Discovery of a Novel Hsp90 Inhibitor by Fragment Linking

Over the past decade, fragment screening has become an increasingly popular method for hit identification in drug discovery. Many methods can be successfully employed to identify fragment hits, however confirmation of a fragment hit and detailed analysis of the binding pose to its target is usually achieved by X-ray crystallographic analysis of the fragment protein complex. Subsequent optimisation involves the evolution of fragments to fully exploit binding pockets of a target or, where the chemistry of combining fragments is tractable, by the linking of fragments. Previously, we reported results from a fragment evolution process based on heat shock protein 90 (Hsp90) fragment hits; in the present report, we describe a fragment-linking approach that resulted in the rapid improvement in the level of Hsp90 inhibition. Hsp90 is a molecular chaperone with ATPase activity involved in the stabilisation of numerous client proteins including those involved in oncogenic transformations, such as BRaf. As such there continues to be considerable interest in the discovery of Hsp90 inhibitors. Previously, we reported the analysis of multiple crystal structures of diverse fragment complexes of Hsp90 derived from the primary fragment screen that demonstrated the flexibility of Hsp90 in the region of the adenosine binding site (see Figure 1). In particular, Hsp90 was found to adopt a helical conformation in the region of Asn 105 to Ile 110 in the presence of a subset of the fragments, including compound 2. The Hsp90–2 complex structure is essentially the same as the “closed” conformation previously reported for Hsp90 in the presence of geldanamycin. The helical conformation of Hsp90 creates a compact and well-defined pocket adjacent to the adenosine binding site. Other fragments, such as fragment 1, exclusively bind to the adenosine pocket and do not trigger the opening of the helical pocket. Both fragments 1 and 2 displayed relatively low inhibitory potencies against Hsp90 (IC50 = 1500 mm