Principles, implementation, and application of biology-oriented synthesis (BIOS)

Biological Chemistry

Volumn 391, Issue 5, 2010, Pages 491-497

  Wilk, Wolfram ^a,b   Zimmermann, Tobias J ^a,b   Kaiser, Markus ^c   Waldmann, Herbert ^a,b  

^a MAX PLANCK INSTITUTE OF MOLECULAR PHYSIOLOGY   (Germany)

^b TU DORTMUND UNIVERSITY   (Germany)

^c CHEMICAL GENOMICS CENTRE OF THE MAX PLANCK SOCIETY   (Germany)

Author keywords

Biology oriented synthesis; Chemical biology; Cheminformatics; Compound libraries; Natural products

Indexed keywords

AJMALICINE; AJMALINE; COLCHICINE; COMPACTIN; DAUNORUBICIN; DISCODERMOLIDE; ESTERASE INHIBITOR; HEXESTROL DIPHOSPHATE; HIRSUTINE; INDOMETACIN; INTEGRAMYCIN; INTEGRASE INHIBITOR; MOLECULAR SCAFFOLD; NAKIJIQUINONE; NATURAL PRODUCT; PACLITAXEL; PHOSPHOTRANSFERASE INHIBITOR; POLYKETIDE; QUININE; UNCLASSIFIED DRUG; VINCA ALKALOID; YOHIMBINE; ZEARALENONE;

BINDING SITE; BIOINFORMATICS; BIOLOGICAL ACTIVITY; BIOLOGY; BIOLOGY ORIENTED SYNTHESIS; CLASSIFICATION; DRUG SCREENING; DRUG STRUCTURE; DRUG SYNTHESIS; HUMAN; INFORMATION SCIENCE; MOLECULAR LIBRARY; PRIORITY JOURNAL; PROTEIN STRUCTURE; SHORT SURVEY;

ANIMALS; BIOLOGICAL PRODUCTS; BIOLOGY; COMBINATORIAL CHEMISTRY TECHNIQUES; DRUG DESIGN; HUMANS; PROTEIN CONFORMATION; SMALL MOLECULE LIBRARIES; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 77952836391     PISSN: 14316730     EISSN: 14374315     Source Type: Journal    
DOI: 10.1515/BC.2010.013     Document Type: Short Survey

References (44)

