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Structure-Property/Activity Modeling of Polyphenols
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Structure-Property/Activity Modeling of Polyphenols

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry, Theoretical and Computational Chemistry".

Deadline for manuscript submissions: closed (31 March 2009) | Viewed by 38030

Special Issue Editors

Prof. Dr. Nenad Trinajstic

E-Mail Website
Guest Editor
Department of Physical Chemistry, The Rugjer Boskovic Institute, Bijenicka 54, P.O.Box 102, HR-10002 Zagreb, Croatia
Interests: chemical graph theory; combinatorial chemistry; molecular modeling; computational chemistry; Mathematical chemistry
Dr. Dragan Amic

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Editorial Advisor
Faculty of Agriculture, The Josip Juraj Strossmayer University, P.O. Box 719, HR-31107 Osijek, Croatia
Dr. Bono Lučić

E-Mail Website
Editorial Advisor
NMR Centre, The Ruđer Bošković Institute, 10000 Zagreb, Croatia
Interests: chemoinformatics; structural bioinformatics; structure–activity modeling; QSAR; QSPR; molecular modeling; computational chemistry; molecular structural biophysics; development of model validation algorithms; variable selection algorithms; classification modeling; chance accuracy estimation; development of accuracy parameters; computational research in bioprospecting research; protein structure analysis and prediction
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Polyphenols (flavonoids, phenolic acids etc.) are abundant phytochemicals in human diet, and evidence for their role in the prevention of various diseases such as cardiovascular and neurodegenerative diseases and cancer is emerging. Mechanisms involved in the health-promoting activities of these compounds are far from clear.

The goal of this special issue is to present novel results about structure-activity relationships (SAR) and quantitative structure-activity (property) relationships (QSAR/QSPR) of polyphenols, which may help in resolving the mode of actions of these food phenolics. They may also help in the design of new and efficient polyphenols, which could be used as potential therapeutic agents.

