The aim of Fragment Based Drug Discovery (FBDD) is to identify interactions between small ligands and target proteins using biophysical techniques such as X-ray crystallography or NMR spectroscopy. Ligands tend to bind at discrete, favoured binding sites, or "hotspots", on the protein surface. Identification of these hotspots early in a fragment screening campaign is likely to enhance the prospects of a successful drug design project. Conversely, the absence of identifiable hotspots on the surface of a candidate protein may be a predictor of difficulties ahead.

Polar solvents such as DMSO are routinely used to dissolve fragment compounds. However, DMSO is often found to bind to protein hotspots where it may compete with fragment binding. This suggests that solvents could be used as probes to identify protein hotspots and to highlight potential problems.

Here, we present NMR studies of several polar solvent interactions with two bacterial thiol-disulphide oxidoreductase enzymes, V. cholerae (Vc)DsbA and S. aureus (Sa)DsbA. We found that hotspots were readily identified on VcDsbA, but non-specific interactions predominated with SaDsbA. These results were corroborated by in silico predictions of solvent binding sites using a web-based server, FTMap, and also by our NMR-based fragment screens.

We conclude that small polar solvents are effective probes of hotspots on candidate proteins. Furthermore, we suggest that currently available in silico techniques represent an efficient and economical first step in identifying favoured solvent binding sites, and hence in assessing the suitability of candidate proteins for further investigation as therapeutic targets by FBDD.