Developing consensus 3D-QSAR and pharmacophore models for several beta-secretase, farnesyl transferase and histone deacetylase inhibitors

Journal of Molecular Modeling

Volumn 18, Issue 2, 2012, Pages 675-692

  Wei, Hsin Yuan ^a   Chen, Guan Ju ^a   Chen, Chih Lun ^a   Lin, Thy Hou ^a  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

Author keywords

3D QSAR; Catalyst; CoMFA; CoMSIA; Consensus QSAR; GOLD

Indexed keywords

BETA SECRETASE INHIBITOR; HISTONE DEACETYLASE INHIBITOR; PROTEIN FARNESYLTRANSFERASE INHIBITOR;

ACCURACY; ARTICLE; CATALYST; COMPARATIVE MOLECULAR FIELD ANALYSIS; COMPARATIVE MOLECULAR SIMILARITY INDICES ANALYSIS; COMPUTER PROGRAM; CONSENSUS THREE DIMENSIONAL QUANTITATIVE STRUCTURE ACTIVITY RELATION; MOLECULAR DOCKING; PARTIAL LEAST SQUARES REGRESSION; PHARMACOPHORE; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

AMYLOID PRECURSOR PROTEIN SECRETASES; CATALYSIS; COMPUTER SIMULATION; ENZYME INHIBITORS; FARNESYLTRANSTRANSFERASE; HISTONE DEACETYLASE INHIBITORS; HISTONE DEACETYLASES; MODELS, MOLECULAR; PROTEIN BINDING; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84861228993     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-011-1094-4     Document Type: Article

References (61)

