Molecular dynamics simulations have showed to be powerful tools when applied to the
preliminary investigations of the interactions of potential molecular targets with its natural subtracts or,
eventually, with their potential inhibitors. When the 3D structure of a molecular target is yet unknown,
sometimes it is possible to build a very consistent model using one of the several softwares available
today for this purpose (see chapter on homology modeling) and, further, use it to analyze the overall
structure of the target, the active site residues and their potential interactions with potential ligands, by
performing MD simulations studies in order to afford additional information towards the rational design
of inhibitors to the molecular target in focus. Literature has reported a few interesting studies using this
approach on leishmaniasis. Those studies have afforded useful information for the experimentalists on
new drug targets for the rational design of new, more selective and powerful antileishmiasis agents.
Keywords: Molecular dynamics simulation, proteins, antileishmaniasis agents.
