Cereblon Crystallography with CRBN-midi: Accelerating Molecular Glue and PROTAC Discovery

Targeted protein degradation is redefining how scientists approach diseases once considered “undruggable.” Instead of simply blocking the activity of proteins, TPD strategies harness the cell’s own machinery to eliminate them, unlocking new possibilities for next-generation therapeutics.

At the heart of many TPD systems is Cereblon (CRBN), a key component of an E3 ubiquitin ligase complex. Acting as a “molecular matchmaker,” CRBN enables degraders to engage non-native targets effectively by bridging target interactions via PROTACs and molecular glues. However, studying CRBN has been challenging due to its dependence on DDB1 for structural stability. Thanks to the development of the CRBN-midi construct, we can now resolve this challenge with remarkable accuracy and confidence.

First introduced by Kroupova et al., the engineered CRBN-midi format preserves CRBN’s functional core while improving stability, solubility, and suitability for structural biology. This construct facilitates X-ray crystallography, enabling structure-based screens and designs for therapeutic applications.

At Sygnature Discovery, we’ve harnessed this design to offer a robust, ready-to-use CRBN-midi system empowering clients to accelerate TPD research with reliable biochemical and biophysical assays. Using the published CRBN-Midi construct, we have enabled an off-the-shelf crystallization system and complementary ligand binding analysis by SPR.

Using crystallization conditions similar to those previously reported, followed by X-ray diffraction techniques, we’ve determined high-resolution CRBN-midi structures that can provide valuable insight into CRBN’s binding behavior:

  • Apo CRBN-midi (3.2 Å Resolution): Reveals the apo conformation of CRBN-midi, forming the baseline for ligand-induced structural changes.
  • CRBN-midi–Lenalidomide Complex (1.96 Å Resolution): Highlights molecular interactions critical for degrader design and optimization.
Figure 1: Size exclusion chromatography and SDS-PAGE data showing purity of CRBN-midi
Figure 2. Crystal structures of CRBN-midi in Apo form
Figure 3. a) Crystal structure of CRBN-midi in complex with Lenalidomide
Figure 3. b) Electron density map of Lenalidomide (yellow), 2mFo-DFc map contoured at 1σ, grey

We’ve enabled ligand-binding analysis with CRBN-midi using SPR. Using immobilized CRBN-midi on the sensor surface, we demonstrate saturable binding of lenalidomide.

Figure 4. Binding of lenalidomide to CRBN-midi by SPR: Saturable binding is observed between lenalidomide and immobilized CRBN-midi.

We now have a complete toolbox to support the design of degraders. The CRBN-midi described here performs well in binary assays, particularly for imids, and is an excellent tool for structure-guided design of new glues and Protacs.  This complements our offer with the full a DDB1/Cereblon complex which performs better in ternary assays, and highlights our deep expertise in the degrader space, delivering high-quality data for complex programs.

Sygnature Discovery offers a fully integrated workflow to support partners at every stage of discovery:

  • Protein Expression and Purification: Optimized systems for challenging targets
  • Compound Screening: To identify binders for molecular glue and PROTAC programs
  • Crystallization and X-ray Structure Determination: Industry-leading resolution and reliability
  • Molecular Glue Characterization: From binding assays to structural and biophysical analysis

Our technical depth, flexibility, and scientific insight deliver structural data that drives informed decisions and accelerates timelines.

Our progress with CRBN-midi does more than deliver faster structural insights, it strengthens CHARMED , Sygnature’s pioneering discovery platform. By integrating these learnings, we expand CHARMED’s ability to accelerate molecular glue and degrader programs for biotech and pharmaceutical innovators.

Contact us today  to learn how our structural biology and ligand screening services can accelerate your next breakthrough.