Molecular Operating Environment (MOE, v2019.01, Chemical Computing Group, Montreal, Canada) was used to simulate the interaction between selected alkaloids and targets (Tian et al., 2022 (link)). The 2D structures of peak 5 (magnoflorine), 19 (berberine), 21 (chelerythrine), and the positive control (rofecoxib and nordihydroguaiaretic acid [NDGA]) were imported to establish a compound database. Then, 3D conformations were prepared to obtain a stereo-structure database. Crystallized structures of the enzymes were downloaded from RCSB PDB (COX-2 PDB: 5KIR; 5-LOX PDB: 6N2W) based on previous studies (Orlando and Malkowski, 2016 (link); Gilbert et al., 2020 (link)). After removing water and adding hydrogen, one chain containing a ligand was kept and optimized for minimum energy conformation. Molecular docking was conducted in the active pocket. London dG scores were produced by using the Triangle Matching method to dock at 30 preferential poses. In addition to energy scores, the interactions of residues, energy, and bonds were displayed, compared, and discussed to evaluate the ligand–target interactions.
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