Azoacetylene Electrophiles for Proteome-wide Ligand and Target Discovery: Supporting Targeted Protein Degradation

Covalent
probes integrated with chemical proteomics have been an
efficient method for disclosing new druggable targets and E3 ubiquitin
ligases supporting targeted protein degradation. However, a large
fraction of the proteome including E3 ligases remains inaccessible
with existing electrophiles. In this work, we developed a new reactive
warhead, terminal azoacetylene, which can be generated by in situ
desilylation for proteome profiling under cellular conditions. A series
of uncharacterized targets and E3 ubiquitin ligases were covalently
engaged. Fragment-based ligand discovery (FBLD) showed that the azoacetylene-containing
fragments can covalently bind a series of essential protein hits at
the active sites such as C130 of TUFM probably modulating the protein
functions. Incorporation of this warhead into BRD4 targeting inhibitor
JQ1 led to generation of novel small molecular degraders that degrade
BRD4 without inducing the hook effect. This provides a new method
for ligand and target discovery, as well as the development of new
types of small molecular degraders.