Natural Product-Derived Compound Libraries and Protein Structure Similarity as Guiding Principles for the Discovery of Drug Candidates

Chemogenomics in Drug Discovery: A Medicinal Chemistry Perspective

Volumn , Issue , 2005, Pages 377-403

  Koch, Marcus A ^a   Waldmann, Herbert ^a  

^a MAX PLANCK INSTITUTE OF MOLECULAR PHYSIOLOGY   (Germany)

Author keywords

Chemogenomics; Development of natural product based inhibitors; Development of natural product based small molecule binders; Natural product derived compound libraries; Protein folds; Protein function; Protein structure similarity

Indexed keywords

LIBRARIES; PROTEIN FOLDING;

CHEMOGENOMICS; COMPOUND LIBRARIES; NATURAL PRODUCTS; PROTEIN FUNCTIONS; PROTEIN STRUCTURES; SMALL MOLECULES;

PROTEINS;

EID: 84954239013     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/3527603948.ch14     Document Type: Chapter

References (77)

1. B.R. Stockwell, Nat. Rev. Genetics 2000, 1, 116-125.
2. P.J. Alaimo, M.A. Shogren-Knaak, K.M. Shokat, Curr. Opin. Chem. Biol.2001, 5, 60-367.
3. R.S. Bohacek, C. McMartin, W.C. Guida, Med. Res. Rev. 1996, 16, 3-50.
4. A. Golebiowski, S.R. Klopfenstein, D.E. Portlock, Curr. Opin. Chem. Biol.2001, 5, 273-284.
5. J.S. Mason, M.A. Hermsmeier, Curr.Opin. Chem. Biol. 1999, 3, 342-349.
6. S.L. Schreiber, Science 2000, 287, 1964-1969.
7. W.P. Walters, Ajay, M.A. Murcko, Curr. Opin. Chem. Biol. 1999, 3, 384-387.
8. Ajay, W.P. Walters, M.A. Murcko, J. Med. Chem. 1998, 41, 3314-3324.
9. J. Sadowski, H. Kubinyi, J. Med. Chem.1998, 41, 3325-3329.
10. A.K. Ghose, V.N. Viswanadhan, J.J. Wendoloski, J. Comb. Chem. 1999, 1, 55-68.
11. M.-L. Lee, G. Schneider, J. Comb. Chem.2001, 3, 284-289.
12. R. Breinbauer, I.R. Vetter, H. Waldmann, Angew. Chem., Int. Ed.2002, 41, 2878-2890.
13. M.A. Koch, R. Breinbauer, H. Waldmann, Biol. Chem. 2003, 384, 1265-1272.
14. D. Brohm, S. Metzger, A. Bhargava, O. Müller, F. Lieb, H. Waldmann, Angew. Chem., Int. Ed. 2002, 41, 307-311.
15. B.E. Evans, K.E. Rittle, M.G. Bock, R.M. DiPardo, R.M. Freidinger, W.L. Whitter, G.F. Lundell, D.F. Veber, P.S. Anderson, R.S.L. Chang, V.J. Lotti, D.J. Cerino, T.B. Chen, P.J. Kling, K.A. Kunkel, J.P. Springer, J. Hirshfield, J. Med.Chem. 1988, 31, 2235-2246.
16. D.A. Horton, G.T. Bourne, M.L. Smythe, Chem. Rev. 2003, 103, 893-930.
17. A.N. Lupas, C.P. Ponting, R.B. Russell, J. Struct. Biol. 2001, 134, 199-203.
18. S. Govindarajan, R. Recabarren, R.A. Goldstein, Proteins 1999, 35, 408-414.
19. C.P. Ponting, J. Schultz, R.P. Copley, M.A. Andrade, P. Bork, Adv. Protein Chem. 2000, 54, 185-244.
20. A.G. Murzin, S.E. Brenner, T. Hubbard, C. Chothia, J. Mol. Biol.1995, 247, 536-540.
21. J.M. Thornton, D.T. Jones, M.W. MacArthur, C.A. Orengo, M.B. Swindells, Philos. Trans. R. Soc.London, Ser. B 1995, 348, 71-79.
22. Y.I. Wolf, N.V. Grishin, E.V. Koonin, J. Mol. Biol. 2000, 299, 897-905.
23. E.V. Koonin, Y.I. Wolf, G.P. Karev, Nature 2002, 420, 218-223.
