Ye, T.; Alamgir, A.; Robertus, C.; Colina, D.; Monticello, C.; Donahue, T. C.; Hong, L.; Vincoff, S.; Goel, S.; Fekkes, P.; Camargo, L. M.; Lam, K.; Heyes, J.; Putnam, D.; Alabi, C. A.; Chatterjee, P.; DeLisa, M. P.

Aberrant activation of Wnt signaling results in unregulated accumulation of cytosolic {beta}-catenin, which subsequently enters the nucleus and promotes transcription of genes that contribute to cellular proliferation and malignancy. Here, we sought to eliminate pathogenic {beta}-catenin from the cytosol using designer ubiquibodies (uAbs), chimeric proteins composed of an E3 ubiquitin ligase and a target-binding domain that redirect intracellular proteins to the proteasome for degradation. To accelerate uAb development, we leveraged a protein language model (pLM)-driven algorithm called SaLT&PepPr to computationally design \"guide\" peptides with affinity for {beta}-catenin, which were subsequently fused to the catalytic domain of a human E3 called C-terminus of Hsp70-interacting protein (CHIP). Expression of the resulting peptide-guided uAbs in colorectal cancer cells led to the identification of several designs that significantly reduced the abnormally stable pool of free {beta}-catenin in the cytosol and nucleus while preserving the normal membrane-associated subpopulation. This selective knockdown of pathogenic {beta}-catenin suppressed Wnt/{beta}-catenin signaling and impaired tumor cell survival and proliferation. Furthermore, one of the best degraders selectively {beta}-catenin levels in livers of BALB/C mice following delivery as a lipid nanoparticle (LNP)-encapsulated mRNA. Collectively, these findings reveal the unique ability of uAbs to selectively eradicate abnormal proteins in vitro and in vivo and open the door to peptide-programmable biologic modulators of other disease-causing proteins.