DFT Computations and Molecular Docking Studies of 3-(6-(3-aminophenyl)thiazolo[1,2,4]triazol-2-yl)-2H-chromen-2-one(ATTC) Molecule

Year 2023, Volume: 10 Issue: 1, 11 - 19, 31.03.2023

Mehmet Bağlan , Kenan Gören , Ümit Yıldıko

https://doi.org/10.17350/HJSE19030000286

Cited By: 3

Abstract

In this study, theoretic analyses were executed on the optimized geometric structure of 3-(6-(3-aminophenyl)thiazolo[3,2-b][1.2.4]triazol-2-yl)-2H-chromen-2-one (ATTC). The basis sets for these theoretical research were B3LYP/DGDZVP and B3LYP/6-311G(d,p). To determine the stability and molecular reactiveness of the molecule, energy range, the HOMO-LUMO energies, softhood (s), hardhood (η), electronic negativity (χ), and chemical potential (μ) characteristics were employed. The second array decay energy E(2) values of the molecule, which indicates the ATTC molecule’s the bioactivite, were determined with the native bond orbital (NBO) analysis. The ATTC molecule’s the reactive behavior is further studied using simulated the molecular electrostatic potential (MEP) surface’s calculations. The overall electron intensity and mulliken atomic charge distribution found by MEP area research gave proof that the molecule's reactive area existed. The ATTC molecule will continue to be a crucial therapeutic agent to Alzheimer disease’s the treatment Alzheimer disease thanks to molecular docking study. The highest binding affinity was observed as a docking score of -10,681 Kcal/mol.

