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 surface is identified by the detection of protein-mediated ILOEs. We demonstrate that a pharmacophore-based search guided by experimental binding data of weakly interacting fragments can be rapidly and efficiently used to identify (or synthesize) high-affinity, selective ligands. Targeting the inactive state of protein kinases represents a promising approach to achieve selectivity and cellular efficacy. In this respect, when we apply the method for the discovery of potent p38alpha 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 macromolecular targets, including not only protein kinases but also those involved in protein-protein interactions or even nucleic acids.