МОЛЕКУЛЯРНИЙ ДОКІНГ БІОІЗОСТЕРІВ ТОСУФЛОКСАЦИНУ ДО БАКТЕРІАЛЬНИХ ТОПОІЗОМЕРАЗ
Ключові слова:
molecular docking, tosufloxacin, bioisosteres, topoisomerase IIАнотація
The molecular docking of 15 tosufloxacin bioisosteres into topoisomerase IV (4KOE) and DNA gyrase (9GGQ) binding sites was performed. The thermodynamic stability of ternary complexes was verified based on binding free energy and metal coordination. Significant affinity was confirmed for the 4KOE target, while steric hindrances in 9GGQ led to ligand displacement. The B4, A1, A11 series candidates were identified as the most promising leaders for further studies.
Посилання
Aldred K. J., Kerns R. J., Osheroff N. Mechanism of quinolone action and resistance. Biochemistry. 2014. Vol. 53, No 10. P. 1565–1574. https://doi.org/10.1021/bi5000564
Uivarosi V. Metal complexes of quinolone antibiotics and their applications: an update. Molecules. 2013. Vol. 18, No 9. P. 11153–11197. https://doi.org/10.3390/molecules180911153
Osypenko O., Marynchenko L. In silico design and physicochemical optimization of novel fluoroquinolone analogs via systematic bioisosteric replacement at N1 and C7 positions. Проблеми та досягнення сучасної біотехнології : тези доп. VI Міжнар. конф, Харків, 2026. С. 86–88.
Cherinka B, et al. Marvin: A tool kit for streamlined access and visualization of the SDSS-IV manga data set. The astronomical journal. 2019. Vol. 158, No 2. P. 74. https://doi.org/10.3847/1538-3881/ab2634
Hanwell M. D., et al. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. Journal of cheminformatics. 2012. Vol. 4, No 1. https://doi.org/10.1186/1758-2946-4-17
RCSB PDB - 4KOE: Quinolone (Trovafloxacin)-DNA cleavage complex of type IV topoisomerase from S. pneumoniae. Protein Data Bank. URL: https://www.rcsb.org/structure/4KOE (дата звернення: 06.04.2026).
Michalczyk E, et al. Structural basis of chiral wrap and T-segment capture by Escherichia coli DNA gyrase. Proceedings of the national academy of sciences. 2024. Vol. 121, No 49. https://doi.org/10.1073/pnas.2407398121
Pettersen E. F., et al. UCSF Chimera—A visualization system for exploratory research and analysis. Journal of computational chemistry. 2004. Vol. 25, No 13. P. 1605–1612. https://doi.org/10.1002/jcc.20084
Trott O., Olson A. J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of computational chemistry. 2009. Vol. 31, No 2. P. 455–461. https://doi.org/10.1002/jcc.21334
Eberhardt J, et al. AutoDock vina 1.2.0: new docking methods, expanded force field, and python bindings. Journal of chemical information and modeling. 2021. Vol. 61, No 8. P. 3891–3898. https://doi.org/10.1021/acs.jcim.1c00203
Stierand K., Rarey M. Drawing the PDB: protein−ligand complexes in two dimensions. ACS medicinal chemistry letters. 2010. Vol. 1, No 9. P. 540–545. https://doi.org/10.1021/ml100164p
Schultes S, et al. Ligand efficiency as a guide in fragment hit selection and optimization. Drug discovery today: technologies. 2010. Vol. 7, No 3. P. e157–e162. https://doi.org/10.1016/j.ddtec.2010.11.003