A fragment-based approach for the discovery of isoform-specific p38? inhibitors

In this study, we describe a novel approach for lead discovery against protein kinases, pharmacophore by interligand nuclear Overhauser effect (ILOE), in which a pair of ligands that bind to adjacent pockets on the target sur- face is identified by the detection of protein-mediated ILOEs. We demonstrate that a pharmacophore-based search guided by experimental binding data of weakly in- teracting fragments can be rapidly and efficiently used to identify (or synthesize) high-affinity, selective ligands. Targeting the inactive state of protein kinases rep- resents a promising approach to achieve selectivity and cellular efficacy. In this re- spect, when we apply the method for the discovery of potent p38 inhibitors, we also demonstrate that the resulting bidentate compounds are highly selective and exhibit a cellular activity that parallels their in vitro binding to the inactive form of the kinase. The method is relatively simple and of general applicability, and as such we anticipate its potential implementation against a variety of macromolecu- lar targets, including not only protein kinases but also those involved in protein- protein interactions or even nucleic acids.