Proteolysis Targeting Chimeras (PROTACs): Design and Mechanism

Proteolysis-targeting chimeras (PROTACs) are driving a fundamental shift in small-molecule drug discovery from the traditional "occupation-driven" to the innovative "event-driven" pharmacological paradigm. This chapter systematically reviews the development of PROTAC technology and provides a detailed analysis of the dynamic process by which it hijacks the ubiquitin-proteasome system (UPS) to mediate the catalytic degradation of the protein of interest (POI). It delves into the thermodynamic effects driving the formation of the "POI-PROTAC-E3 ligase" ternary complex, as well as the hook effect mechanism that determines the therapeutic window. Regarding the rational design and optimization of PROTACs, this chapter comprehensively discusses the development principles for three core modules. It systematically explains the modification rules and covalent strategies for the solvent-exposed regions of POI ligands. It then summarizes the applications of classical E3 ligases and focuses on the expansion of the toolkit of novel E3 ligases, including FEM1B, the RNF family, and DCAF16. In addition, it provides an in-depth analysis of the critical role played by the evolution of linkers, from traditional flexible or rigid structures toward macrocyclization, bioorthogonal self-assembly, and molecular hinges, in enhancing druggability. Combining the revolutionary application of artificial intelligence (AI) in ligand and linker design with the latest clinical translation milestones, this chapter provides comprehensive theoretical support and practical guidance for conquering "undruggable" targets, overcoming clinical drug resistance, and developing the next generation of highly effective PROTACs.