Targeted degradation of extracellular proteins: state of the art and diversity of degrader designs

Abstract

Selective elimination of proteins associated with the pathogenesis of diseases is an emerging therapeutic modality with distinct advantages over traditional inhibitor-based approaches. This strategy, called targeted protein degradation (TPD), is based on hijacking the cellular proteolytic machinery using chimeric degrader molecules that physically link the target protein of interest with the degradation effectors. The TPD era began with the development of PROteolysis TAtrgeting Chimeras (PROTACs) in 2001, with various methods and applications currently available. Classical PROTAC molecules are heterobifunctional chimeras linking target proteins with E3 ubiquitin ligases. This induced interaction leads to the ubiquitylation of the target protein, which is needed for its recognition and subsequent degradation by the cellular proteasomes. However, this technology is limited to intracellular proteins since the effectors involved (E3 ubiquitin ligases and proteasomes) are located in the cytosol. The related methods for selective destruction of proteins present in the extracellular space have only emerged recently and are collectively termed extracellular TPD (eTPD). The prototypic eTPD technology utilizes LYsosomal TArgeting Chimeras (LYTACs) that link extracellular target proteins (secreted or membrane-associated) to lysosome-targeting receptors (LTRs) on the cell surface. The resulting complex is then internalized by endocytosis and trafficked to lysosomes, where the target protein is degraded. The successful elimination of various extracellular proteins via LYTACs and related approaches has been reported, including several important targets in oncology that drive tumor growth and dissemination. This review summarizes current progress in the eTPD field and focuses primarily on the respective technological developments. It discusses the design principles and diversity of degrader molecules and the landscape of available targets and effectors that can be employed for eTPD. Finally, it emphasizes current open questions, challenges, and perspectives of this technological platform to promote the expansion of the eTPD toolkit and further development of its therapeutic applications.

Keywords: LYTAC; Membrane proteins; PROTAC; Secreted proteins; Targeted protein degradation.

Fig. 1

The general principles of TPD approaches for intracellular and extracellular proteins. A Scheme of iTPD with a PROTAC degrader. The PROTAC molecule induces the proximity of the intracellular target protein (POI) and the E3 ubiquitin ligase. The latter catalyzes the attachment of a polyubiquitin chain to the POI (normally with the help of E2 ubiquitin-conjugating enzymes), forming the recognition signal for the proteasomes that ultimately degrade the POI. B Scheme of eTPD with a LYTAC degrader. The LYTAC molecule links the POI with the LTR on the cell surface, which induces the internalization of the formed complex and sorting to lysosomes, where the POI is finally degraded

Fig. 2

The modularity of eTPD degrader design. The chimeric degrader molecule comprises two recognition modules that bind to the target protein (warhead) and the effector protein (ligand), respectively, and are connected by a linker. The diversity of molecules that can constitute each of these modules is illustrated below

Fig. 3

The diversity of eTPD effectors and the respective degradation mechanisms. A IGF2R/CI-M6PR-based degraders: The binding of the degrader induces conformational changes in the LTR and endocytosis. B ASGPR-based degraders: The binding of the degrader induces LTR clustering and endocytosis. C Targeting membrane-associated E3 ubiquitin ligases as eTPD effectors instead of LTRs. D CPP-LSS-based degraders: Direct internalization and lysosomal targeting without LTRs or E3 ubiquitin ligase

Fig. 4

The expression patterns of different LTRs. The expression data of the indicated LTRs across selected tissues were analyzed using the GTEx Portal (https://gtexportal.org/home/) and reported as a heatmap with tissue clustering. The gene names for conventional LTRs reported in Tables 1, 2, 3 were used as input