Abstract
Mycobacterium tuberculosis is the focus of several investigations for design of newer drugs, as tuberculosis remains a major epidemic despite the availability of several drugs and a vaccine. Mycobacteria owe many of their unique qualities to mycolic acids, which are known to be important for their growth, survival, and pathogenicity. Mycolic acid biosynthesis has therefore been the focus of a number of biochemical and genetic studies. It also turns out to be the pathway inhibited by front-line anti-tubercular drugs such as isoniazid and ethionamide. Recent years have seen the emergence of systems-based methodologies that can be used to study microbial metabolism. Here, we seek to apply insights from flux balance analyses of the mycolic acid pathway (MAP) for the identification of anti-tubercular drug targets. We present a comprehensive model of mycolic acid synthesis in the pathogen M. tuberculosis involving 197 metabolites participating in 219 reactions catalysed by 28 proteins. Flux balance analysis (FBA) has been performed on the MAP model, which has provided insights into the metabolic capabilities of the pathway. In silico systematic gene deletions and inhibition of InhA by isoniazid, studied here, provide clues about proteins essential for the pathway and hence lead to a rational identification of possible drug targets. Feasibility studies using sequence analysis of the M. tuberculosis H37Rv and human proteomes indicate that, apart from the known InhA, potential targets for anti-tubercular drug design are AccD3, Fas, FabH, Pks13, DesA1/2, and DesA3. Proteins identified as essential by FBA correlate well with those previously identified experimentally through transposon site hybridisation mutagenesis. This study demonstrates the application of FBA for rational identification of potential anti-tubercular drug targets, which can indeed be a general strategy in drug design. The targets, chosen based on the critical points in the pathway, form a ready shortlist for experimental testing.
Highlights
Genomics is rapidly changing the very foundation of several aspects of drug discovery research, one of them being a systems biology and bioinformatics approach for rational identification of drug targets
The mycolic acid pathway (MAP) has been of great interest, and a large amount of biochemical and genetic information is available in the literature, in addition to the entire genome sequence of M. tuberculosis
We present a comprehensive identification of the components of the mycolic acid pathway and represent it mathematically based on reaction stoichiometry
Summary
Genomics is rapidly changing the very foundation of several aspects of drug discovery research, one of them being a systems biology and bioinformatics approach for rational identification of drug targets. The mycolic acid pathway (MAP) has been of great interest, and a large amount of biochemical and genetic information is available in the literature, in addition to the entire genome sequence of M. tuberculosis. It is possible to exploit these large volumes of data to construct an in silico model of the pathway, which can be simulated and analysed [11] Constructing such models forms an important step in understanding the underlying molecular mechanisms of disease, and facilitates rational approaches to drug design. We present a comprehensive identification of the components of the mycolic acid pathway and represent it mathematically based on reaction stoichiometry Such models are amenable to perturbations and simulations using flux balance analysis, allowing the study of pathways from a metabolic capacity perspective, and yielding information about reaction fluxes. The FAS-I system, present predominantly in eukaryotes, is capable of de novo fatty acid synthesis, whereas the FAS-II system in mycobacteria, similar to that in other
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