Pharmacophore modeling, homology modeling, and in silico screening reveal mammalian target of rapamycin inhibitory activities for sotalol, glyburide, metipranolol, sulfamethizole, glipizide, and pioglitazone

Journal of Molecular Graphics and Modelling

Volumn 42, Issue , 2013, Pages 39-49

  Khanfar, Mohammad A ^a   Abukhader, Majed M ^b   Alqtaishat, Saja ^a   Taha, Mutasem O ^a  

^a UNIVERSITY OF JORDAN   (Jordan)

^b OMAN MEDICAL COLLEGE   (Oman)

Author keywords

HipHop; Homology model; mTOR; Pharmacophore; ROC; Virtual Screening

Indexed keywords

HIPHOP; HOMOLOGY MODELS; MTOR; PHARMACOPHORES; ROC; VIRTUAL SCREENING;

AMINO ACIDS; BINDING ENERGY; DIAGNOSIS; ENZYMES; PHARMACODYNAMICS; QUERY PROCESSING;

ANTIBIOTICS;

GLIBENCLAMIDE; GLIPIZIDE; MAMMALIAN TARGET OF RAPAMYCIN; METIPRANOLOL; PHOSPHATIDYLINOSITOL 3 KINASE GAMMA; PIOGLITAZONE; SOTALOL; SULFAMETHIZOLE;

ARTICLE; COMPUTER MODEL; DATA BASE; DRUG SCREENING; IC 50; MOLECULAR DOCKING; PHARMACOPHORE; PRIORITY JOURNAL; STRUCTURE ACTIVITY RELATION;

ADRENERGIC BETA-ANTAGONISTS; AMINO ACID SEQUENCE; ANTI-INFECTIVE AGENTS; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; GLIPIZIDE; GLYBURIDE; HUMANS; HYPOGLYCEMIC AGENTS; METIPRANOLOL; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; PHOSPHATIDYLINOSITOL 3-KINASES; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; ROC CURVE; SEQUENCE ALIGNMENT; SOTALOL; SULFAMETHIZOLE; THIAZOLIDINEDIONES; TOR SERINE-THREONINE KINASES;

MAMMALIA;

EID: 84875395645     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2013.02.009     Document Type: Article

References (62)

