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Quantum Mechanical Calculations, Hirshfeld Surface Analysis, Molecular Docking, ADME and Toxicology Studies of the Ethyl 4-chloro-2-[(4-nitrophenyl)hydrazono]-3-oxobutrate Compound

Yıl 2023, Cilt: 7 Sayı: 2, 109 - 121, 31.12.2023

Sefa Öztürk Tuğba Aycan Zeynep Demircioğlu Cem Cüneyt Ersanlı

https://doi.org/10.47897/bilmes.1385170

Öz

The theoretical chemical activity parameters of the compound Ethyl 4-chloro-2-[(4-nitrophenyl)hydrazono]-3-oxobutrate, which had previously been synthesized and crystallographically studied, were determined using Density Functional Theory (DFT). With Hirshfeld surface analysis, the effects of molecular interactions on the surface were defined with surface maps and the percentage contribution of the interactions of atoms with each other was determined. In addition, second-order nonlinear optical properties (NLO) and thermodynamic parameters were examined at temperatures between 100 and 1000 K. In addition, molecular docking study was carried out by downloading structure of a B-DNA dodecamer (PDB ID: 1BNA) from PDB (Protein Data Bank). ADME and toxicology properties were examined using the complex, in-silico method and it was discussed whether it had drug properties.

Anahtar Kelimeler

Quantum mechanical calculations Hirshfeld surface analysis molecular docking ADME toxicology

