Compound library development guided by protein structure similarity clustering and natural product structure

Proceedings of the National Academy of Sciences of the United States of America

Volumn 101, Issue 48, 2004, Pages 16721-16726

  Koch, Marcus A ^a,b   Wittenberg, Lars Oliver ^a,b   Basu, Sudipta ^a,b   Jeyaraj, Duraiswamy A ^a,b   Gourzoulidou, Eleni ^a,b   Reinecke, Kerstin ^a,b   Odermatt, Alex ^c   Waldmann, Herbert ^a,b  

^a MAX PLANCK INSTITUTE OF MOLECULAR PHYSIOLOGY   (Germany)

^b TU DORTMUND UNIVERSITY   (Germany)

^c UNIVERSITY OF BERN   (Switzerland)

Author keywords

Bioinformatics; Chemical biology; Combinatorial chemistry; Enzyme inhibition; Ligand sensing core

Indexed keywords

11BETA HYDROXYSTEROID DEHYDROGENASE; ACETYLCHOLINESTERASE; AMINO ACID; DYSIDIOLIDE; PHOSPHATASE;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; EMBRYO; HUMAN; HUMAN CELL; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN STRUCTURE;

11-BETA-HYDROXYSTEROID DEHYDROGENASES; ACETYLCHOLINESTERASE; BIOLOGICAL FACTORS; CDC25 PHOSPHATASE; ENZYME INHIBITORS; MODELS, MOLECULAR; PROTEIN CONFORMATION;

EID: 10044253102     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0404719101     Document Type: Article

References (55)

