Fragment merging on the WBM site of scaffold protein WDR5

Two years ago we highlighted work out of Stephen Fesik’s lab at Vanderbilt University describing potent binders of WDR5, a molecular scaffold that interacts with dozens of other proteins. Those molecules bind at the so-called WIN site, disrupting interactions with proteins such as MLL1. Other proteins, such as the famous anticancer target MYC, bind at a completely different location – the WBM site. This is the focus of a new paper from the same group in J. Med. Chem.

The researchers had previously completed a traditional high-throughput screen and identified molecules such as compound 1. These were further optimized, but, as one might expect looking at the chemical structure, the best molecules had “challenging physicochemical profiles.” The researchers turned to fragments for help.

A two-dimensional (¹H-¹⁵N HMQC) NMR screen of ~14,000 fragments yielded 43 hits, all of them quite weak, with dissociation constants in the millimolar range. The tetrapeptide portion of MYC that binds to the WBM site, Ile-Asp-Val-Val, contains a carboxylic acid flanked by lipophilic residues, and as one would expect many hits were hydrophobic acids. Crystal structures were determined for five, and these suggested a fragment merging opportunity.

The carboxylic acid moiety of fragment F2 makes similar interactions with an asparagine residue in WBM as the sulfonamide moiety of compound 1. The resulting merged compound 2a showed improved potency. More than a dozen replacements for the cyclohexyl ring were attempted but none improved potency significantly. Similarly, moving the cycloalkyl group around the 5-membered heterocycle was not productive. However, introducing a methyl sulfone moiety to engage a lysine residue led to a ten-fold boost in potency for compound 12. The molecule disrupted WDR5-MYC complex formation in cell lysates and also reduced MYC binding to target genes in cells.

This is another nice example of using fragment merging to fix problems across early lead series. Of course, compound 12 still has a long way to go; as the researchers note, the phenol is a likely site of glucuronidation. Still, this and the 2018 paper demonstrate the power of fragments to target two separate protein-protein interfaces on the same protein.