Melanoma Cancer Evaluation with ADME and Molecular Docking Analysis, DFT Calculations of (E)-methyl 3-(1-(4-methoxybenzyl)-2,3-dioxoindolin-5-yl)-acrylate Molecule

Yıl 2024, Cilt: 14 Sayı: 3, 1186 - 1199, 01.09.2024

Kenan Gören , Mehmet Bağlan , Ümit Yıldıko

https://doi.org/10.21597/jist.1467666

Öz

In this study, we performed HOMO-LUMO energy calculations, molecular electrostatic potential surface (MEPS), optimized molecular geometry using B3LYP, B3PW91 methods and 6-311G(d,p) basis set of the target molecule (E)-methyl 3-(1-(4-methoxybenzyl)-2,3-dioxoindolin-5-yl) acrylate (MMDA) that is an isatin derivative, nonlinear optics (NLO), NBO analysis to investigate the stability of the molecule as a function of both hyper-conjugative interactions, charge transfer within the molecule and charge delocalization, and Mulliken atomic charge structure were examined using the Gaussian 09 software, and the results were displayed. In this study, ADME analysis was performed to analyze the problem of our molecule finding application in the field, focusing on producing effective and harmless pharmacological drugs. Finally, molecular docking analysis of the examined compound on melanoma cancer were performed with two different enzymes (PDB:3OG7) and (PDB:5EG3), and docking scores and receptor models were given.

