Histone deacetylases (HDACs) play a pivotal role in various biological pathways and represent interesting drug targets. Therefore, HDAC inhibitors (HDACi) with high isoform selectivity and a zinc-binding group different from hydroxamic acid, because of its low metabolic stability, are required. HDAC11, as a highly potent defatty-acylase, differs from other HDACs in its substrate preference. Starting from this finding, we developed specific inhibitors for HDAC11 based on a peptide containing a fatty-acylated lysine side chain as the selectivity tail. The introduction of different heteroatoms at the fatty acyl residue was used to generate potent zinc-binding groups in combination with the scissile amide bond, as well as to suppress substrate properties of the resulting compounds. Further optimization resulted in a highly potent and selective HDAC11 inhibitor 31, which exhibits low nanomolar inhibition against HDAC11 without targeting other HDACs and is active in cells. The data presented here may help expand the range of zinc-binding groups utilized in HDAC inhibitors. Furthermore, the concept of the selectivity tail was demonstrated to facilitate straightforward access to selective defatty-acylase inhibitors.

Department of Enzymology Charles Tanford Protein Center Institute of Biochemistry and Biotechnology Martin Luther University Halle Wittenberg 06120 Halle Germany

Department of Medicinal Chemistry Institute of Pharmacy Martin Luther University Halle Wittenberg 06120 Halle Germany

Institute of Biotechnology of the Czech Academy of Sciences BIOCEV Prumyslova 595 252 50 Vestec Czech Republic

Zobrazit více v PubMed

Yang X. J., Seto E.. The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men. Nat. Rev. Mol. Cell Biol. 2008;9(3):206–218. doi: 10.1038/nrm2346. PubMed DOI PMC

Robinson E. L., Tharp C. A., Bagchi R. A., McKinsey T. A.. Gravi-D peptide disrupts HDAC11 association with an AKAP to stimulate adipocyte thermogenic signaling. J. Clin Invest. 2024;134(9):e177726. doi: 10.1172/JCI177726. PubMed DOI PMC

Liu H., Hu Q., D’Ercole A J., Ye P.. Histone deacetylase 11 regulates oligodendrocyte-specific gene expression and cell development in OL-1 oligodendroglia cells. Glia. 2009;57(1):1–12. doi: 10.1002/glia.20729. PubMed DOI PMC

Cao J., Sun L., Aramsangtienchai P., Spiegelman N. A., Zhang X., Huang W., Seto E., Lin H.. HDAC11 regulates type I interferon signaling through defatty-acylation of SHMT2. Proc. Natl. Acad. Sci. U. S. A. 2019;116(12):5487–5492. doi: 10.1073/pnas.1815365116. PubMed DOI PMC

Haberland M., Montgomery R. L., Olson E. N.. The many roles of histone deacetylases in development and physiology: implications for disease and therapy. Nat. Rev. Genet. 2009;10(1):32–42. doi: 10.1038/nrg2485. PubMed DOI PMC

Seto E., Yoshida M.. Erasers of histone acetylation: the histone deacetylase enzymes. Cold Spring Harb Perspect Biol. 2014;6(4):a018713. doi: 10.1101/cshperspect.a018713. PubMed DOI PMC

Sauve A. A., Wolberger C., Schramm V. L., Boeke J. D.. The biochemistry of sirtuins. Annu. Rev. Biochem. 2006;75:435–465. doi: 10.1146/annurev.biochem.74.082803.133500. PubMed DOI

Aramsangtienchai P., Spiegelman N. A., He B., Miller S. P., Dai L., Zhao Y., Lin H.. HDAC8 Catalyzes the Hydrolysis of Long Chain Fatty Acyl Lysine. ACS Chem. Biol. 2016;11(10):2685–2692. doi: 10.1021/acschembio.6b00396. PubMed DOI PMC

Feldman J. L., Dittenhafer-Reed K. E., Kudo N., Thelen J. N., Ito A., Yoshida M., Denu J. M.. Kinetic and Structural Basis for Acyl-Group Selectivity and NAD­(+) Dependence in Sirtuin-Catalyzed Deacylation. Biochemistry. 2015;54(19):3037–3050. doi: 10.1021/acs.biochem.5b00150. PubMed DOI PMC

