Plasmepsins (Plm) II (EC number: 3.4.23.39) and IV (EC number: 3.4.23.B14) are aspartic proteases present in the food vacuole of the malaria parasite Plasmodium falciparum and are involved in host hemoglobin degradation. Based on our established efficient synthetic sequence, a series of inhibitors for Plm II and IV has been synthesized bearing a 2,3,4,7-tetrahydro-1H-azepine scaffold as the core structural element. During the computational design cycle, thorough investigations were carried out in order to find a reasonable theoretical binding mode for Plm II and IV. The conformation of Plm II in the crystal structure (PDB code: 1LF2) provides a good starting geometry for our virtual screening approach. In contrast, the only available co-crystal structure for Plm IV of P. falciparum (PDB code: 1LS5) appears inappropriate for inhibitor design. Therefore, a homology model was constructed based on the Plm II 1LF2 structure. A combinatorial docking run using FlexX(c) suggested compounds which, after synthesis, turned out to exhibit affinities in the sub-micromolar range. The observed structure-activity relationships of the synthesized compounds confirm the assumed binding mode for Plm II and IV. The best-binding inhibitors designed for Plm II and IV are devoid of any inhibitory potency against human cathepsin D (EC number: 3.4.23.5).