Analyzing Thiol-Dependent Redox Networks in the Presence of Methylene Blue and Other Antimalarial Agents with RT-PCR-Supported in silico Modeling

Abstract

BackgroundIn the face of growing resistance in malaria parasites to drugs, pharmacological combination therapies are important. There is accumulating evidence that methylene blue (MB) is an effective drug against malaria. Here we explore the biological effects of both MB alone and in combination therapy using modeling and experimental data.ResultsWe built a model of the central metabolic pathways in P. falciparum. Metabolic flux modes and their changes under MB were calculated by integrating experimental data (RT-PCR data on mRNAs for redox enzymes) as constraints and results from the YANA software package for metabolic pathway calculations. Several different lines of MB attack on Plasmodium redox defense were identified by analysis of the network effects. Next, chloroquine resistance based on pfmdr/and pfcrt transporters, as well as pyrimethamine/sulfadoxine resistance (by mutations in DHF/DHPS), were modeled in silico. Further modeling shows that MB has a favorable synergism on antimalarial network effects with these commonly used antimalarial drugs.ConclusionsTheoretical and experimental results support that methylene blue should, because of its resistance-breaking potential, be further tested as a key component in drug combination therapy efforts in holoendemic areas.

Aspergillus fumigatus Challenged by Human Dendritic Cells: Metabolic and Regulatory Pathway Responses Testify a Tight Battle

“…The gene expression data were fitted to the enzymes in the metabolic network model and we calculated the activities of all the enzymes in the model. The calculation error of fitting the expression data to enzyme activity has been estimated to be only a few percent (Cecil et al, 2011, 2015; Zirkel et al, 2012). YanaSquare uses an evolutionary algorithm (EA) to calculate flux activities using estimates of flux strength either from direct flux measurements (almost never available) or estimates from protein or gene expression data.…”

Identification of Antifungal Targets Based on Computer Modeling

“…One strategy is to target proteins present in both the eukaryotic pathogen and its host, but aiming at differences in domain structure so that the drug affects mainly the protein in the pathogen. Zirkel et al combined in silico modelling and PCR data to demonstrate that methylene blue selectively inhibits glutathione reductase of Plasmodium falciparum without affecting the human glutathione reductase much [ 9 ]. Pharmacologically interesting CA/C1 peptidases have also shown several functional overlaps in P. falciparum , P. berghei , and their hosts— Mus musculus and Homo sapiens .…”

Elementary mode analysis reveals that Clostridium acetobutylicum modulates its metabolic strategy under external stress

“…Elementary Mode Analysis (EMA), a constraint-based approach, has been used for studying the metabolic network of a number of organisms. 9,14,[20][21][22][23][24][25][26] An elementary mode is defined as a possible sub-pathway, which has a minimal set of enzymes that can operate at the steady state (with irreversible reactions in the network). [27][28][29] In this approach, a network is first converted into smaller elementary modes.…”