Malaria is a major cause of human mortality, with over one million deaths worldwide every year. Four Plasmodium species infects humans; among them, Plasmodium falciparum is the most lethal. The increased resistance of P. falciparum to most currently available drugs challenges the control of malaria. Catabolism of host-cell hemoglobin represents an essential pathway that is being currently investigated for antimalarial drug discovery. P. falciparum catabolizes large quantities of host-cell hemoglobin. In the final stages of hemoglobin digestion, the parasite is hypothesised to employ aminopeptidase activity to complete the digestion process. The aminopeptidases M1, M17 and M18 have been validated as drug targets as they appear to be pivotal for the survival of the parasite.  We employed a fast virtual screening approach for the identification of novel chemical scaffolds that could act as antimalarial agents targeting the M1, M17 and M18 enzymes. The X-ray crystal structure of the three enzymes bound to known inhibitors was analysed to derive a shared 3D pharmacophore. The derived pharmacophore was subsequently used to screen and filter the Ambinter database, which stores six million of purchasable compounds. The identified virtual hits were further filtered by means of molecular docking simulations. Finally, the recently developed HYDE scoring function was used to predict the binding free energy of interaction and rank the obtained virtual hits. Our results identified twelve virtual hits with different chemical scaffolds that were predicted to bind to all three enzymes. We have initiated in vitro testing of these compounds to validate our in silico approach.