Discovery of multi-target mur enzymes inhibitors with anti-mycobacterial activity through a Scaffold approach

References

• Abraham, M. J., Murtola, T., Schulz, R., P? All, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Anuradha, C. M., Mulakayala, C., Babajan, B., Naveen, M., Rajasekhar, C., & Kumar, C. S. (2010). Probing ligand binding modes of Mycobacterium tuberculosis MurC ligase by molecular modeling, dynamics simulation and docking. Journal of Molecular Modeling, 16(1), 77–85.
   PubMed Web of Science ®Google Scholar
• Arvind, A., Kumar, V., Saravanan, P., & Mohan, C. G. (2012). Homology modeling, molecular dynamics and inhibitor binding study on MurD ligase of Mycobacterium tuberculosis. Interdisciplinary Sciences, Computational Life Sciences, 4(3), 223–‐238. https://doi.org/10.1007/s12539-012-0133-x
   PubMed Web of Science ®Google Scholar
• Bansal, R., & Singh, R. (2020). Steroidal pyrazolines as a promising scaffold in drug discovery. Future Medicinal Chemistry, 12(10), 949–959. https://doi.org/10.4155/fmc-2019-0325
   PubMed Web of Science ®Google Scholar
• Basavannacharya, C., Moody, P. R., Munshi, T., Cronin, N., Keep, N. H., & Bhakta, S. (2010). Essential residues for the enzyme activity of ATP-dependent MurE ligase from Mycobacterium tuberculosis. Protein & Cell, 1(11), 1011–1022. https://doi.org/10.1007/s13238-010-0132-9
   PubMed Web of Science ®Google Scholar
• Bemis, G. W., & Murcko, M. A. (1996). The properties of known drugs. 1. Molecular frameworks. Journal of Medicinal Chemistry, 39(15), 2887–2893. https://doi.org/10.1021/jm9602928
   PubMed Web of Science ®Google Scholar
• Brown, N. (2013). Part one Scaffolds: Identification, representation diversity, and navigation. Scaffold Hopping in Medicinal Chemistry., Chapter 1, page 7., Wiley‐VCH.
   Google Scholar
• Burman, W. J., Cohn, D. L., Rietmeijer, C. A., Judson, F. N., Sbarbaro, J. A., & Reves, R. R. (1997). Noncompliance with directly observed therapy for tuberculosis. Epidemiology and effect on the outcome of treatment. Chest, 111(5), 1168–1173. https://doi.org/10.1378/chest.111.5.1168
   PubMed Web of Science ®Google Scholar
• Chiu, S. W., Pandit, S. A., Scott, H. L., & Jakobsson, E. (2009). An improved united atom force field for simulation of mixed lipid bilayers. The Journal of Physical Chemistry. B, 113(9), 2748–2763. https://doi.org/10.1021/jp807056c
   PubMed Web of Science ®Google Scholar
• Chung, B. C., Zhao, J., Gillespie, R. A., Kwon, D. Y., Guan, Z., Hong, J., Zhou, P., & Lee, S. Y. (2013). Crystal structure of MraY, an essential membrane enzyme for bacterial cell wall synthesis. Science (New York, N.Y.), 341(6149), 1012–1016. https://doi.org/10.1126/science.1236501
   PubMed Web of Science ®Google Scholar
• Davies, M., Nowotka, M., Papadatos, G., Dedman, N., Gaulton, A., Atkinson, F., Bellis, L., & Overington, J. P. (2015). ChEMBL web services: streamlining access to drug discovery data and utilities. Nucleic Acids Research, 43(W1), W612–W620. https://doi.org/10.1093/nar/gkv352
   PubMed Web of Science ®Google Scholar
• DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsletter on Protein Crystallography, 40, 82–92.
   Google 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, 35134. https://doi.org/10.1038/srep35134
   PubMedGoogle Scholar
• Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., & Pedersen, L. G. (1995). A smooth particle mesh Ewald method. The Journal of Chemical Physics, 103(19), 8577–8593. https://doi.org/10.1063/1.470117
   Web of Science ®Google Scholar
• Ferreira, L. G., Dos Santos, R. N., Oliva, G., & Andricopulo, A. D. (2015). Molecular docking and structure-based drug design strategies. Molecules (Basel, Switzerland), 20(7), 13384–13421. https://doi.org/10.3390/molecules200713384
   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. J Med Chem, 47(7), 1739–1749. https://doi.org/10.1021/jm0306430
   PubMed Web of Science ®Google Scholar
• Giacomini, E., Rupiani, S., Guidotti, L., Recanatini, M., & Roberti, M. (2016). The use of stilbene scaffold in medicinal chemistry and multi- target drug design. Current Medicinal Chemistry, 23(23), 2439–2489. https://doi.org/10.2174/0929867323666160517121629
   PubMed Web of Science ®Google Scholar
• Gjorgjieva, M., Tomašič, T., Kikelj, D., & Mašič, L. P. (2018). Benzothiazole-based compounds in antibacterial drug discovery. Current Medicinal Chemistry, 25(38), 5218–5236. https://doi.org/10.2174/0929867324666171009103327
   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
• Kumar, V., Saravanan, P., Arvind, A., & Mohan, C. G. (2011). Identification of hotspot regions of MurB oxidoreductase enzyme using homology modeling, molecular dynamics and molecular docking techniques. Journal of Molecular Modeling, 17(5), 939–953.
