ABSTRACT
Enzymes are powerful biological catalysts that are essential for the proper maintenance and propagation of any organism. These properties make them excellent candidates as therapeutic targets to combat diseases of either genetic or pathogenic origin. In this regard, one goal of molecular medicine is to develop and implement effective agents that can modulate the activity of various enzymes involved in essential biological pathways. The process of developing and characterizing these small molecules, i.e., rational drug design, often requires a priori knowledge of the enzyme in question. This chapter provides a rational approach to first characterizing the dynamic behavior of enzymes in the absence of potential modulators such as inhibitors or activators by studying the kinetics of enzyme-catalyzed reactions. To lay the foundation for understanding these catalysts, a brief discussion is provided regarding the principles of chemical catalysis as well as how these general principles are applied to the more complex biological catalysts. This is followed by a quantitative evaluation of single-substrate reactions, which includes sections on how to monitor enzyme activity, the various ways to analyze the generated rate data, and how to interpret the information derived from these experiments. A thorough discussion of the biologically relevant kinetic parameters Vmax, Km, and Vmax/Km is provided. Building upon the analysis for a simple single-substrate reaction, more complex scenarios involving multisubstrate reactions are discussed. Here again, the focus is on first designing the proper kinetic experiments and then interpreting the
generated initial velocity data within the context of several possible kinetic mechanisms. These include distinguishing between a sequential-and a double-displacement mechanism, providing information regarding the order of substrate binding and product release, and identifying the location of the rate-limiting step along the reaction pathway. Finally, a discussion of the utility of applying pre-steady-state kinetic techniques to measure individual rate constants is provided. In general, the various kinetic sections outlined here provide the cornerstone for understanding the effects of therapeutically relevant inhibitors and inactivators of enzyme activity. Furthermore, understanding the kinetic behavior of an enzyme is essential to understanding the chemical mechanism, transition state structure, and regulation of any enzyme that again can be used for the rational design of therapeutic agents.