Keywords

DFT calculation, FMO, NBO, Molecular docking

References

• Kotian, S.Y., et al., Small molecule based five-membered heterocycles: A view of liquid crystalline properties beyond the biological applications. Journal of Molecular Liquids, 2020. 297: p. 111686.
• Lohith, T.N., et al., Synthesis, molecular structure, Hirshfeld surface, energy framework and DFT studies of 1,3,4 oxadiazole derivative. Journal of Molecular Structure, 2022. 1252: p. 132203.
• Ding, J., et al., One-step fabrication of nitrogen-deficient carbon nitride through pyrolysis of melamine and 1,2,4-triazole for its enhanced photocatalytic degradation. Green Chemical Engineering, 2021. 2(3): p. 317-326.
• Sanina, N.A., et al., Synthesis, structure and antibacterial activity of dinitrosyl iron complexes (DNICs) dimers functionalized with 5-(nitrophenyl) -4-H-1,2,4-triazole-3-thiolyls. Polyhedron, 2022. 220: p. 115822.
• Sadeghian, S., et al., 1,2,4-Triazole derivatives as novel and potent antifungal agents: Design, synthesis and biological evaluation. Journal of Molecular Structure, 2023. 1271: p. 134039.
• Suresh Kumar, G.V., et al., Synthesis of some novel 2-substituted-5-[isopropylthiazole] clubbed 1,2,4-triazole and 1,3,4-oxadiazoles as potential antimicrobial and antitubercular agents. European journal of medicinal chemistry, 2010. 45(5): p. 2063-74.
• Lao, Y., et al., Discovery of 1,2,4-triazole derivatives as novel neuroprotectants against cerebral ischemic injury by activating antioxidant response element. Bioorganic Chemistry, 2022. 128: p. 106096.
• Grytsai, O., et al., Synthesis and biological evaluation of 3-amino-1,2,4-triazole derivatives as potential anticancer compounds. Bioorg Chem, 2020. 104: p. 104271.
• Abdelazeem, A.H., et al., Design, synthesis and anti-inflammatory/analgesic evaluation of novel di-substituted urea derivatives bearing diaryl-1,2,4-triazole with dual COX-2/sEH inhibitory activities. Journal of Molecular Structure, 2021. 1240: p. 130565.
• Martínez-Escudero, C.M., et al., Remediation of triazole, anilinopyrimidine, strobilurin and neonicotinoid pesticides in polluted soil using ozonation and solarization. Journal of Environmental Management, 2022. 310: p. 114781.
• Abdelli, A., et al., Recent advances in the chemistry of 1,2,4-triazoles: Synthesis, reactivity and biological activities. Tetrahedron Letters, 2021. 86: p. 153518.
• Minto-García, A., et al., Lexical relations in Spanish-Speaking older adults with Alzheimer's disease: An approach to semantic memory. Journal of Neurolinguistics, 2022. 62: p. 101059.
• Mustafa, I.H., et al., Effect of cholineacetyltransferase activity and choline recycle ratio on diffusion-reaction modeling, bifurcation and chaotic behavior of acetylcholine neurocycle and their relation to Alzheimer's and Parkinson's diseases. Chemical Engineering Science, 2012. 68(1): p. 19-35.
• Gao, H., et al., Pharmacophore-based drug design of AChE and BChE dual inhibitors as potential anti-Alzheimer's disease agents. Bioorg Chem, 2021. 114: p. 105149.
• Aidoo, A.Y. and K. Ward, Spatio-temporal concentration of acetylcholine in vertebrate synaptic cleft. Mathematical and Computer Modelling, 2006. 44(9): p. 952-962.
• Ahmad, W., Glucose enrichment impair neurotransmission and induce Aβ oligomerization that cannot be reversed by manipulating O-β-GlcNAcylation in the C. elegans model of Alzheimer's disease. The Journal of Nutritional Biochemistry, 2022. 108: p. 109100.
• Liu, J., et al., Choline acetyltransferase and vesicular acetylcholine transporter are required for metamorphosis, reproduction, and insecticide susceptibility in Tribolium castaneum. Gene, 2022. 842: p. 146794.
• Marucci, G., et al., Efficacy of acetylcholinesterase inhibitors in Alzheimer's disease. Neuropharmacology, 2021. 190: p. 108352.
• Dos Santos, R., et al., Acetylcholinesterase and butyrylcholinesterase inhibition by nectriapyrone and tryptophol isolated from endophytic fungus Phomopsis sp. Nat Prod Res, 2022. 36(16): p. 4153-4158.
• Ahmed Sameer, K. and T. Mohammed Hussein, Study geometrical, electronic and spectroscopic properties of BeO wurtzoids via DFT. Materials Today: Proceedings, 2021. 42: p. 2629-2637.
• Sharma, D. and S. Nath Tiwari, Molecular Structure and Vibrational Dynamics Studies of 4-n-propyl-4′-cyanobiphenyl using Ab initio and DFT Methods. Materials Today: Proceedings, 2018. 5(7, Part 2): p. 15325-15334.
• Deepa, H.R., S. Chandrasekhar, and J. Thipperudrappa, Investigation of FRET from organic dyes to silver nanoparticles and structural properties using the DFT/TD-DFT approach. Chemical Physics Impact, 2022. 4: p. 100075.
• Frisch, M.J. and e. al, Gaussian 09, . Revision E.01.
• Hernández, J.G., et al., Understanding of [RuL(ONO)](n+) acting as nitric oxide precursor, a theoretical study of ruthenium complexes of 1,4,8,11-tetraazacyclo- tetradecane having different substituents: How spin multiplicity influences bond angle and bond lengths (Ru-O-NO) in releasing of NO. J Inorg Biochem, 2021. 218: p. 111406.
