Identification of potent EGFR inhibitors from TCM Database@Taiwan

PLoS Computational Biology

Volumn 7, Issue 10, 2011, Pages

  Yang, Shun Chieh ^a   Chang, Su Sen ^a   Chen, Hsin Yi ^b   Chen, Calvin Yu Chian ^a,b,c  

^a CHINA MEDICAL UNIVERSITY   (Taiwan)

^b ASIA UNIVERSITY   (Taiwan)

^c CHINA MEDICAL UNIVERSITY BEIGANG HOSPITAL   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; COMPUTATIONAL CHEMISTRY; DATABASE SYSTEMS; ENZYMES; MEDICINE; MOLECULAR DYNAMICS; SUPPORT VECTOR MACHINES;

CANCEROUS CELLS; COMPARATIVE MOLECULAR FIELD ANALYSIS; COMPARATIVE-MOLECULAR-SIMILARITY-INDICES ANALYSIS; EPIDERMAL GROWTH FACTOR RECEPTORS; H-BONDS; MULTIPLE LINEAR REGRESSIONS; OVEREXPRESSIONS; PROTEIN KINASE; QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP; TARTARIC ACIDS;

MULTIPLE LINEAR REGRESSION;

2 O CAFFEOYL TARTARIC ACID; 2 O FERULOYL TARTARIC ACID; EMITINE; EPIDERMAL GROWTH FACTOR RECEPTOR KINASE; EPIDERMAL GROWTH FACTOR RECEPTOR KINASE INHIBITOR; GEFITINIB; PROTEIN KINASE; ROSMARICINE; UNCLASSIFIED DRUG; EPIDERMAL GROWTH FACTOR RECEPTOR; LIGAND;

ARTICLE; BINDING AFFINITY; BINDING SITE; CHINESE MEDICINE; CONTROLLED STUDY; DRUG PROTEIN BINDING; DRUG STRUCTURE; FACTUAL DATABASE; HUMAN; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PREDICTION; PROTEIN DOMAIN; QUANTITATIVE STRUCTURE ACTIVITY RELATION; SCORING SYSTEM; STEREOSPECIFICITY; TAIWAN; THREE DIMENSIONAL IMAGING; VALIDATION PROCESS; ALGORITHM; CHEMICAL STRUCTURE; CHEMISTRY; DRUG ANTAGONISM; METABOLISM; PROTEIN CONFORMATION;

ALGORITHMS; DATABASES, FACTUAL; HYDROGEN BONDING; LIGANDS; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; RECEPTOR, EPIDERMAL GROWTH FACTOR; TAIWAN;

EID: 80055077153     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002189     Document Type: Article

References (57)

