Genome‐Guided Discovery of Antimalarial 4‐Amino‐2,4‐Pentadienoate‐Containing Cyclolipodepsipeptides

Abstract

ABSTRACT 4‐Amino‐2,4‐pentadienoate‐containing cyclolipodepsipeptides (APD‐CLDs) represent a structurally distinctive family of natural products known for their selective activity against hypoxic cancer cells. To explore the structural diversity of APD‐CLDs, we have identified and prioritized cryptic APD‐CLD biosynthetic gene clusters (BGCs) for compound discovery. Using a combination of genetic and chemical methods, we successfully activated three dormant BGCs, leading to the discovery of 12 new APD‐CLDs. These newly discovered metabolites significantly expanded the diversity of the APD‐CLD family, with chloromalamides and arabimalamides representing the first halogenated and glycosylated members, respectively. Unexpectedly, chloromalamides and arabimalamides exhibited potent antiplasmodial activity, with IC 50 values in the 25–161 nM range against drug‐sensitive and multidrug‐resistant Plasmodium falciparum strains. Phenotypic studies revealed arabimalamide B halted parasite development during the asexual blood stage life cycle, resulting in enlarged digestive vacuoles, dispersed hemozoin, and ultimately reduced reinvasion efficiency. These phenotypes are reminiscent of the effect of chloroquine and other 4‐aminoquinoline drugs, suggesting that arabimalamides may disrupt the parasite's heme detoxification mechanism. Biosynthetic studies identified key scaffold‐forming and modifying enzymes, including a rare membrane glycosyltransferase in arabimalamide biosynthesis. Together, these findings unveil APD‐CLDs as new antimalarial lead scaffolds and set the stage for structural diversification and optimization.