Pharmacophore modelling, validation, 3D virtual screening, docking, design and in silico ADMET simulation study of histone deacetylase class-1 inhibitors

Medicinal Chemistry Research

Volumn 23, Issue 11, 2014, Pages 4853-4864

  Gupta, Nirzari ^a   Sitwala, Nikum ^a   Patel, Keyur ^a  

^a NIRMA UNIVERSITY   (India)

Author keywords

ADMET; Docking; HDAC; Pharmacophore modelling; Virtual screening

Indexed keywords

EID: 84939881377     PISSN: 10542523     EISSN: 15548120     Source Type: Journal    
DOI: 10.1007/s00044-014-1057-2     Document Type: Article

References (48)

1. Abujamra AL, Santos MP, Roesler R, Schwartsmann G, Brunetto AL (2010) Histone deacetylase inhibitors: a new perspective for the treatment of leukemia. Leuk Res 34:687-695
2. Chen PC, Patil V, Guerrant W, Green P, Oyelere AK (2008) Synthesis and structure-activity relationship of histone deacetylase (HDAC) inhibitors with triazole-linked cap group. Bioorg Med Chem Lett 16:4839-4953
3. Cheng F, Li W, Zhou Y, Shen J, Wu Z, Liu G, Lee PW, Tang Y (2012) admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties. J Chem Inf Model 52:3099-3105
4. Choi E, Lee C, Park JE, Seo JJ, Cho M, Kang JS, Kimb HM, Park S, Lee K, Han G (2011) Structure and property based design, synthesis and biological evaluation of c-lactam based HDAC inhibitors. Bioorg Med Chem Lett 21:1218-1221
5. Clement OO, Freeman CM, Hartmann RW, Handratta VD, Vasaitis TS, Brodie AHM, Njar VCO (2003) Three dimensional pharmacophore modeling of human CYP17 inhibitors. Potential agents for prostate cancer therapy. J Med Chem 46:2345-2351
6. Curtin ML, Garland RB, Heyman HR, Frey RR, Michaelides MR, Li J, Pease LJ, Glaser KB, Marcotte PA, Davidsen SK (2002) Succinimide hydroxamic acids as potent inhibitors of histone deacetylase (HDAC). Bioorg Med Chem Lett 12:2919-2923
7. Dai Y, Guo Y, Curtin ML, Li J, Pease LJ, Guo J, Marcotte PA, Glaser KB, Davidsen SK, Michaelides MR (2003a) A novel series of histone deacetylase inhibitors incorporating hetero aromatic ring systems as connection units. Bioorg Med Chem Lett 13:3817-3820
8. Dai Y, Guo Y, Guo J, Pease LJ, Li J, Marcotte PA, Glaser KB, Tapang P, Albert DH, Richardson PL, Davidsen SK, Michaelides MR (2003b) Indole amide hydroxamic acids as potent inhibitors of histone deacetylases. Bioorg Med Chem Lett 13:1897-1901
9. Dallavalle S, Pisano C, Zunino F (2012) Development and therapeutic impact of HDAC6-selective inhibitors. Biochem Pharmacol 84:756-765
10. Dokmanovic M, Clarke C, Marks PA (2007) Histone deacetylase inhibitors: overview and perspectives. Mol Cancer Res 5:981-989
11. Elumalai P, Liu H, Zhao J, Chen W, Lin DS, Chuang C, Tsai WY, Ho Y (2012) Pharmacophore modeling, Virtual Screening and docking studies to identify novel HNMT inhibitors. J Taiwan Inst Chem Eng 43:493-503
12. Equbal T, Silakari O, Rambabu G, Ravikumar M (2007) Pharmacophore mapping of diverse classes of farnesyltransferase inhibitor. Bioorg Med Chem Lett 17:1594-1600
13. Fawcett T (2006) An introduction to ROC analysis. Pattern Recognit Lett 27:861-874
14. Finnin MS, Donigian JR, Cohen A, Richon VM, Rifkind RA, Marks PA, Breslow R, Pavletich NP (1999) Structure of a histone deacetylase homologue bound to the TSA and SAHA inhibitor. Nature 401:188-193
15. Fournel M, Bonfils C, Hou Y, Yan PT, Trachy-Bourget MC, Kalita A, Liu J, Lu AH, Zhou NZ, Robert MF, Gillespie J, Wang JJ, Ste-Croix H, Rahil J, Lefebvre S, Moradei O, Delorme D, MacLeod AR, Besterman JM, Li Z (2008) MGCD01303, a novel isotype-selective histone deacetylase inhibitor, has broad spectrum antitumor activity in vitro and in vivo. Mol Cancer Ther 7:759-765
