An Integrated Approach Combining Surface Plasmon Resonance Screening with Proteomics Enables Discovery of Natural Molecular Glue Degraders

Targeted protein degradation, particularly through molecular
glue
degraders (MGDs), offers a promising strategy for targeting “undruggable”
proteins. However, existing fluorescence-based screening approaches,
such as time-resolved fluorescence resonance energy transfer, may
be constrained by conformational changes or inefficient labeling of
targets, necessitating more efficient screening approaches. Here,
we present a MGDs screening approach based on surface plasmon resonance
(SPR) coupled with degradomics and interactomics (SPR-DI). This approach
leverages the high-throughput and label-free SPR for screening E3
ligands, followed by an unbiased “dual filter” of degradomics
and interactomics to identify candidate proteins of interests (POIs).
The feasibility of SPR-DI was validated using previously established
MGD VH032, which can drive VHL to induce CDO1 degradation. Employing
VHL and Keap1 as drivers E3, we then screened a natural product library
and successfully identified triptolide and pycropodophyllin as potential
MGDs. Subsequent investigations demonstrated that triptolide facilitates
VHL-mediated degradation of IMP3, whereas picropodophyllin promotes
Keap1-mediated degradation of DDX52 and LDHB. These degradation events
were confirmed to depend on the respective E3 and ubiquitin-proteasome
system, underscoring the capacity of these compounds to induce ternary
complex formation. In conclusion, the establishment of SPR-DI provides
a promising tool for the discovery of MGDs and their corresponding
POIs, offering instructive insights to advance future MGD screening
methodologies.