Mercaptoacetamide histone deacetylase inhibitors are neuroprotective agents that do not exhibit the genotoxicity associated with more commonly used hydroxamate inhibitors. Here, we present the crystal structure of a selective mercaptoacetamide complexed with the C-terminal catalytic domain of HDAC6. When compared with the structure of a mercaptoacetamide bound to the class I isozyme HDAC8, different interactions are observed with the conserved tandem histidine pair in the active site. These differences likely contribute to the selectivity for inhibition of HDAC6, an important target for cancer chemotherapy and the treatment of neurodegenerative disease.

Department of Medicinal Chemistry and Pharmacognosy Drug Discovery Program University of Illinois at Chicago Chicago Illinois 60612 United States

Laboratory of Structural Biology Institute of Biotechnology of the Czech Academy of Sciences Prumyslova 595 252 50 Vestec Czech Republic

Roy and Diana Vagelos Laboratories Department of Chemistry University of Pennsylvania Philadelphia Pennsylvania 19104 6323 United States

StarWise Therapeutics LLC 505 South Rosa Road Madison Wisconsin 53719 United States

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López J. E.; Sullivan E. D.; Fierke C. A. Metal-dependent deacetylases: cancer and epigenetic regulators. ACS Chem. Biol. 2016, 11, 706–716. 10.1021/acschembio.5b01067. PubMed DOI PMC

Zhao S.; Xu W.; Jiang W.; Yu W.; Lin Y.; Zhang T.; Yao J.; Zhou L.; Zeng Y.; Li H.; Li Y.; Shi J.; An W.; Hancock S. M.; He F.; Qin L.; Chin J.; Yang P.; Chen X.; Lei Q.; Xiong Y.; Guan K. L. Regulation of cellular metabolism by protein lysine acetylation. Science 2010, 327, 1000–1004. 10.1126/science.1179689. PubMed DOI PMC

Wang Q.; Zhang Y.; Yang C.; Xiong H.; Lin Y.; Yao J.; Li H.; Xie L.; Zhao W.; Yao Y.; Ning Z. B.; Zeng R.; Xiong Y.; Guan K. L.; Zhao S.; Zhao G. P. Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. Science 2010, 327, 1004–1007. 10.1126/science.1179687. PubMed DOI PMC

Choudhary C.; Weinert B. T.; Nishida Y.; Verdin E.; Mann M. The growing landscape of lysine acetylation links metabolism and cell signaling. Nat. Rev. Mol. Cell Biol. 2014, 15, 536–550. 10.1038/nrm3841. PubMed DOI

Gregoretti I. V.; Lee Y. M.; Goodson H. V. Molecular evolution of the histone deacetylase family: functional implication of phylogenetic analysis. J. Mol. Biol. 2004, 338, 17–31. 10.1016/j.jmb.2004.02.006. PubMed DOI

Kanyo Z. F.; Scolnick L. R.; Ash D. E.; Christianson D. W. Structure of a unique binuclear manganese cluster in arginase. Nature 1996, 383, 554–557. 10.1038/383554a0. PubMed DOI

Ash D. E.; Cox J. D.; Christianson D. W. Arginase: a binuclear manganese metalloenzyme. Met. Ions Biol. Syst. 2000, 37, 407–428. PubMed

Lombardi P. M.; Cole K. E.; Dowling D. P.; Christianson D. W. Structure, mechanism, and inhibition of histone deacetylases and related metalloenzymes. Curr. Opin. Struct. Biol. 2011, 21, 735–743. 10.1016/j.sbi.2011.08.004. PubMed DOI PMC

Gantt S. L.; Gattis S. G.; Fierke C. A. Catalytic activity and inhibition of human histone deacetylase 8 is dependent on the identity of the active site metal ion. Biochemistry 2006, 45, 6170–6178. 10.1021/bi060212u. PubMed DOI

Vannini A.; Volpari C.; Gallinari P.; Jones P.; Mattu M.; Carfi A.; De Francesco R.; Steinkühler C.; Di Marco S. Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8-substrate complex. EMBO Rep. 2007, 8, 879–884. 10.1038/sj.embor.7401047. PubMed DOI PMC

Dowling D. P.; Gantt S. L.; Gattis S. G.; Fierke C. A.; Christianson D. W. Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrates and inhibitors. Biochemistry 2008, 47, 13554–13563. 10.1021/bi801610c. PubMed DOI PMC

Gantt S. L.; Joseph C. G.; Fierke C. A. Activation and inhibition of histone deacetylase 8 by monovalent cations. J. Biol. Chem. 2010, 285, 6036–6043. 10.1074/jbc.M109.033399. PubMed DOI PMC

Gantt S. M.; Decroos C.; Lee M. S.; Gullett L. E.; Bowman C. M.; Christianson D. W.; Fierke C. A. General base-general acid catalysis in human histone deacetylase 8. Biochemistry 2016, 55, 820–832. 10.1021/acs.biochem.5b01327. PubMed DOI PMC

