The CRBN interactome: a map of starting points for molecular glues

A protein interaction map has identified 43 new starting points for molecular glue drugs

On August 13, Nature Biotechnology published a study of proteins that interact with CRBN in the presence of the drug pomalidomide. By combining computational screening with a large-scale experiment, the researchers identified six known and 43 previously unknown binding domains. A subsequent chemical screen found a compound that induced degradation of one RNF39 domain in cells.

CRBN, also called cereblon, is part of the cellular protein disposal system. A molecular glue holds another protein close to CRBN. The resulting complex attaches a molecular tag called ubiquitin to the target protein, which the cell then breaks down. This approach can reach proteins that conventional drugs cannot readily bind. Lenalidomide, a treatment for multiple myeloma, already acts through CRBN.

The search for a new molecular glue begins with a specific question: which proteins can come into close contact with CRBN? A 2025 study showed that the shape of a protein region may be more important for this interaction than similarity in its amino acid sequence. The authors of the new study tested this idea across a large protein library.

In the GluePCA assay, the researchers attached two fragments of the enzyme DHFR to CRBN and a candidate protein. If pomalidomide brought the proteins together, the fragments reassembled into an active enzyme that allowed yeast to grow. This converted physical proximity into a measurable signal. The library contained 8 363 zinc fingers, which are short protein regions. Of these, 201 showed a dose-dependent interaction with the CRBN–pomalidomide complex.

The MaSIF-mimicry algorithm then compared the surface of a known interaction with computational protein models and selected 1 959 candidates. GluePCA identified six known and 43 new binding domains among them. NanoBiT, a cell-based assay that also measures protein proximity, confirmed some of the new interactions.

For RNF39, the authors tested 960 pomalidomide analogues. Eight compounds increased its interaction with CRBN by at least twofold relative to pomalidomide, while the two strongest compounds increased it by about fivefold. In cells, Z5000181945 induced degradation of the RING domain, one of the domains within RNF39.