Skip to content
Licensed Unlicensed Requires Authentication Published by De Gruyter December 22, 2018

Kinetically selective and potent inhibitors of HDAC8

  • Markus Schweipert , Niklas Jänsch , Wisely Oki Sugiarto and Franz-Josef Meyer-Almes EMAIL logo
From the journal Biological Chemistry


Histone deacetylase 8 (HDAC8) is an established and validated target for T-cell lymphoma and childhood neuroblastoma. The active site binding pocket of HDAC8 is highly conserved among all zinc-containing representatives of the histone deacetylase (HDAC) family. This explains that most HDACs are unselectively recognized by similar inhibitors featuring a zinc binding group (ZBG), a hydrophobic linker and a head group. In the light of this difficulty, the creation of isoenzyme-selectivity is one of the major challenges in the development of HDAC inhibitors. In a series of trifluoromethylketone inhibitors of HDAC8 compound 10 shows a distinct binding mechanism and a dramatically increased residence time (RT) providing kinetic selectivity against HDAC4. Combining the binding kinetics results with computational docking and binding site flexibility analysis suggests that 10 occupies the conserved catalytic site as well as an adjacent transient sub-pocket of HDAC8.


Akaike, H. (1974). A new look at the statistical model identification. IEEE Trans Automatic Control 19, 716–723.10.1007/978-1-4612-1694-0_16Search in Google Scholar

Balasubramanian, S., Ramos, J., Luo, W., Sirisawad, M., Verner, E., and Buggy, J. J. (2008). A novel histone deacetylase 8 (HDAC8)-specific inhibitor PCI-34051 induces apoptosis in T-cell lymphomas. Leukemia 22, 1026–1034.10.1038/leu.2008.9Search in Google Scholar PubMed

Bradshaw, J.M., McFarland, J.M., Paavilainen, V.O., Bisconte, A., Tam, D., Phan, V.T., Romanov, S., Finkle, D., Shu, J., Patel, V., et al. (2015). Prolonged and tunable residence time using reversible covalent kinase inhibitors. Nat. Chem. Biol. 11, 525–531.10.1038/nchembio.1817Search in Google Scholar PubMed PubMed Central

Copeland, R.A., Pompliano, D.L., and Meek, T.D. (2006). Drug-target residence time and its implications for lead optimization. Nat. Rev. Drug Discov. 5, 730–739.10.1038/nrd2082Search in Google Scholar PubMed

Corbeil, C. R., Williams, C. I. and Labute, P. (2012). Variability in docking success rates due to dataset preparation. J. Comput. Aided. Mol. Des. 26, 775–786.10.1007/s10822-012-9570-1Search in Google Scholar PubMed PubMed Central

Decroos, C., Clausen, D.J., Haines, B.E., Wiest, O., Williams, R.M., and Christianson, D.W. (2015). Variable active site loop conformations accommodate the binding of macrocyclic largazole analogues to HDAC8. Biochemistry 54, 2126–2135.10.1021/acs.biochem.5b00010Search in Google Scholar PubMed PubMed Central

Deschamps, N., Simões-Pires, C.A., Carrupt, P.-A., and Nurisso, A. (2015). How the flexibility of human histone deacetylases influences ligand binding: an overview. Drug Discov. Today 20, 736–742.10.1016/j.drudis.2015.01.004Search in Google Scholar PubMed

Dowling, D.P., Gantt, S.L., Gattis, S.G., Fierke, C.A., and Christianson, D.W. (2008). Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors. Biochemistry 47, 13554–13563.10.1021/bi801610cSearch in Google Scholar PubMed PubMed Central

Fenichel, M.P. (2015). FDA approves new agent for multiple myeloma. J. Natl. Cancer Inst. 107, djv165. doi: 10.1093/jnci/djv165.10.1093/jnci/djv165Search in Google Scholar PubMed

