Abstract
New methods and strategies have been developed to design and use small molecules that allow the functional dissection of molecular pathways, cells, and organisms by selective small-molecule ligands or modulators. In this overview, we are focusing on diversity aspects, design methods, and chemical synthesis strategies for the application of small molecules as tools for chemical genomics. Examples for different successful chemical-genomics strategies include the selection of diverse drug-like molecules, target family—focused compound libraries, natural-product chemistry, and diversity-oriented synthesis.
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References
Schreiber, S. L. (1998) Chemical genetics resulting from a passion for synthetic organic chemistry. Bio. Med. Chem. 6, 1127–1152.
Kubinyi, H. and Müller, G. (eds.). (2004) Chemogenomics in drug discovery, a medicinal chemistry perspective. In Methods and Principles in Medicinal Chemistry, Wiley-VCH, Weinheim, Germany.
Ferenc Darvas, F., Guttman, A., and Dormann, G. (2004) Chemical Genomics. Marcel Dekker, New York.
Salemme, F. R. (2003) Chemical genomics as an emerging paradigm for postgenomic drug discovery. Pharmacogenomics 4, 1–11.
Crews, C. M. and Splittgerber, U. (1999) Chemical genetics: exploring and controlling cellular processes with chemical probes. TIBS 5, 317–320.
Morphy, R., Kay, C., and Rankovic, Z. (2004) From magic bullets to designed multiple ligands. Drug Discovery Today 9, 641–651.
Kuntz, I. D., Chen, K., Sharp, K. A., and Kollmann, P. A. (1999) The maximal affinity of ligands. Proc. Natl. Acad. Sci. USA 96, 9997–10,002.
Spencer, R. (1998) High-throughput screening of historic collections: observations on file size, biological targets, and file diversity. Biotechnol. Bioeng. 61, 61–67.
Lipinski, C. A., Lombardo, F., Dominy, B. W., and Feeney, P. J. (1997) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug. Delivery Rev. 23, 4–25.
Proudfoot, J. R. (2002) Drugs, leads, and drug-likeness: an analysis of some recently launched drugs. Bioorg. Med. Chem. Lett. 12, 1647–1650.
Ertl, P., Rohde, B., and Selzer, P. (2000) Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. J. Med. Chem. 43, 3714–3717.
http://www.cosmologic.de. Accessed on March 30, 2005.
Brown, R. D. and Martin, Y. C. (1996) Use of structure-activity data to compare structure-based clustering methods and descriptors for use in compound selection. J. Chem. Inf. Comput. Sci. 36, 572–584.
Shemetulskis, N. A., Dunbar, J. B., Dunbar, B. W., Moreland, D. W., and Humblet, C. (1995) Enhancing the diversity of a corporate database using chemical clustering and analysis. J. Comp. Aided Mol. Design 9, 407–416.
Rishton, G. M. (1997) Reactive compounds and in vitro false positives in HTS. Drug Discovery Today 2, 382–384.
Mayer, T. U., Kapoor, T. M., Haggarty, S. J., King, R. W., Schreiber, S. L., and Mitchtison, T. J. (1999) Small molecule inhibitor of spindle bipolarity identified in a phenotype-based screen. Science 286, 971–974.
Kato-Stankiewicz, J., Hakimi, I., Zhi, G., et al. (2002) Inhibitors of Ras-Raf-1 interaction identified by two-hybrid screening revert Ras-dependent transformation phenotypes in human cancer cells. Proc. Nat. Acad. Sci. USA 99, 14, 14,398–14,403.
Dubowchik, G. M., Vrudhula, V. M., Dasgupta, B., et al. (2001) 2-Aryl-2,2-difluoroacetamide FKBP12 ligands: synthesis and X-ray structural studies. Org. Lett. 3, 3987–3990.
Lu, Y., Sakamuri, S., Chen, Q.-Z., et al. (2004) Solution phase parallel synthesis and evaluation of MAPK inhibitory activities of close structural analogues of a Ras pathway modulator. Bioorg. Med. Chem. Lett. 14, 3957–3962.
Martin, E. J., Blaney, J. M., Siani, M. A., Spellmeyer, D. C., Wong, A. K., and Moos, W. H. (1995) Measuring diversity: experimental design of combinatorial libraries for drug discovery. J. Med. Chem. 38, 1431–1436.
Schneider, G., Chomienne-Clement, O., Hilfiger, L., et al. (2000) Virtual screening for bioactive molecules by evolutionary de novo design. Angew. Chemie Int. Ed. 39, 4130–4133.
Schneider, G., Lee, M.-L., Stahl, M., and Schneider, P. (2000) De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks. J. Comput. Aided Mol. Des. 14, 487–494.
Manning, G., Whyte, D. B., Martinez, R., Hunter, T., and Sudarsanam, S. (2002) The protein kinase complement of the human genome. Science 298, 1912–1934.
