76
Views
1
CrossRef citations to date
0
Altmetric
Original Research

Identification of potent histone deacetylase 8 inhibitors using pharmacophore-based virtual screening, three-dimensional quantitative structure–activity relationship, and docking study

, , , &
Pages 21-39 | Published online: 25 Jun 2015

References

  • Glozak MA, Sengupta N, Zhang X, Seto E. Acetylation and deacetylation of non-histone proteins. Gene. 2005;363:15–23.
  • Suzuki T, Nagano Y, Matsuura A, et al. Novel histone deacetylase inhibitors: design, synthesis, enzyme inhibition, and binding mode study of SAHA-based non-hydroxamates. Bioorg Med Chem Lett. 2003;13(24):4321–4326.
  • Di Gennaro E, Bruzzese F, Caraglia M, Abruzzese A, Budillon A. Acetylation of proteins as novel target for antitumor therapy: review article. Amino Acids. 2004;26(4):435–441.
  • Bolden JE, Peart MJ, Johnstone RW. Anticancer activities of histone deacetylase inhibitors. Nat Rev Drug Discov. 2006;5(9):769–784.
  • Minucci S, Pelicci PG. Histone deacetylase inhibitors and the promise of epigenetic (and more) treatments for cancer. Nat Rev Cancer. 2006;6(1):38–51.
  • Nam NH, Huong TL, Dungdo TM, et al. Novel isatin-based hydroxamic acids as histone deacetylase inhibitors and antitumor agents. Eur J Med Chem. 2013;70:477–486.
  • Wang C, Eessalu TE, Barth VN, et al. Design, synthesis, and evaluation of hydroxamic acid-based molecular probes for in vivo imaging of histone deacetylase (HDAC) in brain. Am J Nucl Med Mol Imaging. 2013;4(1):29–38.
  • Zhang Y, Feng J, Liu C, Fang H, Xu W. Design, synthesis and biological evaluation of tyrosine-based hydroxamic acid analogs as novel histone deacetylases (HDACs) inhibitors. Bioorg Med Chem. 2011;19(15):4437–4444.
  • Montero A, Beierle JM, Olsen CA, Ghadiri MR. Design, synthesis, biological evaluation, and structural characterization of potent histone deacetylase inhibitors based on cyclic alpha/beta-tetrapeptide architectures. J Am Chem Soc. 2009;131(8):3033–3041.
  • Vaidya AS, Karumudi B, Mendonca E, et al. Design, synthesis, modeling, biological evaluation and photoaffinity labeling studies of novel series of photoreactive benzamide probes for histone deacetylase 2. Bioorg Med Chem Lett. 2012;22(15):5025–5030.
  • Moradei OM, Mallais TC, Frechette S, et al. Novel aminophenyl benzamide-type histone deacetylase inhibitors with enhanced potency and selectivity. J Med Chem. 2007;50(23):5543–5546.
  • Ilies M, Dowling DP, Lombardi PM, Christianson DW. Synthesis of a new trifluoromethylketone analogue of l-arginine and contrasting inhibitory activity against human arginase I and histone deacetylase 8. Bioorg Med Chem Lett. 2011;21(19):5854–5858.
  • Bora-Tatar G, Dayangaç-Erden D, Demir AS, Dalkara S, Yelekçi 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):5219–5228.
  • Prince HM, Bishton MJ, Harrison SJ. Clinical studies of histone deacetylase inhibitors. Clin Cancer Res. 2009;15(12):3958–3969.
  • Thurn KT, Thomas S, Moore A, Munster PN. Rational therapeutic combinations with histone deacetylase inhibitors for the treatment of cancer. Future Oncol. 2011;7(2):263–283.
  • Hess-Stumpp H, Bracker TU, Henderson D, Politz O. MS-275, a potent orally available inhibitor of histone deacetylases – the development of an anticancer agent. Int J Biochem Cell Biol. 2007;39(7–8):1388–1405.
  • Gregoretti IV, Lee YM, Goodson HV. Molecular evolution of the histone deacetylase family: functional implications of phylogenetic analysis. J Mol Biol. 2004;338(1):17–31.
  • Oehme I, Deubzer HE, Wegener D, et al. Histone deacetylase 8 in neuroblastoma tumorigenesis. Clin Cancer Res. 2009;15(1):91–99.