Finnin, M.S., Donigian, J.R., Cohen, A., Richon, V.M., Rifkind, R.A., Marks, P.A., Breslow, R., and Pavletich, N.P. (1999). Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors. Nature 401, 188–193.10.1038/43710Search in Google Scholar PubMed

Frey, R.R., Wada, C.K., Garland, R.B., Curtin, M.L., Michealides, M.R., Li, J., Pease, L.J., Glaser, K.B., Marcotte, P.A., Bouska, J.J., et al. (2002). Trifluoromethyl ketones as inhibitors of histone deacetylase. Bioorg. Med. Chem. Lett. 12, 3443–3447.10.1016/S0960-894X(02)00754-0Search in Google Scholar PubMed

Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P., and Kummer, U. (2006). COPASI – a COmplex PAthway SImulator. Bioinformatics 22, 3067–3074.10.1093/bioinformatics/btl485Search in Google Scholar PubMed

Huang, W.J., Wang, Y.C., Chao, S.W., Yang, C.Y., Chen, L.C., Lin, M.H., Hou, W.C., Chen, M.Y., Lee, T.L., Yang, P., et al. (2012). Synthesis and biological evaluation of ortho-aryl N-hydroxycinnamides as potent histone deacetylase (HDAC) 8 isoform-selective inhibitors. Chem. Med. Chem. 7, 1815–1824.10.1002/cmdc.201200300Search in Google Scholar PubMed

Jänsch, N., Meyners, C., Muth, M., Kopranovic, A., Witt, O., Oehme, I., and Meyer-Almes, F.-J. (2019). The enzyme activity of histone deacetylase 8 is modulated by a redox-switch. Redox Biol. 20, 60–67.10.1016/j.redox.2018.09.013Search in Google Scholar PubMed PubMed Central

Kleinschek, A., Meyners, C., Digiorgio, E., Brancolini, C., and Meyer-Almes, F.J. (2016). Potent and selective non-hydroxamate histone deacetylase 8 inhibitors. Chem. Med. Chem. 11, 2598–2606.10.1002/cmdc.201600528Search in Google Scholar PubMed

Kokh, D.B., Czodrowski, P., Rippmann, F., and Wade, R.C. (2016). Perturbation approaches for exploring protein binding site flexibility to predict transient binding pockets. J. Chem. Theory Comput. 12, 4100–4113.10.1021/acs.jctc.6b00101Search in Google Scholar PubMed

Koshland Jr, D. (1958). Application of a theory of enzyme specificity to protein synthesis. Proc. Nat. Acad. Sci. USA 44, 98.10.1073/pnas.44.2.98Search in Google Scholar PubMed PubMed Central

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. Bioorg. Med. Chem. Lett. 17, 2874–2878.10.1016/j.bmcl.2007.02.064Search in Google Scholar PubMed

Kunze, M.B., Wright, D.W., Werbeck, N.D., Kirkpatrick, J., Coveney, P.V., and Hansen, D.F. (2013). Loop interactions and dynamics tune the enzymatic activity of the human histone deacetylase 8. J. Am. Chem. Soc. 135, 17862–17868.10.1021/ja408184xSearch in Google Scholar PubMed PubMed Central

Lee, H.Z., Kwitkowski, V.E., Del Valle, P.L., Ricci, M.S., Saber, H., Habtemariam, B.A., Bullock, J., Bloomquist, E., Li Shen, Y., Chen, X.H., et al. (2015). FDA approval: Belinostat for the treatment of patients with relapsed or refractory peripheral T-cell lymphoma. Clin. Cancer. Res. 21, 2666–2670.10.1158/1078-0432.CCR-14-3119Search in Google Scholar PubMed

Lu, H. and Tonge, P.J. (2010). Drug-target residence time: critical information for lead optimization. Curr. Opin. Chem. Biol. 14, 467–474.10.1016/j.cbpa.2010.06.176Search in Google Scholar PubMed PubMed Central