Kutil Z., Novakova Z., Meleshin M., Mikesova J., Schutkowski M., Barinka C.. Histone Deacetylase 11 Is a Fatty-Acid Deacylase. ACS Chem. Biol. 2018;13(3):685–693. doi: 10.1021/acschembio.7b00942. PubMed DOI

Moreno-Yruela C., Galleano I., Madsen A. S., Olsen C. A.. Histone Deacetylase 11 Is an epsilon-N-Myristoyllysine Hydrolase. Cell Chem. Biol. 2018;25(7):849–856.e8. doi: 10.1016/j.chembiol.2018.04.007. PubMed DOI

Gao L., Cueto M. A., Asselbergs F., Atadja P.. Cloning and functional characterization of HDAC11, a novel member of the human histone deacetylase family. J. Biol. Chem. 2002;277(28):25748–55. doi: 10.1074/jbc.M111871200. PubMed DOI

Wang W., Fu L., Li S., Xu Z., Li X.. Histone deacetylase 11 suppresses p53 expression in pituitary tumor cells. Cell Biol. Int. 2017;41(12):1290–1295. doi: 10.1002/cbin.10834. PubMed DOI

Gong D., Zeng Z., Yi F., Wu J.. Inhibition of histone deacetylase 11 promotes human liver cancer cell apoptosis. Am. J. Transl Res. 2019;11(2):983–990. PubMed PMC

Hurtado E., Nunez-Alvarez Y., Munoz M., Gutierrez-Caballero C., Casas J., Pendas A. M., Peinado M. A., Suelves M.. HDAC11 is a novel regulator of fatty acid oxidative metabolism in skeletal muscle. FEBS J. 2021;288(3):902–919. doi: 10.1111/febs.15456. PubMed DOI

Villagra A., Cheng F., Wang H. W., Suarez I., Glozak M., Maurin M., Nguyen D., Wright K. L., Atadja P. W., Bhalla K., Pinilla-Ibarz J., Seto E., Sotomayor E. M.. The histone deacetylase HDAC11 regulates the expression of interleukin 10 and immune tolerance. Nat. Immunol. 2009;10(1):92–100. doi: 10.1038/ni.1673. PubMed DOI PMC

Bagchi R. A., Ferguson B. S., Stratton M. S., Hu T., Cavasin M. A., Sun L., Lin Y. H., Liu D., Londono P., Song K., Pino M. F., Sparks L. M., Smith S. R., Scherer P. E., Collins S., Seto E., McKinsey T. A.. HDAC11 suppresses the thermogenic program of adipose tissue via BRD2. JCI Insight. 2018;3(15):e120159. doi: 10.1172/jci.insight.120159. PubMed DOI PMC

Sun L., Marin de Evsikova C., Bian K., Achille A., Telles E., Pei H., Seto E.. Programming and Regulation of Metabolic Homeostasis by HDAC11. EBioMedicine. 2018;33:157–168. doi: 10.1016/j.ebiom.2018.06.025. PubMed DOI PMC

Zhang F., Yue K., Sun S., Lu S., Jia G., Zha Y., Zhang S., Chou C. J., Liao C., Li X., Duan Y.. Targeting Histone Deacetylase 11 with a Highly Selective Inhibitor for the Treatment of MASLD. Adv. Sci. (Weinh) 2025;12:e2412903. doi: 10.1002/advs.202412903. PubMed DOI PMC

Deubzer H. E., Schier M. C., Oehme I., Lodrini M., Haendler B., Sommer A., Witt O.. HDAC11 is a novel drug target in carcinomas. Int. J. Cancer. 2013;132(9):2200–8. doi: 10.1002/ijc.27876. PubMed DOI

Bora-Singhal N., Mohankumar D., Saha B., Colin C. M., Lee J. Y., Martin M. W., Zheng X., Coppola D., Chellappan S.. Novel HDAC11 inhibitors suppress lung adenocarcinoma stem cell self-renewal and overcome drug resistance by suppressing Sox2. Sci. Rep. 2020;10(1):4722. doi: 10.1038/s41598-020-61295-6. PubMed DOI PMC

