DFT CALCULATIONS AND MOLECULAR DOCKING STUDY IN 6-(2”-PYRROLIDINONE-5”-YL)-(-) EPICATECHIN MOLECULE FROM FLAVONOIDS

Year 2023, Volume: 11 Issue: 1, 43 - 55, 28.02.2023

Mehmet Bağlan Ümit Yıldıko Kenan Gören

https://doi.org/10.20290/estubtdb.1126604

Abstract

The 6-311G(d,p) and SDD basis sets have been used to calculate the vibration frequencies, and the DFT/B3LYP approach was used to optimize the structure. The energy gap of the molecule has been calculated using the lowest unoccupied molecular orbital (LUMO) with the highest occupied molecular orbital (HOMO). The stability and charge delocalization of the Title molecule have been investigated using natural bond orbital (NBO) analysis. The dipole moment, polarizability, and first-order hyperpolarizability, as well as the molecular electrostatic potentially (MEP) and thermodynamic features, have been used to compute the nonlinear optical (NLO) behavior of the title molecule. The Schrödinger program was used to conduct molecular docking works to determine information about the interactions between the AChE and BChE enzymes and the chemical. In addition, a molecular docking study was analyzed for compounds PEP with AChE and BChE synthase binding protenins (PDB:4M0E) and (PDB:6SAM) using the Discovery Studio 2021 Client program. Compound AChE showed -7.105 kcal/mol while compounds BChE showed a inding score of -7.784 kcal/mol.

Keywords

PEP, DFT, HOMO-LUMO, NBO, Molecular docking

FLAVONOİDLERDEN 6-(2”-PYROLİDİNONE-5”-YL)-(-)EPİCATECHİN MOLEKÜLÜNDE DFT HESAPLAMALARI VE MOLEKÜLER YERLEŞTİRME ÇALIŞMASI

Abstract

Titreşim frekanslarını hesaplamak için 6-311G(d,p) ve SDD temel setleri kullanıldı ve yapıyı optimize etmek için DFT/B3LYP yaklaşımı kullanıldı. En yüksek dolu moleküler orbital (HOMO) ve en düşük boş moleküler orbital (LUMO) ile molekülün enerji boşluğu hesaplandı. Başlık molekülünün stabilitesini ve yük delokalizasyonunu araştırmak için doğal bağ orbitali (NBO) analizi ile incelemiştir. Başlıktaki bileşiğin doğrusal olmayan optik (NLO) davranışı, dipol momenti, polarize edilebilirlik ve birinci dereceden hiperpolarize edilebilirliğin yanı sıra moleküler elektrostatik potansiyeli (MEP) ve termodinamik özellikleri açısından hesaplandı. AChE ve BChE enzimleri ile bileşik arasındaki etkileşimler hakkındaki bilgileri belirlemek için Schrödinger yazılımı tarafından moleküler yerleştirme çalışmaları yapıldı. Ek olarak, Discovery Studio 2021 İstemci programı kullanılarak AChE ve BChE sentaz bağlayıcı proteinler (PDB:4M0E) ve (PDB:6SAM) içeren PEP bileşikleri için bir moleküler yerleştirme çalışması analiz edildi. AChE bileşiği -7.105 kcal/mol gösterirken, BChE bileşikleri -7.784 kcal/mol'lük bir sonuç puanı gösterdi.

