Moleculer Docking and Theoretical Analysis of the (E)-5-((Z)-4-methylbenzylidene)-2-(((E)-4-methylbenzylidene)hydrazineylidene)-3-phenylthiazolidin-4-one Molecule

Yıl 2024, Cilt: 13 Sayı: 3, 659 - 672, 26.09.2024

Kenan Gören , Efdal Çimen , Veysel Tahiroğlu , Ümit Yıldıko

https://doi.org/10.17798/bitlisfen.1471235

Öz

Theoretically ideal molecular structure of (E)-5-((Z)-4-methylbenzylidene)-2-(((E)-4-methylbenzylidene)hydrazineylidene)-3-phenylthiazolidin-4-one (1) Gaussian 09 software program was researched using. The theoretically ideal chemical structure of molecule (1) has been examined. The 6-311G basis of DFT(B3LYP) approaches and the 6-311G basis of DFT(B3PW91) approaches were used to perform quantum chemical calculations. To find out how the molecule transfers charge, LUMO and HOMO analyses were done. The stability of the molecule was investigated as a function of charge dispersion and hyperconjugative interaction using NBO analysis. MEP was reported to be performed using a DFT technique. Molecular docking studies were performed using enzyme codes PDB: 5FGK and PDB: 5HBE to determine the binding affinity and possible fundamental interaction betwith the inhibitors and the target enzyme. Finally, in our study, ADME analysis of Molecule (1) was performed and many parameters were examined using virtual screening methods on small molecules, Molecular characteristics, cell permeability, HIA drug solubility S, medicament paralely point and polar surface area PSA are among them.

Anahtar Kelimeler

DFT, MEP, NBO, ADME, Molecular Docking.

