110
Views
1
CrossRef citations to date
0
Altmetric
Articles

From a computational point of view: deciphering the molecular synergism between oxidative stress-induced lipid peroxidation products and metabolic dysfunctionality of human liver mitochondrial aldehyde dehydrogenase-2

, , &
Pages 652-665 | Received 04 Oct 2018, Accepted 28 Jan 2019, Published online: 22 Feb 2019

References

  • Harada S, Agarwal DP, Goedde HW, et al. Possible protective role against alcoholism for aldehyde dehydrogenase isozyme deficiency in Japan. The Lancet. 1982;320:827.
  • Yoval-Sánchez B, Rodríguez-Zavala JS. Differences in susceptibility to inactivation of human aldehyde dehydrogenases by lipid peroxidation Byproducts. Chem Res Toxicol. 2012;25(3):722–729.
  • O’Brien P, Siraki A, Shangari N. Aldehyde sources, metabolism, molecular toxicity mechanisms, and possible effects on human health. Crit Rev Toxicol.. 2005;35:609–662.
  • Doorn JA, Hurley TD, Petersen DR. Inhibition of human mitochondrial aldehyde dehydrogenase by 4-hydroxynon-2-Enal and 4-Oxonon-2-Enal. Chem Res Toxicol.. 2006;19:102–110.
  • Adeniji EA, Olotu FA, Soliman MES. Alcohol metabolic inefficiency: structural characterization of polymorphism-induced ALDH2 dysfunctionality and allosteric site identification for design of potential wildtype reactivators. Protein J. 2018;37(3):216–222.
  • Weber D, Milkovic L, Bennett SJ, et al. Measurement of HNE-protein adducts in human plasma and serum by ELISA—comparison of two primary antibodies. Redox Biol. 2013;1(1):226–233.
  • Seitz HK, Stickel F. Molecular mechanisms of alcohol-mediated carcinogenesis. Nat Rev Cancer. 2007;7:599–612.
  • Oberley TD, Toyokuni S, Szweda LI. Localization of hydroxynonenal protein adducts in normal human kidney and selected human kidney cancers. Free Radic Biol Med. 1999;27(5–6):695–703.
  • Zanetti D, Poli G, Vizio B, et al. 4-Hydroxynonenal and transforming growth factor-Β1 expression in colon cancer. Mol Aspects Med. 2003;24:273–280.
  • Skrzydlewska E, Sulkowski S, Koda M, et al. Lipid peroxidation and antioxidant status in colorectal cancer. World J Gastroenterol. 2005;11(3):403–406.
  • Marquez-Quiñones A, Čipak A, Žarkovic K, et al. HNE-protein adducts formation in different pre-carcinogenic stages of hepatitis in LEC rats. Free Radic Res. 2010;44(2):119–127.
  • Chang B, Nishikawa M, Nishiguchi S, et al. L-carnitine inhibits hepatocarcinogenesis via protection of mitochondria. Int J Cancer. 2005;113(5):719–729.
  • Zhong H, Yin H. Role of lipid peroxidation derived 4-hydroxynonenal (4-HNE) in cancer: focusing on mitochondria. Redox Biol. 2015;4:193–199.
  • Gupta V, Carroll KS. Profiling the reactivity of cyclic C-nucleophiles towards electrophilic sulfur in cysteine sulfenic acid. Chem Sci. 2016;7(1):400–415.
  • Guéraud F, Atalay M, Bresgen N, et al. Chemistry and biochemistry of lipid peroxidation products. Free Radic Res. 2010;44:1098–1124.
  • Liu W, Porter NA, Schneider C, et al. Formation of 4-hydroxynonenal from cardiolipin oxidation: intramolecular peroxyl radical addition and decomposition. Free Radic Biol Med. 2011;50(1):166–178.
  • Doorn JA, Petersen DR. Covalent modification of amino acid nucleophiles by the lipid peroxidation products 4-hydroxy-2-nonenal and 4-Oxo-2-nonenal. Chem Res Toxicol. 2002;15(11):1445–1450.
  • Pawlosky RJ, Salem N. Perspectives on alcohol consumption: liver polyunsaturated fatty acids and essential fatty acid metabolism. Alcohol. 2004;34:27–33.
  • Macario AJL, De Macario EC. The pathology of cellular anti-stress mechanisms: a new frontier. Stress. 2004;7:243–249.
  • Jayasekara H, MacInnis RJ, Room R, et al. Long-term alcohol consumption and breast, upper aero-digestive tract and colorectal cancer Risk: a systematic review and meta-analysis. Alcohol Alcohol. 2016;51(3):315–330.
  • Hwa Lee S, Blair IA. Characterization of 4-oxo-2-nonenal as a novel product of lipid peroxidation. Chem Res Toxicol. 2000;13(8):698–702.
  • Barrera G, Pizzimenti S, Ciamporcero ES, et al. Role of 4-hydroxynonenal-protein adducts in human diseases. Antioxid Redox Signal. 2014;22(18):150127063122000–150127063122000.
  • González-Segura L, Ho KK, Perez-Miller S, et al. Catalytic contribution of threonine 244 in human ALDH2. Chem Biol Interact.. 2013;202:32–40.
  • Perez-Miller SJ, Hurley TD. Coenzyme isomerization is integral to catalysis in aldehyde dehydrogenase. Biochemistry. 2003;42(23):7100–7109.
