From chance to design: systematic method finds a molecular glue that selectively destroys a leukemia protein

The cellular recycling system as a weapon against cancer proteins

Every cell maintains an elaborate quality-control system that identifies damaged, misfolded, or surplus proteins and marks them for destruction. This ubiquitin-proteasome system operates continuously, tagging proteins with a molecular label that sends them to the cell's disposal machinery. For decades, pharmaceutical researchers have looked at this system and seen an opportunity: if a disease-causing protein could be brought into contact with the tagging machinery, the cell would destroy it automatically.

The strategy has produced a class of compounds called molecular glues - small molecules that induce connections between proteins that would not otherwise interact. If a molecular glue can bring a disease-causing protein close to an ubiquitin ligase (the enzyme that applies the destruction tag), the target protein gets eliminated by the cell's own machinery rather than by an externally administered drug. The approach is elegant and, in principle, applicable to proteins that cannot be blocked by conventional inhibitors.

The problem has been discovery. Most molecular glues found so far were identified by accident - observed to work before researchers understood why. Building them deliberately, starting with a design goal and ending with a functional molecule, has been the unsolved challenge. A collaboration between the groups of Georg Winter at the AITHYRA Research Institute in Vienna and Michael Erb at the Scripps Research Institute in California describes a systematic method that changes this picture.

From one molecule to thousands of variants

The approach starts with a molecule already known to bind to the target protein of interest. Using established chemical synthesis methods, the team generated thousands of variants of that starting molecule by systematically attaching different molecular building blocks to various positions. Each variant subtly alters the surface of the target protein, potentially creating new interfaces that could recruit other proteins - including ubiquitin ligases - into contact with the target.

The crucial innovation is how these thousands of compounds were screened. Rather than purifying each compound and testing it in biochemical assays - which would be impractical at this scale - the team screened crude synthesis reactions directly in living cells using a sensitive assay that reports whether the target protein is being degraded. This live-cell readout collapses the gap between chemical synthesis and functional testing, enabling rapid identification of active compounds from a vast chemical space without the intermediate step of purification.

"Our approach combines high-throughput chemistry with functional testing in cells," said Miquel Munoz i Ordono, co-first author and PhD student in Georg Winter's lab. "This allows us to explore chemical diversity at a scale that was previously impractical, while immediately seeing which compounds have a desired biological effect."

Proof of principle: ENL and acute leukemia

The team chose ENL as their test target. ENL is a protein that plays a central role in certain forms of acute leukemia - specifically leukemias driven by chromosomal translocations that dysregulate gene expression programs controlled by ENL. Inhibiting or eliminating ENL is a validated therapeutic goal, but conventional drug approaches have faced challenges in selectively disrupting its activity without affecting other cellular functions.

From the thousands of compounds screened, the team identified one molecule that efficiently and selectively triggers ENL degradation in leukemia cells. The selectivity is important: the compound primarily affects ENL and the downstream gene programs it controls, rather than producing broad cellular toxicity. This specificity is characteristic of the molecular glue mechanism.

Mechanistic studies revealed how the compound works. It first binds to ENL, reshaping the protein's surface. This reshaping creates a new interaction interface that recruits a specific ubiquitin ligase, which then marks ENL for proteasomal degradation. The cooperative nature of this mechanism - binding one protein to create a surface that recruits a second - is what distinguishes molecular glues from conventional inhibitors and gives them their remarkable selectivity.

"This cooperative mode of action is what makes molecular glues both powerful and selective," Winter explained. "The molecule doesn't just block ENL - it turns the cell's own machinery against it."

Beyond this particular compound

The leukemia application validates the method but is not its final destination. The approach - generating diverse chemical variants from a known protein-binding starting point, then screening them in living cells for degradation activity - is in principle applicable to any protein target for which at least one binding molecule exists.

Many disease-relevant proteins have been considered "undruggable" by conventional approaches because they lack the deep binding pockets that small-molecule inhibitors require. Molecular glues do not need to occupy such pockets - they need only to bind a protein and reshape its surface enough to recruit a degradation partner. The systematic discovery method described here could extend the reach of molecular glue approaches to proteins that have previously resisted therapeutic targeting.

The current work represents a proof-of-concept demonstration using cell-based models. The ENL-degrading compound identified would require substantial additional development - optimization for potency and selectivity, pharmacokinetic studies, and eventual clinical testing - before any clinical application. The value of the current publication is primarily methodological: a scalable, systematic approach to a class of compounds that has largely been discovered by chance.