Combining docking, molecular dynamics and MM/PBSA methods to identify the binding modes of Congo red towards amyloid protofibrils

In this study, molecular docking, molecular dynamics (MD) simulations and binding free energy calculation were conducted to investigate the binding modes of Congo red toward the protofibril formed by an amyloidogenic fragment (GNNQQNY) from yeast prion protein Sup35. Four specific binding sites were indentified in our simulations. In the primary binding site, it shows that Congo red bound to a regular groove formed by the first three residues (G1-N2-N3) of the β-strands along the β-sheet extension direction with a strong binding free energy as estimated by the MM-PBSA method (-24.4 kcal/mol), which is consistent with recent theoretical measurements using the MM-GBSA method (-22.8±1.6 kcal/mol). Moreover, our simulations further indentified other binding sites: the long groove between two β-sheet layers, the aromatic pitch of Y7 and the top or bottom of the protofibril, implying that these binding sites could be bound by Congo red and other long flat molecules. These results not only yield valuable insight into the nature of the molecular form in which the amyloid dye binds the fibril and the binding locations on the fibril, but also provide a clue to design new compounds for clinical purposes.