Summary
Enzymes, the catalytic proteins, are playing pivotal roles in regulating basic cell functions. Drugs that inhibit enzyme activities cover varying aspects of diseases and offer potential cures. One of the major technologies used in the drug discovery industry for finding the enzyme inhibitors is high-throughput screening, which is facing a daunting challenge due to the fast-growing numbers of drug targets arising from genomic and proteomic research and the large chemical libraries generated from high-throughput synthesis. Chemical microarray, as a new technology, could be an excellent alternative for traditional well-based screening, since the technology can screen more compounds against more targets in parallel with a minimum amount of materials, reducing cost and increasing productivity. In this chapter, we have introduced the basic techniques and applications of chemical microarrays, and how to use them routinely for identifying enzyme inhibitors with functional-based assays. Sample assays for kinases, proteases, histone deacetylases, and phosphatases are demonstrated.
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References
Ma, H. and Horiuchi, K.Y. (2006) Chemical microarray: a new tool for drug screening and discovery. Drug Discov. Today 11, 661–668
Sundberg, S.A. (2000) High-throughput and ultra-high-throughput screening: solution- and cell-based approaches. Curr. Opin. Biotechnol. 11, 47–53
MacBeath, G., Koehler, A.N. and Schreiber, S.L. (1999) Printing small molecules as micro-arrays and detecting protein-ligand interactions en masse. J. Am. Chem. Soc. 121, 7967–7968
Kuruvilla, F.G., Shamji, A.F., Sternson, S.M., Hergenrother, P.J. and Schreiber, S.L. (2002) Dissecting glucose signaling with diversity-oriented synthesis and small-molecule microarrays. Nature 416, 653–657
Uttamchandani, M. (2005) Small molecule microarrays, recent advances and applications. Curr. Opin. Chem. Biol. 9, 4–13
Uttamchandani, M., Wang, J. and Yao, S.Q. (2006) Protein and small molecule microarrays: powerful tools for high-throughput proteo-mics. Mol. Biosyst. 2, 58–68
David, C.A., Middleton, T., Montgomery, D., Lim, H.B., Kati, W., Molla, A., Xuei, X., Warrior, U., Kofron, J.L. and Burns, D.J. (2002) Microarray compound screening (microARCS) to identify inhibitors of HIV integrase. J. Biomol. Screen. 7, 259–266
Gopalakrishnan, S.M., Karvinen, J., Kofron, J.L., Burns, D.J. and Warrior, U. (2002) Application of Micro Arrayed Compound Screening (microARCS) to identify inhibitors of caspase-3. J. Biomol. Screen. 7, 317–323
Anderson, S.N. (2004) Microarrayed Compound Screening (µARCS) to identify activators and inhibitors of AMP-activated protein kinase. J. Biomol. Screen. 9, 112–121
Gosalia, D.N. and Diamond, S.L. (2003) Printing chemical libraries on microarrays for fluid phase nanoliter reactions. Proc. Natl. Acad. Sci. U.S.A. 100, 8721–8726
Ma, H., Horiuchi, K.Y., Wang, Y., Kucharewicz, S.A. and Diamond, S.L. (2005) Nanoliter homogeneous ultra-high throughput screening microarray for lead discoveries and IC50 profiling. Assay Drug Dev. Technol. 3, 177–187
Horiuchi, K.Y., Wang, Y. and Ma, H. (2006) Biochemical microarrays for studying chemical biology interaction: DiscoveryDotTM techno-logy. Chem. Biol. Drug Des. 67, 87–88
Ma, H., Wang, Y., Pomabo, A. and Tcai, C. (2006) A homogenous microarray for enzymatic functional assays. In: Frontiers in Biochip Technology. Springer, New York, pp. 3–18
Horiuchi, K.Y., Wang, Y., Diamond, S.L. and Ma, H. (2006) Microarrays for the functional analysis of the chemical-kinase interactome. J. Biomol. Screen. 11, 48–56
Simmons, G., Gosalia, D.N., Rennekamp, A.J., Reeves, J.D., Diamond, S.L. and Bates, P. (2005) Inhibitors of cathepsin L prevent severe acute respiratory syndrome coronavirus entry. Proc. Natl. Acad. Sci. U.S.A. 102, 11876–11881
Gosalia, D.N., Salisbury, C.M., Maly, D.J., Ellman, J.A. and Diamond, S.L. (2005) Profiling serine protease substrate specificity with solution phase fluorogenic peptide microarrays. Proteomics 5, 1292–1298
Gosalia, D.N., Salisbury, C.M., Ellman, J.A. and Diamond, S.L. (2005) High throughput substrate specificity profiling of serine and cysteine proteases using solution-phase fluorogenic peptide microarrays. Mol. Cell. Proteomics 4, 626–636
Zong, Y., Wang, Y., Shi, J., and Zhang, Z., (2006) The Application of Novel Multi-Functional Microarray Slides for Immobilization Biomolecules. In: Frontiers in Biochip TechÂnology. Springer, New York, pp. 3–18
Mann, C.J., Stephens, S.K., and Burke, J.F. (2004) Production of Protein Microarries. In: Protein Microarray Technology. Wieley-VCH, Weinheim, pp. 165–194
Acknowledgments
We would like to thank Ms. Debra Barninger for critical editing. This work is partially supported by NIH grant RO1HG003818, R44CA114995, and R44DE017485 to H.M.
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Liang, S., Xu, W., Horiuchi, K.Y., Wang, Y., Ma, H. (2010). Chemical Microarrays: A New Tool for Discovery Enzyme Inhibitors. In: Roque, A. (eds) Ligand-Macromolecular Interactions in Drug Discovery. Methods in Molecular Biology, vol 572. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-244-5_9
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DOI: https://doi.org/10.1007/978-1-60761-244-5_9
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