[PDF][PDF] Lessons in PROTAC design from selective degradation with a promiscuous warhead

DP Bondeson, BE Smith, GM Burslem… - Cell chemical …, 2018 - cell.com
DP Bondeson, BE Smith, GM Burslem, AD Buhimschi, J Hines, S Jaime-Figueroa, J Wang…
Cell chemical biology, 2018cell.com
Inhibiting protein function selectively is a major goal of modern drug discovery. Here, we
report a previously understudied benefit of small molecule proteolysis-targeting chimeras
(PROTACs) that recruit E3 ubiquitin ligases to target proteins for their ubiquitination and
subsequent proteasome-mediated degradation. Using promiscuous CRBN-and VHL-
recruiting PROTACs that bind> 50 kinases, we show that only a subset of bound targets is
degraded. The basis of this selectivity relies on protein-protein interactions between the E3 …
Summary
Inhibiting protein function selectively is a major goal of modern drug discovery. Here, we report a previously understudied benefit of small molecule proteolysis-targeting chimeras (PROTACs) that recruit E3 ubiquitin ligases to target proteins for their ubiquitination and subsequent proteasome-mediated degradation. Using promiscuous CRBN- and VHL-recruiting PROTACs that bind >50 kinases, we show that only a subset of bound targets is degraded. The basis of this selectivity relies on protein-protein interactions between the E3 ubiquitin ligase and the target protein, as illustrated by engaged proteins that are not degraded as a result of unstable ternary complexes with PROTAC-recruited E3 ligases. In contrast, weak PROTAC:target protein affinity can be stabilized by high-affinity target:PROTAC:ligase trimer interactions, leading to efficient degradation. This study highlights design guidelines for generating potent PROTACs as well as possibilities for degrading undruggable proteins immune to traditional small-molecule inhibitors.
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