Assessment of fragment docking and scoring with the endothiapepsin model system

Fragment-based screening has become indispensable in drug discovery. Yet, the weak binding affinities of these small molecules still represent a challenge for the reliable detection of fragment hits. The extent of this issue was illustrated in the literature for the aspartic protease endothiapepsin: When seven biochemical and biophysical in vitro screening methods were applied to screen a library of 361 fragments, very poor overlap was observed between the hit fragments identified by the individual approaches, resulting in high levels of false positive and/or false negative results depending on the mutually compared methods. Here, the reported in vitro findings are juxtaposed with the results from in silico docking and scoring approaches. The docking programs GOLD and Glide were considered with the scoring functions ASP, ChemScore, ChemPLP, GoldScore, DSXCSD, and GlideScore. First, the ranking power and scoring power were assessed for the named scoring functions. Second, the capability of reproducing the crystallized fragment binding modes was tested in a structure-based redocking approach. The redocking success notably depended on the ligand efficiency of the considered fragments. Third, a blinded virtual screening approach was employed to evaluate whether in silico screening can compete with in vitro methods in the enrichment of fragment databases. An extensive docking and scoring analysis of a 361-fragment library with the model system endothiapepsin is reported and juxtaposed to experimental in vitro results from the literature. Docking with GOLD and Glide was assessed with scoring functions ASP, ChemScore, ChemPLP, GoldScore, DSX, and GlideScore. Analysis of the scoring functions' ranking power and scoring power is provided besides a redocking analysis and a blinded virtual screening approach. image