Table of Contents Author Guidelines Submit a Manuscript
Advances in Bioinformatics
Volume 2014, Article ID 812148, 11 pages
http://dx.doi.org/10.1155/2014/812148
Research Article

Ligand Based Pharmacophore Modeling and Virtual Screening Studies to Design Novel HDAC2 Inhibitors

Department of Chemistry, Sathyabama University, Jeppiaar Nagar, Chennai 600119, India

Received 11 July 2014; Revised 8 October 2014; Accepted 22 October 2014; Published 26 November 2014

Academic Editor: Gilbert Deleage

Copyright © 2014 Naresh Kandakatla and Geetha Ramakrishnan. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. A. Mai, S. Massa, R. Ragno et al., “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,” Journal of Medicinal Chemistry, vol. 46, no. 4, pp. 512–524, 2003. View at Publisher · View at Google Scholar · View at Scopus
  2. C. Monneret, “Histone deacetylase inhibitors,” European Journal of Medicinal Chemistry, vol. 40, no. 1, pp. 1–13, 2005. View at Publisher · View at Google Scholar · View at Scopus
  3. D. D. Leipe and D. Landsman, “Histone deacetylases, acetoin utilization proteins and acetylpolyamine amidohydrolases are members of an ancient protein superfamily,” Nucleic Acids Research, vol. 25, no. 18, pp. 3693–3697, 1997. View at Publisher · View at Google Scholar · View at Scopus
  4. X.-J. Yang and E. Seto, “The Rpd3/Hda1 family of lysine deacetylases: from bacteria and yeast to mice and men,” Nature Reviews Molecular Cell Biology, vol. 9, no. 3, pp. 206–218, 2008. View at Publisher · View at Google Scholar · View at Scopus
  5. A. V. Bieliauskas and M. K. H. Pflum, “Isoform-selective histone deacetylase inhibitors,” Chemical Society Reviews, vol. 37, no. 7, pp. 1402–1413, 2008. View at Publisher · View at Google Scholar · View at Scopus
  6. J. M. Denu, “The Sir2 family of protein deacetylases,” Current Opinion in Chemical Biology, vol. 9, no. 5, pp. 431–440, 2005. View at Publisher · View at Google Scholar · View at Scopus
  7. X.-J. Yang and S. Grégoire, “Class II histone deacetylases: from sequence to function, regulation, and clinical implication,” Molecular and Cellular Biology, vol. 25, no. 8, pp. 2873–2884, 2005. View at Publisher · View at Google Scholar · View at Scopus
  8. I. V. Gregoretti, Y.-M. Lee, and H. V. Goodson, “Molecular evolution of the histone deacetylase family: functional implications of phylogenetic analysis,” Journal of Molecular Biology, vol. 338, no. 1, pp. 17–31, 2004. View at Publisher · View at Google Scholar · View at Scopus
  9. O. H. Krämer, “HDAC2: a critical factor in health and disease,” Trends in Pharmacological Sciences, vol. 30, no. 12, pp. 647–655, 2009. View at Publisher · View at Google Scholar · View at Scopus
  10. M. Kilgore, C. A. Miller, D. M. Fass et al., “Inhibitors of class 1 histone deacetylases reverse contextual memory deficits in a mouse model of alzheimer's disease,” Neuropsychopharmacology, vol. 35, no. 4, pp. 870–880, 2010. View at Publisher · View at Google Scholar · View at Scopus
  11. J. M. Wagner, B. Hackanson, M. Lübbert, and M. Jung, “Histone deacetylase (HDAC) inhibitors in recent clinical trials for cancer therapy,” Clinical Epigenetics, vol. 1, no. 3-4, pp. 117–136, 2010. View at Publisher · View at Google Scholar · View at Scopus
  12. D. R. Walkinshaw and X.-J. Yang, “Histone deacetylase inhibitors as novel anticancer therapeutics,” Current Oncology, vol. 15, no. 5, pp. 237–243, 2008. View at Google Scholar · View at Scopus
