7ZWU image
Entry Detail
PDB ID:
7ZWU
Keywords:
Title:
Crystal structure of human BCL6 BTB domain in complex with compound 15
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2022-05-19
Release Date:
2022-11-16
Method Details:
Experimental Method:
Resolution:
1.56 Å
R-Value Free:
0.17
R-Value Work:
0.15
R-Value Observed:
0.15
Space Group:
P 61 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:B-cell lymphoma 6 protein
Chain IDs:A
Chain Length:128
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:ALA-TRP-VAL-ILE-PRO-ALA
Chain IDs:B
Chain Length:6
Number of Molecules:1
Biological Source:synthetic construct
Primary Citation
Discovering cell-active BCL6 inhibitors: effectively combining biochemical HTS with multiple biophysical techniques, X-ray crystallography and cell-based assays.
Sci Rep 12 18633 18633 (2022)
PMID: 36329085 DOI: 10.1038/s41598-022-23264-z

Abstact

By suppressing gene transcription through the recruitment of corepressor proteins, B-cell lymphoma 6 (BCL6) protein controls a transcriptional network required for the formation and maintenance of B-cell germinal centres. As BCL6 deregulation is implicated in the development of Diffuse Large B-Cell Lymphoma, we sought to discover novel small molecule inhibitors that disrupt the BCL6-corepressor protein-protein interaction (PPI). Here we report our hit finding and compound optimisation strategies, which provide insight into the multi-faceted orthogonal approaches that are needed to tackle this challenging PPI with small molecule inhibitors. Using a 1536-well plate fluorescence polarisation high throughput screen we identified multiple hit series, which were followed up by hit confirmation using a thermal shift assay, surface plasmon resonance and ligand-observed NMR. We determined X-ray structures of BCL6 bound to compounds from nine different series, enabling a structure-based drug design approach to improve their weak biochemical potency. We developed a time-resolved fluorescence energy transfer biochemical assay and a nano bioluminescence resonance energy transfer cellular assay to monitor cellular activity during compound optimisation. This workflow led to the discovery of novel inhibitors with respective biochemical and cellular potencies (IC50s) in the sub-micromolar and low micromolar range.

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Primary Citation of related structures