1. D.H. Kim, D.D. Sarbassov, S.M. Ali, J.E. King, R.R. Latek, H. Erdjument-Bromage, P. Tempst, and D.M. Sabatini mTOR interacts with raptor to form a nutrient-sensitive complex that signals to the cell growth machinery Cell 110 2002 163 175
2. N. Hay, and N. Sonenberg Upstream and downstream of mTOR Genes and Development 18 2004 1926 1945
3. F. Meric-Bernstam, and A.M. Gonzalez-Angulo Targeting the mTOR signaling network for cancer therapy Journal of Clinical Oncology 27 2009 2278 2287
4. L.A. Engelman Targeting PI3K signalling in cancer: opportunities, challenges and limitations Nature Reviews Cancer 9 2009 550 562
5. S. Di Paolo, A. Teutonico, D. Leogrande, C. Capobianco, and P.F. Schena Chronic inhibition of mammalian target of rapamycin signaling downregulates insulin receptor substrates 1 and 2 and AKT activation: a crossroad between cancer and diabetes? Journal of the American Society of Nephrology 17 2006 2236 2244
6. E. Jacinto, R. Loewith, A. Schmidt, S. Lin, M.A. Ruegg, A. Hall, and M.N. Hall Mammalian TOR complex 2 controls the actin cytoskeleton and is rapamycin insensitive Nature Cell Biology 6 2004 1122 1128
7. S.C. Land, and A.R. Tee Hypoxia-inducible factor 1alpha is regulated by the mammalian target of rapamycin (mTOR) via an mTOR signaling motif Journal of Biological Chemistry 282 2007 20534 20543
8. N. Gao, D.C. Flynn, Z. Zhang, X.S. Zhong, V. Walker, K.J. Liu, X. Shi, and B.H. Jiang G1 cell cycle progression and the expression of G1 cyclins are regulated by PI3K/AKT/mTOR/p70S6K1 signaling in human ovarian cancer cells. American journal of physiology American Journal of Physiology 287 2004 C281 C291
9. A.S. Don, and X.F. Zheng Recent clinical trials of mTOR-targeted cancer therapies Reviews on Recent Clinical Trials 6 2011 24 35
10. T. Chano, H. Okabe, and C.M. Hulette RB1CC1 insufficiency causes neuronal atrophy through mTOR signaling alteration and involved in the pathology of Alzheimer's diseases Brain Research 1168 2007 97 105
11. A. Caccamo, S. Majumder, A. Richardson, R. Strong, and S. Oddo Molecular interplay between mammalian target of rapamycin (mTOR), amyloid-beta, and Tau: effects on cognitive impairments Journal of Biological Chemistry 285 2010 13107 13120
12. R. Zoncu, A. Efeyan, and D.M. Sabatini mTOR: from growth signal integration to cancer, diabetes and ageing. Nature reviews Nature Reviews Molecular Cell Biology 12 2011 21 35
13. K.A. Menear, S. Gomez, K. Malagu, C. Bailey, K. Blackburn, X.L. Cockcroft, S. Ewen, A. Fundo, G.A. Le, G. Hermann, L. Sebastian, M. Sunose, T. Presnot, E. Torode, I. Hickson, N.M. Martin, G.C. Smith, and K.G. Pike Identification and optimisation of novel and selective small molecular weight kinase inhibitors of mTOR Bioorganic and Medicinal Chemistry Letters 19 2009 5898 5901
14. K. Tanneeru, and L. Guruprasad Ab initio study of electron transport in 4-(3-nitro-4-tetrafluorophenylthiolate-ethynyl, phenylethynyl) benzenethiolate Journal of Molecular Modeling 18 2012 611 621
15. S.B. Bharate, B. Singh, J.B. Bharate, S.K. Jain, S. Meena, and R.A. Vishwakarma QSAR and pharmacophore modeling of N-acetyl-2-aminobenzothiazole class of phosphoinositide-3-kinase-α inhibitors Medicinal Chemistry Research 2012 10.1007/s00044-012-0081-3
16. H. Li, J. Sutter, and R. Hoffmann HipHop: pharmacophores based on multiple common-feature alignment O.F. Gner, Pharmacophore Perception, Development, and Use in Drug Design 2000 International University Line California 69 84
