Blinded evaluation of cathepsin S inhibitors from the D3RGC3 dataset using molecular docking and free energy calculations.

During the last few years, we have developed a docking protocol involving two steps: (i) the choice of the most appropriate docking software and parameters for the system of interest using structural and functional information available in public databases (PDB, ChEMBL, PubChem Assay, BindingDB, etc.); (ii) the docking of ligand dataset to provide a prediction for the binding modes and ranking of ligands. We applied this protocol to the D3R Grand Challenge 3 dataset containing cathepsin S (CatS) inhibitors. Considering the size and conformational flexibility of ligands, the docking calculations afforded reasonable overall pose predictions, which are however dependent on the specific nature of each ligand. As expected, the correct ranking of docking poses is still challenging. Post-processing of docking poses with molecular dynamics simulations in explicit solvent provided a significantly better prediction, whereas free energy calculations on a subset of compounds brought no significant improvement in the ranking prediction compared with the direct ranking obtained from the scoring function.