Molecular Docking and DFT Analysis of Thiazolidinone-Bis Schiff Base for anti-Cancer and anti-Urease Activity

Yıl 2024, Cilt: 14 Sayı: 2, 822 - 834, 01.06.2024

Kenan Gören Mehmet Bağlan Ümit Yıldıko Veysel Tahiroğlu

https://doi.org/10.21597/jist.1416223

Öz

This reearch focused on the structural characterization of (2Z,5E)-2-(((E)-benziliden) hidraziniliden)-5-(nitro(fenil)metilen)-3-feniltiazolidin-4-on molecule (Thiazolidinone-Bis Schiff Base). Depending on the molecule's stability phase geometry, all analyses have been carried out utilizing the B3PW91 technique with 6-311++G(d,p) and SDD basis sets, for structural characterisation. Many computations were performed in our work, including inter-orbital and inter-orbital bond interactions, HOMO-LUMO energy deficiencies, and electrostatic surface mapping processes of the Thiazolidinone-Bis Schiff Base. In a subsequent investigation, we have used molecular docking to analyze the particular binding place and method of the ligand onto the protein. Schiff Thiazolidinone Molecular docking results against cancer and urease enzymes were obtained.

Anahtar Kelimeler

DFT, MEP, NBO, Molecular doking, Thiazolidinone-bis schiff base

Anti-Kanser ve Anti-Üreaz Aktivitesi için Tiazolidinon-Bis Schiff Bazının Moleküler Yerleştirme ve DFT Analizi

Öz

Bu araştırma (2Z,5E)-2-(((E)-benziliden)hidraziniliden)-5-(nitro(fenil)metilen)-3-feniltiazolidin-4-on molekülün (Tiazolidinon-Bis Schiff Bazı) yapısal karakterizasyonuna odaklanmıştır. Molekülün kararlı faz geometrisine dayanarak yapısal karakterizasyon için SDD ve 6-311++G(d,p) temel setleri ile B3PW91 tekniği kullanılarak tüm hesaplamalar yapıldı. Çalışmamızda yörüngeler arası ve yörüngeler arası bağ etkileşimleri, HOMO-LUMO enerji boşlukları ve Tiazolidinon-Bis Schiff Bazı’ın elektrostatik yüzey haritalama işlemleri dahil olmak üzere birçok hesaplama gerçekleştirildi. Daha sonraki bir araştırmada, protein üzerindeki ligandın özel bağlanma bölgesini ve mekanizmasını analiz etmek için moleküler yerleştirmeyi kullandık. Schiff Thiazolidinone Kansere ve üreaz enzimlerine karşı moleküler yerleştirme sonuçları elde edildi.

