Computational protocol: Ampelopsin Improves Insulin Resistance by Activating PPARγ and Subsequently Up-Regulating FGF21-AMPK Signaling Pathway

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Protocol publication

[…] Based on the ‘lock-and-key’ principle of interaction between ligands and receptors, molecular docking method, which simulate the interaction between a small molecule ligand and a bio-macromolecule receptor, was used to investigate the interaction between APL and PPARγ as described []. Briefly, we determined the 3D structure of APL based on initial molecular data from PubChem (PubChem ID 161557). A structural model of the catalytic domain of PPARγ was constructed using Auto Dock Tools from the published crystal structure of PPARγ (PDB ID 1ZGY) as the modeling template. NAMD (version 2.7) was employed during the molecular dynamics simulation to obtain a refined structure. During the molecular dynamics simulations, the entire structure was surrounded by a cubic water box of simple point charge (SPC) water molecules that extended 10 Å from the protein, and periodic boundary conditions were applied in all directions. The systems were neutralized with Na+ and Cl- counter ions that replaced the water molecules. Energy minimization was performed for 5000 steps, followed by a 500-ps production molecular dynamics simulation with a time-step of 2 fs at constant pressure (1 atm) and temperature (300 K). Furthermore, docking parameters were adjusted to enable the search space of Autodock-Vina to include the potential binding region of APL. In our docking computation, we assumed that APL would interact with PPARγ via the catalytic domain. The binding energy of PPARγ and APL was calculated using Autodock-Vina software assuming the lower the binding energy, the higher the affinity of a particular combination []. […]

Pipeline specifications

Software tools NAMD, AutoDock Vina
Application Protein interaction analysis
Diseases Diabetes Mellitus
Chemicals Glucose