1. Croog SH, Burleson JA, Sudilovsky A, Baume RM (2006) Spouse caregivers of Alzheimer patients: problem responses to caregiver burden. Aging Ment Health 10:87-100 (Pubitemid 43355118)
2. Hardy J, Selkoe DJ (2002) Thyamyloid hypothesis of Alzheimer's disease: progress and problems on the road to the therapeutics. Science 297:353-356 (Pubitemid 34790756)
3. De Strooper BD, Köning G (1999) Alzheimer's disease a firm base for drug development. Nature 402:471-472
4. Plaques and Tangles: The Hallmarks of AD, A. D. E. A. R Center, National Institute on Aging, http://www.nia.nih.gov/Alzheimers/ Publications/ UnravelingTheMystery/Part1/Hallmarks.htm
5. Cai H, Wang Y, McCarthy D, Wen H, Borchelt DR, Price DL, Wong PC (2001) BACE1 is the major β-secretase for generation of Aβpeptides by neurons. Nat Neurosci 4:233-234 (Pubitemid 32194867)
6. Iserloh U, Pan J, Stamford AW, Kennedy ME, Zhang Q, Zhang L, Parker EM, McHugh NA, Favreau L, Strickland C, Voigt J (2008) Discovery of an orally efficacious 4-phenoxypyrrolidine-based BACE-1 inhibitors. Bioorg Med Chem Lett 18:418-422
7. Lindsley SR, Moore KP, Rajapakse HA, Seinick HG, Young MB, Zhu H, Munshi S, Kuo L, McGaughey GB, Colussi D, Crouthamel MC, Lai MT, Pietrak B, Price EA, Sankaranarayanan S, Simon AJ, Seabrook GR, Hazuda DJ, Pudvah NT, Hochman JH, Graham SL, Vacca JP, Nantermet PG (2007) Design, Synthesis, and SAR of macrocyclic tertitary carbinamine BACE- 1 inhibitors. Bioorg Med Chem Lett 17:4057-4061 (Pubitemid 46920916)
8. Stachel SJ, Colourn CA, Steele TG, Crouthamel MC, Pietrak BL, Lai MT, Holloway MK, Munshi SK, Graham SL, Vacca JP (2006) Conformationally based P3 amide replacements of beta-secretase inhibitors. Bioorg Med Chem Lett 16:641-644 (Pubitemid 43014850)
9. Limongelli V, Marinelli L, Cosconati S, Braun HA, Schmidt B, Novellino E (2007) Ensemble-docking approach on BACE-1: pharmacophore perception and guidelines for drug design. Chem Med Chem 2:667-678
10. Gerschwinder S, Olsson LL, Albert JS, Deinum J, Edwards PD, de Beer T, Folmer RH (2007) Discovery of a novel warhead against beta-secretase through fragment-based lead generation. J Med Chem 50:5903-5911
11. Yang W, Fucini RV, Fahr BT, Randal M, Lind KE, Lam MB, Lu W, Lu Y, Cary DR, Ramanowski MJ, Colussi D, Pietrak B, Allison TJ, Munshi SK, Penny DM, Pham P, Sun J, Thomas AE, Wilkinson JM, Jacobs JW, McDowell RS, Ballinger MD (2009) Fragment-based discovery of nonpeptidic BACE-1 inhibitors using tethering. Biochemistry 48:4488-4496
12. Cramer RD III, Patterson DE, Bunce JS (1988) Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J Am Chem Soc 110:5959-5967
13. KlebeG,Abraham U,Mietzner T (1994)Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J Med Chem 37:4130-4146
14. Pandey A, Mungalpara J, Mohan CG (2010) Comparative molecular field analysis and comparative molecular similarity indices analysis of hydroxyethylamine derivatives as selective human BACE-1 inhibitor. Mol Divers 14:39-49
15. Pazin MJ, Kadonaga JT (1997) What's up and down with histone deacetylation and transcription? Cell 89:325-328 (Pubitemid 27220876)
16. Stemer DE, Berger SL (2000) Acetylation of histones and transcription-related factors. Microbiol Mol Biol Rev 64:435-439
17. Konstantinopoulos PA, Karamouzis MV, Papavassiliou AG (2007) Focus on acetylation: the role of histone deacetylase inhibitors in cancer therapy and beyond. Expert Opin Investig Drugs 16:569-571 (Pubitemid 46723267)
18. Yosida M, Kijima M, Akita M, Beppu T (1990) Potent and specific inhibition of mammalian histone deacetylase both in vivo and in vitro by trichostatin. J Biol Chem 265:17174-17179
19. Richon VM, Emiliani S, Verdin E, Webb Y, Breslow R, Rifkind RA, Marks PA (1998) A class of hybrid polar inducers of transformed cell differentiation inhibits histone deacetylase. Proc Natl Acad Sci USA 95:3003-3007 (Pubitemid 28135844)
20. Plumb JA, Finn PW, Williams RJ, Bandara MJ, Romero MR, Watkins CJ, La Thangue NB, Brown R (2003) Pharmacodynamic response and inhibition of growth of human tumor xenografts by the novel histone deacetylase inhibitor PXD101. Mol Cancer Ther 2:721-728
21. 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 (Pubitemid 29370445)
