Inside HDAC with HDAC inhibitors

European Journal of Medicinal Chemistry

Volumn 45, Issue 6, 2010, Pages 2095-2116

  Bertrand, Philippe ^a  

^a UNIVERSITÉ DE POITIERS   (France)

Author keywords

Cancer; HDAC; Inhibitors; Molecular modelling; QSAR

Indexed keywords

4 [N (2 HYDROXYETHYL) N [2 (3 INDOLYL)ETHYL]AMINOMETHYL]CINNAMOHYDROXAMIC ACID; AMINO ACID; APICIDIN; BORON DERIVATIVE; HISTONE DEACETYLASE; HISTONE DEACETYLASE 1; HISTONE DEACETYLASE 10; HISTONE DEACETYLASE 2; HISTONE DEACETYLASE 3; HISTONE DEACETYLASE 4; HISTONE DEACETYLASE 5; HISTONE DEACETYLASE 6; HISTONE DEACETYLASE 7; HISTONE DEACETYLASE 8; HISTONE DEACETYLASE 9; HISTONE DEACETYLASE INHIBITOR; KETONE DERIVATIVE; N (2 AMINOPHENYL) 4 (3 PYRIDINYLMETHOXYCARBONYLAMINOMETHYL)BENZAMIDE; N (2 AMINOPHENYL) 4 [4 (3 PYRIDINYL) 2 PYRIMIDINYLAMINOMETHYL]BENZAMIDE; PANOBINOSTAT; PHOSPHORUS DERIVATIVE; SULFUR DERIVATIVE; UNCLASSIFIED DRUG; VORINOSTAT;

ACETYLATION; APOPTOSIS; CANCER CELL CULTURE; CATALYSIS; CELL PROLIFERATION; CHROMATIN ASSEMBLY AND DISASSEMBLY; CRYSTAL STRUCTURE; DEACETYLATION; DRUG SYNTHESIS; ENZYME ACTIVITY; ENZYME INHIBITION; HUMAN; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE; PROTEIN EXPRESSION; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REVIEW; TUMOR SUPPRESSOR GENE; X RAY CRYSTALLOGRAPHY;

ANIMALS; DRUG DISCOVERY; HISTONE DEACETYLASE INHIBITORS; HISTONE DEACETYLASES; HUMANS; MODELS, MOLECULAR; ZINC;

EID: 77950860448     PISSN: 02235234     EISSN: 17683254     Source Type: Journal    
DOI: 10.1016/j.ejmech.2010.02.030     Document Type: Review

References (100)

1. Miller T.A., Witter D.J., and Belvedere S. Histone deacetylase inhibitors. J. Med. Chem. 46 (2003) 5097
2. Mai A., and Altucci L. Epi-drugs to fight cancer: from chemistry to cancer treatment, the road ahead. Int. J. Biochem. Cell Biol. 41 (2009) 199
3. Frew A.J., Johnstone R.W., and Bolden J.E. Enhancing the apoptotic and therapeutic effects of HDAC inhibitors. Cancer Lett. 280 (2009) 125
4. Acharya M.R., Sparreboom A., Venitz J., and Figg W.D. Rational development of histone deacetylases inhibitors as anti-cancer agents: a review. Mol. Pharmacol. (2005)
5. Marmorstein R. Structure of histone deacetylases: review insights into substrate recognition and catalysis. Structure 9 (2001) 1127
6. Khan N., Jeffers M., Kumar S., Hackett C., Boldog F., Khramtsov N., Qian X., Mills E., Berghs S.C., Carey N., Finn P.W., Collins L.S., Tumber A., Ritchie J.W., Jensen P.B., Lichenstein H.S., and Sehested M. Determination of the class and isoform selectivity of small-molecule histone deacetylase inhibitors. Biochem. J. 409 (2008) 581
7. Ocker M., and Schneider-Stock R. Histone deacetylase inhibitors: signalling towards p21cip1/waf1. Int. J. Biochem. Cell Biol. 39 (2007) 1367
8. Porcu M., and Chiarugi A. The emerging therapeutic potential of sirtuin-interacting drugs: from cell death to lifespan extension. Trends Pharmacol. Sci. 26 (2005) 94