Anahtar Kelimeler

DFT, Moleküler Docking, MEP, ADME, NBO

Kaynakça

• Arivazhagan, M., Manivel, S., Jeyavijayan, S., & Meenakshi, R. (2015). Vibrational spectroscopic (FTIR and FT-Raman), first-order hyperpolarizablity, HOMO, LUMO, NBO, Mulliken charge analyses of 2-ethylimidazole based on Hartree–Fock and DFT calculations. Spectrochim Acta A Mol Biomol Spectrosc, 134, 493-501.
• Bağlan, M., Gören, K., & Yıldıko, Ü. (2023). HOMO–LUMO, NBO, NLO, MEP analysis and molecular docking using DFT calculations in DFPA molecule. Int. J. Chem. Technol, 7(1), 38-47.
• Bhavani, R., Kanagathara, N., Marchewka, M. K., Janczak, J., Senthilkumar, K., & Azam, M. (2024). Single crystal analysis and DFT studies of the novel hybrid material-based on 2-hydroxypyridine and selenic acid. Results in Chemistry, 7, 101239.
• Bouachrıne, M., Azaıd, A., Abram, T., Kacimi, R., Raftanı, M., Sbai, A., & Lakhlıfı, T. (2021). DFT/TDDFT studies of the structural, electronic, NBO and non-linear optical proper-ties of triphenylamine functionalized tetrathiafulvalene. J. Turkish chem. soc, 5(2), 24-34.
• Cetin, A., Toptas, M., & Türkan, F. (2022). Synthesis, biological evaluation, and bioinformatics analysis of indole analogs on AChE and GST activities. Med. Chem. Res., 31(12), 2119-2131.
• 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. J. Mol. Struct., 1134, 404-415.
• Elangovan, N., & Sowrirajan, S. (2021). Synthesis, single crystal (XRD), Hirshfeld surface analysis, computational study (DFT) and molecular docking studies of (E)-4-((2-hydroxy-3,5-diiodobenzylidene)amino)-N-(pyrimidine)-2-yl) benzenesulfonamide. Heliyon, 7(8), e07724.
• Guo, H. (2019). Isatin derivatives and their anti-bacterial activities. Eur. J. Med, 164, 678-688.
• Gümüş, H. P., Tamer, Ö., Avcı, D., & Atalay, Y. (2015). 4-(Metoksimetil)-1, 6-dimetil-2-okso-1, 2-dihidropiridin-3-karbonitril molekülünün teorik olarak incelenmesi. Sakarya University Journal of Science, 19(3), 303-311.
• Gyamfi, J., Kim, J., & Choi, J. (2022). Cancer as a metabolic disorder. Int. J. Mol. Sci, 23(3), 1155.
• Kenan, G., Bağlan, M., & Çakmak, İ. (2022). Theoretical Investigation of 1H and 13C NMR Spectra of Diethanol Amine Dithiocarbamate RAFT Agent. TJST, 12(3), 1677-1689.
• Khan, A. U., Khera, R. A., Anjum, N., Shehzad, R. A., Iqbal, S., Ayub, K., & Iqbal, J. (2021). DFT study of superhalogen and superalkali doped graphitic carbon nitride and its non-linear optical properties. RSC Adv, 11(14), 7779-7789.
• Khodja, I. A., Boulebd, H., Bensouici, C., & Belfaitah, A. (2020). Design, synthesis, biological evaluation, molecular docking, DFT calculations and in silico ADME analysis of (benz) imidazole-hydrazone derivatives as promising antioxidant, antifungal, and anti-acetylcholinesterase agents. J. Mol. Struct, 1218, 128527.
• Kızılbey, K., & Akdeste, Z. M. (2013). Melanoma cancer. SIGMA J ENG NAT SCI, 31(4), 555-569.
• Kloeden, P. E., Platen, E., & Schurz, H. (2012). Numerical solution of SDE through computer experiments. Springer Sci. Rev.
• Mehmet, B., Yıldıko, Ü., & Gören, K. (2023). DFT Calculatıons And Molecular Dockıng Study In 6-(2”-pyrrolıdınone-5”-yl)-(-) epıcatechın Molecule From Flavonoıds. Eskişehir Teknik Üniversitesi Bilim ve Teknoloji Dergisi B-Teorik Bilimler, 11(1), 43-55.
• Özlük, A. A., Oytun, M. G., & Günenç, D. (2017). Kanser immünoterapisi. İstanbul Bilim Üniversitesi Florence Nightingale Transplantasyon Dergisi, 2(1), 21-23.
• Raju, R., Panicker, C. Y., Nayak, P. S., Narayana, B., Sarojini, B., Van Alsenoy, C., & Al-Saadi, A. A. (2015). FT-IR, molecular structure, first order hyperpolarizability, MEP, HOMO and LUMO analysis and NBO analysis of 4-[(3-acetylphenyl) amino]-2-methylidene-4-oxobutanoic acid. Spectrochim Acta A Mol Biomol Spectrosc, 134, 63-72.
• Ramalingam, S., Karabacak, M., Periandy, S., Puviarasan, N., & Tanuja, D. (2012). Spectroscopic (infrared, Raman, UV and NMR) analysis, Gaussian hybrid computational investigation (MEP maps/HOMO and LUMO) on cyclohexanone oxime. Spectrochim Acta A Mol Biomol Spectrosc, 96, 207-220.
• Release, S., (2019). 3: Maestro Schrödinger. LLC, New York
• Sakr, M. A., Sherbiny, F. F., & El-Etrawy, A.-A. S. (2022). Hydrazone-based materials; DFT, TD-DFT, NBO analysis, fukui function, MESP analysis, and solar cell applications. J. Fluoresc., 32(5), 1857-1871.
• Saraç, K. (2018). 4-Klorometil-6, 8-dimetilkumarin Bileşiğinin Sentezi ve Teorik Kimyasal Hesaplamaları. Bitlis Eren Üniversitesi Fen Bilimleri Dergisi, 7(2), 311-319.
• Sehout, I., Boulebd, H., Boulcina, R., Nemouchi, S., Bendjeddou, L., Bramki, A., Merazig, H., & Debache, A. (2021). Synthesis, crystal structure, Hirshfeld surface analysis, biological evaluation, DFT calculations, and in silico ADME analysis of 4-arylidene pyrazolone derivatives as promising antibacterial agents. J. Mol. Struct., 1229, 129586.
• Shokr, E. K., Kamel, M. S., Abdel-Ghany, H., Ali, M. A. E. A. A., & Abdou, A. (2022). Synthesis, characterization, and DFT study of linear and non-linear optical properties of some novel thieno [2, 3-b] thiophene azo dye derivatives. Mater. Chem. Phys, 290, 126646.
• T. Michael J. Frisch, G. W., Bernhard Schlegel, Gustavo Scuseria. (2016). (Version In Revision E.01 )
• Teng, Y.-O., Zhao, H.-Y., Wang, J., Liu, H., Gao, M.-L., Zhou, Y., Han, K.-L., Fan, Z.-C., Zhang, Y.-M., & Sun, H. (2016). Synthesis and anti-cancer activity evaluation of 5-(2-carboxyethenyl)-isatin derivatives. Eur. J. Med. Chem, 112, 145-156.
• Torre, L. A., Bray, F., Siegel, R. L., Ferlay, J., Lortet‐Tieulent, J., & Jemal, A. (2015). Global cancer statistics, 2012. CA: CA Cancer J, 65(2), 87-108.
• Umar, A. B., Uzairu, A., Shallangwa, G. A., & Uba, S. (2020). QSAR modelling and molecular docking studies for anti-cancer compounds against melanoma cell line SK-MEL-2. Heliyon, 6(3).
• Wang, X., & Yao, J. (2017). Improvement of the self-consistent-charge density-functional-tight-binding theory by a modified Mulliken charge. Theor. Chem. Acc, 136(10), 124.
• Weinhold, F., Landis, C., & Glendening, E. (2016). What is NBO analysis and how is it useful? Int Rev Phys Chem, 35(3), 399-440.
• Xavier, R. J., & Gobinath, E. (2012). FT-IR, FT-Raman, ab initio and DFT studies, HOMO–LUMO and NBO analysis of 3-amino-5-mercapto-1, 2, 4-triazole. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 86, 242-251. Molecular and Biomolecular Spectroscopy
• Zaboli, M., & Raissi, H. (2015). The analysis of electronic structures, adsorption properties, NBO, QTAIM and NMR parameters of the adsorbed hydrogen sulfide on various sites of the outer surface of aluminum phosphide nanotube: a DFT study. Structural Chemistry, 26, 1059-1075.