   PubMed 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
• Kumari, M., Singh, R., & Subbarao, N. (2021). Exploring the interaction mechanism between potential inhibitor and multi-target Mur enzymes of mycobacterium tuberculosis using molecular docking, molecular dynamics simulation, principal component analysis, free energy landscape, dynamic cross-correlation matrices, vector movements, and binding free energy calculation. Journal of Biomolecular Structure and Dynamics, 1–30. Advance online publication. https://doi.org/10.1080/07391102.2021.1989040
   Google Scholar
• Lange, O. F., Grubmüller, H., & de Groot, B. L. (2005). Molecular dynamics simulations of protein G challenge NMR-derived correlated backbone motions. Angewandte Chemie (International ed. in English), 44(22), 3394–3399. https://doi.org/10.1002/anie.200462957
   PubMed Web of Science ®Google Scholar
• Maitra, A., Munshi, T., Healy, J., Martin, L. T., Vollmer, W., Keep, N. H., & Bhakta, S. (2019). Cell wall peptidoglycan in Mycobacterium tuberculosis: An Achilles' heel for the TB-causing pathogen. FEMS Microbiology Reviews, 43(5), 548–575. https://doi.org/10.1093/femsre/fuz016
   PubMed Web of Science ®Google Scholar
• Markush, E. A. U.S. Patent 1,506,316, (1924).
   Google Scholar
• Nicolaou, C. A., Tamura, S. Y., Kelley, B. P., Bassett, S. I., & Nutt, R. F. (2002). Analysis of large screening data sets via adaptively grown phylogenetic-like trees. Journal of Chemical Information and Computer Sciences, 42(5), 1069–1079. https://doi.org/10.1021/ci010244i
   PubMedGoogle Scholar
• Parate, S., Kumar, V., Danishuddin, Hong, J. C., & Lee, K. W. (2021). Computational investigation identified potential chemical scaffolds for heparanase as anticancer therapeutics. International Journal of Molecular Sciences, 22(10), 5311. https://doi.org/10.3390/ijms22105311
   PubMed Web of Science ®Google Scholar
• Patel, B., Ryan, P., Makwana, V., Zunk, M., Rudrawar, S., & Grant, G. (2019). Caprazamycins: Promising lead structures acting on a novel antibacterial target MraY. European Journal of Medicinal Chemistry, 171, 462–474. https://doi.org/10.1016/j.ejmech.2019.01.071
   PubMed Web of Science ®Google Scholar
• Sadowski, J., Gasteiger, J., & Klebe, G. (1994). Comparison of automatic three-dimensional model builders using 639 X-ray structures. Journal of Chemical Information and Modeling, 34, 4.
   Web of Science ®Google Scholar
• Sali, A., & Blundell, T. L. (1993). Comparative protein modelling by satisfaction of spatial restraints. Journal of Molecular Biology, 234(3), 779–815. https://doi.org/10.1006/jmbi.1993.1626
   PubMed Web of Science ®Google Scholar
• Sander, T., Freyss, J., von Korff, M., & Rufener, C. (2015). DataWarrior: an open-source program for chemistry aware data visualization and analysis. Journal of Chemical Information and Modeling, 55(2), 460–473. https://doi.org/10.1021/ci500588j
   PubMed Web of Science ®Google Scholar
• Schuffenhauer, A., Ertl, P., Roggo, S., Wetzel, S., Koch, M. A., & Waldmann, H. (2007). The scaffold tree-visualization of the scaffold universe by hierarchical scaffold classification. Journal of Chemical Information and Modeling, 47(1), 47–58. https://doi.org/10.1021/ci600338x
   PubMed Web of Science ®Google Scholar
• Schüttelkopf, 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(Pt 8), 1355–1363. https://doi.org/10.1107/S0907444904011679
   PubMedGoogle Scholar
• Smith, T., Wolff, K. A., & Nguyen, L. (2013). Molecular biology of drug resistance in Mycobacterium tuberculosis. Current Topics in Microbiology and Immunology, 374, 53–80. https://doi.org/10.1007/82_2012_279.
   PubMed Web of Science ®Google Scholar
• Trivedi, A. R., Bhuva, V. R., Dholariya, B. H., Dodiya, D. K., Kataria, V. B., & Shah, V. H. (2010). Novel dihydropyrimidines as a potential new class of antitubercular agents. Bioorganic & Medicinal Chemistry Letters, 20(20), 6100–6102. https://doi.org/10.1016/j.bmcl.2010.08.046
   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
• Xu, L., Wu, D., Liu, L., Zheng, Q., Song, Y., Ye, L., Sha, S., Kang, J., Xin, Y., & Ma, Y. (2014). Characterization of mycobacterial UDP-N-acetylglucosamine enolpyruvyle transferase (MurA). Research in Microbiology, 165(2), 91–101. https://doi.org/10.1016/j.resmic.2014.01.004
   PubMed Web of Science ®Google Scholar