Chemical proteomics applications

Taken together, in vitro display of cDNA libraries are an integral part of modern reverse chemical proteomics applications, where the goal is to functionally display all proteins and to minimize selection bias in the identification of protein ligands for natural products. 

The approach recruited to chemical proteomics in Reference [17] is called SILAC (stable isotope labeling with amino acids in cell culture) and is important in comparative proteomics (Figure 1). SILAC works well with cultured mammalian cells, but prokaryotes defeat it by metabolizing the label (usually supplied in lysine and arginine) into other amino acids. For applications beyond cultured eukaryotic cells, the reductive methylation route to differential labeling [18] is among the alternatives [15]-... 

Jeffery DA, Bogyo M. Chemical proteomics and its application to drug discovery. Curr Opin Biotechnol 2003 14 87-95. 

Of the approaches listed above the last two (chemical proteomics and ABPP) are currently receiving the most interest and have complementary fields of applications. The affinity-based approach is perfectly suitable for reversible inhibitors, but is limited to quite strong binders. The focus of this chapter will be on the other of these two approaches, namely the activity-based approach to natural product identification. An essential requirement for this approach is that the natural product of investigation contains a reactive functional group that reacts with the protein target, forming a covalent bond. Fortunately, a considerable number of natural products contain such reactive groups [19]. Mostly, electrophilic moieties such as epoxides, Michael acceptors, disulfides, lactones, (3-lactams, quinones, etc. can be found. 

The goal of this chapter is to detail the need for such activity-based methods, and to describe the development and application of ABPP by highlighting several studies that have established the utility of this chemical proteomic method as a powerful strategy for the discovery and functional analysis of complex biological proteomes, as well as their individual constituents. 

Molnar, E., Hackler, L., Jr., Jankovics, T., Uige, L., Darvas, F., and Feh4r, L. Z. 2006. Application of small molecule microarrays in comparative chemical proteomics. QSAR Comb. Sci. 25(ll) 1020-27. 

Besides protein microarray proteome profiling, the term chemical proteomics (also chemoproteomics or pull-downs ) is mostly used in reference to the application of affinity chromatography protein purification when small molecules are the bait, and liquid chromatography separation of peptides precludes mass spectrometry as the universal readout (LC-MS/MS). 

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