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Targeting Cullin-RING E3 ubiquitin ligases for drug discovery: structure, assembly and small-molecule modulation.

Bulatov E, Ciulli A - Biochem. J. (2015)

Bottom Line: In the present review, we provide an account of the assembly and structure of CRL complexes, and outline the current state of the field in terms of available knowledge of small-molecule inhibitors and modulators of CRL activity.A comprehensive overview of the reported crystal structures of CRL subunits, components and full-size complexes, alone or with bound small molecules and substrate peptides, is included.This information is providing increasing opportunities to aid the rational structure-based design of chemical probes and potential small-molecule therapeutics targeting CRLs.

View Article: PubMed Central - PubMed

Affiliation: *College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.

ABSTRACT
In the last decade, the ubiquitin-proteasome system has emerged as a valid target for the development of novel therapeutics. E3 ubiquitin ligases are particularly attractive targets because they confer substrate specificity on the ubiquitin system. CRLs [Cullin-RING (really interesting new gene) E3 ubiquitin ligases] draw particular attention, being the largest family of E3s. The CRLs assemble into functional multisubunit complexes using a repertoire of substrate receptors, adaptors, Cullin scaffolds and RING-box proteins. Drug discovery targeting CRLs is growing in importance due to mounting evidence pointing to significant roles of these enzymes in diverse biological processes and human diseases, including cancer, where CRLs and their substrates often function as tumour suppressors or oncogenes. In the present review, we provide an account of the assembly and structure of CRL complexes, and outline the current state of the field in terms of available knowledge of small-molecule inhibitors and modulators of CRL activity. A comprehensive overview of the reported crystal structures of CRL subunits, components and full-size complexes, alone or with bound small molecules and substrate peptides, is included. This information is providing increasing opportunities to aid the rational structure-based design of chemical probes and potential small-molecule therapeutics targeting CRLs.

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Related in: MedlinePlus

Crystal structure of Skp1–Cdc4–SCF-I2 complex (PDB code 3MKS)Left: the Cdc4–Skp1 protein complex and bound SCF-I2 ligand are shown as molecular surface representations. Right: the expanded inset shows the key residues of Cdc4 (light blue carbons) forming the protein interface that binds SCF-I2 and the ligand chemical structure (yellow carbons); oxygen atoms are in red, and nitrogen atoms are in blue.
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Figure 5: Crystal structure of Skp1–Cdc4–SCF-I2 complex (PDB code 3MKS)Left: the Cdc4–Skp1 protein complex and bound SCF-I2 ligand are shown as molecular surface representations. Right: the expanded inset shows the key residues of Cdc4 (light blue carbons) forming the protein interface that binds SCF-I2 and the ligand chemical structure (yellow carbons); oxygen atoms are in red, and nitrogen atoms are in blue.

Mentions: Although many of the CRL inhibitors directly target the substrate–receptor interface, there is an interesting example of small molecule SCF-I2 that exerts long-range allosteric modulation of the yeast F-box protein Cdc4 to disrupt its interaction with substrate Sic1 and prevent subsequent ubiquitination of Sic1 by CRL1Cdc4 [159] (Figure 5). The biplanar dicarboxylic acid ligand SCF-I2 was discovered by screening a library of ~50000 compounds using an FP (fluorescence polarization) assay. The compound constitutes a racemic mixture; however, only the (R)-(+) enantiomer was found to bind Cdc4. Structural studies revealed that SCF-I2 intercalates between adjacent blades 5 and 6 of the conserved WD40 β-propeller domain of Cdc4 in such a way that it induces formation of its own binding pocket located at ~25 Å (1 Å=0.1 nm) distance from the substrate-binding site. Interestingly, this pocket is not present in the apo-form of the Skp1–Cdc4 complex [185]. SCF-I2 was selective towards Cdc4 and showed only little effect on related F-box proteins including the human orthologue of Cdc4 (Fbw7) and the yeast homologous protein Met30. Although SCF-I2 demonstrated significant activity in vitro, it failed to inhibit Cdc4 in vivo probably because of its poor cell permeability. The authors propose that similar allosteric approaches could be employed for developing inhibitors of other WD40 domain proteins that serve as receptor subunits within many CRLs.