Kaynakça

  • [1] J. Pisk et al., "Pyridoxal hydrazonato molybdenum(vi) complexes: assembly, structure and epoxidation (pre)catalyst testing under solvent-free conditions," Rsc Adv, 10.1039/C4RA08179J vol. 4, no. 73, pp. 39000-39010, 2014, doi: https://doi.org/10.1039/C4RA08179J.
  • [2] O. Pouralimardan, A.-C. Chamayou, C. Janiak, and H. Hosseini-Monfared, "Hydrazone Schiff base-manganese(II) complexes: Synthesis, crystal structure and catalytic reactivity," Inorganica Chimica Acta, vol. 360, no. 5, pp. 1599-1608, 2007/04/01/ 2007, doi: https://doi.org/10.1016/j.ica.2006.08.056.
  • [3] M. Bakir, O. Green, and W. H. Mulder, "Synthesis, characterization and molecular sensing behavior of [ZnCl2(η3-N,N,O-dpkbh)] (dpkbh=di-2-pyridyl ketone benzoyl hydrazone)," Journal of Molecular Structure, vol. 873, no. 1, pp. 17-28, 2008/02/17/ 2008, doi: https://doi.org/10.1016/j.molstruc.2007.03.001.
  • [4] M. Alagesan, N. S. P. Bhuvanesh, and N. Dharmaraj, "Potentially cytotoxic new copper(ii) hydrazone complexes: synthesis, crystal structure and biological properties," Dalton Transactions, 10.1039/C3DT50371B vol. 42, no. 19, pp. 7210-7223, 2013, doi: https://doi.org/10.1039/C3DT50371B.
  • [5] I. M. Kapetanovic, "Computer-aided drug discovery and development (CADDD): In silico-chemico-biological approach," Chemico-Biological Interactions, vol. 171, no. 2, pp. 165-176, 2008/01/30/ 2008, doi: https://doi.org/10.1016/j.cbi.2006.12.006.
  • [6] N. Aydin and E. K. DOĞAN, "Focusing on the Structural, Electronic, Optic and Elastic Behaviours of RhBiSe Compound by Ab initio Calculations," International Scientific and Vocational Studies Journal, vol. 6, no. 1, pp. 13-21, 2022.
  • [7] M. Odabaşoğlu, Ö. Özdamar, and O. Büyükgüngör, "Ethyl 4-chloro-2-[(4-nitro­phen­yl)hydrazono]-3-oxobutyrate," Acta Crystallographica Section E, vol. 61, no. 7, pp. o2068-o2070, 2005/07/01 2005, doi: https://doi.org/10.1107/S1600536805017629.
  • [8] Gaussian 09, Revizyon A.02. (2009). Wallingford CT. [Online]. Available: https://gaussian.com/
  • [9] CrystalExplorer17. (2017). The University of Western Australia Perth, WA, Australia.
  • [10] O. Trott and A. J. Olson, "AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading," Journal of computational chemistry, vol. 31, no. 2, pp. 455-461, 2010, doi: https://doi.org/10.1002/jcc.21334.
  • [11] D. S. BIOVIA, "BIOVIA Discovery Studio Visualizer, v16. 1.0. 15350, San Diego: Dassault Systemes; 2015 [cited: 2017 Mar 20]," ed.
  • [12] 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-Uk, vol. 7, no. 1, p. 42717, 2017/03/03 2017, doi: https://doi.org/10.1038/srep42717.
  • [13] U. Norinder and C. A. Bergström, "Prediction of ADMET properties," ChemMedChem: Chemistry Enabling Drug Discovery, vol. 1, no. 9, pp. 920-937, 2006, doi: https://doi.org/10.1002/cmdc.200600155.
  • [14] P. Banerjee, A. O. Eckert, A. K. Schrey, and R. Preissner, "ProTox-II: a webserver for the prediction of toxicity of chemicals," Nucleic acids research, vol. 46, no. W1, pp. W257-W263, 2018, doi: https://doi.org/10.1093/nar/gky318.
  • [15] P. Banerjee, F. O. Dehnbostel, and R. Preissner, "Prediction Is a Balancing Act: Importance of Sampling Methods to Balance Sensitivity and Specificity of Predictive Models Based on Imbalanced Chemical Data Sets," (in English), Frontiers in Chemistry, Original Research vol. 6, 2018-August-28 2018, doi: https://doi.org/10.3389/fchem.2018.00362.
  • [16] M. N. Drwal, P. Banerjee, M. Dunkel, M. R. Wettig, and R. Preissner, "ProTox: a web server for the in silico prediction of rodent oral toxicity," Nucleic Acids Research, vol. 42, no. W1, pp. W53-W58, 2014, doi: https://doi.org/10.1093/nar/gku401.
  • [17] D. Sajan, H. Joe, V. S. Jayakumar, and J. Zaleski, "Structural and electronic contributions to hyperpolarizability in methyl p-hydroxy benzoate," Journal of Molecular Structure, vol. 785, no. 1, pp. 43-53, 2006/03/06/ 2006, doi: https://doi.org/10.1016/j.molstruc.2005.09.041.
  • [18] Y.-X. Sun et al., "Experimental and density functional studies on 4-(3,4-dihydroxybenzylideneamino)antipyrine, and 4-(2,3,4-trihydroxybenzylideneamino)antipyrine," Journal of Molecular Structure: THEOCHEM, vol. 904, no. 1, pp. 74-82, 2009/06/30/ 2009, doi: https://doi.org/10.1016/j.theochem.2009.02.036.
  • [19] T. Aycan, F. Öztürk, T. Doruk, S. Demir, M. Fidan, and H. Paşaoğlu, "Synthesis, structural, spectral and antimicrobial activity studies of copper-nalidixic acid complex with 1,10-phenanthroline: DFT and molecular docking," Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, vol. 241, p. 118639, 2020/11/05/ 2020, doi: https://doi.org/10.1016/j.saa.2020.118639.
  • [20] J. Hodgson, "ADMET—turning chemicals into drugs," Nature biotechnology, vol. 19, no. 8, pp. 722-726, 2001, doi: https://doi.org/10.1038/90761.
  • [21] E. Lipiński, Semitic languages: outline of a comparative grammar. Peeters Publishers, 2001.
  • [22] F. İslamoğlu and E. Hacıfazlıoğlu, "Investigation of the Usability of Some Triazole Derivative Compounds as Drug Active Ingredients by ADME and Molecular Docking Properties," Moroccan Journal of Chemistry, vol. 10, no. 3, 2022, doi: https://doi.org/10.48317/IMIST.PRSM/morjchem-v10i3.30855.

