Repurposing of FDA-approved drugs to target MurB and MurE enzymes in Mycobacterium tuberculosis

References

• Andronis, C., Sharma, A., Virvilis, V., Deftereos, S., & Persidis, A. (2011). Literature mining, ontologies and information visualization for drug repurposing. Briefings in Bioinformatics, 12(4), 357–368. doi: 10.1093/bib/bbr005
   PubMed Web of Science ®Google Scholar
• Basavannacharya, C., Robertson, G., Munshi, T., Keep, N. H., & Bhakta, S. (2010). ATP-dependent MurE ligase in Mycobacterium tuberculosis: Biochemical and structural characterisation. Tuberculosis, 90(1), 16–24. doi: 10.1016/j.tube.2009.10.007
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J., Postma, J. V., van Gunsteren, W. F., DiNola, A. R. H. J., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. doi: 10.1063/1.448118
   Web of Science ®Google Scholar
• Bronson, J. J.,Denbleyker, K. L.,Falk, P. J.,Mate, R. A.,Ho, H. T.,Pucci, M. J., &Snyder, L. B. (2003). Discovery of the first antibacterial small molecule inhibitors of MurB. Bioorganic & Medicinal Chemistry Letters, 13(5), 873–875.
   PubMed Web of Science ®Google Scholar
• Critchley, J. A., Young, F., Orton, L., & Garner, P. (2013). Corticosteroids for prevention of mortality in people with tuberculosis: A systematic review and meta-analysis. The Lancet. Infectious Diseases, 13(3), 223–237. doi: 10.1016/S1473-3099(12)70321-3
   PubMed Web of Science ®Google Scholar
• D'Ambrosio, L., Centis, R., Sotgiu, G., Pontali, E., Spanevello, A., & Migliori, G. B. (2015). New anti-tuberculosis drugs and regimens: 2015 update. ERJ Open Research, 1(1), 00010–2015. doi: 10.1183/23120541.00010-2015
   PubMedGoogle Scholar
• Darden, T., Perera, L., Li, L., & Pedersen, L. (1999). New tricks for modelers from the crystallography toolkit: The particle mesh Ewald algorithm and its use in nucleic acid simulations. Structure, 7(3), R55–R60. doi: 10.1016/S0969-2126(99)80033-1
   PubMed Web of Science ®Google Scholar
• Dooley, K. E., Eric, L. N., & Andreas, H. D. (2013). Pipeline of drugs for related diseases: Tuberculosis. Current Opinion in HIV and AIDS, 8(6), 579. doi: 10.1097/COH.0000000000000009
   PubMed Web of Science ®Google Scholar
• Douguet, D. (2010). e-LEA3D: A computational-aided drug design web server. Nucleic Acids Research, 38(Web Server issue), W615–W621. doi: 10.1093/nar/gkq322
   PubMedGoogle Scholar
• Eniyan, K., Kumar, A., Rayasam, G. V., Perdih, A., & Bajpai, U. (2016). Development of a one-pot assay for screening and identification of Mur pathway inhibitors in Mycobacterium tuberculosis. Scientific Reports, 6(1), 35134. doi: 10.1038/srep35134
   PubMed Web of Science ®Google Scholar
• Eniyan, K., Dharavath, S., Vijayan, R., Bajpai, U., & Gourinath, S. (2018). Crystal structure of UDP-N-acetylglucosamine-enolpyruvate reductase (MurB) from Mycobacterium tuberculosis. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 1866(3), 397–406. doi: 10.1016/j.bbapap.2017.11.013
   PubMed Web of Science ®Google Scholar
• Francisco, G. D., Li, Z., Albright, J. D., Eudy, N. H., Katz, A. H., Petersen, P. J., … Lin, Y. I. (2004). Phenyl thiazolyl urea and carbamate derivatives as new inhibitors of bacterial cell-wall biosynthesis. Bioorganic & Medicinal Chemistry Letters, 14(1), 235–238. doi: 10.1016/j.bmcl.2003.09.082
   PubMed Web of Science ®Google Scholar
• Girgis, N. I., Farid, Z. O. H. E. I. R., Kilpatrick, M. E., Sultan, Y., & Mikhail, I. A. (1991). Dexamethasone adjunctive treatment for tuberculous meningitis. The Pediatric Infectious Disease Journal, 10(3), 179–183.
   PubMed Web of Science ®Google Scholar
• Haller, L., Sossouhounto, R., Coulibaly, I. M., Dosso, M., Kone, M., Adom, H., … Lobognon, L. R. (1999). Isoniazid plus sulphadoxine-pyrimethamine can reduce morbidity of HIV-positive patients treated for tuberculosis in Africa: A controlled clinical trial. Chemotherapy, 45(6), 452–465. doi: 10.1159/000007239
   PubMed Web of Science ®Google Scholar
• Hess, B.,Bekker, H.,Berendsen, H. J., &Fraaije, J. G. (1997). LINCS: a linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472.
