Structures of Aβ17-42 Trimers in Isolation and with Five Small-Molecule Drugs Using a Hierarchical Computational Procedure

The amyloid-beta protein (A beta) oligomers are believed to be the main culprits in the cytoxicity of Alzheimer's disease (AD) and p3 peptides (A beta 17-42 fragments) are present in AD amyloid plaques. Many small molecule or peptide based inhibitors are known to slow down A beta aggregation and reduce the toxicity in vitro, but their exact modes of action remain to be determined since there has been no atomic level of A beta(p3)-drug oligomers. In this study, we have determined the structure of A beta 17-42 trimers both in aqueous solution and in the presence of five small molecule inhibitors using a multiscale computational study. These inhibitors include 2002-H20, curcumin, EGCG, Nqtrp, and resveratrol. First, we used replica exchange molecular dynamics simulations coupled to the coarse grained (CG) OPEP force field. These CG simulations reveal that the conformational ensemble of A beta 17-42 turner can be described by 14 clusters with each peptide essentially adopting turn/random coil configurations, although the most populated duster is characterized by one peptide with a beta-hairpin at Phe19-Leu31. Second, these 14 dominant dusters and the less-frequent fibril-like state with parallel register of the peptides were subjected to atomistic Autodock simulations. Our analysis reveals that the drugs have multiple binding modes with different binding affinities for trimeric A beta 17-42 although they interact preferentially with the CHC region (residues 17-21). The compounds 2002-H20 and Nqtrp are found to be the worst and best binders, respectively, suggesting that the drugs may interfere at different stages of A beta oligomerization. Finally, explicit solvent molecular dynamics of two predicted Nqtrp-A beta 17-42 conformations describe at atomic level some possible modes of action for Nqtrp.