Quantum Mechanical Calculations, Hirshfeld Surface Analysis, Molecular Docking, ADME and Toxicology Studies of the Ethyl 4-chloro-2-[(4-nitrophenyl)hydrazono]-3-oxobutrate Compound

Yıl 2023, Cilt: 7 Sayı: 2, 109 - 121, 31.12.2023

Sefa Öztürk Tuğba Aycan Zeynep Demircioğlu Cem Cüneyt Ersanlı

https://doi.org/10.47897/bilmes.1385170

Öz

The theoretical chemical activity parameters of the compound Ethyl 4-chloro-2-[(4-nitrophenyl)hydrazono]-3-oxobutrate, which had previously been synthesized and crystallographically studied, were determined using Density Functional Theory (DFT). With Hirshfeld surface analysis, the effects of molecular interactions on the surface were defined with surface maps and the percentage contribution of the interactions of atoms with each other was determined. In addition, second-order nonlinear optical properties (NLO) and thermodynamic parameters were examined at temperatures between 100 and 1000 K. In addition, molecular docking study was carried out by downloading structure of a B-DNA dodecamer (PDB ID: 1BNA) from PDB (Protein Data Bank). ADME and toxicology properties were examined using the complex, in-silico method and it was discussed whether it had drug properties.

Anahtar Kelimeler

Quantum mechanical calculations Hirshfeld surface analysis molecular docking ADME toxicology

