Research Article
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Imidazole Based Novel Schiff Base: Synthesis, Characterization, Quantum Chemical Calculations, In Silico Investigation of ADMEt Properties and Molecular Docking Simulations against VEGFR2 Protein

Year 2024, Volume: 13 Issue: 1, 62 - 78, 24.03.2024
https://doi.org/10.17798/bitlisfen.1332971

Abstract

The potential drug candidate novel Schiff base, 2-(((3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl)imino)methyl)phenol (MITPIM) was synthesized by the reaction of salicylaldehyde and 3-(4-methyl-1H-imidazol-1-yl)-5-(trifluoromethyl)aniline which is the precursor of the nilotinib molecule used in the cancer treatment. It was characterizated by using spectroscopic techniques such as 1H-NMR, 13C-NMR, 19F-NMR, FT-IR and UV-Vis. DFT computational technique was used for further investigation. DFT/B3LYP method and the 6-311G(d,p) basis set were used to determine optimized geometry. Then by using optimized geometry and DFT approach three-dimensional molecular electrostatic potential (MEP), vibration frequencies, NMR chemical shift values, HOMOs-LUMOs and molecular orbital energies were calculated. It was observed that the experimental and theoretical datas were in good agreement. The ADME and toxicity properties were investigated by using online servers. According to the results, it was concluded that the MITPIM has low toxicity and high oral bioavailability. Molecular docking simulations of the MITPIM with VEGFR2 protein (PDB ID: 2XIR) were investigated. According to molecular docking studies, the binding energy of the complex formed by the MITPIM with VEGFR2 protein (PDB ID: 2XIR) was −9.34 kcal/mol and the value was close to nilotinib’s binding score which was -9.69 kcal/mol. Molecular docking and ADMEt results shown that the newly synthesized MITPIM has the potential to be drug.

Thanks

The author would like to thank Prof. Dr. Tahir TİLKİ, Prof. Dr. Bülent DEDE and Assoc. Prof. Dr. Çiğdem KARABACAK ATAY for technical and theoretical support.

References

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Year 2024, Volume: 13 Issue: 1, 62 - 78, 24.03.2024
https://doi.org/10.17798/bitlisfen.1332971

