Computational protocol: Nimbolide, a neem limonoid inhibits Phosphatidyl Inositol-3 Kinase to activate Glycogen Synthase Kinase-3β in a hamster model of oral oncogenesis

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Protocol publication

[…] Molecular docking was performed by using Discovery Studio 2.7 package from Biosystems Technologies, San Diego, USA on O2 (R12000) workstation. Nimbolide was retrieved from PubChem (www.ncbi.nlm.nih.gov/pccompound) (CID 100017). X-ray crystal structures of oncogenic signalling kinases PI3Kγ (1E8Y), Akt2 (2JDO), ERK2 (1TVO), and GSK-3β (4ACC) were retrieved from Protein Data Bank (PDB) (www.rcsb.org). Nimbolide ligand structure was minimized by charmM force field, and the stable energy conformation was taken for docking studies. The retrieved proteins were processed by removing heteroatoms, metal ions and water molecules, followed by addition of H-bonds to satisfy valencies and minimized by charmM force field. Docking analysis was carried out using Ligandfit module of Accelrys Discovery Studio (ADS). The ligand nimbolide was docked independently with the receptor proteins. The targeted protein was built as a receptor molecule to predict the active binding site and compute interaction parameters with the ligand. After docking, poses were viewed and analysed by DS Visualizer 3.5. […]

Pipeline specifications

Software tools CHARMM, PHENIX
Application Protein structure analysis
Organisms Azadirachta indica
Diseases Carcinoma, Leukoedema, Oral, Neoplasms
Chemicals 9,10-Dimethyl-1,2-benzanthracene