9. Minucci S., and Pelicci G. Histone deacetylase inhibitors and the promise of epigenetic (and more) treatments for cancer. Nat. Rev. Cancer 6 (2006) 38
10. Stimson L., and La Thangue N.B. Biomarkers for predicting clinical responses to HDAC inhibitors. Cancer Lett. 280 (2009) 177
11. Finnin M.S., Donigian J.R., Cohen A., Richon V.M., Rifkind R.A., Marks P.A., Breslow R., and Pavletich N.P. Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors. Nature 401 (1999) 188
12. Vannini A., Volpari C., Filocamo G., Casavola E.C., Brunetti M., Renzoni D., Chakravarty P., Paolini C., De Francesco R., Gallinari P., Steinkuhler C., and 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. 101 (2004) 15064
13. Vannini A., Volpari C., Gallinari P., Jones P., Mattu M., Carfí A., De Francesco R., Steinkühler C., and Di Marco S. Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8-substrate complex. EMBO Rep. 8 (2007) 879
14. 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., and Tari L.W. Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases. Structure 12 (2004) 1325
15. Min J.R., Schuetz A., Allali-Hassani A., Loppnau P., Kwiatkowski N.P., Mazitschek R., Weigelt J., Sundstrom M., Arrowsmith C.H., Edwards A.M., Vedadi M., Bochkarev A., and Plotnikov A.N. Catalytic domain of human histone deacetylase Hdac7 (2006/8/22), Structural Genomics Consortium (SGC)
16. 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., and Arrowsmith C.H. Human HDAC7 harbors a class IIa histone deacetylase-specific zinc binding motif and cryptic deacetylase activity. J. Biol. Chem. 283 (2008) 11355
17. Schäfer S., Saunders L., Eliseeva E., Velena A., Jung M., Schwienhorst A., Strasser A., Dickmanns A., Ficner R., Schlimme S., Sippl W., Verdin E., and Jung M. Phenylalanine-containing hydroxamic acids as selective inhibitors of class IIb histone deacetylases (HDACs). Bioorg. Med. Chem. 16 (2008) 2011
18. Bottomley M.J., Lo Surdo P., Di Giovine P., Cirillo A., Scarpelli R., Ferrigno F., Jones P., Neddermann P., De Francesco R., Steinkuhler C., Gallinari P., and Carfi A. Structural and functional analysis of the human Hdac4 catalytic domain reveals a regulatory zinc-binding domain. J. Biol. Chem. 283 (2008) 26694
19. Dong A., Ravichandran M., Schuetz A., Loppnau P., Li Y., Mackenzie F., Kozieradzki I., Edwards A.M., Arrowsmith C.H., Weigelt J., Bountra C., Bochkarev A., Dhe-Paganon S., Min J., and Ouyang H. Crystal structure of human Hdac6 zinc finger domain (2008/1/31), Structures Genomics Consortium (SGC)
20. Nielsen T.K., Hildmann C., Dickmanns A., Schwienhorst A., and Ficner R. Crystal structure of a bacterial class 2 histone deacetylase homologue. J. Mol. Biol. 354 (2005) 107
21. Hildmann C., Ninkovic M., Dietrich R., Wegener D., Riester D., Zimmermann T., Birch O.M., Bernegger C., Loidl P., and A Schwienhorst A. New amidohydrolase from Bordetella or Alcaligenes strain FB188 with similarities to histone deacetylases. J. Bacteriol. 186 (2004) 2328
