Native Mass Spectrometry Can Effectively Predict PROTAC Efficacy

Protein degraders,
also known as proteolysis targeting chimeras
(PROTACs), are bifunctional small molecules that promote cellular
degradation of a protein of interest (POI). PROTACs act as molecular
mediators, bringing an E3 ligase and a POI into proximity, thus promoting
ubiquitination and degradation of the targeted POI. Despite their
great promise as next-generation pharmaceutical drugs, the development
of new PROTACs is challenged by the complexity of the system, which
involves binary and ternary interactions between components. Here,
we demonstrate the strength of native mass spectrometry (nMS), a label-free
technique, to provide novel insight into PROTAC-mediated protein interactions.
We show that nMS can monitor the formation of ternary E3-PROTAC-POI
complexes and detect various intermediate species in a single experiment.
A unique benefit of the method is its ability to reveal preferentially
formed E3-PROTAC-POI combinations in competition experiments with
multiple substrate proteins, thereby positioning it as an ideal high-throughput
screening strategy during the development of new PROTACs.