Examination of anti-oxidant properties and molecular docking parameters of some compounds in human body

Year 2020, , 76 - 87, 15.12.2020

Burak Tüzün

https://doi.org/10.33435/tcandtc.781008

Cited By: 15

Abstract

There are many hormones and molecules in the human body. Many of these take place in different jobs and tasks. Some of these hormones are serotonin (A1), testosterone (A2), dopamine (A3), adrenaline (A4), methylcytosine (A5) and creatine (A6). The anti-oxidant properties of these molecules in both gas and water phases of the HF/6-31g(d,p) basis set were calculated with the Gaussian package program. After this process, molecular docking calculations were made to compare the activities of molecules against proteins with anti-oxidant properties whose name are human peroxiredoxin-5 (HP5) and bovine xanthine oxidase (BXO), were compared.

Keywords

antioxidant, molecular docking, DFT, human body, hormone

Project Number

RGD-020

References

• N.F. Boyd and V.McGuire, The possible role of lipid peroxidation in breast cancer risk. Free Radical Biology and Medicine, 10(3-4) (1991) 185-190.
• P. Knekt, A. Reunanen, H. Takkunen, A. Aromaa, M. Heliovaara, and T. Hakuunen, Body iron stores and risk of cancer. International journal of cancer, 56(3) (1994) 379-382.
• G.S. Omenn, G.E.Goodman, M.D. Thornquist, J. Balmes, M.R. Cullen, A. Glass, J.P. Keogh, F.L. Meyskens, B. Valanis, J.H. Williams, S. Barnhart, and S. Hammar, Effects of a combination of beta carotene and vitamin A on lung cancer and cardiovascular disease. New England journal of medicine, 334(18) (1996) 1150-1155.
• M. Valko, C.J. Rhodes, J. Moncola, M. Izakovic, and M. Mazura, Free radicals, metals and antioxidants in oxidative stress-induced cancer. Chemico-biological interactions, 160(1) (2006) 1-40.
• D.A. Street, G. Comstock, R. Salkeldy, and M. Klag, Serum antioxidants and myocardial infarction. Are low levels of carotenoids and alpha-tocopherol risk factors for myocardial infarction?. Circulation, 90(3) (1994) 1154-1161.
• L.H. Kushi, A.R. Folsom, R.J. Prineas, P.J. Mink, Y. Wu, and R. Bostick, N. Engl. Dietary antioxidant vitamins and death from coronary heart disease in postmenopausal women. New England Journal of Medicine, 334(18) (1996) 1156-1162.
• U. Singh and I. Jialal, Oxidative stress and atherosclerosis. Pathophysiology, 13(3) (2006) 129-142.
• Q. Huang, G.D. Lu, H.M. Shen, M.C.M. Chung, and C.N. Ong, Anti‐cancer properties of anthraquinones from rhubarb. Medicinal research reviews, 27(5) (2007) 609-630.
• S. Ghosh, M.D. Sarma, A. Patra, and B. Hazra, Anti‐inflammatory and anticancer compounds isolated from Ventilago madraspatana Gaertn., Rubia cordifolia Linn. and Lantana camara Linn. Journal of pharmacy and pharmacology, 62(9) (2010) 1158-1166.
• J.D.D. Tamokou, M.F. Tala,H.K.Wabo, J.R. Kuiate, and P. Tane, Antimicrobial activities of methanol extract and compounds from stem bark of Vismia rubescens. Journal of ethnopharmacology, 124(3) (2009) 571-575.
• D.O. Andersen, N.D. Weber, S.G. Wood, B.G. Hughes, B.K. Murray, and J.A. North, In vitro virucidal activity of selected anthraquinones and anthraquinone derivatives. Antiviral research, 16(2) (1991) 185-196.