Targeting Cullin-RING E3 ubiquitin ligases for drug discovery: structure, assembly and small-molecule modulation.

Bulatov E, Ciulli A - Biochem. J. (2015)

Crystal structure of Skp1–Cdc4–SCF-I2 complex (PDB code 3MKS)Left: the Cdc4–Skp1 protein complex and bound SCF-I2 ligand are shown as molecular surface representations. Right: the expanded inset shows the key residues of Cdc4 (light blue carbons) forming the protein interface that binds SCF-I2 and the ligand chemical structure (yellow carbons); oxygen atoms are in red, and nitrogen atoms are in blue.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4403949&req=5

Figure 5: Crystal structure of Skp1–Cdc4–SCF-I2 complex (PDB code 3MKS)Left: the Cdc4–Skp1 protein complex and bound SCF-I2 ligand are shown as molecular surface representations. Right: the expanded inset shows the key residues of Cdc4 (light blue carbons) forming the protein interface that binds SCF-I2 and the ligand chemical structure (yellow carbons); oxygen atoms are in red, and nitrogen atoms are in blue.
Mentions: Although many of the CRL inhibitors directly target the substrate–receptor interface, there is an interesting example of small molecule SCF-I2 that exerts long-range allosteric modulation of the yeast F-box protein Cdc4 to disrupt its interaction with substrate Sic1 and prevent subsequent ubiquitination of Sic1 by CRL1Cdc4 [159] (Figure 5). The biplanar dicarboxylic acid ligand SCF-I2 was discovered by screening a library of ~50000 compounds using an FP (fluorescence polarization) assay. The compound constitutes a racemic mixture; however, only the (R)-(+) enantiomer was found to bind Cdc4. Structural studies revealed that SCF-I2 intercalates between adjacent blades 5 and 6 of the conserved WD40 β-propeller domain of Cdc4 in such a way that it induces formation of its own binding pocket located at ~25 Å (1 Å=0.1 nm) distance from the substrate-binding site. Interestingly, this pocket is not present in the apo-form of the Skp1–Cdc4 complex [185]. SCF-I2 was selective towards Cdc4 and showed only little effect on related F-box proteins including the human orthologue of Cdc4 (Fbw7) and the yeast homologous protein Met30. Although SCF-I2 demonstrated significant activity in vitro, it failed to inhibit Cdc4 in vivo probably because of its poor cell permeability. The authors propose that similar allosteric approaches could be employed for developing inhibitors of other WD40 domain proteins that serve as receptor subunits within many CRLs.

Bottom Line: In the present review, we provide an account of the assembly and structure of CRL complexes, and outline the current state of the field in terms of available knowledge of small-molecule inhibitors and modulators of CRL activity.A comprehensive overview of the reported crystal structures of CRL subunits, components and full-size complexes, alone or with bound small molecules and substrate peptides, is included.This information is providing increasing opportunities to aid the rational structure-based design of chemical probes and potential small-molecule therapeutics targeting CRLs.

View Article: PubMed Central - PubMed

Affiliation: *College of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K.

ABSTRACT
In the last decade, the ubiquitin-proteasome system has emerged as a valid target for the development of novel therapeutics. E3 ubiquitin ligases are particularly attractive targets because they confer substrate specificity on the ubiquitin system. CRLs [Cullin-RING (really interesting new gene) E3 ubiquitin ligases] draw particular attention, being the largest family of E3s. The CRLs assemble into functional multisubunit complexes using a repertoire of substrate receptors, adaptors, Cullin scaffolds and RING-box proteins. Drug discovery targeting CRLs is growing in importance due to mounting evidence pointing to significant roles of these enzymes in diverse biological processes and human diseases, including cancer, where CRLs and their substrates often function as tumour suppressors or oncogenes. In the present review, we provide an account of the assembly and structure of CRL complexes, and outline the current state of the field in terms of available knowledge of small-molecule inhibitors and modulators of CRL activity. A comprehensive overview of the reported crystal structures of CRL subunits, components and full-size complexes, alone or with bound small molecules and substrate peptides, is included. This information is providing increasing opportunities to aid the rational structure-based design of chemical probes and potential small-molecule therapeutics targeting CRLs.

Show MeSH
Related in: MedlinePlus