title: Using a genome-scale metabolic network model to elucidate the mechanism of chloroquine action in Plasmodium falciparum.
abstract: Chloroquine, long the default first-line treatment against malaria, is now abandoned in large parts of the world because of widespread drug-resistance in Plasmodium falciparum. In spite of its importance as a cost-effective and efficient drug, a coherent understanding of the cellular mechanisms affected by chloroquine and how they influence the fitness and survival of the parasite remains elusive. Here, we used a systems biology approach to integrate genome-scale transcriptomics to map out the effects of chloroquine, identify targeted metabolic pathways, and translate these findings into mechanistic insights. Specifically, we first developed a method that integrates transcriptomic and metabolomic data, which we independently validated against a recently published set of such data for Krebs-cycle mutants of P. falciparum. We then used the method to calculate the effect of chloroquine treatment on the metabolic flux profiles of P. falciparum during the intraerythrocytic developmental cycle. The model predicted dose-dependent inhibition of DNA replication, in agreement with earlier experimental results for both drug-sensitive and drug-resistant P. falciparum strains. Our simulations also corroborated experimental findings that suggest differences in chloroquine sensitivity between ring- and schizont-stage P. falciparum. Our analysis also suggests that metabolic fluxes that govern reduced thioredoxin and phosphoenolpyruvate synthesis are significantly decreased and are pivotal to chloroquine-based inhibition of P. falciparum DNA replication. The consequences of impaired phosphoenolpyruvate synthesis and redox metabolism are reduced carbon fixation and increased oxidative stress, respectively, both of which eventually facilitate killing of the parasite. Our analysis suggests that a combination of chloroquine (or an analogue) and another drug, which inhibits carbon fixation and/or increases oxidative stress, should increase the clearance of P. falciparum from the host system.
authors.affiliation: Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Ft. Detrick, MD 21702, USA. Electronic address: stewari@bhsai.org.
authors.forename: Shivendra G
authors.initials: SG
authors.lastname: Tewari
authors.affiliation: Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD 21205, USA. Electronic address: sprigge2@jhu.edu.
authors.forename: Sean T
authors.initials: ST
authors.lastname: Prigge
authors.affiliation: Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Ft. Detrick, MD 21702, USA. Electronic address: jaques.reifman.civ@mail.mil.
authors.forename: Jaques
authors.initials: J
authors.lastname: Reifman
authors.affiliation: Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Ft. Detrick, MD 21702, USA. Electronic address: sven.a.wallqvist.civ@mail.mil.
authors.forename: Anders
authors.initials: A
authors.lastname: Wallqvist
mesh_terms: D000962:Antimalarials / Q000494:pharmacology*; D002470:Cell Survival / Q000187:drug effects; D002738:Chloroquine / Q000494:pharmacology*; D003198:Computer Simulation; D004261:DNA Replication / Q000187:drug effects; D020869:Gene Expression Profiling; D056084:Genetic Fitness / Q000187:drug effects; D053858:Metabolic Networks and Pathways / Q000187:drug effects*; D055432:Metabolomics; D010963:Plasmodium falciparum / Q000187:drug effects*; D049490:Systems Biology
chemical_list: D000962:Antimalarials; D002738:Chloroquine
keywords: Carbon fixation; Chloroquine; Metabolic network modeling; Plasmodium; Redox metabolism