Explore on screening COX-2 inhibitors from the essential oil of Solanum lyratum Thunb. By molecular docking and molecular dynamics simulation

Abstract

This study aimed to investigate Solanum lyratum Thunb. with respect to the potential ingredients with anti-inflammatory activity from its essential oil by silico study. To this regard, the essential oil of Solanum lyratum Thunb. was extracted by hydrodistillation. 25 compounds were identified by GC-MS. Using virtual screening, molecular docking and molecular dynamics simulation of the 25 identified compounds, the ones showing anti-inflammatory activity on COX-2 were identified. According to the drug-like principle and the prediction of ADEMT properties, the six compounds of Spathulenol, Cedrol, Juniper camphor, Santalol, Nootkatone and 7,9-Di-tert-butyl-1-oxaspiro[4.5]deca-6,9-diene-2,8-dione were identified and then studied for molecular docking, and based on which the top two compounds of binding free energy were studied by the molecular dynamics simulation. The molecular docking data indicated that the binding free energies of Spathulenol, Cedrol, Juniper camphor, Santalol, Nootkatone and 7,9-Di-tert-butyl-1-oxaspiro[4.5]deca-6,9-diene-2,8-dione to COX-2 protein were −5.65, −7.19, −6.35, −4.94, −5.82 and −5.14 kcal/mol, respectively. The findings showed the steady interactions of hydrogen bonds and hydrophobic bonds between both the top two compounds of binding free energy and the active site residues of COX-2 (4M11) throughout the simulation via hydrogen bonds and hydrophobic bonds. The very study shall be supportive for in vitro and in vivo studies in developing drug products using the lead bioactive ingredients for anti-inflammatory in the future.

Keywords

• Essential oil
• Solanum lyratum Thunb.
• Molecular docking
• Molecular dynamics simulation
• COX-2 enzyme