The ligand-bound (1W51) structure of BACE-1 was used [52] . The procedure used to prepare the structure was as follows: hydrogen was added, the protonation states were assigned, and a highly limited optimization was performed to reduce bad contacts and the overall strain energy in the protein structure. The aspartate located on the active site was adjusted to an ideal protonation state, the Asp32 was protonated, the Asp228 was ionized [46] .