12 April 2021

Fragment merging on c-MET

Fragment-based inhibitors of kinases are legion, particularly those that bind in the so-called hinge region where the adenine of ATP normally sits. However, even among these there are many different flavors of inhibitors. In particular, about 10 kinases can adopt a “folded P-loop” conformation, in which the phosphate-binding loop collapses into the ATP binding site. This was the focus of a recent open-access paper in ACS Med. Chem. Lett. by Gavin Collie and colleagues at AstraZeneca.
The researchers were interested in the oncology target c-MET. A ligand-based NMR screen of 1150 fragments (in pools of 6 at 200 ┬ÁM each) yielded a 6% hit rate, of which 20 confirmed by SPR. Crystallography was attempted unsuccessfully on most of these, but compound 1 was found to snuggle into the active site with the protein in the folded P-loop conformation.
A computational similarity search of AstraZeneca’s internal library identified compound 2, which crystallography revealed to bind in a similar manner, with two hydrogen bonds to the hinge region and the benzyl group buried in a hydrophobic pocket. A second similarity search of the library – this time based on compound 2 – identified compound 3. Crystallography confirmed that the core azaindole moieties of compounds 2 and 3 overlay, and thus fragment merging was attempted.

The resulting compound 5 bound as expected. This prompted yet another computational search of the internal library, and after a bit of medicinal chemistry compound 7 was identified as a mid-nanomolar inhibitor with low micromolar cell-based activity. Crystallography revealed that it too binds to the folded P-loop conformation of c-MET.
Because the folded P-loop conformation is rare among kinases, the researchers hoped that the resulting molecule would be selective. Unfortunately, when profiled against a panel of 140 kinases at the low concentration of 100 nM, 27 of them were inhibited by at least 60%. This is perhaps not surprising given the 7-azaindole core, which has been found to bind to more than 90 kinases, though some compounds containing this moiety are selective.
Nonetheless, this paper is a nice example of structure-guided fragment merging. A cynic could point out that had the researchers screened the entire AstraZeneca compound collection they likely would have identified molecules very similar to compound 7 anyway, but this may have cost more and would not be an option at smaller organizations without million-compound libraries. And the approach is useful for more difficult targets for which high-affinity molecules may not exist – yet.

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