Non-peptide macrocyclic histone deacetylase inhibitors

Journal of Medicinal Chemistry

Volumn 52, Issue 2, 2009, Pages 456-468

  Oyelere, Adegboyega K ^a   Chen, Po C ^a   Guerrant, William ^a   Mwakwari, Sandra C ^a   Hood, Rebecca ^a   Zhang, Yunzhe ^a   Fan, Yuhong ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE DEACETYLASE 1; HISTONE DEACETYLASE 2; HISTONE DEACETYLASE 8; HISTONE DEACETYLASE INHIBITOR; MACROCYCLIC COMPOUND; ENZYME INHIBITOR; HISTONE DEACETYLASE;

ARTICLE; CONCENTRATION RESPONSE; DRUG SELECTIVITY; DRUG SYNTHESIS; ENZYME INHIBITION; HUMAN; HUMAN CELL; IC 50; REACTION ANALYSIS; STRUCTURE ACTIVITY RELATION; CELL LINE; CHEMISTRY; DRUG ANTAGONISM; FAST ATOM BOMBARDMENT MASS SPECTROMETRY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

CELL LINE; ENZYME INHIBITORS; HISTONE DEACETYLASES; HUMANS; MACROCYCLIC COMPOUNDS; MAGNETIC RESONANCE SPECTROSCOPY; SPECTROMETRY, MASS, FAST ATOM BOMBARDMENT; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 60549102514     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm801128g     Document Type: Article

References (45)

