Research Article
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Investigation of the interactions of anticancer drugs with tyrosine kinase enzyme using semi-empirical methods and comparisons with DFT Calculations

Year 2022, Volume: 6 Issue: 2, 22 - 37, 15.12.2022

Yusuf İş

https://doi.org/10.33435/tcandtc.1089782

Abstract

In this work, the interaction energies of some commercial molecules that are still used clinically with aminoacids in the active region of the tyrosine kinase were calculated by semi-empirical methods such as AM1 and PM3. There are already some results calculated with DFT methods and published in an article previously. By comparing the results there with those found here, it has been discussed whether semi-empirical methods with much shorter computation times can be used to estimate the most critical aminoacids for the tyrosine kinase enzyme instead of DFT methods which take much more time. According to the results obtained here, in order for semi-empirical methods to be used instead of DFT methods for this purpose, the examined ligands must have an electrical charge in the physiological environment. In other words, the hypothesis put forward remains valid only if the ligand under consideration has a charge. The use of semi-empirical methods such as AM1 and PM3 instead of DFT methods to estimate the residues with which a molecule that does not have any electrical charge interacts most strongly did not yield overlapping results.

Keywords

Tyrosine kinase anticancer semi-empirical DFT interaction energy

References

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  • L. N. Johnson, Protein kinase inhibitors: Contributions from structure to clinical compounds, Quarterly Reviews of Biophysics, 42(1) (2009) 1–40.
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  • S. C. Druker BJ, Talpaz M, Resta DJ, Peng B, Buchdunger E, Ford JM, Lydon NB, Kantarjian H, Capdeville R, Ohno-Jones S, Numb Er 14 Efficacy and Safety of a Specific Inhibitor of the Bcr-Abl Tyrosine, The New England Journal of Medicine, 344(14) (2001) 1031–1037.
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  • Is, YS, Elucidation of Ligand/Protein Interactions between BCR-ABL Tyrosine Kinase and Some Commercial Anticancer Drugs Via DFT Methods, Journal of Computational Biophysics and Chemistry, 20(4) (2021) 433-447.
  • M.J.S. Dewar, E.G. Zoebisch, E.F. Heally, J.J.P. Stweart, Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model, Journal of American Chemical Society, 107 (1985) 3902-3909.
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  • F. Neese, The ORCA program system, Wiley Interdisciplinary ReviewsComputatioanlMolecular Science, 2(1) (2012) 73–78.
  • M. D. Hanwell, D. E. Curtis, D. C. Lonie, T. Vandermeerschd, E. Zurek, and G. R. Hutchison, Avogadro: An advanced semantic chemical editor, visualization, and analysis platform, Journal of Cheminformatics, 4(8) (2012) 4-17.
  • Sterling, T.; Irwin, J. J. ZINC 15 — Ligand Discovery for Everyone, Journal of Chemical. Information and Modeling, 55 (2015) 2324–2337.

Year 2022, Volume: 6 Issue: 2, 22 - 37, 15.12.2022

Yusuf İş

https://doi.org/10.33435/tcandtc.1089782

Abstract

References

  • S. McGuire, World Cancer Report 2014. Geneva, Switzerland: World Health Organization, International Agency for Research on Cancer. WHO Press, Advances in Nutrition 7 (2) 2016 418–419.
  • L. N. Johnson, Protein kinase inhibitors: Contributions from structure to clinical compounds, Quarterly Reviews of Biophysics, 42(1) (2009) 1–40.
  • J. T. Metz, E. F. Johnson, N. B. Soni, P. J. Merta, L. Kifle, and P. J. Hajduk, Navigating the kinome, Nature Chemical Biology, 7(4) (2011) 200–202.
  • L. N. Johnson and R. J. Lewis, ChemInform Abstract: Structural Basis for Control by Phosphorylation, ChemInform, 32(40) (2010) 2209-2242.
  • G. Manning, Genomic overview of protein kinases, WormBook. 2005; 1–19.
  • S. C. Druker BJ, Talpaz M, Resta DJ, Peng B, Buchdunger E, Ford JM, Lydon NB, Kantarjian H, Capdeville R, Ohno-Jones S, Numb Er 14 Efficacy and Safety of a Specific Inhibitor of the Bcr-Abl Tyrosine, The New England Journal of Medicine, 344(14) (2001) 1031–1037.
  • M. Radi et al., Discovery and SAR of 1,3,4-thiadiazole derivatives as potent Abl tyrosine kinase inhibitors and cytodifferentiating agents, Bioorganic Medicinal Chemistry Letters, 18(3) (2008) 1207–1211.
  • D. Y. Duveau et al., Synthesis and biological evaluation of analogues of the kinase inhibitor nilotinib as Abl and Kit inhibitors, Bioorganic Medicinal Chemistry Letters, 23(3) (2013) 682–686.
  • K. D. Dubey and R. P. Ojha, Binding free energy calculation with QM/MM hybrid methods for Abl-Kinase inhibitor Journal of Biological Physics, 37(1) (2011) 69–78.
  • Is, YS, Elucidation of Ligand/Protein Interactions between BCR-ABL Tyrosine Kinase and Some Commercial Anticancer Drugs Via DFT Methods, Journal of Computational Biophysics and Chemistry, 20(4) (2021) 433-447.
  • M.J.S. Dewar, E.G. Zoebisch, E.F. Heally, J.J.P. Stweart, Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model, Journal of American Chemical Society, 107 (1985) 3902-3909.
  • G.A. Segal, Semiempirical Methods of Electronic Structure Calculation, Part A: Techniques, University of Southern California, Los Angeles, (1997).
  • F. Neese, The ORCA program system, Wiley Interdisciplinary ReviewsComputatioanlMolecular Science, 2(1) (2012) 73–78.
  • M. D. Hanwell, D. E. Curtis, D. C. Lonie, T. Vandermeerschd, E. Zurek, and G. R. Hutchison, Avogadro: An advanced semantic chemical editor, visualization, and analysis platform, Journal of Cheminformatics, 4(8) (2012) 4-17.
  • Sterling, T.; Irwin, J. J. ZINC 15 — Ligand Discovery for Everyone, Journal of Chemical. Information and Modeling, 55 (2015) 2324–2337.
There are 15 citations in total.