• H. Hussain, A. Al-Harrasi, A. Al-Rawahi, I.R. Green, R. Csuk, I. Ahmed, A. Shah, G. Abbas, N.U. Rehman, R. Ullah, In vitro virucidal activity of selected anthraquinones and anthraquinone derivatives. Antiviral research, 16(2) (1991) 185-196.
• G.C. Yen, P.D. Duh, and D.Y. Chuang, Antioxidant activity of anthraquinones and anthrone. Food chemistry, 70(4) (2000) 437-441.
• S.K. Agarwal, S.S. Singh, S. Verma, and S. Kumar, Antifungal activity of anthraquinone derivatives from Rheum emodi. Journal of ethnopharmacology, 72(1-2) (2000) 43-46.
• D. Kremer, I. Kosalec, M. Locatelli, F. Epifano, S. Genovese, G. Carlucci, and M.Z. Konˇci´c, Anthraquinone profiles, antioxidant and antimicrobial properties of Frangula rupestris (Scop.) Schur and Frangula alnus Mill. bark. Food Chemistry, 131(4) (2012) 1174-1180.
• H.F. Brown, D. DiFrancesco, S.J. Noble, How does adrenaline accelerate the heart?. Nature, 280(5719) (1979) 235-236.
• H.L. Judd, S.S. Yen, Serum androstenedione and testosterone levels during the menstrual cycle. The Journal of Clinical Endocrinology & Metabolism, 36(3) (1973) 475-481.
• P. Seeman, H.H. Van Tol, Dopamine receptor pharmacology. Trends in pharmacological sciences, 15(7) (1994) 264-270.
• H. Sternbach, The serotonin syndrome. Am J Psychiatry, 148(6) (1991) 705-713.
• E. Nieschlag, H.M. Behre, S. Nieschlag, Testosterone: action, deficiency, substitution. Cambridge University Press(2012).
• J.P. Declercq, C. Evrard, A. Clippe, D. Vander Stricht, A. Bernard, B. Knoops, Crystal structure of human peroxiredoxin 5, a novel type of mammalian peroxiredoxin at 1.5 Å resolution. Journal of molecular biology, 311(4) (2001) 751-759.
• H. Cao, J.M. Pauff, R. Hille, Substrate orientation and catalytic specificity in the action of xanthine oxidase the sequential hydroxylation of hypoxanthine to uric acid. Journal of Biological Chemistry, 285(36) (2010) 28044-28053.
• Z. Marković, S. Jeremić, J.D. Marković, M.S. Pirković, D. Amić, Influence of structural characteristics of substituents on the antioxidant activity of some anthraquinone derivatives. Computational and Theoretical Chemistry, 1077 (2016) 25-31.
• S. Sari, B. Barut, A. Özel, D. Şöhretoğlu, Tyrosinase inhibitory effects of Vinca major and its secondary metabolites: Enzyme kinetics and in silico inhibition model of the metabolites validated by pharmacophore modelling. Bioorganic chemistry, 92 (2019) 103259.
• E. Koç, A. Üngördü, F. Candan, Antioxidant properties of methanolic extract of ‘Veronica multifida’and DFT and HF analyses of its the major flavonoid component. Journal of Molecular Structure, 1197 (2019) 436-442.
• A. Urbaniak, M. Szeląg, M. Molski, Theoretical investigation of stereochemistry and solvent influence on antioxidant activity of ferulic acid. Computational and Theoretical Chemistry, 1012 (2013) 33-40.
• R. Kheirabadi, M. Izadyar, Antioxidant activity of selenenamide-based mimic as a function of the aromatic thiols nucleophilicity, a DFT-SAPE model. Computational biology and chemistry, 75(2018) 213-221.
• R. Dennington, T. Keith, J. Millam, GaussView, Version 6, Semichem Inc., Shawnee Mission, KS (2016)