  13. Á. Jóna, N. Khaskhely, D. Buglio et al., “The histone deacetylase inhibitor entinostat (sndx-275) induces apoptosis in hodgkin lymphoma cells and synergizes with bcl-2 family inhibitors,” Experimental Hematology, vol. 39, no. 10, pp. 1007.e1–1017.e1, 2011. View at Publisher · View at Google Scholar · View at Scopus
  14. A. Younes, Y. Oki, R. G. Bociek et al., “Mocetinostat for relapsed classical Hodgkin's lymphoma: an open-label, single-arm, phase 2 trial,” The Lancet Oncology, vol. 12, no. 13, pp. 1222–1228, 2011. View at Publisher · View at Google Scholar · View at Scopus
  15. H. M. Prince, M. J. Bishton, and S. J. Harrison, “Clinical studies of histone deacetylase inhibitors,” Clinical Cancer Research, vol. 15, no. 12, pp. 3958–3969, 2009. View at Publisher · View at Google Scholar · View at Scopus
  16. S.-Y. Yang, “Pharmacophore modeling and applications in drug discovery: challenges and recent advances,” Drug Discovery Today, vol. 15, no. 11-12, pp. 444–450, 2010. View at Publisher · View at Google Scholar · View at Scopus
  17. S. Vadivelan, B. N. Sinha, G. Rambabu, K. Boppana, and S. A. R. P. Jagarlapudi, “Pharmacophore modeling and virtual screening studies to design some potential histone deacetylase inhibitors as new leads,” Journal of Molecular Graphics and Modelling, vol. 26, no. 6, pp. 935–946, 2008. View at Publisher · View at Google Scholar · View at Scopus
  18. T. Sundarapandian, J. Shalini, S. Sugunadevi, and L. K. Woo, “Docking-enabled pharmacophore model for histone deacetylase 8 inhibitors and its application in anti-cancer drug discovery,” Journal of Molecular Graphics and Modelling, vol. 29, no. 3, pp. 382–395, 2010. View at Publisher · View at Google Scholar · View at Scopus
  19. N. Kandakatla, G. Ramakrishnan, S. Vadivelan, and S. Jagarlapudi, “QSAR studies of N-(2-Aminophenyl)-Benzamide derivatives as histone deacetylase2 inhibitors,” International Journal of PharmTech Research, vol. 4, no. 3, pp. 1110–1121, 2012. View at Google Scholar · View at Scopus
  20. R. R. Frey, C. K. Wada, R. B. Garland et al., “Trifluoromethyl ketones as inhibitors of histone deacetylase,” Bioorganic & Medicinal Chemistry Letters, vol. 12, no. 23, pp. 3443–3447, 2002. View at Publisher · View at Google Scholar · View at Scopus
  21. P. Siliphaivanh, P. Harrington, D. J. Witter et al., “Design of novel histone deacetylase inhibitors,” Bioorganic & Medicinal Chemistry Letters, vol. 17, no. 16, pp. 4619–4624, 2007. View at Publisher · View at Google Scholar · View at Scopus
  22. D. J. Witter, P. Harrington, K. J. Wilson et al., “Optimization of biaryl selective HDAC1&2 inhibitors (SHI-1:2),” Bioorganic and Medicinal Chemistry Letters, vol. 18, no. 2, pp. 726–731, 2008. View at Publisher · View at Google Scholar · View at Scopus
  23. J. L. Methot, P. K. Chakravarty, M. Chenard et al., “Exploration of the internal cavity of histone deacetylase (HDAC) with selective HDAC1/HDAC2 inhibitors (SHI-1:2),” Bioorganic & Medicinal Chemistry Letters, vol. 18, no. 3, pp. 973–978, 2008. View at Publisher · View at Google Scholar · View at Scopus
  24. K. J. Wilson, D. J. Witter, J. B. Grimm et al., “Phenylglycine and phenylalanine derivatives as potent and selective HDAC1 inhibitors (SHI-1),” Bioorganic and Medicinal Chemistry Letters, vol. 18, no. 6, pp. 1859–1863, 2008. View at Publisher · View at Google Scholar · View at Scopus
  25. P. Tessier, D. V. Smil, A. Wahhab et al., “Diphenylmethylene hydroxamic acids as selective class IIa histone deacetylase inhibitors,” Bioorganic & Medicinal Chemistry Letters, vol. 19, no. 19, pp. 5684–5688, 2009. View at Publisher · View at Google Scholar · View at Scopus
