discovery of novel potential se-lective HDAC8 inhibitors by combine ligand-based, structurebased virtual screening and in-vitro biological evaluation,Scientific Reports. 9(1): 1-14
  • [36] Chakrabarti, A., Oehme, I., Witt, O., et al. (2015), HDAC8: a multifaceted target for therapeutic interventions,Trends in Pharmacological Sciences. 36(7): 481-492
  • [37] Cai, J., Wei, H., Hong, K. H., et al. (2015), Discovery, bioactivity and docking simulation of Vorinostat analogues containing 1, 2, 4- oxadiazole moiety as potent histone deacetylase inhibitors and antitumor agents,Bioorganic & Medicinal Chemistry. 23(13): 3457-3471
  • [38] Buggy, J. J., Sideris, M. L., Mak, P., Lorimer, D. D., Mcintosh, B., and Clark, J. M. (2000), Cloning and c-haracterization of a novel human histone deacetylase, HDAC8,Biochemical Journal. 350(1): 199-205
  • [39] Bolden, J. E., Peart, M. J., Johnstone, R. W. (2006), Anticancer activities of histone deacetylase inhibitors,Nature Reviews Drug Discovery. 5(9): 769-784
  • [40] Araújo, P., da Silva, L. P. and Esteves da Silva, J. (2015), Theoretical Analysis of the Binding of Potential Inhibitors to Protein Kinases MK2 and MK3,Med. Chem. 11(6): 573-579
  • [41] Anantharaju, P. G., Reddy, D. B., Padukudru, M. A., Chitturi, C. M. K., Vimalambike, M. G. and Madhunapantula, S. V. (2017), Induction of colon and cervical cancer cell death by cinnamic acid derivatives is mediated through the inhibition of Histone Deacetylases (HDAC),PloS One. 12(11): e0186208
  • [42] Alsawalha, M., Bolla, S. R., Kandakatla, N., Srinivasadesikan, V., Veeraraghavan, V. P. and Surapaneni, K. M. (2019), Molecular docking and ADMET analysis of hydroxamic acids as HDAC2 inhibitors,Bioinformation, 15(6): 380- 387