22. Leoni F, Zaliani A, Bertolini G, Porro G, Pagani P, Pozzi P, Dona G, Fossati G, Sozzani S, Azam T, Bufler P, Fantuzzi G, Goncharov I, Kim SH, Pomerantz BJ, Reznikov LL, Siegmund B, Dinarello CA, Mascagni P (2002) The antitumor histone deacetylase inhibitor suberoylanilide hydroxamic acid exhibits anti-inflammatory properties via suppression of cytokines. Proc Natl Acad Sci USA 99:2995-3000 (Pubitemid 34240574)
23. De Ruijter AJ, van Gennip AH, Caron HN, Kemp S, van Kuilenburg AB (2003) Histone deacetylase (HDACs): characterization of the classical HDAC family. Biochem J 370:737-749 (Pubitemid 36399066)
24. Grant S, Easley C, Kirkpatrick P (2007) Vorinostat Nat. Rev Drug Discov 6:21-22
25. Ryan QC, Headlee D, Acharya M, Sparreboom A, Trepel JB, Ye J, Figg WD, Hwang K, Chung EJ, Murgo A, Melillo G, Elsayed Y, Monga M, Kalnitskiy M, Zwiebel J, Sausville EA (2005) Phase 1 and pharmacokinetic study of MS-275, a histone deacetylase inhibitors in patients with advanced and refractory solid tumors or lymphoma. J Clin Oncol 23:3912-3922 (Pubitemid 46218694)
26. Byrd JC, Marcucci G, Parthun MR, Xiao JJ, Klisovic RB, Moran M, Lin TS, Liu S, Sklenar AR, Davis ME, Lucas DM, Fisher B, Shank R, Tejaswi SL, Binkley P, Wright J, Chan KK, Grever MR (2005) A phase 1 and pharmacodynamic study of depsipeptide (FK228) in chronic lymphocytic leukemia and acute myeloid leukemia. Blood 105:959-967 (Pubitemid 40170861)
27. Wang DF, Wiest OG, Helquist P, Lan-Hargest HY, Wiech NL (2004) QSAR studies of PC-3 cell line inhibition activity of TSA and SAHA-like hydroxamic acids. Bioorg Med Chem Lett 14:707-711 (Pubitemid 38114857)
28. Xie A, Liao C, Li Z, Ning Z, Hu W, Lu X, Shi L, Zhou J (2004) Quantitative structure-activity relationship study of histone deacetylase inhibitors. Curr Med Chem Anticancer Agents 4:273-299 (Pubitemid 38647587)
29. Juvale DC, Kulkarni VV, Deokar HS, Wagh NK, Padhye SB, Kulkarni VM (2006) 3D-QSAR of histone deacetylase inhibitors: hydroxamate analogues. Org Biomol Chem 4:2858-2868 (Pubitemid 44100284)
30. Bos JL (1989) Ras oncogenes in human cancer: a review. Cancer Res 49:4682-4689 (Pubitemid 19213607)
31. Gibbs JB (1991) Ras C-terminal processing enzymes-new drug targets? Cell 65:1-4 (Pubitemid 121001207)
32. Willumsen BM, Norris K, Papageorge AG, Hubbert NL, Lowy DR (1984) Harvey murine sarcoma virus p21 ras protein: biological and biochemical significance of the cysteine nearest the carboxy terminus. EMBO J 3:2581-2585
33. Casey PJ, Solski PA, Der CJ, Buss JE (1989) p21 ras is modified by a farnesyl isoprenoid. Proc Natl Acad Sci USA 86:8323-8327 (Pubitemid 19286052)
34. Roberts PJ, Der CJ (2007) Targeting the Raf-MEK-ERK mitogenactivated protein kinase cascade for the treatment of cancer. Oncogene 26:3291-3310 (Pubitemid 46763022)
35. Chen WJ, Andres DA, Goldstein JL, Brown MS (1991) Cloning and expression of a cDNA encoding the alpha subunit of rat p21ras protein farnesyltransferase. Proc Natl Acad Sci USA 88:11368-11372 (Pubitemid 21916042)
36. Chen WJ, Andres DA, Goldstein JL, Russell DW, Brown MS (1991) cDNA cloning and expression of the peptide-binding beta subunit of rat p21ras farnesyltransferase, the counterpart of yeast DPR1/RAM1. Cell 66:327-334 (Pubitemid 121001370)
37. Puntambekar DS, Giridhar R, Yadav MR (2008) Insights into the structural requirements of farnesyltransferase inhibitors as potential anti-tumor agents based on 3D-QSAR CoMFA and CoMSIA models. Eur J Med Chem 43:142-154
38. Leonard DM (1997) Ras farnesyltransferase: a new therapeutic target. J Med Chem 40:2971-2990 (Pubitemid 27391526)
39. Perrin D, Halazy S, Hill B (1997) Inhibitors of Ras farnesyltransferase: tomorrows' anticancer agents? Bull Cancer 84:635-642 (Pubitemid 27351532)
40. Gibbs JB, Graham SL, Hartman GD, Koblan KS, Kohl NE, Omer CA, Oliff A (1997) Farnesyltransferase inhibitors versus Ras inhibitors. Curr Opin Chem Biol 1:197-203 (Pubitemid 127437145)
41. Qian Y, Sebti SM, Hamilton AD (1997) Farnesyltransferase as a target for anticancer drug design. Biopolymers 43:25-41 (Pubitemid 127570809)
42. Sun J, Qian Y, Hamilton AD, Sebti SM (1998) Both farnesyltransferase and geranylgeranyltransferase 1 inhibitors are required for inhibition of oncogenic K-Ras prenylation but each alone is sufficient to suppress human tumor growth in nude mouse xenografts. Oncogene 16:1467-1473 (Pubitemid 28151853)
