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

Nguyen Cuong Quoc , Nguyen Trong Tuan , Bui Thi Buu Hue and Tran Quang De *

* Corresponding author (tqde@ctu.edu.vn)

Article Sidebar

Full Text: PDF

Received: 26 Jun 2020
Revised: 10 Sep 2020
Accepted: 28 Dec 2020
Published: 28 Dec 2020
Title: Interactive study of vorinostat with enzyme HDAC8 (1T67) by Autodock
DOI: 10.22144/ctu.jvn.2020.145
Views
177
Downloads
216
Crossref
Scopus
Google Scholar
Europe PMC
How to Cite
Quốc, N. C., Tuân, N. T., Huê, B. T. B., & Đệ, T. Q. (2020). Interactive study of vorinostat with enzyme HDAC8 (1T67) by Autodock. CTU Journal of Science, 56(6), 77-88. https://doi.org/10.22144/ctu.jvn.2020.145
Issue
Vol. 56 No. 6 (2020)
Section
Natural Sciences

Abstract

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.
Keywords: Autodock, docking, enzyme HDAC, tumor cells, vorinostat 

Tóm tắt

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.
Từ khóa: Autodock, molecular docking, HDAC, ung thư, vorinostat

Article Details

Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

References

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.

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.

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.

Bolden, J. E., Peart, M. J. and Johnstone, R. W., 2006. Anticancer activities of histone deacetylase inhibitors. Nature Reviews Drug Discovery.5(9): 769-784.

Buggy, J. J., Sideris, M. L., Mak, P., Lorimer, D. D., Mcintosh, B., and Clark, J. M., 2000. Cloning and characterization of a novel human histone deacetylase, HDAC8. Biochemical Journal. 350(1): 199-205.

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.

Chakrabarti, A., Oehme, I., Witt, O., et al., 2015. HDAC8: a multifaceted target for therapeutic interventions. Trends in Pharmacological Sciences.36(7): 481-492.

Debnath, S., Debnath, T., Bhaumik, S., et al., 2019. Discovery of novel potential selective HDAC8 inhibitors by combine ligand-based, structure-based virtual screening and in-vitro biological evaluation. Scientific Reports.9(1): 1-14.

Decroos, C., Christianson, N. H., Gullett, L. E., et al., 2015. Biochemical and structural characterization of HDAC8 mutants associated with Cornelia de Lange syndrome spectrum disorders. Biochemistry. 54(42): 6501-6513.

Estiu, G., West, N., Mazitschek, R., et al., 2010. On the inhibition of histone deacetylase 8. Bioorganic & Medicinal Chemistry.18(11): 4103-4110.

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.

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.

Gohlke, H., Hendlich, M. and Klebe, G., 2000. Knowledge-based scoring function to predict protein-ligand interactions. Journal of Molecular Biology.295(2): 337-356.

Grant, S., Easley, C. and Kirkpatrick, P., 2007. Vorinostat. Nature Reviews Drug Discovery.6(1): 21-22.

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.

Hu, E., Chen, Z., Fredrickson, T., et al., 2000. Cloning and characterization of a novel human class I histone deacetylase that functions as a transcription repressor. Journal of Biological Chemistry. 275(20): 15254-15264.

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.

Hutchison, G. R., Morley, C., James, C., et al., 2011. Open Babel Documentation.

Johnstone, R. W., 2002. Histone-deacetylase inhibitors: novel drugs for the treatment of cancer. Nature Reviews Drug Discovery.1(4): 287-299.

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.

KrennHrubec, K., Marshall, B. L., Hedglin, M., Verdin, E. and Ulrich, S. M., 2007. Design and evaluation of ‘Linkerless’ hydroxamic acids as selective HDAC8 inhibitors. Bioorganic & Medicinal Chemistry Letters.17(10): 2874-2878.

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 from ubiquitin-mediated degradation. Molecular and Cellular Biology.26(14): 5259-5269.

Li, Y. and Seto, E., 2016. HDACs and HDAC inhibitors in cancer development and therapy.Cold Spring Harbor Perspectives in Medicine.6(10): a026831.

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.

Marek, M., Shaik, T. B., Heimburg, T., et al., 2018. Characterization of histone deacetylase 8 (HDAC8) selective inhibition reveals specific active site structural and functional determinants. Journal of Medicinal Chemistry.61(22): 10000-10016.

Mottamal, M., Zheng, S., Huang, T. L. and Wang, G., 2015. Histone deacetylase inhibitors in clinical studies as templates for new anticancer agents. Molecules. 20(3): 3898-3941.

Oehme, I., Deubzer, H. E., Lodrini, M., Milde, T. and Witt, O., 2009. Targeting of HDAC8 and investigational inhibitors in neuroblastoma. Expert Opinion on Investigational Drugs.18(11): 1605-1617.

Ortore, G., Colo, F. D. and Martinelli, A., 2009. Docking of hydroxamic acids into HDAC1 and HDAC8: a rationalization of activity trendsand selectivities. Journal of Chemical information and Modeling. 49(12): 2774-2785.

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.

Porter, N. J. and 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.

Porter, N. J., Christianson, N. H., Decroos, C. and 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.

Rizvi, S. M. D., Shakil, S. and Haneef, M., 2013. A simple click by click protocol to perform docking: AutoDock 4.2 made easy for non-bioinformaticians. EXCLI Journal. 12: 831-857.

Siegel, D., Hussein, M., Belani, C., et al., 2009. Vorinostat in solid and hematologic malignancies. Journal of Hematology & Oncology. 2(1): 31-42.

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.

Son, C. H., Keum, J. H., Yang, K., et al., 2014. Synergistic enhancement of NK cell-mediated cytotoxicity by combination of histone deacetylase inhibitor andionizing radiation. Radiation Oncology. 9(1): 49-59.

Tabackman, A. A., Frankson, R., Marsan, E. S., Perry, K. and 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.

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.

Van den Wyngaert, I., de Vries, W., Kremer, A., et al., 2000. Cloning and characterization of human histone deacetylase 8. FEBS Letters. 478(1-2): 77-83.

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.

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.

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.

Whitehead, L., Dobler, M. R., Radetich, B., et al., 2011. Human HDAC isoform selectivity achieved via exploitation of the acetate release channel with structurally unique small molecule inhibitors. Bioorganic & Medicinal Chemistry.19(15): 4626-4634.

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.