1. de Oliveira AN, Bocca CC, Carvalho JE, Ruiz AL, Silva TP, et al. (2010) New substituted 4-arylaminoquinazolines as potent inhibitors of breast tumor cell lines: in vitro and docking experiments. Eur J Med Chem 45: 4339-4342.
2. El-Azab AS, Al-Omar MA, Abdel-Aziz AA, Abdel-Aziz NI, el-Sayed MA, et al. (2010) Design, synthesis and biological evaluation of novel quinazoline derivatives as potential antitumor agents: molecular docking study. Eur J Med Chem 45: 4188-4198.
3. Wang P, Hu L, Liu G, Jiang N, Chen X, et al. (2011) Prediction of antimicrobial peptides based on sequence alignment and feature selection methods. PLoS One 6: e18476.
4. Herbst RS, (2004) Review of epidermal growth factor receptor biology. Int J Radiat Oncol Biol Phys 59: 21-26.
5. Oda K, Matsuoka Y, Funahashi A, Kitano H, (2005) A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol 1: 1-17.
6. Franklin WA, Veve R, Hirsch FR, Helfrich BA, Bunn PA Jr, (2002) Epidermal growth factor receptor family in lung cancer and premalignancy. Semin Oncol 29: 3-14.
7. Linggi B, Carpenter G, (2006) ErbB receptors: new insights on mechanisms and biology. Trends Cell Biol 16: 649-656.
8. Chan TO, Rittenhouse SE, Tsichlis PN, (1999) AKT/PKB and other D3 phosphoinositide-regulated kinases: kinase activation by phosphoinositide-dependent phosphorylation. Ann Rev Biochem 68: 965-1014.
9. Either SP, (2002) Signal transduction pathways: the molecular basis for targeted therapies. Semin Radiat Oncol 12: 3-10.
10. Shibata T, Kawano T, Nagayasu H, Okumura K, Arisue M, et al. (1996) Enhancing effects of epidermal growth factor on human squamous cell carcinoma motility and matrix degradation but not growth. Tumour Biol 17: 168-175.
11. Petit AM, Rak J, Hung MC, Rockwell P, Goldstein N, et al. (1997) Neutralizing antibodies against epidermal growth factor and ErbB-2/neu receptor tyrosine kinases down-regulate vascular endothelial growth factor production by tumor cells in vitro and in vivo: angiogenic implications for signal transduction therapy of solid tumors. Am J Pathol 151: 1523-1530.
12. Mitsudomi T, Yatabe Y, (2010) Epidermal growth factor receptor in relation to tumor development: EGFR gene and cancer. FEBS J: 277: 301-308.
13. Sordella R, Bell DW, Haber DA, Settleman J, (2004) Gefitinib-sensitizing EGFR mutations in lung cancer activate anti-apoptotic pathways. Science 305: 1163-1167.
14. Wakeling AE, Barker AJ, Davies DH, Brown DS, Green LR, et al. (1996) Specific inhibition of epidermal growth factor receptor tyrosine kinase by 4-anilinoquinazolines. Breast Cancer Res Treat 38: 67-73.
15. Merlo V, Longo M, Novello S, Scagliotti GV, (2011) EGFR pathway in advanced non-small cell lung cancer. Front Biosci 3: 501-517.
16. Van den Eynde M, Baurain JF, Mazzeo F, Machiels JP, (2011) Epidermal growth factor receptor targeted therapies for solid tumours. Acta Clin Belg 66: 10-17.
17. Sherman SI, (2011) Targeted therapies for thyroid tumors. Mod Pathol 24: S44-52.
18. Medina PJ, Goodin S, (2008) Lapatinib: a dual inhibitor of human epidermal growth factor receptor tyrosine kinases. Clin Ther 30: 1426-1447.
19. Johnston SR, Leary A, (2006) Lapatinib: a novel EGFR/HER2 tyrosine kinase inhibitor for cancer. Drugs Today (Barc) 42: 441-453.
20. Forsythe B, Faulkner K, (2004) Overview of the tolerability of gefitinib (IRESSA) monotherapy: clinical experience in non-small-cell lung cancer. Drug Saf 27: 1081-1092.
21. AustraZeneca Pharmaceuticals, (2011) Iressa Product Information. Available: http://www.iressa.com/product-information. Accessed 15 May 2011.
22. Chen L, Huang T, Shi XH, Cai YD, Chou KC, (2010) Analysis of protein pathway networks using hybrid properties. Molecules 15: 8177-8192.
23. Huang T, Shi XH, Wang P, He Z, Feng KY, et al. (2010) Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks. PLoS One 5: e10972.
24. Chou KC, (1996) Review: Prediction of HIV protease cleavage sites in proteins. Anal Biochem 233: 1-14.
25. Chou KC, (2001) Prediction of protein cellular attributes using pseudo-amino acid composition. Proteins 43: 246-255.
26. Shen HB, Chou KC, (2008) HIVcleave: a web-server for predicting HIV protease cleavage sites in proteins. Anal Biochem 375: 388-390.
27. Chou KC, Wu ZC, Xiao X, (2011) iLoc-Euk: A multi-label classifier for predicting the subcellular localization of singleplex and multiplex eukaryotic proteins. PLoS One 6: e18258.
28. Chou KC, (2004) Structural bioinformatics and its impact to biomedical science. Curr Med Chem 11: 2105-2134.
29. Chou KC, Shen HB, (2009) Review: Recent advances in developing web-servers for predicting protein attributes. Nat Sci 2: 63-92.
30. Liao QH, Gao QZ, Wei J, Chou KC, (2011) Docking and molecular dynamics study on the inhibitory activity of novel inhibitors on epidermal growth factor receptor (EGFR). Med Chem 7: 24-31.
