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!
2 comments:
Thanks for posting. Indeed stay tuned! Fun project and terrific team science. Post-doc's KyuOk Jeon and Feng Wang worked tirelessly in driving this series from its inception.
I miss my days working on WDR5-MLL /WDR5-MyC interactions . Great job
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