1. Marks, P. A. Discovery and development of SAHA as an anticancer agent. Oncogene 2007, 26, 1351-1356.
2. Kelly, W. K.; O'Connor, O. A.; Marks, P. A. Histone deacetylase inhibitors: from target to clinical trials. Expert. Opin. Invest. Drugs 2002, 11, 1695-1713.
3. Miller, T. A.; Witter, D. J.; Belvedere, S. Histone deacetylase inhibitors. J. Med. Chem. 2003, 46, 5097-5116.
4. Rosato, R. R.; Grant, S. Histone deacetylase inhibitors in clinical development. Expert Opin. Invest. Drugs 2004, 13, 21-38.
5. Monneret, C. Histone deacetylase inhibitors. Eur. J. Med. Chem. 2005, 40, 1-13.
6. Yoo, C. B.; Jones, P. A. Epigenetic therapy of cancer: past, present and future. Nat.Rev. DrugDiscoveri 2006, 5, 37-50.
7. Finnin, M. S.; Donigian, J. R.; Cohen, A.; Richon, V. M.; Rifkind, R. A.; Marks, P. A.; Breslow, R.; Pavletich, N. P. Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors. Nature 1999, 401, 188-193.
8. (a) Vannini, A.; Volpari, C.; Filocamo, G.; Casavola, E. C.; Brunetti, M.; Renzoni, D.; Chakravarty, P.; Paolini, C.; De Francesco, R.; Gallinari, P.; Steinkuhler, C.; Di Marco, S. Crystal structure of a eukaryotic zinc-dependent histone deacetylase, human HDAC8, com- plexed with a hydroxamic acid inhibitor. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 15064-15069.
9. (b) 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. W.; 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. (c) Schuetz, A.; Min, J.; Allali-Hassani, A.;Schapira, M.; Shuen, M.; Loppnau, P.; Mazitschek, R.; Kwiatkowski, N. P.; Lewis, T. A.; Maglathin, R. L.; McLean, T. H.; Bochkarev, A.; Plotnikov, A. N.; Vedadi, M.; Arrowsmith, C. H. Human HDAC7 harbors a class Ila histone deacetylase-specific zinc binding motif and cryptic deacetylase activity. J Biol Chem. 2008, 283, 11355-11363.
11. http://www.clinicaltrials.gov/ct/show/NCT00106431.
12. (a) Furumai, R.; Komatsu, Y.; Nishino, N.; Khochbin, S.; Yoshida, M.; Horinouchi, S. Potent histone deacetylase inhibitors built from trichostatin A and cyclic tetrapeptide antibiotics including trapoxin. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 87-92.
13. (b) Yurek-George, A.; Cecil, A. R. L.; Mo, A. H. K.; Wen, S.; Rogers, H.; Habens, F.; Maeda, S.; Yoshida, M.; Packham, G.; Ganesan, A. The first biologically active synthetic analogues of FK228, the depsipeptide histone deacetylase inhibitor. J. Med. Chem. 2007, 50, 5720-5726.
14. (c) Gomez-Paloma, L.; Bruno, I.; Cini, E.; Khochbin, S.; Rodriquez, M.; Taddei, M.; Terracciano, S.; Sadoul, K. Design and synthesis of cyclopeptide analogues of the potent histone deacetylase inhibitor FR235222. ChemMedChem 2007, 2, 1511-1519.
15. Tsai, W. C.; Standiford, T. J. Immunomodulatory effects of macrolides in the lung: lessons from in-vitro and in-vivo models. Curr. Pharm. Des. 2004, 10, 3081-3093.
16. Shinkai, M.; Park, C. S.; Rubin, B. K. Immunomodulatory effects of macrolide antibiotics. Interstitial, inflammatory, and occupational lung disease. Clin. Pulm. Med. 2005, 12, 341-348.
17. Randolph, J. T.; Waid, P.; Nichols, C.; Sauer, D.; Haviv, F.; Diaz, G.; Bammert, G.; Besecke, L. M.; Segreti, J. A.; Mohning, K. M.; Bush, E. N.; Wegner, C. D.; Greer, J. Nonpeptide luteinizing hormone- releasing hormone antagonists derived from erythromycin A: design, synthesis, and biological activity of cladinose replacement analogues. J. Med. Chem. 2004, 47, 1085-1097.
18. (a) Freiberg, L. A. U.S. Patent 3725385, 1973.
19. (b) Lartey, P. A.; Nellans, H. N.; Faghih, R.; Petersen, A.; Edwards, C. M.; Freiberg, L.; Quigley, S.; Marsh, K.; Klein, L. L.; Plattner, J. J. Synthesis of 4''-deoxy motilides: identification of a potent and orally active prokinetic drug candidate. J. Med. Chem. 1995, 38, 1793-1798.
20. (c) Stenmark, H. G.; Brazzale, A.; Ma, Z. Biomimetic synthesis of macrolide/ketolide metabolites through a selective N-demethylation reaction. J. Org. Chem. 2000, 65, 3875-3876.
21. Awan, A.; Brennan, R. J.; Regan, A. C.; Barber, J. The conformations of the macrolide antibiotics erythromycin A, azithromycin and clarithromycin in aqueous solution: a 1H NMR study. J. Chem. Soc., Perkin Trans. 2000, 2, 1645-1652.
22. Elliott, R. L.; Pireh, D.; Nilius, A. M.; Johnson, P. M.; Flamm, R. K.; Chu, D. T. W.; Plattner, J. J.; Or, Y. S. Novel 3-deoxy-3-descladinosyl- 6-O-methyl erythromycin A analogues. Synthesis and in vitro activity. Bioorg. Med. Chem. Lett. 1997, 7, 641-646.
23. HDAC Fluorimetric Assay/Drug Discovery Kit. AK-500 Manual. Fluorescent Assay System; BIOMOL International, L.P.: Plymouth Meeting, PA, 2005.
