Subtle Changes in Endochin-Like Quinolone Structure Alter the Site of Inhibition within the Cytochrome bc 1 Complex of Plasmodium falciparum

The cytochrome bc 1 complex (cyt bc 1 ) is the third component of the mitochondrial electron transport chain and is the target of several potent antimalarial compounds, including the naphthoquinone atovaquone (ATV) and the 4(1 H )-quinolone ELQ-300. Mechanistically, cyt bc 1 facilitates the transfer of electrons from ubiquinol to cytochrome c and contains both oxidative (Q o ) and reductive (Q i ) catalytic sites that are amenable to small-molecule inhibition. Although many antimalarial compounds, including ATV, effectively target the Q o site, it has been challenging to design selective Q i site inhibitors with the ability to circumvent clinical ATV resistance, and little is known about how chemical structure contributes to site selectivity within cyt bc 1 . Here, we used the proposed Q i site inhibitor ELQ-300 to generate a drug-resistant Plasmodium falciparum clone containing an I22L mutation at the Q i region of cyt b . Using this D1 clone and the Y268S Q o mutant strain, P. falciparum Tm90-C2B, we created a structure-activity map of Q i versus Q o site selectivity for a series of endochin-like 4(1 H )-quinolones (ELQs). We found that Q i site inhibition was associated with compounds containing 6-position halogens or aryl 3-position side chains, while Q o site inhibition was favored by 5,7-dihalogen groups or 7-position substituents. In addition to identifying ELQ-300 as a preferential Q i site inhibitor, our data suggest that the 4(1 H )-quinolone scaffold is compatible with binding to either site of cyt bc 1 and that minor chemical changes can influence Q o or Q i site inhibition by the ELQs.