Hybrid Screening Approach for Very Small Fragments: X‑ray and Computational Screening on FKBP51

Fragment-based
drug discovery (FBDD) permits efficient sampling
of the vast chemical space for hit identification. Libraries are screened
biophysically and fragment:protein co-structures are determined by
X-ray crystallography. In parallel, computational methods can derive pharmacophore models or screen
virtual libraries. We screened 15 very small fragments (VSFs) (HA
≤ 11) computationally, using site identification by ligand
competitive saturation (SILCS), and experimentally, by X-ray crystallography,
to map potential interaction sites on the FKBP51 FK1 domain. We identified
three hot spots and obtained 6 X-ray co-structures, giving a hit rate
of 40%. SILCS FragMaps overlapped with X-ray structures. The compounds
had millimolar affinities as determined by 15N HSQC NMR.
VSFs identified the same interactions as known FK1 binder and provide
new chemical starting points. We propose a hybrid screening strategy
starting with SILCS, followed by a pharmacophore-derived X-ray screen
and 15N HSQC NMR based KD determination to rapidly identify
hits and their binding poses.