• Gaussian 09, Revision D.01, M. J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G.A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H.P. Hratchian, A.F. Izmaylov, J. Bloino, G. Zheng, J.L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J.A. Montgomery, Jr., J.E. Peralta, F. Ogliaro, M. Bearpark, J.J. Heyd, E. Brothers, K.N. Kudin, V.N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S.S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J.M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, R.L. Martin, K. Morokuma, V.G. Zakrzewski, G.A. Voth, P. Salvador, J.J. Dannenberg, S. Dapprich, A. D. Daniels, Ö. Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski, and D.J. Fox, Gaussian, Inc., Wallingford CT, 2009. D. Vautherin, D.M. Brink, Hartree-Fock calculations with skyrme’s interaction. I. Spherical nuclei, Phys. Rev. C, 5 (1972) 626-647
• A.D. Becke, Density-functional thermochemistry. III. The role of exact exchange, J. Chem. Phys., 98 (1993) 5648-5652
• J.S. Wright, E.R. Johnson, G.A. DiLabio, Predicting the activity of phenolic antioxidants: theoretical method, analysis of substituent effects, and application to major families of antioxidants. Journal of the American Chemical Society, 123-6 (2001) 1173-1183.
• J.E. Bartmess, Thermodynamics of the electron and the proton. The Journal of Physical Chemistry, 98-25 (1994) 6420-6424.
• L. Schrodinger, (2019). Small-Molecule Drug Discovery Suite 2019-4
• Schrödinger Release 2019-4: Protein Preparation Wizard; Epik, Schrödinger, LLC, New York, NY, 2016; Impact, Schrödinger, LLC, New York, NY, 2016; Prime, Schrödinger, LLC, New York, NY, 2019.
• R.A. Friesner, R.B. Murphy, M.P. Repasky, L.L. Frye, J.R. Greenwood, T.A. Halgren, P.C. Sanschagrin, D.T. Mainz, Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein−ligand complexes. Journal of medicinal chemistry. 49 (2006) 6177–6196.
• G.M. Sastry, M. Adzhigirey, T. Day, R. Annabhimoju, W. Sherman, Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. Journal of computer-aided molecular design, 27(3) (2013) 221-234.
• Schrödinger Release 2019-4: LigPrep, Schrödinger, LLC, New York, NY, 2019.
• D. Kısa, N. Korkmaz, P. Taslimi, B. Tuzun, Ş. Tekin, A. Karadag, F. Şen, Bioactivity and molecular docking studies of some nickel complexes: New analogues for the treatment of Alzheimer, glaucoma and epileptic diseases. Bioorganic chemistry, 101 (2020) 104066.
• F. Türkan, P. Taslimi, S.M. Abdalrazaq, A. Aras, Y. Erden, H.U. Celebioglu, B. Tüzün, M.S. Ağırtaş, İ. Gülçin, Determination of anticancer properties and inhibitory effects of some metabolic enzymes including acetylcholinesterase, butyrylcholinesterase, alpha glycosidase of some compounds with molecular docking study. Journal of Biomolecular Structure and Dynamics (2020) 1-17.
• H.G. Bilgiçli, A.T. Bilgiçli, A. Günsel, B. Tüzün, D. Ergön, M.N. Yarasir, M. Zengin, Turn‐on fluorescent probe for Zn2+ ions based on thiazolidine derivative. Applied Organometallic Chemistry, 34(6) (2020) e5624.
• S. Akkoç, B. Tüzün, İ.Ö. İlhan, M. Akkurt, Investigation of structural, spectral, electronic, and biological properties of 1, 3-disubstituted benzimidazole derivatives. Journal of Molecular Structure, (2020) 128582.
• L.K. Ojha, B. Tüzün, J. Bhawsar, Experimental and Theoretical Study of Effect of Allium sativum Extracts as Corrosion Inhibitor on Mild Steel in 1 M HCl Medium. Journal of Bio-and Tribo-Corrosion, 6(2) (2020) 1-10.