  • Eswar N, Webb B, Marti-Renom MA, et al. Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci. 2007;50(1):2.9.1–2.9.31.
  • Shen MY, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Sci. 2006;15:2507–2524.
  • Kim S, Thiessen PA, Bolton EE, et al. Pubchem substance and compound databases. Nucleic Acids Res. 2016;44(D1):D1202–D1213.
  • Hanwell MD, Curtis DE, Lonie DC, et al. Avogadro: an advanced semantic chemical editor, visualization, and analysis platform. J Cheminformatics. 2012;4(1):17.
  • 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.
  • Pettersen EF, Goddard TD, Huang CC, et al. UCSF chimera: a visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605–1612.
  • Sastry G, Adzhigirey M, Day T, et al. Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aid Mol Des. 2013;27(3):221–234.
  • Olotu FA, Soliman MES. From mutational inactivation to aberrant gain-of-function: unraveling the structural basis of mutant P53 oncogenic transition. J Cell Biochem. 2018;119(3):2646–2652.
  • Khan S, Bjij I, Betz RM, et al. Reversible versus irreversible inhibition modes of ERK2: a comparative analysis for ERK2 protein kinase in cancer therapy. Future Med Chem. 2018;10(9):1003–1015.
  • Case DA, Cheatham TE, Darden T, et al. The amber biomolecular simulation programs. J Comput Chem. 2005;26:1668–1688.
  • Wang J, Wolf RM, Caldwell JW, et al. Development and testing of a general amber force field. J Comput Chem. 2004;25(9):1157–1174.
  • Maier JA, Martinez C, Kasavajhala K, et al. Ff14SB: improving the accuracy of protein side chain and backbone parameters from Ff99SB. J Chem Theory Comput. 2015;11(8):3696–3713.
  • Kumalo HM, Bhakat S, Soliman MES. Theory and applications of covalent docking in drug discovery: merits and pitfalls. Molecules. 2015;20:1984–2000.
  • Parameterization with Dabble — Dabble 2.7.3 documentation [cited 2018 Mar 15]. http://dabble.robinbetz.com/parameter_api.html.
  • Seifert E. Originpro 9.1: scientific data analysis and graphing software—software review. J Chem Inf Model. 2014;54(5):1552.
  • Genheden S, Ryde U. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin Drug Discov. 2015;10(5):449–461.
  • Hou T, Wang J, Li Y, et al. Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. J Chem Inf Comput Sci. 2011;51(1):69–82.
  • David CC, Jacobs DJ. Principal component analysis: a method for determining the essential dynamics of proteins. Methods Mol Biol. 2014;1084:193–226.
  • Roe DR, Cheatham TE, III. PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J Chem Theory Com. 2013;9(7):3084–3095.
  • Arnold GE, Ornstein RL. Molecular dynamics study of time-correlated protein domain motions and molecular flexibility: cytochrome P450BM-3. Biophys J. 1997;73(3):1147–1159.
  • Brooks PJ, Theruvathu JA. DNA adducts from acetaldehyde: implications for alcohol-related carcinogenesis. Alcohol. 2005;35:187–193.
  • Bös F, Pleiss J. Multiple molecular dynamics simulations of TEM β-Lactamase: dynamics and water binding of the Ω-Loop. Biophys J. 2009;97(9):2550–2558.
  • Larson HN, Weiner H, Hurley TD. Disruption of the coenzyme binding site and dimer Interface revealed in the crystal structure of mitochondrial aldehyde dehydrogenase “asian” Variant. J Biol Chem. 2005;280(34):30550–30556.
  • Malleshappa Gowder S, Chatterjee J, Chaudhuri T, et al. Prediction and analysis of surface hydrophobic residues in tertiary structure of proteins. Sci World J. 2014;2014:971258.
  • Hurley TD, Perez-Miller S, Breen H. Order and disorder in mitochondrial aldehyde dehydrogenase. Chem Biol Interact.. 2001;130–132:3–14.
  • Lobanov MI, Bogatyreva NS, Galzitskaia OV. Radius of gyration as an indicator of protein structure compactness. Mol Biol. 2008;42(4):623–628.
  • Huynh T, Smith JC, Sanson A. Protein unfolding transitions in an intrinsically unstable annexin domain: molecular dynamics simulation and comparison with nuclear magnetic resonance data. Biophys J. 2002;83(2):681–698.
  • Hou T, Wang J, Li Y, et al. Assessing the performance of the MM/PBSA and MM/GBSA Methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. J Chem Inf Model. 2011;51(1):69–82.
  • Chen C-H, Ferreira JCB, Gross ER, et al. Targeting aldehyde dehydrogenase 2: new therapeutic opportunities. Physiol Rev. 2014;94(1):1–34.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.