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Published:
Jul 11, 2026DOI:
10.4314/tjpr.v25i6.8Keywords:
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Main Article Content
Computational docking study of naproxen binding to COX-2 (6COX) using AutoDock and visualization tools
Abstract
Purpose: To investigate the molecular interaction of Naproxen and cyclooxygenase (COX) using a docking approach.
Methods: Naproxen structure was built and energy minimized in HyperChem to attain its stable conformation. The COX receptor (PDB ID: 6COX) was prepared by stripping water molecules and co-crystal ligands, adding polar hydrogens and assigning charge prior to performing molecular docking. AutoDock Vina was used to dock Naproxen to predict its orientation within the COX active site.
Results: The docking yielded five binding modes with the best-ranked pose having a binding affinity of −7.643 kcal/mol, which indicates favorable binding. Visualization by PyMOL indicates that Naproxen fits well inside the COX binding pocket, where the aromatic core is buried deep in the hydrophobic channel, while the carboxylic group is directed toward the pocket entrance, supporting stabilizing interactions.
Conclusion: Naproxen binds within the COX active site with a predicted binding affinity of −7.643 kcal/mol. The ligand is stabilized by hydrophobic interactions and hydrogen bonding.
