Emerging protein degradation strategies: expanding the scope to extracellular and membrane proteins

Abstract

Classic small molecule inhibitors that directly target pathogenic proteins typically rely on the accessible binding sites to achieve prolonged occupancy and influence protein functions. The emerging targeted protein degradation (TPD) strategies exemplified by PROteolysis TArgeting Chimeras (PROTACs) are revolutionizing conventional drug discovery modality to target proteins of interest (POIs) that were categorized as "undruggable" before, however, these strategies are limited within intracellular POIs. The novel new degrader technologies such as LYsosome-TArgeting Chimaeras (LYTACs) and Antibody-based PROTACs (AbTACs) have been successfully developed to expand the scope of TPD to extracellular and membrane proteins, fulfilling huge unmet medical needs. Here, we systematically review the currently viable protein degradation strategies, emphasize that LYTACs and AbTACs turn a new avenue for the development of TPD, and highlight the potential challenges and directions in this vibrant field.

Keywords: AbTAC; LYTAC; extracellular and membrane proteins; targeted protein degradation (TPD).

Figure 1

An overview of the novel protein degradation technologies. LYTAC and AbTAC utilizes lysosome system to degrade extracellular and membrane POIs. Intracellular POIs are targeted and degraded by PROTAC through the UPS. AUTAC and ATTEC technologies take advantages of autophagy-lysosome system to selectively degrade intracellular proteins and even organelles. Figure created with BioRender.com.

Figure 2

The schematic diagram of LYTAC and AbTAC. (A) M6Pn-LYTAC targets extracellular or membrane protein and is recognized by lysosome shuttling receptor CI-M6PR at the cell surface, to form ternary complex, while GalNAc-LYTAC binds target protein and liver cell-surface ASGPR simultaneously. The resulting complex is engulfed by the cell membrane, endocytosed into endosomes, and degraded in lysosomes. (B) AbTAC binds to RNF43 and cell-surface proteins simultaneously, inducing RNF43-AbTAC-protein complexes internalization and lysosomal degradation. Figure created with BioRender.com.

Figure 3

A toolbox of functional LYTAC. (A) The design of LTR-binding ligands. (B) The currently targeted extracellular and transmembrane POIs and their ligands. Figure created with BioRender.com.

Figure 4

Generation of bispecific IgG AbTAC. The recombinant antibody for RNF43 and POI was generated using phage display. These two IgGs are assembled to form an AbTAC utilizing the knobs-into-holes technology. Figure created with BioRender.com.