22. Vanommeslaeghe K., De Proft F., Loverix S., Tourwé D., and Geerlings P. Theoretical study revealing the functioning of a novel combination of catalytic motifs in histone deacetylase. Bioorg. Med. Chem. 13 (2005) 3987
23. Corminboeuf C., Hu P., Tuckerman M.E., and Zhang Y. Unexpected deacetylation mechanism suggested by a density functional theory QM/MM Study of histone-deacetylase-like protein. J. Am. Chem. Soc. 128 (2006) 4530
24. Vanommeslaeghe K., Loverix S., Geerlings P., and Tourwé D. DFT-based ranking of zinc-binding groups in histone deacetylase inhibitors. Bioorg. Med. Chem. 13 (2005) 6070
25. Wang D., Helquist P., and Wiest O. Zinc binding in HDAC inhibitors: a DFT study. J. Org. Chem. 72 (2007) 5446
26. Puerta D.T., Griffin M.O., Lewis J.A., Romero-Perez D., Garcia R., Villarreal F.J., and Cohen S.M. Heterocyclic zinc-binding groups for use in the next-generation matrix metalloproteinase inhibitors: potency, toxicity, and reactivity. J. Biol. Inorg. Chem. (2005)
27. Dobbs K.D., Rinehart A.M., Howard M.H., Zheng Y.-J., and Kleier D.A. Computational characterization of metal binding groups for metalloenzyme inhibitors. J. Chem. Theory Comput. 2 (2006) 990
28. Auld D.S. Zinc coordination sphere in biochemical zinc sites. BioMetals 14 (2001) 271
29. Gantt S.L., Gattis S.G., and Fierke C.A. Catalytic activity and inhibition of human histone deacetylase 8 is dependant on the identity of the active site metal ion. Biochemistry 45 (2006) 6170
30. Schultz B.E., Misialek S., Wu J., Tang J., Conn M.T., Tahilramani R., and Wong L. Kinetics and comparative reactivity of human class I and class Iib histone deacetylases. Biochemistry 43 (2004) 11083
31. Paris M., Porcelloni M., Binaschi M., and Fattori D. Histone deacetylase inhibitors: from bench to clinic. J. Med. Chem. 51 (2008) 1505
32. Suzuki T., and Miyata N. Non-hydroxamate histone deacetylase inhibitors. Curr. Med. Chem. 12 (2005) 2867
33. Nishino N., Jose B., Okamura S., Ebisusaki S., Kato T., Sumida Y., and Yoshida M. Cyclic tetrapeptides bearing a sulfhydryl group potently inhibit histone deacetylases. Org. Lett. 5 (2003) 5079
34. Suzuki T., Kouketsu A., Matsuura A., Kohara A., Ninomiya S.-I., Kohda K., and Miyata N. Thiol-based SAHA analogues as potent histone deacetylase inhibitors. Bioorg. Med. Chem. Lett. 14 (2004) 3313
35. Nishino N., Yoshikawa D., Watanabe L.A., Kato T., Jose B., Komatsu Y., Sumida Y., and Yoshida M. Synthesis and histone deacetylase inhibitory activity of cyclic tetrapeptides containing a retrohydroxamate as zinc ligand. Bioorg. Med. Chem. Lett. 14 (2004) 2427
36. Wu T.Y.H., Hassig C., Wu Y., Ding S., and Schultz P.G. Design, synthesis, and activity of HDAC inhibitors with a N-formyl hydroxylamine head group. Bioorg. Med. Chem. Lett. 14 (2004) 449
