There is experimental evidence that the astaxanthin, betanin and EGCG (epigallocatechin-3-gallate) compounds slow down the aggregation kinetics and the toxicity of the amyloid-beta (Aβ) peptide. How these inhibitors affect self-assembly at the atomic level remains elusive. To address this issue, we have performed for each ligand atomistic replica exchange molecular dynamics (REMD) simulations in explicit solvent of the Aβ11-40 trimer from the U-shape conformation, and MD simulations starting from Aβ1-40 dimer and tetramer structures characterized by different intra- and inter-peptide conformations. We find that the three ligands have similar binding free energies on small Aβ40 oligomers, but very distinct transient binding sites that will affect aggregation of larger assemblies and fibril elongation of Aβ40 peptide.