Protein kinase inhibition: Different approaches to selective inhibitor design

Current Drug Targets

Volumn 7, Issue 11, 2006, Pages 1443-1454

  Scapin, Giovanna ^a  

^a MERCK RESEARCH LABORATORIES   (United States)

Author keywords

ATP competitive; Chemogenomics; Focused library; Protein kinase inhibition; Specificity; Structural biology; Substrate competitive

Indexed keywords

4 (4 FLUOROPHENYL) 2 (4 METHYLSULFINYLPHENYL) 5 (4 PYRIDYL)IMIDAZOLE; 5 (2,6 DICHLOROPHENYL) 2 (2,4 DIFLUOROPHENYLTHIO)PYRIMIDO[1,6 B]PYRIDAZIN 6 ONE; ABELSON KINASE; ADENOSINE TRIPHOSPHATE; CHIR 98023; CYCLIC AMP DEPENDENT PROTEIN KINASE INHIBITOR; CYCLIN DEPENDENT KINASE 4; DORAMAPIMOD; EPIDERMAL GROWTH FACTOR RECEPTOR KINASE INHIBITOR; ERLOTINIB; FLAVOPIRIDOL; GEFITINIB; GLYCOGEN SYNTHASE KINASE 3 INHIBITOR; GLYCOGEN SYNTHASE KINASE 3BETA; IMATINIB; IMIDAZOLE; MITOGEN ACTIVATED PROTEIN KINASE P38 INHIBITOR; PD 173074; PD 173955; PHOSPHOTRANSFERASE INHIBITOR; PROTEIN KINASE; PROTEIN KINASE C INHIBITOR; PROTEIN KINASE INHIBITOR; PROTEIN TYROSINE KINASE; QUINAZOLINE; SCIO 469; SEMAXANIB; STRESS ACTIVATED PROTEIN KINASE INHIBITOR; UNCLASSIFIED DRUG; UNINDEXED DRUG; VATALANIB;

AUTOIMMUNE DISEASE; CANCER; CELL FUNCTION; COMPETITIVE INHIBITION; DRUG DESIGN; DRUG SCREENING; DRUG TARGETING; ENZYME ACTIVITY; ENZYME INHIBITION; ENZYME STRUCTURE; HEART DISEASE; HUMAN; INFLAMMATORY DISEASE; NONHUMAN; PROTEIN FUNCTION; PROTEIN TARGETING; REVIEW; STRUCTURE ACTIVITY RELATION;

EID: 33750892907     PISSN: 13894501     EISSN: None     Source Type: Journal    
DOI: 10.2174/1389450110607011443     Document Type: Review

References (116)