37. J.C. Bressi, J. Brown, A.R. Gangloff, J.A. Stafford, P.H. Vu, Histone Deacetylase Inhibitors. WO2006122319, 2006.
38. Wada C.K., Frey R.R., Ji Z., Curtin M.L., Garland R.B., Holms J.H., Li J., Pease L.J., Guo J., Glaser K.B., Marcotte P.A., Richardson P.L., Murphy S.S., Bouska J.J., Tapang P., Magoc T.J., Albert D.H., Davidsen S.K., and Michaelides M.R. α-Keto amides as inhibitors of histone deacetylase. Bioorg. Med. Chem. Lett. 13 (2003) 3331
39. Pérez-Balado C., Nebbioso A., Rodriguez-Graña P., Minichiello A., Miceli M., Altucci L., and de Lera A.R. Bispyridinium dienes: histones deacetylase inhibitors with selective activities. J. Med. Chem. 50 (2007) 2497
40. Jones P., Altamura S., Chakravarty P.K., Cecchetti O., De Francesco R., Gallinari P., Ingenito R., Meinke P.T., Petrocchi A., Rowley M., Scarpelli R., Serafini S., and Steinkuhler C. A series of novel, potent, and selective histone deacetylase inhibitors. Bioorg. Med. Chem. Lett. 16 (2006) 5948
41. Furumai R., Matsuyama A., Kobashi N., Lee K.-H., Nishiyama M., Nakajima H., Tanaka A., Komatsu Y., Nishino N., Yoshida M., and Horinouchi S. FK228 (depsipeptide) as a natural prodrug that inhibits class I histone deacetylases. Cancer Res. 62 (2002) 4916
42. Piña I.C., Gautschi J.T., Wang G.-Y.-S., Sanders M.L., Schmitz F.J., France D., Cornell-Kennon S., Sambucetti L.C., Remiszewski S.W., Perez L.B., Bair K.W., and Crews P. Psammaplins from the sponge Pseudoceratina purpurea: inhibition of both histone deacetylase and DNA methyltransferase. J. Org. Chem. 68 (2003) 3866
43. Kinzel O., Llauger-Bufi L., Pescatore G., Rowley M., Schultz-Fademrecht C., Monteagudo E., Fonsi M., Paz O.G., Fiore F., Steinkühler C., and Jones P. Discovery of a potent class I selective ketone histone deacetylase inhibitor with antitumor activity in vivo and optimized pharmacokinetic properties. J. Med. Chem. 52 (2009) 3453
44. Suzuki T., Nagano Y., Kouketsu A., Matsuura A., Maruyama S., Kurotaki M., Nakagawa H., and 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. 48 (2005) 1019
45. Suzuki T., Matsuura A., Kouketsu A., Nakagawa H., and Miyata N. Identification of a potent non-hydroxamate histone deacetylase inhibitor by mechanism-based drug design. Bioorg. Med. Chem. Lett. 15 (2005) 331
46. Chen B., Petukhov P.A., Jung M., Velena A., Eliseeva E., Dritshilo A., and Kozikowski A.P. Chemistry and biology of mercaptoacetamides as novel histones deacetylases inhibitors. Bioorg. Med. Chem. Lett. 15 (2005) 1389
47. Vannini A., Volpari C., Gallinari P., Jones P., Mattu M., Carfi{dotless} A., De Francesco R., Steinkuhler C., and Di Marco S. Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8-substrate complex. EMBO Rep. 8 (2007) 879
48. Suzuki T., Matsuura A., Kouketsu A., Hisakawa S., Nakagawa H., and Miyata N. Design and synthesis of non-hydroxamate histone deacetylase inhibitors: identification of a selective histone acetylating agent. Bioorg. Med. Chem. 13 (2005) 4332
49. Suzuki T., Kouketsu A., Itoh Y., Hisawa S., Maeda S., Yoshida M., Nakagawa H., and Miyata N. Highly potent and selective histone deacetylase 6 inhibitors designed based on a small-molecular substrate. J. Med. Chem. 49 (2006) 4809