• M. Akin, A. Günsel, A.T. Bilgiçli, B. Tüzün, G. Arabaci, N. Şaki, M.N. Yarasir, The Water-Soluble Peripheral Substituted Phthalocyanines as Corrosion Inhibitors for Copper in 0.1 N HCl: Gravimetric, Electrochemical, SEM-EDS, and Quantum Chemical Calculations. Protection of Metals and Physical Chemistry of Surfaces, 56(3) (2020) 609-618.
• D. Douche, H. Elmsellem, L. Guo, B. Hafez, B. Tüzün, A. El Louzi, K. Bougrina, K. Karrouchi, B. Himmi, Anti-corrosion performance of 8-hydroxyquinoline derivatives for mild steel in acidic medium: Gravimetric, electrochemical, DFT and molecular dynamics simulation investigations. Journal of Molecular Liquids, (2020) 113042.
• A. Urbaniak, M. Szeląg, M. Molski, Theoretical investigation of stereochemistry and solvent influence on antioxidant activity of ferulic acid. Computational and Theoretical Chemistry, 1012 (2013) 33-40.
• R. Kheirabadi, M. Izadyar, Antioxidant activity of selenenamide-based mimic as a function of the aromatic thiols nucleophilicity, a DFT-SAPE model. Computational biology and chemistry, 75 (2018) 213-221.
• B. Tüzün, E. Saripinar, Molecular docking and 4D-QSAR model of methanone derivatives by electron conformational-genetic algorithm method. Journal of the Iranian Chemical Society, 17 (2020) 985–1000.
• B. Tüzün, Investi̇gati̇on of pyrazoly derivatives schi̇ff base li̇gands and thei̇r metal complexes used as anti-cancer drug. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 227 (2020) 117663.
• B. Tüzün, Investigation of the Molecules Obtained from Marijuana: Computational Study of Spectral, Structural and Docking 16(3,4) (2020) 59-74.
• H.U. Celebioglu, Y. Erden, F. Hamurcu, P. Taslimi, O.S. Şentürk, Ü.Ö. Özmen, B. Tüzün, İ. Gulçin, Cytotoxic effects, carbonic anhydrase isoenzymes, α-glycosidase and acetylcholinesterase inhibitory properties, and molecular docking studies of heteroatom-containing sulfonyl hydrazone derivatives. Journal of Biomolecular Structure and Dynamics, (2020) 1-12.
• H.G. Bilgicli, P. Taslimi, B. Akyuz, B. Tuzun, I. Gulcin, Synthesis, characterization, biological evaluation, and molecular docking studies of some piperonyl‐based 4‐thiazolidinone derivatives. Archiv der Pharmazie, 353(1) (2020) 1900304.
• H.G. Bilgiçli, D. Ergön, P. Taslimi, B. Tüzün, İ.A. Kuru, M. Zengin, İ. Gülçin, Novel Propanolamine Derivatives Attached to 2-Metoxifenol Moiety: Synthesis, Characterization, Biological Properties, and Molecular Docking Studies. Bioorganic Chemistry, (2020) 103969.
• K. Sayin, A. Üngördü, Investigations of structural, spectral and electronic properties of enrofloxacin and boron complexes via quantum chemical calculation and molecular docking. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 220 (2019) 117102.
• K. Sayin, D. Karakaş, Investigation of structural, electronic properties and docking calculations of some boron complexes with norfloxacin: A computational research. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 202 (2018) 276-283.
• K. Sayin, D. Karakaş, Quantum chemical investigation of levofloxacin-boron complexes: a computational approach. Journal of Molecular Structure, 1158 (2018) 57-65.
• K. Sayin, A. Üngördü, Investigation of anticancer properties of caffeinated complexes via computational chemistry methods. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 193 (2018) 147-155.
