Reconstruction and flux-balance analysis of the Plasmodium falciparum metabolic network

Center for Computational Biology and Bioinformatics, Columbia University, New York City, NY 10032, USA.
Molecular Systems Biology (Impact Factor: 10.87). 09/2010; 6(1):408. DOI: 10.1038/msb.2010.60
Source: PubMed


Genome-scale metabolic reconstructions can serve as important tools for hypothesis generation and high-throughput data integration. Here, we present a metabolic network reconstruction and flux-balance analysis (FBA) of Plasmodium falciparum, the primary agent of malaria. The compartmentalized metabolic network accounts for 1001 reactions and 616 metabolites. Enzyme-gene associations were established for 366 genes and 75% of all enzymatic reactions. Compared with other microbes, the P. falciparum metabolic network contains a relatively high number of essential genes, suggesting little redundancy of the parasite metabolism. The model was able to reproduce phenotypes of experimental gene knockout and drug inhibition assays with up to 90% accuracy. Moreover, using constraints based on gene-expression data, the model was able to predict the direction of concentration changes for external metabolites with 70% accuracy. Using FBA of the reconstructed network, we identified 40 enzymatic drug targets (i.e. in silico essential genes), with no or very low sequence identity to human proteins. To demonstrate that the model can be used to make clinically relevant predictions, we experimentally tested one of the identified drug targets, nicotinate mononucleotide adenylyltransferase, using a recently discovered small-molecule inhibitor. © 2010 EMBO and Macmillan Publishers Limited All rights reserved.

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Available from: Germán Plata, Aug 05, 2014
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    • "Several bioinformatic approaches have previously been employed to help identify or prioritize drug targets for Plasmodium parasites. These include techniques based on automated identification of important steps in metabolic pathways (Yeh et al., 2004; Fatumo et al., 2009; Huthmacher et al., 2010; Plata et al., 2010), techniques that combine chemical starting points and proteinbased queries (Joubert et al., 2009), as well as the use of the TDRtargets web-resource ( (Magarinos et al., 2012) to prioritize drug targets through the combination of multiple data types relevant to drug development (Crowther et al., 2010). "
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    ABSTRACT: Aminoacyl-tRNA synthetases (aaRSs) are housekeeping enzymes that couple cognate tRNAs with an amino acid so as to transmit genomic information for protein translation. Plasmodium falciparum nuclear genome encodes two copies of methionyl-tRNA synthetases (PfMRS(cyt) and PfMRS(api)). Phylogenetic analyses reveal that both proteins are of primitive origin and related to heterokonts (PfMRS(cyt)) or proteo/primitive bacteria (PfMRS(api)). We show that PfMRS(cyt) localizes in parasite cytoplasm while PfMRS(api) localizes to apicoplast in asexual stages of malaria parasites. Two of the known bacterial MRS inhibitors, REP3123 and REP8839 hampered Plasmodium growth very effectively in early and late stages of parasite development. Small molecule drug-like libraries were screened against modeled PfMRS structures and several 'hits' showed significant effects on parasite growth. We then tested the effect of 'hit' compounds on protein translation by labeling nascent proteins with S(35) labeled cysteine and methionine. Three of the tested compounds reduced protein synthesis and also blocked parasite growth progression from ring to trophozoite stages. Drug docking studies suggest distinct modes of binding for three compounds when compared with the enzyme product methionyl adenylate. This study therefore provides new targets (PfMRSs) and hit compounds that together can be explored for development as anti-malarials. Copyright © 2015, American Society for Microbiology. All Rights Reserved.
    Antimicrobial Agents and Chemotherapy 01/2015; 59(4). DOI:10.1128/AAC.02220-13 · 4.48 Impact Factor
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    • "We enzymatically characterized the parasite nicotinate mononucleotide adenylyltransferase (PfNMNAT) in vitro using purified recombinant protein and we demonstrate its ability to complement the Escherichia coli homolog in vivo. Following up on previous predictions that PfNMNAT is essential to P. falciparum development [25], we synthesized and screened derivatives of previously identified inhibitors of bacterial NMNATs [26] against purified PfNMNAT and live parasite culture. This work validates the parasite NAD+ metabolic pathway as a novel drug target and identifies viable lead compounds for further development as antimalarial drugs. "
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    ABSTRACT: Nicotinamide adenine dinucleotide (NAD+) is an essential metabolite utilized as a redox cofactor and enzyme substrate in numerous cellular processes. Elevated NAD+ levels have been observed in red blood cells infected with the malaria parasite Plasmodium falciparum, but little is known regarding how the parasite generates NAD+. Here, we employed a mass spectrometry-based metabolomic approach to confirm that P. falciparum lacks the ability to synthesize NAD+ de novo and is reliant on the uptake of exogenous niacin. We characterized several enzymes in the NAD+ pathway and demonstrate cytoplasmic localization for all except the parasite nicotinamidase, which concentrates in the nucleus. One of these enzymes, the P. falciparum nicotinate mononucleotide adenylyltransferase (PfNMNAT), is essential for NAD+ metabolism and is highly diverged from the human homolog, but genetically similar to bacterial NMNATs. Our results demonstrate the enzymatic activity of PfNMNAT in vitro and demonstrate its ability to genetically complement the closely related Escherichia coli NMNAT. Due to the similarity of PfNMNAT to the bacterial enzyme, we tested a panel of previously identified bacterial NMNAT inhibitors and synthesized and screened twenty new derivatives, which demonstrate a range of potency against live parasite culture. These results highlight the importance of the parasite NAD+ metabolic pathway and provide both novel therapeutic targets and promising lead antimalarial compounds.
    PLoS ONE 04/2014; 9(4):e94061. DOI:10.1371/journal.pone.0094061 · 3.23 Impact Factor
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    • "Applying a constraint-based framework, we systematically explored strain-specific models based on the differential expression of mRNA data. Although this method does not take into account any post-translational modifications or the specific activity of enzymes, mRNA expression has previously been shown to be useful in determining relative metabolic flux capacity (Colijn et al, 2009; Plata et al, 2010). "
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    ABSTRACT: Increasingly, metabolic potential is proving to be a critical determinant governing a pathogen's virulence as well as its capacity to expand its host range. To understand the potential contribution of metabolism to strain-specific infectivity differences, we present a constraint-based metabolic model of the opportunistic parasite, Toxoplasma gondii. Dominated by three clonal strains (Type I, II, and III demonstrating distinct virulence profiles), T. gondii exhibits a remarkably broad host range. Integrating functional genomic data, our model (which we term as iCS382) reveals that observed strain-specific differences in growth rates are driven by altered capacities for energy production. We further predict strain-specific differences in drug susceptibilities and validate one of these predictions in a drug-based assay, with a Type I strain demonstrating resistance to inhibitors that are effective against a Type II strain. We propose that these observed differences reflect an evolutionary strategy that allows the parasite to extend its host range, as well as result in a subsequent partitioning into discrete strains that display altered virulence profiles across different hosts, different organs, and even cell types.
    Molecular Systems Biology 11/2013; 9(1):708. DOI:10.1038/msb.2013.62 · 10.87 Impact Factor
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