Ellmeier W.; Seiser C. Histone deacetylase function in CD4+ T cells. Nat. Rev. Immunol. 2018, 18, 617–634. 10.1038/s41577-018-0037-z. PubMed DOI

Falkenberg K. J.; Johnstone R. W. Histone deacetylases and their inhibitors in cancer, neurological diseases and immune disorders. Nat. Rev. Drug Discovery 2014, 13, 673–691. 10.1038/nrd4360. PubMed DOI

Hubbert C.; Guardiola A.; Shao R.; Kawaguchi Y.; Ito A.; Nixon A.; Yoshida M.; Wang X. F.; Yao T. P. HDAC6 is a microtubule-associated deacetylase. Nature 2002, 417, 455–458. 10.1038/417455a. PubMed DOI

Haggarty S. J.; Koeller K. M.; Wong J. C.; Grozinger C. M.; Schreiber S. L. Domain-selective small-molecule inhibitor of histone deacetylase 6 (HDAC6)-mediated tubulin deacetylation. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 4389–4394. 10.1073/pnas.0430973100. PubMed DOI PMC

Zhang Y.; Li N.; Caron C.; Matthias G.; Hess D.; Khochbin S.; Matthias P. HDAC-6 interacts with and deacetylates tubulin and microtubules in vivo. EMBO J. 2003, 22, 1168–1179. 10.1093/emboj/cdg115. PubMed DOI PMC

Yang P. H.; Zhang L.; Zhang Y. J.; Zhang J.; Xu W. F. HDAC6: physiological function and its selective inhibitors for cancer treatment. Drug Discoveries Ther. 2013, 7, 233–242. 10.5582/ddt.2013.v7.6.233. PubMed DOI

Rivieccio M. A.; Brochier C.; Willis D. E.; Walker B. A.; D’Annibale M. A.; McLaughlin K.; Siddiq A.; Kozikowski A. P.; Jaffrey S. R.; Twiss J. L.; Ratan R. R.; Langley B. HDAC6 is a target for protection and regeneration following injury in the nervous system. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 19599–19604. 10.1073/pnas.0907935106. PubMed DOI PMC

Simões-Pires C.; Zwick V.; Nurisso A.; Schenker E.; Carrupt P. A.; Cuendet M. HDAC6 as a target for neurodegenerative diseases: what makes it different from the other HDACs?. Mol. Neurodegener. 2013, 8, 7.10.1186/1750-1326-8-7. PubMed DOI PMC

Butler K. V.; Kalin J.; Brochier C.; Vistoli G.; Langley B.; Kozikowski A. P. Rational design and simple chemistry yield a superior, neuroprotective HDAC6 inhibitor, Tubastatin A. J. Am. Chem. Soc. 2010, 132, 10842–10846. 10.1021/ja102758v. PubMed DOI PMC

Hai Y.; Christianson D. W. Histone deacetylase 6 structure and molecular basis of catalysis and inhibition. Nat. Chem. Biol. 2016, 12, 741–747. 10.1038/nchembio.2134. PubMed DOI PMC

Miyake Y.; Keusch J. J.; Wang L.; Saito M.; Hess D.; Wang X.; Melancon B. J.; Helquist P.; Gut H.; Matthias P. Structural insights into HDAC6 tubulin deacetylation and its selective inhibition. Nat. Chem. Biol. 2016, 12, 748–754. 10.1038/nchembio.2140. PubMed DOI

Porter N. J.; Mahendran A.; Breslow R.; Christianson D. W. Unusual zinc binding mode of HDAC6-selective hydroxamate inhibitors. Proc. Natl. Acad. Sci. U. S. A. 2017, 114, 13459–13464. 10.1073/pnas.1718823114. PubMed DOI PMC

Porter N. J.; Wagner F. F.; Christianson D. W. Entropy as a driver of selectivity for inhibitor binding to histone deacetylase 6. Biochemistry 2018, 57, 3916–3924. 10.1021/acs.biochem.8b00367. PubMed DOI PMC

Porter N. J.; Osko J. D.; Diedrich D.; Kurz T.; Hooker J. M.; Hansen F. K.; Christianson D. W. Histone deacetylase 6-selective inhibitors and the influence of capping groups on hydroxamate-zinc denticity. J. Med. Chem. 2018, 61, 8054–8060. 10.1021/acs.jmedchem.8b01013. PubMed DOI PMC

Richon V. M.; Webb Y.; Merger R.; Sheppard T.; Jursic B.; Ngo L.; Civoli F.; Breslow R.; Rifkind R. A.; Marks P. A. Second generation hybrid polar compounds are potent inducers of transformed cell differentiation. Proc. Natl. Acad. Sci. U. S. A. 1996, 93, 5705–5708. 10.1073/pnas.93.12.5705. PubMed DOI PMC

