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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

Yıl 2024, , 62 - 78, 24.03.2024
https://doi.org/10.17798/bitlisfen.1332971

Öz

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.

Teşekkür

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.

Kaynakça

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Yıl 2024, , 62 - 78, 24.03.2024
https://doi.org/10.17798/bitlisfen.1332971

Öz

Kaynakça

  • [1] R. L. Siegel, K. D. Miller, H. E. Fuchs, and A. Jemal, “Cancer statistics, 2022,” CA Cancer J Clin, vol. 72, no. 1, pp. 7–33, Jan. 2022.
  • [2] D. T. Debela, S. G. Muzazu, K. D. Heraro, M. T. Ndalama, B. W. Mesele, D. C. Haile, S. K. Kitui, T. Manyazewal, “New approaches and procedures for cancer treatment: Current perspectives,” SAGE Open Med, vol. 9, p. 205031212110343, Aug. 2021.
  • [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.
  • [5] S. Kakkar, S. Kumar, B. Narasimhan, S. M. Lim, K. Ramasamy, V. Mani, S. A. A.Shah, “Design, synthesis and biological potential of heterocyclic benzoxazole scaffolds as promising antimicrobial and anticancer agents,” Chem Cent J, vol. 12, no. 1, p. 96, Sep. 2018.
  • [6] T. Tahir, M. Ashfaq, M. Saleem, M. Rafiq, M. I. Shahzad, K. K. Mojzych, M. Mojzych, “Pyridine Scaffolds, Phenols and Derivatives of Azo Moiety: Current Therapeutic Perspectives,” Molecules, vol. 26, no. 16, p. 4872, Aug. 2021.
  • [7] A. Verma, S. Joshi, and D. Singh, “Imidazole: Having Versatile Biological Activities,” J Chem, vol. 2013, p. 329402, Oct. 2013.
  • [8] A. Abula, Z. Xu, Z. Zhu, C. Peng, Z. Chen, W. Zhu, H. A. Aisa, “Substitution Effect of the Trifluoromethyl Group on the Bioactivity in Medicinal Chemistry: Statistical Analysis and Energy Calculations,” J Chem Inf Model, vol. 60, no. 12, pp. 6242–6250, Dec. 2020.
  • [9] J. B. I. Sap, N. J. W. Straathof, T. Knauber, C. F. Meyer, M. Médebielle, L. Buglioni, C. Genicot, A. A. Trabanco, T. Noël, C.W. A. Ende, and V. Gouverneur, “Organophotoredox Hydrodefluorination of Trifluoromethylarenes with Translational Applicability to Drug Discovery,” J Am Chem Soc, vol. 142, no. 20, pp. 9181–9187, May 2020.
  • [10] A. S. Nair, A. K. Singh, A. Kumar, S. Kumar, S. Sukumaran, V. P. Koyiparambath, L. K. Pappachen, T. M. Rangarajan, H. Kim, and B. Mathew, “FDA-Approved Trifluoromethyl Group-Containing Drugs: A Review of 20 Years,” Processes, vol. 10, no. 10, p. 2054, Oct. 2022.
  • [11] Y. Zhang, P. Cai, G. Cheng, and Y. Zhang, “A Brief Review of Phenolic Compounds Identified from Plants: Their Extraction, Analysis, and Biological Activity,” Nat Prod Commun, vol. 17, no. 1, Jan. 2022.
  • [12] A. Basli, N. Belkacem, and I. Amrani, “Health Benefits of Phenolic Compounds Against Cancers,” in Phenolic Compounds - Biological Activity, InTech, 2017, pp. 193–210, March 2017.
  • [13] P. G. Anantharaju, P. C. Gowda, M. G. Vimalambike, and S. V. Madhunapantula, “An overview on the role of dietary phenolics for the treatment of cancers,” Nutr J, vol. 15, no. 1, p. 99, Dec. 2016.
  • [14] A. Kajal, S. Bala, S. Kamboj, N. Sharma, and V. Saini, “Schiff Bases: A Versatile Pharmacophore,” Journal of Catalysts, vol. 2013, p. 893512, Aug. 2013.
  • [15] A. P. Hnatiuk, A. A. N. Bruyneel, D. Tailor, M. Pandrala, A. Dheeraj, W. Li, R. Serrano, D. A. M. Feyen, M. M. Vu, P. Amatya, S. Gupta, Y. Nakauchi, I. Morgado, V. Wiebking, R. Liao, M. H. Porteus, R. Majeti, S. V. Malhotra, M. Mercola, “Reengineering Ponatinib to Minimize Cardiovascular Toxicity,” Cancer Res, vol. 82, no. 15, pp. 2777–2791, Aug. 2022.
  • [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.
