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Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC.

Aziz RK, Khaw VL, Monk JM, Brunk E, Lewis R, Loh SI, Mishra A, Nagle AA, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Palsson BØ, Charusanti P - Front Microbiol (2015)

Bottom Line: Here, we reconcile this disparity by providing evidence that aldA and prpC form a synthetic lethal pair, as the double knockout could only be created through complementation with a plasmid-borne copy of aldA.Moreover, virtual and biological screening against the two proteins led to a set of compounds that inhibited the growth of E. coli and Salmonella enterica serovar Typhimurium synergistically at 100-200 μM individual concentrations.These results highlight the power of metabolic models to drive basic biological discovery and their potential use to discover new combination antibiotics.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University Cairo, Egypt ; Department of Bioengineering, University of California, San Diego La Jolla, CA, USA.

ABSTRACT
Mathematical models of biochemical networks form a cornerstone of bacterial systems biology. Inconsistencies between simulation output and experimental data point to gaps in knowledge about the fundamental biology of the organism. One such inconsistency centers on the gene aldA in Escherichia coli: it is essential in a computational model of E. coli metabolism, but experimentally it is not. Here, we reconcile this disparity by providing evidence that aldA and prpC form a synthetic lethal pair, as the double knockout could only be created through complementation with a plasmid-borne copy of aldA. Moreover, virtual and biological screening against the two proteins led to a set of compounds that inhibited the growth of E. coli and Salmonella enterica serovar Typhimurium synergistically at 100-200 μM individual concentrations. These results highlight the power of metabolic models to drive basic biological discovery and their potential use to discover new combination antibiotics.

No MeSH data available.


Related in: MedlinePlus

Comparative structural analysis of (A) PrpC and (B) AldA. In the left panel of (A), the region with the highest overlapping structural similarity between PrpC and AldA is shown in green. The putative binding site with catalytic residues H274 and D325 are shown in blue. In the native reaction, 2-methyl citrate synthase, oxaloacetate reacts with a CoA-ester (e.g., propionyl-CoA) to form (2R,3S)-2-hydroxybutane-1,2,3-tricarboxylate. The NADH binding site is 15 Å away from the closest residue in the green overlapping region, and is therefore not considered a part of the overlap. Shown in the right panel of (A) is a magnification of the putative binding site. In the left panel of (B), the region with the highest overlapping structural similarity is again shown in green. The putative binding site (violet) shows where lactic acid binds to the protein. The putative binding orientation of lactic acid is taken from an alignment with PDB entry 3o8j.
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Figure 3: Comparative structural analysis of (A) PrpC and (B) AldA. In the left panel of (A), the region with the highest overlapping structural similarity between PrpC and AldA is shown in green. The putative binding site with catalytic residues H274 and D325 are shown in blue. In the native reaction, 2-methyl citrate synthase, oxaloacetate reacts with a CoA-ester (e.g., propionyl-CoA) to form (2R,3S)-2-hydroxybutane-1,2,3-tricarboxylate. The NADH binding site is 15 Å away from the closest residue in the green overlapping region, and is therefore not considered a part of the overlap. Shown in the right panel of (A) is a magnification of the putative binding site. In the left panel of (B), the region with the highest overlapping structural similarity is again shown in green. The putative binding site (violet) shows where lactic acid binds to the protein. The putative binding orientation of lactic acid is taken from an alignment with PDB entry 3o8j.

Mentions: We compared the protein structures for AldA and PrpC to investigate whether PrpC might have unrecognized promiscuous dehydrogenase activity. AldA is comprised of 61.3% alpha helix/beta sheet content versus 58.8% for PrpC, and the two differ in length by 90 amino acids (479 versus 389 for AldA and PrpC, respectively, Figure 3). A pairwise comparison using DALI (Holm and Rosenstrom, 2010), however, indicates very little sequence and secondary structural similarity. Only 47 of the 479 (10%) residues in AldA have structural similarity to residues in PrpC, and PrpC lacks any indication of an NADH binding site (Figure 3). The likelihood that PrpC exhibits promiscuous dehydrogenase activity is therefore low.


Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC.

