Abstract
Free energy changes upon the binding of three triazole derivatives in the active site of imidazole glycerol phosphate dehydratase from Arabidopsis thaliana and Mycobacterium tuberculosis were calculated by computer simulation. These data were correlated with the previously evaluated inhibition constants for the binding of these inhibitors with the enzyme from Arabidopsis thaliana. The free energy changes for both enzymes calculated by the MM-PBSA method correlate with the inhibition constants of the plant enzyme determined by experimental methods.
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REFERENCES
B. N. Ames, B. Garry, and L. A. Herzenberg, J. Mol. Biol. 33, 533 (1960).
I. Mori, R. Fonne-Pfister, S. Matsunaga, et al., Plant Physiol. 107, 719 (1995).
M. S. Ahangar, Y. Khandokar, N. Nasir, et al., Acta Crystallogr. F. 67, 1451 (2011).
D. D. Podshivalov, Yu. B. Mandzhieva, D. D. Sidorov-Biryukov, et al., Crystallogr. Rep. 63 (1), 74 (2018).
Yu. K. Agapova, V. I. Timofeev, and A. S. Komolov, Crystallogr. Rep. 64 (4), 608 (2019).
S. Rawson, C. Bisson, and D. L. Hurdiss, Proc. Natl. Acad. Sci. U. S. A. 115, 1795 (2018).
C. Bisson, K. L. Britton, S. E. Sedelnikova, et al., Ang. Chem. Int. Ed. Engl. 55, 13485 (2016).
C. Bisson, K. L. Britton, S. E. Sedelnikova, et al., Structure 23, 1236 (2015).
A. J. Trott and O. Olson, J. Comput. Chem. 31, 455 (2010).
D. A. Case, T. Cheatham, and T. Darden, J. Comput. Chem. 26, 1668 (2005).
R. Salomon-Ferrer, A. W. Goetz, D. Poole, et al., J. Chem. Theor. Comput. 9, 3878 (2013).
J. A. Maier, C. Martinez, K. Kasavajhala, et al., J. Chem. Theor. Comput. 11, 3696 (2015).
M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids (Oxford Univ. Press, New York, 1991).
P. J. Steinbach, Proteins 57, 665 (2004).
S. Genheden and U. Ryde, Expert Opin. Drug Discovery 10, 449 (2015).
Funding
The study was supported by the Russian Foundation for Basic Research (project no. 18-34-00876; calculations of the free energy changes upon the binding of inhibitors) and the Ministry of Science and Higher Education of the Russian Federation within the framework of the State assignment of the Federal Scientific Research Centre “Crystallography and Photonics” of the Russian Academy of Sciences (analysis of molecular simulation data).
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Translated by T. Safonova
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Agapova, Y.K., Komolov, A.S. & Timofeev, V.I. Molecular Dynamics Calculations of the Interaction Energy of Imidazole Glycerol Phosphate Dehydratase from Mycobacterium tuberculosis with Triazole Derivatives. Crystallogr. Rep. 65, 755–756 (2020). https://doi.org/10.1134/S1063774520050028
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DOI: https://doi.org/10.1134/S1063774520050028