Biochemical principles of targeted protein degradation

The therapeutic strategy of targeted protein degradation (TPD) has undergone a massive growth in interest over the last several years. Founded in 2015, C4 Therapeutics was one of the first companies to focus exclusively on the development of therapies that employ the TPD modality. In this chapter, we share our perspectives on the advancement of TPD therapies, focusing on biochemical principles and biological considerations that differentiate TPD from traditional inhibition-based approaches. First, we review the steps in the biological mechanism by which the destruction of a desired protein is chemically induced, highlighting the key interactions and the catalytic nature of degrader compounds. By dissecting the mechanism of TPD, advantages of the TPD modality relative to inhibitors will emerge. Next, the chemical design of degraders is described, and assays commonly used in the field to screen degraders are analyzed. Additionally, we discuss how structure-activity relationships can be built from these assays and inform on the relationship between binding affinity and degradation activity. Third, we review validation strategies to verify that degraders showing degradation of a target are indeed following the TPD modality. Mechanisms of selective degradation, including its relationship to binding selectivity, are also discussed. Next, we touch on topics related to the ubiquitination of the target, specifically the identification of the site of ubiquitination, considerations related to the kinetic rate of ubiquitination of the target, and utilization of the ubiquitin-proteasome system components. Finally, we conclude with how TPD fits in with the larger framework of protein turnover and homoeostasis.