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Malaria is one of the most devastating infectious diseases that has spread to multiple countries. This protozoal-borne disease is caused by Plasmodium spp. carried by female Anopheles mosquito as the vector to human. However, as chloroquine-drug resistance malaria case was found, and more natural compounds should be tested as antimalarial drug. Neem (Azadirachta indica) is one of the plant natives in Southeast Asia, including Indonesia. In this study, leaf extract compounds were identified using Liquid Chromatography Tandem Mass Spectrophotometry (LC-MS/MS) and further characterized by in silico screening against 3 virulence factors known to be involved in the pathogenesis of P. falciparum, including purine nucleoside phosphorylases (PNP), dihydroorotate dehydrogenase (DHODH), and erythrocyte membrane protein 1 (EMP1). The LC-MS/MS resulted in 237 compounds identified, and 5 quinone-derivates were selected for further screening, dubbed compound A to E. From all 5 compounds, compound C is nominated for the best anti-malarial drug candidate in the screening as it topped the frontier molecular orbitals energy gaps (top 3), passed the Lipinski Rules of 5, bioavailability, and synthetic accessibility in ADME test, only has 1 more intermediate than quinine in biosynthetic pathway prediction, and it has some shared enzyme targets. Compound C only has no predicted activity for antiprotozoal in PASS screening. However, in molecular docking and dynamics, compound C has strong binding affinity compared to controls in PNP and DHODH, although it was the second strongest in EMP1. Compound C also belongs to the top 3 with the strongest binding free energy tested with MM/GBSA.
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