An experimental and theoretical study of ROS scavenging by organosulfur compounds from garlic: In silico analysis of metabolic pathways and interactions on CYP2E1

References

• Manda G, Nechifor MT, Neagu T. Reactive oxygen species: cancer and anti-cancer therapies. Curr Chem Biol. 2009;3(1):22–46.
   Google Scholar
• Schieber M, Chandel NS. ROS function in redox signaling and oxidative stress. Curr Biol. 2014;24(10):453–462.
   PubMed Web of Science ®Google Scholar
• Zamora J. Antioxidantes: micronutrientes en lucha por la salud. Rev Chil Nutr. 2007;34(1):17–26.
   Google Scholar
• Rahman K. Garlic and aging: new insights into an old remedy. Ageing Res Rev. 2003;2(1):39–56.
   PubMedGoogle Scholar
• Moyer S. Garlic in health, history and world cuisine. St. Petersburg: Sun Coast Press; 1996.
   Google Scholar
• Randle W, Lancaster J. Sulphur compounds in Alliums in relation to flavour quality. In: Rabbinowitch HD, Currah L, editors. Allium crop science: recent advances. Wallingford: CABI Publishing; 2002. p. 329–357.
   Google Scholar
• Scherz H. Food composition and nutrition tables. 5th ed. Stuttgart: CRC Press; 1994.
   Google Scholar
• Ambati S. Garlic derivatives: role in obesity and related disorders. OA Biotechnol. 2013;2(1):1–5.
   Google Scholar
• Müller A, Eller J, Albrecht F, et al. Allicin induces thiol stress in bacteria through S-allylmercapto modification of protein cysteines. J Biol Chem. 2016;291(22):11477–11490.
   PubMed Web of Science ®Google Scholar
• Kaschula CH, Hunter R, Hassan HT, et al. Anti-proliferative activity of synthetic ajoene analogues on cancer cell-lines. Anti-Cancer Agents Med Chem. 2011;11(3):260–266.
   PubMedGoogle Scholar
• Shang A, Cao SY, Xu XY, et al. Bioactive compounds and biological functions of garlic (Allium sativum L.). Foods. 2019;8(7):1–31.
   Google Scholar
• Jinxin X, Benjian L, Ri-Yuan T. Functional application of sulfur-containing spice compounds. J Agric. Food Chem. 2020;68(45):12505–12526.
   PubMedGoogle Scholar
• Wang X, Liu R, Yang Y, et al. Isolation, purification and identification of antioxidants in an aqueous aged garlic extract. Food Chem. 2015;187:37–43.
   PubMed Web of Science ®Google Scholar
• Li FM, Li T, Li W, et al. Changes in antioxidant capacity, levels of soluble sugar, total polyphenol, organosulfur compound and constituents in garlic clove during storage. Ind Crop Prod. 2015;69:137–142.
   Google Scholar
• Dehghani S, Alipoor E, Salimzadeh A, et al. The effect of a garlic supplement on the pro-inflammatory adipocytokines, resistin and tumor necrosis factor-alpha, and on pain severity, in overweight or obese women with knee osteoarthritis. Phytomedicine. 2018;48:70–75.
   PubMedGoogle Scholar
• Lawson LD, Hunsaker SM. Allicin bioavailability and bioequivalence from garlic supplements and garlic foods. Nutrients. 2018;10(7):1–49.
   Google Scholar
• Brady JF, Ishizaki H, Fukuto JM, et al. Inhibition of Cytochrome P-450 2E1 by Diallyl sulfide and its metabolites. Chem Res Toxicol. 1991;4(6):642–647.
   PubMed Web of Science ®Google Scholar
• Weltman M, Farrell G, Hall P, et al. Hepatic cytochrome P450 2E1 is increased in patients with nonalcoholic steatohepatitis. Hepatology. 1998;27(1):128–133.
   PubMed Web of Science ®Google Scholar
• Kim YC, Lee AK, Lee JH, et al. Pharmacokinetics of theophylline in diabetes mellitus rats: induction of CYP1A2 and CYP2E1 on 1,3-dimethyluric acid formation. Eur J Pharm Sci. 2005;26(1):114–123.
   PubMed Web of Science ®Google Scholar
• Kaut O, Schmitt I, Wullner U. Genome-scale methylation analysis of Parkinson's disease patients brains reveals DNA hypomethylation and increased mRNA expression of cytochrome P450 2E1. Neurogenetics. 2012;13(1):87–91.
   PubMed Web of Science ®Google Scholar
• Mari M, Wu D, Nieto N, et al. CYP2E1-dependent toxicity and up-regulation of antioxidant genes. J Biomed Sci. 2001;8(1):52–58.
