Unraveling the Metabolic Interactions in Plasmodium Falciparum Using a Novel Genome-Scale Model Reconstruction

The identification of novel and more efficient antimalarial therapies is a highly pressing need to fight against multi-drug-resistant parasites. Computational methods that analyze the metabolism of the pathogen can provide testable hypotheses and guide the experimental efforts for the identification of drug targets in metabolic networks. In this study, we aim at answering the following questions: (i) which of the substrates available at the blood stage are essential for growth simulation? (ii) what metabolic enzymes are essential in silico for replication? (iii) what are the intracellular metabolites that determine the directionality and function of metabolic enzymes? For this purpose, we have first developed iPfa, a newly reconstructed genome-scale metabolic model of P. falciparum, which extends the scope of the existing metabolic models of this parasite. We have then performed advanced computational analyses of iPfa, which involve the integration in iPfa of metabolomics data measured in P. falciparum at the blood stage and its thermodynamics-based flux analysis (TFA).

In our computational studies, we identify the minimal nutritional requirements of P. falciparum at the blood stage and we identify the in silico minimal media, which is composed of only 23 substrates that are required for growth. We also identify the genes and enzymes that may represent drug targets for the blood-stage P. falciparum infection. With TFA and metabolomics data integrated, we predict 63 genes and 25 pairs of genes to be essential for the intraerythrocytic growth of the parasite.  In total, we found supporting evidence for 35 of these predictions and no information was found for 28 genes that remain to be tested. We also identify metabolites, like glutamine or CDP-ethanolamine, whose intracellular concentration determines the directionality and function of key reactions in the metabolic network. Our computational results provide novel insights about the metabolic capabilities and interactions of P. falciparum that can guide experimental efforts towards better understanding of the pathogen’s physiology and, ultimately, towards the identification of novel antimalarial drug targets.