1. Hunter, T. (1995) Cell, 80, 225-236.
2. Johnson, L.N. and Lewis, R.J. (2001) Chem. Rev., 101, 2209-2242.
3. Saito, H. (2001) Chem. Rev., 101, 2497-2510.
4. Chen, Z., Gibson, T.B., Robinson, F., Silvestro, L., Pearson, G., Xu, B.E., Wright, A., Vanderbilt, C. and Cobb, M.H. (2001) Chem. Rev., 101, 2449-2476.
5. Harper, S. J. and LoGrasso, P. (2001) Drugs of the Future, 26, 957-973.
6. Adams, J.L., Badger, A.M., Kumar, S. and Lee, J.C. (2001) in Progress in Medicinal Chemistry, (F.D. King, and Oxford, A.W., Eds.), Elsevier Sciences B.V.: Amsterdam, The Netherlands. p. 1-60.
7. Dong, C., Davis, R.J. and Flavell, R.A. (2002) Ann. Rev. Immunol., 20, 55-72.
8. Webster, K.R. (1998) Exp. Opin. Investig. Drugs, 7, 865.
9. Cohen, P. (1999) Curr. Opin. Chem. Bio., 3, 459-465.
10. Fischer, P.M. and Lane, D. P. (2000) Curr. Med. Chem., 7, 1213-1245.
11. Alonso, M. and Martinez, A. (2004) Curr. Med. Chem., 11, 755-763.
12. Cohen, P. (2002) Nat.Rev. Drug Disc., 1, 309-315.
13. Yaish, P., Gazit, A., Gilon, C. and Levitzki, A. (1988) Science, 242, 933-935.
14. Druker, B.J., tamura, S., Buchdunger, E., Ohno, S., Segal, G.M., Fanning, S., Zimmermann, J. and Lydon, N.B. (1996) Nat. Med., 2, 561-566.
15. Druker, B.J. and Lydon, N.B. (2000) J. Clinic. Investig., 105, 3-7.
16. Druker, B.J. (2002) Trends Mol. Med., 8, S14-S18.
17. Shah, S.R., Walsh, T. L., Williams, C. B. and Soefje, S. A. (2003) J. Oncol. Pharm. Practice, 9, 161-160.
18. Grunwald, V. and Hidalgo, M. (2003) J. Natl. Cancer Inst., 95, 851-867.
19. Fong, T.A.T., Shawver, L. K., Sun, L., Tang, C., App, H., Powell, T. J., Kim, Y. H., Schreck, R., Wang, X., Risau, W., Ullrich, A., Hirth, K. P. and McMahon, G. (1999) Cancer Res., 59, 99-106.
20. Zhu, Z., Bohlen, P. and Witte, L. (2002) Curr. Cancer Drug Targets, 2, 135-156.
21. Madhusudan, S. and Ganesan, T. S. (2004) Clin. Biochem., 37, 618-635.
22. Shah, N.P., Tran, C., Lee, F. Y., Chen, P., Norris, D. and Sawyers, C. L. (2004) Science, 305, 399-401.
23. Daub, H., Specht, K. and Ullrich, A. (2004) Nat. Rev. Drug Disc., 3, 1001-1010.
24. Shapiro, G.I. (2004) Clin. Cancer Res., 10, 4270S-4275.
25. Regan, J., Breitfelder, S., Cirillo, P., Gilmore, T., Graham, A.G., Hickey, E., Klaus, B., Madwed, J., Moriak, M., Moss, N., Pargellis, C., Pav, S., Proto, A., Swinamer, A., Tong, L. and Torcellini, C. (2002) J. Med. Chem., 45, 2994-3008.
26. Hardy, L.a.M., A. (2003) www.currentdrugdiscovery.com, 15, (December 2003)
27. Nikas, S.N. and Drosos, A. A. (2004) Curr. Opin. Investig. Drugs, 5, 1205-12.
28. Tuttle, K. and Anderson, P. (2003) Am. J. Kidney Dis., 42, 456-465.
29. Mortlock A., K.N.J., Jung F. H., Heron N. M., Foote K. M., Wilkinson R. and Green S. (2005) Curr. Top. Med. Chem., 5, 199-213.
