Docking belinostat into HDAC 8 using autodock tool

Huynh Nhu Thao * , Bui Thi Buu Hue , Le Thi Bach , Tran Quang De , Ha Thi Kim Quy , Nguyen Thanh Si , Nguyen Huu Toan , Nguyen Cuong Quoc and Nguyen Trong Tuan

* Corresponding authorHuynh Nhu Thao

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Received: 04 Mar 2020
Revised: 23 Apr 2020
Accepted: 31 Jul 2020
Published: 31 Jul 2020
DOI: 10.22144/ctu.jen.2020.009
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Huynh, N. T., Bui, T. B. H., Le, T. B., Tran, Q. D., Ha, T. K. Q., Nguyen, T. S., Nguyen, H. T., Nguyen, C. Q., & Nguyen, T. T. (2020). Docking belinostat into HDAC 8 using autodock tool. CTU Journal of Innovation and Sustainable Development , 12(2), 1-8. https://doi.org/10.22144/ctu.jen.2020.009
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Vol. 12 No. 2 (2020)

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Abstract

Belinostat, a histone deacetylases inhibitor, was reached the marketing approval by FDA for the treatment of relapsed and refractory peripheral T-cell lymphomas in 2014. Among 18 Histone Deacetylase (HDAC) enzymes, HDAC 8 has grabbed considerable attention from chemists as a promising target for cancer treatment, which leads to an ever-growing demand for the discovery of novel HDAC 8 inhibitors. With the advent of technologies, a useful and free-of-charge software – Autodock Tool was introduced to dock belinostat into the active site of HDAC 8 in this report. Nevertheless, docking to HDACs, known as metalloenzymes, still remains a challenge due to the interaction with Zn2+ ion at the bottom of the active binding site of the enzyme. For this reason, the extension of the Autodock forcefield to the new one named Autodock4Zn was utilized. The outcomes showed significant improvements in performance in both free energy of binding estimation as well as binding capacity of belinostat with different amino acids of HDAC8.
Keywords: Autodock4, Autodock4Zn, HDAC 8, metalloenzymes

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References

Balasubramanian, S., Ramos, J., Luo, W., Sirisawad, M., Verner, E., & Buggy, J. J., 2008. A novel histone deacetylase 8 (HDAC8)-specifc inhibitor PCI-34051 induces apoptosis in T-cell lymphomas. Leukemia. 22(5): 1026–1034.

Barneda-Zahonero, B., & Parra, M., 2012. Histone deacetylases and cancer. Molecular Oncology, 6(6): 579-589.

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

Chakrabarti, Ina Oehme, Olaf Witt and et al., 2015. HDAC8: a multifaceted target for therapeutic interventions. Trends in Pharmacological Sciences. 36: 481-492.

Chakrabarti, A., Melesina, J., Kolbinger, F. R., et al., 2016. Targeting histone deacetylase 8 as a therapeutic approach to cancer and neurodegenerative diseases. Future Medicinal Chemistry. 8(13): 1609-1634.

Chang, S., McKinsey, T. A., Zhang, C. L., Richardson, J. A., Hill, J. A., & Olson, E. N., , 2014. Histone Deacetylases 5 and 9 Govern Responsiveness of the Heart to a Subset of Stress Signals and Play Redundant Roles in Heart Development. Mol. Cell. Bio. 24: 8467–8476.

Ruijter, A. J. D., Gennip, A. H. V., Caron, H. N., Kemp, S., & Kuilenburg, A. B. V., 2003. Histone deacetylases (HDACs): characterization of the classical HDAC family. Biochemical Journal, 370(3): 737-749.

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.

Finnin, M.S.; Donigian, J.R.; Cohen, A.; Richon, V.M.; Rifkind, R.A.; Marks, P.A.; Breslow, R.; Pavletich, N.P, 1999. Structures of a histone deacetylase homologue bound to the tsa and saha inhibitors. Nature, 401: 188–193.

Grant, S., Easley, C., & Kirkpatrick, P., 2007. Vorinostat.

Haberland M, M. R. O. E., 2009. The many roles of histone deacetylases in development and physiology: implications for disease and therapy. Nat Rev Genet. 10: 32-42.

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, D., Li, X., & Xiu, Z., 2012. Molecular modeling of the interactions between histone deacetylase 8 and inhibitors. Journal of Theoretical and Computational Chemistry. 11: 907-924.

Kelly WK, O. O., K. L., C. J. et al., 2005. Phase I study of an oral histone deacetylase inhibitor, suberoylanilide hydroxamic acid, in patients with advanced cancer. J Clin Oncol. 23: 3923-3931.

KrennHrubec, K., Marshall, B. L., Hedglin, M., Verdin, E., & Ulrich, S. M., 2007. Design and evaluation of ‘linkerless’ hydroxamic acids as selective HDAC8 inhibitors. Bioorg. Med. Chem. Lett. 17(10): 2874–2878.

Oehme I, Deubzer HE, Wegener D et al., 2009. Histone deacetylase 8 in neuroblastoma tumorigenesis. Clin. Cancer Res. 15(1): 91–99.

Olson DE, Wagner FF, Kaya T et al., 2013. Discovery of the first histone deacetylase 6/8 dual inhibitors. J. Med. Chem. 56(11): 4816–4820.

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

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

Micelli, C., Rastelli, G., 2015. Histone deacetylases: structural determinants of inhibitor selectivity. Drug Discov. Today 20(6): 718–735.

Montgomery, R.L., Potthoff, M.J., Haberland, M., et al., 2008. Maintenance of Cardiac Energy Metabolism by Histone Deacetylase 3 in Mice. J. Clin. Invest. 118: 3588–3597.

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.

Morris, 2007. AutoDock. [Online]. Available at: http://autodock.scripps.edu/wiki/AutoGrid

Saha and Pahan, 2006. HDACs in neurodegeneration: a tale of disconcerted acetylation homestasis. Cell Death & Differentiation. 13: 539-550.

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: 1325-1334.

Parbin, S., Kar, S., Shilpi, A., Sengupta et al., 2014. Histone deacetylases: a saga of pertubed acetylation homeostasis in cancer. Journal of Histochemistry & Cytochemistry. 62: 11-33.

Santos-Martins, D., Forli, S., Ramos et al., 2014. AutoDock4Zn: An improved AutoDock forcefield for small-molecule docking to zinc metalloproteins. Journal of Chemical Information and Modeling. 54: 2371-2379.

Roohani, N., Hurrell, R., Kelishadi, R., & Schulin, R., 2013. Zinc and its importance for human health: An integrative review. Journal of Research in Medical Sciences: The Official Journal of Isfahan University of Medical Sciences, 18(2): 144.

Thien, H. D., 2019. Molecular docking studies of synthesized benzimidazole derivatives as Hepatitis C virus NS5B inhibitors. Master Thesis. Can Tho University. Can Tho City

Uba, A. I., & Yelekci, K., 2017. Exploration of the binding pocket of histone deacetylases: the design of potent and isoform-selective inhibitors. Turkish Journal of Biology, 41(6): 901-918.

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

Walkinshaw, D. R., & Yang, X. J., 2008. Histone deacetylase inhibitors as novel anticancer therapeutics. Current Oncology, 15(5): 237.

Zhang, L., Zhang, J., Jiang, Q., et al., 2018. Zinc binding groups for histone deacetylase inhibitors. Journal of enzyme inhibition and medicinal chemistry, 33(1): 714-721.