  • [17] D. Zhu, H. Huang, D. M. Pinkas, J. Luo, D. Ganguly, A. E. Fox, E. Arner, Q. Xiang, Z. C. Tu, A. N. Bullock, A. R. Brekken, K. Ding, X. Lu, “2-Amino-2,3-dihydro-1 H -indene-5-carboxamide-Based Discoidin Domain Receptor 1 (DDR1) Inhibitors: Design, Synthesis, and in Vivo Antipancreatic Cancer Efficacy,” J Med Chem, vol. 62, no. 16, pp. 7431–7444, Aug. 2019.
  • [18] H. G. Choi, P. Ren, F. Adrian, F. Sun, H. S. Lee, X. Wang, Q. Ding, G. Zhang, Y. Xie, J. Zhang, Y. Liu, T. Tuntland, M. Warmuth, P. W. Manley, J. Mestan, N. S. Gray, T.Sim “A Type-II Kinase Inhibitor Capable of Inhibiting the T315I ‘Gatekeeper’ Mutant of Bcr-Abl,” J Med Chem, vol. 53, no. 15, pp. 5439–5448, Aug. 2010.
  • [19] M. Pandrala, A. A. N. Bruyneel, A. P. Hnatiuk, M. Mercola, and S. V. Malhotra, “Designing Novel BCR-ABL Inhibitors for Chronic Myeloid Leukemia with Improved Cardiac Safety,” J Med Chem, vol. 65, no. 16, pp. 10898–10919, Aug. 2022.
  • [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.
  • [26] Frisch, M. J., G. W., Trucks, H. B., Schlegel, G. E., Scuseria, M. A., Robb, J. R., Cheeseman, G., Scalmani, V., Barone, G. A., Petersson, H., Nakatsuji, X., Li, M., Caricato, A., Marenich, J., Bloino, B. G., Janesko, R., Gomperts, B., Mennucci, H. P., Hratchian, J. V., Ortiz, A. F I., D. J. F. 2016. Gaussian 09, Revision E.01. Gaussian, Inc.
  • [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.
  • [28] Chemcraft - graphical software for visualization of quantum chemistry computations. Version 1.8, build 654. https://www.chemcraftprog.com [Accessed: July. 25, 2023].
  • [29] A. D. Becke, “Density-functional exchange-energy approximation with correct asymptotic behavior,” Phys Rev A (Coll Park), vol. 38, no. 6, pp. 3098–3100, Sep. 1988.
  • [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.
  • [34] R. Ditchfield, “Molecular Orbital Theory of Magnetic Shielding and Magnetic Susceptibility,” J Chem Phys, vol. 56, no. 11, pp. 5688–5691, Jun. 1972.
  • [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.
  • [40] A. Daina, O. Michielin, and V. Zoete, “SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules,” Sci Rep, vol. 7, no. 1, p. 42717, Mar. 2017.
  • [41] P. Banerjee, A. O. Eckert, A. K. Schrey, and R. Preissner, “ProTox-II: a webserver for the prediction of toxicity of chemicals,” Nucleic Acids Res, vol. 46, no. W1, pp. W257–W263, Jul. 2018.
  • [42] B. Raimer, P. G. Jones, and T. Lindel, “Quantum chemical calculation of 19F NMR chemical shifts of trifluoromethyl diazirine photoproducts and precursors,” J Fluor Chem, vol. 166, pp. 8–14, Oct. 2014.
  • [43] Ç. K. Atay, Y. Kara, M. Gökalp, I. Kara, T. Tilki, and F. Karci, “Disazo dyes containing pyrazole and indole moieties: Synthesis, characterization, absorption characteristics, theoretical calculations, structural and electronic properties,” J Mol Liq, vol. 215, pp. 647–655, Mar. 2016.
  • [44] M. Gökalp, T. Tilki, and Ç. K. Atay, “Newly Synthesized Aminothiazole Based Disazo Dyes and Their Theoretical Calculations,” Polycycl Aromat Compd, pp. 1–23, Feb. 2023.
  • [45] B. Sezgin, T. Tilki, Ç. K. Atay, and B. Dede, “Comparative in vitro and DFT antioxidant studies of phenolic group substituted pyridine-based azo derivatives,” J Biomol Struct Dyn, vol. 40, no. 11, pp. 4921–4932, Jul. 2022.
Toplam 45 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Organik Kimyasal Sentez
Bölüm Araştırma Makalesi
Yazarlar

Ömer Dilek 0000-0003-1409-782X

Erken Görünüm Tarihi 21 Mart 2024
Yayımlanma Tarihi 24 Mart 2024
Gönderilme Tarihi 26 Temmuz 2023
Kabul Tarihi 9 Ocak 2024
Yayımlandığı Sayı Yıl 2024

Kaynak Göster

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, c. 13, sy. 1, ss. 62–78, 2024, doi: 10.17798/bitlisfen.1332971.



Bitlis Eren Üniversitesi
Fen Bilimleri Dergisi Editörlüğü

Bitlis Eren Üniversitesi Lisansüstü Eğitim Enstitüsü        
Beş Minare Mah. Ahmet Eren Bulvarı, Merkez Kampüs, 13000 BİTLİS        
E-posta: fbe@beu.edu.tr