MD simulations of Mycobacterium tuberculosis tyrosyl-tRNA synthetase in complex with SB-219383 inhibitor using QM/MM approach

Authors

  • V. V. Mykuliak Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kiev
  • I. S. Voiteshenko Institute of High Technologies, Taras Shevchenko National University of Kiev
  • A. I. Kornelyuk Institute of Molecular Biology and Genetics of the NAS of Ukraine, Kiev

DOI:

https://doi.org/10.15407/dopovidi2016.01.099

Keywords:

inhibitor, Mycobacterium tuberculosis, QM/MM approach, tyrosyl-tRNA synthetase

Abstract

Mycobacterium tuberculosis tyrosyl-tRNA synthetase (MtTyrRS) is one of the key enzymes at the pre-ribosomal step of protein synthesis. Therefore, its inhibition is a promising way for the development of new antibiotics. Effective and one of the most studied bacterial TyrRS inhibitors is SB-219383 compound. We have studied the nature of the interactions between SB-219383 and MtTyrRS using the hybrid approach of QM/MM simulations. In particular, a special attention has been paid to the identification of hydrogen bonds and their structural and physico-chemical parameters.

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References

Odynets K. A., Kornelyuk A. I. The Ukrainian Biochemical Journal, 2008, 80, No 5: 62–75 (in Ukranian).

Bonnefond L., Giegé R., Rudinger-Thirion J. Biochimie, 2005, 87, No 9-10: 873–883. doi: https://doi.org/10.1016/j.biochi.2005.03.008, PMid:16164994

Stefanska A. L., Coates N. J., Mensah L. M., Pope A. J., Ready S. J., Warr S. R. J. Antibiot. (Tokyo), 2000, 53, No 4: 345–350. doi: https://doi.org/10.7164/antibiotics.53.345

Mykuliak V. V., Kornelyuk A. I. Biopolymers and Cell, 2014, 30, No 2: 157–162. doi: https://doi.org/10.7124/bc.000890

Mykuliak V. V., Kornelyuk A. I. Reports of the National Academy of Sciences of Ukraine, 2014, 6: 156–159 (in Ukranian). doi: https://doi.org/10.15407/dopovidi2014.06.156

Mykuliak V. V., Dubey I. Ya., Kornelyuk A. I. Reports of the National Academy of Sciences of Ukraine, 2014, 10: 167–174 (in Ukranian). doi: https://doi.org/10.15407/dopovidi2014.10.167

Páll S., Abraham M.J., Kutzner C., Hess B., Lindahl E. Solving Software Challenges for Exascale, Cham, Switzerland: Springer, 2015: 3–27.

Neese F. WIREs Comput. Mol. Sci., 2012, 2, Iss. 1: 73–78. doi: https://doi.org/10.1002/wcms.81

Hornak V., Abel R., Okur O., Strockbine B., Roitberg A., Simmerling C. Proteins, 2006, 65, No 3: 712–725. doi: https://doi.org/10.1002/prot.21123, PMid:16981200 PMCid:PMC4805110

Bussi G., Donadio D., Parrinello M. J. Chem. Phys., 2007, 126: 014101. doi: https://doi.org/10.1063/1.2408420, PMid:17212484

Beider R. Atoms in molecules. Quantum theory, Moscow, Mir: 2001 (in Russian).

Bader R., Nguyen-Dang T. T., Tal Y. J. Chem. Phys., 1979, 70, No 9: 4316–4329. doi: https://doi.org/10.1063/1.438006

Bader R. F. W., Essen H. J. Chem. Phys., 1984, 80, No 5: 1943–1960. doi: https://doi.org/10.1063/1.446956

Espinosa E., Molinsa E., Lecomte C. Chem. Phys. Lett., 1998, 285, No 3–4: 170-173. doi: https://doi.org/10.1016/S0009-2614(98)00036-0

Keith T. A. AIMAll (Version 10.05.04). – 2010. – Resource access mode: http://aim.tkgristmill.com

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Published

29.09.2024

How to Cite

Mykuliak, V. V., Voiteshenko, I. S., & Kornelyuk, A. I. (2024). MD simulations of Mycobacterium tuberculosis tyrosyl-tRNA synthetase in complex with SB-219383 inhibitor using QM/MM approach . Reports of the National Academy of Sciences of Ukraine, (1), 99–104. https://doi.org/10.15407/dopovidi2016.01.099

Issue

No. 1 (2016): Reports of the National Academy of Sciences of Ukraine

Section

Biophysics

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