Structure-based ensemble-QSAR model: a novel approach to the study of the EGFR tyrosine kinase and its inhibitors
Tóm tắt
Từ khóa
Tài liệu tham khảo
Citri A, Yarden Y . EGF-ERBB signalling: towards the systems level. Nat Rev Mol Cell Biol 2006; 7: 505–16.
Downward J, Parker P, Waterfield MD . Autophosphorylation sites on the epidermal growth factor receptor. Nature 1984; 311: 483–5.
Oda K, Matsuoka Y, Funahashi A, Kitano H . A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol 2005; 1: E11–E17.
Zhang H, Berezov A, Wang Q, Zhang G, Drebin J, Murali R, et al. ErbB receptors: from oncogenes to targeted cancer therapies. J Clin Invest 2007; 117: 2051–8.
Pao W, Chmielecki J . Rational, biologically based treatment of EGFR-mutant non-small-cell lung cancer. Nat Rev Cancer 2010; 10: 760–74.
Moyer JD, Barbacci EG, Iwata KK, Arnold L, Boman B, Cunningham A, et al. Induction of apoptosis and cell cycle arrest by CP-358,774, an inhibitor of epidermal growth factor receptor tyrosine kinase. Cancer Res 1997; 57: 4838–48.
Barker AJ, Gibson KH, Grundy W, Godfrey AA, Barlow JJ, Healy MP, et al. Studies leading to the identification of ZD1839 (IRESSA): an orally active, selective epidermal growth factor receptor tyrosine kinase inhibitor targeted to the treatment of cancer. Bioorg Med Chem Lett 2001; 11: 1911–4.
Sorscher SM . EGFR mutations and sensitivity to gefitinib. N Engl J Med 2004; 351: 1260–1; author reply 60–1.
Liu T, Lin Y, Wen X, Jorissen RN, Gilson MK . BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities. Nucleic Acids Res 2007; 35: D198–201.
Aparna V, Rambabu G, Panigrahi SK, Sarma JARP, Desiraju GR . Virtual screening of 4-anilinoquinazoline analogues as EGFR kinase inhibitors: Importance of hydrogen bonds in the evaluation of poses and scoring functions. J Chem Inf Model 2005; 45: 725–38.
Gundla R, Kazemi R, Sanam R, Muttineni R, Sarma JA, Dayam R, et al. Discovery of novel small-molecule inhibitors of human epidermal growth factor receptor-2: combined ligand and target-based approach. J Med Chem 2008; 51: 3367–77.
Li S, Sun X, Zhao H, Tang Y, Lan M . Discovery of novel EGFR tyrosine kinase inhibitors by structure-based virtual screening. Bioorg Med Chem Lett 2012; 22: 4004–9.
Chen Z, Li HL, Zhang QJ, Bao XG, Yu KQ, Luo XM, et al. Pharmacophore-based virtual screening versus docking-based virtual screening: a benchmark comparison against eight targets. Acta Pharmacol Sin 2009; 30: 1694–708.
Li J, Du Y, Liu X, Shen QC, Huang Al, Zheng MY, et al. Binding sensitivity of adefovir to the polymerase from different genotypes of HBV: molecular modeling, docking and dynamics simulation studies. Acta Pharmacol Sin 2013; 34: 319–28.
Pasha FA, Muddassar M, Srivastava AK, Cho SJ . In silico QSAR studies of anilinoquinolines as EGFR inhibitors. J Mol Model 2010; 16: 263–77.
La Motta C, Sartini S, Tuccinardi T, Nerini E, Da Settimo F, Martinelli A . Computational studies of epidermal growth factor receptor: docking reliability, three-dimensional quantitative structure-activity relationship analysis, and virtual screening studies. J Med Chem 2009; 52: 964–75.
Peng T, Pei J, Zhou J . 3D-QSAR and receptor modeling of tyrosine kinase inhibitors with flexible atom receptor model (FLARM). J Chem Inf Comput Sci 2003; 43: 298–303.
Cox R, Green DS, Luscombe C, Malcolm N, Pickett S . QSAR workbench: automating QSAR modeling to drive compound design. J Comput Aid Mol Des 2013; 27: 321–36.
