Chemical genomics: A challenge for de novo drug design

Molecular Biotechnology

Volumn 37, Issue 3, 2007, Pages 237-245

  Dean, P M ^a  

^a De Novo Pharmaceuticals Ltd   (United Kingdom)

Author keywords

Design criteria; Drug design; Gene expression; Metabolism; Pharmacogenomics; Polymorphism; Site similarity; Structure based design

Indexed keywords

BIOINFORMATICS; GENE EXPRESSION; GENETIC ALGORITHMS; METABOLISM; PHARMACODYNAMICS; POLYMORPHISM;

DRUG DESIGN; PHARMACOGENOMICS; SITE SIMILARITY; STRUCTURE-BASED DESIGN;

MOLECULAR STRUCTURE;

DASATINIB; IMATINIB;

DRUG DESIGN; GENE EXPRESSION; GENE SEQUENCE; PHARMACOGENOMICS; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

COMPUTATIONAL BIOLOGY; DRUG DESIGN; GENOMICS; HUMANS; MODELS, BIOLOGICAL; PHARMACOGENETICS; SMALL MOLECULE LIBRARIES; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 36949018707     PISSN: 10736085     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12033-007-0037-x     Document Type: Review

References (23)

1. Read, J., Pearce, J., Li, X., Muirhead, H., Chirgwin, J., & Davies, C. (2001). The crystal structure of human phosphoglucose isomerase at 1.6A resolution: Implications for catalytic mechanism, cytokine activity and haemolytic anaemia. Journal of Molecular Biology, 309, 447-463.
2. Tsutsumi, S., Yanagawa, T., Shimura, T., Fukumori, T., Hogan, V., Kuwano, H., & Raz, A. (2003). Regulation of cell proliferation by autocrine motility factor/phospoglucose isomerase signaling. Journal of Biological Chemistry, 278, 32165-32172.
3. Ohi, M. D., Vander Kooi, C. W., Rosenberg, J. A., Chazin, W. J., & Gould, K. L. (2003). Structural insights into the U-box, a domain associated with multi-ubiquitination. Nature Structural Biology, 10, 250-255.
4. Bohacek, R. S., Martin, C., & Guida, W. C. (1996). The art and practice of structure-based drug design: A molecular modeling perspective. Medical Research Review, 16, 3-50.
5. Magwene, P. M., & Kim, J. (2004). Estimating genomic coexpression networks using first-order conditional independence. Genome Biology 5, R100.1-R100.16.
6. di Bernardo, D., Thompson, M. J., Gardener, T. S., Chobot, S. E., Eastwood, E. L., Wojtovich, A. P., Elliot, S. J., Schaus, S. E., & Collins, J. J. (2005). Chemogenomic profiling on a genome-wide scale using reverse-engineered gene networks. Nature Biotechnology, 23, 377-383.
7. Zhou, X., Wang, X., & Dougherty, E. R. (2003). Construction of genomic networks using mutual-information clustering and reversible-jump Markov chain Monte-Carlo predictor design. Signal Processing, 83, 745-761.
8. Hartemink, A. J., Gifford, D. K., Jaakola, T. S., & Young, R. A. (2001). Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks. Pacific Symposium in Biocomputing, 6, 422-433.
9. Shah, N. P., et al. (2002). Multiple BRC-ABL kinase domain mutations confer polyclonal resistance to the tyrosine kinase inhibitor imatinib (ST1571) in chronic phase and blast crisis chronic myeloid leukemia. Cancer Cell, 2, 117-125.
10. Shah, N. P., et al. (2004). Overriding imatinib resistance with a novel ABL kinase inhibitor. Science, 305, 399-400.
11. Azam, M., Nardi, V., Shakespeare, W. C., Metcalf, C. A., Bohacek, R. S., Wang, Y., Sundaramoorthi, R., Sliz, P., Veach, D. R., Bornmann, W. G., Clarkson, B., Dalgarno, D. C., Sawyer, T. K., & Daley, G. Q. (2006). Activity of dual SRC/ABL inhibitors highlights the role of BCR/ABL kinase dynamics in drug resistance. PNAS, 103, 9244-9249.
12. Duarte, N. C., Becker, S. A., Jamshidi, N., Thiele, I., Mo, M. L., Vo, T. D., Srivas, R., & Palsson, B. O. (2007). Global reconstruction of the human metabolic network based on genomic and bibliomic data. PNAS, 104, 1777-1782.
13. Koonin, E. V. (1999). http://kr.expasy.org/cgi-bin/prosite-searchac? PDOC00017
14. Deng, Z., Chuaqui, C., & Singh, J. (2004). Structural interaction fingerprint (SIFt): A novel method for analyzing three-dimensional protein-ligand binding interactions. Journal of Medical Chemistry 47, 337-344.
15. Levitt, M. (2007). Growth of novel protein structural data. PNAS, 104, 3183-3188.
16. O'Toole, N., Raymond, S., & Cygler, M. (2003). Coverage of protein sequence space by current structural genomics. Journal of Structural and Functional Genomics, 4, 47-55.
17. Todorov, N. P., Alberts, I. L., Dean, P. M. (2007). De novo design. In J. Mason (Ed.), Comprehensive medicinal chemistry II, Vol. 4, Chapter 13, (pp. 283-305). Elzevier Ltd.
18. Todorov, N. P., & Dean, P. M. (1997). An evaluation of a method for controlling molecular scaffold diversity in de novo ligand design. Journal of Computer-Aided Molecular Design, 11, 175-192.
19. Mancera, R. L. (2002). De novo ligand design with explicit water molecules: an application to bacterial neuraminidase. Journal of Computer-Aided Molecular Design, 16, 479-499.
20. Lloyd, G. G., Garcia-Sosa, A., Alberts, I. L., Todorov, N. P., & Mancera, R. L. (2004a). The effect of tightly bound water molecules on the structural interpretation of ligand-derived pharmacophore models. Journal of Computer-Aided Molecular Design, 18, 89-100.
21. Stahl, M., Todorov, N. P., Tames, T., Mauser, H., Boehm, H.-J., & Dean, P. M. (2002). A validation study on the practical use of de novo design. Journal of Computer-Aided Molecular Design, 16, 459-478.
22. Firth-Clark, S., Todorov, N. P., Alberts, I. L., Williams, A., James, T., & Dean, P. M. (2006). Exhaustive de novo design of low-molecular weight fragments against the ATP-binding site of DNA-gyrase. Journal of Chemical Information Modelling, 46, 1168-1173.
23. Lloyd, D. G., Buenemann, C. L., Todorov, N. P., Manallack, D. T., & Dean, P. M. (2004b). Scaffold hopping in de novo drug design - ligand generation in the absence of receptor information. Journal of Medical Chemistry, 47, 493-496.