Cytochrome bc1 (EC 1.10.2.2, bc1) is an essential component of the cellular respiratory chain, which catalyzes electron transfer from quinol to cytochrome c and concomitantly the translocation of protons across the membrane. It has been identified as a promising target in malaria parasites. The structure-based pharmacophore modelling and molecular dynamic simulation approach have been employed to identify novel inhibitors of cytochrome bc1. The best structure-based pharmacophore hypothesis (Hypo1) consists of one hydrogen bond acceptor (HBA), one general hydrophobic (HY), and two hydrophobic aromatic features (HYAr). Further, hydrogen interactions and hydrophobic interactions of known potent inhibitors with cytochrome bc1 were compared with Hypo1, which showed that the Hypo1 has good predictive ability. The validated Hypo1 was used to screen the chemical databases. The hits obtained were subsequently subjected to the molecular docking analysis to identify false-positive hits. Moreover, the molecular docking results were further validated by molecular dynamics simulations. Binding-free energy analysis using MM-GBSA method reveals that the van der Waals interactions and the electrostatic energy provide the basis for favorable absolute free energy of the complex. The five virtual hits were identified as possible candidates for the designing of potent cytochrome bc1 inhibitors. 1. Introduction The cytochrome bc1 complex (EC 1.10.2.2, bc1) is a vital component of the cellular respiratory chain and the photosynthetic apparatus in photosynthetic bacteria [1]. It is found on the plasma membrane of bacteria and in the inner mitochondrial membrane of eukaryotes [2]. It consists of two heme groups, cytochrome b, iron-sulfur protein (ISP), with a Rieske-type Fe2S2 cluster and cytochrome c1 that undergoes reduction and oxidation during turnover of the enzyme [3]. The role of cytochrome bc1 complex is to catalyze the electron transfer from quinol to a soluble cytochrome c (cyt c), and this electron transfer couples to the translocation of protons across the membrane [4]. Due to its important role in the life cycle, inhibition of the bc1 complex has become an important target in the discovery of new antimalarial agent [5]. Atovaquone is a competitive inhibitor of the quinol oxidation site of cytochrome bc1. It has also shown potential role against pneumocystis pneumonia and toxoplasmosis in immunocompromised individuals [6–8]. So far, two separate catalytic sites within the bc1 complex have been identified and confirmed by X-ray crystallographic studies: the quinol
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