2.15. Molecular Docking

eIF4A1 three-dimensional structure was obtained from the Protein Data Bank ID 5ZC9, which corresponds to the structure of human eIF4A1-ATP with a resolution of 2Å [42]. The structures of ligand molecules were obtained from the PubChem database [43], Cry (CID 160254) and rocaglamide (CID 331783). The protein structure was prepared by removing water and small molecules, leaving only the protein structure. Ligand and receptor were 3D-protonated, and energy minimization was performed using Molecular Operating Environment (MOE) software with default parameters under the AMBER89 force field. For the ligand, it generates different conformations by the use of a stochastic search in MOE default parameters.

The active site was predicted by employing the site finder option of the MOE software [44]. Molecular docking was set at default parameters for MOE software, and the pre-conformations were employed. For the interpretation of docking results, MOE identifies salt bridges, hydrogen bonds, hydrophobic interactions, sulfur-LP, cation-π, and solvent exposure and gives the S score. Ligand interactions with target proteins were predicted on the basis of the S score [45].