Abstract

References

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  • [3] V. V. Padma, “An overview of targeted cancer therapy,” Biomedicine (Taipei), vol. 5, no. 4, p. 19, Nov. 2015.
  • [4] P. Martins, J. Jesus, S. Santos, L. R. Raposoi, C. Roma-Rodrigues, P. V. Baptista, A. R. Fernandes, “Heterocyclic Anticancer Compounds: Recent Advances and the Paradigm Shift towards the Use of Nanomedicine’s Tool Box,” Molecules, vol. 20, no. 9, pp. 16852–16891, Sep. 2015.
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  • [16] H. Jung, J. Kim, D. Im, H. Moon, and J.-M. Hah, “Design, synthesis, and in vitro evaluation of N-(3-(3-alkyl-1H-pyrazol-5-yl) phenyl)-aryl amide for selective RAF inhibition,” Bioorg Med Chem Lett, vol. 29, no. 4, pp. 534–538, Feb. 2019.
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  • [20] E. Kalinichenko, A. Faryna, T. Bozhok, and A. Panibrat, “Synthesis, In Vitro and In Silico Anticancer Activity of New 4-Methylbenzamide Derivatives Containing 2,6-Substituted Purines as Potential Protein Kinases Inhibitors,” Int J Mol Sci, vol. 22, no. 23, p. 12738, Nov. 2021.
  • [21] X. Lu, Z. Zhang, X. Ren, X. Pan, D. Wang, X. Zhuang, J. Luo, R. Yu, K. Ding, “Hybrid pyrimidine alkynyls inhibit the clinically resistance related Bcr-AblT315I mutant,” Bioorg Med Chem Lett, vol. 25, no. 17, pp. 3458–3463, Sep. 2015.
  • [22] E. Kalinichenko, A. Faryna, V. Kondrateva, A. Vlasova, V. Shevchenko, A. Melnik, O. Avdoshko and Alla Belko, “Synthesis, Biological Activities and Docking Studies of Novel 4-(Arylaminomethyl)benzamide Derivatives as Potential Tyrosine Kinase Inhibitors,” Molecules, vol. 24, no. 19, p. 3543, Sep. 2019.
  • [23] E. Kalinichenko, A. Faryna, T. Bozhok, A. Golyakovich, and A. Panibrat, “Novel Phthalic-Based Anticancer Tyrosine Kinase Inhibitors: Design, Synthesis and Biological Activity,” Curr Issues Mol Biol, vol. 45, no. 3, pp. 1820–1842, Feb. 2023.
  • [24] G. Faudone, R. Zhubi, F. Celik, S. Knapp, A. Chaikuad, J. Heering, D. Merk, “Design of a Potent TLX Agonist by Rational Fragment Fusion,” J Med Chem, vol. 65, no. 3, pp. 2288–2296, Jan. 2022.
  • [25] Ç. K. Atay, Ö. Dilek, T. Tilki, and B. Dede, “A novel imidazole-based azo molecule: synthesis, characterization, quantum chemical calculations, molecular docking, molecular dynamics simulations and ADMET properties,” J Mol Model, vol. 29, no. 8, p. 226, Aug. 2023.
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  • [27] M. D. Hanwell, D. E. Curtis, D. C. Lonie, T. Vandermeersch, E. Zurek, and G. R. Hutchison, “Avogadro: an advanced semantic chemical editor, visualization, and analysis platform,” J Cheminform, vol. 4, no. 1, p. 17, Aug. 2012.
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  • [30] C. Lee, W. Yang, and R. G. Parr, “Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density,” Phys Rev B, vol. 37, no. 2, pp. 785–789, Jan. 1988.
  • [31] J. P. Merrick, D. Moran, and L. Radom, “An Evaluation of Harmonic Vibrational Frequency Scale Factors,” J Phys Chem A, vol. 111, no. 45, pp. 11683–11700, Oct. 2007.
  • [32] R. Bauernschmitt and R. Ahlrichs, “Treatment of electronic excitations within the adiabatic approximation of time dependent density functional theory,” Chem Phys Lett, vol. 256, no. 4–5, pp. 454–464, Jul. 1996.
  • [33] M. E. Casida, C. Jamorski, K. C. Casida, and D. R. Salahub, “Molecular excitation energies to high-lying bound states from time-dependent density-functional response theory: Characterization and correction of the time-dependent local density approximation ionization threshold,” J Chem Phys, vol. 108, no. 11, pp. 4439–4449, Mar. 1998.
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  • [35] K. Wolinski, J. F. Hinton, and P. Pulay, “Efficient implementation of the gauge-independent atomic orbital method for NMR chemical shift calculations,” J Am Chem Soc, vol. 112, no. 23, pp. 8251–8260, Nov. 1990.
  • [36] A. Grosdidier, V. Zoete, and O. Michielin, “SwissDock, a protein-small molecule docking web service based on EADock DSS,” Nucleic Acids Res, vol. 39, no. suppl, pp. W270–W277, Jul. 2011.
  • [37] E. F. Pettersen et al., “UCSF Chimera--A visualization system for exploratory research and analysis,” J Comput Chem, vol. 25, no. 13, pp. 1605–1612, Oct. 2004.
  • [38] H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, P. E. Bourne, “The Protein Data Bank,” Nucleic Acids Res, vol. 28, no. 1, pp. 235–242, Jan. 2000.
  • [39] J. Jiménez, S. Doerr, G. Martínez-Rosell, A. S. Rose, and G. De Fabritiis, “DeepSite: protein-binding site predictor using 3D-convolutional neural networks,” Bioinformatics, vol. 33, no. 19, pp. 3036–3042, Oct. 2017.
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There are 45 citations in total.

Details

Primary Language English
Subjects Organic Chemical Synthesis
Journal Section Araştırma Makalesi
Authors

Ömer Dilek 0000-0003-1409-782X

Early Pub Date March 21, 2024
Publication Date March 24, 2024
Submission Date July 26, 2023
Acceptance Date January 9, 2024
Published in Issue Year 2024 Volume: 13 Issue: 1

Cite

IEEE Ö. Dilek, “Imidazole Based Novel Schiff Base: Synthesis, Characterization, Quantum Chemical Calculations, In Silico Investigation of ADMEt Properties and Molecular Docking Simulations against VEGFR2 Protein”, Bitlis Eren Üniversitesi Fen Bilimleri Dergisi, vol. 13, no. 1, pp. 62–78, 2024, doi: 10.17798/bitlisfen.1332971.

Bitlis Eren University
Journal of Science Editor
Bitlis Eren University Graduate Institute
Bes Minare Mah. Ahmet Eren Bulvari, Merkez Kampus, 13000 BITLIS