USD Conference Systems, International Conference on Sustainable Natural Products in Healthcare 2025

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Molecular Docking and Dynamics Simulation of ZINC000085595326 Compound as an Acetylcholinesterase Inhibitor Assisted by YASARA Structure
Chrisologus Ivan Prasetyo, Stephanus Satria Wira Waskitha

Last modified: 2025-06-06

Abstract


Alzheimer's disease (AD) is a progressive disorder worsening over time and can affect cognition, behavior, and functional capacity. As an alternative therapy for AD, one of natural products that could be potentially used is  compound ZINC000085595326. This study aimed to analyze the stability of the interaction of  ZINC000085595326 against acetylcholinesterase (AChE) enzyme through molecular docking and dynamics simulations. The methods used were molecular and 15-ns molecular dynamics (MD) simulations at body temperature using the YASARA-Structure. The results were analyzed by observing the RMSD values of redocking and docking to cluser the best-docked compounds. The results showed that the redocking value of native ligand huprine X had RMSD values ≤ 2.000 Å, suggesting the validity of the protocol. The MD simulations results also showed that in the last 5 ns of the production phase, the ΔRMSD Backbone and LigandMovement values were ≤ 2.000 Å and had a binding energy of 8,374-10,860 KJ/mol. The aromatic and hydrophobic interactions in the ZINC000085595326-AChE complex had similar inhibitory interactions to the native ligand based on simulation results. These results indicated that compound ZINC000085595326 was stable during the MD simulations, involving key residues such as Tyr70, Asp72, Trp84, Tyr121, Trp279, Phe330, and Tyr334.


Keywords


Acetylcholinesterase; Alzheimer’s; Molecular Docking; Molecular Dynamics; ZINC000085595326