Flipping fragments in CDK8

The cyclin-dependent kinases (CDKs) are targets for a variety of diseases, particularly cancers. One of the earliest posts at Practical Fragments discussed the clinical-stage AT7519, which inhibits several CDKs. A new paper in Bioorg. Med. Chem. Lett. by Xingchun Han, Song Yang, and their colleagues at Roche Innovation Center Shanghai describes the discovery of a selective CDK8 inhibitor.

The researchers started with a biochemical screen (at 100 µM) of ~6500 fragments, all with less than 19 non-hydrogen atoms. A whopping 403 compounds showed >70% inhibition, and of 227 tested in full dose-response curves, 48 had IC₅₀ < 50 µM with ligand efficiency > 0.3 kcal/mol/atom. Compound 1 was both potent and structurally interesting.

SAR by catalog led to several more active analogs, including compound 4, which was crystallographically characterized bound to CDK8 (blue). The pyridine nitrogen makes a hydrogen bond with the hinge-region of the kinase, while the pyrrole nitrogen makes a water-mediated bond to the protein. Interestingly though, benzylation of the pyrrole slightly improved affinity, suggesting that the molecule can bind in a flipped orientation, with the pyrrole nitrogen pointing out towards solvent. This binding mode would provide easy access to a small hydrophobic pocket, a hypothesis that was supported when compound 17 showed a dramatic increase in affinity. A crystal structure of compound 17 bound to CDK8 confirmed the flipped binding mode.

A closely related molecule (replacing the chlorine atom with a trifluoromethyl group) showed oral bioavailability and good pharmacokinetics in mice. And another closely related compound (methyl instead of chlorine) showed excellent selectivity against a panel of 43 kinases.

There are several practical lessons in this brief paper. First, very minor changes can lead to massive improvements in affinity. Indeed, compound 17 has the same number of non-hydrogen atoms as the initial fragment, yet binds almost 1000-fold more tightly. Second, it is possible to discover selective kinase inhibitors while staying well within the ATP-binding pocket, and doing so may cut down on molecular obesity too (compare this paper with the CK2 story highlighted last week.) And finally, while structural information can be enabling, it is always important to remember that molecules – even reasonably potent ones – can dramatically change binding modes with the slightest modification. Remaining alert to this possibility can open new opportunities.