16. Fréchette S, Leit S, Woo SH, Lapointe G, Jeannotte G, Moradei O, Paquin I, Bouchain G, Raeppel S, Gaudette F, Zhou N, Vaisburg A, Fournel M, Yan PT, Trachy-Bourget M, Kalita A, Robert M, Lu A, Rahil J, MacLeod AR, Besterman JM, Li Z, Delorme D (2008) 4-(Heteroarylaminomethyl)- N-(2-aminophenyl)-benzamides and their analogs as a novel class of histone deacetylase inhibitors. Bioorg Med Chem Lett 18:1502-1506
17. Frikeche J, Peric Z, Brissot E, Grégoire M, Gaugler B, Mohty M (2012) Impact of HDAC inhibitors on dendritic cell functions. Exp Hematol 40:783-791
18. Garcia-Manero G, Assouline S, Cortes J, Estrov Z, Kantarjian H, Yang H, Newsome WM, Miller WH, Rousseau C, Kalita A, Bonfils C, Dubay M, Patterson TA, Li Z, Besterman JM, Reid G, Laille E, Martell RE, Minden M (2008) Phase I study of the oral isotope specific histone deacetylase inhibitor MGCD01303 in leukemia. Blood 112:981-989
19. Gimsing P, Hansen M, Knudsen LM, Knoblauch P, Christensen IJ, Ooi CE, Buhl-Jensen P (2008) A Phase I clinical trials of the histone deacetylase inhibitors belinostat in patient with advanced hematological neoplasia. Eur J Hematol 81:170-176
20. Gopalan B, Ponpandian T, Kachhadia V, Mohan KB, Vignesh R, Sivasudar V, Narayanan S, Mandar B, Praveen R, Saranya N, Rajagopal S, Rajagopal S (2013) Discovery of adamantane based highly potent HDAC inhibitors. Bioorg Med Chem Lett 23: 2532-2537
21. Gore L, Rothenberg ML, O'Bryant CL, Schultz MK, Sandler AB, Coffin D, McCoy C, Schott A, Scholz C, Eckhardt SG (2008) A Phase I clinical and pharmacokinetic study of the oral histone deacetylase inhibitor, MS-275, in patient with refractory solid tumor and lymphomas. Clin Cancer Res 14:4517-4525
22. Güner OF (2000) Pharmacophore perception, development, and use in drug design. International University Line, La Jolla, pp 213-236
23. Güner OF, Henry DR (2000) Metric for analyzing hit lists and pharmacophores. In: Güner OF (ed) Pharmacophore perception, development, and use in drug design. International University Line, La Jolla, pp 191-211
24. Güner OF, Henry DR, Moock TE, Pearlman RS (1990) Flexible queries in 3D searching techniques in 3D query formulation. Tetrahedron Lett 3:557-563
25. Gupta N, Patel B, Vyas V, Ghate M (2014) Predictive 3D-QSAR and HQSAR model generation of isocitrate lyase (ICL) inhibitors by various alignment methods combined with docking study. Med Chem Res 23:2757-2768
26. Kell J (2007) Drug evaluation: MGCD-0103, a novel histone deacetylase inhibitor for the treatment of cancer. Curr Opin Investig Drugs 8:485-492
27. Kim H, Bae S (2011) Histone deacetylase inhibitors: molecular mechanisms of action and clinical trials as anti-cancer drugs. Am J Transl Res 3:166-179
28. Kim HM, Hong SH, Kim MS, Lee CW, Kang JS, Lee K, Park S, Han JH, Lee HY, Kwon HJ (2007) Modification of cap group in d-lactam-based histone deacetylase (HDAC) inhibitors. Bioorg Med Chem Lett 17:6234-6238
29. Landgrebe TCW, Duin RPW (2007) Approximating the multiclass ROC by pairwise analysis. Pattern Recognit Lett 28:1747-1758
30. Landgrebe TCW, Paclik P (2010) The ROC skeleton for multiclass ROC estimation. Pattern Recognit Lett 31:949-958
31. Lee S, Shinji C, Ogura K, Shimizu M, Maeda S, Sato M, Yoshida M, Hashimotoa M, Miyachi H (2007) Design, synthesis, and evaluation of isoindolinone-hydroxamic acid derivatives as histone deacetylase (HDAC) inhibitors. Bioorg Med Chem Lett 17:4895-4900
