molecular dynamics simulations

MD simulations were performed using the Amber 24 software package to assess the binding stability between COX‑2 and 13(S)‑HOTrE. The system was built with the LEaP module, employing the GAFF2 and ff14SB force fields for the small molecule and the protein, respectively. A 100 ns MD simulation was conducted under constant temperature and constant pressure. Trajectories were analyzed using CPPTRAJ to calculate root‑mean‑square deviation (RMSD), radius of gyration (Rg), solvent‑accessible surface area (SASA), root‑mean‑square fluctuation (RMSF), and the number of hydrogen bonds. Binding free energies were estimated using the MM/GBSA method. One hundred frames extracted from the last 1 ns of the 100 ns trajectory were used to decompose the contributions of van der Waals, electrostatic interactions, polar and non‑polar solvation terms, with results expressed in kJ/mol.