Synthetic Strategies for Activity-Based Probes to Decode Ubiquitin-Like Modifiers

Area of Science:

• Biochemistry
• Chemical Biology
• Molecular Biology

Background:

• Ubiquitin-like proteins (Ubls) regulate cellular homeostasis through conjugation-deconjugation cycles.
• These cycles involve E1, E2, E3 enzymes and Ubl-specific proteases (ULPs).
• Understanding active enzyme forms requires specialized tools like activity-based probes (ABPs).

Purpose of the Study:

• To review chemistry-centric strategies for designing and synthesizing Ubl-targeting ABPs.
• To highlight methods for probe development targeting various Ubl pathway enzymes.
• To showcase applications of ABPs in dissecting Ubl biology.

Main Methods:

• Summarizing synthetic and semisynthetic approaches for Ubl ABP construction.
• Detailing methods for C-terminal ligation (native chemical ligation, activated cysteine ligation, hydrazide chemistry).
• Discussing strategies for incorporating reporter tags and bioorthogonal handles.

Main Results:

• Ubl ABP development is organized by target class: Ubl isopeptidases, E1/E2 conjugating enzymes, and E3 ligases.
• Chemical design choices are tailored for specific applications like live-cell profiling and proteomic mapping.
• Methodologies enable discovery of novel enzymes and substrate networks.

Conclusions:

• A versatile chemical toolkit for dissecting Ubl biology has been established.
• These tools facilitate the discovery of novel Ubl enzymes and mapping of substrate networks.
• ABP development aids in identifying potential therapeutic modulators for Ubl pathways.