Rational drug design and high-throughput for RNA targets

Combinatorial Chemistry and High Throughput Screening

Volumn 3, Issue 3, 2000, Pages 219-234

  Hermann, Thomas ^a   Westhof, Eric ^b  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

CONFORMATIONAL TRANSITION; DRUG DESIGN; DRUG SCREENING; DRUG TARGETING; GENE EXPRESSION; GENE FUNCTION; GENE TARGETING; MOLECULAR RECOGNITION; PRIORITY JOURNAL; REVIEW; RNA BINDING; RNA STRUCTURE;

EID: 0033933433     PISSN: 13862073     EISSN: None     Source Type: Journal    
DOI: 10.2174/1386207003331652     Document Type: Review

References (130)

1. Hermann, T. Angew. Chem. Int. Ed. Engl., 2000, 39, 4000-4015.
2. Wilson, W.D.; Li, K. Curr. Med. Chem., 2000, 7, 73.
3. Afshar, M.; Prescott, C.D.; Varani, G. Curr. Opin. Biotech., 1999, 10, 59.
4. Tor, Y. Angew. Chem. Int. Ed. Engl, 1999, 38, 1579.
5. Ecker, D.J.; Griffey, R.H. Drug Discovery Today, 1999, 4, 420.
6. Hermann, T.; Westhof, E. Curr. Opin. Biotech., 1998, 9, 66.
7. Pearson, N.D.; Prescott, C.D. Chem. Biol., 1997, 4, 409.
8. Zweiger, G.; Scott, R.W. Curr. Opin. Biotechnol., 1997, 8, 684.
9. Dunham, I. et al. Nature, 1999, 402, 489.
10. Lenz, G.R.; Nash, H.M.;Jindal, J.D. Drug Discovery Today, 2000, 5, 145.
11. Masquida, B.; Westhof, E. In Oxford Handbook of Nucleic Acid Structure; Neidle, S., Ed.; Oxford University Press; Oxford, 1999, pp.533-565.
12. Nowakowski, J.; Tinoco, I. jr. In Oxford Handbook of Nucleic Acuid Structure; Neidle, S., Ed.; Oxford University Press; Oxford, 1999, pp.567-602.
13. Batey, R.T.; Rambo, R.P.; Doudna, J.A. Angew. Chem. Int. Ed. Engl., 1999, 38, 2326.
14. Hermann, T.; Patel, D.J. J. Mol. Biol., 1999, 294, 829.
15. Hermann, T.; Westhof, E. Biopolymers (Nucleic Acid Sciences), 1998, 48, 155.
16. Puglisi, J.D.; Williamson, J.R. In The RNA World, 2nd ed.; Gesteland, R.F.; Cech, T.R.; Atkins, J.F., Eds.; Cold Spring Harbor Laboratory Press; New York, 1999, pp.403-425,.
17. Hermann, T.; Patel, D.J. Science, 2000, 287, 820-825.
18. Brion, P.; Westhof, E. Annu. Rev. Biophys. Biomol. Struct., 1997, 26, 113.
19. Tinoco, I.; Bustamante, C. J. Mol. Biol., 1999, 293, 271.
20. Saenger, W. Principles of nucleic acid structure, Springer-Verlag: New York, 1984.
21. Leontis, N.B.; Westhof, E. Quart. Rev. Biophys., 1998, 31, 399.
22. Westhof, E.; Fritsch, V. Structure, 2000, 8, R55.
23. Hermann, T.; Westhof, E. Chem. Biol., 1999, 6, R335.
24. Leontis, N.B.; Westhof, E. J. Mol. Biol., 1998, 283, 571.
25. Peterson, R.D.; Bartel, D.P.; Szostak, J.W.; Horvath, S.J.; Feigon, J. Biochemistry, 1994, 33, 5357.
26. Ippolito, J.A.; Steitz, T.A. J. Mol. Biol., 2000, 295, 711.
27. Peterson, R.D.; Feigon, J. J. Mol. Biol., 1996, 264, 863.
28. Battiste, J.L.; Mao, H; Rao, M.S.; Tan, R.; Muhandiram, D.R.; Kay, L.E.; Frankel, A.D; Williamson, J.R. Science, 1996, 273, 1547.
29. Werstuck, G.; Zapp, M.L.; Green, M.R. Chem. Biol., 1996, 3, 129.
