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Tans-Atovaquone is widely used as an effective drug to treat uncomplicated malaria. But its cis-isomer is not a drug. In the present study, we report energy minimized binding pattern of trans-Atovaquone and its cisisomer with cytochrome bc1 (cytbc1) of yeast. The new feature of this molecular docking computation is that structural parameters of the drug molecules have been determined from their crystal structures. The energy minimized structures of protein-drug complexes show that H-bond distant between His-181 of cytochrome bc1 and C=O of Atovaquone for trans-Atovaquone is 2.85 A and 5.3 A with the cis-isomer. The role of this H-bonding interaction in dictating drug potency is in conformity with proton-coupled electron transport mechanism of drug action.

Binding Study of Cis-Atovaquone with Cytochrome bc1 of Yeast