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Research Articles

In silico discovery of potential drug molecules to improve the treatment of isoniazid-resistant Mycobacterium tuberculosis

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Pages 3388-3398 | Received 12 Apr 2018, Accepted 15 Aug 2018, Published online: 04 Nov 2018

References

  • Ballell, L., Bates, R. H., Young, R. J., Alvarez-Gomez, D., Alvarez-Ruiz, E., Barroso, V., … Cammack, N. (2013). Fueling open ‐ source drug discovery: 177 small molecule leads against tuberculosis. ChemMedChem, 8(2), 313–321.
  • Banerjee, A., Dubnau, E., Quemard, A., Balasubramanian, V., Um, K. S., Wilson, T., … Jacobs, W. R. (1994). inhA, a gene encoding a target for isoniazid and ethionamide in Mycobacterium tuberculosis. Science (New York, N.Y.), 263(5144), 227–230.
  • Baragaña, B., Hallyburton, I., Lee, M. C. S., Norcross, N. R., Grimaldi, R., Otto, T. D., … Gilbert, I. H. (2015). A novel multiple-stage antimalarial agent that inhibits protein synthesis. Nature, 522(7556), 315.
  • Basso, L. A., Zheng, R., Musser, J. M., Jacobs, W. R. Jr., & Blanchard, J. S. (1998). Mechanisms of isoniazid resistance in Mycobacterium tuberculosis: Enzymatic characterization of enoyl reductase mutants identified in isoniazid-resistant clinical isolates. The Journal of Infectious Diseases, 178(3), 769–775.
  • Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., & Weissig, H. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242.
  • Binkowski, T. A., Naghibzadeh, S., & Liang, J. (2003). CASTp: Computed atlas of surface topography of proteins. Nucleic Acids Research, 31(13), 3352–3355.
  • Bobrik, A., Danishevski, K., Eroshina, K., & McKee, M. (2005). Prison health in Russia: The larger picture. Journal of Public Health Policy, 26(1), 30–59.
  • Bryk, R., Lima, C. D., Erdjument-Bromage, H., Tempst, P., & Nathan, C. (2002). Metabolic enzymes of mycobacteria linked to antioxidant defense by a thioredoxin-like protein. Science, 295(5557), 1073–1077.
  • Chan, R. C. Y., Hui, M., Chan, E. W. C., Au, T. K., Chin, M. L., Yip, C. K., … Cheng, A. F. B. (2007). Genetic and phenotypic characterization of drug-resistant Mycobacterium tuberculosis isolates in Hong Kong. Journal of Antimicrobial Chemotherapy, 59(5), 866–873.
  • Czabotar, P. E., Westphal, D., Dewson, G., Ma, S., Hockings, C., Fairlie, W. D., … Colman, P. M. (2013). Bax crystal structures reveal how BH3 domains activate Bax and nucleate its oligomerization to induce apoptosis. Cell, 152(3), 519–531.
  • DeLano, W. L. (2010). The Pymol molecular graphics system, Version 1.2 r3pre. New York, NY: Schrödinger, LLC.
  • Dookie, N., Rambaran, S., Padayatchi, N., Mahomed, S., & Naidoo, K. (2018). Evolution of drug resistance in Mycobacterium tuberculosis: A review on the molecular determinants of resistance and implications for personalized care. Journal of Antimicrobial Chemotherapy, 73(5), 1138–1151.
  • Dowdy, D. W., Theron, G., Tornheim, J. A., & Kendall, E. A. (2017). Drug-resistant tuberculosis in 2017: At a crossroads. The Lancet Respiratory Medicine, 5(4), 241–242.
  • Duan, X., Xiang, X., & Xie, J. (2014). Crucial components of mycobacterium type II fatty acid biosynthesis (Fas-II) and their inhibitors. FEMS Microbiology Letters, 360(2), 87–99.
  • Dundas, J., Ouyang, Z., Tseng, J., Binkowski, A., Turpaz, Y., & Liang, J. (2006). CASTp: Computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Research, 34, W116–W118.