Li R., Wu X., Zhao P., Xue K., Li J.. A pan-cancer analysis identifies HDAC11 as an immunological and prognostic biomarker. FASEB J. 2022;36(7):e22326. doi: 10.1096/fj.202101742RR. PubMed DOI

Yang M., Zhao W., Zhang J., Liu L., Tian S., Miao Y., Jia Y., Wang L., Chai Q., Wang Q., Liu F., Zhang Y., You X.. HDAC11 Inhibition as a Potential Therapeutic Strategy for AML: Target Identification, Lead Discovery, Antitumor Potency, and Mechanism Investigation. J. Med. Chem. 2025;68(8):8124–8142. doi: 10.1021/acs.jmedchem.4c02550. PubMed DOI

Bolden J. E., Peart M. J., Johnstone R. W.. Anticancer activities of histone deacetylase inhibitors. Nat. Rev. Drug Discov. 2006;5(9):769–84. doi: 10.1038/nrd2133. PubMed DOI

Duvic M., Talpur R., Ni X., Zhang C., Hazarika P., Kelly C., Chiao J. H., Reilly J. F., Ricker J. L., Richon V. M., Frankel S. R.. Phase 2 trial of oral vorinostat (suberoylanilide hydroxamic acid, SAHA) for refractory cutaneous T-cell lymphoma (CTCL) Blood. 2007;109(1):31–9. doi: 10.1182/blood-2006-06-025999. PubMed DOI PMC

Molife L. R., de Bono J. S.. Belinostat: clinical applications in solid tumors and lymphoma. Expert Opin Investig Drugs. 2011;20(12):1723–32. doi: 10.1517/13543784.2011.629604. PubMed DOI

Garnock-Jones K. P.. Panobinostat: first global approval. Drugs. 2015;75(6):695–704. doi: 10.1007/s40265-015-0388-8. PubMed DOI

Celesia A., Notaro A., Franzo M., Lauricella M., D’Anneo A., Carlisi D., Giuliano M., Emanuele S.. The Histone Deacetylase Inhibitor ITF2357 (Givinostat) Targets Oncogenic BRAF in Melanoma Cells and Promotes a Switch from Pro-Survival Autophagy to Apoptosis. Biomedicines. 2022;10(8):1994. doi: 10.3390/biomedicines10081994. PubMed DOI PMC

Friedrich A., Assmann A. S., Schumacher L., Stuijvenberg J. V., Kassack M. U., Schulz W. A., Roos W. P., Hansen F. K., Pflieger M., Kurz T., Fritz G.. In Vitro Assessment of the Genotoxic Hazard of Novel Hydroxamic Acid- and Benzamide-Type Histone Deacetylase Inhibitors (HDACi) Int. J. Mol. Sci. 2020;21(13):4747. doi: 10.3390/ijms21134747. PubMed DOI PMC

Shen S., Kozikowski A. P.. Why Hydroxamates May Not Be the Best Histone Deacetylase Inhibitors--What Some May Have Forgotten or Would Rather Forget? ChemMedChem. 2016;11(1):15–21. doi: 10.1002/cmdc.201500486. PubMed DOI PMC

Lee M. S., Isobe M.. Metabolic activation of the potent mutagen, 2-naphthohydroxamic acid, in Salmonella typhimurium TA98. Cancer Res. 1990;50(14):4300–4307. PubMed

Bornes K. E., Moody M. A., Huckaba T. M., Benz M. C., McConnell E. C., Foroozesh M., Barnes V. H., Collins-Burow B. M., Burow M. E., Watt T. J., Toro T. B.. Lysine deacetylase inhibitors have low selectivity in cells and exhibit predominantly off-target effects. FEBS Open Bio. 2025;15(1):94–107. doi: 10.1002/2211-5463.13896. PubMed DOI PMC