With best regards,
Prof. Dr. Nenad Trinajstic
Guest Editor

Leading Papers and Reviews

  1. Amic, D.; Davidovic-Amic, D.; Beslo, D.; Rastija, V; Lucic, B.; Trinajstic, N. SAR and QSAR of the Antioxidant Activity of Flavonoids. Curr. Med. Chem. 2007, 14, 827-845.
  2. Reis, M.; Lobato, B.; Lameira, J.; Santos, A.S.; Alves, C.N. A theoretical study of phenolic compounds with antioxidant properties. Eur. J. Med. Chem. 2007, 42, 440-446.
  3. Khlebnikov, A.I.; Schepetkin, I.A.; Domina, N.G.; Kirpotina, L.N.; Quinn, M.T. Improved quantitative structure–activity relationship models to predict antioxidant activity of flavonoids in chemical, enzymatic, and cellular systems. Bioorg. Med. Chem. 2007, 15, 1749-1770.
  4. Cabrera, M.; Simoens, M.; Falchi, G.; Lavaggi, M.L.; Piro, O.E.; Castellano, E.E.; Vidal, A.; Azqueta, A.; Monge, A.; de Cerain, A.L.; Sagrera, G.; Seoane, G.; Cerecetto H.; Gonzalez, M. Synthetic chalcones, flavanones, and flavones as antitumoral agents: Biological evaluation and structure-activity relationships. Bioorg. Med. Chem. 2007, 15, 3356-3367.
  5. Cai, Y.Z.; Sun, M.; Xing, J.; Luo, Q.; Corke H. Structure-radical scavenging activity relationships of phenolic compounds from traditional Chinese medicinal plants. Life Sci. 2006, 78, 2872-2888.
  6. Raad, I.; Terreux, R.; Richomme, P.; Matera, E.L.; Dumontet, C.; Raynaud, J.; Guilet, D. Structure–activity relationship of natural and synthetic coumarins inhibiting the multidrug transporter P-glycoprotein. Bioorg. Med. Chem. 2006, 14, 6979-6987.
  7. Brand, W.; Schutte, M.E.; Williamson, G.; van Zanden, J.J.; Cnubben, N. H.P.; Groten, J.P.; van Bladeren P.J.; Rietjens I.M.C.M. Flavonoid-mediated inhibition of intestinal ABC transporters may affect the oral bioavailability of drugs, food-borne toxic compounds and bioactive ingredients. Biomed. Pharmacother. 2006, 60, 508-519.
  8. Lameira, J.; Medeiros, I.G.; Reis, M.; Santos, A.S.; Alves, C.N. Structure-activity relationships study of flavone compounds with anti-HIV-1 integrase activity: A density functional theory study. Bioorg. Med Chem. 2006, 14, 7105-7112.
  9. Prabhakar, Y.S.; Gupta, M.K.; Roy, N.; Venkateswarlu, Y. A high dimensional QSAR study on the aldose reductase inhibitory activity of some flavones: Topological descriptors in modeling the activity. J. Chem Inf. Model. 2006, 46, 86-92.
  10. Sadeghipour, M.; Terreux, R.; Phipps J. Flavonoids and tyrosine nitration: structure–activity relationship correlation with enthalpy of formation. Toxic. in Vitro 2005, 19, 155-165.
  11. van Zanden, J.J.; Wortelboer, H.M.; Bijlsma, S.; Punt, A.; Usta, M.; van Bladeren, P.J.; Rietjens, I.M.C.M.; Cnubben, N.H.P. Quantitative structure activity relationship studies on the flavonoid mediated inhibition of multidrug resistance proteins 1 and 2. Biochem. Pharmacol.2005, 69, 699-708.
  12. Zhang, H.Y. Structure-Activity Relationships and Rational Design Strategies for Radical-Scavenging Antioxidants. Curr. Comp.-Aided Drug Des. 2005, 1, 257-273.
  13. Zhang, S.; Yang, X.; Coburn, R.A.; Morris, M.E. Structure activity relationships and quantitative structure activity relationships for the flavonoid-mediated inhibition of breast cancer resistance protein. Biochem.Pharmacol. 2005, 70, 627-639.
  14. Fernández, M.; Caballero, J.; Helguera, A.M.; Castro, E.A.; González, M.P. Quantitative structure–activity relationship to predict differential inhibition of aldose reductase by flavonoid compounds. Bioorg. Med.Chem. 2005, 13, 3269-3277.
  15. Mukherjee, S.; Mukherjee, A.; Saha, A. QSAR modeling on binding affinity of diverse estrogenic flavonoids: electronic, topological and spatial functions in quantitative approximation. J. Mol. Struct. (Theochem) 2005, 715, 85-90.
  16. Rasulev, B.F.; Abdullaev, N.D.; Syrov, V.N.; Leszczynski, J.A Quantitative Structure-Activity Relationship (QSAR) Study of the Antioxidant Activity of Flavonoids. QSAR Comb. Sci. 2005, 24, 1056-1065.
  17. Nemeikaite-Ceniene, A.; Imbrasaite, A.; Sergediene, E.; Cenas, N. Quantitative structure-activity relationships in prooxidant cytotoxicity of polyphenols: Role of potential of phenoxyl radical/phenol redox couple. Arch. Biochem. Biophys. 2005, 441, 182-190.
  18. Rackova, L.; Firakova, S.; Kostalova, D.; Steferk, M.; Sturdik, E.; Majekova, M. Oxidation of liposomal membrane suppressed by flavonoids: Quantitative structure-activity relationship. Bioorg. Med Chem. 2005, 13, 6477-6484.
  19. Fylaktakidou K.C.; Hadjipavlou-Litina D.J.; Litinas K.E.; Nicolaides D.N. Natural and synthetic coumarin derivatives with anti-inflammatory/antioxidant activities Current Pharmaceutical Design. 2004, 10, 3813-3833.
  20. Amic, D.; Davidovic-Amic, D.; Beslo, D.; Trinajstic, N. Structure-Radical Scavenging Activity Relationships of Flavonoids. Croat. Chem. Acta 2003, 76, 55-61.
  21. Sadik, C.D.; Sies, H.; Schewe, T. Inhibition of 15-lipoxygenases by flavonoids: structure-activity relations and mode of action. Biochem. Pharmacol. 2003, 65, 773-781.
  22. Van Hoorn, D.E.C.; Nijveldt, R.J.; Van Leeuwen, P.A.M.; Hofman, Z.; M'Rabet, L.; De Bont, D.BA.; Norren, K.V. Accurate prediction of xanthine oxidase inhibition based on the structure of flavonoids. Eur. J. Pharm. 2002, 451, 111-118
  23. Kim, D.O.; Lee, C.Y. Comprehensive Study on Vitamin C Equivalent Antioxidant Capacity (VCEAC) of Various Polyphenolics in Scavenging a Free Radical and its Structural Relationship. Crit. Rev. Food Sci. Nutr. 2004, 44, 253-273.
 