  • Ellis, C. R., Tsai, C. C., Hou, X., & Shen, J. (2016). Constant pH molecular dynamics reveals pH-modulated binding of two small-molecule BACE1 inhibitors. The Journal of Physical Chemistry Letters, 7(6), 944–949. doi:10.1021/acs.jpclett.6b00137.
  • Gaulton, A., Bellis, L. J., Bento, A. P., Chambers, J., Davies, M., Hersey, A., … Overington, J. P. (2012). ChEMBL: A large-scale bioactivity database for drug discovery. Nucleic Acids Research, 40(D1), D1100–D1107.
  • Guardia, A., Gulten, G., Fernandez, R., Gómez, J., Wang, F., Convery, M., … Castro-Pichel, J. (2016). N‐Benzyl‐4‐((heteroaryl) methyl) benzamides: A new class of direct NADH‐dependent 2‐trans enoyl–acyl carrier protein reductase (InhA) inhibitors with antitubercular activity. ChemMedChem, 11(7), 687–701.
  • Harris, R. C., Tsai, C. C., Ellis, C. R., & Shen, J. (2017). Proton-coupled conformational allostery modulates the inhibitor selectivity for β-secretase. The Journal of Physical Chemistry Letters, 8(19), 4832–4837.
  • Hazbón, M. H., Brimacombe, M., Bobadilla del Valle, M., Cavatore, M., Guerrero, M. I., Varma-Basil, M., … Alland, D. (2006). Population genetics study of isoniazid resistance mutations and evolution of multidrug-resistant Mycobacterium tuberculosis. Antimicrobial Agents and Chemotherapy, 50(8), 2640–2649.
  • Heep, M., Rieger, U., Beck, D., & Lehn, N. (2000). Mutations in the beginning of the rpoB gene can induce resistance to rifamycins in both Helicobacter pylori and Mycobacterium tuberculosis. Antimicrobial Agents and Chemotherapy, 44(4), 1075–1077.
  • Heym, B., Honoré, N., Schurra, C., Cole, S. T., Heym, B., Truffot-Pernot, C., … van Embden, J. D. A. (1994). Implications of multidrug resistance for the future of short-course chemotherapy of tuberculosis: A molecular study. The Lancet, 344(8918), 293–298.
  • Hillas, P. J., del Alba, F. S., Oyarzabal, J., Wilks, A., & de Montellano, P. R. O. (2000). The AhpC and AhpD antioxidant defense system of Mycobacterium tuberculosis. Journal of Biological Chemistry, 275(25), 18801–18809.
  • Hitchcock, S. A., & Pennington, L. D. (2006). Structure − brain exposure relationships. Journal of Medicinal Chemistry, 49(26), 7559–7583.
  • Iseman, M. D. (1993). Treatment of multidrug-resistant tuberculosis. The New England Journal of Medicine, 329(11), 784–791.
  • Jadaun, A., Sudhakar, D. R., Subbarao, N., & Dixit, A. (2015). In silico screening for novel inhibitors of DNA polymerase III alpha subunit of Mycobacterium tuberculosis (M.tbDnaE2, H37Rv). PLoS One, 10(3), e0119760.
  • Jena, L., Waghmare, P., Kashikar, S., Kumar, S., & Harinath, B. C. (2014). Computational approach to understanding the mechanism of action of isoniazid, an anti-TB drug. International Journal of Mycobacteriology, 3(4), 276–282.
  • Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. (1997). Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology, 267(3), 727–748.
  • Kiepiela, P., Bishop, K. S., Smith, A. N., Roux, L., & York, D. F. (2000). Genomic mutations in the katG, inhA and aphC genes are useful for the prediction of isoniazid resistance in Mycobacterium tuberculosis isolates from Kwazulu Natal, South Africa. Tubercle and Lung Disease, 80(1), 47–56.
  • Kitchen, D. B., Decornez, H., Furr, J. R., & Bajorath, J. (2004). Docking and scoring in virtual screening for drug discovery: Methods and applications. Nature Reviews. Drug Discovery, 3(11), 935.
  • Kujawski, J., Popielarska, H., Myka, A., Drabińska, B., & Bernard, M. K. (2012). The log P parameter as a molecular descriptor in the computer-aided drug design – An overview. Computational Methods in Science and Technology, 18(2), 81–88.
