A Chemical Genomic Analysis of Decoquinate, a <i>Plasmodium falciparum</i> Cytochrome <i>b</i> Inhibitor

Decoquinate has single-digit nanomolar activity against <i>in vitro</i> blood stage <i>Plasmodium falciparum</i> parasites, the causative agent of human malaria. <i>In vitro</i> evolution of decoquinate-resistant parasites and subsequent comparative genomic analysis to the drug-sensitive parental strain revealed resistance was conferred by two nonsynonymous single nucleotide polymorphisms in the gene encoding cytochrome <i>b</i>. The resultant amino acid mutations, A122T and Y126C, reside within helix C in the ubiquinol-binding pocket of cytochrome <i>b</i>, an essential subunit of the cytochrome <i>bc</i>₁ complex. As with other cytochrome <i>bc</i>₁ inhibitors, such as atovaquone, decoquinate has low nanomolar activity against <i>in vitro</i> liver stage <i>P. yoelii</i> and provides partial prophylaxis protection when administered to infected mice at 50 mg kg^–1. In addition, transgenic parasites expressing yeast dihydroorotate dehydrogenase are >200-fold less sensitive to decoquinate, which provides additional evidence that this drug inhibits the parasite’s mitochondrial electron transport chain. Importantly, decoquinate exhibits limited cross-resistance to a panel of atovaquone-resistant parasites evolved to harbor various mutations in cytochrome <i>b</i>. The basis for this difference was revealed by molecular docking studies, in which both of these inhibitors were shown to have distinctly different modes of binding within the ubiquinol-binding site of cytochrome <i>b