IAP-based biodegraders can convert necroptosis to apoptosis and eliminate cancer driving protein complexes

Targeted protein degradation holds significant therapeutic potential. Intrabodies, such as nanobodies and monobodies, can degrade intracellular proteins via fusion to E3 ubiquitin ligases. Here, we developed multi-targeting biodegrader intrabodies using the RING domain of inhibitor of apoptosis (IAP) proteins, or the IAP-binding motif from Smac/DIABLO. When fused to monobodies recognizing the necroptosis effector mixed lineage kinase domain-like pseudokinase (MLKL), IAP-based intrabodies degraded both MLKL and IAPs, blocking necroptosis and sensitizing cells to apoptosis. The potent degradative ability of the IAP RING was demonstrated via fusion to distinct intrabodies, with those targeting RAS enabling IAP and RAS proto-oncogenes to be concurrently eliminated. Quantitative proteomics of select IAP-based intrabodies revealed additional degradation of the BAF chromatin-remodelling complex, uncovering IAP and BAF co-dependencies in cancer. This work establishes IAP-based intrabodies as a modular class of protein biodegraders, whose multi-targeting capacity can enable the redirection of damaging necrotic cell death toward apoptosis, and the eradication of cancer-drivers.