Insights from the molecular mechanism of pyrazinamide to mutated pyrazinamidase linked to the pncA gene in clinical isolates of Mycobacterium tuberculosis

References

• Alame-Emane, A. K., Xu, P., Pierre-Audigier, C., Cadet-Daniel, V., Shen, X., Sraouia, M., Siawaya, J. F. D., Takiff, H., Gao, Q., & Gicquel, B. (2015). Pyrazinamide resistance in Mycobacterium tuberculosis arises after rifampicin and fluoroquinolone resistance. The International Journal of Tuberculosis and Lung Disease, 19(6), 679–684. https://doi.org/10.5588/ijtld.14.0768
   PubMed Web of Science ®Google Scholar
• Caren, G. J., Iskandar, D., Pitaloka, D. A. E., Abdulah, R., & Suwantika, A. A. (2022). COVID-19 pandemic disruption on the management of tuberculosis treatment in Indonesia. Journal of Multidisciplinary Healthcare, 15, 175–183. https://doi.org/10.2147/JMDH.S341130
   PubMed Web of Science ®Google Scholar
• Chaidir, L., Ruesen, C., Dutilh, B. E., Ganiem, A. R., Andryani, A., Apriani, L., Huynen, M. A., Ruslami, R., Hill, P. C., van Crevel, R., & Alisjahbana, B. (2019). Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Indonesia. Journal of Global Antimicrobial Resistance, 16, 170–177. https://doi.org/10.1016/j.jgar.2018.08.018
   PubMed Web of Science ®Google Scholar
• Chen, F., Liu, H., Sun, H., Pan, P., Li, Y., Li, D., & Hou, T. (2016). Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein-protein binding free energies and re-rank binding poses generated by protein-protein docking. Physical Chemistry Chemical Physics, 18(32), 22129–22139. https://doi.org/10.1039/c6cp03670h
   PubMed Web of Science ®Google Scholar
• Junaid, M., Tahir Khan, M., Malik, S.-I., & Wei, D.-Q. (2019). Insights into the mechanisms of the pyrazinamide resistance of three pyrazinamidase mutants N11K, P69T, and D126N. Journal of Chemical Information and Modeling, 59(1), 498-508. https://doi.org/10.1021/acs.jcim.8b00525
   Web of Science ®Google Scholar
• Kumari, R., & Kumar, R. & Lynn, A. (2014). g_mmpbsa—A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Molavi Tabrizi, A., Goossens, S., Mehdizadeh Rahimi, A., Knepley, M., & Bardhan, J. P. (2017). Predicting solvation free energies and thermodynamics in polar solvents and mixtures using a solvation-layer interface condition. The Journal of Chemical Physics, 146(9), 094103. https://doi.org/10.1063/1.4977037
   Web of Science ®Google Scholar
• Nettleman, M. D. (2005). Multidrug-resistant tuberculosis: News from the front. JAMA, 293(22), 2788–2790. https://doi.org/10.1001/jama.293.22.2788
   PubMed Web of Science ®Google Scholar
• Njire, M., Tan, Y., Mugweru, J., Wang, C., Guo, J., Yew, W., Tan, S., & Zhang, T. (2016). Pyrazinamide resistance in Mycobacterium tuberculosis: Review and update. Advances in Medical Sciences, 61(1), 63–71. https://doi.org/10.1016/j.advms.2015.09.007
   PubMed Web of Science ®Google Scholar
• Pantsar, T., & Poso, A. (2018). Binding affinity via docking: Fact and fiction. Molecules, 23(8), 1899. https://doi.org/10.3390/molecules23081899
   PubMed Web of Science ®Google Scholar
• Petrella, S., Gelus-Ziental, N., Maudry, A., Laurans, C., Boudjelloul, R., & Sougakoff, W. (2011). Crystal structure of the pyrazinamidase of Mycobacterium tuberculosis: Insights into natural and acquired resistance to pyrazinamide. PLoS One. 6(1), e15785. https://doi.org/10.1371/journal.pone.0015785
   PubMed Web of Science ®Google Scholar
• Petrov, D., & Zagrovic, B. (2014). Are current atomistic force fields accurate enough to study proteins in crowded environments? PLoS Computational Biology, 10(5), e1003638. https://doi.org/10.1371/journal.pcbi.1003638
   PubMed Web of Science ®Google Scholar
• Pitaloka, D. A. E., Ramadhan, D. S. F., Arfan, Chaidir, L., & Fakih, T. M. (2021). Docking-based virtual screening and molecular dynamics simulations of quercetin analogs as enoyl-acyl carrier protein reductase (InhA) inhibitors of Mycobacterium tuberculosis. Scientia Pharmaceutica, 89(2), 20. https://doi.org/10.3390/scipharm89020020
   Web of Science ®Google Scholar
• Ramirez-Busby, S. M., & Valafar, F. (2015). Systematic review of mutations in pyrazinamidase associated with pyrazinamide resistance in Mycobacterium tuberculosis clinical isolates. Antimicrobial Agents and Chemotherapy, 59(9), 5267–5277. https://doi.org/10.1128/AAC.00204-15