24. C. Chothia, Nature 1992, 357, 543-544.
25. P. Green, D. Lipman, L. Hillier, R. Waterston, D. Stobes, J.M. Claverie, Science 1993, 259, 1711-1716.
26. N. Alexandrov, N. Go, Abstract presented at the Bioinformatics Genome Regulation Structure Conference (Novosibirsk) 1998.
27. M. Weir, M. Swindells, J. Overington, Trends Biotechnol. 2001, 19, S61-S66.
28. A. Danchin, Curr. Opin. Struct. Biol.1999, 9, 363-367.
29. R.L. Tatusov, D.A. Natale, I.V. Garkavtsev, T.A. Tatusova, U.T. Shankavaram, B.S. Rao, B. Kiryutin, M.Y. Galperin, N.D. Fedorova, E.V. Koonin, Nucleic Acids Res. 2001, 29, 22-28.
30. W. Anantharaman, L. Aravind, E.V. Koonin, Curr. Opin. Chem. Biol.2003, 7, 12-20.
31. J.A. Gerlt, P.C. Babbitt, Annu. Rev.Biochem. 2001, 70, 209-246.
32. A.E. Todd, C.A. Orengo, J.M. Thornton, Curr. Opin. Chem. Biol.1999, 3, 548-556.
33. S.V. Frye, Chem. Biol. 2001, 6, R3-R7.
34. E. Jacoby, A. Schuffenhauer, P. Floersheim, Drug News Perspect. 2003, 16, 93-102.
35. P.R. Caron, M.D. Mullican, R.D. Mashal, K.P. Wilson, M.S. Su, M.A. Murcko, Curr. Opin. Chem. Biol.2001, 5, 464-470.
36. R.B. Russell, P.D. Sasieni, M.J.E. Sternberg, J. Mol. Biol. 1998, 282, 903-918.
37. A.G. Murzin, Curr. Opin. Struct. Biol.1998, 8, 380-387.
38. P. Stahl, L. Kissau, R. Mazitschek, A. Huwe, P. Furet, A. Giannis, H. Waldmann, J. Am. Chem. Soc. 2001, 123, 11586-11593.
39. P. Stahl, L. Kissau, R. Mazitschek, A. Giannis, H. Waldmann, Angew.Chem., Int. Ed. 2002, 41, 1174-1178.
40. D. Brohm, N. Philippe, S. Metzger, A. Bhargava, O. Müller, F. Lieb, H. Waldmann, J. Am. Chem. Soc. 2002, 124, 13171-13178.
41. D. Brohm, S. Metzger, A. Bhargava, O. Müller, F. Lieb, H. Waldmann, Angew. Chem., Int. Ed. 2002, 41, 307-311.
42. S.P. Gunasekera, P.J. McCarthy, M. Kelly-Borges, E. Lobkovsky, J. Clardy, J. Am. Chem. Soc. 1996, 118, 8759-8760.
43. S. Danishefsky, S.R. Magnuson, N. Rosen, Patent WO 99/40079, 1999.
44. M. Takahashi, K. Dodo, Y. Hashimoto, R. Shirai, Tetrahedron Lett. 2000, 41, 2111-2114.
45. L. Holm, Curr. Opin. Struct. Biol. 1998, 8, 372-379.
46. N.V. Grishin, J. Struct. Biol. 2001, 134, 167-185.
47. M.M.G.M. Thunnissen, P. Nordlund, J.Z. Haeggström, Nat. Struct. Biol. 2001, 8, 131-135.
48. L. Orning, G. Krivi, F.A. Fitzpatrick, J. Biol. Chem. 1991, 266, 1375-1378.
49. W. Yuan, B. Munoz, C.-H. Wong, J.Z. Haeggström, A. Wetterholm, B. Samuelsson, J. Med. Chem. 1993, 36, 211-220.
50. I.R. Ollmann, J.H. Hogg, B. Munoz, J.Z. Haeggström, B. Samuelsson, C.-H. Wong, Bioorg. Med. Chem. 1995, 3, 969-995.
51. J.H. Hogg, I.R. Ollmann, J.Z. Haeggström, A. Wetterholm, B. Samuelsson, C.-H. Wong, Bioorg.Med. Chem. 1995, 3, 1405-1415.
52. M.-Q. Zhang, Curr. Med. Chem. 1997, 4, 67-78.
53. M.M.G.M. Thunnissen, B. Andersson, B. Samuelsson, C.-H. Wong, J.Z. Haeggström, FASEB J. 2002, 16, 1648-1650.
54. T.C. Norman, N.S. Gray, J.T. Koh, P.G. Schultz, J. Am. Chem. Soc. 1996, 118, 7430-7431.
