Molecular Docking of Plant Metabolites

Docking was performed with the AutoDock Vina package [88 (link)]. The AutoDock Tools 1.5.7 module was used to prepare and analyse the computational calculations. After optimization, the structures of the plant metabolites were positioned in the central portion of the respective catalytic site of each selected target (Cys145 to Mpro, Asp618 to RdRp, Tyr264 to PLpro, His250 to NSP15, Gln493 to RDB Spro and Arg273 to ACE-2). Gasteiger charges and polar hydrogens, required for potential calculations, were added after removal of water molecules, drugs and/or artefacts from the target structures [89 (link)]. The targets macromolecules structures were kept rigid, while the ligands did not have their mobility restricted, remaining free. The size of the grid box was set to 22.5 Å for each axis. The number of modes was set to 50, and the exhaustiveness was set to 24. The conformations of the best interaction energy of the ‘ligand + receptor’ complexes identified in molecular docking were selected based on free energy of binding, by visual inspection and analysis of residues that best interacted with the ligand [19 (link),20 (link),90 (link)]. Molecular analyses and complex representations were obtained using the UCSF Chimera package [91 (link)] and PoseView [92 (link)].