Ibrahim H. S., Guo M., Hilscher S., Erdmann F., Schmidt M., Schutkowski M., Sheng C., Sippl W.. Probing class I histone deacetylases (HDAC) with proteolysis targeting chimera (PROTAC) for the development of highly potent and selective degraders. Bioorg Chem. 2024;153:107887. doi: 10.1016/j.bioorg.2024.107887. PubMed DOI

Sun P., Wang J., Khan K. S., Yang W., Ng B. W., Ilment N., Zessin M., Bulbul E. F., Robaa D., Erdmann F., Schmidt M., Romier C., Schutkowski M., Cheng A. S., Sippl W.. Development of Alkylated Hydrazides as Highly Potent and Selective Class I Histone Deacetylase Inhibitors with T cell Modulatory Properties. J. Med. Chem. 2022;65(24):16313–16337. doi: 10.1021/acs.jmedchem.2c01132. PubMed DOI

Bora-Tatar G., Dayangac-Erden D., Demir A. S., Dalkara S., Yelekci K., Erdem-Yurter H.. Molecular modifications on carboxylic acid derivatives as potent histone deacetylase inhibitors: Activity and docking studies. Bioorg. Med. Chem. 2009;17(14):5219–28. doi: 10.1016/j.bmc.2009.05.042. PubMed DOI

Fruhauf A., Meyer-Almes F. J.. Non-Hydroxamate Zinc-Binding Groups as Warheads for Histone Deacetylases. Molecules. 2021;26(17):5151. doi: 10.3390/molecules26175151. PubMed DOI PMC

McKinsey T. A.. Isoform-selective HDAC inhibitors: closing in on translational medicine for the heart. J. Mol. Cell Cardiol. 2011;51(4):491–6. doi: 10.1016/j.yjmcc.2010.11.009. PubMed DOI

Ho T. T., Peng C., Seto E., Lin H.. Trapoxin A Analogue as a Selective Nanomolar Inhibitor of HDAC11. ACS Chem. Biol. 2023;18(4):803–809. doi: 10.1021/acschembio.2c00840. PubMed DOI PMC

Son S. I., Cao J., Zhu C. L., Miller S. P., Lin H.. Activity-Guided Design of HDAC11-Specific Inhibitors. ACS Chem. Biol. 2019;14(7):1393–1397. doi: 10.1021/acschembio.9b00292. PubMed DOI PMC

Martin M. W., Lee J. Y., Lancia D. R. Jr., Ng P. Y., Han B., Thomason J. R., Lynes M. S., Marshall C. G., Conti C., Collis A., Morales M. A., Doshi K., Rudnitskaya A., Yao L., Zheng X.. Discovery of novel N-hydroxy-2-arylisoindoline-4-carboxamides as potent and selective inhibitors of HDAC11. Bioorg. Med. Chem. Lett. 2018;28(12):2143–2147. doi: 10.1016/j.bmcl.2018.05.021. PubMed DOI

Baselious F., Hilscher S., Hagemann S., Tripathee S., Robaa D., Barinka C., Hüttelmaier S., Schutkowski M., Sippl W.. Utilization of an Optimized AlphaFold Protein Model for Structure-Based Design of a Selective HDAC11 Inhibitor with Anti-neuroblastoma Activity. Arch Pharm. 2024;357(10):e2400486. doi: 10.1002/ardp.202400486. PubMed DOI

Baselious F., Hilscher S., Robaa D., Barinka C., Schutkowski M., Sippl W.. Comparative Structure-Based Virtual Screening Utilizing Optimized AlphaFold Model Identifies Selective HDAC11 Inhibitor. Int. J. Mol. Sci. 2024;25(2):1358. doi: 10.3390/ijms25021358. PubMed DOI PMC

Son S. I., Su D., Ho T. T., Lin H.. Garcinol Is an HDAC11 Inhibitor. ACS Chem. Biol. 2020;15(11):2866–2871. doi: 10.1021/acschembio.0c00719. PubMed DOI PMC

