Structure-based discovery of Plasmodium falciparum DPAP-1 inhibitor and its experimental validation as an antimalarial agent.

Malaria remains one of the world’s most persistent and deadly infectious diseases, largely driven by Plasmodium falciparum (P. falciparum) strains that have developed resistance to conventional treatments. To explore new therapeutic options, the food vacuole enzyme Dipeptidyl Aminopeptidase-1 (DPAP-1) of P. falciparum was selected due to its crucial biological role. A comprehensive virtual screening of a natural compound library derived from plants led to the identification of three promising molecules (Hesperidin methylchalcone, Cepharanthine, and 6-Methoxydihydroavicine). These ligands demonstrated strong docking interactions and complex stability during 500-ns molecular dynamics simulations. Furthermore, the MM-GBSA calculation revealed that all these molecules exhibited relatively high binding affinities, particularly Hesperidin methylchalcone, which had a low free energy of binding (ΔG = -63.73 kcal/mol). Machine learning predictions estimated high biological activity, with Hesperidin methylchalcone achieving a pIC₅₀ value of 8.6. Experimental validation through P. falciparum 3D7 growth inhibition assays confirmed a dose-dependent reduction in parasitemia at nanomolar concentrations (50–1000 nM), demonstrating strong inhibition at 500 nM and 1000 nM. Together, these computational and experimental results highlight Hesperidin methylchalcone as a potent antimalarial candidate with favorable pharmacological and dynamic properties, warranting further preclinical investigation for the development of malaria therapy.