5,5'',7''-trihidroksi-3,7-dimetoksi-4'-4'''-O-biflavon Bileşiğinde DFT ve Moleküler Doking Çalışması

Yıl 2022, Cilt: 12 Sayı: 2, 283 - 298, 30.12.2022

Mehmet Bağlan Ümit Yıldıko Kenan Gören

https://doi.org/10.37094/adyujsci.1121018

Öz

Bu çalışmada, 5,5'',7''-trihidroksi-3,7-dimetoksi-4'-4'''-O-biflavon (TDOB) molekülünün yapısal karakterizasyonu yapıldı. Bu molekülün yapısal karakterizasyonu için, molekülün kararlı faz geometrisine dayalı olarak, tüm hesaplamalar sırasıyla CAM-B3LYP ve PBEPBE metotlarını SDD ve LanL2DZ temel seti kullanılarak yapıldı. Çalışmamızda TDOB molekülünün HOMO-LUMO enerji boşlukları, yörüngeler arası ve yörüngeler arası bağ etkileşimleri, elektrostatik yüzey haritalama işlemleri gibi birçok hesaplamalarda yapılmıştır. Çalışmamızın devamında moleküler doking kullanılarak ligandın protein üzerindeki spesifik bağlanma yeri ve mekanizması araştırıldı. Doking çalışmasında, TDOB- aldoz reduktaz (PDB: 4ICC) ve TDOB- aldoz reduktaz (PDB: 4IGS) ile afinite skorları sırasıyla -8.559 kcal/mol ve -5.461 kcal/mol olarak bulundu. TDOB- aldoz reduktaz (PDB: 4ICC) reseptör bağlanma skoru daha büyük olduğu tespit edildi. Moleküler doking çalışmasının devamında TDOB'nin inhibitör özellikleri, her ikisi de etkili inhibisyon gösteren (PDB: 4ICC) ve (PDB: 4IGS) enzimlerine karşı araştırıldı ve TDOB molekülünün, (PDB: 4ICC) ve (PDB: 4IGS) aldoz reduktaz enzimlerini etkili bir şekilde inhibe ettiği görüldü.

Computational Investigation of 5.5'',7''-trihydroxy-3,7-dimethoxy-4'-4'''-O-biflavone from Flavonoids Using DFT Calculations and Molecular Docking

Öz

The structural characterization of the 5.5",7"-trihydroxy-3,7-dimethoxy-4'-4'''-O-biflavone (TDOB) molecule was done in this study. For the structural characterization of this molecule, based on the molecule's stable phase geometry, entire calculations were done using the CAM-B3LYP and PBEPBE approaches with SDD and LanL2DZ basis sets respectively. In our study, many calculations, such as HOMO-LUMO energy gaps, inter-orbital, and inter-orbital bond interactions, and electrostatic surface mapping processes of the TDOB molecule, have also been made. In the continuation of our study, the specific binding site and mechanism of the ligand on the protein were investigated using molecular docking. In the molecular docking study, affinity scores for TDOB- aldose reductase (PDB: 4ICC) and (PDB: 4IGS) were found to be -8.559 kcal/mol and -5.461 kcal/mol, respectively. The 4ICC receptor binding score was found to be greater. In the continuation of the molecular docking study, the inhibitory properties of TDOB were investigated against the aldose reductase enzymes (PDB: 4ICC) and (PDB: 4IGS), both of which showed effective inhibition, and it was seen that the TDOB molecule effectively inhibited the enzymes (PDB: 4ICC) and aldose reductase (PDB: 4IGS).

