Mapping the latent CRBN-molecular glue degrader interactome
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Abstract
Molecular glue degraders (MGDs) are a transformative modality in drug discovery. MGDs that work in concert with the E3 ligase CRL4 CRBN can degrade a range of substrates through tailored MGDs. To explore CRL4 CRBN reprogrammability, we tested whether reported CRBN-MGD substrates are part of a network of latent CRBN interactors, detectable with generic CRBN-MGDs. Leveraging highly parallel interaction measurement (GluePCA) between CRL4 CRBN and human zinc-fingers (ZFs), we identified ∼210 ZFs bound to CRBN-pomalidomide, where top binders are already reported as degraded by dedicated MGDs. To map latent CRBN-MGDs interactions proteome-wide, and thus define the immediately accessible CRBN target space, we combined AI-derived protein surface queries (MaSIF-mimicry) with GluePCA. This pipeline identified 6 known and 43 novel CRBN-pomalidomide binders, thereby providing privileged starting points for MGD development. We expect this binding-focused, highly parallel workflow to be readily applicable to other MGD/E3 ligase systems, extending the target landscape of this emerging drug class.
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Mapping the latent CRBN-molecular glue degrader interactome
The combination of MaSIF-mimicry and GluePCA provides a powerful framework for mapping the latent CRBN-MGD interactome, and the scale at which you identify both ZF and non-ZF binders is impressive. The work makes a strong case that CRBN’s binding landscape is far broader than its known degradome.
I have a few questions about the bonsai library, its expression in yeast, and the interpretation of the latent interactome:
Because all bonsai constructs are expressed in yeast, some human ZFs and non-ZF fragments may misfold, fail to coordinate Zn²⁺, or depend on mammalian PTMs or chaperones. These would appear as GluePCA negatives even if they are true binders in human cells. Have you assessed folding in yeast, estimated how much of the “non-binder” space may reflect yeast-specific …
Mapping the latent CRBN-molecular glue degrader interactome
The combination of MaSIF-mimicry and GluePCA provides a powerful framework for mapping the latent CRBN-MGD interactome, and the scale at which you identify both ZF and non-ZF binders is impressive. The work makes a strong case that CRBN’s binding landscape is far broader than its known degradome.
I have a few questions about the bonsai library, its expression in yeast, and the interpretation of the latent interactome:
Because all bonsai constructs are expressed in yeast, some human ZFs and non-ZF fragments may misfold, fail to coordinate Zn²⁺, or depend on mammalian PTMs or chaperones. These would appear as GluePCA negatives even if they are true binders in human cells. Have you assessed folding in yeast, estimated how much of the “non-binder” space may reflect yeast-specific false negatives, or tested any GluePCA-negative constructs in a mammalian binding assay?
GluePCA reports proximity-driven binding, but degradation requires a very specific geometry relative to the CRL4^CRBN ubiquitination machinery. Many binders may be sterically dead: capable of engaging CRBN-MGD but oriented such that lysines are inaccessible to the E2. Have you explored whether certain ZF orientations, linker patterns, lysine positions, or accessory elements distinguish productive binders from non-productive ones? And do you think the dataset is sufficient to computationally separate these classes? Such an analysis could help predict productively oriented binders that are more amenable to rational MGD design.
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