24. (a) Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function. J. Comput. Chem. 1998, 19, 1639-1662; http://www. scripps.edu/pub/olson-web/doc/ autodock/.
25. (b) Wang, D.-F.; Wiest, O.; Helquist, P.; Lan-Hargest, H.-Y.; Wiech, N. L. On the function of the 14 A long internal cavity of histone deacetylase-like protein: implications for the design of histone deacetylase inhibitors. J. Med. Chem. 2004, 47, 3409-3417.
26. (c) Lu, Q.; Wang, D.-S.; Chen, C.-S.; Hu, Y.- D.; Chen, C.-S. Structure-based optimization of phenylbutyrate-derived histone deacetylase inhibitors. J. Med. Chem. 2005, 48, 5530-5535.
27. Chen, P. C.; Patil, V.; Guerrant, W.; Green, P.; Oyelere, A. K. Synthesis and structure-activity relationship of histone deacetylase (HDAC) inhibitors with triazole-linked cap group. Bioorg. Med. Chem.2008, 16, 4839-4853.
28. Numerous examples of Cu(I) catalyzed Huigsen cycloaddition reaction have appeared in the literature (a comprehensive list is available at www.scripps.edu/chem/sharpless/click.html). Cited here are two pioneering examples:(a) Rostovtsev, V. V.; Green, L. G.; Fokin, V. V.; Sharpless, K. B. A stepwise huigsen cycloaddition process: copper (I)-catalyzed regioselective "ligation" of azides and terminal alkynes. Angew. Chem., Int. Ed. 2002, 41, 2596-2599.
29. (b) Tornoe, C. W.; Christensen, C.; Meldal, M. Peptidotriazoles on solid phase: [1,2,3]- triazoles by regiospecific copper(I)-catalyzed 1,3-dipolar cycloadditions of terminal alkynes to azides. J. Org. Chem. 2002, 67, 3057-3064.
30. (a) Salisbury, C. M.; Cravatt, B. F. Activity-based probes for proteomic profiling of histone deacetylase complexes. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 1171-1176.
31. (b) Salisbury, C. M.; Cravatt, B. F. Optimization of activity-based probes for proteomic profiling of histone deacetylase complexes. J. Am. Chem. Soc. 2008, 130, 2184-2194.
32. (a) KrennHrubec, K.; Marshall, B. L.; Hedglin, M.; Verdin, E.; Ulrich, S. M. Design and evaluation of "linkerless" hydroxamic acids as selective HDAC8 inhibitors. Bioorg. Med. Chem. Lett. 2007, 17, 28742878.
33. (b) Gurard-Levin, Z. A.; Mrksich, M. The activity of HDAC8 depends on local and distal sequences of its peptide substrates. Biochemistry 2008, 47, 6242-6250.
34. (c) 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.
35. Freshney, R. Culture of Animal Cells: A Manual of Basic Technique; Alan R. Liss, Inc.: New York, 1987; p 117.
36. Suzuki, T.; Nagano, Y.; Kouketsu, A.; Matsuura, A.; Maruyama, S.; Kurotaki, M.; Nakagawa, H.; Miyata, N. Novel inhibitors of human histone deacetylases: design, synthesis, enzyme inhibition, and cancer cell growth inhibition of SAHA-based non-hydroxamates. J. Med. Chem. 2005, 48, 1019-1032.
37. Rundlett, S. E.; Carmen, A. A.; Kobayashi, R.; Bavykin, S.; Turner, B. M.; Grunstein, M. HDA1 and RPD3 are members of functionally distinct yeast histone deacetylase complexes. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 14503-14508.
38. Marks, P.; Rifkind, R. A.; Richon, V. M.; Breslow, R.; Miller, T.; Kelly, W. K. Histone deacetylases and cancer: causes and therapies. Nat. Rev. Cancer 2001, 1, 194-202.
39. WAFI1 expression and gene- associated histone acetylation. Proc. Natl. Acad. Sci. U.S.A. 2000, 97,10014-10019.
40. Danesi, R.; Lupetti, A.; Barbara, C.; Ghelardi, E.; Chella, A.; Malizia, T.; Senesi, S.; Angeletti, C. A.; Del Tacca, M.; Campa, M. Comparative distribution of azithromycin in lung tissue of patients given oral daily doses of 500 and 1000 mg. J. Antimicrob. Chemother. 2003,51, 939-945.
41. Savariar, E. N.; Aathimanikandan, S. V.; Thayumanavan, S. Supramo- lecular assemblies from amphiphilic homopolymers: testing the scope. J. Am. Chem. Soc. 2006, 128, 16224-16230.
42. Heine, H. W.; Becker, E. B.; Lane, J. F. On cyclic intermediates in substitution reactions. III. The alkaline hydrolysis of £-bromocaproic and £-bromoenanthic acids. J. Am. Chem. Soc. 1953, 75, 4514-4515.
43. (a) Collman, J. P.; Devaraj, N. K.; Chidsey, C. E. D. "Clicking" functionality onto electrode surfaces. Langmuir 2004, 20, 1051-1053.
44. (b) Shon, Y.-S.; Kelly, K. F.; Halas, N. J.; Lee, T. R. Fullerene- terminated alkanethiolate SAMs on gold generated from unsymmetrical disulfides. Langmuir 1999, 15, 5329-5332.
45. Muri, D.; Bode, J. W.; Carreira, E. M. A novel, general method for the synthesis of nitrile oxides: dehydration of O-silylated hydroxamicacids. Org. Lett. 2000, 2, 539-541.JM801128G