Assessing the in vitro efficacy of in silico designed compounds targeting the malarial Qi site of cytochrome bc1

Abstract

Plasmodium falciparum is the causative agent of the most commonly fatal form of malaria in Africa with annual deaths of more than 300 000. The rapid development and spread of antimalarial drug resistance by the parasite have stimulated research into the development of new drug classes. Target-based drug discovery have been used as a prominent and efficient tool to identify lead drugs. Reports suggest that selectively inhibiting the parasite mitochondrial electron transport could be a potential treatment effective at multi-stages of the parasite life cycle. Inhibitors of cytochrome bc1 (Cyt bc1), an essential inner mitochondrial membrane protein that drives ATP synthesis in the mitochondria are claimed to be lethal to apicomplexan species including Plasmodium. The emergence of resistance to atovaquone, a Cyt bc1 complex Qo site inhibitor, casts doubt over the long-term efficacy of new drugs targeting these mitochondrial proteins. Many aspects of potential drugs must be investigated to assess the suitability of new emerging drugs targeting the mitochondrion. In silico target-based drug design methods using Autodock vina were used to design compounds that would theoretically bind to and inhibit the Qi site of Cyt bc1 of the P. falciparum. The potential candidate compounds were selected from compounds defined by Gamo et al., (2010) and tested using in silico docking experiments. Homology models were developed and modified to improve their drug-likeness according to the Lipinski rule, QED parameters and synthesised by Wuxi App Tec. This study assessed the antiproliferative activity of six candidate compounds on P. falciparum parasites in vitro following in silico compound docking and drug likeness assessment. Initial in vitro screening data was obtained for the test compounds at 1 and 5 ?M over 96 h and full dose-response curves was performed for compounds showing >70% proliferation inhibition at 1 ?M against the 3D7 strain. Four of the test compounds, EE1, EE3, EE5 and EE7 gave IC50 values of 89 nM, 664 nM, 64 nM and 249 nM, respectively. The candidate compounds had a marginal >2-fold selectivity towards malaria parasites but did not show cross resistance, with resistance indices of >120. In conclusion, in silico docking using software programs could be utilised as a potential tool for rapidly identifying feasible target-based antimalarial compounds while avoiding high throughput screening. Other possible target sites on the mitochondrion can be used to design new chemotypes. All the designed compounds showed significant antimalarial activity against the asexual stages tested on 3D7 strain with a significant resistance index. However, these compounds showed minimal activity on the gametocyte stage. Finally, compound EE5 showed to be the most potent, more selective and with higher resistance index, hence this can be further optimised for preclinical studies.