Recent advances in structure-based drug design and virtual screening of VEGFR tyrosine kinase inhibitors

Methods

Volumn 71, Issue C, 2015, Pages 85-91

  Hoi, Pui Man ^a   Li, Shang ^a   Vong, Chi Teng ^a   Tseng, Hisa Hui Ling ^a   Kwan, Yiu Wa ^b   Lee, Simon Ming Yuen ^a  

^a China Macau University of Science and Technology Zhuhai MUST Science and Technology Research Institute   (Macao)

^b Prince of Wales Hospital   (Hong Kong)

Author keywords

Molecular docking; Pharmacophore modeling; VEGFR2; VEGFR2 inhibitors; Virtual screening

Indexed keywords

VASCULOTROPIN INHIBITOR; VASCULOTROPIN RECEPTOR; PROTEIN KINASE INHIBITOR; VASCULOTROPIN RECEPTOR 2;

ANALYTIC METHOD; ANGIOGENESIS; ANTIANGIOGENIC ACTIVITY; ARTICLE; BINDING AFFINITY; BINDING SITE; CANCER THERAPY; COMPUTER MODEL; CONCEPTUAL FRAMEWORK; CRYSTAL STRUCTURE; DRUG DESIGN; DRUG IDENTIFICATION; DRUG SCREENING; DRUG STABILITY; DRUG STRUCTURE; HIGH THROUGHPUT SCREENING; HUMAN; MOLECULAR DOCKING; MOLECULAR INTERACTION; MOLECULAR MODEL; PHARMACOPHORE; PRIORITY JOURNAL; PROCESS OPTIMIZATION; X RAY CRYSTALLOGRAPHY; ANTAGONISTS AND INHIBITORS; CHEMISTRY; PROCEDURES;

DRUG DESIGN; DRUG EVALUATION, PRECLINICAL; MOLECULAR DOCKING SIMULATION; PROTEIN KINASE INHIBITORS; VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR-2;

EID: 84927729299     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2014.09.004     Document Type: Article

References (81)