  26. S. Raeppel, N. Zhou, F. Gaudette et al., “SAR and biological evaluation of analogues of a small molecule histone deacetylase inhibitor N-(2-aminophenyl)-4-((4-(pyridin-3-yl)pyrimidin-2-ylamino)methyl)benzamide (MGCD0103),” Bioorganic & Medicinal Chemistry Letters, vol. 19, no. 3, pp. 644–649, 2009. View at Publisher · View at Google Scholar · View at Scopus
  27. R. W. Heidebrecht Jr., M. Chenard, J. Close et al., “Exploring the pharmacokinetic properties of phosphorus-containing selective HDAC 1 and 2 inhibitors (SHI-1:2),” Bioorganic and Medicinal Chemistry Letters, vol. 19, no. 7, pp. 2053–2058, 2009. View at Publisher · View at Google Scholar · View at Scopus
  28. K. V. Butler and A. P. Kozikowski, “Chemical origins of isoform selectivity in histone deacetylase inhibitors,” Current Pharmaceutical Design, vol. 14, no. 6, pp. 505–528, 2008. View at Publisher · View at Google Scholar · View at Scopus
  29. P. Jones and C. Steinkühler, “From natural products to small molecule ketone histone deacetylase inhibitors: development of new class specific agents,” Current Pharmaceutical Design, vol. 14, no. 6, pp. 545–561, 2008. View at Publisher · View at Google Scholar · View at Scopus
  30. L. Zuomei and K. Murakami, “Combination therapy,” US 20090124631 A1.
  31. J. C. Bressi, A. J. Jennings, R. Skene et al., “Exploration of the HDAC2 foot pocket: synthesis and SAR of substituted N-(2-aminophenyl)benzamides,” Bioorganic and Medicinal Chemistry Letters, vol. 20, no. 10, pp. 3142–3145, 2010. View at Publisher · View at Google Scholar · View at Scopus
  32. J. B. Joseph and B. Sriram, “Uses of selective inhibitors of hdac8 for treatment of t-cell proliferative disorders,” US Patent no. 20080112889 A1, 2008.
  33. D. V. Smil, S. Manku, Y. A. Chantigny et al., “Novel HDAC6 isoform selective chiral small molecule histone deacetylase inhibitors,” Bioorganic & Medicinal Chemistry Letters, vol. 19, no. 3, pp. 688–692, 2009. View at Publisher · View at Google Scholar · View at Scopus
  34. G. Giannini, M. Marzi, M. D. Marzo et al., “Exploring bis-(indolyl)methane moiety as an alternative and innovative CAP group in the design of histone deacetylase (HDAC) inhibitors,” Bioorganic and Medicinal Chemistry Letters, vol. 19, no. 10, pp. 2840–2843, 2009. View at Publisher · View at Google Scholar · View at Scopus
  35. H. Li, J. Sutter, and R. Hoffmann, “HypoGen: an automated system for generating predictive 3D pharmacophore models,” in Pharmacophore Perception, Development, and use in Drug Design, O. F. Güner, Ed., pp. 173–189, International University Line, La Jolla, Calif, USA, 2000.
  36. T. Langer and G. Wolber, “Pharmacophore definition and 3D searches,” Drug Discovery Today: Technologies, vol. 1, no. 3, pp. 203–207, 2004. View at Publisher · View at Google Scholar · View at Scopus
  37. National Cancer Institute (NCI) database, http://dtp.nci.nih.gov/.
  38. Maybride Database, http://www.maybridge.com/.
  39. C. M. Venkatachalam, X. Jiang, T. Oldfield, and M. Waldman, “LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites,” Journal of Molecular Graphics and Modelling, vol. 21, no. 4, pp. 289–307, 2003. View at Publisher · View at Google Scholar · View at Scopus
  40. N. Noureen, S. Kalsoom, and H. Rashid, “Ligand based pharmacophore modelling of anticancer histone deacetylase inhibitors,” African Journal of Biotechnology, vol. 9, no. 25, pp. 3923–3931, 2010. View at Google Scholar · View at Scopus