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Tuncbag, N., Gursoy, A. and Keskin, O. (2009) Identification of Computational Hotspots in Protein Interfaces: Combining Solvent Accessibility and Inter-Residue Potentials Improves the Accuracy. Bioinformatics, 25, 1513-1520.
http://dx.doi.org/10.1093/bioinformatics/btp240

has been cited by the following article:

  • TITLE: Computational Analyses of Docosahexaenoic Acid (DHA, C22:6, n-3) with Alzheimer’s Disease-Causing Amyloid Peptide Aβ1-42 Reassures Its Therapeutic Utility

    AUTHORS: Michio Hashimoto, Shahdat Hossain, Kentaro Matsuzaki, Abdullah Al Mamun, Hiroyuki Arai, Osamu Shido

    KEYWORDS: Docosahexaenoic Acid, Alzheimer’s Disease, Amyloid Beta Peptide, Molecular Docking, In Silico, Drug Design, Protein Data Bank

    JOURNAL NAME: Advances in Alzheimer's Disease, Vol.5 No.2, June 29, 2016

    ABSTRACT: The accumulation of amyloid β peptide1-42 (Aβ1-42) masses in the brains of Alzheimer’s Disease (AD) patients is associated with neuronal loss and memory deficits. We have previously reported that oral administration of docosahexaenoic acid (DHA, C22:6, n-3) significantly decreases Aβ burden in the brains of AD model rats and that direct in vitro incubation of DHA with Aβ1-42 curbs the progression of amyloid fibrillation. In the present in silico study, we investigated whether DHA computationally binds with amyloid peptides. The NMR solution structures of Aβ1-42 were downloaded from the Protein Data Bank (PDB IDs: 1Z0Q and 2BEG). The binding of DHA to Aβ peptides was assessed by molecular docking using both a flexible and rigid docking system. Thioflavin T (ThT) was used as positive control. The chemical structures of ThT and DHA were modeled and converted to the PDB format using PRODRUG. Drug-like properties of DHA were evaluated by ADME (Absorption, Distribution, Metabolism, and Excretion). DHA was found to successfully dock with Aβ1-42. Computational analyses of the binding of DHA to Aβ1-42, as evaluated by docking studies, further corroborated the inhibitory effect of DHA on in vitro Aβ1-42 fibrillogenesis and might explain the in vivo reduction of amyloid burden observed in the brains of DHA-administered AD model rats demonstrated in our previous study. These computational data suggest the potential utility of DHA as a preventive medication in Aβ-induced neurodegenerative diseases, including AD.