Fragments vs PDK1

Kinases have been a particularly productive target class for fragment-based drug discovery (and drug discovery in general), with nearly half of reported FBDD-derived clinical candidates targeting kinases. The latest dispatch from this field can be found in the November issue of ACS Medicinal Chemistry Letters.

In this paper, Jeffrey Axten and colleagues at GlaxoSmithKline describe their use of fragment screening to identify inhibitors of PDK1, a popular anti-cancer target. They started by assembling a library of fragments biased towards the purine-binding site of kinases, and tested 1065 of these in a biochemical screen at 400 micromolar concentration. Of these, 193 inhibited activity at least 60% and were further characterized; 89 had IC50 values better than 400 micromolar. A set of 36 of these, chosen on the basis of ligand efficiency and chemical tractability, were chosen for follow-up.

Saturation transfer difference (STD) NMR was used to confirm which fragments bound to PDK, which cut the number of hits in half. X-ray crystallography experiments were started before NMR and performed on 7 fragments; only the fragments that were confirmed by NMR gave interpretable data. One of these was the aminoindazole compound 8 (see figure).

A substructure search was conducted to find more elaborated molecules within the corporate screening collection, leading to compound 19, which has sub-micromolar potency. This compound also showed some signs of selectivity for PDK1 over other kinases. Although the paper stops here, Jeffrey Axten gave a nice presentation at FBLD 2010 in which he discussed subsequent medicinal chemistry that ultimately led to novel, high picomolar inhibitors of PDK1.

There are at least two lessons from this story. First, the significant attrition from the biochemical screen again emphasizes the need for orthogonal methods of fragment validation. Second, even though the fragment identified has been around the block with respect to kinases (as of last year, the aminoindazole substructure had appeared in over 70 kinase patents), skillful medicinal chemistry can still get you to novel compounds.