Modeling the Effect of Cooperativity in Ternary Complex Formation and Targeted Protein Degradation Mediated by Heterobifunctional Degraders

Chemically induced proximity between certain endogenousenzymesand a protein of interest (POI) inside cells may cause post-translationalmodifications to the POI with biological consequences and potentialtherapeutic effects. Heterobifunctional (HBF) molecules that bindwith one functional part to a target POI and with the other to anE3 ligase induce the formation of a target-HBF-E3 ternary complex,which can lead to ubiquitination and proteasomal degradation of thePOI. Targeted protein degradation (TPD) by HBFs offers a promisingapproach to modulate disease-associated proteins, especially thosethat are intractable using other therapeutic approaches, such as enzymaticinhibition. The three-way interactions among the HBF, the target POI,and the ligase including the protein-protein interactionbetween the POI and the ligase contribute to the stabilityof the ternary complex, manifested as positive or negative bindingcooperativity in its formation. How such cooperativity affects HBF-mediateddegradation is an open question. In this work, we develop a pharmacodynamicmodel that describes the kinetics of the key reactions in the TPDprocess, and we use this model to investigate the role of cooperativityin the ternary complex formation and in the target POI degradation.Our model establishes the quantitative connection between the ternarycomplex stability and the degradation efficiency through the former'seffect on the rate of catalytic turnover. We also develop a statisticalinference model for determining cooperativity in intracellular ternarycomplex formation from cellular assay data and demonstrate it by quantifyingthe change in cooperativity due to site-directed mutagenesis at thePOI-ligase interface of the SMARCA2-ACBI1-VHL ternary complex. Ourpharmacodynamic model provides a quantitative framework to dissectthe complex HBF-mediated TPD process and may inform the rational designof effective HBF degraders.