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Updated: Jan 3, 2026
Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells
Published on: March 3, 2015
Fragment screening for a protein-protein interaction inhibitor to WDR5
Matthew L Dennis1, Benjamin J Morrow, Olan Dolezal1
1Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria 3052, Australia.
Abstract:
The WD40-repeat protein WDR5 scaffolds various epigenetic writers and is a critical component of the mammalian SET/MLL histone methyltransferase complex. Dysregulation of the MLL1 catalytic function is associated with mixed-lineage leukemia, and antagonism of the WDR5-MLL1 interaction by small molecules has been proposed as a therapeutic strategy for MLL-rearranged cancers. Small molecule binders of the "WIN" site of WDR5 that cause displacement from chromatin have been additionally implicated to be of broader use in cancer treatment. In this study, a fragment screen with Surface Plasmon Resonance (SPR) was used to identify a highly ligand-efficient imidazole-containing compound that is bound in the WIN site. The subsequent medicinal chemistry campaign-guided by a suite of high-resolution cocrystal structures with WDR5-progressed the initial hit to a low micromolar binder. One outcome from this study is a moiety that substitutes well for the side chain of arginine; a tripeptide containing one such substitution was resolved in a high resolution structure (1.5 Å) with a binding mode analogous to the native tripeptide. SPR furthermore indicates a similar residence time (k d = ∼0.06 s-1) for these two analogs. This novel scaffold therefore represents a possible means to overcome the potential permeability issues of WDR5 ligands that possess highly basic groups like guanidine. The series reported here furthers the understanding of the WDR5 WIN site and functions as a starting point for the development of more potent WDR5 inhibitors that may serve as cancer therapeutics.
Insights
Researchers developed novel WDR5 WIN site inhibitors for cancer therapy. These compounds target the WDR5-MLL1 interaction, offering a new strategy against MLL-rearranged cancers and potentially other malignancies.
Area of Science:
- Epigenetics
- Medicinal Chemistry
- Structural Biology
Background:
- WDR5 protein is crucial for epigenetic regulation and forms part of the SET/MLL histone methyltransferase complex.
- MLL1 dysregulation is linked to mixed-lineage leukemia, making WDR5-MLL1 interaction antagonism a therapeutic target for MLL-rearranged cancers.
- Small molecules binding WDR5's WIN site can displace it from chromatin, suggesting broader anti-cancer applications.
Purpose of the Study:
- To identify and develop novel small molecule inhibitors targeting the WDR5 WIN site.
- To explore a new scaffold for WDR5 ligands that may overcome permeability issues.
Main Methods:
- Fragment screening using Surface Plasmon Resonance (SPR) to identify initial hits.
- Medicinal chemistry optimization guided by high-resolution co-crystal structures of WDR5.
- SPR analysis to assess binding kinetics and residence time.
Main Results:
- Identified a ligand-efficient imidazole-containing compound binding to the WDR5 WIN site.
- Optimized the initial hit to a low micromolar binder through medicinal chemistry.
- Developed a novel moiety mimicking arginine side chains, with SPR data showing similar residence times to native peptides.
Conclusions:
- The novel WDR5 WIN site scaffold offers a potential solution for permeability challenges associated with existing WDR5 ligands.
- This work advances the understanding of WDR5 WIN site interactions and provides a foundation for developing potent WDR5 inhibitors as cancer therapeutics.
