Computational protocol: α-Mangostin Extraction from the Native Mangosteen (Garcinia mangostana L.) and the Binding Mechanisms of α-Mangostin to HSA or TRF

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Protocol publication

[…] Interaction models of drug and proteins were established by molecular simulation via DOCK 4.0 at SGI O2 workstation. The crystal structures of HSA and TRF were obtained from Brookhaven Protein Data Bank (encoding: 1H9Z and 1D4N, respectively). In the process of molecular docking, following some reports [–], we use the Chain A of HSA for the docking studies. Molecular structure of α-mangostin was built by ChemDraw and then molecular modeling based on the force field optimization of MM2 molecular mechanics was established. In the pretreatment process of molecular docking, receptor and ligand could be optimized with AutoDock Tools (ADT). Ligand had been handled with adding hydrogenation, adding charge and adding the atomic type, While the entire protein had been pretreatmented about deleting water, adding hydrogens and computing gasteiger by AutoDock Tools. The pretreatment of α-mangostin were automatically docked into the binding cavity of HSA/TRF by autodock 4.2. The active sites of HSA and TRF were confirmed through molecular docking and in order to find the best binding mode of ligand and receptor, we adopted the empirical potential-energy function as the evaluation function [–]. […]

Pipeline specifications

Software tools ChemDraw, AutoDock
Applications Drug design, Protein interaction analysis
Chemicals Hydrogen