Aziz RK, Khaw VL, Monk JM, Brunk E, Lewis R, Loh SI, Mishra A, Nagle AA, Satyanarayana C, Dhakshinamoorthy S, Luche M, Kitchen DB, Andrews KA, Palsson BØ, Charusanti P - Front Microbiol (2015)

Comparative structural analysis of (A) PrpC and (B) AldA. In the left panel of (A), the region with the highest overlapping structural similarity between PrpC and AldA is shown in green. The putative binding site with catalytic residues H274 and D325 are shown in blue. In the native reaction, 2-methyl citrate synthase, oxaloacetate reacts with a CoA-ester (e.g., propionyl-CoA) to form (2R,3S)-2-hydroxybutane-1,2,3-tricarboxylate. The NADH binding site is 15 Å away from the closest residue in the green overlapping region, and is therefore not considered a part of the overlap. Shown in the right panel of (A) is a magnification of the putative binding site. In the left panel of (B), the region with the highest overlapping structural similarity is again shown in green. The putative binding site (violet) shows where lactic acid binds to the protein. The putative binding orientation of lactic acid is taken from an alignment with PDB entry 3o8j.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4585216&req=5

Figure 3: Comparative structural analysis of (A) PrpC and (B) AldA. In the left panel of (A), the region with the highest overlapping structural similarity between PrpC and AldA is shown in green. The putative binding site with catalytic residues H274 and D325 are shown in blue. In the native reaction, 2-methyl citrate synthase, oxaloacetate reacts with a CoA-ester (e.g., propionyl-CoA) to form (2R,3S)-2-hydroxybutane-1,2,3-tricarboxylate. The NADH binding site is 15 Å away from the closest residue in the green overlapping region, and is therefore not considered a part of the overlap. Shown in the right panel of (A) is a magnification of the putative binding site. In the left panel of (B), the region with the highest overlapping structural similarity is again shown in green. The putative binding site (violet) shows where lactic acid binds to the protein. The putative binding orientation of lactic acid is taken from an alignment with PDB entry 3o8j.
Mentions: We compared the protein structures for AldA and PrpC to investigate whether PrpC might have unrecognized promiscuous dehydrogenase activity. AldA is comprised of 61.3% alpha helix/beta sheet content versus 58.8% for PrpC, and the two differ in length by 90 amino acids (479 versus 389 for AldA and PrpC, respectively, Figure 3). A pairwise comparison using DALI (Holm and Rosenstrom, 2010), however, indicates very little sequence and secondary structural similarity. Only 47 of the 479 (10%) residues in AldA have structural similarity to residues in PrpC, and PrpC lacks any indication of an NADH binding site (Figure 3). The likelihood that PrpC exhibits promiscuous dehydrogenase activity is therefore low.

Bottom Line: Here, we reconcile this disparity by providing evidence that aldA and prpC form a synthetic lethal pair, as the double knockout could only be created through complementation with a plasmid-borne copy of aldA.Moreover, virtual and biological screening against the two proteins led to a set of compounds that inhibited the growth of E. coli and Salmonella enterica serovar Typhimurium synergistically at 100-200 μM individual concentrations.These results highlight the power of metabolic models to drive basic biological discovery and their potential use to discover new combination antibiotics.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University Cairo, Egypt ; Department of Bioengineering, University of California, San Diego La Jolla, CA, USA.

ABSTRACT
Mathematical models of biochemical networks form a cornerstone of bacterial systems biology. Inconsistencies between simulation output and experimental data point to gaps in knowledge about the fundamental biology of the organism. One such inconsistency centers on the gene aldA in Escherichia coli: it is essential in a computational model of E. coli metabolism, but experimentally it is not. Here, we reconcile this disparity by providing evidence that aldA and prpC form a synthetic lethal pair, as the double knockout could only be created through complementation with a plasmid-borne copy of aldA. Moreover, virtual and biological screening against the two proteins led to a set of compounds that inhibited the growth of E. coli and Salmonella enterica serovar Typhimurium synergistically at 100-200 μM individual concentrations. These results highlight the power of metabolic models to drive basic biological discovery and their potential use to discover new combination antibiotics.

No MeSH data available.


Related in: MedlinePlus