Development of pharmacophore model to identify potential DNA gyrase inhibitors

References

• Anquetin, G., Greiner, J., Mahmoud, N., Santillana, H. M., Gozalbes, R., Farhati, K., Derouin, F., Aubry, A., Cambau, E., & Vierling, P. (2006). Design, synthesis and activity against Toxoplasma gondii, Plasmodium spp., and Mycobacterium tuberculosis of new 6-fluoroquinolones. European Journal of Medicinal Chemistry, 41(12), 1478–1493.
   PubMed Web of Science ®Google Scholar
• Bates, A. D., & Maxwell, A. (2005). DNA topology. Oxford University Press.
   Google Scholar
• Bates, A. D., & Maxwell, A. (2007). Energy coupling in type ii topoisomerases: Why do they hydrolyzeatp? Biochemistry, 46(27), 7929–7941. https://doi.org/10.1021/bi700789g
   PubMed Web of Science ®Google Scholar
• Boucher, H. W., Talbot, G. H., Bradley, J. S., Edwards, J. E., Gilbert, D., Rice, L. B., Scheld, M., Spellberg, B., & Bartlett, J. (2009). Bad bugs, no drugs: No ESKAPE! An update from the Infectious Diseases Society of America. Clinical Infectious Diseases, 48(1), 1–12. https://doi.org/10.1086/595011
   PubMed Web of Science ®Google Scholar
• Bowers, K. J., Chow, 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. In Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida.
   Google Scholar
• Choi, C. (2001). Bacterial meningitis in aging adults. Clinical Infectious Diseases, 33(8), 1380–1385. https://doi.org/10.1086/322688
   PubMed Web of Science ®Google Scholar
• Collin, F., Karkare, S., & Maxwell, A. (2011). Exploiting bacterial DNA gyrase as a drug target: Current state and perspectives. Applied Microbiology and Biotechnology, 92(3), 479–497. https://doi.org/10.1007/s00253-011-3557-z
   PubMed Web of Science ®Google Scholar
• Domagala, J. M., Hanna, L. D., Heifetz, C. L., Hutt, M. P., Mich, T. F., Sanchez, J. P., & Solomon, M. (1986). New structure-activity relationships of the quinolone antibacterials using the target enzyme. The development and application of a DNA gyrase assay. Journal of Medicinal Chemistry, 29(3), 394–404. doi: https://doi.org/10.1021/jm00153a015
   PubMed Web of Science ®Google Scholar
• Dong, K. C., & Berger, J. M. (2008). Structure and function of DNA topoisomerases. In Rice, P. A., & Correll, C. C. (Eds.), Protein-nucleic acid interactions: Structural biology. RSC Biomolecular Sciences (Vol. 1, pp. 234–269). Royal Society of Chemistry.
   Google Scholar
• Furst, A. L., & Francis, M. B. (2019). Impedance-based detection of bacteria. Chemical Reviews, 119(1), 700–726. https://doi.org/10.1021/acs.chemrev.8b00381
   PubMed Web of Science ®Google Scholar
• Guex, N., & Peitsch, M. C. (1997). SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis, 18(15), 2714–2723. https://doi.org/10.1002/elps.1150181505
   PubMed Web of Science ®Google Scholar
• Guo, H. (2019). Isatin derivatives and their anti-bacterial activities. European Journal of Medicinal Chemistry, 164, 678–688. https://doi.org/10.1016/j.ejmech.2018.12.017
   PubMed Web of Science ®Google Scholar
• Habibi, N., Uddin, S., Lyons, B., Al-Sarawi, H. A., Behbehani, M., Shajan, A., Razzack, A. N., Zakir, F., & Alam, F. (2022). Antibiotic resistance genes associated with marine surface sediments: A baseline from the shores of Kuwait. Sustainability, 14(13), 8029. https://doi.org/10.3390/su14138029
   Web of Science ®Google Scholar
• Jakhar, R., Khichi, A., Kumar, D., Dangi, M., & Anil Kumar Chhillar, A. K. (2022). Discovery of novel inhibitors of bacterial DNA gyrase using a QSAR-based approach. ACS Omega, 7(36), 32665–32678. https://doi.org/10.1021/acsomega.2c04310
   PubMed Web of Science ®Google Scholar
• Kayastha, K., Dhungel, B., Karki, S., Adhikari, B., Banjara, M. R., Rijal, K. R., & Ghimire, P. (2020). Extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella species in pediatric patients visiting International Friendship Children’s Hospital, Kathmandu, Nepal. Infectious Diseases, 13, 1178633720909798. https://doi.org/10.1177/1178633720909798
   Google Scholar
• LigPrep. (2021). Schrödinger Release 2021-4. Schrödinger, LLC, New York, NY.
   Google Scholar
• Lykov, I. N., Galemina, I. E., Zaitseva, N. S., & Kapinus, Y. A. (2022). Antibiotic resistance of bacteria isolated from domestic animals and their owners [Paper presentation]. AIP Conference Proceedings, 2467, 070045. https://doi.org/10.1063/5.0093319
   Google Scholar
• Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). Autodock4 and AutoDockTools4: Automated docking with selective receptor flexiblity. Journal of Computational Chemistry, 16, 2785–2791.
   Web of Science ®Google Scholar
• NCI. (2022). https://cactus.nci.nih.gov/download/nci/index.html.
   Google Scholar
• Nollmann, M., Crisona, N. J., & Arimondo, P. B. (2007). Thirty years of Escherichia coli DNA gyrase: From in vivo function to single-molecule mechanism. Biochimie, 89(4), 490–499. https://doi.org/10.1016/j.biochi.2007.02.012
   PubMed Web of Science ®Google Scholar
• O’Neill, J. (2016). Tackling drug-resistant infections globally: Final report and recommendations. The Wellcome Trust.
   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. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Proekt, A., & Hemmings, H. C J. (2013). Chapter 1 - Mechanisms of drug action. In: Pharmacology and Physiology for Anesthesia (pp. 3–19). Elsevier. https://doi.org/10.1016/B978-1-4377-1679-5.00001-6
   Google Scholar
• QikProp. (2021). Schrödinger Release 2021-4. Schrödinger, LLC, New York, NY.
   Google Scholar
• Ramanan, L., & Chaudhury, R. R. (2016). Antibiotic resistance in India: Drivers and opportunities for action. PLoS Medicine, 13(3), e1001974.
   PubMed Web of Science ®Google Scholar
• Schoeffler, A. J., & Berger, J. M. (2008). DNA topoisomerases: Harnessing and constraining energy to govern chromosome topology. Quarterly Reviews of Biophysics, 41(1), 41–101. https://doi.org/10.1017/S003358350800468X
   PubMed Web of Science ®Google Scholar
• Simon, S. (2019). What causes disease? Cross MD FRCPath. In Underwood’s Pathology. Elsevier.
   Google Scholar
• Wang, J. C. (2009). A journey in the world of DNA rings and beyond. Annual Review of Biochemistry, 78, 31–54. https://doi.org/10.1146/annurev.biochem.78.030107.090101
   PubMed Web of Science ®Google Scholar