Traditional small-molecule drugs inhibit protein function by binding to active or allosteric sites, modulating enzymatic activity or protein conformation. In contrast, molecular glues stabilise weak, pre-existing interactions between target proteins and E3 ligases, redirecting ubiquitination pathways for targeted protein degradation. These interactions often involve degrons, short peptide motifs within substrate proteins that are directly recognised by E3 ligases through specific binding events. By harnessing the ubiquitin-proteasome system and altering the binding specificity of E3 ligases, molecular glues facilitate the recruitment of target proteins for ubiquitination and subsequent degradation. This approach enables the selective removal of disease-associated proteins, including those that cannot be readily targeted by conventional inhibitors, providing an alternative strategy for treating conditions such as cancer.
Targeted protein degradation can also be achieved using proteolysis-targeting chimeras (PROTACs), which are bifunctional molecules that contain separate ligands for a target protein and an E3 ligase, connected by a linker. While PROTACs have demonstrated strong efficacy, their large sizes can limit oral viability and bioavailability, often leading to complex pharmacokinetics. In contrast, molecular glues are small, monovalent molecules, making them more drug-like.
Despite their promise, only two primary classes of molecular glues have been discovered: (i) immunomodulatory imide drugs, which induce the degradation of transcription factors via CRBN; and (ii) sulfonamide-based molecular glues, which act through DCAF15 to degrade RBM39. Both classes were identified serendipitously.
A central challenge in molecular glue discovery is identifying E3 ligase–substrate interactions that are inherently gluable. Without knowing which interactions can be stabilised, systematic screening remains elusive with traditional approaches. However, recent research has demonstrated that both major classes of molecular glues enhance pre-existing E3 ligase–substrate interactions, increasing binding affinities by approximately an order of magnitude from their initially weak nominal affinity. This finding provides a potential framework for discovering weak E3 ligase-protein interactions that could be used in molecular glue discovery.
Thus, we developed a mass spectrometry-based approach integrating affinity selection mass spectrometry with native mass spectrometry to enable proteome-wide degron screening. This pipeline can be used to directly detect low-affinity interactions, providing a path to uncover previously unrecognised degron motifs and E3 ligase pairs that could be used for molecular glue discovery. Applying this workflow across multiple E3 ligases revealed both known and previously unreported degron motifs, expanding the landscape of potential molecular glue targets.
Additionally, our group has developed new methods to enhance signal and resolution in native mass spectrometry, improving the ability to characterise biomolecular assemblies, including E3 ligase complexes, in heterogeneous biological mixtures. These advancements will also be reported.