Kaynakça

  • [1] J. Pisk et al., "Pyridoxal hydrazonato molybdenum(vi) complexes: assembly, structure and epoxidation (pre)catalyst testing under solvent-free conditions," Rsc Adv, 10.1039/C4RA08179J vol. 4, no. 73, pp. 39000-39010, 2014, doi: https://doi.org/10.1039/C4RA08179J.
  • [2] O. Pouralimardan, A.-C. Chamayou, C. Janiak, and H. Hosseini-Monfared, "Hydrazone Schiff base-manganese(II) complexes: Synthesis, crystal structure and catalytic reactivity," Inorganica Chimica Acta, vol. 360, no. 5, pp. 1599-1608, 2007/04/01/ 2007, doi: https://doi.org/10.1016/j.ica.2006.08.056.
  • [3] M. Bakir, O. Green, and W. H. Mulder, "Synthesis, characterization and molecular sensing behavior of [ZnCl2(η3-N,N,O-dpkbh)] (dpkbh=di-2-pyridyl ketone benzoyl hydrazone)," Journal of Molecular Structure, vol. 873, no. 1, pp. 17-28, 2008/02/17/ 2008, doi: https://doi.org/10.1016/j.molstruc.2007.03.001.
  • [4] M. Alagesan, N. S. P. Bhuvanesh, and N. Dharmaraj, "Potentially cytotoxic new copper(ii) hydrazone complexes: synthesis, crystal structure and biological properties," Dalton Transactions, 10.1039/C3DT50371B vol. 42, no. 19, pp. 7210-7223, 2013, doi: https://doi.org/10.1039/C3DT50371B.
  • [5] I. M. Kapetanovic, "Computer-aided drug discovery and development (CADDD): In silico-chemico-biological approach," Chemico-Biological Interactions, vol. 171, no. 2, pp. 165-176, 2008/01/30/ 2008, doi: https://doi.org/10.1016/j.cbi.2006.12.006.
  • [6] N. Aydin and E. K. DOĞAN, "Focusing on the Structural, Electronic, Optic and Elastic Behaviours of RhBiSe Compound by Ab initio Calculations," International Scientific and Vocational Studies Journal, vol. 6, no. 1, pp. 13-21, 2022.
  • [7] M. Odabaşoğlu, Ö. Özdamar, and O. Büyükgüngör, "Ethyl 4-chloro-2-[(4-nitro­phen­yl)hydrazono]-3-oxobutyrate," Acta Crystallographica Section E, vol. 61, no. 7, pp. o2068-o2070, 2005/07/01 2005, doi: https://doi.org/10.1107/S1600536805017629.
  • [8] Gaussian 09, Revizyon A.02. (2009). Wallingford CT. [Online]. Available: https://gaussian.com/
  • [9] CrystalExplorer17. (2017). The University of Western Australia Perth, WA, Australia.
  • [10] O. Trott and A. J. Olson, "AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading," Journal of computational chemistry, vol. 31, no. 2, pp. 455-461, 2010, doi: https://doi.org/10.1002/jcc.21334.
  • [11] D. S. BIOVIA, "BIOVIA Discovery Studio Visualizer, v16. 1.0. 15350, San Diego: Dassault Systemes; 2015 [cited: 2017 Mar 20]," ed.
  • [12] 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-Uk, vol. 7, no. 1, p. 42717, 2017/03/03 2017, doi: https://doi.org/10.1038/srep42717.
  • [13] U. Norinder and C. A. Bergström, "Prediction of ADMET properties," ChemMedChem: Chemistry Enabling Drug Discovery, vol. 1, no. 9, pp. 920-937, 2006, doi: https://doi.org/10.1002/cmdc.200600155.
  • [14] P. Banerjee, A. O. Eckert, A. K. Schrey, and R. Preissner, "ProTox-II: a webserver for the prediction of toxicity of chemicals," Nucleic acids research, vol. 46, no. W1, pp. W257-W263, 2018, doi: https://doi.org/10.1093/nar/gky318.
  • [15] P. Banerjee, F. O. Dehnbostel, and R. Preissner, "Prediction Is a Balancing Act: Importance of Sampling Methods to Balance Sensitivity and Specificity of Predictive Models Based on Imbalanced Chemical Data Sets," (in English), Frontiers in Chemistry, Original Research vol. 6, 2018-August-28 2018, doi: https://doi.org/10.3389/fchem.2018.00362.
  • [16] M. N. Drwal, P. Banerjee, M. Dunkel, M. R. Wettig, and R. Preissner, "ProTox: a web server for the in silico prediction of rodent oral toxicity," Nucleic Acids Research, vol. 42, no. W1, pp. W53-W58, 2014, doi: https://doi.org/10.1093/nar/gku401.
  • [17] D. Sajan, H. Joe, V. S. Jayakumar, and J. Zaleski, "Structural and electronic contributions to hyperpolarizability in methyl p-hydroxy benzoate," Journal of Molecular Structure, vol. 785, no. 1, pp. 43-53, 2006/03/06/ 2006, doi: https://doi.org/10.1016/j.molstruc.2005.09.041.
  • [18] Y.-X. Sun et al., "Experimental and density functional studies on 4-(3,4-dihydroxybenzylideneamino)antipyrine, and 4-(2,3,4-trihydroxybenzylideneamino)antipyrine," Journal of Molecular Structure: THEOCHEM, vol. 904, no. 1, pp. 74-82, 2009/06/30/ 2009, doi: https://doi.org/10.1016/j.theochem.2009.02.036.
  • [19] T. Aycan, F. Öztürk, T. Doruk, S. Demir, M. Fidan, and H. Paşaoğlu, "Synthesis, structural, spectral and antimicrobial activity studies of copper-nalidixic acid complex with 1,10-phenanthroline: DFT and molecular docking," Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, vol. 241, p. 118639, 2020/11/05/ 2020, doi: https://doi.org/10.1016/j.saa.2020.118639.
  • [20] J. Hodgson, "ADMET—turning chemicals into drugs," Nature biotechnology, vol. 19, no. 8, pp. 722-726, 2001, doi: https://doi.org/10.1038/90761.
  • [21] E. Lipiński, Semitic languages: outline of a comparative grammar. Peeters Publishers, 2001.
  • [22] F. İslamoğlu and E. Hacıfazlıoğlu, "Investigation of the Usability of Some Triazole Derivative Compounds as Drug Active Ingredients by ADME and Molecular Docking Properties," Moroccan Journal of Chemistry, vol. 10, no. 3, 2022, doi: https://doi.org/10.48317/IMIST.PRSM/morjchem-v10i3.30855.
Toplam 22 adet kaynakça vardır.

