Abstract
Advances in computational methodologies have ushered in innovations in visualization, calculations, and prediction of factors relating to aging processes and concomitant diseases with novel strategies like comparative genomics, protein interactive networks, and systems biology. Molecular level investigations of antiaging agents like phytochemicals such as curcumin, resveratrol, and quercetin have been carried out by electronic structure calculations by density functional theory and molecular docking studies to cytochrome P450 3A4 protein. It is found that both hydrogen bonding and hydrophobic interactions play a crucial role in the interaction between these phytochemicals and CY3A4 protein, which may provide important insights into modulations of drug metabolism in aging populations.
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References
Alvers AL, Fishwick LK, Wood MS, Hu D, Chung HS, Dunn WA Jr, Aris JP (2009) Autophagy and amino acid homeostasis are required for chronological longevity in Saccharomyces cerevisiae. Aging Cell 8(4):353–369
Benayoun, BA, Pollina EA, and Brunet A (2015) Epigenetic regulation of ageing: linking environmental inputs to genomic stability. Nat Rev Mol Cell Biol 16(10):593
Bissoyi A, Pattanayak SK, Bit A, Patel A, Singh AK, Behera SS, Satpathy D (2018) Alphavirus nonstructural proteases and their inhibitors. In: Viral proteases and their inhibitors, pp 77–104
Bissoyi A, Singh AK, Pattanayak SK, Bit A, Sinha SK, Patel A et al (2017) Understanding the molecular mechanism of improved proliferation and osteogenic potential of human mesenchymal stem cells grown on a polyelectrolyte complex derived from non-mulberry silk fibroin and chitosan. Biomed Mater 13(1):015011
Bock C, Konstantin H, Joachim B, Thomas L (2009) EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi) genomic data. Genome Biol 10(2):R14
Bock C, Thomas L (2008) Computational epigenetics. Bioinformatics 24(1):1–10
Boyd D, Crawford K (2012) Critical questions for big data: provocations for a cultural, technological, and scholarly phenomenon. Inf Commun Soc 15(5):662–679
Brazhnik P, de la Fuente A, Mendes P (2002) Gene networks: how to put the function in genomics. Trends Biotechnol 20(11):467–472
Cevenini E, Bellavista E, Tieri P, Castellani G, Francesco L, Francesconi M, Mishto M (2010) Systems biology and longevity: an emerging approach to identify innovative anti-aging targets and strategies. Curr Pharm Des 16(7):802–813
Chand A, Chettiyankandy P, Pattanayak SK, Chowdhuri S (2017) Effects of trimethylamine-N-oxide (TMAO) on aqueous N-methylacetamide solution: a comparison of different force fields of TMAO. J Mol Liq 225:926–935
Cho Y, Richard K (2017) Thermodynamic and electrostatic analysis of Flavonol and tocopherol analogues in anti-aging products. Bull Am Phys Soc 62
Chowdhuri S, Pattanayak SK (2013) Pressure effects on the dynamics of ions and solvent molecules in liquid methanol under ambient and cold conditions: importance of solvent’s H-bonding network. J Mol Liq 180:172–178
Christensen K, Doblhammer G, Rau R, Vaupel JW (2009) Ageing populations: the challenges ahead. Lancet 374(9696):1196–1208
Comfort A (1964) Ageing. The biology of senescence. Holt, Rinehart and Winston, New York
De Magalhães JP, Toussaint O (2004) How bioinformatics can help reverse engineer human aging. Ageing Res Rev 3(2):125–141
Deng R, Xu C, Chen X, Chen P, Wang Y, Zhou X, Bi H (2014) Resveratrol suppresses the inducible expression of CYP3A4 through the pregnane X receptor. J Pharmacol Sci 126(2):146–154