30. Kostich, M., English, J., Madison, V., Gheyas, F., Wang, L., Qiu, P., Greene, J. and Laz, T. M. (2002) Genome Biol., 3, Research 043.1.
31. Manning, G., Whyte, D. B., Martinez, R., Hunter, T. and Sudarsanam, S. (2002) Science, 298, 1912-1934.
32. Denessiouk, K.A. and Johnson, M. S. (2000) Proteins, 38, 310-326.
33. Vieth, M., Higgs, R. E., Robertson, D. H., Shapiro, M., Gragg, E. A. and Hemmerle, H. (2004) Biochim. Biophys. Acta, 1697, 243-257.
34. Toledo, L.M., Lydon, N.B. and Elbaum, D. (1999) Curr. Med. Chem., 6, 775-805.
35. Scapin, G. (2002) DDT, 7, 601-611.
36. Wilson, K.P., McCaffrey, P.G., Hsiao, K., Pazhanisamy, S., Galullo, V., Bemis, G.W., Fitzgibbon, M.J., Caron, P.R., Murcko, M.A. and Su, M.S.S. (1997) Chem. Biol., 4, 423-431.
37. Lisnock, J.M., Tebben, A., Frantz, B., O'Neill, E.A., Croft, G., O'Keefe, S.J., Li, B., Hacker, C., de Laszlo, S., Smith, A., Libby, B., Liverton, N., Hermes, J.D. and LoGrasso, P. (1998) Biochemistry, 37, 16573-16581.
38. Wang, Z., Canagarajah, B.J., Boehm, J,.C., Kassisa, S., Cobb, M.H., Young, P.R., Abdel-Meguid, S., Adams, J.L. and Goldsmith, E.J. (1998) Structure, 6, 1117-1128.
39. Tong, L., Pav, S., White, D.M., Rogers, S., Crane, K.M., Cywin, C.L., Brown, M.L. and Pargellis, C.A. (1997) Nat. Struct. Biol., 4, 311-316.
40. Johnson, L.N., Noble, M.E.M. and Owen, D.J. (1996) Cell, 85, 149-158.
41. Huse, M. and Kuriyan, J. (2002) Cell, 109, 275-282.
42. Adams, J.A. (2001) Chem. Rev., 101, 2271-2290.
43. Atwell, S., Adams, J. M., Badger, J., Buchanan, M. D., Feil, I. K., Froning, K. J., Gao, X., Hendle, J., Keegan, K., Leon, B. C., Muller-Dieckmann, H. J., Nienaber, V. L., Noland, B. W., Post, K., Rajashankar, K. R., Ramos, A., Russell, M., Burley, S. K. and Buchanan, S. G. (2004) J. Biol. Chem., 279, 55827-55832.
44. Schindler, T., Bornmann, W., Pellicena, P., Miller, W.T., Clarkson, B. and Kuriyan, J. (2000) Science, 289, 1938-1942.
45. Nagar, B., Bornmann, W. G., Pellicena, P., Schindler, T., Veach, D. R., Miller, W. T., Clarkson, B. and Kuriyan, J. (2002) Cancer Res., 62, 4236-4243.
46. Pargellis, C., Tong, L., Churchill, L., Cirillo, P.F., Gilmore, T., Graham, A.G., Grob, P.M., Hickey, E.R., Moss, N., Pav, S. and Regan, J. (2002) Nat. Struct. Biol., 9, 268-272.
47. Mohammadi, M., McMahon, G., Sun, L., Tang, C., Hirth, P., Yeh, B.K., Hubbard, S.R. and Schlessinger, J. (1997) Science, 276, 955-960.
48. Bredel, M. and Jacoby, E. (2004) Nat. Rev. Genet., 5, 262-275.
49. Hantschel, O. and Superti-Furga, G. (2004) Nat. Rev. Mol. Cell. Biol., 5, 33-44.
50. Wientjes, F.B.a.S., A. W. (2003) Curr. Opin. Hematol., 10, 2-7.
51. Bradshaw, J.M. and Waksman, G. (2002) Adv. Protein Chem., 61, 161-210.
52. Musacchio, A. (2002) Adv. Protein Chem., 61, 211-268.
