Antimalarial 4(1H)-pyridones bind to the Q _i site of cytochrome bc ₁

Abstract

Cytochrome bc 1 is a proven drug target in the prevention and treatment of malaria. The rise in drug-resistant strains of Plasmodium falciparum, the organism responsible for malaria, has generated a global effort in designing new classes of drugs. Much of the design/redesign work on overcoming this resistance has been focused on compounds that are presumed to bind the Q o site (one of two potential binding sites within cytochrome bc 1 ) using the known crystal structure of this large membrane-bound macromolecular complex via in silico modeling. Cocrystallization of the cytochrome bc 1 complex with the 4(1H)-pyridone class of inhibitors, GSK932121 and GW844520, that have been shown to be potent antimalarial agents in vivo, revealed that these inhibitors do not bind at the Q o site but bind at the Q i site. The discovery that these compounds bind at the Q i site may provide a molecular explanation for the cardiotoxicity and eventual failure of GSK932121 in phase-1 clinical trial and highlight the need for direct experimental observation of a compound bound to a target site before chemical optimization and development for clinical trials. The binding of the 4(1H)-pyridone class of inhibitors to Q i also explains the ability of this class to overcome parasite Q o -based atovaquone resistance and provides critical structural information for future design of new selective compounds with improved safety profiles. malaria | cytochrome bc 1 | drug discovery | Plasmodium falciparum | membrane protein

Genetic Evidence for Cytochrome b Q i Site Inhibition by 4(1 H )-Quinolone-3-Diarylethers and Antimycin in Toxoplasma gondii

“…If the Lys228 residue does function in this manner, the apicomplexan Q i site has an alternate mechanism of proton uptake, given the tolerance of proline, serine, threonine, asparagine, cysteine, or leucine at this position. Cocrystallization of bovine cytochrome bc 1 with 4(1H)-pyridones suggests that the pyridone carbonyl forms a hydrogen bond with the highly conserved adjacent aspartic acid, which has also been proposed to interact with ubiquinone (10,21,22). In silico modeling of ELQ-300 docking in this structure suggests similar positioning of ELQ-300 within the Q i pocket (10).…”

“…Among the large panel of ELQs that we have synthesized, ELQ-316 was found to have the greatest efficacy against T. gondii and did not inhibit human cytochrome bc 1 at concentrations up to 10 M. Previous genetic mutations in Saccharomyces cerevisiae and Plasmodium falciparum suggest that ELQ-271 and ELQ-300, respectively, inhibit the apicomplexan cytochrome bc 1 Q i site (10,12,14). However, no direct experimental evidence for the mechanism of action of ELQs in T. gondii or of ELQ-316 has been described.…”

“…Inhibitors of the cytochrome bc 1 Q i site, such as antimycin, an antifungal compound made by Streptomyces species, have long been known, but Q i site inhibitors have not been used clinically (9). Recently, antimalarial pyridones, which inhibit the Q i site, were advanced for the first time to human studies but were withdrawn due to cardiotoxicity in rats that was related to activity against host cytochrome bc 1 (10). The endochinlike quinolone (ELQ) series of 4(1H)-quinolone-3-diarylethers are suspected to target the Q i site and have been optimized to avoid human cytochrome bc 1 inhibition (11).…”

New Opportunities in the Structure-based Design of Anti-Protozoan Agents

“…In 2015 Capper et al [42] solved two bovine cytochrome bc1 crystal structures (PDB ID 4D6T and 4D6U) bound to GSK's clopidol derivatives GW844520 and GSK932121 [43] (4 and 5, Fig. 1), determining that these compounds bind at the Qi (reduction) site ( Fig.…”

“…Both of these conclusions are promising indicators of a reduced propensity for the development of resistance in the enzyme itself. If this is the case the possibility of a combination of Qi and Qo inhibitors may require an infeasible fitness cost for the parasite target to develop resistance [42].…”