50. Itoh Y., Suzuki T., Kouketsu A., Suzuki N., Maeda S., Yoshida M., Nakagawa H., and Miyata N. Design, synthesis, structure-selectivity relationship, and effect on human cancer cells of a novel series of histone deacetylase 6-selective inhibitors. J. Med. Chem. 50 (2007) 5425
51. Kapustin G.V., Fejér G., Gronlund J.L., McCafferty D.G., Seto E., and Etzkorn F.A. Phosphorus-based SAHA analogues as histone deacetylase inhibitors. Org. Lett. 5 (2003) 3053
52. Suzuki N., Suzuki T., Ota Y., Nakano T., Kurihara M., Okuda H., Yamori T., Tsumoto H., Nakagawa H., and Miyata N. Design, synthesis, and biological activity of boronic acid-based histone deacetylase inhibitors. J. Med. Chem. 52 (2009) 2909
53. Jose B., Oniki Y., Kato T., Nishino N., Sumida Y., and Yoshida M. Novel histone deacetylase inhibitors: cyclic tetrapeptide with trifluoromethyl and pentafluoromethyl ketones. Bioorg. Med. Chem. Lett. 14 (2004) 5343
54. Weerasinghe S.V.W., Estiu G., Wiest O., and Pflum M.K.H. Residues in the 11 Å channel of histone deacetylase 1 promote catalytic activity: implications for designing isoform-selective histone deacetylase inhibitors. J. Med. Chem. 51 (2008) 5542
55. Charrier C., Bertrand P., Gesson J.-P., and Roche J. Synthesis of rigid trichostatin A analogs as HDAC inhibitors. Bioorg. Med. Chem. Lett. 16 (2006) 5339
56. Charrier C., Roche J., Gesson J.-P., and Bertrand P. Antiproliferative activities of a library of hybrids between indanones and HDAC inhibitor SAHA and MS-275 analogues. Bioorg. Med. Chem. Lett. 17 (2007) 6142
57. Wang D.F., Wiest O., Helquist P., Lan-Hargest H.-Y., and Wiech N.L. On the function of the 14 Å long internal cavity of histone deacetylase-like protein: implications for the design of histone deacetylase inhibitors. J. Med. Chem. 47 (2004) 3409
58. Wang D.F., Helquist P., Wiech N.L., and Wiest O. Toward selective histone deacetylase inhibitor design: homology modeling, docking studies, and molecular dynamics simulations of human class I histone deacetylases. J. Med. Chem. 48 (2005) 6936
59. Moradei O.M., Mallais T.C., Frechette S., Paquin I., Tessier P.E., Leit S.M., Fournel M., Bonfils C., Trachy-Bourget M.-C., Liu J., Yan T.P., Lu A.-H., Rahil J., Wang J., Lefebvre S., Li Z., Vaisburg A.F., and Besterman J.M. Novel aminophenyl benzamide-type histone deacetylase inhibitors with enhanced potency and selectivity. J. Med. Chem. 50 (2007) 5543
60. Siliphaivanh P., Harrington P., Witter D.J., Otte K., Tempest P., Kattar S., Kral A.M., Fleming J.C., Deshmukh S.V., Harsch A., Secrist P.J., and Miller T.A. Design of novel histone deacetylase inhibitors. Bioorg. Med. Chem. Lett. 17 (2007) 4619
61. Methot J.L., Hamblett C.L., Mampreian D.M., Jung J., Harsch A., Szewczak A.A., Dahlberg W.K., Middleton R.E., Hughes B., Fleming J.C., Wang H., Kral A.M., Ozerova N., Cruz J.C., Haines B., Chenard M., Kenific C.M., Secrist J.P., and Miller T.A. SAR profiles of spirocyclic nicotinamide derived selective HDAC1/HDAC2 inhibitors (SHI-1:2). Bioorg. Med. Chem. Lett. 18 (2008) 6104
62. Hamblett C.L., Methot J.L., Mampreian D.M., Sloman D.L., Stanton M.G., Kral A.M., Fleming J.C., Cruz J.C., Chenard M., Ozerova N., Hitz A.M., Wang H., Deshmukh S.V., Nazef N., Harsch A., Hughes B., Dahlberg W.K., Szewczak A.A., Middleton R.E., Mosley R.T., Secrist J.P., and Miller T.A. The discovery of 6-amino nicotinamides as potent and selective histone deacetylase inhibitors. Bioorg. Med. Chem. Lett. 17 (2007) 5300
