ABSTRACT
Enzyme catalysis involves the conversion of a natural ligand (the substrate) into a different chemical species (the product), most often through a process of chemical bond breaking and formation steps. The chemical transformation of substrate to product almost always involves the formation of a sequential series of intermediate chemical species along the reaction pathway. Paramount in this reaction pathway is the formation of a short-lived, high-energy species referred to as the transition state. To facilitate this sequential process of intermediate species formation, the ligand-binding pocket(s) of enzymes must undergo speci c conformational changes that induce strains at correct locations and align molecular orbitals to augment the chemical reactivity of the appropriate functionalities on the substrate molecule(s), at de ned moments during the reaction cycle. The bases of mechanistic enzymology include understanding the chemical nature of the various intermediate species formed, and their interactions with those elements of the enzymebinding pocket that facilitate chemical transformations. When these studies are coupled with structural biology methods, such as x-ray crystallography and multidimensional nuclear magnetic resonance (NMR) spectroscopy, a rich understanding of the structure-activity relationships (SAR) that attend enzyme catalysis can be obtained. What is germane to the present discussion is that this structural and mechanistic understanding can be exploited to discover and design small molecule inhibitors-mimicking key structural features of reaction intermediates-that form high-af nity interactions with speci c conformational states of the ligand-binding pocket of the target enzyme. In this chapter, we describe the application of mechanistic and structural enzymology to drug discovery efforts with an emphasis on the evolution of structural changes that attend catalysis and the exploitation of these various conformational forms for high-af nity inhibitor development.
