Resistance related metabolic pathways for drug target identification in mycobacterium tuberculosis
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Authors
Cloete, Ruben
Oppon, Ekow
Murungi, Edwin
Schubert, Wolf-Dieter
Christoffels, Alan
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
Abstract
BACKGROUND : Increasing resistance to anti-tuberculosis drugs has driven the need for developing new drugs.
Resources such as the tropical disease research (TDR) target database and AssessDrugTarget can help to prioritize
putative drug targets. Hower, these resources do not necessarily map to metabolic pathways and the targets are not
involved in dormancy. In this study, we specifically identify drug resistance pathways to allow known drug resistant
mutations in one target to be offset by inhibiting another enzyme of the same metabolic pathway. One of the putative
targets, Rv1712, was analysed by modelling its three dimensional structure and docking potential inhibitors.
RESULTS : We mapped 18 TB drug resistance gene products to 15 metabolic pathways critical for mycobacterial growth
and latent TB by screening publicly available microarray data. Nine putative targets, Rv1712, Rv2984, Rv2194, Rv1311,
Rv1305, Rv2195, Rv1622c, Rv1456c and Rv2421c, were found to be essential, to lack a close human homolog, and to
share >67 % sequence identity and >87 % query coverage with mycobacterial orthologs. A structural model was
generated for Rv1712, subjected to molecular dynamic simulation, and identified 10 compounds with affinities better
than that for the ligand cytidine-5′-monophosphate (C5P). Each compound formed more interactions with the protein
than C5P.
CONCLUSIONS : We focused on metabolic pathways associated with bacterial drug resistance and proteins unique to
pathogenic bacteria to identify novel putative drug targets. The ten compounds identified in this study should be
considered for experimental studies to validate their potential as inhibitors of Rv1712.
Description
Additional file 1: Table S1. KEGG pathways for genes known to be
associated with 1st and 2nd line drug resistance. The 10 mutations (eight
genes) indicated in bold were verified by the BROAD institute, while the
remainder were identified from literature. Abbreviations used: A-Adenine,
Ala-Alanine, Arg-Arginine, Asn-Glutamine, Asp-Aspartate, Gly-Glycine,
His-Histidine, indel-insertion deletion, Ileu-Isoleucine, Leu-Leucine,
Met-Methionine, N.A-Not available, Pro-Proline, Ser-Serine, T-Thymidine,
Thr-Threonine, Tyr-Tyrosine, Val-Valine. (PDF 143 kb)
Additional file 2: Table S2. Criteria used to filter high priority M.tuberculosis drug targets. The genes highlighted in bold satisfied all the selection criteria. The hyphen (−) indicates exclusion from further analysis. Abbreviations used: NUI- Not under investigation, PDB- Protein Data Bank, TBSGC- TB Structural Genome Consortium. References 12-Sassetti et al., 2003; 34-Lamichhane et al., 2003. Data can be viewed in Microsoft excel. (XLS 12 kb)
Additional file 3: Table S3. The 24 sequenced Mycobacterium strains. Data can be viewed in Microsoft excel. (XLS 34 kb)
Additional file 4: Table S4. Blast hits obtained for Rv1712, Rv2984, Rv2194, Rv1311, Rv1305, Rv2195, Rv1622c, Rv1456c and Rv2421c against three host intestinal bacteria. Bacterial species highlighted in bold showed homology to the query gene. Data can be viewed in Microsoft excel. (XLS 13 kb)
Additional file 5: Figure S1. KEGG metabolic pathway map for Nucleotide metabolism (pyrimidine metabolism) in M. tuberculosis H37rV strain. Rv1712 or cmk selected for investigation is shown in red highlighted boxes and involved in step 2.7.4.14 of this specific pathway. Known drug resistance gene Rv0667 or rpoB is shown in blue highlighted box and involved in step 2.7.7.6 of this pathway. M. tuberculosis specific genes are coloured in green. (PDF 111 kb)
