Bioorthogonal Reactions in Activity-Based Protein Profiling

Abstract

Activity-based protein profiling (ABPP) is a powerful technique to label and detect active enzyme species within cell lysates, cells, or whole animals. In the last two decades, a wide variety of applications and experimental read-out techniques have been pursued in order to increase our understanding of physiological and pathological processes, to identify novel drug targets, to evaluate selectivity of drugs, and to image probe targets in cells. Bioorthogonal chemistry has substantially contributed to the field of ABPP, as it allows the introduction of tags, which may be bulky or have unfavorable physicochemical properties, at a late stage in the experiment. In this review, we give an overview of the bioorthogonal reactions that have been implemented in ABPP, provide examples of applications of bioorthogonal chemistry in ABPP, and share some thoughts on future directions.

Bioorthogonal Chemistry and Its Applications

“…The advantage of employing bioorthogonal functionality such as an azide or alkyne moiety as the tag for a probe is that allows small and relatively nonperturbing groups to be used, yielding results more consistent with the behavior of the enzymes in the absence of probe. 113 Many desirable tags such as biotin impair the cell permeability of probes bearing them. Reaction of probes with smaller tags in cells followed by lysis removes the need for cell-permeable tagging moieties.…”

Identification of fungal lignocellulose-degrading biocatalysts secreted by Phanerochaete chrysosporium via activity-based protein profiling

“…In ABPP, activity-based probes (ABPs) consisting of a reactive "warhead", an enzyme inhibitory moiety that forms a covalent irreversible bond with their target protein(s) and often ensures a high enzyme class specificity, a linker, and a reporter tag are used to label, identify and report on active enzymes under native, physiological conditions. As reporters, biotin, fluorophores, or so-called two-step reporter tags such as alkyne or azide moieties are frequently used 6 . In the last years, intensive efforts have been undertaken, both to develop new ABPs targeting new enzyme families and to establish their use in, amongst others, drug discovery (target and lead discovery, target engagement) [7][8][9][10][11][12] , plant biology 13 , or microbiology [14][15][16][17][18] .…”

Modern Wound Dressings: Hydrogel Dressings

“…Such crosslinking reactions are conventionally called “bioorthogonal”, because all components used for polymerization (precursors, cofactors, initiators, etc.) participate only in the formation of the polymer network, but do not interact with biomolecules [ 45 ].…”