Activity‐Based Protein Profiling: Recent Advances in Probe Development and Applications

Abstract

The completion of the human genome sequencing project has provided a wealth of new information regarding the genomic blueprint of the cell. Although, to date, there are roughly 20,000 genes in the human genome, the functions of only a handful of proteins are clear. The major challenge lies in translating genomic information into an understanding of their cellular functions. The recently developed activity-based protein profiling (ABPP) is an unconventional approach that is complementary for gene expression analysis and an ideal utensil in decoding this overflow of genomic information. This approach makes use of synthetic small molecules that covalently modify a set of related proteins and subsequently facilitates identification of the target protein, enabling rapid biochemical analysis and inhibitor discovery. This tutorial review introduces recent advances in the field of ABPP and its applications.

Activity-based protein profiling as a robust method for enzyme identification and screening in extremophilic Archaea

“…Notably, the here described ABPP methodology has a broad application potential and also allows use of other enzyme class/family-specific ABPs1618. As chemical biologists constantly develop novel ABPs19, many more enzyme classes should therefore be addressable by our approach.…”

“…In bacteria and eukaryotes, ABPP is an established methodology for measuring the activity state of enzymes under physiological conditions16171819. It relies on the use of activity-based probes (ABPs) that irreversibly label active enzymes, either in vitro or even in vivo .…”

“…For example, serine hydrolase, cysteine or threonine protease, tyrosine phosphatase, glycosidase or ATPase and kinase-specific ABPs are available16171819. Consequently, in vivo application of such ABPs to archaea could be used to detect and functionally annotate enzymes of a selected family/class in a target-oriented manner (Fig.…”

Transition from identity to bioactivity‐guided proteomics for biomarker discovery with focus on the PF2D platform

“…Another emerging area that complements proteomics, is detection and bioactivity of enzymes in complex proteomes using activity‐based probes (ABPs) . Click chemistry can engineer these synthetic ABPs with both a reactive and a reporting group .…”

Activity‐Based Probes for HECT E3 Ubiquitin Ligases

“…To this end, the expansion of the Ub toolbox with activity‐based probes (ABPs) has contributed to a rapid increase in our understanding of deubiquitinases (DUBs) . First‐generation ABPs (Ub‐ABPs) comprise a Ub for selective recognition by DUBs, with the C‐terminal G76 chemically modified with an electrophilic warhead to covalently label the catalytic Cys.…”