Additional file 6: Figure S2. KEGG metabolic pathway map for Oxidative phosphorylation in M. tuberculosis H37rV strain. Rv2984 or ppk selected for investigation is shown in blue highlighted box and involved in step 2.7.4.1 of this specific pathway. Rv2194 or qcrC selected for investigation is shown in the red highlighted box. Both Rv1305 (atpE) and Rv1311 (atpC) selected for investigation are shown in brown highlighted box and involved in step 3.6.3.14 of this specific pathway. Rv2195 or qcrA selected for investigation is shown in the yellow highlighted box involved in cytochrome C reductase. Rv1456c or COX15 selected for investigation is shown in the magenta highlighted box involved in cytochrome C oxidase. Rv1622c or CydB selected for investigation is shown in the light blue highlighted box involved in cytochrome C oxidase. Known drug resistance gene Rv1854c or ndh is shown in orange highlighted box and involved in step 1.6.99.3 of this pathway. M. tuberculosis specific genes are coloured in green. (PDF 157 kb)
Additional file 7: Figure S3. KEGG metabolic pathway map for Nicotinate and Nicotinamide metabolism in M. tuberculosis H37rV strain. Rv2421c or nadD selected for investigation is shown in red highlighted box and involved in step 2.7.7.18 of this specific pathway. Known drug resistance gene Rv2043c or pncA is shown in blue highlighted box and involved in step 3.5.1.19 of this pathway. M. tuberculosis specific genes are coloured in green. (PDF 106 kb)
Additional file 8: Table S5. KEGG pathway descriptors for M. tuberculosis genes retained after prioritization. Data can be viewed in Microsoft excel. (XLS 7 kb)
Additional file 9: Figure S4. DOPE score energy profiles graph of the structural model for Rv1712 (red) and templates 1Q3T (green), 1CKE (dark blue), 1KDO (light blue) and 2H92 (purple). Generated using Gnuplotv4.2 [41]. (PDF 68 kb)
Additional file 10: Figure S5. RMSD of the backbone atoms of model Rv1712 (green) and substrate C5P (red) during the 30000 ps simulation. Generated using Gnuplotv4.2 [41]. (PDF 198 kb)
Additional file 11: Figure S6. The variation in total (green) and potential energy (red) for the Rv1712-C5P complex during the 30000 ps simulation. Generated using Gnuplotv4.2 [41]. (PDF 69 kb)
Additional file 12: Figure S7. RMS fluctuations of all Cα residues for Rv1712 over the 30000 ps simulation. (PDF 55 kb)
Additional file 13: Figure S8. Radius of gyration of all bacbone atoms for Rv1712 over the 30000 ps simulation. (PDF 29 kb)
Additional file 14: Figure S9. Superimposition of lowest DOPE score models for the initial and newly generated structures. The blue model represents the initial model without 3R20 used as a template while the red model consist of 3R20 used as a template for model construction. Ligands SO4 and CMP are shown as sticks. RMSD = 0.387 Å. (PDF 33 kb)
Additional file 15: Table S6. Docking scores and number of interactions for the top ten compounds to Rv1712. The residues highlighted in bold are conserved catalytic residues while ligand C5P is highlighted in red. The numbers inside the () indicate the number of interactions formed between residue and the compound atom. Data can be viewed in Microsoft excel. (XLS 8 kb)
Additional file 2: Table S2. Criteria used to filter high priority M.tuberculosis drug targets. The genes highlighted in bold satisfied all the selection criteria. The hyphen (−) indicates exclusion from further analysis. Abbreviations used: NUI- Not under investigation, PDB- Protein Data Bank, TBSGC- TB Structural Genome Consortium. References 12-Sassetti et al., 2003; 34-Lamichhane et al., 2003. Data can be viewed in Microsoft excel. (XLS 12 kb)
Additional file 3: Table S3. The 24 sequenced Mycobacterium strains. Data can be viewed in Microsoft excel. (XLS 34 kb)
Additional file 4: Table S4. Blast hits obtained for Rv1712, Rv2984, Rv2194, Rv1311, Rv1305, Rv2195, Rv1622c, Rv1456c and Rv2421c against three host intestinal bacteria. Bacterial species highlighted in bold showed homology to the query gene. Data can be viewed in Microsoft excel. (XLS 13 kb)
