Plasmepsins II (EC number: 126.96.36.199) 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. A series of pyrrolidine derivatives, originally synthesized as HIV-1 protease inhibitors, were tested for activity against plasmepsin (Plm). Inhibitors in the nanomolar range were discovered for the Plm II and IV isoforms. Detailed studies were carried out to identify putative binding modes that help to explain the underlying structure–activity relationships. Reasonable binding modes were generated for pyrrolidine-3,4-diester derivatives and a substituted 3,4-diaminopyrrolidine inhibitor by using a crystal structure of inhibitor-bound Plm II (PDB ID: 1LEE). Modeling studies indicated that the flap of available Plm crystal structures is not sufficiently opened to accommodate the 3,4-bis(aminomethylene)pyrrolidines. Molecular dynamics simulations were performed to analyze the flexibility of the protein in greater detail, leading to a binding mode hypothesis for the 3,4-bis(aminomethylene)pyrrolidines and providing further insight and general implications for the design of Plm II inhibitors.