1. Folkman J. N. Engl. J. Med. 1971, 285(21):1182-1186.
2. Chung A.S., Lee J., Ferrara N. Nat. Rev. Cancer 2010, 10(7):505-514.
3. Ferrara N. Eur. Cytokine Netw. 2009, 20(4):158-163.
4. Jain R.K., et al. Nat. Clin. Pract. Oncol. 2006, 3(1):24-40.
5. Des Guetz G., et al. Br. J. Cancer 2006, 94(12):1823-1832.
6. Yuan A., et al. Int. J. Cancer 2000, 89(6):475-483.
7. Duda D.G., et al. Trends Mol. Med. 2007, 13(6):223-230.
8. Ferrara N. Oncology 2005, 69(Suppl. 3):11-16.
9. Ellis L.M., Hicklin D.J. Nat. Rev. Cancer 2008, 8(8):579-591.
10. McTigue M., et al. Proc. Natl. Acad. Sci. U.S.A. 2012, 109(45):18281-18289.
11. Ferrara N. EXS 2005, 94:209-231.
12. Fan T.P., et al. Trends Pharmacol. Sci. 2006, 27(6):297-309.
13. Ferrara N., Bunting S. Curr. Opin. Nephrol. Hypertens. 1996, 5(1):35-44.
14. Koolwijk P., et al. Angiogenesis 2001, 4(1):53-60.
15. Wu L.W., et al. J. Biol. Chem. 2000, 275(7):5096-5103.
16. Holmqvist K., et al. J. Biol. Chem. 2004, 279(21):22267-22275.
17. Singh N.K., et al. Blood 2013, 121(10):1911-1923.
18. Koch S., et al. Biochem. J. 2011, 437(2):169-183.
19. Ferrara N., Gerber H.P., LeCouter J. Nat. Med. 2003, 9(6):669-676.
20. Zhang J., Yang P.L., Gray N.S. Nat. Rev. Cancer 2009, 9(1):28-39.
21. Wilhelm S., et al. Nat. Rev. Drug Discov. 2006, 5(10):835-844.
22. Chow L.Q., Eckhardt S.G. J. Clin. Oncol. 2007, 25(7):884-896.
23. Harris P.A., et al. J. Med. Chem. 2008, 51(15):4632-4640.
24. Hu-Lowe D.D., et al. Clin. Cancer Res. 2008, 14(22):7272-7283.
25. Kerbel R.S. N. Engl. J. Med. 2008, 358(19):2039-2049.
26. Krueger J., et al. Development 2011, 138(10):2111-2120.
27. Fong G.H., et al. Nature 1995, 376(6535):66-70.
28. Lee H.K., et al. Blood 2011, 117(21):5762-5771.
29. Wang F., et al. J. Biol. Chem. 2011, 286(11):9097-9106.
30. Luttun A., et al. Nat. Med. 2002, 8(8):831-840.
31. Aiello L.P., et al. Proc. Natl. Acad. Sci. U.S.A. 1995, 92(23):10457-10461.
32. Hiratsuka S., et al. Cancer Res. 2001, 61(3):1207-1213.
33. Henrick K., et al. Nucleic Acids Res. 2008, 36:D426-433. (Database issue).
34. Standley D.M., et al. Brief. Bioinform. 2008, 9(4):276-285.
35. Wolber G., Langer T. J. Chem. Inf. Model. 2005, 45(1):160-169.
36. Chen J., Lai L. J. Chem. Inf. Model. 2006, 46(6):2684-2691.
37. Ortuso F., Langer T., Alcaro S. Bioinformatics 2006, 22(12):1449-1455.
38. Baroni M., et al. J. Chem. Inf. Model. 2007, 47(2):279-294.
39. An J., Totrov M., Abagyan R. Mol. Cell. Proteomics 2005, 4(6):752-761.
40. Accerlrys Discovery Studio Version 2.5 User Manual 2009, Accerlrys Inc., San Diego, CA.
41. Barnum D., et al. J. Chem. Inf. Comput. Sci. 1996, 36(3):563-571.
42. Dixon S.L., et al. J. Comput. Aided Mol. Des. 2006, 20(10-11):647-671.
43. Ligand Fit, DS Modeling 1.7, Cerius2, LigandFit and InsightII are Software Packages Available from Accelrys Inc., 9685 Scranton Road, San Diego, CA 92121-3752.
44. Morris G.M., Huey R., Olson A.J. Curr. Protoc. Bioinform. 2008, (Chapter 8: Unit 8.14).
45. Friesner R.A., et al. J. Med. Chem. 2004, 47(7):1739-1749.
46. Jones G., et al. J. Mol. Biol. 1997, 267(3):727-748.
47. Neves M.A., Totrov M., Abagyan R. J. Comput. Aided Mol. Des. 2012, 26(6):675-686.
48. Johnson L.N., et al. FEBS Lett. 1998, 430(1-2):1-11.
49. Manning G., et al. Science 2002, 298(5600):1912-1934.
50. Traxler P., Furet P. Pharmacol. Ther. 1999, 82(2-3):195-206.
51. Liu Y., Gray N.S. Nat. Chem. Biol. 2006, 2(7):358-364.
52. Traxler P., et al. J. Med. Chem. 1999, 42(6):1018-1026.
53. Soares P., et al. Biomed. Res. Int. 2013, 2013:154856.
54. Kankanala J., et al. Br. J. Pharmacol. 2012, 166(2):737-748.
55. Pasha F.A., et al. J. Mol. Graph. Model. 2009, 28(1):54-61.
56. Diller D.J., Li R. J. Med. Chem. 2003, 46(22):4638-4647.
57. Noble M.E., Endicott J.A., Johnson L.N. Science 2004, 303(5665):1800-1805.
58. Lee K., et al. Eur. J. Med. Chem. 2010, 45(11):5420-5427.
59. Cavasotto C.N., Abagyan R.A. J. Mol. Biol. 2004, 337(1):209-225.
60. Cavasotto C.N. Methods Mol. Biol. 2012, 819:157-168.
61. Teodoro M.L., Kavraki L.E. Curr. Pharm. Des. 2003, 9(20):1635-1648.
62. Cavasotto C.N., Orry A.J. Curr. Top. Med. Chem. 2007, 7(10):1006-1014.
63. Dubinina G.G., et al. Anticancer Agents Med. Chem. 2007, 7(2):171-188.
64. Harris P.A., et al. J. Med. Chem. 2005, 48(5):1610-1619.
65. Mohammadi M., et al. EMBO J. 1998, 17(20):5896-5904.
66. Oguro Y., et al. Bioorg. Med. Chem. 2010, 18(20):7260-7273.
67. Miyamoto N., et al. Bioorg. Med. Chem. 2012, 20(24):7051-7058.
68. Miyamoto N., et al. Bioorg. Med. Chem. 2013, 21(8):2333-2345.
69. Wang C., et al. Bioorg. Med. Chem. 2014, 22(1):277-284.
70. Seo E.J., et al. Evid. Based Complement. Alternat. Med. 2013, 2013:131306.
71. Drwal M.N., Griffith R. Drug Discov. Today Technol. 2013, 10(3):e395-e401.
72. Wilson G.L., Lill M.A. Future Med. Chem. 2011, 3(6):735-750.
73. Tanrikulu Y., Kruger B., Proschak E. Drug Discov. Today 2013, 18(7-8):358-364.
74. Zhang Y., et al. J. Chem. Inf. Model. 2013, 53(12):3163-3177.
75. Dixit A., Verkhivker G.M. J. Chem. Inf. Model. 2012, 52(10):2501-2515.
76. Lau K.M., et al. J. Ethnopharmacol. 2012, 141(1):250-256.
77. Cui G., et al. Int. J. Cardiol. 2013, 168(2):1349-1359.
78. Hu G., et al. Vasc. Cell 2012, 4(1):2.
79. Zhao H., et al. Eur. J. Dermatol. 2012, 22(1):58-67.
80. Tonnesen M.G., Feng X., Clark R.A. J. Investig. Dermatol. Symp. Proc. 2000, 5(1):40-46.
81. Annex B.H. Nat. Rev. Cardiol. 2013, 10(7):387-396.