Kaynakça

• [1] A.-R. L. H. Ismail, N. M. Ismael, and M. Abu-Dief, “Co (II) and Cd (II) complexes based on a tetradentate ONNO donor Schiff base ligand,” DFT calculations and biological studies of Mn (II), Fe (II), vol. 1134, pp. 851–862, 2017.
• [2] M. Salihović et al., “Synthesis, characterization, antimicrobial activity and DFT study of some novel Schiff bases,” J. Mol. Struct., vol. 1241, no. 130670, p. 130670, 2021.
• [3] L. Touafri, A. Hellal, S. Chafaa, A. Khelifa, and A. Kadri, “Synthesis, characterisation and DFT studies of three Schiff bases derived from histamine,” J. Mol. Struct., vol. 1149, pp. 750–760, 2017.
• [4] E. Ermiş, “Synthesis, spectroscopic characterization and DFT calculations of novel Schiff base containing thiophene ring,” J. Mol. Struct., vol. 1156, pp. 91–104, 2018.
• [5] R. M. Issa, M. K. Awad, and F. M. Atlam, “DFT theoretical studies of antipyrine Schiff bases as corrosion inhibitors: Schiff bases as corrosion inhibitors,” Mater. Corros, vol. 61, no. 8, pp. 709–714, 2010.
• [6] T. Bensafi, “Synthesis, characterization and DFT calculations of linear and NLO properties of novel (Z)-5-benzylidene-3-N (4-methylphenyl)-2-thioxothiazolidin-4-one,” Journal of Sulfur Chemistry, vol. 42, no. 6, pp. 645–663, 2021.
• [7] M. Rashid, J. Yaqoob, N. Khalil, R. Jamil, M. U. Khan, and M. A. Gilani, “Nonlinear optical (NLO) response of boron phosphide nanosheet by alkali metals doping: A DFT study,” Mater. Sci. Semicond. Process., vol. 151, no. 107007, p. 107007, 2022.
• [8] M. Ishaq, R. A. Shehzad, M. Yaseen, S. Iqbal, K. Ayub, and J. Iqbal, “DFT study of superhalogen-doped borophene with enhanced nonlinear optical properties,” J. Mol. Model., vol. 27, no. 6, p. 188, 2021.
• [9] T. Michael, J. Frisch, G.W, Bernhard. Schlegel, Gustavo. Scuseria, 2016.
• [10] M. Bağlan, “Theoretical Investigation of 1H and 13C NMR Spectra of Diethanol Amine Dithiocarbamate RAFT Agent,” Journal of the Institute of Science and Technology, vol. 12, no. 3, pp. 1677–1689, 2022.
• [11] A. Voityuk Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys, 23, 08010 Barcelona, Spain. alexander. voityuk@gmail. com, A. J. Stasyuk, and S. F. Vyboishchikov, “A simple model for calculating atomic charges in molecules,” Phys. Chem. Chem. Phys., vol. 20, no. 36, pp. 23328–23337, 2018.
• [12] P. Bultinck et al., “The electronegativity equalization method II: Applicability of different atomic charge schemes,” J. Phys. Chem. A, vol. 106, no. 34, pp. 7895–7901, 2002.
• [13] M. Bağlan, K. Gören, and Ü. Yildiko, “HOMO–LUMO, NBO, NLO, MEP analysis and molecular docking using DFT calculations in DFPA molecule,” Int. J. Chem. Technol., pp. 208–217, 2023.
• [14] V. Choudhary, A. Bhatt, D. Dash, and N. Sharma, “DFT calculations on molecular structures, HOMO-LUMO study, reactivity descriptors and spectral analyses of newly synthesized diorganotin (IV) 2-chloridophenylacetohydroxamate complexes,” J. Comput. Chem., pp. 2354–2363, 2019.
• [15] F. Pereira, K. Xiao, D. A. R. S. Latino, C. Wu, Q. Zhang, and J. Aires-de-Sousa, “Machine learning methods to predict density functional theory B3LYP energies of HOMO and LUMO orbitals,” J. Chem. Inf. Model., vol. 57, no. 1, pp. 11–21, 2017.
• [16] E. S. Marinho and M. M. Marinho, “A DFT study of synthetic drug topiroxostat: MEP, HOMO, LUMO,” Int. J. Sci. Eng. Res, vol. 7, no. 8, 2016.
• [17] S. Chandrasekar, V. Balachandran, and H.-S. Evans, “Synthesis, crystal structures HOMO-LUMO analysis and DFT calculation of new complexes of p-substituted dibenzyltin chlorides and 1, 10-phenanthroline,” Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, vol. 143, pp. 136–146, 2015.
• [18] V. Balachandran, G. Mahalakshmi, A. Lakshmi, and A. Janaki, “DFT, FT-Raman, FT-IR, HOMO-LUMO and NBO studies of 4-Methylmorpholine,” Spectrochim. Acta A Mol. Biomol. Spectrosc., vol. 97, pp. 1101–1110, 2012.
• [19] Ü. Yildiko and G. K. Dft, “DFT Calculatıons and Molecular Dockıng Study ın 6-(2”-pyrrolıdınone-5”-Yl)-(,” Epıcatechın Molecule From Flavonoıds. Eskişehir Teknik Üniversitesi Bilim ve Teknoloji Dergisi B-Teorik Bilimler, vol. 11, pp. 43–55, 2023.
• [20] S. Guidara and H. Feki, “Structural, vibrational, NLO, MEP, NBO analysis and DFT calculation of bis 2, 5-dimethylanilinium sulfate,” Journal of Molecular Structure, vol. 1080, pp. 176–187, 2015.
• [21] B. K. Shukla, “DFT calculations on molecular structure, MEP and HOMO-LUMO study of 3-phenyl-1-(methyl-sulfonyl)-1H-pyrazolo pyrimidine-4-amine,” Materials Today: Proceedings, vol. 49, pp. 3056–3060, 2022.
• [22] N. Uludağ, G. Serdaroğlu, Ir, and N. Uv-Vis, “An improved synthesis, spectroscopic (FT-IR, NMR) study and DFT computational analysis (IR, NMR, UV-Vis, MEP diagrams, NBO, NLO, FMO) of the 1, 5-methanoazocino indole core structure,” Journal of Molecular Structure, vol. 1155, pp. 548–560, 2018.
• [23] S. Sevvanthi, “MEP) studies and molecular docking on benzodiazepine derivatives-heterocyclic organic arenes,” Chemical Data Collections, vol. 30, 2020.
• [24] Ü. Yildiko, “Computational Investigation of 5.5’’, 7’’-trihydroxy-3, 7-dimethoxy-4’-4’’’-O-biflavone from Flavonoids Using DFT Calculations and Molecular Docking,” Adıyaman University Journal of Science, vol. 12, no. 2, pp. 283–298, 2022.
• [25] R. Saravanan, S. Seshadri, S. Gunasekaran, and R. Mendoza-Meroño, “Crystallographic, experimental (FT-IR and FT-RS) and theoretical (DFT) investigation, UV-Vis, MEP, HOMO-LUMO and NBO/NLMO of (E)-1-[1-(4-Chlorophenyl) ethylidene] thiosemicarbazide,” Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, vol. 121, pp. 268–275, 2014.
• [26] K. Gören, “DFT Computations and Molecular Docking Studies of 3-(6-(3-aminophenyl) thiazolo [1, 2, 4] triazol-2-yl)-2H-chromen-2-one (ATTC) Molecule,” Hittite Journal of Science and Engineering, vol. 10, no. 1, pp. 11–19, 2023.
• [27] S. Sundaram, V. N. Vijayakumar, and V. Balasubramanian, “Electronic and structure conformational analysis (HOMO-LUMO, MEP, NBO, ELF, LOL, AIM) of hydrogen bond binary liquid crystal mixture: DFT/TD-DFT approach,” Comput. Theor. Chem., vol. 1217, no. 113920, p. 113920, 2022.
• [28] M. Khattab and A. A. Al-Karmalawy, “Revisiting activity of some Nocodazole analogues as a potential anticancer drugs using molecular docking and DFT calculations,” Front. Chem., vol. 9, p. 628398, 2021.
• [29] N. A. Dlala, Y. Bouazizi, H. Ghalla, and N. Hamdi, “DFT calculations and molecular docking studies on a chromene derivative,” J. Chem., vol. 2021, pp. 1–17, 2021.
• [30] V. K. Singh et al., “Docking, ADMET prediction, DFT analysis, synthesis, cytotoxicity, antibacterial screening and QSAR analysis of diarylpyrimidine derivatives,” J. Mol. Struct., vol. 1247, no. 131400, p. 131400, 2022.
• [31] C. A. Lipinski, “Lead-and drug-like compounds: the rule-of-five revolution,” Drug discovery today: Technologies, vol. 1, no. 4, pp. 337–341, 2004.
• [32] A.-S. Badran and M. A. Ibrahim, “Synthesis, spectral characterization, DFT and in silico ADME studies of the novel pyrido[1,2-a]benzimidazoles and pyrazolo[3,4-b]pyridines,” J. Mol. Struct., vol. 1274, no. 134454, p. 134454, 2023.