Anahtar Kelimeler

DFT, NBO, MEP, Moleküler yerleştirme, Tiazolidinon-bis schiff bazı

Kaynakça

• Abdelsattar, A. S., Dawoud, A., & Helal, M. A. (2021). Interaction of nanoparticles with biological macromolecules: a review of molecular docking studies. Nanotoxicology, 15(1), 66-95.
• Ak, F., & Kebiroglu, H. (2023). Molecular Structure, Geometry Properties, HOMO-LUMO, and MEP Analysis of Acrylic Acid Based on DFT Calculations. Journal of Physical Chemistry and Functional Materials, 6(2), 92-100.
• Al-Sharif, M. S. (2023). 2,4-dihydroxybenzaldehyde based Schiff base derivatives as an effective corrosion inhibitor for steel corrosion in 1 M hydrochloric acid solution. International Journal of Electrochemical Science, 18(12), 100384.
• Alkorta, I., & Villar, H. O. (1994). Molecular electrostatic potential of D1 and D2 dopamine agonists. Journal of Medicinal Chemistry, 37(1), 210-213.
• Assfeld, X., & Rivail, J.-L. (1996). Quantum chemical computations on parts of large molecules: the ab initio local self consistent field method. Chemical Physics Letters, 263(1), 100-106.
• Baskaran, C., & Ramachandran, M. (2012). Computational molecular docking studies on anticancer drugs. Asian Pacific Journal of Tropical Disease, 2, S734-S738.
• Berhanu, A. L., Gaurav, Mohiuddin, I., Malik, A. K., Aulakh, J. S., Kumar, V., & Kim, K.-H. (2019). A review of the applications of Schiff bases as optical chemical sensors. TrAC Trends in Analytical Chemistry, 116, 74-91.
• Callahan, B. P., Yuan, Y., & Wolfenden, R. (2005). The Burden Borne by Urease. Journal of the American Chemical Society, 127(31), 10828-10829.
• Cuesta, I. G., Pedersen, T. B., Koch, H., & Sánchez de Merás, A. (2006). Carbon Nanorings: A Challenge to Theoretical Chemistry. ChemPhysChem, 7(12), 2503-2507.
• da Silva, C. M., da Silva, D. L., Modolo, L. V., Alves, R. B., de Resende, M. A., Martins, C. V. B., & de Fátima, Â. (2011). Schiff bases: A short review of their antimicrobial activities. Journal of Advanced Research, 2(1), 1-8.
• Demir, P., & Akman, F. (2017). Molecular structure, spectroscopic characterization, HOMO and LUMO analysis of PU and PCL grafted onto PEMA-co-PHEMA with DFT quantum chemical calculations. Journal of Molecular Structure, 1134, 404-415.
• El-Hassab, M. A. E.-M., El-Bastawissy, E. E., & El-Moselhy, T. F. (2020). Identification of potential inhibitors for HCV NS5b of genotype 4a by combining dynamic simulation, protein–ligand interaction fingerprint, 3D pharmacophore, docking and 3D QSAR. Journal of Biomolecular Structure and Dynamics, 38(15), 4521-4535.
• Ergan, E. (2021). Theoretical Studies via DFT Calculation of Pyrimidine Derivatives as Potential Corrosion Inhibitor [Potansiyel Korozyon İnhibitörü Olarak Pirimidin Türevlerinin DFT Hesaplaması ile Teorik Çalışmalar]. Journal of the Institute of Science and Technology, 11(3), 2142-2151.
• Eşme, A., & Sağdınç, S. G. (2017). Spectroscopic (FT–IR, FT–Raman, UV–Vis) analysis, conformational, HOMO-LUMO, NBO and NLO calculations on monomeric and dimeric structures of 4-pyridazinecarboxylic acid by HF and DFT methods. Journal of Molecular Structure, 1147, 322-334.
• Goh, G. B., Hodas, N. O., & Vishnu, A. (2017). Deep learning for computational chemistry. Journal of Computational Chemistry, 38(16), 1291-1307.
• Govindarajan, M., & Karabacak, M. (2012). Spectroscopic properties, NLO, HOMO–LUMO and NBO analysis of 2,5-Lutidine. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 96, 421-435.
• Hodnett, E. M., & Dunn, W. J. (1970). Structure-antitumor activity correlation of some Schiff bases. Journal of Medicinal Chemistry, 13(4), 768-770.
• Hratchian, H. P., Parandekar, P. V., Raghavachari, K., Frisch, M. J., & Vreven, T. (2008). QM:QM electronic embedding using Mulliken atomic charges: Energies and analytic gradients in an ONIOM framework. The Journal of Chemical Physics, 128(3).
• Kaltsoyannis, N. (2018). Transuranic Computational Chemistry. Chemistry – A European Journal, 24(12), 2815-2825.
• Kar, T., & Sannigrahi, A. B. (1988). Effect of basis set on Mulliken and Löwdin atomic charges, bond orders and valencies of some polar molecules. Journal of Molecular Structure: THEOCHEM, 165(1), 47-54.
• Kolandaivel, P., & Nirmala, V. (2004). Study of proper and improper hydrogen bonding using Bader's atoms in molecules (AIM) theory and NBO analysis. Journal of Molecular Structure, 694(1), 33-38.