63. Kattar S.D., Surdi L.M., Zabierek A., Methot J.L., Middleton R.E., Hughes B., Szewczak A.A., Dahlberg W.K., Kral A.M., Ozerova N., Fleming J.C., Wang H., Secrist P., Harsch A., Hamill J.E., Cruz J.C., Kenific C.M., Chenard M., Miller T.A., Berk S.C., and Tempest P. Parallel medicinal chemistry approaches to selective HDAC1/HDAC2 inhibitor (SHI-1:2) optimization. Bioorg. Med. Chem. Lett. 19 (2009) 1168
64. Methot J.L., Chakravarty P.K., Chenard M., Close J., Cruz J.C., Dahlberg W.K., Fleming J., Hamblett C.L., Hamill J.E., Harrington P., Harsch A., Heidebrecht R., Hughes B., Jung J., Kenific C.M., Kral A.M., Meinke P.T., Middleton R.E., Ozerova N., Sloman D.L., Stanton M.G., Szewczak A.A., Tyagarajan S., Witter D.J., Secrist J.P., and Miller T.A. Exploration of the internal cavity of histone deacetylase (HDAC) with selective HDAC1/HDAC2 inhibitors (SHI-1:2). Bioorg. Med. Chem. Lett. 18 (2008) 973
65. Charrier C., Clarhaut J., Gesson J.-P., Estiu G., Wiest O., Roche J., and Bertrand P. Synthesis and modeling of new benzofuranone histone deacetylase inhibitors that stimulate tumor suppressor gene expression. J. Med. Chem. 52 (2009) 3112
66. Mai A., Massa S., Rotili D., Pezzi R., Bottoni P., Scatena R., Meranr J., and Brosh G. Exploring the connection unit in the HDAC inhibitor pharmacophore model: novel uracil-based hydroxamates. Bioorg. Med. Chem. Lett. 15 (2005) 4656
67. Dai Y., Guo Y., Curtin M.L., Li J., Pease L.J., Guo J., Marcotte P.A., Glaser K.B., Davidsen S.K., and Michaelides M.R. A novel series of histone deacetylase inhibitors incorporating hetero aromatic ring systems as connection units. Bioorg. Med. Chem. Lett. 13 (2003) 3817
68. Chen P.C., Patil V., Guerrant W., Green P., and Oyelere A.K. Synthesis and structure-activity relationship of histone deacetylase (HDAC) inhibitors with triazole-linked cap group. Bioorg. Med. Chem. 16 (2008) 4839
69. KrennHrubec K., Marshall B.L., Hedglin M., Verdin E., and Ulrich S.M. Desgn and evaluation of 'Linkerless' hydroxamic acids as selective HDAC8 inhibitors. Bioorg. Med. Chem. Lett. 17 (2007) 2874
70. Witter D.J., Belvedere S., Chen L., Secrist J.P., Mosley R.T., and Miller T.A. Benzo[b]thiophene-based histone deacetylase inhibitors. Bioorg. Med. Chem. Lett. 17 (2007) 4562
71. Price S., Bordogna W., Bull R.J., Clark D.E., Crackett P.H., Dyke H.J., Gill M., Harris N.V., Gorski J., Lloyd J., Lockey P.M., Mullett J., Roach A.G., Roussel F., and White A.B. Identification and optimisation of a series of substituted 5-(1H-pyrazol-3-yl)-thiophene-2-hydroxamic acids as potent histone deacetylase (HDAC) inhibitors. Bioorg. Med. Chem. Lett. 17 (2007) 370
72. Estiu G., Greenberg E., Harrison C.B., Kwiatkowski N.P., Mazitschek R., Bradner J.E., and Wiest O. Structural origin of selectivity in class II-selective histone deacetylase inhibitors. J. Med. Chem. 51 (2008) 2898
73. Haggarty S.J., Koeller K.M., Wong J.C., Grozinger C.M., and Schreiber S.L. Domain-selective small molecule inhibitor of histone deacetylase 6 (HDAC6)-mediated tubulin deacetylation. Proc. Nat. Acad. Sci. 100 (2003) 4389