   Web of Science ®Google Scholar
• Hess, B., Kutzner, C., Van Der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4(3), 435–447. doi: 10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Kaufmann, S. H., Lange, C., Rao, M., Balaji, K. N., Lotze, M., Schito, M., … Maeurer, M. (2014). Progress in tuberculosis vaccine development and host-directed therapies—A state of the art review. The Lancet Respiratory Medicine, 2(4), 301–320. doi: 10.1016/S2213-2600(14)70033-5
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., Lynn, A., & Open Source Drug Discovery Consortium. (2014). A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. doi: 10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Maitra, A., Bates, S., Kolvekar, T., Devarajan, P. V., Guzman, J. D., & Bhakta, S. (2015). Repurposing-a ray of hope in tackling extensively drug resistance in tuberculosis. International Journal of Infectious Diseases, 32, 50–55. doi: 10.1016/j.ijid.2014.12.031
   PubMed Web of Science ®Google Scholar
• Maitra, A., Bates, S., Shaik, M., Evangelopoulos, D., Abubakar, I., McHugh, T. D., … Bhakta, S. (2016). Repurposing drugs for treatment of tuberculosis: A role for non-steroidal anti-inflammatory drugs. British Medical Bulletin, 118(1), 138. doi: 10.1093/bmb/ldw019
   PubMed Web of Science ®Google Scholar
• Moraes, G. L., Gomes, G. C., Monteiro de Sousa, P. R., Alves, C. N., Govender, T., Kruger, H. G., … Lameira, J. (2015). Structural and functional features of enzymes of Mycobacterium tuberculosis peptidoglycan biosynthesis as targets for drug development. Tuberculosis, 95(2), 95–111. doi: 10.1016/j.tube.2015.01.006
   PubMed Web of Science ®Google Scholar
• Munshi, T., Gupta, A., Evangelopoulos, D., Guzman, J. D., Gibbons, S., Keep, N. H., & Bhakta, S. (2013). Characterisation of ATP-dependent Mur ligases involved in the biogenesis of cell wall peptidoglycan in Mycobacterium tuberculosis. PLoS One, 8(3), e60143. doi: 10.1371/journal.pone.0060143
   PubMed Web of Science ®Google Scholar
• 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.doi: 10.1186/1758-2946-3-33
   PubMed Web of Science ®Google Scholar
• Opravil, M., Pechère, M., Lazzarin, A., Heald, A., Rüttimann, S., Iten, A., … Hirschel, B. (1995). Dapsone/pyrimethamine may prevent mycobacterial disease in immunosuppressed patients infected with the human immunodeficiency virus. Clinical Infectious Diseases, 20(2), 244–249. doi: 10.1093/clinids/20.2.244
   PubMed Web of Science ®Google Scholar
• Palomino, J. C., & Martin, A. (2013). Is repositioning of drugs a viable alternative in the treatment of tuberculosis? Journal of Antimicrobial Chemotherapy, 68(2), 275–283. doi: 10.1093/jac/dks405
   PubMed Web of Science ®Google Scholar
• Pearson, W. R., & Wood, T. C. (2001). Statistical significance in biological sequence comparison. In Handbook of statistical genetics. John Wiley & Sons. doi: 10.1002/0470022620.bbc02
   Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera—A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. doi: 10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Rani, J., Shah, A. R., & Ramachandran, S. (2015). pubmed.mineR: An R package with text-mining algorithms to analyse PubMed abstracts. Journal of Biosciences, 40(4), 671–682. doi: 10.1007/s12038-015-9552-2
   PubMed Web of Science ®Google Scholar
• SchuÈttelkopf, A. W., & Van Aalten, D. M. (2004). PRODRG: A tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallographica Section D Biological Crystallography, 60(8), 1355–1363. doi: 10.1107/S0907444904011679
   PubMedGoogle Scholar
• Song, D., Zhang, J., Wang, Y., Hu, J., Xu, S., Xu, Y., … Sun, Z. (2019). Molecular mechanism study of several inhibitors binding to BRD9 bromodomain based on molecular simulations. Journal of Biomolecular Structure and Dynamics 37(11), 2970–2979. doi: 10.1080/07391102.2018.1502097
   Google Scholar
• Štrancar, K., Boniface, A., Blanot, D., & Gobec, S. (2007). Phosphinate Inhibitors of UDP-N-acetylmuramoyl-L-alanyl-D-glutamate: L-lysine ligase (MurE). Archiv der Pharmazie (Weinheim), 340(3), 127–134. doi: 10.1002/ardp.200600191
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. doi: 10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Wahid, B., Saleem, K., Waqar, M., Wasim, M., & Idrees, M. (2018). Successful treatment of HCV/TB co-infected patient with sofosbuvir and daclatasvir: a case report. Future Virology, 13(5), 317–321.
   Web of Science ®Google Scholar
• Wishart, D. S., Knox, C., Guo, A. C., Cheng, D., Shrivastava, S., Tzur, D., … Hassanali, M. (2007). DrugBank: A knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Research, 36(Suppl 1), D901–D906. doi: 10.1093/nar/gkm958
   PubMedGoogle Scholar
• World Health Organization. (2016). WHO treatment guidelines for drug-resistant tuberculosis 2016 update. Geneva, Switzerland: World Health Organization.
   Google Scholar
• Živec, M.,Turk, S.,Blanot, D., &Gobec, S. (2011). Design and Synthesis of New Peptidomimetics as Potential Inhibitors of MurE. Acta Chimica Slovenica, 58(1).
   PubMed Web of Science ®Google Scholar
• Zumla, A., Rao, M., Dodoo, E., & Maeurer, M. (2016). Potential of immunomodulatory agents as adjunct host-directed therapies for multidrug-resistant tuberculosis. BMC Medicine, 14(1), 89. doi: 10.1186/s12916-016-0635-1
   PubMedGoogle Scholar