Covalent Reprogramming of Kinase Binders to Modulate Protein Abundance

ABSTRACT Small molecules that modulate protein abundance through induced proximity expand the landscape beyond traditional inhibition. Here, we explore how introducing covalent or latent electrophilic groups into a multi‐kinase binder scaffold reprograms protein abundance within the kinase family. Using the broad‐spectrum kinase ligand TL13‐87 as a template, we synthesize analogs bearing α‐chloroacetamide, acrylamide, or terminal amine groups. Quantitative proteomics reveals that while most analogs have minimal global impact, MKI‐AA, a multi‐kinase inhibitor bearing an acrylamide warhead, uniquely stabilizes Aurora kinase A (AURKA). Mechanistic studies show that MKI‐AA acts post‐translationally to suppress AURKA ubiquitination and proteasomal degradation. Proteomic mapping of MKI‐AA‐induced AURKA interactors reveals changes in protein associations upon treatment, providing mechanistic insights into how MKI‐AA influences AURKA stability. Intriguingly, adding a short linker to MKI‐AA converts it from a stabilizer into a degrader, highlighting how subtle structural variations can invert functional outcomes.