1. Arya, P., Joseph, R., Gan, Z., and Rakic, B. (2005). Exploring new chemical space by stereocontrolled diversity-oriented synthesis. Chem. Biol. 12, 163-180.
2. Balamurugan, R., Dekker, F.J., and Waldmann, H. (2005). Design of compound libraries based on natural product scaffolds and protein structure similarity clustering (PSSC). Mol. Biosyst. 1, 36-45.
3. Barun, O., Kumar, K., Sommer, S., Langerak, A., Mayer, T.U., Muller, O., and Waldmann, H. (2005). Natural product-guided synthesis of a spiroacetal collection reveals modulators of tubulin cytoskeleton integrity. Eur. J. Org. Chem. 22, 4773-4788.
4. Bialy, L. and Waldmann, H. (2004). Total synthesis and biological evaluation of the protein phosphatase 2A inhibitor cytostatin and analogues. Chem. Eur. J. 10, 2759-2780.
5. Bohacek, R.S., McMartin, C., and Guida, W.C. (1996) The art and practice of structure-based drug design: a molecular modeling perspective. Med. Res. Rev. 16, 3-50.
6. Brohm, D., Metzger, S., Bhargava, A., Muller, O., Lieb, F., and Waldmann, H. (2002a). Natural products are biologically validated starting points in structural space for compound library development: solid-phase synthesis of dysidiolide-derived phosphatase inhibitors. Angew. Chem. Int. Ed. Engl. 41, 307-311.
7. Brohm, D., Philippe, N., Metzger, S., Bhargava, A., Muller, O., Lieb, F., and Waldmann, H. (2002b). Solid-phase synthesis of dysidiolide-derived protein phosphatase inhibitors. J. Am. Chem. Soc. 124, 13171-13178. (Pubitemid 35247129)
8. Burke, M.D. and Schreiber, S.L. (2004). A planning strategy for diversity-oriented synthesis. Angew. Chem. Int. Ed. Engl. 43, 46-58.
9. Clardy, J., Fischbach, M.A., and Currie, C.R. (2009). The natural history of antibiotics. Curr. Biol. 19, 437-441.
10. Corrêa, I.R. Jr., Nören-Müller, A., Ambrosi, H.-D., Jakupovic, S., Saxena, K., Schwalbe, H., Kaiser, M., and Waldmann, H. (2007). Identification of inhibitors for Mycobacterial protein tyrosine phosphatase B (MptpB) by Biology-Oriented Synthesis (BIOS). Chem. Asian J. 2, 1109-1126.
11. Cragg, G.M. and Newman, D.J. (2005). Biodiversity: a continuing source of novel drug leads. Pure Appl. Chem. 77, 7-24.
12. Dekker, F.J., Koch, M.A., and Waldmann, H. (2005). Protein structure similarity clustering (PSSC) and natural product structure as inspiration sources for drug development and chemical genomics. Curr. Opin. Chem. Biol. 9, 232-239. (Pubitemid 40804545)
13. Dobson, C.M. (2004). Chemical space and biology. Nature 432, 824-828.
14. Gallagher, B.M. Jr. (2007). Microtubule-stabilizing natural products as promising cancer therapeutics. Curr. Med. Chem. 14, 2959-2967.
15. Groll, M., Schellenberg, B., Bachmann, A.S., Archer, C.S., Huber, R., Powell, T.K., Lindow, S., Kaiser, M., and Dudler, R. (2008). A plant pathogen virulence factor inhibits the eukaryotic proteasome by a novel mechanism. Nature 452, 755-758.
16. Kaiser, M., Wetzel, S., Kumar, K., and Waldmann, H. (2008). Biology-inspired synthesis of compound libraries. Cell. Mol. Life Sci. 65, 1186-1201.
17. Kissau, L., Stahl, P., Mazitschek, R., Giannis, A., and Waldmann, H. (2003). Development of natural product-derived receptor tyrosine kinase inhibitors based on conservation of protein domain fold. J. Med. Chem. 46, 2917-2931.
18. Koch, M.A., Wittenberg, L.-O., Basu, S., Jeyaraj, D.A., Gourzoulidou, E., Reinecke, K., Odermatt, A., and Waldmann, H. (2004). Compound library development guided by protein structure similarity clustering and natural product structure. Proc. Natl. Acad. Sci. USA 101, 16721-16726.
19. Koch, M.A., Schuffenhauser, A., Scheck, M., Wetzel, S., Casaulta, M., Odermatt, A., Ertl, P., and Waldmann, H. (2005). Charting biologically relevant chemical space: a structural classification of natural products (SCONP). Proc. Natl. Acad. Sci. USA 102, 17272-17277.
20. Leßmann, T. and Waldmann, H. (2006). Enantioselective synthesis on the solid phase. Chem. Commun. 32, 3380-3389.
21. Leßmann, T., Leuenberger, M.G., Menninger, S., Lopez-Canet, M., Müller, O., Hümmer, S., Bormann, J., Korn, K., Fava, E., Zerial, M., et al. (2007). Natural product-derived modulators of cell cycle progression and viral entry by enantioselective oxa Diels-Alder reactions on the solid phase. Chem. Biol. 14, 443-451.
22. Lipinski, C. and Hopkins, A. (2004) Navigating chemical space for biology and medicine. Nature 432, 855-861.
23. McArdle, B.M. and Quinn, R.J. (2007). Identification of protein fold topology shared between different folds inhibited by natural products. ChemBioChem 8, 788-798.