Marks P. A. Discovery and development of SAHA as an anticancer agent. Oncogene 2007, 26, 1351–1356. 10.1038/sj.onc.1210204. PubMed DOI

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, 15–21. 10.1002/cmdc.201500486. PubMed DOI PMC

Kerr J. S.; Galloway S.; Lagrutta A.; Armstrong M.; Miller T.; Richon V. M.; Andrews P. A. Nonclinical safety assessment of the histone deacetylase inhibitor vorinostat. Int. J. Toxicol. 2010, 29, 3–19. 10.1177/1091581809352111. PubMed DOI

Kozikowski A. P.; Chen Y.; Gaysin A.; Chen B.; D’Annibale M. A.; Suto C. M.; Langley B. C. Functional differences in epigenetic modulators – superiority of mercaptoacetamide-based histone deacetylase inhibitors relative to hydroxamates in cortical neuron neuroprotection studies. J. Med. Chem. 2007, 50, 3054–3061. 10.1021/jm070178x. PubMed DOI

Segretti M. C. F.; Vallerini G. P.; Brochier C.; Langley B.; Wang L.; Hancock W. W.; Kozikowski A. P. Thiol-based potent and selective HDAC6 inhibitors promote tubulin acetylation and T-regulatory cell suppressive function. ACS Med. Chem. Lett. 2015, 6, 1156–1161. 10.1021/acsmedchemlett.5b00303. PubMed DOI PMC

Lv W.; Zhang G.; Barinka C.; Eubanks J. H.; Kozikowski A. P. Design and synthesis of mercaptoacetamides as potent, selective, and brain permeable histone deacetylase 6 inhibitors. ACS Med. Chem. Lett. 2017, 8, 510–515. 10.1021/acsmedchemlett.7b00012. PubMed DOI PMC

Chakrabarti P. Geometry of interaction of metal ions with sulfur-containing ligands in protein structures. Biochemistry 1989, 28, 6081–6085. 10.1021/bi00440a052. PubMed DOI

Cole K. E.; Dowling D. P.; Boone M. A.; Phillips A. J.; Christianson D. W. Structural basis of the antiproliferative activity of largazole, a depsipeptide inhibitor of the histone deacetylases. J. Am. Chem. Soc. 2011, 133, 12474–12477. 10.1021/ja205972n. PubMed DOI PMC

Stolfa D. A.; Marek M.; Lancelot J.; Hauser A.-T.; Walter A.; Leproult E.; Melesina J.; Rumpf T.; Wurtz J.-M.; Cavarelli J.; Sippl W.; Pierce R. J.; Romier C.; Jung M. Molecular basis for the antiparasitic activity of a mercaptoacetamide derivative that inhibits histone deacetylase 8 (HDAC8) from the human pathogen Schistosoma mansoni. J. Mol. Biol. 2014, 426, 3442–3453. 10.1016/j.jmb.2014.03.007. PubMed DOI

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.; Tang J.; Sang B.-C.; Verner E.; Wynands R.; Leahy E. M.; Dougan D. R.; Snell G.; Navre M.; Knuth M. A.; Swanson R. V.; McRee D. E.; Tari L. W. Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases. Structure 2004, 12, 1325–1334. 10.1016/j.str.2004.04.012. PubMed DOI

Vannini A.; Volpari C.; Filocamo G.; Casavola E. C.; Brunetti M.; Renzoni D.; Chakravarty P.; Paolini C.; De Francesco R.; Gallinari P.; Steinkühler C.; Di Marco S. Crystal structure of a eukaryotic zinc-dependent histone deacetylase, human HDAC8, complexed with a hydroxamic acid inhibitor. Proc. Natl. Acad. Sci. U. S. A. 2004, 101, 15064–15069. 10.1073/pnas.0404603101. PubMed DOI PMC

Bertos N. R.; Gilquin B.; Chen G. K. T.; Yen T. J.; Khochbin S.; Yang X.-J. Role of the tetradecapeptide repeat domain of human histone deacetylase 6 in cytoplasmic retention. J. Biol. Chem. 2004, 12, 48246–48254. 10.1074/jbc.M408583200. PubMed DOI

Ondetti M. A.; Rubin B.; Cushman D. W. Design of specific inhibitors of angiotensin-converting enzyme: new class of orally active antihypertensive agents. Science 1977, 196, 441–444. 10.1126/science.191908. PubMed DOI

Cushman D. W.; Ondetti M. A. History of the design of Captopril and related inhibitors of angiotensin converting enzyme. Hypertension 2001, 17, 589–592. 10.1161/01.HYP.17.4.589. PubMed DOI

Lee J.-H.; Yao Y.; Mahendran A.; Ngo L.; Venta-Perez G.; Choy M. L.; Breslow R.; Marks P. A. Creation of a histone deacetylase 6 inhibitor and its biological effects. Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 12005–12010. 10.1073/pnas.1515882112. PubMed DOI PMC

2015, 112, E5899. 10.1073/pnas.1519546112 PubMed

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