Fragments score a win against WDR5-WIN

Protein-protein interactions (PPIs) can be difficult targets for multiple reasons. First, the contacts often cover large, flattish areas with few “ligandable” pockets. Second, they can involve multiple proteins; imagine trying to disrupt a huge multicomponent machine with a little widget. The protein WDR5 falls into the second category. It serves as a scaffold around which other proteins assemble to regulate epigenetics. One of these proteins, MLL1, is implicated in certain leukemias and binds to WDR5 through the WDR5 INteraction (WIN) motif, making this protein-protein interaction an intriguing anti-cancer target. In a recent paper in J. Med. Chem., Stephen Fesik and colleagues at Vanderbilt University describe their efforts towards this target.

Unlike some PPIs, the WIN motif does contain a nice little pocket which normally recognizes arginine residues. However, since the highly basic guanidine moiety of arginine is undesirable in drugs, the researchers conducted a fragment screen to find new WIN-site binders. A two-dimensional (¹H-¹⁵N HMQC) NMR screen of a large fragment library (>13,800 fragments, more than the majority of respondents in the poll to the right) identified 47 hits that produced similar spectral changes as a peptide that binds in the WIN site. Compound F-1 was the most potent.

A crystal structure of compound F-1 bound to WDR5 revealed that the imidazole moiety binds in the same deep pocket normally occupied by the arginine side chain, with the phenyl ring pointing up out of the pocket. Initial growing off the phenyl ring into nearby hydrophobic pockets produced more potent compounds, but at best these were still micromolar binders. The researchers had more success by targeting a slightly more distant pocket with compounds such as 4a and subsequently compound 4i. A crystal structure of compound 4a bound to WDR5 suggested that the biologically active conformation might not be the lowest energy conformation of the free molecule. Introducing a ring to restrict the conformation led to more potent molecules such as 6e, with sub-nanomolar affinity.

Unfortunately, though potent in biochemical assays, compound 6e and related molecules were about 2800-fold less potent in cell-based assays. The compound is cell permeable and not effluxed, so the disconnect must be due to something else – perhaps the multiple other proteins in the cellular environment. Anyone who has spent much time doing medicinal chemistry will have encountered frustrating situations like this. Perhaps a new chemotype is needed, or perhaps the compounds need to be made even more potent. Indeed, several years ago the Fesik group reported nanomolar binders of MCL-1, but it was not until they improved affinity to picomolar that they saw good cell potency. Stay tuned!