Activity-Based Protein Profiling ABPP

Activity-based protein profiling (ABPP) is a chemical proteomic strategy in which active-site-directed covalent probes are used to profile the functional states of enzymes in complex proteomes. Activity-based probes (ABPs) can distinguish active enzymes from their inactive zymogens or inhibitor-bound forms. They contain a reactive group intended to modify enzyme active sites covalently and a reporter group (typically rhodamine or biotin) that assists in detection and identification of protein targets. 

The rise of global analysis methods for nucleic acids [6-8] and proteins [9-11] demonstrates the value of unbiased analysis in molecular biology. Activity-based protein profiling (ABPP), for example, measures changes in enzyme activity between biological samples. This method has been used to discover enzymes that are associated with disease processes, such as cancer cell invasiveness [12, 13]. Similarly, unbiased analysis of the metabolome led to the development of metabolomics approaches [5,14—19]. 

Activity-based Protein Profiling (ABPP) - A Chemical Strategy for the Global Profiling of Enzyme Activities in Complex Proteomes... 

Fig. 7.3-3 General strategy for activity-based protein profiling (ABPP). Proteomes are treated with chemical probes that label active enzymes of a particular class (or classes) in a manner that allows for their detection, isolation, and identification. Active enzymes are denoted by open/unshaded active sites, with their inactive counterparts (e.g., zymogen or inhibitor-bound forms) shaded in black.

Scheme 73 A Principle of conventional activity-based protein profiling (ABPP) [255]. B Synthesis of Rhodamine- and Rhodamine-biotin-tagged molecules 364 and 365 of the natural product FR182877 in order to investigate its mechanism of action by the conventional ABPP technique [258]...

Activity-based protein profiling (ABPP) is a powerful technique to identify enzymatic activities and to study their functioning - and the effect of inhibitors on this - in vitro, in situ, and in vivo. In this chapter some case studies on activity-based profiling of mammalian proteasomes are discussed. Both direct and two-step bioorthogonal ABPP strategies and their merits are discussed, and the value of ABPP in the establishment of previously uncharted enzymatic activities and the direct visualization of inhibitor specificity are presented. 

Capture compounds (Figure 18.3) as used in activity-based protein profiling (ABPP) have been designed for MT profiling based on modified SAH 2 and are... 

Another area in chemical biology that the triazole-forming click reactions have revolutionized is activity-based protein profiling (ABPP). ABPP is a chemical biology platform that uses active site-directed probes [61] to study the dymamic expression and function of mechanistically similar enzymes in their various... 

Exceptions certainly exist in the realm of clinical therapeutics such as the proteasome inhibitor carfilzomib and in the emerging chemical biology field of activity-based protein profiling (ABPP) however, without a direct hypothesis relating to electrophilic modification, early elimination of these hit compounds may prove fortuitous [25, 26]. 

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