Fragments vs DYRK1A and DYRK1B: Part 2

Last week we highlighted work out of Vernalis and Servier in which fragment-based methods were used to identify potent and selective inhibitors of DYRK1A and 1B, potential targets for cancer and neurodegenerative diseases. The NMR screens yielded 166 hits, only one of which was advanced in that paper. A second J. Med. Chem. paper by Andras Kotschy and collaborators describes the optimization of another fragment.

 

Compound 1 is a whoppingly potent fragment with impressive ligand efficiency. If you’ve ever worked on kinases you probably think you know how it binds, as the diaminopyrimidine moiety is a common hinge-binding motif. In fact, crystallography revealed that the molecule binds in a completely different orientation and that the methoxy group makes a single hydrogen bond to the hinge amide NH. Cyclizing the molecule led to compound 10, with a satisfying boost in affinity.

 

Unfortunately, compound 10 was also a potent inhibitor of the kinase CKD9. To gain selectivity, the researchers took advantage of the fact that one of the backbone carbonyl oxygens in the hinge adopts an unusual orientation in DYRK1A, making room for the methyl group in compound 33. Next, the researchers replaced the benzofuran core for reasons of “synthetic tractability, metabolic stability, and freedom to operate.” This exercise ultimately led to compound 40.

 

This compound was profiled against 442 kinases and found to be quite selective, with only 8 kinases significantly inhibited at 1 µM. One of these was the related kinase DYRK2, but further growing led to selective compound 58. An overlay of the initial fragment (blue) with compound 58 (gray) reveals how the binding mode has been maintained, in contrast to the series described last week.

Compound 40 had only modest antiproliferative activity against human cancer cell lines that were grown in 2D culture but was more active when the cells were grown in 3D culture. The molecule had good oral bioavailability in mice, and xenograft studies revealed that it inhibited tumor growth, though it was also toxic at higher doses. The researchers do not mention brain penetration, though given the number of hydrogen bond donors I would be surprised if it crosses the blood-brain barrier.

 

This paper is a nice example of how getting high affinity is often only the beginning of a long journey. In combination with the story from last week it is also a useful reminder of how many starting points a single fragment screen can provide: just two fragments led to two completely independent series. Whether molecules from these series advance to the clinic, they provide useful tools to further understand the biology of DYRK1A.