31. Mustafa M, Mirza A, Kannan N, (2011) Conformational regulation of the EGFR kinase core by the juxtamembrane and C-terminal tail: a molecular dynamics study. Proteins 79: 99-114.
32. Krug M, Wichapong K, Erlenkamp G, Sippl W, Schachtele C, et al. (2011) Discovery of 4-benzylamino-substituted alpha-carbolines as a novel class of receptor tyrosine kinase inhibitors. ChemMedChem 6: 63-72.
33. Zheng Y, Wu X, Xue B, Li M, Ji M, (2010) Design, synthesis, docking and antitumor activity of quinazolino [3, 4-a] thieno [3, 2-d] pyrimidin-8-one derivatives. Chem Biol Drug Des 76: 285-290.
34. Qian Y, Zhang HJ, Zhang H, Xu C, Zhao J, et al. (2010) Synthesis, molecular modeling, and biological evaluation of cinnamic acid metronidazole ester derivatives as novel anticancer agents. Bioorg Med Chem 18: 4991-4996.
35. Lv PC, Li HQ, Sun J, Zhou Y, Zhu HL, (2010) Synthesis and biological evaluation of pyrazole derivatives containing thiourea skeleton as anticancer agents. Bioorg Med Chem 18: 4606-4614.
36. Ali HI, Nagamatsu T, Akaho E, (2011) Structure-based drug design and AutoDock study of potential protein tyrosine kinase inhibitors. Bioinformation 5: 368-374.
37. Nandi S, Bagchi MC, (2010) 3D-QSAR and molecular docking studies of 4-anilinoquinazoline derivatives: a rational approach to anticancer drug design. Mol Divers 14: 27-38.
38. Cheng WY, Wu SL, Hsiang CY, Li CC, Lai TY, et al. (2008) Relationship between San-Huang-Xie-Xin-Tang and its herbal components on the gene expression profiles in HepG2 cells. Am J Chin Med 36: 783-797.
39. Liu SH, Liu YF, Liou SH, Lin YL, Hsiao YC, et al. (2010) Mortality and cancer incidence among physicians of traditional Chinese medicine: a 20-year national follow-up study. Occup Environ Med 67: 166-169.
40. Hsu CH, Yu MC, Lee CH, Lee TC, Yang SY, (2003) High eosinophil cationic protein level in asthmatic patients with "heat" Zheng. Am J Chin Med 31: 277-283.
41. Huang HJ, Lee KJ, Yu HW, Chen CY, Hsu CH, et al. (2010) Structure-based and ligand-based drug design for HER2 receptor. J Biomol Struct Dyn 28: 23-37.
42. Chen CY, Chen CYC, (2010) Insights into designing the dual-targeted HER2/HSP90 inhibitors. J Mol Graph Model 29: 21-31.
43. Choowongkomon K, Sawatdichaikul O, Songtawee N, Limtrakul J, (2010) Receptor-based virtual screening of EGFR kinase inhibitors from the NCI diversity database. Molecules 15: 4041-4054.
44. Abou-Seri SM, (2010) Synthesis and biological evaluation of novel 2,4′-bis substituted diphenylamines as anticancer agents and potential epidermal growth factor receptor tyrosine kinase inhibitors. Eur J Med Chem 45: 4113-4121.
45. Pasha FA, Muddassar M, Srivastava AK, Cho SJ, (2010) In silico QSAR studies of anilinoquinolines as EGFR inhibitors. J Mol Model 16: 263-277.
46. Coumar MS, Chu CY, Lin CW, Shiao HY, Ho YL, et al. (2010) Fast-forwarding hit to lead: aurora and epidermal growth factor receptor kinase inhibitor lead identification. J Med Chem 53: 4980-4988.
47. Konkimalla VB, Efferth T, (2010) Inhibition of epidermal growth factor receptor-overexpressing cancer cells by camptothecin, 20-(N,N-diethyl) glycinate. Biochem Pharmacol 80: 39-49.
48. Chen CYC, (2011) TCM Database@Taiwan: the world's largest traditional Chinese medicine database for drug screening in silico.PLoS One 6: e15939.
49. Chou KC, (2011) Some remarks on protein attribute prediction and pseudo amino acid composition. J Theor Biol 273: 236-247.
50. The UniProt Consortium, (2010) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 39: D214-D219.
51. Yun CH, Boggon TJ, Li Y, Woo MS, Greulich H, et al. (2007) Structures of lung cancer-derived EGFR mutants and inhibitor complexes: mechanism of activation and insights into differential inhibitor sensitivity. Cancer Cell 11: 217-227.
52. Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, et al. (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30: 1545-1614.
53. Fidanze SD, Erickson SA, Wang GT, Mantei R, Clark RF, et al. (2010) Imidazo[2,1-b]thiazoles: multitargeted inhibitors of both the insulin-like growth factor receptor and members of the epidermal growth factor family of receptor tyrosine kinases. Bioorg Med Chem Lett 20: 2452-2455.
54. Picard RR, Cook RD, (1984) Cross-validation of regression models. J Am Stat Assoc 79: 575-583.
55. Fan RE, Chen PH, Lin CJ, (2005) Working set selection using second order information for training support vector machines. J Mach Learn Res 6: 1889-1918.
56. Chou KC, Shen HB, (2007) Review: Recent progresses in protein subcellular location prediction. Anal Biochem 370: 1-16.
57. Pernas FG, Allen CT, Winters ME, Yan B, Friedman J, et al. (2009) Proteomic Signatures of Epidermal Growth Factor Receptor and Survival Signal Pathways Correspond to Gefitinib Sensitivity in Head and Neck Cancer. Clin Cancer Res 15: 2361-2372.