Ma, B., Kumar, S., Tsai, C.-J., and Nussinov, R. (1999). Folding funnels and binding mechanisms. Prot. Eng. 12, 713–720.10.1093/protein/12.9.713Search in Google Scholar PubMed

Madsen, A.S., Kristensen, H.M.E., Lanz, G., and Olsen, C.A. (2014). The effect of various zinc binding groups on inhibition of histone deacetylases 1-11. ChemMedChem. 9, 614–626.10.1002/cmdc.201300433Search in Google Scholar PubMed

Mann, B.S., Johnson, J.R., Cohen, M.H., Justice, R., and Pazdur, R. (2007). FDA approval summary: vorinostat for treatment of advanced primary cutaneous T-cell lymphoma. Oncologist 12, 1247–1252.10.1634/theoncologist.12-10-1247Search in Google Scholar PubMed

Meyer-Almes, F.J. (2016). Discrimination between conformational selection and induced fit protein-ligand binding using integrated global fit analysis. Eur. Biophys. J. 45, 245–257.10.1007/s00249-015-1090-1Search in Google Scholar PubMed

Meyners, C., Baud, M.G., Fuchter, M.J., and Meyer-Almes, F.J. (2014a). Kinetic method for the large-scale analysis of the binding mechanism of histone deacetylase inhibitors. Anal. Biochem. 460, 39–46.10.1016/j.ab.2014.05.014Search in Google Scholar PubMed

Meyners, C., Wawrzinek, R., Kramer, A., Hinz, S., Wessig, P., and Meyer-Almes, F.J. (2014b). A fluorescence lifetime-based binding assay for acetylpolyamine amidohydrolases from Pseudomonas aeruginosa using a [1,3]dioxolo[4,5-f][1,3]benzodioxole (DBD) ligand probe. Anal. Bioanal. Chem. 406, 4889–4897.10.1007/s00216-014-7886-5Search in Google Scholar PubMed

Meyners, C., Mertens, M., Wessig, P., and Meyer-Almes, F.J. (2017). A fluorescence-lifetime-based binding assay for class IIa histone deacetylases. Chemistry 23, 3107–3116.10.1002/chem.201605140Search in Google Scholar PubMed

Niegisch, G., Knievel, J., Koch, A., Hader, C., Fischer, U., Albers, P., and Schulz, W.A. (2013). Changes in histone deacetylase (HDAC) expression patterns and activity of HDAC inhibitors in urothelial cancers. Urol. Oncol. 31, 1770–1779.10.1016/j.urolonc.2012.06.015Search in Google Scholar PubMed

Oehme, I., Deubzer, H.E., Wegener, D., Pickert, D., Linke, J.P., Hero, B., Kopp-Schneider, A., Westermann, F., Ulrich, S.M., von Deimling, A., et al. (2009). Histone deacetylase 8 in neuroblastoma tumorigenesis. Clin. Cancer. Res. 15, 91–99.10.1158/1078-0432.CCR-08-0684Search in Google Scholar PubMed

Park, S.Y., Jun, J.A., Jeong, K.J., Heo, H.J., Sohn, J.S., Lee, H.Y., Park, C.G., and Kang, J. (2011). Histone deacetylases 1, 6 and 8 are critical for invasion in breast cancer. Oncol. Rep. 25, 1677–1681.10.3892/or.2011.1236Search in Google Scholar PubMed

Seeliger, D., Haas, J., and de Groot, B.L. (2007). Geometry-based sampling of conformational transitions in proteins. Structure 15, 1482–1492.10.1016/j.str.2007.09.017Search in Google Scholar PubMed

Singh, J., Petter, R.C., Baillie, T.A., and Whitty, A. (2011). The resurgence of covalent drugs. Nat. Rev. Drug Discov. 10, 307–317.10.1038/nrd3410Search in Google Scholar PubMed