24. Meseguer, B., Alonso-Diaz, D., Griebenow, N., Herget, T., and Waldmann, H. (1999). Natural product synthesis on polymeric supports - synthesis and biological evaluation of an indolactam library. Angew. Chem. Int. Ed. Engl. 38, 2902-2906.
25. Meseguer, B., Alonso-Diaz, D., Griebenow, N., Herget, T., and Waldmann, H. (2000). Solid-phase synthesis and biological evaluation of a Teleocidin library - discovery of a selective PKCd down regulator. Chem. Eur. J. 6, 3943-3957.
26. Nandy, J.P., Prakesch, M., Khadem, S., Reddy, P.T., Sharma, U., and Arya, P. (2009). Advances in solution- and solid-phase synthesis toward the generation of natural-product-like libraries. Chem. Rev. 109, 1999-2060.
27. Newman, D.J. and Cragg, G.M. (2007). Natural products as sources of new drugs over the last 25 years. J. Nat. Prod. 70, 461-477.
28. Nören-Müller, A., Reis-Correa, I. Jr., Prinz, H., Rosenbaum, C., Saxena, K., Schwalbe, H.J., Vestweber, D., Cagna, G., Schunk, S., Schwarz, O., et al. (2006). From the cover: discovery of protein phosphatase inhibitor classes by biology-oriented synthesis. Proc. Natl. Acad. Sci. USA 103, 10606-10611.
29. Nören-Müller, A., Wilk, W., Saxena, K., Schwalbe, H., Kaiser, M., and Waldmann, H. (2008). Discovery of a new class of inhibitors of Mycobacterium tuberculosis protein tyrosine phosphatase B by biology-oriented synthesis. Angew. Chem. Int. Ed. Engl. 47, 5973-5977.
30. Oh, D.-C., Poulsen, M., Currie, C.R., and Clardy, J. (2009). Dentigerumycin: a bacterial mediator of an ant-fungus symbiosis. Nat. Chem. Biol. 5, 391-393.
31. Renner, S., van Otterlo, W.A., Dominguez Seoane, M., Möcklinghoff, S., Hofmann, B., Wetzel, S., Schuffenhauer, A., Ertl, P., Oprea, T.I., Steinhilber, D., et al. (2009). Bioactivity-guided mapping and navigation of chemical space. Nat. Chem. Biol. 5, 585-592.
32. Rosenbaum, C., Baumhof, P., Mazitschek, R., Muller, O., Giannis, A., and Waldmann, H. (2004). Synthesis and biological evaluation of an indomethacin library reveals a new class of angiogenesis-related kinase inhibitors. Angew. Chem. Int. Ed. Engl. 43, 224-228.
33. Russell, R.B., Sasieni, P.D., and Sternberg, M.J.E. (1998). Supersites within superfolds. Binding site similarity in the absence of homology. J. Mol. Biol. 282, 903-918.
34. Smith, J.M. (1970). Natural selection and the concept of a protein space. Nature 225, 563-564.
35. Spring, D.R. (2005). Chemical genetics to chemical genomics: small molecules offer big insights. Chem. Soc. Rev. 34, 472-482.
36. Stahl, P., Kissau, L., Mazitschek, R., Huwe, A., Furet, P., Giannis, A., and Waldmann, H. (2001). Total synthesis and biological evaluation of the Nakijiquinones. J. Am. Chem. Soc. 123, 11586-11593.
37. Stahl, P., Kissau, L., Mazitschek, R., Giannis, A., and Waldmann, H. (2002). Natural product derived receptor tyrosine kinase inhibitors: identification of IGF1R, Tie-2, and VEGFR-3 inhibitors. Angew. Chem. Int. Ed. Engl. 41, 1174-1178.
38. Umarye, J.D., Lessmann, T., Garcia, A.B., Mamane, V., Sommer, S., and Waldmann, H. (2007). Biology-oriented synthesis of stereochemically diverse natural-product-derived compound collections by iterative allylations on a solid support. Chem. Eur. J. 13, 3305-3319.
39. Wetzel, S., Klein, K., Renner, S., Rauh, D., Oprea, T.I., Mutzel, P., and Waldmann, H. (2009). Interactive exploration of chemical space with scaffold hunter. Nat. Chem. Biol. 5, 581-583.
40. Wilk, W., Nören-Müller, A., Kaiser, M., and Waldmann, H. (2009a). Biology-oriented combined solid- and solution phase synthesis of a macroline-like compound collection. Chem. Eur. J. 15, 11976-11984.
41. Wilk, W., Waldmann, H., and Kaiser, M. (2009b). g-Pyrone natural products - a privileged compound class provided by nature. Bioorg. Med. Chem. 17, 2304-2309.
42. Wilks, H.M., Cortes, A., Emery, D.C., Halsall, D.J., Clarke, A.R., and Holbrook, J.J. (1992). Opportunities and limits in creating new enzymes. Experiences with the NAD-dependent lactate dehydrogenase frameworks of humans and bacteria. Ann. N. Y. Acad. Sci. 672, 80-93.
43. Yoshida, M., Hedberg, C., Kaiser, M., and Waldmann, H. (2009). Traceless solid phase synthesis of natural product inspired cis-1,2-dehydrodecalins. Chem. Commun. 20, 2926-2928.
44. Zimmermann, T.J., Niesen, F.H., Pilka, E.S., Knapp, S., Oppermann, U., and Maier, M.E. (2009). Discovery of a potent and selective inhibitor for human carbonyl reductase 1 from propionate scanning applied to the macrolide zearalenone. Bioorg. Med. Chem. 17, 530-536.