Small-molecule probes elucidate global enzyme activity in a proteomic context

Abstract

The recent dramatic improvements in high-resolution mass spectrometry (MS) have revolutionized the speed and scope of proteomic studies. Conventional MS-based proteomics methodologies allow global protein profiling based on expression levels. Although these techniques are promising, there are numerous biological activities yet to be unveiled, such as the dynamic regulation of enzyme activity. Chemical proteomics is an emerging field that extends these types proteomic profiling. In particular, activity-based protein profiling (ABPP) utilizes small-molecule probes to monitor enzyme activity directly in living intact subjects. In this mini-review, we summarize the unique roles of smallmolecule probes in proteomics studies and highlight some recent examples in which this principle has been applied. [BMB Reports 2014; 47(3): 149-157]

Proteome-wide Map of Targets of T790M-EGFR-Directed Covalent Inhibitors

“…These benefits, however, are counterbalanced by the risk for inadvertent or excessive covalent modification of other proteins in the proteome, which could lead to cell and/or organism toxicity. The special combination of opportunities and challenges afforded by covalent drugs has stimulated the emergence of methods to globally assess the protein reactivity of electrophilic small molecules in native biological systems (Johnson et al, 2010, Lee et al, 2014). Such approaches draw inspiration from chemical proteomic technologies such as activity-based protein profiling (ABPP) (Cravatt et al, 2008, Sanman and Bogyo, 2014, Patricelli et al, 2011) and have been used, for instance, to: i) provide target engagement assays for measuring the fraction of inhibited kinase in native biological systems (Advani et al, 2013), ii) identify targets and off-targets of covalent kinase inhibitors in human cells and to correlate these profiles with cytotoxicity (Lanning et al, 2014), and iii) more broadly map the portion of the human proteome that can interact with cysteine-directed small-molecule electrophiles (Backus et al, 2016).…”

Targets Fishing and Identification of Calenduloside E as Hsp90AB1: Design, Synthesis, and Evaluation of Clickable Activity-Based Probe

“…Samples were denatured by heating in 2 × SDS-loading buffer and analyzed by SDS-PAGE. The resulting bands were visualized with Coomassie blue staining (Lee et al, 2014 ). Next, trypsin digestion was performed on selected visible protein bands.…”

Applications of Activity‐Based Protein Profiling (ABPP) and Bioimaging in Drug Discovery

“…Screening against proteins that have low abundance or are membrane-bound has been proved to be extremelyc hallenging. [40] Wang et al recently developed an ovel reaction-based turn-on probe capable of no-wash imaging of BTK in live cells with high sensitivity and selectivity by conjugation of maleimidecoumarin with ibrutinib (Figure 3, IB-4). [25] In this case, the turnon fluorescence difference caused by competition with drug candidates can be detectedi na384-wellp late, allowing screening of potential drugs in ah igh throughput format.…”

“…Structures of activity-based probes( ABPs) for target identification and parent inhibitors originating from target-based drug design.Chem. Asian J 2020,15,[34][35][36][37][38][39][40][41]. …”