Targeted Degradation of IRAK4 Protein Via Heterobifunctional Small Molecules for Treatment of MYD88 Mutant Lymphoma
Authors: Kelleher Joseph , Audoly Laurent , Campbell Veronica , Chen Jesse , Ji Nan , Kamadurai Hari , Li Henry , Loh Christine , Rong Haojing , Vigil Dominico , Weiss Matt , Yuan Karen , Zhang Yi , Mainolfi Nello 
Published: October 2019

Abstract
Recurrent mutations in the scaffolding protein MYD88 are present in 30-40% of activated B cell diffuse lymphocytic B cell lymphoma (ABC-DLBCL)(Ngo et al. Nature 2011). MYD88 links activated interleukin 1 receptor (IL1R) and Toll-like receptors (TLRs) to downstream effectors by nucleating assembly of the Myddosome, a multi-protein complex containing MYD88, the protein kinases IRAK4 and IRAK1 and the pseudokinase IRAK2, via oligomerization of the N-terminal Death Domains in each of these proteins (Motshwene et al. JBC 2009; Lin, Lo and Wu. Nature 2010). The most prevalent MYD88 mutation, L265P, constitutively activates assembly of the Myddosome, causing IRAK4-dependent NFκB and MAP kinase signaling and leading to lymphoma survival and proliferation (Ngo et al. Nature 2011).
Constitutive activation of the Myddosome has proven to be difficult to drug. MYD88 and IRAK2 lack enzymatic activity and cannot be targeted by conventional small molecule catalytic inhibitors. There are no IRAK1 inhibitors in clinical trials. Specific inhibitors of the kinase activity of IRAK4 have shown limited activity as single agents in preclinical models of MYD88 mutant lymphoma (Lim et al. Blood 2012; Booher et al. Blood 2014). This is consistent with the observations that there is kinase-independent activity of IRAK4 in mediating downstream signals, such as those leading to induction of NFκB (Qin et al. JBC 2004; Fraczek et al. JBC 2008; Sun et al. Sci Signal. 2016). IRAK4 kinase inhibitors thus might not provide optimal blockade of NFκB-dependent tumor survival signals driven by MYD88 mutations in ABC-DLBCL.
Kymera Therapeutics is advancing a new class of drugs based on targeted protein degradation: heterobifunctional molecules that recruit disease-causing proteins to specific E3 ubiquitin ligases, resulting in their ubiquitination and subsequent degradation. We have developed a portfolio of potent and specific degraders of IRAK4 with drug-like properties
Our lead molecules cause potent and specific degradation of IRAK4 in the ABC-DLBCL cell lines OCI-LY10 (MYD88 L265P) and U2932 (MYD88 WT) while showing selective cytotoxic effects on OCI-LY10 vs U2932. The apoptotic response is triggered within 24-48 h in OCI-LY10, demonstrated by appearance of cleaved caspase 3 and PARP. Quantitative proteomic studies show selective degradation of IRAK4 vs five to six thousand other proteins detected in OCI-LY10.
IRAK4 degraders were tested in an OCI-LY10 xenograft model with daily dosing for 28 days, to determine the level of IRAK4 degradation and impact of that degradation on tumor growth in vivo. We observed that degraders mediated decrease in IRAK4 in vivo and produced a statistically significant decrease in tumor growth rate.
Here we will present in vitro and in vivo activity and mechanism of action of our most advanced IRAK4 degraders. These IRAK4 degrader molecules represent a new therapeutic modality and provide an exciting opportunity to treat MYD88 mutation-driven ABC-DLBCL.

Disclosures
Kelleher: Kymera Therapeutics: Employment, Equity Ownership. Audoly:Kymera Therapeutics: Employment, Equity Ownership, Membership on an entity's Board of Directors or advisory committees. Campbell:Kymera Therapeutics: Employment, Equity Ownership. Chen:Kymera Therapeutics: Employment, Equity Ownership. Ji:Kymera Therapeutics: Employment, Equity Ownership. Kamadurai:Kymera Therapeutics: Employment, Equity Ownership. Li:Kymera Therapeutics: Employment, Equity Ownership. Loh:Kymera Therapeutics: Employment, Equity Ownership. Rong:Kymera Therapeutics: Employment, Equity Ownership. Vigil:Kymera Therapeutics: Employment, Equity Ownership. Weiss:Kymera Therapeutics: Employment, Equity Ownership. Yuan:Kymera Therapeutics: Employment, Equity Ownership. Zhang:Kymera Therapeutics: Employment, Equity Ownership. Mainolfi:Kymera Therapeutics: Employment, Equity Ownership.