Anahtar Kelimeler

Flavonoids, TDOB, HOMO-LUMO, Molecular docking

Kaynakça

• Panche, A.N., Diwan, A.D., and Chandra, S.R., Flavonoids: an overview, Journal of Nutritional Science, 5 (47), 1-15, 2016.
• Oyeleke, M.B. and Owoyele, B.V., Saponins and flavonoids from Bacopa floribunda plant extract exhibit antioxidant and anti-inflammatory effects on amyloid beta 1-42-induced Alzheimer's disease in BALB/c mice, Journal of Ethnopharmacology, 288, 114997, 2022.
• Chauhan, B.S., Kumar, R., Kumar, P., Kumar, P., Sinha, S., Mishra, S.K., Kumar, P., Tiwari, K.N., Critchley, A.T., Prithiviraj, B., and Srikrishna, S., Neuroprotective potential of flavonoid rich Ascophyllum nodosum (FRAN) fraction from the brown seaweed on an Aβ(42) induced Alzheimer's model of Drosophila, Phytomedicine, 95, 153872, 2022.
• Wang, B., Ding, Y., Zhao, P., Li, W., Li, M., Zhu, J., and Ye, S., Systems pharmacology-based drug discovery and active mechanism of natural products for coronavirus pneumonia (COVID-19): An example using flavonoids, Computers in Biology and Medicine, 143, 105241, 2022.
• Mitra, S., Lami, M.S., Uddin, T.M., Das, R., Islam, F., Anjum, J., Hossain, M.J., and Emran, T.B., Prospective multifunctional roles and pharmacological potential of dietary flavonoid narirutin, Biomedicine and Pharmacotherapy, 150, 112932, 2022.
• Heimfarth, L., Nascimento, L.D.S., Amazonas da Silva, M.J., Lucca Junior, W., Lima, E.S., Quintans-Junior, L.J., and Veiga-Junior, V.F.D., Neuroprotective and anti-inflammatory effect of pectolinarigenin, a flavonoid from Amazonian Aegiphila integrifolia (Jacq.), against lipopolysaccharide-induced inflammation in astrocytes via NFκB and MAPK pathways, Food and Chemical Toxicology, 157, 112538, 2021.
• Onishi, S., Nishi, K., Yasunaga, S., Muranaka, A., Maeyama, K., Kadota, A., and Sugahara, T., Nobiletin, a polymethoxy flavonoid, exerts anti-allergic effect by suppressing activation of phosphoinositide 3-kinase, Journal of Functional Foods, 6, 606-614, 2014.
• Young, D.A. and Sterner, R.W., Leaf flavonoids of primitive dicotyledonous angiosperms: Degeneria vitiensis and Idiospermum australiense, Biochemical Systematics and Ecology, 9 (2), 185-187, 1981.
• Truchado, P., Ferreres, F., and Tomas-Barberan, F.A., Liquid chromatography-tandem mass spectrometry reveals the widespread occurrence of flavonoid glycosides in honey, and their potential as floral origin markers, Journal of Chromatography. A, 1216 (43), 7241-8, 2009.
• Solgun, D.G., Tanriverdi, A.A., Yildiko, U., and Ağirtaş, M.S., Synthesis of axially silicon phthalocyanine substituted with bis- (3,4-dimethoxyphenethoxy) groups, DFT and molecular docking studies, Journal of Inclusion Phenomena and Macrocyclic Chemistry, 102 (11), 851-860, 2022.
• Cui, W., Chen, J., Insight into mineral flotation fundamentals through the DFT method, International Journal of Mining Science and Technology, 31 (6), 983-994, 2021.
• Chauhan, A., Singh, K.M., Recursive sliding DFT algorithms: A review, Digital Signal Processing, 127, 103560, 2022.
• Shang, Y., Duan, X., Wang, S., Yue, Q., Gao, B., and Xu, X., Carbon-based single atom catalyst: Synthesis, characterization, DFT calculations, Chinese Chemical Letters, 33 (2), 663-673, 2022.
• Frisch, M.J., Trucks, G.W., Schlegel, H.B., and Scuseria, G.E., Gaussian 09, Revision E.01, 2016.
• Wang, G., Liu, W., Gong, Z., Huang, Y., Li, Y., and Peng, Z., Design, synthesis, biological evaluation and molecular docking studies of new chalcone derivatives containing diaryl ether moiety as potential anticancer agents and tubulin polymerization inhibitors, Bioorganic Chemistry, 95, 103565, 2020.
• Altun, K., Yildiko, Ü., Tanrıverdi, A.A., Tekeş, A.T., Ata, A.Ç., Kartal, B., and Çakmak, İ., Structural and Spectral Properties of 4-(5-methyl-[1, 2, 4] triazolo [1, 5-a] pyrimidine-7-yloxy) phthalonitrile: Analysis by TD-DFT Method, ADME Analysis, and Molecular Docking Simulations, Journal of the Institute of Science Technology, 12 (4), 2340-2351, 2022.
• Yildiko, Ü., Türkan, F., Tanriverdi, A.A., Ata, A.C., Atalar, M.N., and Cakmak, İ., Synthesis, enzymes inhibitory properties and characterization of 2-(bis (4-aminophenyl) methyl) butan-1-ol compound: Quantum simulations, and in-silico molecular docking studies, Journal of the Indian Chemical Society, 98 (11), 100206, 2021.
• Akinpelu, O.I., Lawal, M.M., Kumalo, H.M., and Mhlongo, N.N., Drug repurposing: Fusidic acid as a potential inhibitor of M. tuberculosis FtsZ polymerization – Insight from DFT calculations, molecular docking and molecular dynamics simulations, Tuberculosis, 121, 101920, 2020.