55. N.S. Gray, L. Wodicka, A.-M.W.H. Thunnissen, T.C. Norman, S. Kwon, F.H. Espinoza, D.O. Morgan, G. Barnes, S. LeClerc, L. Meijer, S.-H. Kim, D.J. Lockhart, P.G. Schultz, Science 1998, 281, 533-538.
56. Y.-T. Chang, N.S. Gray, G.R. Rosania, D.P. Sutherlin, S. Kwon, T.C. Norman, R. Sarohia, M. Leost, L. Meijer, P.G. Schultz, Chem. Biol.1999, 6, 361-375.
57. Y.-T. Chang, G. Choi, Y.-S. Bae, M. Burdett, H.-S. Moon, J.W. Lee, N.S. Gray, P.G. Schultz, L. Meijer, S.-K. Chung, K.Y. Choi, P.-G. Suh, S.H. Ryu, ChemBioChem 2002, 9, 897-901.
58. S. Ding, N.S. Gray, Q. Ding, P.G. Schultz, J. Org. Chem. 2001, 66, 8273-8276.
59. J. Jin, T.L. Graybill, M.A. Wang, L.D. Davis, M.L. Moore, J. Comb.Chem. 2001, 3, 97-101.
60. Y. Kakuta, L.G. Pedersen, C.W. Carter, M. Negishi, L.C. Pedersen, Nat. Struct.Biol. 1997, 4, 904-908.
61. Y. Kakuta, E.V. Petrotchenko, L.C. Pedersen, M. Negishi, J. Biol.Chem. 1998, 273, 27325-27330.
62. J.I. Armstrong, A.R. Portley, Y.-T. Chang, D.M. Nierengarten, B.N. Cook, K.G. Bowman, A. Bishop, N.S. Gray, K.M. Shokat, P.G. Schultz, C.R. Bertozzi, Angew.Chem., Int. Ed. 2000, 39, 1303-1306.
63. D.E. Verdugo, M.T. Cancilla, X. Ge, N.S. Gray, Y.-T. Chang, P.G. Schultz, M. Negishi, J.A. Leary, C.R. Bertozzi, J. Med. Chem. 2001, 44, 2683-2686.
64. E. Chapman, S. Ding, P.G. Schultz, C.-H. Wong, J. Am. Chem. Soc. 2002, 124, 14524-14525.
65. M. Robinson-Rechavi, H. Escriva Garcia, V. Laudet, J. Cell Sci. 2003, 116, 585-586.
66. M. Schapira, Curr. Cancer Drug Targets 2002, 2, 243-256.
67. M. Schapira, B.M. Raaka, H.H. Samuels, R. Abagyan, Proc. Natl.Acad. Sci. USA 2000, 97, 1008-1013.
68. A.A. Bogan, F.E. Cohen, T.S. Scanlan, Nat. Struct. Biol. 1998, 5, 679-681.
69. N.L. Urizar, A.B. Liverman, D.T. Dodds, F.V. Silva, P. Ordentlich, Y. Yan, F.J. Gonzalez, R.A. Heyman, D.J. Mangelsdorf, D.D. Moore, Science 2002, 296, 1703-1706.
70. E. Owsley, J.Y. Chiang, Biochem.Biophys. Res. Commun. 2003, 304, 191-195.
71. A.C.W. Pike, A.M. Brzozowski, R.E. Hubbard, T. Bonn, A.-G. Thorsell, O. Engström, J. Ljunggren, J.-Å. Gustafsson, M. Carlquist, EMBO J. 1999, 18, 4608-4618.
72. Z.-C. Dang, V. Audinot, S.E. Papapoulos, J.A. Boutin, C.W.G. M Lowik, J. Biol. Chem. 2003, 278, 962-967.
73. L. Van Gaal, A.J. Scheen, Diabetes Metab. Res. Rev. 2002, 18, S1-S4.
74. K.C. Nicolaou, J.A. Pfefferkorn, A.J. Roecker, G.-Q. Cao, S. Barluenga, H.J. Mitchell, J. Am. Chem. Soc. 2000, 122, 9939-9953.
75. K.C. Nicolaou, J.A. Pfefferkorn, H.J. Mitchell, A.J. Roecker, S. Barluenga, G.-Q. Cao, R.L. Affleck, J.E. Lillig, J. Am. Chem. Soc. 2000, 122, 9954-9967.
76. K.C. Nicolaou, R.M. Evans, A.J. Roecker, R. Hughes, M. Downes, J.A. Pfefferkorn, Org. Biomol. Chem.2003, 1, 908-920.
77. M. Downes, M.A. Verdecia, A.J. Roecker, R. Hughes, J.B. Hogenesch, H.R. Kast-Woelbern, M.E. Bowman, J.-L. Ferrer, A.M. Anisfeld, P.A. Edwards, J.M. Rosenfeld, J.G. Alvarez, J.P. Noel, K.C. Nicolaou, R.M. Evans, Mol. Cell 2003, 11, 1079-1092.