The peptide PROTAC modality: a novel strategy for targeted protein ubiquitination

Abstract

Despite dramatic advances in drug discovery over the decades, effective therapeutic strategies for cancers treatment are still in urgent demands. PROteolysis TArgeting Chimera (PROTAC), a novel therapeutic modality, has been vigorously promoted in preclinical and clinical applications. Unlike small molecule PROTAC, peptide PROTAC (p-PROTAC) with advantages of high specificity and low toxicity, while avoiding the limitations of shallow binding pockets through large interacting surfaces, provides promising substitutions for E3 ubiquitin ligase complex-mediated ubiquitination of "undruggable proteins". It is worth noting that successful applications of p-PROTAC still have some obstacles, including low stability and poor membrane permeability. Hence, we highlight that p-PROTAC combined with cell-penetrating peptides, constrained conformation technique, and targeted delivery systems could be the future efforts for potential translational research.

Keywords: E3 ligase; peptide PROTAC; ubiquitination; undruggable proteins.

Figure 1

The schematic diagram of p-PROTAC. (A) With ATP, the enzyme E1 adheres to the Cys residue of the ubiquitin molecule. Then E1 transfers the activated ubiquitin molecule to the E3 ubiquitin ligase via the ubiquitin-binding enzyme E2. (B) Bifunctional p-PROTAC molecule binds to the POI with one end while the other end binding to an E3 ligase to form ternary complex. (C) Different types of E3 enzymes jointly recognize POI with polyubiquitinated modification to mediate degradation through ubiquitin proteasome, and then freed p-PROTAC can be recycled.

Figure 2

A toolbox of functional peptide PROTACs. (A) The design of peptide targeting warhead using chemical epitope targeting strategy (PDB code: 1QZ7). (B) The commonly used E3 ligase ligands. (C) Linkers-1 connecting POI and E3 ligase ligand. (D) Cell penetrating peptides used to increase membrane permeability. (E) Linkers-2 connecting POI and tag. (F) Functional tags used in p-PROTAC.

Figure 3

Different pathways in cancer targeted by p-PROTAC. (A) ^ErbB2PP_PI3K and PROTAC_AKT inhibit breast tumor growth and promote apoptosis through the classic PI3K/AKT signaling pathway. c-Src promotes the transcription of ERα in the nucleus through the MAPK signaling pathway. The degradation of ERα by TD-PROTAC inhibits the transcription of downstream target genes and mediates the killing effect on ERα-positive breast cancer. (B) Reduced expression of E-cadherin is closely related to disruption of cell-cell contacts and enhanced cancer cell invasion. When E-cadherin expression is suppressed, β-catenin is released and translocated to the nucleus, which can be antagonized by PROTAC_X-protein. (C) PRTC proficiently inhibits cell proliferation and motility in pancreatic by inhibiting transcription initiation upon Wnt signaling as well as downstream target gene cyclin D1 thus inducing cycle arrest and DNA damage.