The diverse roles of cysteine proteases in parasites and their suitability as drug targets

Protozoan and metazoan parasites are the causative agents of many neglected diseases of global health import. Because these are diseases of poor people in resource-poor areas, there has been little economic incentive to develop new drugs in the pharmaceutical industry. Attention has therefore focused on suitable molecular targets in these parasites that could be exploited for new drugs at a relatively low cost. Cysteine proteases are particularly attractive for several reasons. They are ubiquitous in parasites; they are known to be druggable; and much is known about their structure, mechanism of action, and how to inhibit them. This compendium of reviews will focus attention on selected proteases and their function. Cysteine proteases are named because of the importance of a cysteine thiol group as the key nucleophile in the active site of the enzyme. The thiol group acts as a nucleophile in the initial steps of catalytic cleavage of the peptide bond (see [1,2] for a diagram). However, classification of cysteine proteases into distinct families is dependent both on sequence homology as well as on the specificity of the protease for amino acid sidechains in the “P1” position of the substrate (Fig 1). Remember, “cysteine” proteases are not named because they cleave a peptide bond next to a cysteine. Several types of cysteine proteases are represented in the genomes of human and veterinary parasites. These include Clan CA (papain family) cysteine proteases, Clan CD asparaginyl endopeptidases (legumains), and caspases [1]. Whereas trypsin family serine proteases are the dominant gene family in vertebrates, Clan CA cysteine proteases are the dominant gene family of proteases in protozoa and metazoan [4,5]. This differential is particularly striking if one observes the proteases primarily involved in gut protein digestion. With the evolution of the pancreas, S1 serine proteases became the digestive enzymes, but invertebrates’ cysteine cathepsins still play that role. The accompanying reviews on helminth parasites drive home this point. Because of the presence of an additional atomic “shell” in sulfur, the thiol group of cysteine is a much more effective nucleophile than the hydroxyl group of serine proteases. Therefore, primitive eukaryotes, like protozoa and metazoa, may have used a “more effective” family of proteases for their important biological and parasitic functions. However, this hypothesis also suggests a drawback. Cysteine proteases are more easily inactivated than serine proteases in an oxygen-rich environment. There was certainly a change in the relative abundance of serine versus cysteine protease genes in insects, mollusks, and crustaceans. The exact reasons for this shift remain unknown, but one might envision that the change reflected adaptation to terrestrial life with higher oxygen tension or the primacy of aerobic metabolism. Clan CA (papain family) cysteine proteases are the focus of this review. This is not to suggest that other cysteine proteases of parasites are not suitable drug targets. In fact, much research is now centered on drug discovery targeting legumains, metacaspases, caspases, and