53. Dalgarno, D.C., Botfield, M.C. and Rickles, R.J, (1997) Biopolymers (Peptide Science), 43, 383-400.
54. Kuriyan, J. and Cowburn, D. (1997) Annu. Rev. Biophys. Biomol. Struct., 26, 259-288.
55. Wybenga-Groot, L.E., Baskin, B., Ong, S.H., Tong, J.F., Pawson, T. and Sicheri, F. (2001) Cell, 106, 745-757.
56. Shewchuk, L.M., Hassell, A. M., Ellis, B., Holmes, W. D., Davis, R., Horne, E. L., Kadwell, S. H., McKee, D. D. and Moore, J. T. (2000) Structure, 8, 1105-1113.
57. Meng, W., Swenson, L.L., Fitzgibbon, M.J., Hayakawa, K., Haar, E., Behrens, A.E., Fulghum, J.R. and Lippke, J.A. (2002) J. Biol. Chem., 277, 37401-37405.
58. Underwood, K.W., Parris, K.D., Federico, E., Mosyak, L., Czerwinski, R.M., Shane, T., Taylor, M., Svenson, K., Liu, Y., Hsiao, C.L., Wolfrom, S., Maguire, M., Malakian, K., Telliez, J.B., Lin, L.L., Kriz, R.W., Seehra, J., Somers, W.S. and Stahl, M.L. (2003) Structure, 11, 627-636.
59. Broadbridge, R.J. and Sharma, R. P. (2000) Curr. Drug Targets, 1, 365-386.
60. Shakespeare, W., Yang, M., Bohacek, R., Cerasoli, F., Stebbins, K., Sundaramoorthi, R., Azimioara, M., Vu, C., Pradeepan, S., Metcalf, C., III, Haraldson, C., Merry, T., Dalgarno, D., Narula, S., Hatada, M., Lu, X., van Schravendijk, M.R., Adams, S., Violette, S., Smith, J., Guan, W., Bartlett, C., Herson, J., Iuliucci, J., Weigele, M. and Sawyer, T.K. (2000) Proc. Natl. Acad. Sci. USA, 97, 9373-9378.
61. Cody, W.L., Lin, Z., Panek, R.L., Rose, D.W. and Rubin, J.R. (2000) Curr. Pharm. Des., 6, 59-98.
62. Yeh, R.-H., Lee, T.R. and Lawrence, D.S. (2001) J. Biol. Chem., 276, 12235-12240.
63. Harris, T.K. (2003) IUBMB Life, 55, 117-126.
64. Shakespeare, W.C., Metcalf, C. A., 3rd, Wang, Y., Sundaramoorthi, R., Keenan, T., Weigele, M., Bohacek, R. S., Dalgarno, D. C. and Sawyer, T. K. (2003) Curr. Opin. Drug. Discov. Devel., 6, 729-741.
65. Li, B., Liu, Y., Uno, T. and Gray, N. (2004) Comb. Chem. and HTS, 7, 453-472.
66. Liu, W.Q., Vidal, M., Olszowy, C., Million, E., Lenoir, C., Dhotel, H. and Garbay, C. (2004) J. Med. Chem., 47, 1223-1233.
67. Stout, T.J., Foster, P.G. and Matthews, D.J. (2004) Curr. Pharm. Design, 10, 1069-1082.
68. Kuhn, P., Wilson, K., Patch, M.G. and Stevens, R.C. (2002) Curr. Opin. Struct. Biol., 6, 704-710.
69. Tickle, I., Sharff, A., Vinkovic, M., Yon, J. and Jhoti, H. (2004) Chem. Soc. Rev., 33, 558-565.
70. Kunick, C., Zeng, Z., Gussio, R., Zaharevitz, D., Leost M., Totzke, F., Schächtele, C., Kubbutat, M.H.G., Meijer, L. and Lemcke, T. (2005) Chembiochem, 6, 541-549.
71. Asano, T., Nakamura, H., Uehara, Y. and Yamamoto, Y. (2004) Chembiochem, 5, 483-490.
72. Fischer, P.M. (2004) Curr. Med. Chem., 11, 1563-1583.
73. Baba, Y., Ogoshi, Y., Hirai, G., Yanagisawa, T., Nagamatsu, K., Mayumi, S., Hashimoto, Y., Sodeoka, M. (2004) Bioorg. Med. Chem. Lett., 14, 2963-2967.
