Discovery of NEK9 and Aurora A PROTACs using a proteomics-based screening approach

Abstract

Chemically induced degradation has emerged as a valuable tool in chemical biology and medicinal chemistry for both potential therapies, and to investigate protein function. Proteolysis targeting chimeras (PROTACs) are small molecules that can hijack E3 ligases, the protein complexes that catalyse ubiquitination, to direct proteasomal degradation of selected targets. Simultaneous binding of both the E3 ligase recruiting moiety and warhead to their respective targets induces ternary (E3-PROTAC-target) complex formation, allowing the E3 ligase to perform ubiquitination on non-native substrates. Subsequent polyubiquitination of the target protein signals for proteasome dependant degradation. Despite significant strides in PROTAC development, including multiple early phase clinical trials, currently only proteins with known binders can be targeted for degradation. We hypothesise that to improve the target landscape of PROTACs and increase the degradable proteome, we could implement a proteomics-based screen of promiscuous kinase focussed PROTACs. An array of small molecular weight kinase binding PROTACs were synthesised and triaged through proteomics analysis, identifying selective NEK9 and Aurora kinase A (AURKA) hit degraders. Subsequent validation confirmed degradation of NEK9, however, through a neddylation and CRBN independent mechanism. Warhead alterations were explored to determine what component of the degrader conferred the unexpected degradation mechanism. A selective AURKA PROTAC was found to be active at low nM concentrations, affording robust reductions in protein levels over a 2-72 hour treatment. Warhead substitutions to previously published AURKA inhibitors in addition to truncation of the warhead afforded reduced degradation potency. Through the use of small molecular weight warheads, we highlight the ternary complex driven degradation or AURKA, and demonstrate that some PROTACs may not require high affinity warheads. Our approach has the potential to afford degraders of underexplored proteins and provide valuable chemical tools to elucidate protein function.