  • Lee, A. S., Lim, I. H., Tang, L. L., Telenti, A., & Wong, S. Y. (1999). Contribution of kasA analysis to detection of isoniazid-resistant Mycobacterium tuberculosis in Singapore. Antimicrobial Agents and Chemotherapy, 43(8), 2087–2089.
  • Lee, H., Cho, S. N., Bang, H. E., Lee, J. H., Bai, G. H., Kim, S. J., & Kim, J. D. (2000). Exclusive mutations related to isoniazid and ethionamide resistance among Mycobacterium tuberculosis isolates from Korea. The International Journal of Tuberculosis and Lung Disease, 4(5), 441–447.
  • Leung, E. T. Y., Ho, P. L., Yuen, K. Y., Woo, W. L., Lam, T. H., Kao, R. Y., … Yam, W. C. (2006). Molecular characterization of isoniazid resistance in Mycobacterium tuberculosis: Identification of a novel mutation in inhA. Antimicrobial Agents and Chemotherapy, 50(3), 1075–1078.
  • Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2012). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 64, 4–17.
  • Lordi, G. M., & Reichman, L. B. (1991). Treatment of tuberculosis. American Family Physician, 44(1), 219–224.
  • Louw, G. E., Warren, R. M., van Pittius, N. G., McEvoy, C. R. E., Van Helden, P. D., & Victor, T. C. (2009). A balancing act: Efflux/influx in mycobacterial drug resistance. Antimicrobial Agents and Chemotherapy, 53(8), 3181–3189.
  • Master, S. S., Springer, B., Sander, P., Boettger, E. C., Deretic, V., & Timmins, G. S. (2002). Oxidative stress response genes in Mycobacterium tuberculosis: Role of ahpC in resistance to peroxynitrite and stage-specific survival in macrophages. Microbiology, 148(10), 3139–3144.
  • Morlock, G. P., Metchock, B., Sikes, D., Crawford, J. T., & Cooksey, R. C. (2003). ethA, inhA, and katG loci of ethionamide-resistant clinical Mycobacterium tuberculosis isolates. Antimicrobial Agents and Chemotherapy, 47(12), 3799–3805.
  • Morton, D. J., Whitby, P. W., Jin, H., Ren, Z., & Stull, T. L. (1999). Effect of multiple mutations in the hemoglobin-and hemoglobin-haptoglobin-binding proteins, HgpA, HgpB, and HgpC, of Haemophilus influenzae Type b. Infection and Immunity, 67(6), 2729–2739.
  • Musser, J. M., Kapur, V., Williams, D. L., Kreiswirth, B. N., Van Soolingen, D., & Van Embden, J. D. (1996). Characterization of the catalase-peroxidase gene (katG) and inhA locus in isoniazid-resistant and-susceptible strains of Mycobacterium tuberculosis by automated DNA sequencing: Restricted array of mutations associated with drug resistance. The Journal of Infectious Diseases, 173(1), 196–202.
  • O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 33.
  • Ohlrogge, J., & Browse, J. (1995). Lipid biosynthesis. The Plant Cell, 7(7), 957.
  • Ramaswamy, S., & Musser, J. M. (1998). Molecular genetic basis of antimicrobial agent resistance in Mycobacterium tuberculosis: 1998 update. Tubercle and Lung Disease, 79(1), 3–29.
  • Ramaswamy, S. V., Reich, R., Dou, S.-J., Jasperse, L., Pan, X., Wanger, A., … Graviss, E. A. (2003). Single nucleotide polymorphisms in genes associated with isoniazid resistance in Mycobacterium tuberculosis. Antimicrobial Agents and Chemotherapy, 47(4), 1241–1250.
  • Rebollo-Lopez, M. J., Lelièvre, J., Alvarez-Gomez, D., Castro-Pichel, J., Martínez-Jiménez, F., Papadatos, G., … Barros-Aguire, D. (2015). Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery. PLoS One, 10(12), e0142293. doi:10.1371/journal.pone.0142293.
  • Ristow, M., Möhlig, M., Rifai, M., Schatz, H., Feldmann, K., & Pfeiffer, A. (1995). New isoniazid/ethionamide resistance gene mutation and screening for multidrug-resistant Mycobacterium tuberculosis strains. The Lancet, 346(8973), 502–503.