Dresser GK, Spence JD, Bailey DG (2000) Pharmacokinetic-pharmacodynamic consequences and clinical relevance of cytochrome P450 3A4 inhibition. Clin Pharmacokinet 38(1):41–57
Fontana L, Partridge L, Longo VD (2010) Extending healthy life span-from yeast to humans. Science 328:321–326
Fraga MF, Esteller M (2007) Epigenetics and aging: the targets and the marks. Trends Genet 23:413–418
Frazer KA, Lior P, Alexander P, Edward MR, Inna D (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Res 32:W273–W279
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA (2013) Gaussian 09, Revision E.01. Gaussian Inc Wallingford CT
Gelino S, Hansen M (2012) Autophagy-an emerging anti-aging mechanism. J Clin Exp Pathol. Suppl 4: 006
George J, Karen B, Geoffrey CF (1995) Age but not gender selectively affects expression of individual cytochrome P450 proteins in human liver. Biochem Pharmacol 50(5):727–730
Goñi J, Francisco JE, Nieves VM, Jorge S, Sergio A, Ion A, Villoslada P (2008) A computational analysis of protein-protein interaction networks in neurodegenerative diseases. BMC Syst Biol 2(1):52
Hoffman TE, Katherine JB, Lyle W, William HH (2017) A multimethod computational simulation approach for investigating mitochondrial dynamics and dysfunction in degenerative aging. Aging Cell 16(6):1244–1255
Hsu S, Shih-Ming H, Ann C, Chiao-Yin S, Shih-Hua L, Jin-Shuen C, Shu-Ting L, Yu-Juei H (2014) Resveratrol increases anti-aging klotho gene expression via the activating transcription factor 3/c-Jun complex-mediated signaling pathway. Int J Biochem Cell Biol 53:361–371
Kaladhar DSVGK (2011) Computational studies of Sirtuins in the treatment of type II diabetes mellitus. Asian J Pharm Res Health Care 3(2):38–42
Karabacak M, Sinha L, Prasad O, Cinar Z, Cinar M (2012) The spectroscopic (FT-Raman, FT-IR, UV and NMR), molecular electrostatic potential, polarizability and hyperpolarizability, NBO and HOMO–LUMO analysis of monomeric and dimeric structures of 4-chloro-3, 5-dinitrobenzoic acid. Spectrochim Acta A Mol Biomol Spectrosc 93:33–46
Khan M, Kalim A, Salman A, Arif JM (2017) Development of in silico protocols to predict structural insights into the metabolic activation pathways of xenobiotics. Interdiscip Sci Comput Life Sci:1–17
Kinirons MT, O’Mahony MS (2004) Drug metabolism and ageing. Br J Clin Pharmacol 57(5):540–544
Kirkwood TBL (2005) Understanding the odd science of aging. Cell 120:437–447
Koopmans T (1933) Ordering of wave functions and eigenenergies to the individual electrons of an atom. Physica 1(1):104–113
Laye MJ, ViLinh T, Dean PJ, Pankaj K, Daniel ELP (2015) The effects of age and dietary restriction on the tissue-specific metabolome of Drosophila. Aging Cell 14(5):797–808
López-OtÃn C et al (2013) The hallmarks of aging. Cell 153:1194–1217
Lu L, Shufang Z, Haijun Z, Shaowei Z (2013) Improvement of antioxidative activity of resveratrol by elongating conjugated chain: a DFT theoretical study. Comput Theor Chem 1019:39–47
Marino G, Federico P, Frank M, Guido K (2014) Caloric restriction mimetics: natural/physiological pharmacological autophagy inducers. Autophagy 10(11):1879–1882
Miki Y, Suzuki T, Tazawa C, Blumberg B, Sasano H (2005) Steroid and xenobiotic receptor (SXR), cytochrome P450 3A4 and multidrug resistance gene 1 in human adult and fetal tissues. Mol Cell Endocrinol 231(1):75–85
Miller JA, Michael CO, Daniel HG (2008) A systems level analysis of transcriptional changes in Alzheimer’s disease and normal aging. J Neurosci 28(6):1410–1420
Misaka S, Keisuke K, Satomi O, José PW, Monica G, Sekihiro T, Toshiyuki K, Junko K, Hiroshi W, Shizuo Y (2013) Effects of green tea catechins on cytochrome P450 2B6, 2C8, 2C19, 2D6 and 3A activities in human liver and intestinal microsomes. Drug Metab Pharmacokinet 28(3):244–249
