Discovery of Proteolysis-Targeting Chimera Molecules that Selectively Degrade the IRAK3 Pseudokinase

Abstract

We report the first disclosure of IRAK3 degraders in the scientific literature. Taking advantage of an opportune byproduct obtained during our efforts to identify IRAK4 inhibitors, we identified ready-to-use, selective IRAK3 ligands in our compound collection with the required properties for conversion into proteolysis-targeting chimera (PROTAC) degraders. This work culminated with the discovery of PROTAC 23, which we demonstrated to be a potent and selective degrader of IRAK3 after 16 h in THP1 cells. 23 induced proteasome-dependent degradation of IRAK3 and required both CRBN and IRAK3 binding for activity. We conclude that PROTAC 23 constitutes an excellent in vitro tool with which to interrogate the biology of IRAK3.

Dimeric Structure of the Pseudokinase IRAK3 Suggests an Allosteric Mechanism for Negative Regulation

“…A similar approach has been established for small molecules that disrupt the conformation of the pseudokinase ROR1 ( Sheetz et al., 2020 ). Alternatively, inhibitors could be used to develop PROTACs for targeted degradation, as has been demonstrated recently ( Degorce et al., 2020 ).…”

Targeting key proteins involved in transcriptional regulation for cancer therapy: Current strategies and future prospective

“…Although the PROTACs have been advertised as having significant potential for targeting the “undruggable,” especially the TFs, the majority of reported TF‐targeted PROTACs are highly dependent on previously developed ligands, such as those inhibitors of nuclear receptor LBDs or TF PPIs, stressing the preference for druggable TFs for the development of TF‐targeting PROTACs 16,336–340 . Nevertheless, one important feature of PROTACs that is often ignored is the warhead, which as part of an effective PROTAC can bind with any region of the POI, even those domains that are functionally inactive 223,341–343 . Besides, considerable evidence have proved that even those relatively weak warheads for POIs can still make highly potent PROTACs 219,344,345 .…”

“…16,[336][337][338][339][340] Nevertheless, one important feature of PROTACs that is often ignored is the warhead, which as part of an effective PROTAC can bind with any region of the POI, even those domains that are functionally inactive. 223,[341][342][343] Besides, considerable evidence have proved that even those relatively weak warheads for POIs can still make highly potent PROTACs. 219,344,345 Therefore, the strategy for the expansion of PROTAC warheads should discard the traditional methods of the development of occupancy-based modulators and instead focus on optimizing the binding activity.…”

IRAK1 and IRAK4 as emerging therapeutic targets in hematologic malignancies

“…No inhibitors or degraders of IRAK2 or IRAK3 are currently being vetted for therapeutic application, though an IRAK3-selective PROTAC has recently been developed [ 147 ]. It will be fascinating to see whether targeting IRAK3 demonstrates broad utility in stimulating antitumor immune responses, possibly as part of a combination with checkpoint inhibitors as proposed elsewhere [ 148 ].…”