NMR assessment of ternary complex formation by targeted protein degraders

Targeted protein degradation (TPD) is an increasingly prominent therapeutic strategy for targeting systems previously thought to be undruggable. Unlike typical small molecule inhibitors or agonists, TPDs induce the degradation of specific proteins by forcing them into proximity with the cell's native proteasomal degradation machinery. Many companies are rapidly developing new TPDs, and several degraders have reached clinical trials. From a chemistry standpoint, there are three main aspects of a TPD to study and optimize: 1) a ligand that binds and recruits a target protein, 2) a ligand that binds an E3 ligase, and 3) a linker that orients the two ligands and their associated proteins at the correct geometry for degradation. TPDs present a more complicated case of lead optimization than traditional programs since they bind simultaneously to two proteins forming a non-native protein:protein complex. The formation of these target protein-TPD-E3 ternary complexes is of particular interest in the field. As in any drug development program, knowing structural details of how TPDs bind to their target proteins provides critical information that may offer new and unique insights into future TPD design. Further, ideal TPDs allow for turnover of the degradation machinery, meaning that these molecules act catalytically to degrade more target protein at low concentrations, which complicates the desired kinetics for the formation and dissolution of ternary complexes. Recent work has shown that these complexes may be fundamentally dynamic and involve non-optimal interactions. Nuclear magnetic resonance (NMR) spectroscopy is uniquely poised to study these TPD complexes since it can be used to study both the structure and dynamics of molecules in solution. We report our use of NMR to characterize ternary complexes consisting of a TPD bound to both its target protein and the E3. Using isotopically labeled proteins, we first study the TPD binary complexes to establish how each end of the TPD binds before assessing additional changes that occur in ternary complexes. With this approach, we have the capacity to discriminate between changes due to ligand binding and those due to novel protein-protein interactions between the target protein and the E3. We find that the presence of the second protein in the ternary complex affects how the TPD binds to each protein, suggesting that these experiments report on the cooperativity of binding and the possible structural basis of this cooperativity. We further explored the use of NMR data acquired across a series of TPDs with different linkers to guide our understanding of the idealized ternary complex structural ensemble when combined with traditional assays for degradation. The study of ternary complex dynamics using NMR offers a new strategy to allow for the design and optimization of the next generation of TPDs. We will be disclosing all the structures related to this study.