Molecular Dynamics as a Tool in Rational Drug Design: Current Status and Some Major Applications

Rational Drug Design has become a well-established discipline in pharmaceutical research. It uses computational chemistry with the aim to discover or study drugs and their related biologically active molecules. The purpose is to reduce the number of targets for a good drug that have to be subjected to expensive and time-consuming synthesis. The advanced methods developed in this field united with the increased potency of the new computer generation are the tools for the scientist to explore the conformational variability and properties of a large number of potentially active molecules and their interaction with each other or with their biological target (i.e. enzyme or receptor). Among these methodologies, Molecular Dynamics (MD) is one of the most useful tools in this process now routinely used to simulate complex dynamic processes that occur in biological systems such as molecular recognition in drug-receptor complexes. This paper reviews the current status of Molecular Dynamics methods, and some of its most recent and interesting applications in the field of Drug Design and Discovery.