Fragments vs DYRK1A and DYRK1B: Part 1

The dual-specificity tyrosine-phosphorylation-regulated kinases 1A and 1B (DYRK1A and DYRK1B) belong to a family of five serine/threonine kinases implicated in several cancers as well as Down’s syndrome and other neurodegenerative diseases. For the latter indications in particular, brain penetration would be essential for any inhibitor, just as in the LRRK2 story last week. In a new (open access) J. Med. Chem. paper, Rod Hubbard and collaborators at Vernalis and Servier describe the discovery of a chemical probe.

 

The researchers started by testing their in-house library of 1063 fragments in pools of six, each at 500 µM, in three ligand-detected NMR screens. This resulted in a whopping 166 hits. Crystal structures of the eight most ligand-efficient fragments bound to DYRK1A were obtained, including compound 5. Fragment growing led to compound 16, which bound the kinase 200-fold more tightly. 

 

The crystal structure of compound 16 bound to DYRK1A was compared to structures of other known ligands and suggested the possibility for an alternative binding mode. This led to the synthesis of compound 24, with low nanomolar affinity against both DYRK1A and DYRK1B (only the former is shown in the figure). This compound turned out to be surprisingly unstable in slightly acidic aqueous solution (below pH 5), but replacing the oxygen with a nitrogen fixed this, and further tweaking ultimately led to compound 34.

 

Compound 34 was profiled at 1 µM against a panel of 442 kinases and found to be fairly selective, with only 15 kinases inhibited by at least 50%. It is orally bioavailable in mice, brain penetrant, and inhibited the proliferation of glioblastoma cells, although the potency was significantly attenuated by serum. In a xenograft study the compound caused tumor growth delays and was well-tolerated.

 

This is a nice example of fragment-based lead discovery heavily dependent on structural information. Comparing the binding mode of compound 34 (gray) with that of compound 5 (light blue) reveals the significant shift in binding mode of the initial fragment.

The paper is also a useful reminder of how long it can take for industry research to be published. Work began in 2009, and Rod presented some of it at the CHI FBDD conference in 2019. But this is not the end of the DYRK1A story: stay tuned for next week!