• Asadi, Z., Golchin, M., Eigner, V., Dusek, M., and Amirghofran, Z., A detailed study on the interaction of a novel water-soluble glycine bridged zinc(II) Schiff base coordination polymer with BSA: Synthesis, crystal structure, molecular docking and cytotoxicity effect against A549, Jurkat and Raji cell lines, Inorganica Chimica Acta, 465, 50-60, 2017.
• Marinho, E.M., Batista de Andrade Neto, J., Silva, J., Rocha da Silva, C., Cavalcanti, B.C., Marinho, E.S., and Nobre Júnior, H.V., Virtual screening based on molecular docking of possible inhibitors of Covid-19 main protease, Microbial Pathogenesis, 148, 104365, 2020.
• Solğun, D.G., Keskin, M.S., yıldıko, Ü., and Ağırtaş, M.S., DFT analysis and electronic properties, and synthesis of tetra (9-phenyl-9H-xanthen-9-yl) oxy peripheral-substituted zinc phthalocyanine, Chemical Papers, 74 (8), 2389-2401, 2020. Khajehzadeh, M. and Moghadam, M., Molecular structure, FT IR, NMR, UV, NBO and HOMO–LUMO of 1-(3-(dimethylamino)propyl)-1-(4-fluorophenyl)-1,3-dihydroisobenzofuran-5-carbonitrile by DFT/B3LYP and PBEPBE methods with LanL2DZ and 6-311++G(d,2p) basis sets, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 180, 51-66, 2017.
• Yildiko, Ü., Ata, A.Ç., Tanriverdi, A.A., and Çakmak, İ., Investigation of novel diethanolamine dithiocarbamate agent for RAFT polymerization: DFT computational study of the oligomer molecules, Bulletin of Materials Science, 44 (3), 186, 2021.
• Li, K., Xu, W., Han, M., Cheng, Y., Wen, G., and Huang, T., Integration of iron-manganese co-oxide (FMO) with gravity-driven membrane (GDM) for efficient treatment of surface water containing manganese and ammonium, Separation and Purification Technology, 282, 119977, 2022.
• Griesbeck, C., Hager-Braun, C., Rogl, H., and Hauska, G., Quantitation of P840 reaction center preparations from Chlorobium tepidum: chlorophylls and FMO-protein, Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1365 (1), 285-293, 1998.
• Tanriverdi, A.A., Yildiko, U., Tekes, A.T., Cakmak, İ., and Ata, A.C., Synthesis, characterization and affinity detection of sulfonated polyimides: confirmation of proton transfer in quantum theory simulations, Polymer Bulletin, 2022. DOI: https://doi.org/10.1007/s00289-022-04536-0
• Tekeş, A.T., Ata, A.Ç., Tanriverdi, A.A., and Çakmak, İ., Insilico Molecular Docking Studies of THBF Compound: TD-DFT Simulations and Drug Design, Journal of the Institute of Science Technology, 11 (4), 2955-2966, 2021.
• Durgadevi, R., Suvitha, A., and Arumanayagam, T., Growth, optical, electrical properties and DFT studies on piperidinium 4-nitrophenolate NLO single crystal in acetone, Journal of Crystal Growth, 582, 126512, 2022.
• Derafa, W., Aggoun, D., Messasma, Z., Houchi, S., Bouacida, S., and Ourari, A., An unexpected single crystal structure of nickel(II) complex: Spectral, DFT, NLO, magnetic and molecular docking studies, Journal of Molecular Structure, 1264, 133190, 2022.
• Al Sabahi, A., Al Busafi, S.N., Suliman, F.O., and Al Kindy, S.M., Photophysical and theoretical studies on the solvatochromic effects and dipole moments evaluation of substituted 1-phenyl-3-naphthyl-5- (4-ethyl benzoate)-2-pyrazoline, Journal of Molecular Liquids, 307, 112967, 2020.
• Arivazhagan, M. and Senthil kumar, J., Molecular structure, vibrational spectral assignments, HOMO–LUMO, MESP, Mulliken analysis and thermodynamic properties of 2,6-xylenol and 2,5-dimethyl cyclohexanol based on DFT calculation, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 137, 490-502, 2015.
• Priya, M.K., Revathi, B.K., Renuka, V., Sathya, S., and Asirvatham, P.S., Molecular Structure, Spectroscopic (FT-IR, FT-Raman, 13C and 1H NMR) Analysis, HOMO-LUMO Energies, Mulliken, MEP and Thermal Properties of New Chalcone Derivative by DFT Calculation, Materials Today: Proceedings, 8, 37-46, 2019.
• Akman, M., Ata, A.C., Yildiko, U., and Çakmak, İ., Molecular structure, frontier molecular orbitals, NBO, MESP and thermodynamic properties of 5,12-dibromo perylene with DFT calculation methods, International Journal of Chemistry and Technology, 4 (1), 49-59, 2020.
• Boshaala, A., Said, M.A., Assirey, E.A., Alborki, Z.S., AlObaid, A.A., Zarrouk, A., and Warad, I., Crystal structure, MEP/DFT/XRD, thione ⇔ thiol tautomerization, thermal, docking, and optical/TD-DFT studies of (E)-methyl 2-(1-phenylethylidene)-hydrazinecarbodithioate ligand, Journal of Molecular Structure, 1238, 130461, 2021.
• Murugan, P., Jeyavijayan, S., Ramuthai, M., and Narmadha, R.B., Structural, Spectroscopic, NBO and Molecular Docking Analysis of 5-Nitrobenzimidazole – A DFT Approach, Polycyclic Aromatic Compounds, 2022. DOI: https://doi.org/10.1080/10406638.2022.2056621