32. Lengauer T, Lemmen C, Rarey M, Zimmermann M (2004) Novel technologies for virtual screening. Drug Discov Today 9:112-116
33. Marks PA, Xu W (2009) Histone deacetylase inhibitors: potential in cancer therapy. J Cell Biochem 107:600-608
34. Nguyen TL, Wilson MG, Hiscott J (2010) Oncolytic viruses and histone deacetylase inhibitors - a multi-pronged strategy to target tumor cells. Cytokine Growth Factor Rev 21:153-159
35. Ooms D, Palm R, Leemans V, Destain MF (2010) A sorting optimization curve with quality and yield requirements. Pattern Recognit Lett 31:983-990
36. Pan L, Lu J, Huang B (2007) HDAC inhibitors: a potential new category of anti-tumor agents. Cell Mol Immunol 4:337-343
37. Qian X, LaRochelle WJ, Ara G, Wu F, Petersen KD, Thougaard A, Sehested M, Lichenstein HS, Jeffers M (2006) Activity of PDX 101, a histone deacetylase inhibitor, in preclinical ovarian cancer studies. Mol Cancer Ther 5:2086-2093
38. Remiszewski SW, Sambucetti LC, Bair KW, Bontempo J, Cesarz D, Chandramouli N, Chen R, Cheung M, Cornell-Kennon S, Dean K, Diamantidis G, France D, Green MA, Howell KL, Kashi R, Kwon P, Lassota P, Martin MS, Mou Y, Perez LB, Sharma S, Smith T, Sorensen E, Taplin F, Trogani N, Versace R, Walker H, Weltchek-Engler S, Wood A, Wu A, Atadja P (2003) N-hydroxy-3-phenyl-2-propenamides as novel inhibitors of human histone deacetylase with in vivo antitumor activity. J Med Chem 46:4609-4624
39. Suzuki T, Ando T, Tsuchiya K, Fukazawa N, Saito A, Mariko Y, Yamashita T, Nakanishi O (1999) Synthesis and histone deacetylase inhibitory activity of new benzamide derivatives. J Med Chem 42:3001-3003
40. Suzuki T, Kouketsu A, Matsuura A, Kohara A, Ninomiya S, Kohdaa K, Miyataa N (2004) Thiol-based SAHA analogues as potent histone deacetylase inhibitors. Bioorg Med Chem Lett 14:3313-3317
41. Tan J, Cang S, Ma Y, Petrillo RL, Liu D (2010) Novel histone deacetylase inhibitors in clinical trials as anti-cancer agents. J Hematol Oncol 3:5-13
42. Tripos Associates (2011) SYBYL X Molecular Modeling Software Version 1.3. Tripos Associates St. Louis. http://www.tripos.com. Accessed 10 Mar 2014
43. Vyas VK, Ghate M, Goel A (2013) Pharmacophore modeling, virtual screening, docking and in silico ADMET analysis of protein kinase B (PKB) inhibitors. J Mol Graph Model 42:17-25
44. Wang X, Wei X, Pang Q, Yi F (2012) Histone deacetylases and their inhibitors: molecular mechanisms and therapeutic implications in diabetes mellitus. Acta Pharm Sin B 2:387-395
45. Witter DJ, Belvedere S, Chen L, Secrist JP, Mosleyd RT, Miller TA (2007) Benzo[b]thiophene-based histone deacetylase inhibitors. Bioorg Med Chem Lett 17:4562-4567
46. Yuan H, Petukhov PA (2006) Improved 3D-QSAR CoMFA of the dopamine transporter blockers with multiple conformations using the genetic algorithm. Bioorg Med Chem Lett 16:6267-6272
47. Zhou N, Moradei O, Raeppel S, Leit S, Frechette S, Gaudette F, Paquin I, Bernstein N, Bouchain G, Vaisburg A, Jin Z, Gillespie J, Wang J, Fournel M, Yan PT, Trachy-Bourget MC, Kalita A, Lu A, Rahil J, MacLeod AR, Li Z, Besterman JM, Delorme D (2008) Discovery of N-(2-aminophenyl)-4-[(4-pyridin-3-ylpyrmidine-2-ylamino)methyl]benzamide, an orally active histone deacetylase inhibitor. J Med Chem 51:4072-4075
48. Zuo M, Zheng Y, Lu S, Li Y, Zhang S (2012) Synthesis and biological evaluation of N-aryl salicylamides with a hydroxamic acid moiety at 5-position as novel HDAC-EGFR dual inhibitors. Bioorg Med Chem 20:4405-4412