30. Long, K.S.; Crothers, D.M. Biochemistry, 1999, 38, 10059.
31. Aboul-ela, F.; Kam, J.; Varani, G. J. Mol. Biol., 1995, 253, 313.
32. Aboul-ela, F.; Karn, J.; Varani, G. Nucleic Acids Res., 1996, 24, 3974.
33. Wang, S.; Huber, P. W.; Cui, M.; Czarnik, A. W.; Mei, H.-Y. Biochemistry, 1998, 37, 5549.
34. Hermann, T.; Westhof, E. J. Med. Chem., 1999, 42, 1250.
35. Eddy, S.R. Curr. Opin. Genet. Dev., 1999, 9, 695.
36. Erdmann, V.A.; Szymanski, M.; Hochberg, A.; de Groot, N.; Barciszewski, J. Nucleic Acids Res., 2000, 28, 197.
37. Hazelrigg, T. Cell, 1998, 95, 451.
38. Gray, N.K.; Wickens, M. Annut. Rev. Cell Dev. Biol., 1998, 14, 399.
39. Pesole, G.; Liuni, S.; Saccone, C. Gene, 1997, 205, 95.
40. Schroeder, R.; Waldsich, C.; Wank, H. EMBO J., 2000, 19, 1.
41. Walter, F.; Vicens, Q.; Westhof, E. Curr. Opin. Chem. Biol., 1999, 3, 694.
42. Moazed, S.; Noller, H.F. Nature, 1987, 327, 389.
43. Mikkelsen, N.E.; Brannvall, M.; Virtanen, A.; Kirsebom, L.A. Proc. Natl. Acad. Sci. USA, 1999, 96, 6155.
44. von Ahsen, U.; Davies, J.; Schroeder, R. Nature, 1991, 353, 368.
45. Stage, T. K.; Hertel, K. J.; Uhlenbeck, O. C. RNA, 1995, 1, 95.
46. Rogers, J.; Chang, A. H.; von Ahsen, U.; Schroeder, R.; Davies, J. J. Mol. Biol., 1996, 259, 916.
47. Tok, J.B.H.; Cho, J.; Rando, R.R. Biochemistry, 1999, 38, 199.
48. Mei, H.-Y.; Galan, A. A.; Halim, N. S.; Mack, D. P.; Moreland, D. W.; Sanders, K. B.; Truong, H. N.; Czarnik, A. W. Bioorg. Med. Chem. Lett., 1995, 5, 2755.
49. Zapp, M. L.; Stern, S.; Green, M. R. Cell, 1993, 74, 969.
50. Fichant, G.A.; Burks, C. J. Mol. Biol., 1991, 220, 659.
51. Eddy, S.R.; Durbin, R. Nucleic Acids Res., 1994, 22, 2079.
52. Sakakibara, Y.; Brown, M.; Hughey, R.; Mian, I.S.; Sjolander, K.; Underwood, R.C.; Haussler, D. Nucleic Acids Res., 1994, 22, 5112.
53. Lowe, T.M.; Eddy, S.R. Nucleic Acids Res., 1997, 25, 955.
54. Lisacek, F.; Diaz, Y.; Michel, F. J. Mol. Biol., 1994, 235, 1206.
55. Ferbeyre, G.; Smith, J.M.; Cedergren, R. Mol. Cell. Biol., 1998, 18, 3880.
56. Ryan, P.C.; Lu, M.; Draper, D.E. J. Mol. Biol., 1991, 221, 1257.
57. Conn, G.L.; Draper, D.E.; Lattmann, E.E.; Gittis, A.G. Science, 1999, 284, 1171.
58. Wimberly, B.T.; Guymon, R.; McCutcheon, J.P.; White, S.W.; Ramakrishnan, V. Cell, 1999, 97, 491.
59. Wallis, M.G.; Streicher, B.; Wank, H.; von Ahsen, U.; Clodi, E.; Wallace, S.T.; Famulok, M.; Schroeder, R. Chem. Biol., 1997, 4, 357.
60. Hermann, T.; Westhof, E. J. Mol. Biol., 1998, 276, 903.
61. Tor, Y.; Hermann, T.; Westhof, E. Chem. Biol., 1998, 5, R277.
62. Fourmy, D.; Recht, M.L; Blanchard, S.C.; Puglisi, J.D. Science, 1996, 274, 1367.
63. Dandekar, T.; Hentze, M.W. Trends Genet., 1995, 11, 45.
64. Bourdeau, V.; Ferbeyre, G.; Pageau, M.; Paquin, B.; Cedergren, R. Nucleic Acids Res., 1999, 27, 4457.
65. Dandekar, T.; Stripecke, R.; Gray, N.K.; Goossen, B.; Constable, A.; Johansson, H.E.; Hentze, M.W. EMBO J., 1991, 10, 1903.
