Linker-rigidified VHL homodimerizers convert degraders into stabilizers of non-ubiquitinable ternary complexes

Abstract

Protein degraders recruit E3 ligases to targets for ubiquitination and subsequent proteasomal degradation. Efficient degradation typically correlates with long-lived ternary complexes that position target lysines for productive ubiquitination. Here, we determine a cryo-EM structure of the Cullin 2 RING VHL (CRL2VHL) ligase dimerized by the VHL homo-PROTAC CM11, wherein one CRLVHL acts as the ligase and a second VHL as the neo-substrate. Guided by this structure, we design side-by-side, linker-rigidified VHL homodimerizers that bias the relative VHL orientation away from the E2[~]Ub active site, contrasting the flexible, head-to-head PEG linkage of CM11. Biophysical binding and in vitro ubiquitination assays show that these compounds form stable, long-lived and compact ternary complexes that are incompatible with VHL cross-ubiquitination. In cells, the compounds stabilize VHL and concomitantly inhibit it to elevate HIF-1 levels. Thus, a stable ternary complex can be non-productive for ubiquitination, and linker architecture can reprogram degraders into stabilizers by controlling target ubiquitinability.