Inhibitor-induced supercharging of kinase turnover via endogenous proteolytic circuits

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: July 10, 2024

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

Language: Английский

Structural basis for C-degron selectivity across KLHDCX family E3 ubiquitin ligases

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Nov. 15, 2024

Abstract Specificity of the ubiquitin-proteasome system depends on E3 ligase-substrate interactions. Many such pairings depend ligases binding to peptide-like sequences - termed N- or C-degrons at termini substrates. However, our knowledge structural features distinguishing closely related C-degron substrate-E3 is limited. Here, by systematically comparing ubiquitylation activities towards a suite common model substrates, and defining interactions biochemistry, crystallography, cryo-EM, we reveal principles recognition across KLHDCX family Cullin-RING (CRLs). First, motif these anchors substrate’s C-terminus. distinct locations this C-terminus anchor in different blades KLHDC2, KLHDC3, KLHDC10 β-propellers establishes relative positioning molecular environments for substrate C-termini. Second, data show KLHDC3 has pre-formed pocket establishing preference an Arg Gln preceding C-terminal Gly, whereas conformational malleability contributes KLHDC10’s varying adjacent Finally, additional non-consensus interactions, mediated grooves and/or distal propeller surfaces globular domains, can substantially impact ubiquitylatability. Overall, combinatorial mechanisms determining specificity plasticity KLDCX-family ligases.

Language: Английский