Many drugs commonly used today to treat infectious diseases, cancers, inflammatory, cardiovascular, and metabolic diseases, are enzyme inhibitors or inactivators. Examples exist for all six classes of enzymes, but inhibitors of hydrolases, transferases, and oxidoreductases predominate. Typically, enzyme inhibitors or inactivators that progress to become drugs exert high potency toward their targets at concentrations of 100 nanomolar or less, and attending these potencies is high selectivity for their targets. Drugs that block the activity of enzymes do so by either covalent reaction with nucleophilic enzymatic residues, or by noncovalent binding. Covalent inactivation by affinity agents and mechanism-based inactivators is generally irreversible, leading to time-dependent loss of enzyme activity that is normally un-recoverable. Drugs that are noncovalent enzyme inhibitors, including bi-substrate analogs, and analogs of enzyme reaction intermediates and transition states, like their covalent counterparts, often display time-dependent inhibition despite the absence of covalent reaction. This pseudoirreversible inhibition is manifest at nanomolar concentrations of inhibitor, and is due to the isomerization of an initial enzyme–inhibitor complex to a tighter binary complex which reverses very slowly, if at all. Natural-product enzyme inhibitors have provided the blueprints for many drugs, including the statins, epoxomicin, and inhibitors of HIV protease. We describe herein the aforementioned types of enzyme inhibitors and inactivators that, through the application of medicinal chemistry have rendered new therapies, including case histories of many of the more important drugs that block the action of enzymes.