Targeted protein degradation: A promise for undruggable proteins

Abstract

Protein homeostasis, or "proteostasis," is indispensable for a balanced, healthy environment within the cell. However, when natural proteostasis mechanisms are overwhelmed from excessive loads of dysregulated proteins, their accumulation can lead to disease initiation and progression. Recently, the induced degradation of such disease-causing proteins by heterobifunctional molecules, i.e., PROteolysis TArgeting Chimeras (PROTACs), is emerging as a potential therapeutic modality. In the 2 decades since the PROTAC concept was proposed, several additional Targeted Protein Degradation (TPD) strategies have also been explored to target previously undruggable proteins, such as transcription factors. In this review, we discuss the progress and evolution of the TPD field, the breadth of the proteins targeted by PROTACs and the biological effects of their degradation.

Keywords: PROTACs; proteasome; targeted protein degradation; ubiquitination; undruggable proteome.

Figure 1.. Components of proteostasis.

Protein synthesis, protein folding and clearance are key components of the proteostasis network.

Figure 2.. Conditional activation of PROTACs.

General PROTAC technology and other complementary strategies to control its activity. PhosphoPROTACs bind to the POI only under conditions where the tyrosine residue of the POI-recruiting peptide is phosphorylated upon activation of intracellular signaling. PhotoPROTACs are activated by cellular irradiation at a particular wavelength. ACBIDs release active PROTACs only upon entry into tumor cells via an antibody-specific tumor antigen.

Figure 3.. Tumor and tissue- specific E3 ligases.

Compared to small molecule inhibitors, PROTACs permit tumor or tissue selective target engagement and subsequent degradation of the target. Numerous E3 ligases are enriched in certain tissues or tumors, suggesting use of such E3 ligases in PROTAC design will accomplish tumor or tissue selective degradation (Khan et al., 2020, Schapira et al., 2019).

Figure 4.. Protein classes targeted by induced degradation.

Receptors, kinases, epigenetic proteins and several transcription factors have been successfully degraded by induced proximity-based approaches.

Figure 5.. Alternative strategies to control protein levels – regulation of gene expression.

Techniques such as CRISPR-mediated gene editing and transcriptional regulation have been widely used to control target proteins level at genetic/transcriptional level. RNA interference, RIBOTAC and synthetic DNA-decoys have also been used to regulate protein levels.

Figure 6.. Applications of transcription factor targeting chimeras (TRAFTACs).

A) Chimeric TRAFTACs induce the proximity between a transcription factor of interest and an E3-ligase complex in the presence of HP14. Subsequent ubiquitination results in the degradation of TF by the proteasome. B) Conversion of TRAFTACs to a standard gRNA that targets a neighboring site of the promoter region could recruit an E3 ligase to the proximity of promoter-bound TF and induce subsequent degradation of TF by the proteasome. Spacer DNA between dCas9 binding site and TF-binding site can be adjusted using different gRNAs to achieve optimal/productive proximity between the recruited E3-ligase and the TF.