  • Gryder BE, Sodji QH, Oyelere AK. Targeted cancer therapy: giving histone deacetylase inhibitors all they need to succeed. Future Med Chem. 2012;4(4):505–524.
  • Balasubramanian S, Ramos J, Luo W, Sirisawad M, Verner E, Buggy JJ. A novel histone deacetylase 8 (HDAC8)-specific inhibitor PCI-34051 induces apoptosis in T-cell lymphomas. Leukemia. 2008;22(5):1026–1034.
  • Song J, Noh JH, Lee JH, et al. Increased expression of histone deacetylase 2 is found in human gastric cancer. APMIS. 2005;113(4):264–268.
  • Zhu P, Martin E, Mengwasser J, Schlag P, Janssen KP, Göttlicher M. Induction of HDAC2 expression upon loss of APC in colorectal tumorigenesis. Cancer Cell. 2004;5(5):455–463.
  • Tang W, Luo T, Greenberg EF, Bradner JE, Schreiber SL. Discovery of histone deacetylase 8 selective inhibitors. Bioorg Med Chem Lett. 2011;21(9):2601–2605.
  • Liu T, Kapustin G, Etzkorn FA. Design and synthesis of a potent histone deacetylase inhibitor. J Med Chem. 2007;50(9):2003–2006.
  • Olson DE, Wagner FF, Kaya T, et al. Discovery of the first histone deacetylase 6/8 dual inhibitors. J Med Chem. 2013;56(11):4816–4820.
  • Chen PC, Patil V, Guerrant W, Green P, Oyelere AK. Synthesis and structure-activity relationship of histone deacetylase (HDAC) inhibitors with triazole-linked cap group. Bioorg Med Chem. 2008;16(9):4839–4853.
  • Grozinger CM, Schreiber SL. Deacetylase enzymes: biological functions and the use of small-molecule inhibitors. Chem Biol. 2002;9(1):3–16.
  • Jung M, Brosch G, Kölle D, Scherf H, Gerhäuser C, Loidl P. Amide analogues of trichostatin A as inhibitors of histone deacetylase and inducers of terminal cell differentiation. J Med Chem. 1999;42(22):4669–4679.
  • 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(1):87–92.
  • Finnin MS, Donigian JR, Cohen A, et al. Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors. Nature. 1999;401(6749):188–193.
  • Patil V, Sodji QH, Kornacki JR, Mrksich M, Oyelere AK. 3-Hydroxypyridin-2-thione as novel zinc binding group for selective histone deacetylase inhibition. J Med Chem. 2013;56(9):3492–3506.
  • Zhang Y, Feng J, Jia Y, et al. Development of tetrahydroisoquinoline-based hydroxamic acid derivatives: potent histone deacetylase inhibitors with marked in vitro and in vivo antitumor activities. J Med Chem. 2011;54(8):2823–2838.
  • Somoza JR, Skene RJ, Katz BA, et al. Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases. Structure. 2004;12(7):1325–1334.
  • Dixon SL, Smondyrev AM, Knoll EH, Rao SN, Shaw DE, Friesner RA. PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J Comput Aided Mol Des. 2006;20(10–11):647–671.
  • Tawari NR, Bag S, Degani MS. Pharmacophore mapping of a series of pyrrolopyrimidines, indolopyrimidines and their congeners as multidrug-resistance-associated protein (MRP1) modulators. J Mol Model. 2008;14(10):911–921.
  • Tetko IV, Tanchuk VY, Villa AE. Prediction of n-octanol/water partition coefficients from PHYSPROP database using artificial neural networks and E-state indices. J Chem Inf Comput Sci. 2001;41(5):1407–1421.
  • Veerasamy R, Rajak H, Jain A, Sivadasan S, Varghese CP, Agrawal RK. Validation of QSAR models – strategies and importance. International Journal of Drug Design and Discovery. 2011;2(3):511–519.
  • Roy DR, Sarkar U, Chattaraj PK, et al. Analyzing toxicity through electrophilicity. Mol Divers. 2006;10(2):119–131.
  • Friesner RA, Banks JL, Murphy RB, et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem. 2004;47(7):1739–1749.
  • Halgren TA, Murphy RB, Friesner RA, et al. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem. 2004;47(7):1750–1759.
  • Friesner RA, Murphy RB, Repasky MP, et al. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem. 2006;49(21):6177–6196.