Techniques for Accelerating the Understanding of PROTAC-Based Ternary Complex

Proteolysis-targeting chimeras (PROTACs) are bifunctional small molecules capable of selectively degrading proteins by forming tertiary complexes with proteins of interest (POIs), E3 ubiquitin ligases, and degraders. Unlike traditional occupancy-driven inhibitors, PROTACs function through an event-driven mechanism, based on the thermodynamic, kinetic, and structural properties of the ternary complex assembly. This chapter provides an overview of the mechanistic and current knowledge of the ternary complexes formed by PROTAC and provides a review of the experimental and computational approaches applied to characterize them. Special emphasis is given to the role of cooperativity, residence time, conformational heterogeneity, and the interaction between ternary complex stability and productive ubiquitination. The structural, biophysical, cellular, proteomic, and computational approaches are presented with respect to their advantages and disadvantages. The representative case studies illustrate the role of the mechanistic insight in degrader design. A ternary complex-based and integrative framework is suggested to be used as the basis for the rational development of specific protein degraders.