In silico antimalarial bioprospecting of neem (Azadirachta indica) quinine-derivative alkaloids

Malaria, driven by the protozoan Plasmodium spp. and transmitted by Anopheles mosquitoes, remains a significant global health threat. With the emergence of chloroquine-resistant malaria, alternative treatments derived from natural compounds are pressing. This study explores neem (Azadirachta indica), a Southeast Asian plant, as a source of antimalarial agents. A Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) analysis of a neem leaf extract identified 184 compounds, of which five quinone-derivative compounds were subject to in silico screening against three Plasmodium falciparum virulence proteins: Purine nucleoside phosphorylases (PNP), dihydroorotate dehydrogenase (DHODH), and erythrocyte membrane protein 1 (EMP1). Among these five compounds (A-E), compound C emerged as the top candidate, ranking highly in molecular stability (FMO energy gaps), drug-likeness (Lipinski’s Rule of 5), bioavailability, and synthetic accessibility. Compound C also exhibited strong binding affinity to PNP and DHODH in molecular docking and dynamics simulations and ranked among the top three for binding free energy in MM/PBSA calculations. However, it lacked predicted antiprotozoal activity in PASS screening, though it shared key enzyme targets with established antimalarial drugs. These findings nominate compound C as a promising candidate for further research as a potential antimalarial agent.