   PubMed Web of Science ®Google Scholar
• Scorpio, A., Lindholm-Levy, P., Heifets, L., Gilman, R., Siddiqi, S., Cynamon, M., & Zhang, Y. (1997). Characterization of pncA mutations in pyrazinamide-resistant Mycobacterium tuberculosis. Antimicrobial Agents and Chemotherapy, 41(3), 540–543. https://doi.org/10.1128/AAC.41.3.540
   PubMed Web of Science ®Google Scholar
• Sheen, P., Ferrer, P., Gilman, R. H., Christiansen, G., Moreno-Román, P., Gutiérrez, A. H., Sotelo, J., Evangelista, W., Fuentes, P., Rueda, D., Flores, M., Olivera, P., Solis, J., Pesaresi, A., Lamba, D., & Zimic, M. (2012). Role of metal ions on the activity of Mycobacterium tuberculosis pyrazinamidase. The American Journal of Tropical Medicine and Hygiene, 87(1), 153–161. https://doi.org/10.4269/ajtmh.2012.10-0565
   PubMed Web of Science ®Google Scholar
• Silva, A. W. S. d., & Vranken, W. (2012). ACPYPE - AnteChamber PYthon Parser interfacE. BMC Research Notes, 5, 367. https://doi.org/10.1186/1756-0500-5-367
   PubMedGoogle Scholar
• Tan, S., Rao, Y., Guo, J., Tan, Y., Cai, X., Kuang, H., Li, Y., Liu, W., Mugweru, J., Wang, B., Cao, Y., Wang, C., Zhang, Y., & Zhang, T. (2016). The influence of pyrazinamide monoresistance on treatment outcomes in tuberculosis patients from Southern China. Journal of Tuberculosis Research, 04(01), 9–17. https://doi.org/10.4236/jtr.2016.41002
   Google Scholar
• Temple, B., Ayakaka, I., Ogwang, S., Nabanjja, H., Kayes, S., Nakubulwa, S., Worodria, W., Levin, J., Joloba, M., Okwera, A., Eisenach, K. D., McNerney, R., Elliott, A. M., Smith, P. G., Mugerwa, R. D., Ellner, J. J., & Jones-López, E. C. (2008). Rate and amplification of drug resistance among previously-treated patients with tuberculosis in Kampala, Uganda. Clinical Infectious Diseases, 47(9), 1126–1134. https://doi.org/10.1086/592252
   PubMed Web of Science ®Google Scholar
• Vats, C., Dhanjal, J., Goyal, S., Gupta, A., Bharadvaja, N., & Grover, A. (2015). Mechanistic analysis elucidating the relationship between Lys96 mutation in Mycobacterium tuberculosis pyrazinamidase enzyme and pyrazinamide susceptibility. BMC Genomics. 16(Suppl 2), S14. https://doi.org/10.1186/1471-2164-16-S2-S14
   PubMed Web of Science ®Google Scholar
• Wang, H., Gao, X., & Fang, J. (2016). Multiple staggered mesh Ewald: Boosting the accuracy of the smooth particle mesh Ewald method. Journal of Chemical Theory and Computation, 12(11), 5596–5608. https://doi.org/10.1021/acs.jctc.6b00701
   PubMed Web of Science ®Google Scholar
• Wang, N., Wang, L., & Xie, X.-Q. (2017). ProSelection: A novel algorithm to select proper protein structure subsets for in silico target identification and drug discovery research. Journal of Chemical Information and Modeling, 57(11), 2686–2698. https://doi.org/10.1021/acs.jcim.7b00277
   PubMed Web of Science ®Google Scholar
• Whitfield, M. G., Engelthaler, D. M., Allender, C., Folkerts, M., Heupink, T. H., Limberis, J., Warren, R. M., Van Rie, A., & Metcalfe, J. Z. (2022). Comparative performance of genomic methods for the detection of pyrazinamide resistance and heteroresistance in Mycobacterium tuberculosis. Journal of Clinical Microbiology, 60(1), e0190721. https://doi.org/10.1128/JCM.01907-21
   PubMed Web of Science ®Google Scholar
• Yamagishi, J., Okimoto, N., Morimoto, G., & Taiji, M. (2014). A new set of atomic radii for accurate estimation of solvation free energy by Poisson–Boltzmann solvent model. Journal of Computational Chemistry, 35(29), 2132–2139. https://doi.org/10.1002/jcc.23728
   PubMed Web of Science ®Google Scholar
• Yee, D. P., Menzies, D., & Brassard, P. (2012). Clinical outcomes of pyrazinamide-monoresistant Mycobacterium tuberculosis in Quebec. The International Journal of Tuberculosis and Lung Disease: The Official Journal of the International Union against Tuberculosis and Lung Disease, 16(5), 604–609. https://doi.org/10.5588/ijtld.11.0376
   PubMed Web of Science ®Google Scholar
• Zhang, H., Deng, J.-Y., Bi, L.-J., Zhou, Y.-F., Zhang, Z.-P., Zhang, C.-G., Zhang, Y., & Zhang, X.-E. (2008). Characterization of Mycobacterium tuberculosis nicotinamidase/pyrazinamidase. The FEBS Journal, 275(4), 753–762. https://doi.org/10.1111/j.1742-4658.2007.06241.x
   PubMed Web of Science ®Google Scholar