74. McInnes, C., Wang, S., Anderson, S., O'Boyle, J., Jackson, W., Kontopidis, G., Meades, C., Mezna, M., Thomas, M. and Wood, G. (2004) Chem. Biol., 11, 525-534.
75. Vangrevelinghe, E., Zimmermann, K., Schoepfer, J., Portmann, R., Fabbro, D. and Furet, P. (2003) J. Med. Chem., 46, 2656-2662.
76. Prabhu, N.V., Sidiqui, S.A., McMurray, J.S. and Pettitt, B.M. (2001) Biopolimers, 59, 167-179.
77. Fitzgerald, C.E., Patel, S.B., Becker, J.W., Cameron, P.M., Zaller, D., Pikounis, V.B., O'Keefe, S.J. and Scapin, G (2003) Nat. Struct. Biol., 10, 764-769.
78. Cherry, M. and Williams, D.H. (2004) Curr. Med. Chem., 11, 663-673.
79. Woolfrey, J.R. and Weston, G. S. (2002) Curr. Pharm. Des., 8, 1527-1545.
80. Naumann, T. and Matter, H. (2002) J. Med. Chem., 45, 2366-2378.
81. Sheridan, R.P., Holloway, M. K., McGaughey, G., Mosley, R. T. and Singh, S. B. (2002) J. Mol. Graph. Model., 21, 71-79.
82. Diller, D.J. and Li, R. (2003) J. Med. Chem., 46, 4638-4647.
83. Bhattacharya, S.K., Cox, E. D., Kath, J. C., Mathiowetz, A. M., Morris, J., Moyer, J. D., Pustilnik, L. R., Rafidi, K., Richter, D. T., Su, C. and Wessel, M. D. (2003) Biochem. Biophys. Res. Comm., 307, 267-273.
84. ter Haar, E., Walters, W. P., Pazhanisamy, S., Taslimi, P., Pierce, A. C., Bemis, G. W., Salituro, F. G. and Harbeson, S. L. (2004) Mini Rev. Med. Chem., 4, 235-253.
85. Gray, N.S., Wodicka, L., Thunnissen, A.-M.W.H., Norman, T.C., Kwon, S., Espinoza, F.H., Morgan, D.O., Barnes, G., LeClerc, S., Meijer, L., Kim, S.-H., Lockhart, D.J. and Schultz, P.G. (1998) Science, 281, 533-538.
86. Stahura, F.L., Xue, L., Godden, J. W. and Bajorath, J. (1999) J. Mol. Graph. Model., 17, 1-9.
87. Golebiowski, A., Klopfenstein, S. R. and Portlock, D. E. (2003) Curr. Opin. Chem. Biol., 7, 308-325.
88. Bradley, E.K., Miller, J. L., Saiah, E. and Grootenhuis, P. D. (2003) J. Med. Chem., 46, 4360-4364.
89. Honma, T., Yoshizumi, T., Hashimoto, N., Hayashi, K., Kawanishi, N., Fukasawa, K., Takaki, T., Ikeura, C., Ikuta, M., Suzuki-Takahashi, I., Hayama, T., Nishimura, S. and Morishima, H. (2001) J. Med. Chem., 44, 4628-4640.
90. Lawrence, D.S. and Niu, J. (1998) Pharmacol. Ther., 77, 81-114.
91. Pinna, L.A. and Ruzzene, M. (1996) Biochim. Biophys. Acta, 14, 191-225.
92. Kamath, J.R., Liu, R., Enstrom, A. M., Lou, Q. and Lam, K. S. (2003) J. Pept. Res., 62, 260-268.
93. Leftheris, K., Ahmed, G., Chan, R., Dyckman, A.J., Hussain, Z., Ho, K., Hynes, J., Letourneau, J., Li, W., Lin, S. Q., Metzger, A., Moriarty, K. J., Riviello, C., Shimshock, Y., Wen, J., Wityak, J., Wrobleski, S. T., Wu, H., Wu, J. J., Desai, M., Gillooly, K. M., Lin, T. H., Loo, D., McIntyre, K. W., Pitt, S., Shen, D. R., Shuster, D. J., Zhang, R., Diller, D., Doweyko, A., Sack, J., Baldwin, J., Barrish, J., Dodd, J., Henderson, I., Kanner, S., Schieven, G. L. and Webb, M. (2004) J. Med. Chem., 47, 6283-6291.