74. Zou H., Wu Y., Navre M., and Sang B.C. Characterization of the two catalytic domains in histone deacetylase 6. Biochem. Biophys. Res. Commun. 341 (2006) 45
75. Massa S., Artico M., Corelli F., Mai A., Di Santo R., Cortes S., Maronglu M.E., Pani A., and La Clla P. Synthesis and antimicrobial and cytotoxic activities of pyrrole-containing analogues of trichostatin A. J. Med. Chem. 33 (1990) 2845
76. Mai A., Massa S., Ragno R., Esposito M., Sbardella G., Nocca G., Scatena R., Jesacher F., Loidl P., and Brosch G. Binding mode analysis of 3-(4-benzoyl-1-methyl-1H-2-pyrrolyl)-N-hydroxy-2-propenamide: a new synthetic histone deacetylase inhibitor inducing histone hyperacetylation, growth inhibition, and terminal cell differentiation. J. Med. Chem. 45 (2002) 1778
77. Mai A., Massa S., Ragno R., Cerbara I., Jesacher F., Loidl P., and Brosch G. 3-(4-Aroyl-1-methyl-1H-2-pyrrolyl)-N-hydroxy-2-alkylamides as a new class of synthetic histone deacetylase inhibitors. 1. Design, synthesis, biological evaluation, and binding mode studies performed through three different docking procedures. J. Med. Chem. 46 (2003) 512
78. Mai A., Massa S., Cerbara I., Valente S., Ragno R., Bottoni P., Scatena R., Loidl P., and Brosch G. 3-(4-Aroyl-1-methyl-1H-2-pyrrolyl)-N-hydroxy-2-propenamides as a new class of synthetic histone deacetylase inhibitors. 2. Effect of pyrrole-C2 and/or -C4 substitutions on biological activity. J. Med. Chem. 47 (2004) 1098
79. Ragno R., Mai A., Massa S., Cerbara I., Valente S., Bottoni P., Scatena R., Jesacher F., Loidl P., and Brosch G. 3-(4-Aroyl-1-methyl-1H-pyrrol-2-yl)-N-hydroxy-2-propenamides as a new class of synthetic histone deacetylase inhibitors. 3. Discovery of novel lead compounds through structure-based drug design and docking studies. J. Med. Chem. 47 (2004) 1351
80. Lu Q., Wang D., Chen C.S., Hu Y.D., and Chen C.S. Structure-based optimization of phenylbutyrate-derived histone deacetylase inhibitors. J. Med. Chem. 48 (2005) 5530
81. Kim H.M., Hong S.H., Kim M.S., Lee C.W., Kang J.S., Lee K., Park S.-K., Han J.W., Lee H.Y., Choi Y., Kwon H.J., and Han G. Modification of cap group in δ-lactam-based histone deacetylase (HDAC) inhibitors. Bioorg. Med. Chem. Lett. 17 (2007) 6234
82. Lee S., Shinji C., Ogura K., Shimizu M., Maeda S., Sato M., Yoshida M., Hashimoto Y., and Miyachi H. Design, synthesis, and evaluation of isoindolinone-hydroxamic acid derivatives as histone deacetylase (HDAC) inhibitors. Bioorg. Med. Chem. Lett. 17 (2007) 4895
83. Shinji C., Maeda S., Imai K., Yoshida M., Hashimoto Y., and Miyachi H. Design, synthesis, and evaluation of cyclic amide/imide-bearing hydroxamic acid derivatives as class-selective histone deacetylase (HDAC) inhibitors. Bioorg. Med. Chem. 14 (2006) 7625
84. Belvedere S., Witter D.J., Yan J., Secrist J.P., Richon V., and Miller T.A. Aminosuberoyl hydoxamic acids (ASHAs): a potent new class of HDAC inhibitors. Bioorg. Med. Chem. Lett. 17 (2007) 3969
85. Charrier C., Roche J., Gesson J.-P., and Bertrand P. Biological activities of substituted trichostatic acid derivatives. J. Chem. Sci. 121 (2009) 471