17. A. Smellie, S.L. Teig, and P.J. Towbin Poling-promoting conformational variation Journal of Computational Chemistry 16 1995 171 187
18. A. Smellie, S.D. Kahn, and S.L. Teig Analysis of conformational coverage. 2. Application of conformational models Journal of Chemical Information and Computer Sciences 35 1995 295 304
19. D. Barnum, J. Greene, A. Smellie, and P. Sprague Identification of common functional configurations among molecules Journal of Chemical Information and Computer Sciences 36 1996 563 571
20. HipHop User Guide Version 3.1, Catalyst 4.10, Accelrys Inc., San Diego, CA, 2005. http://www.accelrys.com/doc/life/catalyst410/help/hipHop/HipHop-23TOC. doc.htm.
21. T. Schwede, J. Kopp, N. Guex, and M.C. Peitsch SWISS-MODEL. An automated protein homology-modeling server Nucleic Acids Research 31 2003 3381 3385
22. K.S. Wilson, S. Butterworth, Z. Dauter, V.S. Lamzin, M. Walsh, S. Wodak, J. Pontius, J. Richelle, A. Vaguine, C. Sander, R.W. Hooft, G. Vriend, J.M. Thornton, R.A. Laskowski, M.W. MacArthur, E.J. Dodson, G. Murshudov, T.J. Old, R. Kaptein, and J.C. Rullmann Who checks the checkers? Four validation tools applied to eight atomic resolution structures. EU 3-D Validation Network Journal of Molecular Biology 276 1998 417 436
23. R. Rodriguez, G. Chinea, N. Lopez, T. Pons, and G. Vriend Homology modeling, model and software evaluation: three related resources Bioinformatics 14 1998 523 528
24. J.D. Thompson, D.G. Higgins, and T.J. Gibson CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Research 22 1994 4673 4680
25. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman Basic local alignment search tool Journal of Molecular Biology 215 1990 403 410
26. E.H. Walker, M.E. Pacold, O. Perisic, L. Stephens, P.T. Hawkins, M.P. Wymann, and R.L. Williams Structural determinants of phosphoinositide 3-kinase inhibition by wortmannin, LY294002, quercetin, myricetin, and staurosporine Molecular Cell 6 2000 909 919
27. 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 21 2003 289 307
28. T.W. Sturgill, and M.N. Hall Activating mutations in TOR are in similar structures as oncogenic mutations in PI3KCalpha ACS Chemical Biology 4 2009 999 1015
29. A.N. Jain Scoring non-covalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities Journal of Computer-Aided Molecular Design 10 1996 427 440
30. A. Krammer, P.D. Kirchhoff, X. Jiang, C.M. Venkatachalam, and M. Waldman LigScore: a novel scoring function for predicting binding affinities Journal of Molecular Graphics and Modelling 23 2005 395 407
31. D.K. Gehlhaar, G.M. Verkhivker, P.A. Rejto, C.J. Sherman, D.B. Fogel, L.J. Fogel, and S.T. Freer Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming Chemistry and Biology 2 1995 317 324
32. D.K. Gehlhaar, D. Bouzida, and P. Rejto Reduced dimensionality in ligand-protein structure prediction: covalent inhibitors of serine proteases and design of site-directed combinatorial libraries L. Parrill, M. Rami Reddy, Rational Drug Design: Novel Methodology and Practical Applications 1999 American Chemical Society Washington, DC 292 311
33. I. Muegge Effect of ligand volume correction on PMF scoring Journal of Computational Chemistry 22 2001 418 425
34. J.M. Garcia-Martinez, J. Moran, R.G. Clarke, A. Gray, S.C. Cosulich, C.M. Chresta, and D.R. Alessi Ku-0063794 is a specific inhibitor of the mammalian target of rapamycin (mTOR) Biochemical Journal 421 2009 29 42