1. Breinbauer, R., Vetter, I. R. & Waldmann, H. (2002) Angew. Chem. Int. Ed. 41, 2878-2890.
2. Koch, M. A., Breinbauer, R. & Waldmann, H. (2003) Biol. Chem. 384, 1265-1272.
3. Walters, W. P., Ajay & Murcko, M. A. (1999) Curr. Opin. Chem. Biol. 3, 384-387.
4. Ajay, Walters, W. P. & Murcko, M. A. (1998) J. Med. Chem. 41, 3314-3324.
5. Sadowski, J. & Kubinyi, H. (1998) J. Med. Chem. 41, 3325-3329.
6. Ghose, A. K., Viswanadhan, V. N. & Wendoloski, J. J. (1999) J. Comb. Chem. 1, 55-68.
7. Lee, M.-L. & Schneider, G. (2001) J. Comb. Chem. 3, 284-289.
8. Golebiowski, A., Klopfenstein, S. R. & Portlock, D. E. (2001) Curr. Opin. Chem. Biol. 5, 273-284.
9. Mason, J. S. & Hermsmeier, M. A. (1999) Curr. Opin. Chem. Biol. 3, 342-349.
10. Schreiber, S. L. (2000) Science 287, 1964-1969.
11. Schuffenhauer, A., Floersheim, P., Acklin, P. & Jacoby, E. (2003) J. Chem. Inf. Comput. Sci. 43, 391-405.
12. Frye, S. V. (1999) Chem. Biol. 6, R3-R7.
13. Jacoby, E., Schuffenhauer, A. & Floersheim, P. (2003) Drug News Perspect. 16, 93-102.
14. Gerlt, J. A. & Babbitt, P. C. (2001) Annu. Rev. Biochem. 70, 209-246.
15. Grishin, N. V. (2001) J. Struct. Biol. 134, 167-185.
16. Russell, R. B., Sasieni, P. D. & Sternberg, M. J. E. (1998) J. Mol. Biol. 282, 903-918.
17. Koonin, E. V., Wolf, Y. I. & Karev, G. P. (2002) Nature 420, 218-223.
18. Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia, C. (1995) J. Mol. Biol. 247, 536-540.
19. Holm, L. & Sander, C. (1996) Nucleic Acids Res. 24, 206-209.
20. Shindyalov, I. N. & Bourne, P. E. (1998) Protein Eng. 11, 739-747.
21. Brohm, D., Metzger, S., Bhargava, A., Müller, O., Lieb, F. & Waldmann, H. (2002) Angew. Chem. Int. Ed. 41, 307-311.
22. Brohm, D., Philippe, N., Metzger, S., Bhargava, A., Müller, O., Lieb, F. & Waldmann, H. (2002) J. Am. Chem. Soc. 124, 13171-13178.
23. Ihara, M., Suzuki, S., Taniguchi, N. & Fukumoto, K. (1993) J. Chem. Soc. Perkin Trans. 1, 2251-2258.
24. Frigerio, M., Santagostino, M., Sputore, S. & Palmisano, G. (1995) J. Org. Chem. 60, 7272-7276.
25. Corey, E. J. & Roberts, B. E. (1997) J. Am. Chem. Soc. 119, 12425-12431.
26. Kernan, M. R. & Faulkner, D. J. (1988) J. Org. Chem. 53, 2773-2776.
27. Brown, S. P., Goodwin, N. C. & MacMillan, D. W. C. (2003) J. Am. Chem. Soc. 125, 1192-1194.
28. Blomberg, I. & Hoffmann, I. (1999) Mol. Cell. Biol. 19, 6183-6194.
29. Baratte, B., Meijer, L., Galaktionov, K. & Beach, D. (1992) Anticancer Res. 12, 873-880.
30. Schweizer, R. A. S., Atanasov, A. G., Frey, B. M. & Odermatt, A. (2003) Mol. Cell. Endocrinol. 212, 41-49.
31. Frick, C., Atanasov, A. G., Arnold, P., Ozols, J. & Odermatt, A. (2004) J. Biol. Chem. 279, 31131-31138.
32. Ellman, G. L., Courtney, K. D., Andres, V., Jr., & Featherstone, R. M. (1961) Biochem. Pharmacol. 7, 88-95.
33. Contreras, J.-M., Parrot, I., Sippl, W., Rival, Y. M. & Wermuth, C. G. (2001) J. Med. Chem. 44, 2707-2718.
34. Fauman, E. B., Cogswell, J. P., Lovejoy, B., Rocque, W. J., Holmes, W., Montana, V. G., Piwnica-Worms, H., Rink, M. J. & Saper, M. A. (1998) Cell 93, 617-625.
35. McCain, D. F., Catrina, I. E., Hengge, A. C. & Zhang, Z.-Y. (2002) J. Biol. Chem. 277, 11190-11200.
36. Zhang, Z.-Y. (2001) Curr. Opin. Chem. Biol. 5, 416-423.
37. Sussman, J. L., Harel, M., Frolow, F., Oefner, C., Goldman, A., Toker, L. & Silman, I. (1991) Science 253, 872-879.
38. Ibach, B. & Haen, E. (2004) Curr. Pharm. Des. 10, 231-251.
39. Walker, B. R. & Seckl, J. R. (2003) Expert Opin. Ther. Targets 7, 771-783.
40. Jörnvall, H., Persson, B., Krook, M., Atrian, S., Gonzàlez-Duarte, R., Jeffery, J. & Ghosh, D. (1995) Biochemistry 34, 6003-6013.
41. Chrousos, G. P. (2004) Proc. Natl. Acad. Sci. USA 101, 6329-6330.
42. Masuzaki, H., Paterson, J., Shinyama, H., Morton, N. M., Mullins, J. J., Seckl, J. R. & Flier, J. S. (2001) Science 294, 2166-2170.
43. Masuzaki, H. & Flier, J. S. (2003) Curr. Drug Targets Immune Endocr. Metab. Disord. 3, 255-262.
44. Paterson, J. M., Morton, N. M., Fievet, C., Kenyon, C. J., Holmes, M. C., Staels, B., Seckl, J. R. & Mullins, J. J. (2004) Proc. Natl. Acad. Sci. USA 101, 7088-7093.
45. Alberts, P., Engblom, L., Edling, N., Forsgren, M., Klingström, G., Larsson, C., Rönquist-Nii, Y., Öhman, B. & Abrahmsén, L. (2002) Diabetologia 45, 1528-1532.
46. Ross, S. A., Gulve, E. A. & Wang, M. (2004) Chem. Rev. 104, 1255-1282.
47. Sandeep, T. C., Yau, J. L. W., MacLullich, A. M. J., Noble, J., Deary, I. J., Walker, B. R. & Seckl, J. R. (2004) Proc. Natl. Acad. Sci. USA 101, 6734-6739.
48. New, M. I. & Wilson, R. C. (1999) Proc. Natl. Acad. Sci. USA 96, 12790-12797.
49. Lyon, M. A., Ducruet, A. P., Wipf, P. & Lazo, J. S. (2002) Nat. Rev. Drug Discov. 1, 961-976.
50. Gunasekera, S. P., McCarthy, P. J., Kelly-Borges, M., Lobkovsky, E. & Clardy, J. (1996) J. Am. Chem. Soc. 118, 8759-8760.
51. McGovern, S. L., Helfand, B. T., Feng, B. & Shoichet, B. K. (2003) J. Med. Chem. 46, 4265-4272.
52. Evans, B. E., Rittle, K. E., Bock, M. G., DiPardo, R. M., Freidinger, R. M., Whitter, W. L., Lundell, G. F., Veber, D. F., Anderson, P. S., Chang, R. S. L., et al. (1988) J. Med. Chem. 31, 2235-2246.
53. Maelicke, A. & Albuquerque, E. X. (1996) Drug Discov. Today 1, 53-59.
54. Kaur, J. & Zhang, M.-Q. (2000) Curr. Med. Chem. 7, 273-294.
55. Koch, M. A. & Waldmann, H. (2004) in Chemogenomics in Drug Discovery: A Medicinal Chemistry Perspective, eds. Kubinyi, H. & Müller, G. (Wiley-VCH, Weinheim, Germany), pp. 377-403.