Inhibitor-induced supercharging of kinase turnover via endogenous proteolytic circuits

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Inhibitor-induced supercharging of kinase turnover via endogenous proteolytic circuits

Authors

Scholes, N. S.; Bertoni, M.; Comajuncosa-Creus, A.; Kladnik, K.; Frommelt, F.; Hinterndorfer, M.; Razumkov, H.; Prokofeva, P.; Schwalm, M. P.; Imrichova, H.; Barone, E.; Schätz, C.; Rukavina, A.; Koren, A.; Kubicek, S.; Knapp, S.; Gray, N. S.; Superti-Furga, G.; Küster, B.; Aloy, P.; Winter, G. E.

Abstract

Targeted protein degradation has emerged as a promising new pharmacologic strategy. Traditionally, it relies on small molecules that induce proximity between a target protein and an E3 ubiquitin ligase to prompt target ubiquitination and degradation by the proteasome. Sporadic reports indicated that ligands designed to inhibit a target can also induce its destabilization. Among others, this has repeatedly been observed for kinase inhibitors. However, we lack an understanding of frequency, generalizability, and mechanistic underpinnings of these phenomena. To address this knowledge gap, we established dynamic abundance profiles of 98 kinases after cellular perturbations with 1570 kinase inhibitors, revealing 160 selective instances of inhibitor-induced kinase destabilization. Kinases prone to degradation are frequently annotated as HSP90 clients, thus affirming chaperone deprivation as an important route of destabilization. However, detailed investigation of inhibitor-induced degradation of LYN, BLK and RIPK2 revealed a differentiated, common mechanistic logic where inhibitors function by inducing a kinase state that is more efficiently cleared by endogenous degradation mechanisms. Mechanistically, effects can manifest by ligand-induced changes in cellular activity, localization, or multimerization and can be prompted by direct target engagement or network effects. In sum, our data indicates that inhibitor-induced kinase degradation is a frequent event and positions supercharging of endogenous degradation circuits as an alternative to classical proximity-inducing degraders.

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