Details

Primary Language English
Subjects Chemical Engineering
Journal Section Research Article
Authors

Yusuf İş 0000-0003-3818-6923

Early Pub Date March 18, 2022
Publication Date December 15, 2022
Submission Date March 18, 2022
Published in Issue Year 2022 Volume: 6 Issue: 2

Cite

APA İş, Y. (2022). Investigation of the interactions of anticancer drugs with tyrosine kinase enzyme using semi-empirical methods and comparisons with DFT Calculations. Turkish Computational and Theoretical Chemistry, 6(2), 22-37. https://doi.org/10.33435/tcandtc.1089782
AMA İş Y. Investigation of the interactions of anticancer drugs with tyrosine kinase enzyme using semi-empirical methods and comparisons with DFT Calculations. Turkish Comp Theo Chem (TC&TC). December 2022;6(2):22-37. doi:10.33435/tcandtc.1089782
Chicago İş, Yusuf. “Investigation of the Interactions of Anticancer Drugs With Tyrosine Kinase Enzyme Using Semi-Empirical Methods and Comparisons With DFT Calculations”. Turkish Computational and Theoretical Chemistry 6, no. 2 (December 2022): 22-37. https://doi.org/10.33435/tcandtc.1089782.
EndNote İş Y (December 1, 2022) Investigation of the interactions of anticancer drugs with tyrosine kinase enzyme using semi-empirical methods and comparisons with DFT Calculations. Turkish Computational and Theoretical Chemistry 6 2 22–37.
IEEE Y. İş, “Investigation of the interactions of anticancer drugs with tyrosine kinase enzyme using semi-empirical methods and comparisons with DFT Calculations”, Turkish Comp Theo Chem (TC&TC), vol. 6, no. 2, pp. 22–37, 2022, doi: 10.33435/tcandtc.1089782.
ISNAD İş, Yusuf. “Investigation of the Interactions of Anticancer Drugs With Tyrosine Kinase Enzyme Using Semi-Empirical Methods and Comparisons With DFT Calculations”. Turkish Computational and Theoretical Chemistry 6/2 (December 2022), 22-37. https://doi.org/10.33435/tcandtc.1089782.
JAMA İş Y. Investigation of the interactions of anticancer drugs with tyrosine kinase enzyme using semi-empirical methods and comparisons with DFT Calculations. Turkish Comp Theo Chem (TC&TC). 2022;6:22–37.
MLA İş, Yusuf. “Investigation of the Interactions of Anticancer Drugs With Tyrosine Kinase Enzyme Using Semi-Empirical Methods and Comparisons With DFT Calculations”. Turkish Computational and Theoretical Chemistry, vol. 6, no. 2, 2022, pp. 22-37, doi:10.33435/tcandtc.1089782.
Vancouver İş Y. Investigation of the interactions of anticancer drugs with tyrosine kinase enzyme using semi-empirical methods and comparisons with DFT Calculations. Turkish Comp Theo Chem (TC&TC). 2022;6(2):22-37.

Journal Full Title: Turkish Computational and Theoretical Chemistry


Journal Abbreviated Title: Turkish Comp Theo Chem (TC&TC)