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Systems level mapping of metabolic complexity in Mycobacterium tuberculosis to identify high-value drug targets.

Vashisht R, Bhat AG, Kushwaha S, Bhardwaj A, OSDD ConsortiumBrahmachari SK - J Transl Med (2014)

Bottom Line: The reconstructed metabolism of Mtb encompasses 961 metabolites, involved in 1152 reactions catalyzed by 890 protein coding genes, organized into 50 pathways.Further, we formulate a novel concept of metabolic persister genes (MPGs) and compared our predictions with published in vitro and in vivo experimental evidence.Through such analyses, we report for the first time that de novo biosynthesis of NAD may give rise to bacterial persistence in Mtb under conditions of metabolic stress induced by conventional anti-tuberculosis therapy.

View Article: PubMed Central - PubMed

Affiliation: CSIR-Open Source Drug Discovery Unit, New Delhi, India. skb@igib.res.in.

ABSTRACT

Background: The effectiveness of current therapeutic regimens for Mycobacterium tuberculosis (Mtb) is diminished by the need for prolonged therapy and the rise of drug resistant/tolerant strains. This global health threat, despite decades of basic research and a wealth of legacy knowledge, is due to a lack of systems level understanding that can innovate the process of fast acting and high efficacy drug discovery.

Methods: The enhanced functional annotations of the Mtb genome, which were previously obtained through a crowd sourcing approach was used to reconstruct the metabolic network of Mtb in a bottom up manner. We represent this information by developing a novel Systems Biology Spindle Map of Metabolism (SBSM) and comprehend its static and dynamic structure using various computational approaches based on simulation and design.

Results: The reconstructed metabolism of Mtb encompasses 961 metabolites, involved in 1152 reactions catalyzed by 890 protein coding genes, organized into 50 pathways. By accounting for static and dynamic analysis of SBSM in Mtb we identified various critical proteins required for the growth and survival of bacteria. Further, we assessed the potential of these proteins as putative drug targets that are fast acting and less toxic. Further, we formulate a novel concept of metabolic persister genes (MPGs) and compared our predictions with published in vitro and in vivo experimental evidence. Through such analyses, we report for the first time that de novo biosynthesis of NAD may give rise to bacterial persistence in Mtb under conditions of metabolic stress induced by conventional anti-tuberculosis therapy. We propose such MPG's as potential combination of drug targets for existing antibiotics that can improve their efficacy and efficiency for drug tolerant bacteria.

Conclusion: The systems level framework formulated by us to identify potential non-toxic drug targets and strategies to circumvent the issue of bacterial persistence can substantially aid in the process of TB drug discovery and translational research.

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Related in: MedlinePlus

Metabolic Persister Genes (MPGs) in the metabolism ofMtbA) Bi-phasic killing and emergence of persisters upon drug exposure; B) Directional re-routing of metabolic fluxes resulting in the adaptation of the bacterium and the emergence of persiters; C) SBSM illustrating the metabolite and reaction connectivity to inhA, the target of Isoniazid; D) Loss of metabolic information in terms of metabolites, genes and reaction following inhA knock-out; E) Gain of function following inhA knock-out showing persister metabolites (PM), persister genes (MPGs) and persister reactions (PR); F-G) Gene expression status of 60 MPG’s on treatment with Isoniazid at 1 μg/ml for 2 hr and 6 hr in vivo H) Transcriptional control of 60 MPGs I) Expression status of nadA ~ E operon on treatment with Isoniazid at 1 μg/ml for 2 hr and 6 hr in vivo.
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Fig4: Metabolic Persister Genes (MPGs) in the metabolism ofMtbA) Bi-phasic killing and emergence of persisters upon drug exposure; B) Directional re-routing of metabolic fluxes resulting in the adaptation of the bacterium and the emergence of persiters; C) SBSM illustrating the metabolite and reaction connectivity to inhA, the target of Isoniazid; D) Loss of metabolic information in terms of metabolites, genes and reaction following inhA knock-out; E) Gain of function following inhA knock-out showing persister metabolites (PM), persister genes (MPGs) and persister reactions (PR); F-G) Gene expression status of 60 MPG’s on treatment with Isoniazid at 1 μg/ml for 2 hr and 6 hr in vivo H) Transcriptional control of 60 MPGs I) Expression status of nadA ~ E operon on treatment with Isoniazid at 1 μg/ml for 2 hr and 6 hr in vivo.

Mentions: Consider a wild-type bacterium in an optimal metabolic steady state, as shown in (Figure 4B). As stress is introduced through antibiotics, the optimal metabolism can undergo changes in three ways such as a) loss of function (shutdown reactions that were active); b) function regulation (increase or decrease in the flux carrying capacity of active reactions); c) gain of function (activation of reactions that were dormant). The gain of function through the activation of reactions is responsible for the directional re-routing of metabolic fluxes, as illustrated in (Figure 4B). This results into alternative metabolic phenotypes. Over a prolonged period of antibiotic stress such phenotypes can eventually be selected, leading to the adaptation of the bacterium, which might demonstrate antibiotic tolerance.Figure 4


Systems level mapping of metabolic complexity in Mycobacterium tuberculosis to identify high-value drug targets.