   PubMedGoogle Scholar
• Lu Y, Cederbaum AI. Cisplatin-induced hepatotoxicity is enhanced by elevated expression of cytochrome P450 2E1. Toxicol Sci. 2006;89(2):515–523.
   PubMed Web of Science ®Google Scholar
• Díaz MG, Vega-Hissi EG, Andrada MF, et al. Scavenging of hydrogen peroxide by allyl methyl sulfide and Diallyl sulfide, two garlic active compounds: a theoretical study. ChemistrySelect. 2020;5(11):3234–3242.
   Google Scholar
• Díaz MG, Andrada MF, Vega-Hissi EG, et al. Density functional theory study of the oxidation reaction in the gas and aqueous phase of allyl methyl disulfide with hydroxyl radical. Struct Chem. 2019;30(1):237–245.
   Google Scholar
• Vega-Hissi EG, Andrada MF, Díaz MG, et al. Computational study of the hydrogen peroxide scavenging mechanism of allyl methyl disulfide, an antioxidant compound from garlic. Mol Diversity. 2019;23(4):985–999.
   PubMedGoogle Scholar
• Heelis PF. The photophysical and photochemical properties of flavins (isoalloxazines). Chem Soc Rev. 1982;11(1):15–39.
   Google Scholar
• Muller F. Chemistry and biochemistry of flavoenzymes. Boca Raton (FL): CRC Press; 1991.
   Google Scholar
• Krishna CM, Uppuluri S, Riesz P, et al. A study of the photodynamic efficiencies of some eye lens constituents. Photochem Photobiol. 1991;54(1):51–58.
   PubMed Web of Science ®Google Scholar
• Wilkinson F, Helman WP, Ross AB. Quantum yields for the photosensitized formation of the lowest electronically excited singlet state of molecular oxygen in solution. J Phys Chem Ref Data. 1993;22(1):113–262.
   Google Scholar
• Becke AD. Density-functional thermochemistry. III. The role of exact exchange. J. Chem Phys. 1993;98(7):5648–5652.
   Web of Science ®Google Scholar
• Raghavachari K, Binkley JS, Seeger R, et al. Self consistent molecular orbital methods. XX. basis set for correlated wave-functions. J Chem Phys. 1980;72(1):650–654.
   Google Scholar
• Davidson ER, Chakravorty S. A test of the Hirshfeld defnition of atomic charges and moments. Theor Chim Acta. 1992;83:319–330.
   Google Scholar
• Rousseau B, Peeters A, Van Alsenoy C. Systematic study of the parameters determining stockholder charges. Chem Phys Lett. 2000;324:189–194.
   Web of Science ®Google Scholar
• Oláh J, Van Alsenoy C, Sannigrahi AB. Condensed Fukui functions derived from stockholder charges: assessment of their performance as local reactivity descriptors. J Phys Chem A. 2002;106(15):3885–3890.
   Web of Science ®Google Scholar
• McIver JW, Komornicki A. Structure of transition states in organic reactions. General theory and an application to the cyclobutene-butadiene isomerization using a semiempirical molecular orbital method. J Am Chem Soc. 1972;94(8):2625–2633.
   Google Scholar
• Zhao Y, Truhlar DG. The M06 suite of density functionals for main group thermochemistry,: thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theor Chem Acc. 2008;120:215–241.
   Web of Science ®Google Scholar
• Deng L, Ziegler T. The determination of intrinsic reaction coordinates by density functional theory. Int J of Quantum Chem. 1994;52(4):731–765.
   Google Scholar
• Peng C, Ayala PY, Schlegel HB, et al. Using redundant internal coordinates to optimize equilibrium geometries and transition states. J Comp Chem. 1996;17(1):49–56.
   Web of Science ®Google Scholar
• Truhlar DG, Garrett BC. Variational transition-state theory. Acc Chem Res. 1980;13(12):440–448.
   Web of Science ®Google Scholar
• Marenich AV, Cramer CJ, Truhlar DG. Universal solvation model based on solute electron density and on a continuum Model of the solvent defined by the bulk dielectric constant and atomic surface tensions. J Phys Chem B. 2009;113(18):6378–6396.
   PubMed Web of Science ®Google Scholar
• Tian P. Computational protein design: from single domain soluble proteins to membraneproteins. Chem Soc Rev. 2010;39(6):2071–2082.
   PubMedGoogle Scholar
• Coster HGL. The physics of cell membranes. J Biol Phys. 2003;29(4):363–399.