Deng, Z., Chuaqui, C., and Singh, J. (2004) Structural Interaction Fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. J. Med. Chem. 47, 337–344.
Weber, L. Fractal theory applied to structure-activity relationships. Euro-QSAR 2004, Istanbul, Turkey, September 5–10, 2005.
Verdine, L. G. (1996) The combinatorial chemistry of nature. Nature 384, 11–13.
Lee, M.-L. and Schneider, G. (2001) Scaffold architecture and pharmacophoric properties of trade drugs and natural products. J. Comb. Chem. 3, 284–289.
Barone, R. and Chanon, M. (2001) A new and simple approach to chemical complexity. Application to the synthesis of natural products. J. Chem. Inf. Comput. Sci. 41, 269–272.
Hann, M. M., Leach, A. R., and Harper, G. (2001) Molecular complexity and its impact on the probability of finding leads for drug discovery. J. Chem. Inf. Comput. Sci. 41, 856–864.
Brohm, D., Metzger, S., Bhargava, A., Müller, O., Lieb, F., and Waldmann, H. (2002) 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. 41, 307–311.
Schreiber, S. L. (2000) Target-oriented and diversity-oriented organic synthesis in drug discovery. Science 287, 1964–1969.
Weber, L. (2000) High-diversity combinatorial libraries. Curr. Opin. Chem. Biol. 4, 295–302.
Creighton, C. J., Zapf, C. W., Bu, J. H., and Goodman, M. (1999) Solid-phase synthesis of pyridones and pyridopyrazines as peptidomimetic scaffolds. Org. Lett. 1, 1647–1649.
Peng, G., Sohn, A., and Gallop, M. A. (1999) Stereoselective solid-phase synthesis of a triaza tricyclic ring system: a new chemotype for lead discovery. J. Org. Chem. 64, 8342–8349.
Brooking, P., Crawshaw, M., Hird, N. W., et al. (1999) The development of a solidphase tsuge reaction and its application in high throughput robotic synthesis. Synthesis 11, 1986–1992.
Paulsen, H., Antons, S., Brandes, A., et al. (1999) Stereoselective Mukaiyama-Michael/Michael/Aldol domino cyclization as the key step in the synthesis of pentasubstituted arenes: an efficient access to highly active inhibitors of cholesteryl ester transfer protein (CETP). Angew. Chem. Int. Ed. 38, 3373–3375.
Lee, D., Sello, J. K., and Schreiber, S. L. (2000) Pairwise use of complexitygenerating reactions in diversity-oriented organic synthesis. Org. Lett. 2, 709–712.
Reichwein, J. F., Wels, B., Kruijtzer, J. A. W., Versluis, C., Liskamp, R. M. J. (1999) Rolling loop scan: an approach featuring ring-closing metathesis for generating libraries of peptides with molecular shapes mimicking bioactive conformations or local folding of peptides and proteins. Angew. Chem. Int. Ed. 38, 3684–3687.
Taylor, S. J., Taylor, A. M., and Schreiber, S. L. (2004) Synthetic strategy toward skeletal diversity via solid-supported, otherwise unstable reactive intermediates. Angewandte Chemie 43, 1681–1685.
Burke, M. D. and Schreiber, S. L. (2004) A planning strategy for diversity-oriented synthesis. Angewandte Chemie 43, 46–58.
Shah, K., Liu, Y., Deirmengian, C., and Shokat, K. M. (1997) Engineering unnatural nucleotide specificity for Rous sarcoma virus tyrosine kinase to uniquely label its direct substrates. Proc. Nat. Acad. Sci. USA 94, 3565–3570.
Huc, I. and Lehn, J.-M. (1997) Virtual combinatorial libraries: dynamic generation of molecular and supramolecular diversity by self-assembly. Proc. Natl. Acad. Sci. USA 94, 2106–2110.
Lewis, W. G., Green, L. G., Grynszpan, F., et al. (2002) Click chemistry in situ: acetylcholinesterase as a reaction vessel for the selective assembly of a femtomolar inhibitor from an array of building blocks. Angew. Chem. Int. Ed. 41, 1053–1057
Illgen, K., Enderle, T., Broger, C., and Weber, L. (2000) Simulated molecular evolution in a full combinatorial library. Chem. Biol. 7, 433–441.
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Weber, L. (2005). Chemistry for Chemical Genomics. In: Zanders, E.D. (eds) Chemical Genomics. Methods in Molecular Biology™, vol 310. Humana Press. https://doi.org/10.1007/978-1-59259-948-6_2
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DOI: https://doi.org/10.1007/978-1-59259-948-6_2
Publisher Name: Humana Press
Print ISBN: 978-1-58829-399-2
Online ISBN: 978-1-59259-948-6
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