Piekarz R. L., Frye R., Turner M., Wright J. J., Allen S. L., Kirschbaum M. H., Zain J., Prince H. M., Leonard J. P., Geskin L. J., Reeder C., Joske D., Figg W. D., Gardner E. R., Steinberg S. M., Jaffe E. S., Stetler-Stevenson M., Lade S., Fojo A. T., Bates S. E.. Phase II multi-institutional trial of the histone deacetylase inhibitor romidepsin as monotherapy for patients with cutaneous T-cell lymphoma. J. Clin Oncol. 2009;27(32):5410–7. doi: 10.1200/JCO.2008.21.6150. PubMed DOI PMC

Kutil Z., Mikesova J., Zessin M., Meleshin M., Novakova Z., Alquicer G., Kozikowski A., Sippl W., Barinka C., Schutkowski M.. Continuous Activity Assay for HDAC11 Enabling Reevaluation of HDAC Inhibitors. ACS Omega. 2019;4(22):19895–19904. doi: 10.1021/acsomega.9b02808. PubMed DOI PMC

Li S., Fossati G., Marchetti C., Modena D., Pozzi P., Reznikov L. L., Moras M. L., Azam T., Abbate A., Mascagni P., Dinarello C. A.. Specific inhibition of histone deacetylase 8 reduces gene expression and production of proinflammatory cytokines in vitro and in vivo. J. Biol. Chem. 2015;290(4):2368–78. doi: 10.1074/jbc.M114.618454. PubMed DOI PMC

Matalon S., Palmer B. E., Nold M. F., Furlan A., Kassu A., Fossati G., Mascagni P., Dinarello C. A.. The histone deacetylase inhibitor ITF2357 decreases surface CXCR4 and CCR5 expression on CD4­(+) T-cells and monocytes and is superior to valproic acid for latent HIV-1 expression in vitro. J. Acquir Immune Defic Syndr. 2010;54(1):1–9. doi: 10.1097/QAI.0b013e3181d3dca3. PubMed DOI PMC

Zessin M., Meleshin M., Simic Z., Kalbas D., Arbach M., Gebhardt P., Melesina J., Liebscher S., Bordusa F., Sippl W., Barinka C., Schutkowski M.. Continuous Sirtuin/HDAC (histone deacetylase) activity assay using thioamides as PET (Photoinduced Electron Transfer)-based fluorescence quencher. Bioorg Chem. 2021;117:105425. doi: 10.1016/j.bioorg.2021.105425. PubMed DOI

Dankova D., Nielsen A. L., Zarda A., Hansen T. N., Hesse M., Benova M., Tsiris A., Bartling C. R. O., Will E. J., Stromgaard K., Moreno-Yruela C., Heinis C., Olsen C. A.. Discovery of De Novo Macrocycle Inhibitors of Histone Deacetylase 11. JACS Au. 2025;5(3):1299–1307. doi: 10.1021/jacsau.4c01148. PubMed DOI PMC

Ranganathan R., Lenti G., Tassone N. M., Scannell B. J., Southern C. A., Karver C. E.. Design and application of a fluorogenic assay for monitoring inflammatory caspase activity. Anal. Biochem. 2018;543:1–7. doi: 10.1016/j.ab.2017.11.023. PubMed DOI

Kopranovic A., Meyer-Almes F. J.. Discovery and Characterization of Novel Non-Hydroxamate HDAC11 Inhibitors. Int. J. Mol. Sci. 2025;26(13):5950. doi: 10.3390/ijms26135950. PubMed DOI PMC

Nishimura O., Suenaga M., Ohmae H., Tsuji S., Suenaga M., Fujino M.. An efficient chemical method for removing N-terminal extra methionine from recombinant methionylated human growth hormone. Chem. Commun. 1998;10:1135–1136. doi: 10.1039/a801297k. DOI

Zessin M., Kutil Z., Meleshin M., Novakova Z., Ghazy E., Kalbas D., Marek M., Romier C., Sippl W., Barinka C., Schutkowski M.. One-Atom Substitution Enables Direct and Continuous Monitoring of Histone Deacylase Activity. Biochemistry. 2019;58(48):4777–4789. doi: 10.1021/acs.biochem.9b00786. PubMed DOI

