Skip to main content

Computational Methods for Developing Novel Antiaging Interventions

  • Chapter
  • First Online:
Molecular Basis and Emerging Strategies for Anti-aging Interventions

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Bock C, Thomas L (2008) Computational epigenetics. Bioinformatics 24(1):1–10

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • Brazhnik P, de la Fuente A, Mendes P (2002) Gene networks: how to put the function in genomics. Trends Biotechnol 20(11):467–472

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Cho Y, Richard K (2017) Thermodynamic and electrostatic analysis of Flavonol and tocopherol analogues in anti-aging products. Bull Am Phys Soc 62

    Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Christensen K, Doblhammer G, Rau R, Vaupel JW (2009) Ageing populations: the challenges ahead. Lancet 374(9696):1196–1208

    Article  Google Scholar 

  • Comfort A (1964) Ageing. The biology of senescence. Holt, Rinehart and Winston, New York

    Google Scholar 

  • De Magalhães JP, Toussaint O (2004) How bioinformatics can help reverse engineer human aging. Ageing Res Rev 3(2):125–141

    Article  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Dresser GK, Spence JD, Bailey DG (2000) Pharmacokinetic-pharmacodynamic consequences and clinical relevance of cytochrome P450 3A4 inhibition. Clin Pharmacokinet 38(1):41–57

    Article  CAS  Google Scholar 

  • Fontana L, Partridge L, Longo VD (2010) Extending healthy life span-from yeast to humans. Science 328:321–326

    Article  CAS  Google Scholar 

  • Fraga MF, Esteller M (2007) Epigenetics and aging: the targets and the marks. Trends Genet 23:413–418

    Article  CAS  Google Scholar 

  • Frazer KA, Lior P, Alexander P, Edward MR, Inna D (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Res 32:W273–W279

    Article  CAS  Google Scholar 

  • 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

    Google Scholar 

  • Gelino S, Hansen M (2012) Autophagy-an emerging anti-aging mechanism. J Clin Exp Pathol. Suppl 4: 006

    Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Google Scholar 

  • Kinirons MT, O’Mahony MS (2004) Drug metabolism and ageing. Br J Clin Pharmacol 57(5):540–544

    Article  CAS  Google Scholar 

  • Kirkwood TBL (2005) Understanding the odd science of aging. Cell 120:437–447

    Article  CAS  Google Scholar 

  • Koopmans T (1933) Ordering of wave functions and eigenenergies to the individual electrons of an atom. Physica 1(1):104–113

    CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • López-Otín C et al (2013) The hallmarks of aging. Cell 153:1194–1217

    Article  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Marino G, Federico P, Frank M, Guido K (2014) Caloric restriction mimetics: natural/physiological pharmacological autophagy inducers. Autophagy 10(11):1879–1882

    Article  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Pandey KB, Rizvi SI (2009) Plant polyphenols as dietary antioxidants in human health and disease. Oxidative Med Cell Longev 2(5):270–278

    Article  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • 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

    PubMed  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • Vincenzo C, Lara E, Kahn A, Fraga MF (2009) Ageing Res Rev 8(4):268–276

    Article  Google Scholar 

  • Visualizer DS (2005) Accelrys Software Inc. Discovery Studio Visualizer, 2

    Google Scholar 

  • Zerrouki M, Farid B (2018) DFT study of the mechanisms of nonenzymatic DNA repair by phytophenolic antioxidants. J Mol Model 24(4):78

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

Download references

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.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Snehasis Chowdhuri .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

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

Download citation

Publish with us

Policies and ethics