The Binding of Thioflavin T and Its Neutral Analog BTA-1 to Protofibrils of the Alzheimer’s Disease Aβ16–22 Peptide Probed by Molecular Dynamics Simulations

Thioflavin T (ThT) is a fluorescent dye commonly used to stain amyloid plaques, but the binding sites of this dye onto fibrils are poorly characterized. We present molecular dynamics simulations of the binding of ThT and its neutral analog BTA-1 [2-(4′-methylaminophenyl)benzothiazole] to model protofibrils of the Alzheimerʹs disease Aβ16–22 (amyloid β) peptide. Our simulations reveal two binding modes located at the grooves of the β-sheet surfaces and at the ends of the β-sheet. These simulations provide new insight into recent experimental work and allow us to characterize the high-capacity, micromolar-affinity site seen in experiment as binding to the β-sheet surface grooves and the low-capacity, nanomolar-affinity site seen as binding to the β-sheet extremities of the fibril. The structure–activity relationship upon mutating charged ThT to neutral BTA-1 in terms of increased lipophilicity and binding affinity was studied, with calculated solvation free energies and binding energies found to be in qualitative agreement with the experimental measurements.