43. Hunt JT, Lee VG, Leftheris K, Seizinger B, Carboni J, Mabus J, Ricca C, Yan N, Manne V (1996) Potent cell active non-thiol tetrapeptide inhibitors of farnesyltransferase. J Med Chem 39:353-358 (Pubitemid 26041449)
44. Tong Y, Lin NH, Wang L, Hasvold L, Wang W, Leonard N, Li T, Li Q, Cohen J, Gu WZ, Zhang H, Stoll V, Bauch J, Marsh K, Rosenberg SH, Sham HL (2003) Discovery of potent imidazole and cyanophenyl containing farnesyltransferase inhibitors with improved oral bioavailability. Bioorg Med Chem Lett 13:1571-1574 (Pubitemid 36428562)
45. Wang L, Wang GT, Wang X, Tong Y, Sullivan G, Park D, Leonard NM, Li Q, Cohen J, Gu WZ, Zhang H, Bauch JL, Jakob CG, Hutchins CW, Stoll VS, Marsh K, Rosenberg SH, Sham HL, Lin NH (2004) Design, synthesis, and biological activity of 4-[(4-cyano-2-arylbenzyloxy0-(3-methyl-3 H-imidazol-4-yl) methyl]benzonitriles as potent and selective farnesyltransferase inhibitors. J Med Chem 47:612-626 (Pubitemid 38129719)
46. Xie A, Odde S, Prasanna S, Doerksen RJ (2009) Imidazolecontaining farnesyltransferase inhibitors: 3D quantitative structureactivity relationships and molecular docking. J Comput Aided Mol Des 23:431-448
47. Equbal T, Silakari O, Rambabu G, Ravikumar M (2007) Pharmacophore mapping of diverse classes of farnesyltransferase inhibitors. Bioorg Med Chem Lett 17:1594-1600
48. Stahle L, Wold S (1986) On the use of some multivariate statistical methods in pharmacological research. J Pharmacol Meth 16:91-110 (Pubitemid 16048587)
49. Catalyst 4.11, Accelrys Inc., San Diego, CA 2005, http://accelrys. com/.
50. Bharatham N, Bharatham K, Lee KW (2006) Pharmacophore identification and virtual screening for methionyl-tRNA synthetase inhibitors. J Mol Graph Model 25:813-823
51. Freskos JN, Fobian YM, Benson TE, Bienkowski MJ, Brown DL, Emmons TL, Heintz R, Laborde A, McDonald J, Mischke BV, Molyneaux JM, Moon JB, Mullins PB, Prince DB, Poddock DJ, Tomasselli AG, Winterrowd G (2007) Design of potent inhibitors of human β-secretase. Part 1. Bioorg Med Chem Lett 17:73-77 (Pubitemid 44959985)
52. Freskos JN, Fobian YM, Benson TE, Moon JB, Bienkowski MJ, Brown DL, Emmons TL, Heintz R, Laborde A, McDonald JJ, Mischke BV, Molyneaux JM, Mullins PB, Prince B, Poddock DJ, Tomasselli AG, Winterrowd G (2007) Design of potent inhibitors of human β-secretase. Part 2. Bioorg Med Chem Lett 17:78-81 (Pubitemid 44959984)
53. Wei HY, Tsai KC, Lin TH (2005) Modelling ligand-receptor interaction for some MHC class II HLA-DR4 peptide mimetic inhibitors using several molecular docking and 3D QSAR techniques. J Chem Inf Model 45:1343-1351
54. Yang L, Tan CH, Hsieh MJ, Wang J, Duan Y, Cieplak P, Caldwell J, Kollman PA, Luo R (2006) New-generation Amber united-atom force field. J Phys Chem B 110:13166-13176 (Pubitemid 44115654)
55. SYBYL 8.0, Tripos Associates, St. Louis, MO
56. GOLD User Guide & Tutorials (2006) The Cambridge Crystallographic Data Centre. http://www.ccdc.cam.ac.uk/
57. Jakalian A, Jack DB, Bayly CI (2002) Fast efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J Comput Chem 23:1623-1641 (Pubitemid 35330860)
58. Case DA, Darden TA, Cheatham TEIII, Simmerling CL, Wang J, Duke RE, Luo R, Merz KM, Pearlman DA, Crowley M, Walker RC, Zhang W, Wang B, Hayik S, Roitberg A, Seabra G, Wong KF, Paesani F, Wu X, Brozell S, Tsui V, Gohlke H, Yang L, Tan C, Mongan J, Hornak V, Cui G, Beroza P, Mathews DH, Schafmeister C, Ross WS, Kollman PA (2006) AMBER 9. University of California, San Francisco
59. Scarpelli R, Marco AD, Ferrigno F, Laufer R, Marcucci I, Muraglia E, Ontoria JM, Rowley M, Serafini S, Steinkühler C, Jones P (2008) Studies of the metabolic stability in cells of 5-(trifluoroacetyl)thiophene-2-carboxamides and identification of more stable class II histone deacetylase (HDAC) inhibitors. Bioorg Med Chem Lett 18:6078-6082
60. Muraglia E, Altamura S, Branca D, Cecchetti O, Ferrigno F, Orsale MV, Palumbi MC, Rowley M, Scarpelli R, Steinkühler C, Jones P (2008) 2-trifluoroacetylthiophene oxadiazoles as potent and selective class II human histone deacetylase inhibitors. Bioorg Med Chem Lett 18:6083-6087
61. Bottomley MJ, Lo Surdo P, Di Giovine P, Cirillo A, Scarpelli R, Ferrigno F, Jones P, Neddermann P, De Francesco R, Steinkühler C, Gallinari P, Carfi A (2008) Structural and functional analysis of the human Hdac 4 catalytic domain reveals a regulatory zinc-binding domain. J Biol Chem 283:26694-26704