Infectious diseases, such as malaria, leishmaniasis, and African trypanosomiasis (sleeping sickness), are public health problems in more than 90 countries with millions of deaths per year. [1] The drugs mainly used today for chemotherapy, especially against the neglected diseases leishmaniasis and trypanosomiasis, were developed decades ago, lack appropriate efficacy, and give rise to severe side effects. The absence of highly effective vaccines and the inadequate control of insect vectors demand new approaches to drug development. Furthermore, resistance of the pathogens causing malaria (Plasmodium falciparum) and African trypanosomiasis (sleeping sickness caused by Trypanosoma brucei gambiense and T. b. rhodesiense, and nagana in livestock, caused by T. b. brucei) against established drugs has been increasing. Therefore, research to identify new drugs, ideally addressing new targets, is more important than ever. [2] Parasite cysteine proteases of clan CA, family C1 (papain family), [3] are considered to be new promising therapeutic targets. These enzymes, namely falcipains [4] in plasmodia, and rhodesain [5] in T. b. rhodesiense, play important roles in the life cycles of the parasites. Cysteine protease inhibitors have been reported to kill African trypanosomes in vitro and in animal models of the disease, [6] however, it is not yet clear whether rhodesain is the only target of the inhibitors.[7] Proteases of malaria parasites play pivotal roles in the processes of host erythrocyte rupture, erythrocyte invasion, and hemoglobin degradation. Treatment with cysteine protease inhibitors blocks hemoglobin hydrolysis and development of the parasite. [4,[8][9][10][11][12] Both enzymes belong to the cathepsin L subfamily of the papain family of cysteine proteases.In a general protease-and cell-based screening using different proteases, we recently discovered hybrid compounds containing both a peptidic and a nonpeptidic moiety, namely a guanidinocarbonyl pyrrole, as potent inhibitors of falcipains with antiplasmodial activity (Scheme 1). The compounds were originally designed as new aspartic protease inhibitors but did not fulfill this expectation. However, the tert-butoxycarbonyl (Boc)-protected intermediates, for example, falcipain inhibitor A with a hybrid structure, unexpectedly displayed inhibitory activity against falcipains and plasmodia (FP-2: IC 50 = 3.1 mm; FP-3: no inhibition at 100 mm; P. f.: IC 50 = 1.7 mm). In order to evaluate which inhibitor fragment is responsible for the remarkable activity, the two building blocks B and C were tested individually. The peptidic fragment C was moderately active in the form of the ester (R = Et: FP-2: IC 50 = 34 mm; FP-3: IC 50 = 49 mm; P. f.: IC 50 = 29 mm; R= H: no inhibition at 100 mm); this was not unexpected, as Michael-acceptor-derived peptides have already been shown to be cysteine protease inhibitors. [13] However, to our surprise, the Boc-protected guanidinocarbonyl moiety B was also an efficient falcipain inhibitor (FP-2: IC 50 = 33 mm).Since preliminary docki...