Additional file 5: Figure S1. KEGG metabolic pathway map for Nucleotide metabolism (pyrimidine metabolism) in M. tuberculosis H37rV strain. Rv1712 or cmk selected for investigation is shown in red highlighted boxes and involved in step 2.7.4.14 of this specific pathway. Known drug resistance gene Rv0667 or rpoB is shown in blue highlighted box and involved in step 2.7.7.6 of this pathway. M. tuberculosis specific genes are coloured in green. (PDF 111 kb)
Additional file 6: Figure S2. KEGG metabolic pathway map for Oxidative phosphorylation in M. tuberculosis H37rV strain. Rv2984 or ppk selected for investigation is shown in blue highlighted box and involved in step 2.7.4.1 of this specific pathway. Rv2194 or qcrC selected for investigation is shown in the red highlighted box. Both Rv1305 (atpE) and Rv1311 (atpC) selected for investigation are shown in brown highlighted box and involved in step 3.6.3.14 of this specific pathway. Rv2195 or qcrA selected for investigation is shown in the yellow highlighted box involved in cytochrome C reductase. Rv1456c or COX15 selected for investigation is shown in the magenta highlighted box involved in cytochrome C oxidase. Rv1622c or CydB selected for investigation is shown in the light blue highlighted box involved in cytochrome C oxidase. Known drug resistance gene Rv1854c or ndh is shown in orange highlighted box and involved in step 1.6.99.3 of this pathway. M. tuberculosis specific genes are coloured in green. (PDF 157 kb)
Additional file 7: Figure S3. KEGG metabolic pathway map for Nicotinate and Nicotinamide metabolism in M. tuberculosis H37rV strain. Rv2421c or nadD selected for investigation is shown in red highlighted box and involved in step 2.7.7.18 of this specific pathway. Known drug resistance gene Rv2043c or pncA is shown in blue highlighted box and involved in step 3.5.1.19 of this pathway. M. tuberculosis specific genes are coloured in green. (PDF 106 kb)
Additional file 8: Table S5. KEGG pathway descriptors for M. tuberculosis genes retained after prioritization. Data can be viewed in Microsoft excel. (XLS 7 kb)
Additional file 9: Figure S4. DOPE score energy profiles graph of the structural model for Rv1712 (red) and templates 1Q3T (green), 1CKE (dark blue), 1KDO (light blue) and 2H92 (purple). Generated using Gnuplotv4.2 [41]. (PDF 68 kb)
Additional file 10: Figure S5. RMSD of the backbone atoms of model Rv1712 (green) and substrate C5P (red) during the 30000 ps simulation. Generated using Gnuplotv4.2 [41]. (PDF 198 kb)
Additional file 11: Figure S6. The variation in total (green) and potential energy (red) for the Rv1712-C5P complex during the 30000 ps simulation. Generated using Gnuplotv4.2 [41]. (PDF 69 kb)
Additional file 12: Figure S7. RMS fluctuations of all Cα residues for Rv1712 over the 30000 ps simulation. (PDF 55 kb)
Additional file 13: Figure S8. Radius of gyration of all bacbone atoms for Rv1712 over the 30000 ps simulation. (PDF 29 kb)
Additional file 14: Figure S9. Superimposition of lowest DOPE score models for the initial and newly generated structures. The blue model represents the initial model without 3R20 used as a template while the red model consist of 3R20 used as a template for model construction. Ligands SO4 and CMP are shown as sticks. RMSD = 0.387 Å. (PDF 33 kb)
Additional file 15: Table S6. Docking scores and number of interactions for the top ten compounds to Rv1712. The residues highlighted in bold are conserved catalytic residues while ligand C5P is highlighted in red. The numbers inside the () indicate the number of interactions formed between residue and the compound atom. Data can be viewed in Microsoft excel. (XLS 8 kb)
Keywords
Anti-tuberculosis drugs, New drugs, Drug targets, Tropical disease research (TDR), Drug resistance pathways, Drug resistant mutations
Sustainable Development Goals
Citation
Cloete, R, Oppon, E, Murungi, E, Schubert, W-D & Christoffels, A 2015, 'Resistance related metabolic pathways for drug target identification in mycobacterium tuberculosis', BMC Bioinformatics, vol. 17, art. #75, pp. 1-10.