Molecular dynamics simulations of anti-aggregation effect of ibuprofen.
Using implicit solvent molecular dynamics and replica exchange simulations, we study the impact of ibuprofen on the growth of wild-type Abeta fibrils. We show that binding of ibuprofen to Abeta destabilizes the interactions between incoming peptides and the fibril. As a result, ibuprofen interference modifies the free energy landscape of fibril growth and reduces the free energy gain of Abeta peptide binding to the fibril by approximately 2.5 RT at 360 K. Furthermore, ibuprofen interactions shift the thermodynamic equilibrium from fibril-like locked states to disordered docked states. Ibuprofen's anti-aggregation effect is explained by its competition with incoming Abeta peptides for the same binding site located on the fibril edge. Although ibuprofen impedes fibril growth, it does not significantly change the mechanism of fibril elongation or the structure of Abeta peptides bound to the fibril.
Chang
Wenling E
WE
Department of Bioinformatics and Computational Biology, George Mason University, Manassas, Virginia, USA.
Takeda
Takako
T
Raman
E Prabhu
EP
Klimov
Dmitri K
DK
D000682:Amyloid / Q000737:chemistry*; D016229:Amyloid beta-Peptides / Q000737:chemistry*; D007052:Ibuprofen / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D010446:Peptide Fragments / Q000737:chemistry; D055503:Protein Multimerization / Q000187:drug effects; D020836:Protein Structure, Quaternary; D013696:Temperature; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D000682:Amyloid; D016229:Amyloid beta-Peptides; D010446:Peptide Fragments; D014867:Water; D007052:Ibuprofen