High-Affinity Peptidomimetic Inhibitors of the DCN1-UBC12 Protein-Protein Interaction
Haibin Zhou, Weihua Zhou, Bing Zhou
1Institute of Translational Medicine , Zhejiang University School of Medicine , Hangzhou , Zhejiang 310029 , China.
Abstract:
The Cullin-RING ligases (CRLs) regulate the turnover of approximately 20% of the proteins in mammalian cells and are emerging therapeutic targets in human diseases. The activation of CRLs requires the neddylation of their cullin subunit, which is controlled by an activation complex consisting of Cullin-RBX1-UBC12-NEDD8-DCN1. Herein, we describe the design, synthesis, and evaluation of peptidomimetics targeting the DCN1-UBC12 protein-protein interaction. Starting from a 12-residue UBC12 peptide, we have successfully obtained a series of peptidomimetic compounds that bind to DCN1 protein with KD values of <10 nM. Determination of a cocrystal structure of a potent peptidomimetic inhibitor complexed with DCN1 provides the structural basis for their high-affinity interaction. Cellular investigation of one potent DCN1 inhibitor, compound 36 (DI-404), reveals that it effectively and selectively inhibits the neddylation of cullin 3 over other cullin members. Further optimization of DI-404 may yield a new class of therapeutics for the treatment of human diseases in which cullin 3 CRL plays a key role.
Insights
Researchers developed novel peptidomimetics targeting the DCN1-UBC12 interaction, crucial for Cullin-RING ligase (CRL) activation. These compounds effectively inhibit neddylation, offering potential new therapeutics for diseases involving CRLs.
Area of Science:
- Biochemistry
- Molecular Biology
- Drug Discovery
Background:
- Cullin-RING ligases (CRLs) control protein turnover, impacting ~20% of mammalian proteins.
- CRLs are critical therapeutic targets for various human diseases.
- CRL activation depends on neddylation, regulated by the Cullin-RBX1-UBC12-NEDD8-DCN1 complex.
Purpose of the Study:
- To design, synthesize, and evaluate peptidomimetics targeting the DCN1-UBC12 protein-protein interaction.
- To identify potent inhibitors of CRL activation.
- To explore therapeutic potential for diseases involving CRLs.
Main Methods:
- Peptide design and synthesis based on a UBC12 peptide.
- Biochemical assays to evaluate binding affinity (KD) to DCN1.
- Co-crystallography to determine inhibitor-DCN1 complex structure.
- Cellular assays to assess inhibition of cullin neddylation.
Main Results:
- Developed peptidomimetics with high affinity for DCN1 (KD <10 nM).
- Determined the co-crystal structure of a DCN1-inhibitor complex, elucidating the binding mechanism.
- Identified compound 36 (DI-404) as a potent and selective inhibitor of cullin 3 neddylation.
Conclusions:
- Peptidomimetics targeting the DCN1-UBC12 interaction are effective CRL inhibitors.
- DI-404 demonstrates selective inhibition of cullin 3 neddylation.
- Optimized DI-404 analogs may represent a new therapeutic strategy for cullin 3-dependent diseases.
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