66. Dandekar, T.; Beyer, K.; Bork, P.; Kenealy, M.R.; Pantopoulos, K.; Hentze, M.W.; Sonntag-Buck, V.; Flouriot, G.; Gannon, F.; Schreiber, S. Bioinformatics, 1998, 14, 271.
67. Beyer, K.; Dandekar, T.; Keller, W. J. Biol. Chem., 1997, 272, 26769.
68. Ferbeyre, G.; Bourdeau, V.; Cedergren, R. Trends Biochem. Sci., 1997, 22, 115.
69. Lowe, T.M.; Eddy, S.R. Science, 1999, 253, 1168.
70. Lescure, A.; Gautheret, D.; Carbon, P.; Krol, A. J. Biol. Chem., 1999, 274, 38147.
71. Kryukov, G.V.; Kryukov, V.M.; Gladyshev, V.N. J. Biol. Chem., 1999, 274, 33888.
72. Pesole, G.; Liuni, S.; Grillo, G.; Licciulli, F.; Larizza, A.; Makalowski, W.; Saccone, C. Nucleic Acids Res., 2000, 28, 193.
73. Olivas, W.M.; Muhlrad, D.; Parker, R. Nucleic Acids Res., 1997, 25, 4619.
74. Bailey, D.S.; Bondar, A.; Furness, L.M. Curr. Opin. Biotechnol., 1998, 9, 595.
75. Evans, W.E.; Relling, M.V. Science, 1999, 286, 487.
76. Shen, L.X.; Basilion, J.P.; Stanton, V.P. Proc. Natl. Acad. Sci. USA, 1999, 96, 7871.
77. Mei, H.-Y.; Cui, M.; Sutton, S.T.; Truong, H.N.; Chung, F.Z.; Czarnik, A.W. Nucleic Acids Res., 1996, 24, 5051.
78. Mei, H.-Y.; Cui, M.; Lemrow, S.M.; Czarnik, A.W. Bioorg. Med. Chem., 1997, 5, 1185.
79. Jenne, A.; Gmelin, W.; Raffler, N.; Famulok, M. Angew. Chem. Int. Ed. Engl., 1999, 38, 1300.
80. Llano-Sotelo, B.; Chow, C.S. Bioorg. Med. Chem. Lett., 1999, 9, 213.
81. Hamasaki, K.; Rando, R.R. Anal. Chem., 1998, 267, 183.
82. Mei, H.-Y.; Mack, D.P.; Galan, A.A.; Halim, N.S.; Heldsinger, A.; Loo, J.A.; Moreland, D.W.; Sannes-Lowery, K.A.; Sharmeen, L.; Truong, H.N.; Czarnik, A.W. Bioorg. Med. Chem. 1997, 5, 1173.
83. Mei, H.-Y.; Cui, M.; Heldsinger, A.; Lamrow, S.M.; Loo, J.A.; Sannes-Lowery, K.A.; Sharmeen, L.; Czarnik, A.W. Biochemistry, 1998, 37, 14204.
84. Sannes-Lowery, K.A.; Hu, P.; Mack, D.P.; Mei, H.-Y.; Loo, J.A. Anal. Chem., 1997, 69, 5130.
85. Grain, P.F.; McCloskey, J.A. Curr. Opin. Biotechnol., 1998, 9, 25.
86. Loo, J.A.; Thanabal, V.; Mei, H.-Y. Mass Spectrom. Biol. Med., 2000, 73.
87. Hofstadler, S.A.; Sannes-Lowery, K.A.; Crooke, S.T.; Ecker, D.J.; Sasmor, H.; Manalili, S.; Griffey, R.H. Anal. Chem., 1999, 71, 3436.
88. Griffey, R.H.; Hofstadler, S.A.; Sannes-Lowery, K.A.; Ecker, D.J.; Crooke, S.T. Proc. Natl. Acad. Sci. USA, 1999, 96, 10129.
89. Griffey, R.H.; Greig, M.J.; An, H.; Sasmor, H.; Manalili, S. J. Am. Chem. Soc., 1999, 121, 474.
90. Hendrix, M.; Priestley, E.S.; Joyce, G.F.; Wong, C.H. J. Am. Chem. Soc., 1997, 119, 3641.
91. Wong, C.-H.; Hendrix, M.; Manning, D.D.; Rosenbohm, C.; Greenberg, W.A. J. Am. Chem. Soc., 1998, 120, 8319.
92. Wong, C.-H.; Hendrix, M.; Priestley, E.S.; Greenberg, W.A.-Chem. Biol., 1998, 5, 397.
93. Alper, P.B.; Hendrix, M.; Sears, P.; Wong, C.-H. J. Am. Chem. Soc., 1998, 120, 1965.
94. Greenberg, W.A.; Priestley, E.S.; Sears, P.S.; Alper, P.B.; Rosenbohm, C.; Hendrix, M.; Hung, S.-C.; Wong, C.-H. J. Am. Chem. Soc., 1999, 121, 6527.