Somoza, J.R., Skene, R.J., Katz, B.A., Mol, C., Ho, J.D., Jennings, A.J., Luong, C., Arvai, A., Buggy, J.J., Chi, E., et al. (2004). Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases. Structure 12, 1325–1334.10.1016/j.str.2004.04.012Search in Google Scholar PubMed

Stank, A., Kokh, D.B., Horn, M., Sizikova, E., Neil, R., Panecka, J., Richter, S., and Wade, R.C. (2017). TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets. Nucleic Acids Res. 45, W325–W330.10.1093/nar/gkx277Search in Google Scholar PubMed PubMed Central

Suzuki, T., Ota, Y., Ri, M., Bando, M., Gotoh, A., Itoh, Y., Tsumoto, H., Tatum, P.R., Mizukami, T., Nakagawa, H., et al. (2012). Rapid discovery of highly potent and selective inhibitors of histone deacetylase 8 using click chemistry to generate candidate libraries. J. Med. Chem. 55, 9562–9575.10.1021/jm300837ySearch in Google Scholar PubMed

Tummino, P.J. and Copeland, R.A. (2008). Residence time of receptor – Ligand complexes and its effect on biological function. Biochemistry 47, 5481–5492.10.1021/bi8002023Search in Google Scholar PubMed

Volund, A. (1978). Application of the four-parameter logistic model to bioassay: comparison with slope ratio and parallel line models. Biometrics 34, 357–365.10.2307/2530598Search in Google Scholar

Wagner, F., Zhang, Y.-L., Fass, D., Joseph, N., Gale, J., Weïwer, M., McCarren, P., Fisher, S., Kaya, T., and Zhao, W.-N. (2015). Kinetically selective inhibitors of histone deacetylase 2 (HDAC2) as cognition enhancers. Chem. Sci. 6, 804–815.10.1039/C4SC02130DSearch in Google Scholar PubMed PubMed Central

Wawrzinek, R., Ziomkowska, J., Heuveling, J., Mertens, M., Herrmann, A., Schneider, E., and Wessig, P. (2013). DBD dyes as fluorescence lifetime probes to study conformational changes in proteins. Chemistry 19, 17349–17357.10.1002/chem.201302368Search in Google Scholar PubMed

Wentsch, H.K., Walter, N.M., Buhrmann, M., Mayer-Wrangowski, S., Rauh, D., Zaman, G.J.R., Willemsen-Seegers, N., Buijsman, R.C., Henning, M., Dauch, D., et al. (2017). Optimized target residence time: type I1/2 inhibitors for p38alpha MAP kinase with improved binding kinetics through direct interaction with the R-spine. Angewandte Chemie 56, 5363–5367.10.1002/anie.201701185Search in Google Scholar PubMed

Whitehead, L., Dobler, M.R., Radetich, B., Zhu, Y., Atadja, P.W., Claiborne, T., Grob, J.E., McRiner, A., Pancost, M.R., Patnaik, A., et al. (2011). Human HDAC isoform selectivity achieved via exploitation of the acetate release channel with structurally unique small molecule inhibitors. Bioorg. Med. Chem. 19, 4626–4634.10.1016/j.bmc.2011.06.030Search in Google Scholar PubMed

Wright, J.S., Anderson, J.M., Shadnia, H., Durst, T., and Katzenellenbogen, J.A. (2013). Experimental versus predicted affinities for ligand binding to estrogen receptor: iterative selection and rescoring of docked poses systematically improves the correlation. J. Comput. Aided Mol. Des. 27, 707–721.10.1007/s10822-013-9670-6Search in Google Scholar PubMed

Supplementary Material

The online version of this article offers supplementary material (

Received: 2018-08-31
Accepted: 2018-11-25
Published Online: 2018-12-22
Published in Print: 2019-06-26

©2019 Walter de Gruyter GmbH, Berlin/Boston

Downloaded on 5.6.2023 from
Scroll to top button