A low-cost molecular docking methodology to predict interactions between inorganic complexes and biomacromolecules: A tutorial

Transition metal complexes (TMC) are involved in several medicinal chemistry studies, but they still need more attention. TMCs have shown promising results related to medical treatments, for instance: contrast agents, biosensors, anticancer and antibacterial agents. In this context, there are several research groups working with inorganic medicinal chemistry combined with molecular modeling to understand the formation of a stable protein-ligand systems for TMCs, to improve and complement their experimental results. Herein, we discuss and implement a low-cost protocol for molecular docking experiments using Autodock vina, visualizing in silico protein-ligand interactions as a structure-based method for drug design. We use free software and web-servers, achieving to reproduce at least 70% of the amino acid residues interactions in comparison with PDB structure and keeping a RMSD<1.1 for two TMCs analyzed. In this context, this methodology can help newcomers to start molecular modeling studies in inorganic medicinal chemistry.