Vashisht R, Bhat AG, Kushwaha S, Bhardwaj A, OSDD ConsortiumBrahmachari SK - J Transl Med (2014)

Metabolic Persister Genes (MPGs) in the metabolism ofMtbA) Bi-phasic killing and emergence of persisters upon drug exposure; B) Directional re-routing of metabolic fluxes resulting in the adaptation of the bacterium and the emergence of persiters; C) SBSM illustrating the metabolite and reaction connectivity to inhA, the target of Isoniazid; D) Loss of metabolic information in terms of metabolites, genes and reaction following inhA knock-out; E) Gain of function following inhA knock-out showing persister metabolites (PM), persister genes (MPGs) and persister reactions (PR); F-G) Gene expression status of 60 MPG’s on treatment with Isoniazid at 1 μg/ml for 2 hr and 6 hr in vivo H) Transcriptional control of 60 MPGs I) Expression status of nadA ~ E operon on treatment with Isoniazid at 1 μg/ml for 2 hr and 6 hr in vivo.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4201925&req=5

Fig4: Metabolic Persister Genes (MPGs) in the metabolism ofMtbA) Bi-phasic killing and emergence of persisters upon drug exposure; B) Directional re-routing of metabolic fluxes resulting in the adaptation of the bacterium and the emergence of persiters; C) SBSM illustrating the metabolite and reaction connectivity to inhA, the target of Isoniazid; D) Loss of metabolic information in terms of metabolites, genes and reaction following inhA knock-out; E) Gain of function following inhA knock-out showing persister metabolites (PM), persister genes (MPGs) and persister reactions (PR); F-G) Gene expression status of 60 MPG’s on treatment with Isoniazid at 1 μg/ml for 2 hr and 6 hr in vivo H) Transcriptional control of 60 MPGs I) Expression status of nadA ~ E operon on treatment with Isoniazid at 1 μg/ml for 2 hr and 6 hr in vivo.
Mentions: Consider a wild-type bacterium in an optimal metabolic steady state, as shown in (Figure 4B). As stress is introduced through antibiotics, the optimal metabolism can undergo changes in three ways such as a) loss of function (shutdown reactions that were active); b) function regulation (increase or decrease in the flux carrying capacity of active reactions); c) gain of function (activation of reactions that were dormant). The gain of function through the activation of reactions is responsible for the directional re-routing of metabolic fluxes, as illustrated in (Figure 4B). This results into alternative metabolic phenotypes. Over a prolonged period of antibiotic stress such phenotypes can eventually be selected, leading to the adaptation of the bacterium, which might demonstrate antibiotic tolerance.Figure 4

Bottom Line: The reconstructed metabolism of Mtb encompasses 961 metabolites, involved in 1152 reactions catalyzed by 890 protein coding genes, organized into 50 pathways.Further, we formulate a novel concept of metabolic persister genes (MPGs) and compared our predictions with published in vitro and in vivo experimental evidence.Through such analyses, we report for the first time that de novo biosynthesis of NAD may give rise to bacterial persistence in Mtb under conditions of metabolic stress induced by conventional anti-tuberculosis therapy.

View Article: PubMed Central - PubMed

Affiliation: CSIR-Open Source Drug Discovery Unit, New Delhi, India. skb@igib.res.in.

ABSTRACT

Background: The effectiveness of current therapeutic regimens for Mycobacterium tuberculosis (Mtb) is diminished by the need for prolonged therapy and the rise of drug resistant/tolerant strains. This global health threat, despite decades of basic research and a wealth of legacy knowledge, is due to a lack of systems level understanding that can innovate the process of fast acting and high efficacy drug discovery.

Methods: The enhanced functional annotations of the Mtb genome, which were previously obtained through a crowd sourcing approach was used to reconstruct the metabolic network of Mtb in a bottom up manner. We represent this information by developing a novel Systems Biology Spindle Map of Metabolism (SBSM) and comprehend its static and dynamic structure using various computational approaches based on simulation and design.

Results: The reconstructed metabolism of Mtb encompasses 961 metabolites, involved in 1152 reactions catalyzed by 890 protein coding genes, organized into 50 pathways. By accounting for static and dynamic analysis of SBSM in Mtb we identified various critical proteins required for the growth and survival of bacteria. Further, we assessed the potential of these proteins as putative drug targets that are fast acting and less toxic. Further, we formulate a novel concept of metabolic persister genes (MPGs) and compared our predictions with published in vitro and in vivo experimental evidence. Through such analyses, we report for the first time that de novo biosynthesis of NAD may give rise to bacterial persistence in Mtb under conditions of metabolic stress induced by conventional anti-tuberculosis therapy. We propose such MPG's as potential combination of drug targets for existing antibiotics that can improve their efficacy and efficiency for drug tolerant bacteria.

Conclusion: The systems level framework formulated by us to identify potential non-toxic drug targets and strategies to circumvent the issue of bacterial persistence can substantially aid in the process of TB drug discovery and translational research.

Show MeSH
Related in: MedlinePlus