35. K. Yu, L. Toral-Barza, C. Shi, W.G. Zhang, J. Lucas, B. Shor, J. Kim, J. Verheijen, K. Curran, D.J. Malwitz, D.C. Cole, J. Ellingboe, S. Ayral-Kaloustian, T.S. Mansour, J.J. Gibbons, R.T. Abraham, P. Nowak, and A. Zask Biochemical, cellular, and in vivo activity of novel ATP-competitive and selective inhibitors of the mammalian target of rapamycin Cancer Research 69 2009 6232 6240
36. Z. Zeng, Y.X. Shi, T. Tsao, Y. Qiu, S.M. Kornblau, K.A. Baggerly, W. Liu, K. Jessen, Y. Liu, H. Kantarjian, C. Rommel, D.A. Fruman, M. Andreeff, and M. Konopleva Targeting of mTORC1/2 by the mTOR kinase inhibitor PP242 induces apoptosis in AML cells under conditions mimicking the bone marrow microenvironment Blood 120 2012 2679 3689
37. M.E. Feldman, B. Apsel, A. Uotila, R. Loewith, Z.A. Knight, D. Ruggero, and K.M. Shokat Active-site inhibitors of mTOR target rapamycin-resistant outputs of mTORC1 and mTORC2 PLoS Biology 7 2009 e38
38. J. Kirchmair, P. Markt, S. Distinto, G. Wolber, and T. Langer Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - what can we learn from earlier mistakes? Journal of Computer-Aided Molecular Design 22 2008 213 228
39. M.L. Verdonk, V. Berdini, M.J. Hartshorn, W.T. Mooij, C.W. Murray, R.D. Taylor, and P. Watson Virtual screening using protein-ligand docking: avoiding artificial enrichment Journal of Chemical Information and Computer Science 44 2004 793 806
40. J. Kaplan, J.C. Verheijen, N. Brooijmans, L. Toral-Barza, I. Hollander, K. Yu, and A. Zask Discovery of 3,6-dihydro-2H-pyran as a morpholine replacement in 6-aryl-1H-pyrazolo[3,4-d]pyrimidines and 2-arylthieno[3,2-d]pyrimidines: ATP-competitive inhibitors of the mammalian target of rapamycin (mTOR) Bioorganic and Medicinal Chemistry Letters 20 2010 640 643
41. A. Zask, J.C. Verheijen, D.J. Richard, J. Kaplan, K. Curran, L. Toral-Barza, J. Lucas, I. Hollander, and K. Yu Discovery of 2- ureidophenyltriazines bearing bridged morpholines as potent and selective ATP-competitive mTOR inhibitors Bioorganic and Medicinal Chemistry Letters 20 2010 2644 2647
42. J.C. Verheijen, K. Yu, L. Toral-Barza, I. Hollander, and A. Zask Discovery of 2-arylthieno[3,2-d]pyrimidines containing 8-oxa-3-azabi-cyclo[3.2. 1]octane in the 4-position as potent inhibitors of mTOR with selectivity over PI3K Bioorganic and Medicinal Chemistry Letters 20 2010 375 379
43. K.J. Curran, J.C. Verheijen, J. Kaplan, D.J. Richard, L. Toral-Barza, L. Hollander, J. Lucas, S. Ayral-Kaloustian, K. Yu, and A. Zask Pyrazolopyrimidines as highly potent and selective, ATP-competitive inhibitors of the mammalian target of rapamycin (mTOR): optimization of the 1-substituent Bioorganic and Medicinal Chemistry Letters 20 2010 1440 1444
44. R.W. Hooft, G. Vriend, C. Sander, and E.E. Abola Errors in protein structures Nature 381 1996 272
45. A. Zask, J. Kaplan, J.C. Verheijen, D.J. Richard, K. Curran, N. Brooijmans, E.M. Bennett, L. Toral-Barza, I. Hollander, S. Ayral-Kaloustian, and K. Yu Morpholine derivatives greatly enhance the selectivity of mammalian target of rapamycin (mTOR) inhibitors Journal of Medicinal Chemistry 52 2009 7942 7945
46. F. Cohen, P. Bergeron, E. Blackwood, K.K. Bowman, H. Chen, A.G. Dipasquale, J.A. Epler, M.F. Koehler, K. Lau, C. Lewis, L. Liu, C.Q. Ly, S. Malek, J. Nonomiya, D.F. Ortwine, Z. Pei, K.D. Robarge, S. Sideris, L. Trinh, T. Truong, J. Wu, X. Zhao, and J.P. Lyssikatos Potent, selective, and orally bioavailable inhibitors of mammalian target of rapamycin (mTOR) kinase based on a quaternary substituted dihydrofuropyrimidine Journal of Medicinal Chemistry 59 2011 3426 3435
