Binding modes of thioflavin T and Congo red to the fibril structure of amyloid-β(1-42)

Chem Commun (Camb). 2020 Jul 14;56(55):7589-7592. doi: 10.1039/d0cc01161d. Epub 2020 Jun 8.


Binding modes for the amyloid-β(1-42) fibril fluorescent dyes thioflavin T and Congo red were predicted by molecular dynamics simulations and binding free energy calculations. Both probes bind on the fibril surface to primarily hydrophobic grooves, with their long axis oriented almost parallel to the fibril axis. The computed binding affinities are in agreement with experimental values. The binding modes also explain observables from previous structural studies and, thus, provide a starting point for the systematic search and design of novel molecules, which may improve in vitro diagnostics for Alzheimer's disease.

Publication types

  • Video-Audio Media

MeSH terms

  • Amyloid beta-Peptides / chemistry
  • Amyloid beta-Peptides / metabolism*
  • Benzothiazoles / metabolism*
  • Binding Sites
  • Congo Red / metabolism*
  • Fluorescent Dyes / metabolism*
  • Molecular Dynamics Simulation
  • Peptide Fragments / chemistry
  • Peptide Fragments / metabolism*
  • Protein Binding
  • Protein Structure, Quaternary
  • Thermodynamics


  • Amyloid beta-Peptides
  • Benzothiazoles
  • Fluorescent Dyes
  • Peptide Fragments
  • amyloid beta-protein (1-42)
  • thioflavin T
  • Congo Red