Identification of novel inhibitors for trigger factor (TF) of M. tb: an in silico investigation

References

• Albanna, A. S., Smith, B. M., Cowan, D., & Menzies, D. (2013). Fixed-dose combination antituberculosis therapy: A systematic review and meta-analysis. The European Respiratory Journal, 42(3), 721–732. https://doi.org/10.1183/09031936.00180612
   PubMed Web of Science ®Google Scholar
• Bochevarov, A. D., Harder, E., Hughes, T. F., Greenwood, J. R., Braden, D. A., Philipp, D. M., Rinaldo, D., Halls, M. D., Zhang, J., & Friesner, R. A. (2013). Jaguar: A high‐performance quantum chemistry software program with strengths in life and materials sciences. International Journal of Quantum Chemistry, 113(18), 2110–2142. https://doi.org/10.1002/qua.24481
   Web of Science ®Google Scholar
• Bowers, K. J., Chow, D. E., Xu, H., Dror, R. O., Eastwood, M. P., Gregersen, B. A., Klepeis, J. L., Kolossvary, I., Moraes, M. A., Sacerdoti, F. D., Salmon, J. K., Shan, Y., & Shaw, D. E. (2006). Scalable algorithms for molecular dynamics simulations on commodity clusters [Paper presentation]. SC 2006 Conference, Proceedings of the ACM/IEEE, 11-17 Nov. 2006.
   Google Scholar
• Canonical Ltd. (2018). Ubuntu 18.04 LTS (Bionic Beaver).
   Google Scholar
• Cohen, A., Mathiasen, V. D., Schön, T., & Wejse, C. (2019). The global prevalence of latent tuberculosis: A systematic review and meta-analysis. European Respiratory Journal, 54(3), 1900655. https://doi.org/10.1183/13993003.00655-2019
   PubMed Web of Science ®Google Scholar
• Fair, R. J., & Tor, Y. (2014). Antibiotics and bacterial resistance in the 21st century. Perspectives in Medicinal Chemistry, 6, 25–64. https://doi.org/10.4137/pmc.S14459
   PubMedGoogle Scholar
• Ferbitz, L., Maier, T., Patzelt, H., Bukau, B., Deuerling, E., & Ban, N. (2004). Trigger factor in complex with the ribosome forms a molecular cradle for nascent proteins. Nature, 431(7008), 590–596. https://doi.org/10.1038/nature02899
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., Shaw, D. E., Francis, P., & Shenkin, P. S. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47(7), 1739–1749. https://doi.org/10.1021/jm0306430
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., Sanschagrin, P. C., & Mainz, D. T. (2006). Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. Journal of Medicinal Chemistry, 49(21), 6177–6196. https://doi.org/10.1021/jm051256o
   PubMed Web of Science ®Google Scholar
• Halgren, T. (2007). New method for fast and accurate binding-site identification and analysis. Chemical Biology & Drug Design, 69(2), 146–148. https://doi.org/10.1111/j.1747-0285.2007.00483.x
   PubMed Web of Science ®Google Scholar
• Halgren, T. A. (2009). Identifying and characterizing binding sites and assessing druggability. Journal of Chemical Information and Modeling, 49(2), 377–389. https://doi.org/10.1021/ci800324m
   PubMed Web of Science ®Google Scholar
• Halgren, T. A., Murphy, R. B., Friesner, R. A., Beard, H. S., Frye, L. L., Pollard, W. T., & Banks, J. L. (2004). Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. Journal of Medicinal Chemistry, 47(7), 1750–1759. https://doi.org/10.1021/jm030644s
   PubMed Web of Science ®Google Scholar
• Hoffmann, A., Bukau, B., & Kramer, G. (2010). Structure and function of the molecular chaperone Trigger Factor. Biochimica et Biophysica Acta, 1803(6), 650–661. https://doi.org/10.1016/j.bbamcr.2010.01.017
   PubMed Web of Science ®Google Scholar
• Houben, R. M., & Dodd, P. J. (2016). The global burden of latent tuberculosis infection: A re-estimation using mathematical modelling. PLoS Medicine, 13(10), e1002152. https://doi.org/10.1371/journal.pmed.1002152
   PubMed Web of Science ®Google Scholar
• Jacobson, M. P., Friesner, R. A., Xiang, Z., & Honig, B. (2002). On the role of the crystal environment in determining protein side-chain conformations. Journal of Molecular Biology, 320(3), 597–608. https://doi.org/10.1016/s0022-2836(02)00470-9
   PubMed Web of Science ®Google Scholar
• Jacobson, M. P., Pincus, D. L., Rapp, C. S., Day, T. J., Honig, B., Shaw, D. E., & Friesner, R. A. (2004). A hierarchical approach to all-atom protein loop prediction. Proteins, 55(2), 351–367. https://doi.org/10.1002/prot.10613
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., Maxwell, D. S., & Tirado-Rives, J. (1996). Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. Journal of the American Chemical Society, 118(45), 11225–11236. https://doi.org/10.1021/ja9621760
   Web of Science ®Google Scholar
• Jorgensen, W. L., & Tirado-Rives, J. (1988). The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. Journal of the American Chemical Society, 110(6), 1657–1666. https://doi.org/10.1021/ja00214a001
   PubMed Web of Science ®Google Scholar
• Ludlam, A. V., Moore, B. A., & Xu, Z. (2004). The crystal structure of ribosomal chaperone trigger factor from Vibrio cholerae. Proceedings of the National Academy of Sciences of the United States of America, 101(37), 13436–13441. https://doi.org/10.1073/pnas.0405868101
   PubMed Web of Science ®Google Scholar
• Polikanov, Y. S., Aleksashin, N. A., Beckert, B., & Wilson, D. N. (2018). The mechanisms of action of ribosome-targeting peptide antibiotics. Frontiers in Molecular Biosciences, 5, 48. https://doi.org/10.3389/fmolb.2018.00048
   PubMed Web of Science ®Google Scholar
• Schmidpeter, P. A. M., & Schmid, F. X. (2015). Prolyl isomerization and its catalysis in protein folding and protein function. Journal of Molecular Biology, 427(7), 1609–1631. https://doi.org/10.1016/j.jmb.2015.01.023
   PubMed Web of Science ®Google Scholar
• Shivakumar, D., Williams, J., Wu, Y., Damm, W., Shelley, J., & Sherman, W. (2010). Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. Journal of Chemical Theory and Computation, 6(5), 1509–1519. https://doi.org/10.1021/ct900587b
   PubMed Web of Science ®Google Scholar
• Stoller, G., Rücknagel, K. P., Nierhaus, K. H., Schmid, F. X., Fischer, G., & Rahfeld, J. U. (1995). A ribosome-associated peptidyl-prolyl cis/trans isomerase identified as the trigger factor. The EMBO Journal, 14(20), 4939–4948. https://doi.org/10.1002/j.1460-2075.1995.tb00177.x
   PubMed Web of Science ®Google Scholar
• The UniProt C. (2021). UniProt: The universal protein knowledgebase in 2021. Nucleic Acids Research, 49(D1), D480–D489. https://doi.org/10.1093/nar/gkaa1100
   PubMed Web of Science ®Google Scholar