  • Rozwarski, D. A., Grant, G. A., Barton, D. H., Jacobs, W. R., & Sacchettini, J. C. (1998). Modification of the NADH of the isoniazid target (InhA) from Mycobacterium tuberculosis. Science (New York, N.Y.), 279(5347), 98–102.
  • Sandgren, A., Strong, M., Muthukrishnan, P., Weiner, B. K., Church, G. M., & Murray, M. B. (2009). Tuberculosis drug resistance mutation database. PLoS Medicine, 6(2), e1000002.
  • Sarkar, A., & Kellogg, G. E. (2010). Hydrophobicity-shake flasks, protein folding and drug discovery. Current Topics in Medicinal Chemistry, 10(1), 67–83.
  • Scheraga, H. A., Némethy, G., & Steinberg, I. Z. (1962). The contribution of hydrophobic bonds to the thermal stability of protein conformations. Journal of Biological Chemistry, 237(8), 2506–2508.
  • Sharma, S. K., & Mohan, A. (2006). Multidrug-resistant tuberculosis: A menace that threatens to destabilize tuberculosis control. Chest, 130(1), 261–272.
  • Silva, M. S. N., Senna, S. G., Ribeiro, M. O., Valim, A. R. M., Telles, M. A., Kritski, A., … Rossetti, M. L. R. (2003). Mutations in katG, inhA, and ahpC genes of Brazilian isoniazid-resistant isolates of Mycobacterium tuberculosis. Journal of Clinical Microbiology, 41(9), 4471–4474.
  • Taniguchi, H., Aramaki, H., Nikaido, Y., Mizuguchi, Y., Nakamura, M., Koga, T., & Yoshida, S. I. (1996). Rifampicin resistance and mutation of the rpoB gene in Mycobacterium tuberculosis. FEMS Microbiology Letters, 144(1), 103–108.
  • Tousif, S., Ahmad, S., Bhalla, K., Moodley, P., & Das, G. (2015). Challenges of tuberculosis treatment with DOTS: An immune impairment perspective. Journal of Cell Science & Therapy, 6(5), 1.
  • Walker, T. M., Merker, M., Knoblauch, A. M., Helbling, P., Schoch, O. D., van der Werf, M. J., … Witschi, M. (2018). A cluster of multidrug-resistant Mycobacterium tuberculosis among patients arriving in Europe from the Horn of Africa: A molecular epidemiological study. The Lancet Infectious Diseases, 18(4), 431.
  • Whitfield, M. G., Soeters, H. M., Warren, R. M., York, T., Sampson, S. L., Streicher, E. M., … van Rie, A. (2015). A global perspective on pyrazinamide resistance: Systematic review and meta-analysis. PLoS One, 10(7), e0133869.
  • WHO. (2015). Multi-drug-resistant tuberculosis (MDR-TB) – Update. Geneva: WHO.
  • Wolber, G., & Kosara, R. (2006). Pharmacophores from macromolecular complexes with LigandScout. Pharmacophores and Pharmacophore Searches, 32, 131–150.
  • Xu, D., & Zhang, Y. (2011). Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophysical Journal, 101(10), 2525–2534.
  • Yang, S. Y. (2010). Pharmacophore modeling and applications in drug discovery: Challenges and recent advances. Drug Discovery Today, 15(11–12), 444–450.
  • Youatt, J. (1969). A review of the action of isoniazid. The American Review of Respiratory Disease, 99(5), 729–749.
  • Zenteno-Cuevas, R., Zenteno, J. C., Cuellar, A., Cuevas, B., Sampieri, C. L., Riviera, J. E., & Parissi, A. (2009). Mutations in rpoB and katG genes in Mycobacterium isolates from the Southeast of Mexico. Memorias Do Instituto Oswaldo Cruz, 104(3), 468–472.
  • Zhang, Y., Heym, B., Allen, B., Young, D., & Cole, S. (1992). The catalase-peroxidase gene and isoniazid resistance of Mycobacterium tuberculosis. Nature, 358(6387), 591.

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