Molecular dynamics simulation analysis of the beta amyloid peptide with docked inhibitors

Bandar Aloufi; Ahmad Mohajja Alshammari; Nawaf Alshammari; Mohammad Jahoor Alam

doi:10.6026/97320630018622

Molecular dynamics simulation analysis of the beta amyloid peptide with docked inhibitors

Bioinformation. 2022 Jul 31;18(7):622-629. doi: 10.6026/97320630018622. eCollection 2022.

Authors

Bandar Aloufi¹, Ahmad Mohajja Alshammari¹, Nawaf Alshammari¹, Mohammad Jahoor Alam¹

Affiliation

¹ Department of Biology, College of Science, University of Hail, Kingdom of Saudi Arabia.

Abstract

Beta amyloid peptide is widely studied due to its association with Alzheimer disease (AD). Various study reported that the accumulation of beta amyloid in brain cells leads to Alzheimer disease. Hence, Beta amyloid peptide could be a potential target of anti-AD therapy. Hence, it is of interest to develop potent inhibitors for Beta amyloid peptide in the context of Alzheimer disease (AD). We report the binding features of Ascorbic acid, Cysteine, Dithioerythriol, Dithiothreitol, Malic acid and α-Tocopherol with beta amyloid having binding energy values of -6.7, -6.5, -6.0, -6.5, -6.7 and - 7.0 kcal/mol respectively. The molecular docking of top-scoring compounds with beta amyloid suggests that amino acids such as ASP23, GLU22, Phe19, are crucial in binding. Molecular dynamics simulation study showed steady-state interaction of compounds with beta amyloid for further consideration.

Keywords: Alzheimer; Beta amyloid; Docking; MD simulation; natural compounds.