8G3C

Crystal structure of human WDR5 in complex with N-[(2'-cyano[1,1'-biphenyl]-4-yl)methyl]-3-hydroxy-6-methyl-4-oxo-4H-pyran-2-carboxamide (compound 1, WDR5-MYC PPI inhibitor)

Summary for 8G3C

• Entry DOI: 10.2210/pdb8g3c/pdb
• Descriptor: WD repeat-containing protein 5, N-[(2'-cyano[1,1'-biphenyl]-4-yl)methyl]-3-hydroxy-6-methyl-4-oxo-4H-pyran-2-carboxamide (3 entities in total)
• Functional Keywords: wdr5, wbm, myc, small molecule, oncoprotein-inhibitor complex, oncoprotein/inhibitor
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 34751.35

Authors

Zhao, M. (deposition date: 2023-02-07, release date: 2023-06-28, Last modification date: 2023-10-25)

Primary citation

Ding, J.,Liu, L.,Chiang, Y.L.,Zhao, M.,Liu, H.,Yang, F.,Shen, L.,Lin, Y.,Deng, H.,Gao, J.,Sage, D.R.,West, L.,Llamas, L.A.,Hao, X.,Kawatkar, S.,Li, E.,Jain, R.K.,Tallarico, J.A.,Canham, S.M.,Wang, H.
Discovery and Structure-Based Design of Inhibitors of the WD Repeat-Containing Protein 5 (WDR5)-MYC Interaction.
J.Med.Chem., 66:8310-8323, 2023

PubMed Abstract: WDR5 is a critical chromatin cofactor of MYC. WDR5 interacts with MYC through the WBM pocket and is hypothesized to anchor MYC to chromatin through its WIN site. Blocking the interaction of WDR5 and MYC impairs the recruitment of MYC to its target genes and disrupts the oncogenic function of MYC in cancer development, thus providing a promising strategy for the treatment of MYC-dysregulated cancers. Here, we describe the discovery of novel WDR5 WBM pocket antagonists containing a 1-phenyl dihydropyridazinone 3-carboxamide core that was identified from high-throughput screening and subsequent structure-based design. The leading compounds showed sub-micromolar inhibition in the biochemical assay. Among them, compound can disrupt WDR5-MYC interaction in cells and reduce MYC target gene expression. Our work provides useful probes to study WDR5-MYC interaction and its function in cancers, which can also be used as the starting point for further optimization toward drug-like small molecules.

PubMed: 37307526
DOI: 10.1021/acs.jmedchem.3c00787

Experimental method

X-RAY DIFFRACTION (1.8 Å)