Targeting the Ubiquinol-Reduction (Q(i)) Site of the Mitochondrial Cytochrome bc(1) Complex for the Development of Next Generation Quinolone Antimalarials

Simple Summary Malaria is a life-threatening disease which infects millions of people a year via mosquito bites, particularly in developing countries. Although many malaria drugs are available in the market today, all of them have been challenged by drug-resistant variants. Developing a new drug to fight mutated malaria is extremely critical. Cytochrome bc(1) complex of malaria parasites is an important drug target focused on by several antimalarial development programs. One of those is the 4(1H)-quinolone series which inhibits cytochrome bc(1) and effectively kills drug-resistant malaria parasites. However, some of these compounds have unexpected toxicity due to cross-species inhibition of human cytochrome bc(1). In this work, we explore by experimental and computational studies how 4(1H)-quinolone compounds work with human and parasite cytochrome bc(1). This information reveals the key to improved selectivity between human and parasite cytochrome bc(1) and helps drug developers to design new compounds with better therapeutic efficiency and safety. Antimalarials targeting the ubiquinol-oxidation (Q(o)) site of the Plasmodium falciparum bc(1) complex, such as atovaquone, have become less effective due to the rapid emergence of resistance linked to point mutations in the Q(o) site. Recent findings showed a series of 2-aryl quinolones mediate inhibitions of this complex by binding to the ubiquinone-reduction (Qi) site, which offers a potential advantage in circumventing drug resistance. Since it is essential to understand how 2-aryl quinolone lead compounds bind within the Qi site, here we describe the co-crystallization and structure elucidation of the bovine cytochrome bc(1) complex with three different antimalarial 4(1H)-quinolone sub-types, including two 2-aryl quinolone derivatives and a 3-aryl quinolone analogue for comparison. Currently, no structural information is available for Plasmodial cytochrome bc(1). Our crystallographic studies have enabled comparison of an in-silico homology docking model of P. falciparum with the mammalian's equivalent, enabling an examination of how binding compares for the 2- versus 3-aryl analogues. Based on crystallographic and computational modeling, key differences in human and P. falciparum Q(i) sites have been mapped that provide new insights that can be exploited for the development of next-generation antimalarials with greater selective inhibitory activity against the parasite bc(1) with improved antimalarial properties.