Inhibitor binding to the plasmepsin IV aspartic protease from Plasmodium falciparum

Plasmepsin IV (P1m IV) is one of the aspartic proteases present in the food vacuole of the malaria parasite Plasmodium falciparum involved in host hemoglobin degradation by the parasite. Using a series of previously synthesized plasmepsin inhibitors [Ersmark, K., et al. (2005) J. Med. Chem. 48, 6090-106], we report here experimental data and theoretical analysis of their inhibitory activity toward P1m IV. All compounds share a 1,2-dihydroxyethylene unit as the transition state mimic. They possess symmetric P1 and P1′ side chains and either a diacylhydrazine, a five-membered oxadiazole ring, or a retroamide at the P2 and P2′ positions. Experimental binding affinities are compared to those predicted by the linear interaction energy (LIE) method and an empirical scoring function, using both a crystal structure and a homology model for the enzyme. Molecular dynamics (MD) simulations of the modeled complexes allow a rational interpretation of the structural determinants for inhibitor binding. A ligand bearing a P2 and P2′ symmetric oxadiazole which is devoid of amide bonds is identified both experimentally and theoretically as the most potent inhibitor of P1m IV. For the P2 and P2′ asymmetric compounds, the results are consistent with earlier predictions regarding the mode of binding of this class of inhibitors to P1m II. Theoretical estimation of selectivity for some compounds is also reported. Significant features of the P1m IV binding pocket are discussed in comparison to related enzymes, and the results obtained here should be helpful for further optimization of inhibitors.