Molecular docking was undertaken with the help of AutoDock 4.0, Autogrid [33 (link)], and AutoDock Tools [34 ]. The standard AutoDock protocol was followed unless otherwise noted. Ligands were drawn and then processed with AutoDock Tools for charge and rotatable bonds assignment. 5-LO crystal structure chosen for docking is PDB ID: 3O8Y [34 ], which is a “stable-5-LOX.” To enable crystallization, several mutations are present in the noncatalytic domain and a small 3 residue sequence in the catalytic domain is replaced from KKK to ENL. The mutations maybe affect the structure, but “stable-5-LOX” catalytic activity was not affected [34 ]. The protein was prepared with AutoDock Tools. Water molecules were removed, polar hydrogens added, and charges assigned. The grid box used a default spacing of 0.375 with a bounding box of 60, 66, and 60 and a grid center of −2.24, 25.69, and −0.94, in both cases X, Y, and Z coordinates. As for the docking settings, 100 runs were completed per ligand and defaults were kept with exceptions for the following values: ga_pop_size 5000, ga_num_evals 100,000,000, ga_num_generations 500,000, and sw_max_its 5000. For analysis, AutoDock Tools (Schrödinger Release; Maestro, version 10.6) and LigPlot+ [35 (link)] were used. Results were clustered with a maximum of 2.00 Å RMSD, and the largest cluster with the lowest binding energy was chosen.
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