Ligand Macromolecule Interactions: Theoretical Principles of Molecular Recognition

Molecular recognition is mediated by three main factors: surface complementarity, thermodynamics, and associated physicochemical properties. These principles are responsible for ligand–target binding and therefore serve as the foundation for the design of new biologically relevant chemical entities. As these principles are involved in nearly all biological processes, a firm understanding of the details involved in binding is necessary for drug design. The consideration of these factors individually has proven useful; however, the combined effect of these governing principles is most important. And despite extensive studies, there are still many gaps in our understanding of this recognition process. The aim of this chapter is to introduce the basic concepts of ligand binding to set the stage for the following chapters, while briefly discussing fundamental techniques of drug design, including the indispensable tools of molecular modeling.