Mechanisms of macromolecular protease inhibitors.

Proteolytic enzymes are ubiquitous in all organisms and constitute 2–4% of encoded gene products. They are critical for diverse biological processes such as digestion, blood clotting, host defense, pathogenic infection, viral replication, wound healing, and disease progression, to name but a few. Because proteases trigger an irreversible event—the cleavage of a protein—their activity must be tightly controlled. Dysregulated proteolytic activity causes a disruption in the homeostatic balance of a biological system and can result in any number of poor biological outcomes. As a result, nature has developed a number of strategies to control proteolysis, including spatial and temporal regulation, zymogen activation and protease degradation, and through the inhibition of proteases by macromolecular inhibitors. Somewhat surprisingly, relatively few design principles underlie the mechanisms of inhibition of a myriad range of macromolecular protease inhibitors. Significant engineering efforts have gone into modifying and improving inhibitor potency and specificity, and to a large extent, the same design principles that work well for naturally occurring protease inhibitors have proved valuable for inhibitors developed in the laboratory. This review aims to survey the mechanisms by which macromolecular protease inhibitors function. To do this, inhibitors have been divided into categories based on their mechanism in order to illustrate that a relatively small number of design principles can be combined to develop new and effective protease inhibitors. These divisions are not strict, and many inhibitors could be grouped in a number of classes. The list of mechanisms presented here is not exhaustive in its treatment of all inhibitors, but aims to be illustrative of the many ways proteases can be inhibited. For more information on genome-wide protease mining, protease mechanism, preclinical inhibition, and drug-discovery efforts, the reader is directed to excellent reviews that have been written in recent years. Figure 1 provides an overview of basic substrate and protease nomenclature that will be used in this review.