The goal in result analysis was to identify novel antimalarial compounds and to compare the used docking tools, parameters and targets and to draw some general conclusions about their impact on virtual screening results.
The different parameter settings and target scenarios had severe influence on the virtual screening results. Although there could be found a high correlation between the scores of the docked compounds under different conditions the differences were significant and partly different compounds were selected as the top-scoring ligands. But the highest diversity was produced by the application of the different docking tools. There was almost no dependence between the docking scores calculated by AutoDock and FlexX. When looking at the chemical properties of the ligands, we found that the docking tools preferred compounds with different properties. FlexX calculated the lowest scores for ligands which possess 3 to 7 donors, 2 to 5 rings and a polar surface area of 50 to 210 2 while AutoDock prefers ligands with 1 to 3 donors, 5 to 7 rings and a polar surface area of 20 to 130 2. What both tools share is a preference for larger molecules with a high molecular mass which corresponds well to the reference ligands co-crystallized with the PDB structures. These findings clearly demonstrate that an application of several docking tools can enrich the candidate set and that parameters and target scenarios should be carefully chosen in advance if it is not possible to perform several experiments.
Several strategies were employed to analyze the results including docking scores, ideal binding modes, and interactions to key residues of the protein. From the 500,000 ligands screened a few hundred compounds that can be tested in experimental laboratories should be identified. Three different classes of structures with thiourea, diphenylurea and guanidino scaffolds were identified to be promising hits. Diphenylurea analogues are already known to be micromolar inhibitors for plasmepsin (Walter Reed compounds, Jiang, S.; Prigge, S. T.; Wei, L.; Gao, Y. E.; Hudson, T. H.; Gerena, L.; Dame, J. B.; Kyle, D. E. New Class of Small Nonpeptidyl Compounds Blocks Plasmodium falciparum Development In Vitro by Inhibiting Plasmepsins. Antimicrob. Agents Chemother. 2001, 45, 2577-2584). This suggests that the overall approach is sensible for the discovery of inhibitors for plasmepsins. Guanidino analogues are likely to be a novel class of compounds, as they have not yet been reported as inhibitors for plasmepsins.