• K. Sayin, D. Karakaş, Determination of structural, spectral, electronic and biological properties of tosufloxacin boron complexes and investigation of substituent effect. Journal of Molecular Structure, 1146 (2017) 191-197.
• R. Jayarajan, R. Satheeshkumar, T. Kottha, S. Subbaramanian, K. Sayin, G. Vasuki, Water mediated synthesis of 6-amino-5-cyano-2-oxo-N-(pyridin-2-yl)-4-(p-tolyl)-2H-[1, 2′-bipyridine]-3-carboxamide and 6-amino-5-cyano-4-(4-fluorophenyl)-2-oxo-N-(pyridin-2-yl)-2H-[1, 2′-bipyridine]-3-carboxamide–An experimental and computational studies with non-linear optical (NLO) and molecular docking analyses. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 229 (2020) 117861.
• A. Üngördü, K. Sayin, Quantum chemical calculations on sparfloxacin and boron complexes. Chemical Physics Letters, 733 (2019) 136677.
• A. Huseynova, R. Kaya, P. Taslimi, V. Farzaliyev, X. Mammadyarova, A. Sujayev, B. Tüzün, U.M. Kocyigit, S. Alwasel, İ. Gulçin. Design, synthesis, characterization, biological evaluation, and molecular docking studies of novel 1, 2-aminopropanthiols substituted derivatives as selective carbonic anhydrase, acetylcholinesterase and α-glycosidase enzymes inhibitors. Journal of Biomolecular Structure and Dynamics, (2020) 1-13.
• A. Aktaş, B. Tüzün, R. Aslan, K. Sayin, H. Ataseven, New anti-viral drugs for the treatment of COVID-19 instead of favipiravir, Journal of Biomolecular Structure and Dynamics, (2020) 1-11.
• A. Aktaş, B. Tüzün, A.H. Taşkin Kafa, K. Sayin, H. Ataseven, clarification of interaction mechanism of arbidol with covid-19 and investigation of the inhibition activity analogues against covid-19, Bratislava Medical Journal 121 (2020) 705-711.
• M.A. Gedikli, B. Tüzün, A. Aktaş, K. Sayin, H. Ataseven, do clarithromycin, azithromycin and their analogues effective in the treatment of COVID-19? Bratislava Medical Journal, 122 (2021).
• P. Taslimi, Y. Erden, S. Mamedov, L. Zeynalova, N. Ladokhina, R. Tas, B. Tüzün, A. Sujayev, N. Sadeghian, S.H. Alwasel, I. Gulcin, The Biological Activities, Molecular Docking Studies, and Anticancer Effects of 1-Arylsuphonylpyrazole Derivatives. Jounal of Biomolecular Structure and Dynamics, (2020) 1-20.
• Y. Demir, P. Taslimi, Ü.M. Koçyiğit, M. Akkuş, M.S. Özaslan, H.E. Duran, Y. Budak, B. Tüzün, M.B. Gürdere, M. Ceylan, S. Taysi, I. Gülçin, Ş. Beydemir, Determination of the inhibition profiles of pyrazolyl–thiazole derivatives against aldose reductase and α‐glycosidase and molecular docking studies. Archiv der Pharmazie, (2020) e2000118.
• S. Kaya, S. Erkan, D. Karakaş, Computational investigation of molecular structures, spectroscopic properties and antitumor-antibacterial activities of some Schiff bases. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 244 (2020) 118829.
• E. Güzel, Ü.M. Koçyiğit, P. Taslimi, İ. Gülçin, S. Erkan, M. Nebioğlu, ... & İ. Şişman, Phthalocyanine complexes with (4-isopropylbenzyl) oxy substituents: preparation and evaluation of anti-carbonic anhydrase, anticholinesterase enzymes and molecular docking studies. Journal of Biomolecular Structure and Dynamics, (2020) 1-9.
• S. Ökten, A. Aydın, Ü.M. Koçyiğit, O. Çakmak, S. Erkan, C.A. Andac, ... İ. Gülçin, Quinoline‐based promising anticancer and antibacterial agents, and some metabolic enzyme inhibitors. Archiv der Pharmazie, 353(9) (2020) 2000086.