• Southern, S.A. and D.L. Bryce, To what extent do bond length and angle govern the 13C and 1H NMR response to weak CH⋯O hydrogen bonds? A case study of caffeine and theophylline cocrystals. Solid State Nuclear Magnetic Resonance, 2022. 119: p. 101795.
• Yildiko, U., et al., Investigation of novel diethanolamine dithiocarbamate agent for RAFT polymerization: DFT computational study of the oligomer molecules. Bulletin of Materials Science, 2021. 44.
• Satheeshkumar, R., et al., Spectroscopic (FT-IR, NMR, single crystal XRD) and DFT studies including FMO, Mulliken charges, and Hirshfeld surface analysis, molecular docking and ADME analyses of 2-amino-4′-fluorobenzophenone (FAB). Journal of Molecular Structure, 2022. 1267: p. 133552.
• Krishna Kumar, V., et al., Vibrational assignment of the spectral data, molecular dipole moment, polarizability, first hyperpolarizability, HOMO–LUMO and thermodynamic properties of 5-nitoindan using DFT quantum chemical calculations. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2014. 118: p. 663-671.
• Oftadeh, M., S. Naseh, and M. Hamadanian, Electronic properties and dipole polarizability of thiophene and thiophenol derivatives via density functional theory. Computational and Theoretical Chemistry, 2011. 966(1): p. 20-25.
• Yahya, M., G. Kurtay, and A. Suvitha, On the Viability of Divergent Donor Moieties in Malononitrile-Based Donor-π-Acceptor NLO active materials: A DFT/TD-DFT Study. Journal of Physical Organic Chemistry, 2022. 35.
• Rashid, M., et al., Nonlinear optical (NLO) response of boron phosphide nanosheet by alkali metals doping: A DFT study. Materials Science in Semiconductor Processing, 2022. 151: p. 107007.
• Bi, Z., et al., Experimental and theoretical study on broadband electromagnetic wave absorption of algae-like NiO/carbon nanotubes absorbers. Journal of Alloys and Compounds, 2022. 926: p. 166821.
• Jothi, A.I., M.W.B. Paul, and V. Alexander, A comparative molecular structure – NLO activity study of ortho-bridged dibenzaldehydes: Synthesis, crystal structure, SHG, and DFT studies. Journal of Molecular Structure, 2022. 1250: p. 131776.
• Derafa, W., et al., An unexpected single crystal structure of nickel(II) complex: Spectral, DFT, NLO, magnetic and molecular docking studies. Journal of Molecular Structure, 2022. 1264: p. 133190.
• Slyvka, Y., et al., Crystal structure, DFT-study and NLO properties of the novel copper(I) nitrate π,σ-coordination compound based on 1-allyl-3-norbornan-thiourea. Polyhedron, 2022. 211: p. 115545.
• Yildiko, U., et al., Computational DFT calculations, photovoltaic properties and synthesis of (2R, 3S)-2, 3, 4-trihydroxybutoxy substituted phthalocyanines. Inorganic and Nano-Metal Chemistry, 2020. 50.
• Buvaneswari, M., et al., 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.
• Sowrirajan, S., et al., (E)-4-((4-Bromobenzylidene) Amino)-N-(Pyrimidin-2-yl) Benzenesulfonamide from 4-Bromobenzaldehyde and Sulfadiazine, Synthesis, Spectral (FTIR, UV–Vis), Computational (DFT, HOMO–LUMO, MEP, NBO, NPA, ELF, LOL, RDG) and Molecular Docking Studies. Polycyclic Aromatic Compounds, 2022.
• Sakr, M.A.S. and M.A. Saad, Spectroscopic investigation, DFT, NBO and TD-DFT calculation for porphyrin (PP) and porphyrin-based materials (PPBMs). Journal of Molecular Structure, 2022. 1258: p. 132699.
• Aboalhassan, A.A., et al., 1,4-bis[β-(2-benzoxazoly1) vinyl] benzene (BBVB) laser dye and sodium salt of meso-tetrakis (4-sulfonatophenyl) porphyrin (TPPS); spectroscopic investigation and DFT, NBO and TD-DFT calculations. Journal of Photochemistry and Photobiology A: Chemistry, 2022. 431: p. 114039.
• Singh, P., et al., Spectroscopic investigation (FT-IR, FT-Raman), HOMO-LUMO, NBO, and molecular docking analysis of N-ethyl-N-nitrosourea, a potential anticancer agent. Journal of Molecular Structure, 2018. 1154: p. 39-50.
• Balachandran, V., et al., Conformational stability, spectroscopic and computational studies, HOMO–LUMO, NBO, ESP analysis, thermodynamic parameters of natural bioactive compound with anticancer potential of 2-(hydroxymethyl)anthraquinone. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 2015. 150: p. 631-640.
• Balachandran, V. and V. Karpagam, Conformational stability, vibrational assignments of 2,3-dihydroxy benzaldehyde as supported by ab initio, hybrid density functional theory and normal coordinate analysis. Journal of Molecular Structure, 2013. 1038: p. 52-61.
• Rezkallah, E., et al., DFT and Thermal Decomposition Studies on Gemcitabine. 2019. 233(10): p. 1503-1527.
• Celik, S., S. Akyuz, and A.E. Ozel, Vibrational spectroscopic characterization and structural investigations of Cepharanthine, a natural alkaloid. Journal of Molecular Structure, 2022. 1258: p. 132693.
• Celik, S., S. Akyuz, and A.E. Ozel, Molecular modeling, DFT quantum chemical analysis, and molecular docking on edotecarin, an indolocarbazole anticancer agent. Molecular Crystals and Liquid Crystals, 2022: p. 1-23.