Ayrıntılar

Birincil Dil Türkçe
Konular Atom ve Molekül Fiziği, Doğrusal Olmayan Optik ve Spektroskopi, Hesaplamalı Kimya
Bölüm Makaleler
Yazarlar

Sefa Öztürk 0000-0003-2036-7734

Tuğba Aycan 0000-0002-5313-7807

Zeynep Demircioğlu 0000-0001-9538-9140

Cem Cüneyt Ersanlı 0000-0002-8113-5091

Yayımlanma Tarihi 31 Aralık 2023
Gönderilme Tarihi 2 Kasım 2023
Kabul Tarihi 29 Aralık 2023
Yayımlandığı Sayı Yıl 2023 Cilt: 7 Sayı: 2

Kaynak Göster

APA Öztürk, S., Aycan, T., Demircioğlu, Z., Ersanlı, C. C. (2023). Quantum Mechanical Calculations, Hirshfeld Surface Analysis, Molecular Docking, ADME and Toxicology Studies of the Ethyl 4-chloro-2-[(4-nitrophenyl)hydrazono]-3-oxobutrate Compound. International Scientific and Vocational Studies Journal, 7(2), 109-121. https://doi.org/10.47897/bilmes.1385170
AMA Öztürk S, Aycan T, Demircioğlu Z, Ersanlı CC. Quantum Mechanical Calculations, Hirshfeld Surface Analysis, Molecular Docking, ADME and Toxicology Studies of the Ethyl 4-chloro-2-[(4-nitrophenyl)hydrazono]-3-oxobutrate Compound. ISVOS. Aralık 2023;7(2):109-121. doi:10.47897/bilmes.1385170
Chicago Öztürk, Sefa, Tuğba Aycan, Zeynep Demircioğlu, ve Cem Cüneyt Ersanlı. “Quantum Mechanical Calculations, Hirshfeld Surface Analysis, Molecular Docking, ADME and Toxicology Studies of the Ethyl 4-Chloro-2-[(4-nitrophenyl)hydrazono]-3-Oxobutrate Compound”. International Scientific and Vocational Studies Journal 7, sy. 2 (Aralık 2023): 109-21. https://doi.org/10.47897/bilmes.1385170.
EndNote Öztürk S, Aycan T, Demircioğlu Z, Ersanlı CC (01 Aralık 2023) Quantum Mechanical Calculations, Hirshfeld Surface Analysis, Molecular Docking, ADME and Toxicology Studies of the Ethyl 4-chloro-2-[(4-nitrophenyl)hydrazono]-3-oxobutrate Compound. International Scientific and Vocational Studies Journal 7 2 109–121.
IEEE S. Öztürk, T. Aycan, Z. Demircioğlu, ve C. C. Ersanlı, “Quantum Mechanical Calculations, Hirshfeld Surface Analysis, Molecular Docking, ADME and Toxicology Studies of the Ethyl 4-chloro-2-[(4-nitrophenyl)hydrazono]-3-oxobutrate Compound”, ISVOS, c. 7, sy. 2, ss. 109–121, 2023, doi: 10.47897/bilmes.1385170.
ISNAD Öztürk, Sefa vd. “Quantum Mechanical Calculations, Hirshfeld Surface Analysis, Molecular Docking, ADME and Toxicology Studies of the Ethyl 4-Chloro-2-[(4-nitrophenyl)hydrazono]-3-Oxobutrate Compound”. International Scientific and Vocational Studies Journal 7/2 (Aralık 2023), 109-121. https://doi.org/10.47897/bilmes.1385170.
JAMA Öztürk S, Aycan T, Demircioğlu Z, Ersanlı CC. Quantum Mechanical Calculations, Hirshfeld Surface Analysis, Molecular Docking, ADME and Toxicology Studies of the Ethyl 4-chloro-2-[(4-nitrophenyl)hydrazono]-3-oxobutrate Compound. ISVOS. 2023;7:109–121.
MLA Öztürk, Sefa vd. “Quantum Mechanical Calculations, Hirshfeld Surface Analysis, Molecular Docking, ADME and Toxicology Studies of the Ethyl 4-Chloro-2-[(4-nitrophenyl)hydrazono]-3-Oxobutrate Compound”. International Scientific and Vocational Studies Journal, c. 7, sy. 2, 2023, ss. 109-21, doi:10.47897/bilmes.1385170.
Vancouver Öztürk S, Aycan T, Demircioğlu Z, Ersanlı CC. Quantum Mechanical Calculations, Hirshfeld Surface Analysis, Molecular Docking, ADME and Toxicology Studies of the Ethyl 4-chloro-2-[(4-nitrophenyl)hydrazono]-3-oxobutrate Compound. ISVOS. 2023;7(2):109-21.
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