Computational protocol: Revealing the potency of Annona muricata leaves extract as FOXO1 inhibitor for diabetes mellitus treatment through computational study

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Protocol publication

[…] Analytical-Descriptive Research Design was used to determine the potential of the Annona muricata leaves active compounds and to determine the binding affinity of the active compounds toward FOXO1 protein computationally. The compound was obtained from the PubChem (https://pubchem.ncbi.nlm.nih.gov) server with a recorded CID. While FOXO1 receptor, that was the inhibitor, was obtained from the data bank (http://www.rcsb.org/pdb/home/home.do) server by ID 3CO6. Inhibitor reference that can inhibit the activity of FOXO1 proteins was taken from calbiochem by CID AS1842856 (Nagashima et al. ). Furthermore, the docking process was performed by using PyRx program (Autodock vina) (Dallakyan and Olson ). The docking process was done specifically with ‘the compound’ as ligand and inhibitor reference (AS1842856). Compound that has the smallest or most negative binding energy was chosen because it showed the best complex conformation. Docking results were stored and visualized by using Ligandscout and PyMOL ligand (DeLano ). The visualization of docking results by using LigPlot showed the interaction between these two molecules (FOXO1-ligand compound or inhibitor reference) (Wallace et al. ). LigPlot results showed hydrophobic bonding and hydrogen bonding that occurred within the complex. Potential inhibition can be seen from the amino acid on FOXO1 active side that was bound by the active compound. […]

Pipeline specifications

Software tools PyRx, LigandScout, PyMOL, LigPlot+
Applications Drug design, Protein interaction analysis
Diseases Diabetes Mellitus
Chemicals Amino Acids, Hydrogen, Rutin