Keywords

PEP, DFT, HOMO-LUMO, NBO, Molecular docking

References

• [1] Ilkei V, Spaits A, Prechl A, Müller J, Könczöl Á, Lévai S, Riethmüller E, Szigetvári Á, Béni Z, Dékány M, Martins A, Hunyadi A, Antus S, Szántay C, Balogh GT, Kalaus G, Bölcskei H, and Hazai L, C8-selective biomimetic transformation of 5,7-dihydroxylated flavonoids by an acid-catalysed phenolic Mannich reaction: Synthesis of flavonoid alkaloids with quercetin and (–)-epicatechin skeletons. Tetrahedron.2017; 73:(11): p. 1503-1510.
• [2] Moyeenudin HM, Thiruchelvi R, Wilfred Lawrence A, and John Williams R, The phytochemical components of caesalpinia sappan in treating respiratory ailments through an herbal soup in addition with sensory evaluation. Materials Today: Proceedings.2022; 56: p. 2167-2171.
• [3] Xiao P-t, Liu S-y, Kuang Y-j, Jiang Z-m, Lin Y, Xie Z-s, and Liu EH, Network pharmacology analysis and experimental validation to explore the mechanism of sea buckthorn flavonoids on hyperlipidemia. Journal of Ethnopharmacology.2021; 264: p. 113380.
• [4] Miao N, Yun C, Han S, Shi Y, Gao Y, Wu S, Zhao Z, Wang H, and Wang W, Postharvest UV-A radiation affects flavonoid content, composition, and bioactivity of Scutellaria baicalensis root. Postharvest Biology and Technology.2022; 189: p. 111933.
• [5] Mora-Granados M, Crevillen AG, González-Gómez D, and Gallego-Picó A, Disposable electrochemical sensor combined with molecularly imprinted solid-phase extraction for catabolites detection of flavan-3-ol in urine samples. Talanta.2021; 235: p. 122734.
• [6] Wojdyło A and Nowicka P, Anticholinergic effects of Actinidia arguta fruits and their polyphenol content determined by liquid chromatography-photodiode array detector-quadrupole/time of flight-mass spectrometry (LC-MS-PDA-Q/TOF). Food Chemistry.2019; 271: p. 216-223.
• [7] Webby RF, Wilson RD, and Ferguson AR, Leaf flavonoids of Actinidia. Biochemical Systematics and Ecology.1994; 22:(3): p. 277-286.
• [8] Teng J, Li J, Zhao Y, and Wang M, Hesperetin, a dietary flavonoid, inhibits AGEs-induced oxidative stress and inflammation in RAW264.7 cells. Journal of Functional Foods.2021; 81: p. 104480.
• [9] Frisch MJ, Trucks GW, and SH, and GE. S, Gaussian 09. Revision E.01.
• [10] Tunç G, Canımkurbey B, Dedeoğlu B, Zorlu Y, Eryılmaz S, and Gürek AG, Synthesis, crystal structure and electronic applications of monocarboxylic acid substituted phthalonitrile derivatives combined with DFT studies. Journal of Molecular Structure.2021; 1240: p. 130545.
• [11] Anuoluwa Bamidele E, Olanrewaju Ijaola A, Bodunrin M, Ajiteru O, Martha Oyibo A, Makhatha E, and Asmatulu E, Discovery and prediction capabilities in metal-based nanomaterials: An overview of the application of machine learning techniques and some recent advances. Advanced Engineering Informatics.2022; 52: p. 101593.
• [12] Solğun DG, Yıldıko Ü, and Ağırtaş MS, Synthesis, DFT Calculations, Photophysical, Photochemical Properties of Peripherally Metallophthalocyanines Bearing (2-(Benzo[d] [1,3] Dioxol-5-Ylmethoxy) Phenoxy) Substituents. Polycyclic Aromatic Compounds.2021: p. 1-19.
• [13] Sonia C, Devi TG, and Karlo T, DFT study on the structural and chemical properties of Janus kinase inhibitor drug Baricitinib. Materials Today: Proceedings.2022.
• [14] Fatima A, Khanum G, Verma I, Butcher RJ, Siddiqui N, Srivastava SK, and Javed S, Synthesis, Characterization, Crystal Structure, Hirshfeld Surface, Electronic Excitation, Molecular Docking, and DFT Studies on 2-Amino Thiophene Derivative. Polycyclic Aromatic Compounds.2022.
• [15] Kole PB, Kollur SP, Revanasiddappa HD, Shivamallu C, Costa RA, Junior ESA, Anselmo LM, da Silva JN, Srinivasa C, Syed A, and Singh FV, Structural, Electronic, Vibrational and Pharmacological Investigations of Highly Functionalized Diarylmethane Molecules Using DFT Calculations, Molecular Dynamics and Molecular Docking. Polycyclic Aromatic Compounds.2022.
• [16] Soni K, Saxena S, and Jain A, Recent advances in DFT assisted optimized energy, stability and distortions of optimized topologies of certain biopotent dimethyltin(IV) complexes. Journal of the Indian Chemical Society.2022; 99:(3): p. 100332.
• [17] Budania S, Saxena S, and Jain A, Assessment of DFT based optimized molecular structure-antioxidant efficacy relationship of trimethylgermanium(IV) complexes. Journal of the Indian Chemical Society.2022; 99:(5): p. 100419.
