Cysteine proteinases are key virulence factors of the protozoan parasite Entamoeba histolytica. We have shown that cysteine proteinases play a central role in tissue invasion and disruption of host defenses by digesting components of the extracellular matrix, immunoglobulins, complement, and cytokines. Analysis of the E. histolytica genome project has revealed more than 40 genes encoding cysteine proteinases. We have focused on E. histolytica cysteine proteinase 1 (EhCP1) because it is one of two cysteine proteinases unique to invasive E. histolytica and is highly expressed and released. Recombinant EhCP1 was expressed in Escherichia coli and refolded to an active enzyme with a pH optimum of 6.0. We used positional-scanning synthetic tetrapeptide combinatorial libraries to map the specificity of the P1 to P4 subsites of the active site cleft. Arginine was strongly preferred at P2, an unusual specificity among clan CA proteinases. A new vinyl sulfone inhibitor, WRR483, was synthesized based on this specificity to target EhCP1. Recombinant EhCP1 cleaved key components of the host immune system, C3, immunoglobulin G, and pro-interleukin-18, in a time-and dose-dependent manner. EhCP1 localized to large cytoplasmic vesicles, distinct from the sites of other proteinases. To gain insight into the role of secreted cysteine proteinases in amebic invasion, we tested the effect of the vinyl sulfone cysteine proteinase inhibitors K11777 and WRR483 on invasion of human colonic xenografts. The resultant dramatic inhibition of invasion by both inhibitors in this human colonic model of amebiasis strongly suggests a significant role of secreted amebic proteinases, such as EhCP1, in the pathogenesis of amebiasis.The intestinal protozoan parasite Entamoeba histolytica is the etiologic agent of amebic colitis and liver abscess, which cause high rates of morbidity and mortality worldwide (49). The mechanism by which Entamoeba histolytica is able to invade and damage the host's target tissues has been the subject of intense research. Several virulence factors have been identified, including secreted cysteine proteinases (39, 42). These amebic enzymes have been implicated in the in vitro cytopathology of cell monolayers (20, 23), which correlates with the observed separation of colonic epithelial cells before invasion (51). Other correlates with invasion include the ability of cysteine proteinases to degrade extracellular matrix components (19) and colonic mucin (31, 32). Furthermore, cysteine proteinases enable E. histolytica to evade the host's immune defenses by activating and locally depleting complement (43), and by degrading anaphylotoxins C3a and C5a (41), human immunoglobulin G (IgG) (53), human IgA (21), and interleukin-18 (IL-18) (37).The recent completion of the Entamoeba histolytica genome project has revealed the presence of at least 40 genes encoding cysteine proteinases (25). Of all the cysteine proteinase genes, only ehcp1 and ehcp5 are unique to E. histolytica, as their orthologs are either absent (ehcp1) or nonfuncti...