Introduction: In the current study, to reduce the side effects of anti-inflammatory drugs and increase their specificity, a new pharmaceutical inhibitor was designed by computational Biology and Bioinformatics knowledge.

Materials & methods: For this purpose, first, 150000 compounds with medicinal properties from ZINC database and also the files related to the structure of the enzyme cyclooxygenase2 from RCSB (Research Collaboratory for Structural Bioinformatics) were extracted. After preparing them, all of these chemical compounds were docked with the target enzyme in order to select the best pharmaceutical inhibitor (ligand).

Findings: After checking the computation, 10 compounds of ligands that were the results of Docking, were selected according to the Gibbs free energy (least ΔG). Based on the results of the docking operation, inhibitor binding to cox2 causes conformational changes of enzyme, potential energy reduction, and increasing the stability of inhibitor-enzyme complex.

Discussion & conclusions: According to the results obtained from the study, the inhibitors can reduce the inflammation and pain in different inflammatory diseases, by placing in the active site on the basis of more specificity and finally less toxicity.