The ability of the prodomains of trypanosomal cysteine proteinases to inhibit their active form was studied using a set of 23 overlapping 15-mer peptides covering the whole prosequence of congopain, the major cysteine proteinase of Trypanosoma congolense. Three consecutive peptides with a common 5-mer sequence YHNGA were competitive inhibitors of congopain. A shorter synthetic peptide consisting of this 5-mer sequence flanked by two Ala residues (AYHNGAA) also inhibited purified congopain. No residue critical for inhibition was identified in this sequence, but a significant improvement in K i value was obtained upon Nterminal elongation. Procongopain-derived peptides did not inhibit lysosomal cathepsins B and L but did inhibit native cruzipain (from Dm28c clone epimastigotes), the major cysteine proteinase of Trypanosoma cruzi, the proregion of which also contains the sequence YHNGA. The positioning of the YHNGA inhibitory sequence within the prosegment of trypanosomal proteinases is similar to that covering the active site in the prosegment of cysteine proteinases, the three-dimensional structure of which has been resolved. This strongly suggests that trypanosomal proteinases, despite their long C-terminal extension, have a prosegment that folds similarly to that in related mammal and plant cysteine proteinases, resulting in reverse binding within the active site. Such reverse binding could also occur for short procongopain-derived inhibitory peptides, based on their resistance to proteolysis and their ability to retain inhibitory activity after prolonged incubation. In contrast, homologous peptides in related cysteine proteinases did not inhibit trypanosomal proteinases and were rapidly cleaved by these enzymes.Cysteine proteinases of the papain superfamily have very similar sequences and a common catalytic mechanism; they are found in bacteria, protozoa, plants, and mammals (1, 2). These enzymes play a critical role in the life cycle of protozoan parasites, in host invasion and alteration of the host immune response (3, 4). Parasite cysteine proteinases from the genus Trypanosoma and Plasmodium, have been reported as putative targets for chemotherapeutic inhibitors (5, 6). The main drawback of this strategy is that cysteine proteinases have a broad substrate specificity, which makes it difficult to develop inhibitors that target individual proteinases.Congopain is a cathepsin L-like cysteine proteinase of Trypanosoma congolense, and cruzipain is the equivalent from Trypanosoma cruzi. These protozoan parasites cause bovine trypanosomiase in Africa and Chagas disease in South America respectively (3, 4). Cruzipain (also called cruzain) is a highly mannosylated glycoprotein and an immunodominant antigen (GP57/51) that is among the best characterized of parasitic cysteine proteinases (7-11). The three-dimensional structure of its recombinant central catalytic domain (215 residues) is very similar to those of papain and cathepsin L (11, 12). Congopain differs only slightly from cruzipain in its enzymatic specifici...