Pandey KB, Rizvi SI (2009) Plant polyphenols as dietary antioxidants in human health and disease. Oxidative Med Cell Longev 2(5):270–278
Pattanayak SK, Chowdhuri S (2013a) Effects of concentrated NaCl and KCl solutions on the behaviour of aqueous peptide bond environment: single-particle dynamics and H-bond structural relaxation. Mol Phys 111(21):3297–3310
Pattanayak SK, Chowdhuri S (2013b) Pressure and temperature dependence on the hydrogen bonding and dynamics of ammonium ion in liquid water: a molecular dynamics simulations study. J Mol Liq 186:98–105
Pattanayak SK, Chowdhuri S (2014) Effects of methanol on the hydrogen bonding structure and dynamics in aqueous N-methylacetamide solution. J Mol Liq 194:141–148
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C et al (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464(7285):59
Schaefer MH, Jean-Fred F, Arunachalam V, Pablo P, Erich EW, Miguel AA (2012) HIPPIE: integrating protein interaction networks with experiment based quality scores. PLoS One 7(2):e31826
Shi R, Wang Y, Zhu X, Lu X (2012) Exploration of the binding of curcumin analogues to human P450 2C9 based on docking and molecular dynamics simulation. J Mol Model 18(6):2599–2611
Song X, Di Giovanni V, He N, Wang K, Ingram A, Rosenblum ND, Pei Y (2009) Systems biology of autosomal dominant polycystic kidney disease (ADPKD): computational identification of gene expression pathways and integrated regulatory networks. Hum Mol Genet 18(13):2328–2343
Suresh Rattan IS, Kryzch V, Schnebert S, Perrier E, Nizard C (2013) Hormesis-based anti-aging products: a case study of a novel cosmetic. Dose-Response 11:99–108
Tanak H, Toy M (2013) Molecular structure, vibrational spectra, NLO and MEP analysis of bis [2-hydroxy-кO-N-(2-pyridyl)-1-naphthaldiminato-кN] zinc (II). Spectrochim Acta A Mol Biomol Spectrosc 115:145–153
Vincenzo C, Lara E, Kahn A, Fraga MF (2009) Ageing Res Rev 8(4):268–276
Visualizer DS (2005) Accelrys Software Inc. Discovery Studio Visualizer, 2
Zerrouki M, Farid B (2018) DFT study of the mechanisms of nonenzymatic DNA repair by phytophenolic antioxidants. J Mol Model 24(4):78
Zahn JM, Rebecca S, Hannes V, Emily C, Krystyna M, Ralph R, Ronald WD, Kevin GB, Art BO, Stuart KK (2006) Transcriptional profiling of aging in human muscle reveals a common aging signature. PLoS Genet 2(7):e115
Acknowledgments
A. Chand is thankful to the Council of Scientific and Industrial Research (CSIR) for the Research Fellowship. A. Bissoyi is thankful to the Department of Science and Technology (DST) Government of India for the financial support through grant number YSS/2015/000618. M. Moharana would like to express his gratitude to the Department of Chemistry, Utkal University. S. N Sahu and S. K Pradhan extend sincere thanks to the Department of Bioinformatics, OUAT. S. K Pattanayak and S. P Mahapatra are obliged to the Department of Chemistry, National Institute of Technology Raipur. A. K. Singh is grateful to the Department of Biochemistry of Allahabad University.
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Chand, A. et al. (2018). Computational Methods for Developing Novel Antiaging Interventions. In: Rizvi, S., Çakatay, U. (eds) Molecular Basis and Emerging Strategies for Anti-aging Interventions. Springer, Singapore. https://doi.org/10.1007/978-981-13-1699-9_12
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DOI: https://doi.org/10.1007/978-981-13-1699-9_12
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