A protease is an enzyme that specifically recognizes and breaks apart a given protein or similar proteins. The destruction of the protein is accomplished by the ability of the protease to break the peptide bonds that link the constituent parts of the protein--the amino acids--together.

Proteases are present in every living cell of every living organism. As soon as the cells are disrupted, the proteases are released and can quickly degrade any given protein of interest. In experimental work this behavior is highly undesirable, as the protease destruction of other proteins greatly reduces the yield of the target protein in isolation experiments.

Fortunately, chemical substances called protease inhibitors can prevent protease activity. A protease inhibitor is any substance that partially or completely blocks functioning of the protease. This can be accomplished by the binding of the inhibitor to the active site within the protease at which the breakage of the peptide bonds occurs. Other protease inhibitors exert their influence by binding to some other place on the protease's structure that prevents, through a conformational (shape) change in the protein, the active site from functioning properly. Because of the binding specificity, a given inhibitor will be active against only one or a certain number of types of protease.

Protease inhibitors have become important clinically because of their promise as a treatment for AIDS--acquired immunodeficiency syndrome. They work by blocking the activity of a protease associated with the AIDS virus, the human immunodeficiency virus (HIV). HIV protease clips a long viral protein into several differently sized smaller proteins. These smaller proteins are necessary for proper HIV assembly and for the ability of these newly-made virus particles to infect other cells once they are released from the infected cell. It is the processing of the long viral protein into the infection-critical smaller proteins that is blocked by protease inhibitors. The spread of the virus to new cells is subsequently halted.

To combat HIV, protease inhibitors are usually administered as a cocktail with other agents that block the transcription of the viral RNA into DNA. This treatment is costly and monitoring of the body's response is important, as resistance to protease inhibitors can develop.