94. Lee, J.H., Nandy, S. K. and Lawrence, D. S. (2004) J. Am. Chem. Soc., 126, 3394-3395.
95. Blum, G., Gazit, A. and Levitzki, A. (2000) Biochemistry, 39, 15705-15712.
96. Plotkin, B., Kaidanovich, O., Talior, I. and Eldar-Finkelman, H. (2003) J. Pharmacol. Exp. Ther., 305, 974-980.
97. Niv, M.Y., Rubin, H., Cohen, J., Tsirulnikov, L., Licht, T., Peretzman-Shemer, A., Cna'an, E., Tartakovsky, A., Stein, I., Albeck, S., Weinstein, I., Goldenberg-Furmanov, M., Tobi, D., Cohen, E., Laster, M., Ben-Sasson, S. A. and Reuveni, H. (2004) J. Biol. Chem., 279, 1242-1255.
98. Parang, K. and Cole, P. A. (2002) Pharmacol. Therap., 93, 145-157.
99. Parang, K., Till, J.H., Ablooglu, A.J., Kohanski, R.A., Hubbard, S.R. and Cole, P.A. (2001) Nat. Struct. Biol., 8, 37-41.
100. Hines, A.C. and Cole, P. A. (2004) Bioorg. Med. Chem. Lett., 14, 2951-2954.
101. Zhou, J. and Adams J.A. (1997) Biochemistry, 36, 15733-15738.
102. Aqvist, J., Kolmodin, K., Florian, J. and Warshel, A. (1999) Chem. Biol., 6, R71-R80.
103. Cole, P.A., Courtney, A. D., Shen, K., Zhang, Z., Qiao, Y., Lu, W. and Williams, D.M. (2003) Acc. Chem. Res., 36, 444-452.
104. Madhusudan Trafny, E.A., Xuong, N. H., Adams, J. A., Ten Eyck, L. F., Taylor, S. S. and Sowadski, J. M. (1994) Protein Sci., 3, 176-187.
105. Madhusudan, A.P., Xuong, N. H. and Taylor, S. S. (2002) Nat. Struct. Biol., 9, 273-277.
106. Valiev, M., Kawai, R., Adams, J. A. and Weare, J. H. (2003) J. Am. Chem. Soc., 125, 9926-9927.
107. Salemme, F.R. (2003) Pharmacogenomics, 4, 257-267.
108. van Duin, M., Woolson, H., Mallinson, D. and Black, D. (2003) Biochem. Soc. Trans., 31, 429-432.
109. Dohrmann, C.E. (2004) DDT, 9, 785-794.
110. Daub, H., Godl, K., Brehmer, D., Klebl, B. and Müller, G. (2004) Assay Drug Dev. Technol., 2, 215-224.
111. Godl, K., Wissing, J., Kurtenbach, A., Habenberger, P., Blencke, S., Gutbrod, H., Salassidis, K., Stein-Gerlach, M., Missio, A., Cotten, M. and Daub, H. (2003) Proc. Natl. Acad. Sci. USA, 100, 15434-15439.
112. Davies, S.P., Reddy, H., Caivano, M. and Cohen, P. (2000) Biochem. J., 351, 95-105.
113. Chou, T.-Y., Chiu, C.-H., Li, L.-H., Hsiao, C.-Y., Tzen, C.-Y., Chang, K.-T., Chen, Y.-M., Perng, R.-P., Tsai, S.-F. and Tsai, C.-M. (2005) Clin. Cancer Res., 11, 3750-3757.
114. Bishop, A.C., Buzko, O. and Shokat, K. M. (2001) Trends Cell Biol., 11, 167-172.
115. Bishop, A.C., Ubersax, J. A., Petsch, D. T., Matheos, D. P., Gray, N. S., Blethrow, J., Shimizu, E., Tsien, J. Z., Schultz, P. G., Rose, M. D., Wood, J. L., Morgan, D. O. and Shokat, K. M. (2000) Nature, 407, 395-401.
116. Shokat, K. and Velleca, M. (2002) DDT, 7, 872-879.