Exploring scaffold architecture for biological degraders: A comparative study for targeted lysosomal degradation

Targeted Protein Degradation (TPD) represents a promising strategy for therapeutic intervention, as it enables the selective removal of specific proteins and provides opportunities to address previously “undruggable” targets. In this study, a modular platform for the design and evaluation of Biological Degraders (BioDegs) is established, by which receptor-mediated uptake and degradation of extracellular proteins are facilitated. Two targeting strategies were explored: (i) glycan-conjugated scaffolds modified with triantennary N-acetylgalactosamine (TGN) to engage the ASGPR, and (ii) fusion proteins incorporating insulin-like growth factor 2 (IGF2) to target the cation-independent mannose-6-phosphate receptor (CI-M6PR). To benchmark the platform, the cytokine interleukin-6 (IL-6) and its soluble receptor (sIL-6R) were used as model substrates due to their well-established therapeutic relevance. A range of BioDeg formats, including full-length antibodies (siltuximab, tocilizumab), a VHH (against IL-6), and receptor-based constructs (sIL-6R), were systematically assessed for binding affinity, thermal stability, cellular uptake, lysosomal trafficking, and degradation efficiency in HepG2 cells. The results reveal that both scaffold design and receptor choice critically influence degradation efficacy. In particular, constructs such as sIL-6R-TGN show efficient uptake but fail to induce substantial degradation, highlighting the importance of high-affinity binding and productive intracellular trafficking. Overall, this study provides a comparative framework for BioDeg development and underscores key principles in designing lysosome-targeting degraders for extracellular proteins. The modular nature of the platform enables broad adaptability for diverse therapeutic targets beyond cytokines.