Structure-based design of novel inhibitors of plasmepsins: A family of anti-malarial targets

The plasmepsins are key enzymes in the life cycle of the Plasmodium parasites responsible for malaria, a disease that afflicts more than 300 million individuals annually. Since plasmepsin inhibition leads to starvation of the parasite, these enzymes have been acknowledged to be important targets for the development of new anti-malarial drugs. The development of effective plasmepsin inhibitors, however, is complicated by their genomic diversity which gives rise not to a unique target for drug development, but to a family of closely related targets. Four related and essential proteases, plasmepsin I, plasmepsin II, plasmepsin IV and the histo-aspartyl protease HAP, have been identified in the parasite. Adaptive ligands are designed to bind with extremely high affinity to a primary target within the family (plasmepsin II) and to maintain significant affinity against the other members. High affinity inhibitors of plasmepsin II mimicking the transition state of the natural substrate were identified and characterized. These inhibitors are based upon an allophenylnorstatine scaffold. The strongest inhibitors of plasmepsin II bind with subnanomolar affinities to their primary target. KNI-10006, an inhibitor with a K_i of 0.5 nM against Plm II, binds with K_i ratios of 0.4, 7.1, 17.7 against plasmepsin IV, I and HAP, respectively. Adaptive ligands have characteristic thermodynamic signatures in that unlike their rigid counterparts, their binding is both enthalpically and entropically favorable. This realization has lead to the development of rigorous thermodynamic design guidelines. These guidelines take advantage of correlations between the structure of lead compounds and the enthalpic and entropic components of the binding affinity. Allophenylnorstatine-based inhibitors bind to plasmepsin II with a strong favorable enthalpy between −1.5 to −6 kcal/mol. Docking of these compounds in the active site of Plm II reveals that the core of these inhibitors faces the conserved areas of plasmepsins whereas the substitutions on the inhibitor core face variable areas of plasmepsins. Adaptive inhibitors are expected to play an important role in the chemotherapy of infectious diseases.