• [18] Solğun DG, Keskin MS, yıldıko Ü, and Ağırtaş MS, DFT analysis and electronic properties, and synthesis of tetra (9-phenyl-9H-xanthen-9-yl) oxy peripheral-substituted zinc phthalocyanine. Chemical Papers.2020; 74:(8): p. 2389-2401.
• [19] Janeoo S, Reenu, Saroa A, Kumar R, and Kaur H, Computational investigation of bioactive 2,3-diaryl quinolines using DFT method: FT- IR, NMR spectra, NBO, NLO, HOMO-LUMO transitions, and quantum-chemical properties. Journal of Molecular Structure.2022; 1253: p. 132285.
• [20] Buvaneswari M, Santhakumari R, Usha C, Jayasree R, and Sagadevan S, Synthesis, growth, structural, spectroscopic, optical, thermal, DFT, HOMO–LUMO, MEP, NBO analysis and thermodynamic properties of vanillin isonicotinic hydrazide single crystal. Journal of Molecular Structure.2021; 1243: p. 130856.
• [21] Janani S, Rajagopal H, Muthu S, Aayisha S, and Raja M, Molecular structure, spectroscopic (FT-IR, FT-Raman, NMR), HOMO-LUMO, chemical reactivity, AIM, ELF, LOL and Molecular docking studies on 1-Benzyl-4-(N-Boc-amino)piperidine. Journal of Molecular Structure.2021; 1230: p. 129657.
• [22] Akman ME, Ata AÇ, Yıldıko Ü, and, Cakmak İ, and Molecular structure, frontier molecular orbitals, NBO, MESP and thermodynamic properties of 5, 12-dibromo perylene with DFT calculation methods. International Journal of Chemistry Technology.2020; 4:(1): p. 49-59.
• [23] Sevvanthi S, Muthu S, Aayisha S, Ramesh P, and Raja M, Spectroscopic (FT-IR, FT-Raman and UV-Vis), computational (ELF, LOL, NBO, HOMO-LUMO, Fukui, MEP) studies and molecular docking on benzodiazepine derivatives- heterocyclic organic arenes. Chemical Data Collections.2020; 30: p. 100574.
• [24] Kargar H, Fallah-Mehrjardi M, Behjatmanesh-Ardakani R, and Munawar KS, Synthesis, spectra (FT-IR, NMR) investigations, DFT, FMO, MEP, NBO analysis and catalytic activity of MoO2(VI) complex with ONO tridentate hydrazone Schiff base ligand. Journal of Molecular Structure.2021; 1245: p. 131259.
• [25] Raveendiran C, Prabukanthan P, Ragavendran V, Harichandran G, Dinakaran K, and Seenuvasakumaran P, Synthesis, crystal growth, crystal investigation, optical, thermal, DFT and NLO studies of 2-methylanilinium- 4-methylbenzenesulfonate organic single crystal: Experimental and computational approach. Materials Today: Proceedings.2022.
• [26] Remiya JP, Sikha TS, Shyni B, Anitha L, Lakshmi CSN, and Jayasree EG, Synthesis, spectral characterization and biological evaluations with DFT analysis on molecular geometry and NLO of 1,4,7,10-tetraazacyclotetradecane-11,14-dione. Journal of the Indian Chemical Society.2021; 98:(9): p. 100132.
• [27] Priya MK, Revathi BK, Renuka V, Sathya S, and Asirvatham PS, 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.2019; 8: p. 37-46.
• [28] 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.2015; 137: p. 490-502.
• [29] Sakr MAS and Saad MA, Spectroscopic investigation, DFT, NBO and TD-DFT calculation for porphyrin (PP) and porphyrin-based materials (PPBMs). Journal of Molecular Structure.2022; 1258: p. 132699.
• [30] Murugan P, Jeyavijayan S, Ramuthai M, and Narmadha RB, Structural, Spectroscopic, NBO and Molecular Docking Analysis of 5-Nitrobenzimidazole – A DFT Approach. Polycyclic Aromatic Compounds.2022.
• [31] Jebasingh Kores J, Antony Danish I, Sasitha T, Gershom Stuart J, Jimla Pushpam E, and Winfred Jebaraj J, Spectral, NBO, NLO, NCI, aromaticity and charge transfer analyses of anthracene-9,10-dicarboxaldehyde by DFT. Heliyon.2021; 7:(11): p. e08377.
• [32] Trabelsi S, Tlili M, Abdelmoulahi H, Bouazizi S, Nasr S, González MA, Bellissent-Funel M-C, and Darpentigny J, Intermolecular interactions in an equimolar methanol-water mixture: Neutron scattering, DFT, NBO, AIM, and MD investigations. Journal of Molecular Liquids.2022; 349: p. 118131.
• [33] Kaya ED, Türkhan A, Gür F, and Gür B, A novel method for explaining the product inhibition mechanisms via molecular docking: inhibition studies for tyrosinase from Agaricus bisporus. Journal of Biomolecular Structure and Dynamics.2021: p. 1-14.
• [34] Altun K, Yıldıko Ü, Tanrıverdi AA, Çakmak İJIJoC, and Technology, Structural and spectral properties of 4-(4-(1-(4-Hydroxyphenyl)-1-phenylethyl) phenoxy) phthalonitrile: Analysis by TD-DFT method, ADME analysis and docking studies. 5:(2): p. 147-155.
• [35] Madadi Mahani N, Mostaghni F, and Shafiekhani H, Cuspareine as alkaloid against COVID-19 designed with ionic liquids: DFT and docking molecular approaches. Journal of Photochemistry and Photobiology B: Biology.2022; 231: p. 112447.