Whitehead L., Dobler M. R., Radetich B., Zhu Y., Atadja P. W., Claiborne T., Grob J. E., McRiner A., Pancost M. R., Patnaik A., Shao W., Shultz M., Tichkule R., Tommasi R. A., Vash B., Wang P., Stams T.. Human HDAC isoform selectivity achieved via exploitation of the acetate release channel with structurally unique small molecule inhibitors. Bioorg. Med. Chem. 2011;19(15):4626–34. doi: 10.1016/j.bmc.2011.06.030. PubMed DOI

Greenwood S. O. R., Chan A. W. E., Hansen D. F., Marson C. M.. Potent non-hydroxamate inhibitors of histone deacetylase-8: Role and scope of an isoindolin-2-yl linker with an alpha-amino amide as the zinc-binding unit. Bioorg. Med. Chem. Lett. 2020;30(5):126926. doi: 10.1016/j.bmcl.2019.126926. PubMed DOI

Włostowski M., Czarnocka S., Maciejewski P.. Efficient S-alkylation of cysteine in the presence of 1,1,3,3-tetramethylguanidine. Tetrahedron Lett. 2010;51(46):5977–5979. doi: 10.1016/j.tetlet.2010.08.097. DOI

Mellini P., Itoh Y., Elboray E. E., Tsumoto H., Li Y., Suzuki M., Takahashi Y., Tojo T., Kurohara T., Miyake Y., Miura Y., Kitao Y., Kotoku M., Iida T., Suzuki T.. Identification of Diketopiperazine-Containing 2-Anilinobenzamides as Potent Sirtuin 2 (SIRT2)-Selective Inhibitors Targeting the ″Selectivity Pocket″, Substrate-Binding Site, and NAD­(+)-Binding Site. J. Med. Chem. 2019;62(12):5844–5862. doi: 10.1021/acs.jmedchem.9b00255. PubMed DOI

Schuster S., Roessler C., Meleshin M., Zimmermann P., Simic Z., Kambach C., Schiene-Fischer C., Steegborn C., Hottiger M. O., Schutkowski M.. A continuous sirtuin activity assay without any coupling to enzymatic or chemical reactions. Sci. Rep. 2016;6:22643. doi: 10.1038/srep22643. PubMed DOI PMC

Baselious F., Robaa D., Sippl W.. Utilization of AlphaFold models for drug discovery: Feasibility and challenges. Histone deacetylase 11 as a case study. Comput. Biol. Med. 2023;167:107700. doi: 10.1016/j.compbiomed.2023.107700. PubMed DOI

Charron G., Zhang M. M., Yount J. S., Wilson J., Raghavan A. S., Shamir E., Hang H. C.. Robust fluorescent detection of protein fatty-acylation with chemical reporters. J. Am. Chem. Soc. 2009;131(13):4967–75. doi: 10.1021/ja810122f. PubMed DOI

Faraco G., Pancani T., Formentini L., Mascagni P., Fossati G., Leoni F., Moroni F., Chiarugi A.. Pharmacological inhibition of histone deacetylases by suberoylanilide hydroxamic acid specifically alters gene expression and reduces ischemic injury in the mouse brain. Mol. Pharmacol. 2006;70(6):1876–84. doi: 10.1124/mol.106.027912. PubMed DOI

Zessin M., Meleshin M., Hilscher S., Schiene-Fischer C., Barinka C., Jung M., Schutkowski M.. Continuous Fluorescent Sirtuin Activity Assay Based on Fatty Acylated Lysines. Int. J. Mol. Sci. 2023;24(8):7416. doi: 10.3390/ijms24087416. PubMed DOI PMC

Noritsugu K., Suzuki T., Dodo K., Ohgane K., Ichikawa Y., Koike K., Morita S., Umehara T., Ogawa K., Sodeoka M., Dohmae N., Yoshida M., Ito A.. Lysine long-chain fatty acylation regulates the TEAD transcription factor. Cell Rep. 2023;42(4):112388. doi: 10.1016/j.celrep.2023.112388. PubMed DOI