Just over a year ago we
highlighted work out of A*STAR describing a series of inhibitors for the cancer
target protein kinase C iota (PKC-ι). We ended by mentioning that the group had
a second undisclosed series. This has now been described in ACS Med. Chem. Lett. by Jacek
Kwiatkowski, Alvin Hung, and colleagues.
Compound 1 was among the fragment
hits from the high-concentration biochemical screen previously mentioned.
Although the researchers did not have a crystal structure, they assumed that
the aminopyridine moiety was acting as a hinge binder, which helped them
produce a computational model. A simple replacement of the phenyl ring with a
pyridyl ring led to compound 2, with a satisfying improvement in potency and
ligand efficiency.
As it turned out lots of diverse
moieties could be substituted in place of the phenyl, including indoles and
phenols. This promiscuity led the researchers to propose that the added
heteroatom was making a water-mediated hydrogen bond to the protein; the water
could rotate to either accept or donate a hydrogen bond to the ligand.
Unfortunately, further growing from this ring did not improve potency.
Returning to their model, the
researchers sought to grow from the aminopyridine ring towards a hydrophobic
region of the protein. Adding a phenyl group (compound 16) was tolerated,
though did not improve the affinity. However, the model suggested that an
aspartic acid might be accessible from the phenyl ring, and indeed adding a
positively charged piperazine as in compound 19 led to a nearly 100-fold boost
in affinity. Unfortunately, the compound’s permeability (measured in a Caco-2
assay) was low, and perhaps because of this it showed only weak
antiproliferative activity against hepatocellular carcinoma cells.
Ultimately the researchers were
able to solve the cocrystal structure of compound 19 with PKC-ι, which mostly
confirmed the model: the aminopyridine interacts with the hinge region, and the
second pyridyl moiety likely makes a water-mediated hydrogen-bond with the
protein, although the low resolution of the structure makes this somewhat
ambiguous. The added piperazine appears to interact with a different aspartic
acid than the one targeted.
Although there is more work to be
done, it is notable that the researchers were able to optimize a fairly weak
fragment to a sub-micromolar compound in the absence of experimental structural
information. As they note, “while the empirical SAR remained our ultimate guide
in fragment optimization, the model aided the successful design of potent
inhibitors.” This is another nice example supporting our 2017 poll results, and recent review, that
drug hunters can successfully advance fragments without NMR or
crystallography.
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