Tuccinardi T, Ortore G, Santos MA, Marques SM, Nuti E, Rossello A, et al. Multitemplate alignment method for the development of a reliable 3D-QSAR model for the analysis of MMP3 inhibitors. J Chem Inf Model 2009; 49: 1715–24.
Huang SY, Grinter SZ, Zou XQ . Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions. Phys Chem Chem Phys 2010; 12: 12899–908.
Osguthorpe DJ, Sherman W, Hagler AT . Exploring protein flexibility: incorporating structural ensembles from crystal structures and simulation into virtual screening protocols. J Phys Chem B 2012; 116: 6952–9.
Osguthorpe DJ, Sherman W, Hagler AT . Generation of receptor structural ensembles for virtual screening using binding site shape analysis and clustering. Chem Biol Drug Des 2012; 80: 182–93.
Lan P, Xie MQ, Yao YM, Chen WN, Chen WM . 3D-QSAR studies and molecular docking on [5-(4-amino-1H-benzoimidazol-2-yl)-furan-2-yl]-phosphonic acid derivatives as fructose-1,6-biphophatase inhibitors. J Comput Aid Mol Des 2010; 24: 993–1008.
Mouchlis VD, Mavromoustakos TM, Kokotos G . Molecular docking and 3D-QSAR CoMFA studies on indole inhibitors of GIIA secreted phospholipase A2. J Chem Inf Model 2010; 50: 1589–601.
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, et al. The Protein Data Bank. Nucleic Acids Res 2000; 28: 235–42.
Maestro. Schordinger, LLC,New York, NY 2008.
Impact. Schrödinger, LLC, New York, NY, 2005.
Jorgensen WL, Maxwell DS, Tirado-Rives J . Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996; 118: 11225–36.
Huang N, Shoichet BK, Irwin JJ . Benchmarking sets for molecular docking. J Med Chem 2006; 49: 6789–801.
Ligprep. Schordinger, LLC,New York, NY 2008.
Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004; 47: 1739–49.
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: 647–71.
Dixon SL, Smondyrev AM, Rao SN . PHASE: a novel approach to pharmacophore modeling and 3D database searching. Chem Biol Drug Des 2006; 67: 370–2.
Li X, Li Y, Cheng T, Liu Z, Wang R . Evaluation of the performance of four molecular docking programs on a diverse set of protein-ligand complexes. J Comput Chem 2010; 31: 2109–25.
Li Y, Shen J, Sun X, Li W, Liu G, Tang Y . Accuracy assessment of protein-based docking programs against RNA targets. J Chem Inf Model 2010; 50: 1134–46.
Sun X, Li Y, Li W, Xu Z, Tang Y . Computational investigation of interactions between human H2 receptor and its agonists. J Mol Graph Model 2011; 29: 693–701.
Cheng T, Li X, Li Y, Liu Z, Wang R . Comparative assessment of scoring functions on a diverse test set. J Chem Inf Model 2009; 49: 1079–93.
Yun CH, Boggon TJ, Li Y, Woo MS, Greulich H, Meyerson M, et al. Structures of lung cancer-derived EGFR mutants and inhibitor complexes: mechanism of activation and insights into differential inhibitor sensitivity. Cancer Cell 2007; 11: 217–27.
B-Rao C, Subramanian J, Sharma SD . Managing protein flexibility in docking and its applications. Drug Discov Today 2009; 14: 394–400.
Tropsha A . Best practices for QSAR model development, Validation, and exploitation. Mol Inf 2010; 29: 476–88.
Wissner A, Overbeek E, Reich MF, Floyd MB, Johnson BD, Mamuya N, et al. Synthesis and structure-activity relationships of 6,7-disubstituted 4-anilinoquinoline-3-carbonitriles. The design of an orally active, irreversible inhibitor of the tyrosine kinase activity of the epidermal growth factor receptor (EGFR) and the human epidermal growth factor receptor-2 (HER-2). J Med Chem 2003; 46: 49–63.
Verdonk ML, Mortenson PN, Hall RJ, Hartshorn MJ, Murray CW . Protein-ligand docking against non-native protein conformers. J Chem Inf Model 2008; 48: 2214–25.