47. J. Yuan, P.P. Mehta, M.J. Yin, S. Sun, A. Zou, J. Chen, K. Rafidi, Z. Feng, J. Nickel, J. Engebretsen, J. Hallin, A. Blasina, E. Zhang, L. Nguyen, M. Sun, P.K. Vogt, A. McHarg, H. Cheng, J.G. Christensen, J.L. Kan, and S. Bagrodia PF-04691502, a potent and selective oral inhibitor of PI3K and mTOR kinases with antitumor activity Molecular Cancer Therapeutics 10 2011 2189 2199
48. R. Wondergem, M. Cregan, L. Strickler, R. Miller, and J. Suttles Membrane potassium channels and human bladder tumor cells: II. Growth properties Journal of Membrane Biology 161 1998 257 262
49. M. Abdul, and N. Hoosein Expression and activity of potassium ion channels in human prostate cancer Cancer Letters 186 2002 99 105
50. H. Malhi, A.N. Irani, P. Rajvanshi, S.O. Suadicani, D.C. Spray, T.V. McDonald, and S. Gupta KATP channels regulate mitogenically induced proliferation in primary rat hepatocytes and human liver cell lines. Implications for liver growth control and potential therapeutic targeting Journal of Biological Chemistry 275 2000 26050 26057
51. K.A. Woodfork, W.F. Wonderlin, V.A. Peterson, and J.S. Strobl Inhibition of ATP-sensitive potassium channels causes reversible cell-cycle arrest of human breast cancer cells in tissue culture Journal of Cellular Physiology 162 1995 163 171
52. 2-terminal kinase pathway in human gastric cancer cell line MGC-803 Biochemical Pharmacology 76 2008 1705 1715
53. X. Chi, E.T. Sutton, G. Hellermann, and J.M. Pric Potassium channel openers prevent beta-amyloid toxicity in bovine vascular endothelial cells Neuroscience Letters 290 2000 9 12
54. E. Gottfried, S. Rogenhofer, H. Waibel, L.A. Kunz-Schughart, A. Reichle, M. Wehrstein, A. Peuker, K. Peter, G. Hartmannsgruber, R. Andreesen, and M. Kreutz Pioglitazone modulates tumor cell metabolism and proliferation in multicellular tumor spheroids Cancer Chemotherapy and Pharmacology 67 2011 117 126
55. Z. Wan, W. Shi, B. Shao, J. Shi, A. Shen, Y. Ma, J. Chen, and Q. Lan Peroxisome proliferator-activated receptor gamma agonist pioglitazone inhibits beta-catenin-mediated glioma cell growth and invasion Molecular and Cellular Biochemistry 349 2011 1 10
56. L. Al-Alem, R.C. Southard, M.W. Kilgore, and T.E. Curry Specific thiazolidinediones inhibit ovarian cancer cell line proliferation and cause cell cycle arrest in a PPARgamma independent manner PLoS ONE 6 2011 e16179
57. Y. Wang, M. James, W. Wen, Y. Lu, E. Szabo, R.A. Lubet, and M. You Chemopreventive effects of pioglitazone on chemically induced lung carcinogenesis in mice. Molecular cancer therapeutics Molecular Cancer Therapeutics 9 2010 3074 3082
58. A. Papi, L. Tatenhorst, D. Terwel, M. Hermes, M.P. Kummer, M. Orlandi, and M.T. Heneka PPARgamma and RXRgamma ligands act synergistically as potent antineoplastic agents in vitro and in vivo glioma models Journal of Neurochemistry 109 2009 1779 1790
59. M. Jafari, B. Khodayari, J. Felgner, I.I. Bussel, M.R. Rose, and L.D. Mueller Pioglitazone: an anti-diabetic compound with anti-aging properties Biogerontology 8 2007 639 651
60. M.O. Taha, L.A. Dahbiyeh, Y. Bustanji, H. Zalloum, and S. Salh Combining ligand-based pharmacophore modeling, quantitative structure-activity relationship analysis and in silico screening for the discovery of new potent hormone sensitive lipase inhibitors Journal of Medicinal Chemistry 51 2008 6478 6494
61. W. Walters, and M. Namchuk Designing screens: how to make your hits a hit Nature Reviews. Drug Discovery 2 2003 259 266
62. K.S. Brian Interpreting steep dose-response curves in early inhibitor discovery Journal of Medicinal Chemistry 49 2006 7274 7277