In silico investigation and targeting of amyloid β oligomers of different size

Aggregation of amyloid beta (A beta) peptides into fibrils has been implicated in the pathogenesis of Alzheimer's disease (AD). As a result, in recent years, substantial efforts have been expended in the study of the mechanism of aggregation of the A beta peptide as well as of its inhibition by potential drug molecules. In this context, we have built a model of the A beta(17-42) deca-oligomer using the solid-state NMR (ssNMR) structure of the A beta(17-42) penta-oligomer as a reference. Both the penta- and deca-oligomer systems have been studied by all-atom molecular dynamics (MD) simulations and used as target systems for the investigation of the mechanism of action of a trehalose-derived A beta aggregation inhibitor. In the deca-oligomer all the main structural features of the putative fibrillar state are retained. Moreover, the simulations reveal a remarkable gain in stability as the oligomer grows. MD studies of the inhibitor in complex with the penta- and deca-oligomers indicate a significant destabilization of the structure beyond the hampering of the addition of successive A beta peptides at the ends of the fibril due to the presence of the inhibitor molecule. Our work provides an easy and effective approach which could be useful for the in silico development of potential drug molecules acting at different stages of the progression of A beta-related diseases.