   PubMedGoogle Scholar
• Panahi A, Feig M. Dynamic heterogeneous dielectric generalized born (DHDGB): an implicit membrane Model with a dynamically varying bilayer thickness. J Chem Theory Comput. 2013;9(3):1709–1719.
   PubMedGoogle Scholar
• Frisch MJ, Trucks GW, Schlegel HB, et al. Gaussian 09. Revision A.02. Gaussian. Inc.Wallingford CT. 2016.
   Google Scholar
• Canneaux S, Bohr F, Henon E. KiSThelP: a program to predict thermodynamic properties and rate constants from quantum chemistry results. J Comput Chem. 2014;35(1):82–93.
   PubMed Web of Science ®Google Scholar
• Filimonov DA, Lagunin AA, Gloriozova TA, et al. Prediction of the biological activity spectra of organic compounds using the pass online Web resource. Chem Heterocycl Compd. 2014;50(3):444–457.
   Web of Science ®Google Scholar
• de Bruyn-Kops C, Šícho M, Mazzolari A, et al. GLORYx: prediction of the metabolites resulting from phase 1 and phase 2 biotransformations of xenobiotics. Chem Res Toxicol. 2020;34(29):286–299.
   PubMedGoogle Scholar
• Stork C, Embruch G, Šícho M, et al. NERDD: a web portal providing access to in silico tools for drug discovery. Bioinformatics. 2020;36(4):1291–1292.
   PubMed Web of Science ®Google Scholar
• Zaretzki J, Matlock M, Swamidass SJ. Xenosite: accurately predicting Cyp-mediated sites of metabolism with neural networks. J Chem Inf Model. 2013;53(12):3373–3383.
   PubMed Web of Science ®Google Scholar
• Le-Dang N, Hughes TB, Matlock MK, et al. The metabolic rainbow: deep learning phase I metabolism in five colors. J Chem Inf Model. 2020;60(3):1146–1164.
   PubMedGoogle Scholar
• Dang NL, Hughes TB, Krishnamurthy V, et al. Simple model predicts UGT-mediated metabolism. Bioinformatics. 2016;32(20):3183–3189.
   PubMed Web of Science ®Google Scholar
• Rudik AV, Dmitriev AV, Lagunin AA, et al. Prediction of reacting atoms for the major biotransformation reactions of organic xenobiotics. J Cheminform. 2016;8(1):1–9.
   PubMedGoogle Scholar
• Trott O, Olson AJ. Autodock vina: improving the speed and accuracy of docking with a new scoring function: efficient optimization and multithreading. J Comput Chem. 2010;31(2):455–461.
   PubMed Web of Science ®Google Scholar
• Bernstein FC, Koetzle TF, Williams GJB, et al. The protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1997;112(3):535–542.
   Google Scholar
• Porubsky PR, Battaile KP, Scott EE. Human cytochrome P450 2E1 structures with fatty acid analogs reveal a previously unobserved binding mode. J Biol Chem. 2010;285(29):22282–22290.
   PubMedGoogle Scholar
• Montaña MP, Massad WA, Amat-Guerri F, et al. Scavenging of riboflavin-photogenerated oxidative species by uric acid, xanthine or hypoxanthine. A kinetic study. J Photochem Photobiol. 2008;193:103–109.
   Google Scholar
• Muñoz VA, Dimarco-Palencia FCD, Sancho MI, et al. Experimental and theoretical study of the stability of the complex fisetin-Cu(ii) and a comparative study of free ligand and complex interaction with molecular singlet oxygen. Photochem Photobiol. 2020;96(4):815–825.
   PubMedGoogle Scholar
• Dimarco-Palencia FCD, Muñoz VA, Posadaz AC, et al. Oregano essential oil interactions with photogenerated singlet molecular oxygen. Photochem Photobiol. 2020;96:1005–1013.
   PubMedGoogle Scholar
• Escalada JP, Pajares A, Gianotti J, et al. Dye-sensitized photodegradation of the fungicide carbendazim and related benzimidazoles. Chemosphere. 2006;65:237–244.
   PubMedGoogle Scholar
• Silva E, Herrera L, Edwards AM, et al. Enhancement of riboflavin-mediated photo-oxidation of glucose 6-phosphate dehydrogenase by uronic acid. Photochem Photobiol. 2005;81:206–211.
   PubMed Web of Science ®Google Scholar
• Rahman MA, Midde NM, Wu X, et al. Kinetic characterizations of diallyl sulfide analogs for their novel role as CYP2E1 enzyme inhibitors. Pharmacol Res Perspect. 2017;5(5):1–7.
   Google Scholar