95. De Guzman, R.N.; Turner, R.B.; Summers, M.F. Biopolymers: Nucleic Acids Sciences, 1998, 48, 181.
96. Cusack, S. Curr. Opin. Struct. Biol., 1999, 9, 66.
97. Patel, D.J. Curr. Opin. Struct. Biol., 1999, 9, 74.
98. Hermann, T.; Westhof, E. In RNA-Binding Antibiotics; Wallis, M.G.; Schroeder, R., Eds.; Landes Bioscience; Austin TX, 2000, pp. 148-158.
99. Wang, H.; Tor, Y. Angew. Chem. Int. Ed. Eng., 1998, 37, 109.
100. Wang, H.; Tor, Y. J. Am. Chem. Soc., 1997, 119, 8734.
101. Park, W.K.C.; Auer, M.; Jaksche, H.; Wong, C.H. J. Am. Chem. Soc., 1996, 118, 10150.
102. Tok, J.B.H.; Rando, R.R. J. Am. Chem. Soc., 1998, 120, 8279.
103. Wang, H.; Tor, Y. Bioorg. Med. Chem. Lett., 1997, 7, 1951.
104. Michael, K.; Wang, H.; Tor, Y. Bioorg. Med. Chem., 1999, 7, 1361.
105. Kirk, S.R.; Luedtke, N.W.; Tor, Y. J. Am. Chem. Soc., 2000, 122, 980.
106. Hamy, F.; Brondani, V.; Flörsheimer, A.; Stark, W.; Blommers, M. J.J.; Klimkait, T. Biochemistry, 1998, 37, 5086.
107. Hamy, F.; Felder, E.R.; Heizmann, G.; Lazdins, J.; Aboul-Ela, F.; Varani, G.; Karn, J.; Klimkait, T. Proc. Natl. Acad. Sci. USA, 1997, 94, 3548.
108. Klimkait, T.; Felder, E.R.; Albrecht, G.; Hamy, F. Biotechnol. Bioeng., 1998, 61, 155.
109. Friesen, J.W.; Darby, M.K. Nat. Struct. Biol., 1998, 5, 543.
110. McColl, D.J.; Honchell, C.D., Frankel, A.D. Proc. Natl. Acad. Sci. USA, 1999, 96, 9521.
111. Blancaford, P.; Steinberg, S.V.; Paquin, B.; Klinck, R.; Scott, J.K.; Cedergren, R. Chem. Biol., 1999, 6, 585.
112. Lee, M.S.; Gippert, G.P.; Soman, K.V.; Case, D.A.; Wright, P.E. Science, 1989, 245, 635.
113. Pavletich, N.P.; Pabo, C.O. Science, 1991, 252, 809.
114. Fairall, L.; Schwabe, J.W.; Chapman, L.; Finch, J.T.; Rhodes, D. Nature, 1993, 366, 483.
115. Michel, F.; Westhof, E. J. Mol. Biol., 1990, 216, 585.
116. Lehnert, V.; Jaeger, L.; Michel, F.; Westhof, E. Chem. Biol., 1996, 3, 993.
117. Massire, C.; Jaeger, L.; Westhof, E. J. Mol. Biol., 1998, 279, 773.
118. Kuntz, I.D.; Meng, E.C.; Shoichet, B.K. Acc. Chem. Res., 1994, 27, 117.
119. Golender, V.E.; Vorpagel, E.R. In 3D-QSAR in Drug Design: Theory, Methods and Applications; Kubinyi, H., Ed.; ESCOM; Leiden, 1993, pp.137-149.
120. Chen, Q.; Shafer, R.H.; Kuntz, I.D. Biochemistry, 1997, 36, 11402.
121. Leclerc, F.; Cedergren, R. J. Med. Chem., 1998, 41, 175.
122. Nadassy, K.; Wodak, S.J.; Janin J. Biochemistry 1999, 38, 1999.
123. Hoch, I.; Berens, C.; Westhof, E.; Schroeder, R. J. Mol. Biol., 1998, 282, 557.
124. Hermann, T.; Westhof, E. Structure, 1998, 6, 1303.
125. Sagui, C; Darden, T.A. Annu. Rev. Biophys. Biomol. Struct., 1999, 28, 155.
126. Auffinger, P.; Westhof, E. Curr. Opin. Struct. Biol., 1998, 8, 227.
127. Szewczak, A.A.; Moore, P.B. J. Mol. Biol., 1995, 247, 81.
128. Correll, C.C.; Wool, I.G.; Munishkin, A. J. Mol. Biol., 1999, 292, 275.
129. Walczak, R.; Westhof, E.; Carbon, P.; Krol, A. RNA, 1996, 2, 367.
130. Botto, R.E.; Coxon, B. J. Am. Chem. Soc., 1983, 105, 1021.