19 September 2016

Fragments vs GSK3β via DOS

Diversity-oriented synthesis, or DOS, enables the rapid and systematic synthesis of multiple related compounds from small sets of molecules and reactants. By creatively choosing the chemistry, DOS practitioners can selectively generate all diastereomers and produce more complicated molecules than are usually found in commercial screening collections. While much of the attention has been focused on larger molecules, DOS offers clear applications for addressing the chemistry challenges of FBLD. This is illustrated nicely by a recent paper in ACS Med. Chem. Lett. by Alvin Hung, Damian Young, and collaborators at the Broad Institute, Harvard, the Albert Einstein College of Medicine, A-STAR, and Baylor College of Medicine.

The researchers started with a very small (86 fragment) library, which Damian is in the process of expanding to 3000 compounds. Differential scanning fluorimetry was used to screen the molecules against the kinase GSK3β, which is implicated in cancer and Alzheimer’s disease. Three related fragments slightly increased the melting temperature of the enzyme, of which the simplest was compound 1S.

One nice feature of DOS is that – by design – analog synthesis is straightforward. Thus the researchers made a dozen or so derivatives to flesh out the SAR. This revealed that the enantiomer, compound 1R, stabilized the protein even more than the initial hit. STD and WaterLOGSY NMR confirmed binding, and isothermal titration calorimetry (ITC) revealed modest but measurable affinity. Synthesis of a few additional analogs led to compound 15R, with low micromolar affinity as assessed both by ITC and an enzymatic assay. Ligand efficiency was also good, though the ligand efficiency by atom number (LEAN) values of the molecules do not quite meet Teddy’s Safran Zunft Challenge – a wager due to be settled at FBLD 2016 in a few weeks.

A key selling point of DOS is that, by accelerating chemistry, it enables optimization even without structural information. In this case the researchers suspected that the fragment binds in the hinge region of the kinase, and subsequent crystallography revealed that this was indeed so. Interestingly though, the quality of the crystal structure was insufficient to unambiguously place compound 1R; perhaps it binds in multiple conformations. The crystal structure of compound 15R, on the other hand, was clear.

Of course, there is still a long way to go for this series, and it remains to be seen how broadly applicable DOS will be for FBLD. I look forward to seeing additional examples.

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