An allosteric inhibitor of substrate recognition by the SCFCdc4 ubiquitin ligase

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Abstract
Although general inhibitors of the ubiquitin-proteasome system have been reported, compounds targeting specific ubiquitylation enzymes should be beneficial in clinical applications and basic research. Orlicky et al. present an allosteric inhibitor specific to the yeast SCFCdc4 E3 ligase that prevents binding of the target protein to the WD40 domain of the complex. The specificity of SCF ubiquitin ligase–mediated protein degradation is determined by F-box proteins1,2. We identified a biplanar dicarboxylic acid compound, called SCF-I2, as an inhibitor of substrate recognition by the yeast F-box protein Cdc4 using a fluorescence polarization screen to monitor the displacement of a fluorescein-labeled phosphodegron peptide. SCF-I2 inhibits the binding and ubiquitination of full-length phosphorylated substrates by SCFCdc4. A co-crystal structure reveals that SCF-I2 inserts itself between the β-strands of blades 5 and 6 of the WD40 propeller domain of Cdc4 at a site that is 25 Å away from the substrate binding site. Long-range transmission of SCF-I2 interactions distorts the substrate binding pocket and impedes recognition of key determinants in the Cdc4 phosphodegron. Mutation of the SCF-I2 binding site abrogates its inhibitory effect and explains specificity in the allosteric inhibition mechanism. Mammalian WD40 domain proteins may exhibit similar allosteric responsiveness and hence represent an extensive class of druggable target.