• Kurt, M., Babu, P. C., Sundaraganesan, N., Cinar, M., & Karabacak, M. (2011). Molecular structure, vibrational, UV and NBO analysis of 4-chloro-7-nitrobenzofurazan by DFT calculations. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 79(5), 1162-1170.
• Kuş, N. (2021). Orbıtal Interactıons and Stabılızatıon Energıes of Methyl 5-6 Dihydro Benzo(H) Quınolıne-4-Carboxylate [Orbital interactions and stabilization energies of methyl 5-6 dihydro benzo(h) quinoline-4-carboxylate]. Eskişehir Teknik Üniversitesi Bilim ve Teknoloji Dergisi B - Teorik Bilimler, 9(Iconat Special Issue 2021), 74-84.
• Mahmood, A., Khan, S. U.-D., Rana, U. A., Janjua, M. R. S. A., Tahir, M. H., Nazar, M. F., & Song, Y. (2015). Effect of thiophene rings on UV/visible spectra and non-linear optical (NLO) properties of triphenylamine based dyes: a quantum chemical perspective. Journal of Physical Organic Chemistry, 28(6), 418-422.
• Michael J. Frisch, T., G.W, Bernhard Schlegel, Gustavo Scuseria. (2016). Gaussian 09. In Revision E.01
• Mobley, H. L. T. (2001). Urease. In Helicobacter pylori (pp. 177-191).
• Pang, Z.-H., & Reed, M. (1998). Theoretical Chemical Thermometry on Geothermal Waters: Problems and Methods. Geochimica et Cosmochimica Acta, 62(6), 1083-1091.
• Parandekar, P. V., Hratchian, H. P., & Raghavachari, K. (2008). Applications and assessment of QM:QM electronic embedding using generalized asymmetric Mulliken atomic charges. The Journal of Chemical Physics, 129(14).
• Pathak, S. K., Srivastava, R., Sachan, A. K., Prasad, O., Sinha, L., Asiri, A. M., & Karabacak, M. (2015). Experimental (FT-IR, FT-Raman, UV and NMR) and quantum chemical studies on molecular structure, spectroscopic analysis, NLO, NBO and reactivity descriptors of 3,5-Difluoroaniline. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 135, 283-295.
• Polacco, J. C., & Holland, M. A. (1993). Roles of Urease in Plant Cells. In K. W. Jeon & J. Jarvik (Eds.), International Review of Cytology (Vol. 145, pp. 65-103). Academic Press.
• Preeti, Jaiswal, A., Kumar, M., & Singh, K. N. (2023). An Efficient Combinatorial Synthesis of Novel Thiazolidinone-Bis Schiff Base Hybrids Using One-Pot Multicomponent Reaction. Asian Journal of Organic Chemistry, 12(2), e202200629.
• Pyykkö, P. (2005). Theoretical chemistry of gold. II. Inorganica Chimica Acta, 358(14), 4113-4130.
• Qin, Y., & Cabral, J. M. S. (2002). Review Properties and Applications of Urease. Biocatalysis and Biotransformation, 20(1), 1-14.
• Rupp, M., Von Lilienfeld, O. A., & Burke, K. (2018). Guest Editorial: Special Topic on Data-Enabled Theoretical Chemistry. The Journal of Chemical Physics, 148(24).
• Sertbakan, T. R. (2021). 4-Amino-2-Metil-7(Triflorometil)Kinolin Molekülünün Bazı Özelliklerinin Deneysel ve Teorik Spektroskopik Yöntemlerle İncelenmesi [Investigation of some properties of 4-amino-2-methyl-7(trifluoromethyl)quinoline molecule by experimental and theoretical spectroscopic methods]. Journal of Anatolian Physics and Astronomy, 1(2), 46-64.
• Shoichet, B. K., McGovern, S. L., Wei, B., & Irwin, J. J. (2002). Lead discovery using molecular docking. Current Opinion in Chemical Biology, 6(4), 439-446.
• Sosa, G. L., Peruchena, N. M., Contreras, R. H., & Castro, E. A. (2002). Topological and NBO analysis of hydrogen bonding interactions involving C–H⋯O bonds. Journal of Molecular Structure: THEOCHEM, 577(2), 219-228.
• Suhasini, M., Sailatha, E., Gunasekaran, S., & Ramkumaar, G. R. (2015). Vibrational and electronic investigations, thermodynamic parameters, HOMO and LUMO analysis on Lornoxicam by density functional theory. Journal of Molecular Structure, 1100, 116-128.
• Tabatabai, M. A., & Bremner, J. M. (1972). Assay of urease activity in soils. Soil Biology and Biochemistry, 4(4), 479-487.
• Topsom, R. D. (1983). Contribution of theoretical chemistry to an understanding of electronic substituent effects. Accounts of Chemical Research, 16(8), 292-298.
• Verma, A., Kumar, V., Naik, B., Masood Khan, J., Singh, P., Erik Joakim Saris, P., & Gupta, S. (2023). Screening and molecular dynamics simulation of compounds inhibiting MurB enzyme of drug-resistant Mycobacterium tuberculosis: An in-silico approach. Saudi Journal of Biological Sciences, 30(8), 103730.