Affinity Chemical Proteomics

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). 

As opposed to protein arrays, chemoproteomics leverages the analytical power of mass spectrometry to interrogate the affinity of the investigational compound against its putative target(s) in the native state and relative abundance of the 

In all cases, the labeled peptides are separated by capillary LC and detected by mass spectrometry. The MS/MS stage provides the peptide fragmentation and releases the unique isobaric tag reporter ion that furnishes the peptide quantification comparing relative peak intensities of the same peptide for each reporter. 

The raw peptide data is searched against known trypsin-digested prophetic peptides with specialized protein databases and the corresponding proteins can be identified within a confidence level and controlled false discovery rate. 

The technical boimdaries of in-lysate chemical proteomics affect not only the ability to identify proteins and complexes that are in low abundance but also 

---

Affinity chemical proteomics relies on the affinity capture of the cellular efficacy targets onto solid support. Therefore, it is critical to introduce a linker... 

The use of affinity probes for in-lysate quantitative affinity chemical proteomics is discussed in Section 3.6, and illustrated with the XAV939 linker-bearing analog. 

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. 

Katayama, H., Oda, Y. (2007). Chemical proteomics for drug discovery based on compound-immobilized affinity chromatography. J. Chromatogr. B, 855, 21-27. 

An increasing number of available protein-binding assays, functional cell-based assays, and methods of chemical proteomics (affinity chromatography, three-hybrid assays, pull-down assays) will allow for a better assignment of the specificity and selectivity of a hit compound. It would be desirable that the data collected during these screening... 

Figure 1.25 Various multitarget kinase inhibitors for chemical proteomics indicating the attachment point to the affinity matrix. (From Daub, H. et al., 2004, Evaluation of Kinase Inhibitor Selectivity by Chemical Proteomics, Assay Drug Dev. Technol., 2(2) 215-24.)...

Chemical proteomics consists of the classical drug-affinity chromatography and modern high-resolution MS analysis for protein identification [3, 11]. The procedure typically involves immobilization of the compound of interest to a solid support through a spacer arm, and the affinity matrix is then used to purify specific interacting proteins from cellular lysate. The complex proteomic mixture is then proteolytically digested, and the resulting peptides are sequenced... 

Fig. 1 SILAC-based affinity chromatography for identification of the target proteins of small molecules, (a) Generation of two cell populations differentially labeled with light or heavy amino acids, (b) Employment of the metabolically labeled cell lysates from (a) in affinity-based chemical proteomics...

---