Activatable covalent labeling probes: design, mechanism, and biological applications

Abstract

Stimuli-activatable covalent labeling probes have emerged as powerful tools for targeted biomolecule labeling, addressing the limitations of conventional covalent probes, such as off-target reactivity, limited spatiotemporal control, and low signal-to-background ratios. These probes remain inert under physiological conditions but are selectively activated by specific endogenous or exogenous stimuli—such as enzymes, reactive oxygen species, light, ultrasound, or X-ray irradiation—initiating a cascade of stimulus-activation-covalent ligation. This mechanism enables precise, on-demand covalent conjugation to target biomolecules, improving labeling specificity, enhancing probe retention at pathological sites, and reducing interference with healthy tissues. Recent advances in molecular design, including enzymatic or light-mediated proximity labeling, have expanded their applications in protein profiling, interaction mapping, cell–cell communication analysis, and in vivo imaging. This review provides a comprehensive overview of the design principles, activation strategies focusing on enzymatic and photochemical triggers, and key biomedical applications, while critically assessing challenges related to stability, pharmacokinetics, and clinical translation. By integrating chemical probe engineering with translational research, we highlight the transformative potential of stimuli-activatable covalent labeling probes for protein profiling, disease diagnosis, therapeutic monitoring, and real-time visualization of biological processes.