86. Dowling D.P., Gantt S.L., Gattis S.G., Fierke C.A., and Christianson D.W. Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors. Biochemistry 47 (2008) 13554
87. Di Micco S., Terracciano S., Bruno I., Rodriquez M., Riccio R., Taddei M., and Bifulco G. Molecular modelling studies toward the structural optimization of new cyclopeptide-based HDAC inhibitors modelled on the natural product FR235222. Bioorg. Med. Chem. 16 (2008) 8635
88. Grolla A.A., Podestà V., Chini M.G., Di Micco S., Vallario A., Genazzani A.A., Canonico P.L., Bifulco G., Tron G.C., Sorba G., and Pirali T. Synthesis, biological evaluation, and molecular docking of Ugi products containing a zinc-chelating moiety as novel inhibitors of histone deacetylases. J. Med. Chem. 52 (2009) 2776
89. Montero A., Beierle J.M., Olsen C.A., and Ghadiri M.R. Design, synthesis, biological evaluation, and structural characterization of potent histone deacetylase inhibitors based on cyclic α/β tetrapeptide architectures. J. Am. Chem. Soc. 131 (2009) 3033
90. Olsen C.A., and Ghadiri M.R. Discovery of potent and selective histone deacetylase inhibitors via focused combinatorial libraries of cyclic α3β-tetrapeptides. J. Med. Chem. 52 (2009) 7836
91. Loudni L., Roche J., Potiron V., Clarhaut J., Bachmann C., Gesson J.-P., and Tranoy-Opalinski I. Design, synthesis and biological evaluation of 1,4-benzodiazepine-2,5-dione-based HDAC inhibitors. Bioorg. Med. Chem. Lett. 17 (2007) 4819
92. Guo Y., Xiao J., Guo Z., Chu F., Cheng Y., and Wu S. Exploration of a binding mode of indole amide analogues as potent histone deacetylase inhibitors and 3D-QSAR analyses. Bioorg. Med. Chem. 13 (2005) 5424
93. Juvale D.C., Kulkarni V.V., Deokar H.S., Wagh N.K., Padhye S.B., and Kulkarni V.M. 3D-QSAR of histone deacetylase inhibitors: hydroxamate analogues. Org. Biomol. Chem. 4 (2006) 2858
94. Wagh N.K., Deokar H.S., Juvale D.C., Kadam S.S., and Kulkarni V.M. 3D-QSAR of histone deacetylase inhibitors as anticancer agents by genetic function approximation. Indian J. Biochem. Biophys. 43 (2006) 360
95. Chen Y., Li H., Tang W., Zhu C., Jiang Y., Zou J., Yu Q., and You Q. 3D-QSAR studies of HDACs inhibitors using pharmacophore based alignment. Eur. J. Med. Chem. 44 (2009) 2868
96. Katritzky A.R., Slavov S.H., Dobchev D.A., and Karelson M. Comparison between 2D and 3D-QSAR approaches to correlate inhibitor activity for a series of indoles amides hydroxamic acids. QSAR Comb. Sci. 26 (2006) 333
97. Vadivelan S., Sinha B.N., Rambabu G., Boppana K., and Jagarlapudi S.A.R.P. Pharmacophore modelling and virtual screening studies to design some potential histone deacetylase inhibitors as new leads. J. Mol. Graph. Model. 26 (2008) 935
98. Chen Y.-D., Jiand Y.-J., Zhou J.-W., Yu Q.-S., and You Q.-D. Identification of ligand features essential for HDACs inhibitors by pharmacophore modeling. J. Mol. Graph. Model. 26 (2008) 1160
99. Ragno R., Simeoni S., Valente S., Massa S., and Mai A. 3-D QSAR studies on histone deacetylase inhibitors. A GOLPE/GRID approach on different series of compounds. J. Chem. Info. Model. 46 (2006) 1420
100. Wang D.-F., Wiest O., Helquist P., Lan-Hargest H.-Y., and Wiech N.L. QSAR studies of PC-3 cell line inhibition activity of TSA and SAHA-like hydroxamic acids. Bioorg. Med. Chem. Lett. 14 (2004) 707