 
 

Keywords

  • QSAR
  • SAR
  • QSPR
  • modeling
  • molecular descriptors
  • polyphenols
  • flavonoids
  • coumarins
  • chalcones
  • structure-activity/property relationship
  • antioxidant activity
  • free redical scavenging
  • enzyme inhibition

Published Papers (3 papers)

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169 KiB  
Article
Dietary Protection Against Free Radicals: A Case for Multiple Testing to Establish Structure-activity Relationships for Antioxidant Potential of Anthocyanic Plant Species
by Martin Philpott, Chiara Cheng Lim and Lynnette R. Ferguson
Int. J. Mol. Sci. 2009, 10(3), 1081-1103; https://doi.org/10.3390/ijms10031081 - 11 Mar 2009
Cited by 33 | Viewed by 15946
Abstract
DNA damage by reactive species is associated with susceptibility to chronic human degenerative disorders. Anthocyanins are naturally occurring antioxidants, that may prevent or reverse such damage. There is considerable interest in anthocyanic food plants as good dietary sources, with the potential for reducing [...] Read more.
DNA damage by reactive species is associated with susceptibility to chronic human degenerative disorders. Anthocyanins are naturally occurring antioxidants, that may prevent or reverse such damage. There is considerable interest in anthocyanic food plants as good dietary sources, with the potential for reducing susceptibility to chronic disease. While structure-activity relationships have provided guidelines on molecular structure in relation to free hydroxyl- radical scavenging, this may not cover the situation in food plants where the anthocyanins are part of a complex mixture, and may be part of complex structures, including anthocyanic vacuolar inclusions (AVIs). Additionally, new analytical methods have revealed new structures in previously-studied materials. We have compared the antioxidant activities of extracts from six anthocyanin-rich edible plants (red cabbage, red lettuce, blueberries, pansies, purple sweetpotato skin, purple sweetpotato flesh and Maori potato flesh) using three chemical assays (DPPH, TRAP and ORAC), and the in vitro Comet assay. Extracts from the flowering plant, lisianthus, were used for comparison. The extracts showed differential effects in the chemical assays, suggesting that closely related structures have different affinities to scavenge different reactive species. Integration of anthocyanins to an AVI led to more sustained radical scavenging activity as compared with the free anthocyanin. All but the red lettuce extract could reduce endogenous DNA damage in HT-29 colon cancer cells. However, while extracts from purple sweetpotato skin and flesh, Maori potato and pansies, protected cells against subsequent challenge by hydrogen peroxide at 0oC, red cabbage extracts were pro-oxidant, while other extracts had no effect. When the peroxide challenge was at 37oC, all of the extracts appeared pro-oxidant. Maori potato extract, consistently the weakest antioxidant in all the chemical assays, was more effective in the Comet assays. These results highlight the dangers of generalising to potential health benefits, based solely on identification of high anthocyanic content in plants, results of a single antioxidant assay and traditional approaches to structure activity relationships. Subsequent studies might usefully consider complex mixtures and a battery of assays. Full article
(This article belongs to the Special Issue Structure-Property/Activity Modeling of Polyphenols)
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329 KiB  
Article
Prodrugs of Fluoro-Substituted Benzoates of EGC as Tumor Cellular Proteasome Inhibitors and Apoptosis Inducers
by Zhiyong Yu, Xu Long Qin, Yan Yan Gu, Di Chen, Qiuzhi Cindy Cui, Tao Jiang, Sheng Biao Wan and Q. Ping Dou
Int. J. Mol. Sci. 2008, 9(6), 951-961; https://doi.org/10.3390/ijms9060951 - 02 Jun 2008
Cited by 17 | Viewed by 12418
Abstract
The most potent catechin in green tea is (-)-epigallocatechin-3-gallate [(-)- EGCG], which, however, is unstable under physiological conditions. To discover more stable and more potent polyphenol proteasome inhibitors, we synthesized several novel fluoro-substituted (-)-EGCG analogs, named F-EGCG analogs, as well as their prodrug [...] Read more.
The most potent catechin in green tea is (-)-epigallocatechin-3-gallate [(-)- EGCG], which, however, is unstable under physiological conditions. To discover more stable and more potent polyphenol proteasome inhibitors, we synthesized several novel fluoro-substituted (-)-EGCG analogs, named F-EGCG analogs, as well as their prodrug forms with all of -OH groups protected by acetate. We report that the prodrug form of one F-EGCG analog exhibited greater potency than the previously reported peracetate of (-)- EGCG to inhibit proteasomal activity, suppress cell proliferation, and induce apoptosis in human leukemia Jurkat T cells, demonstrating the potential of these compounds to be developed into novel anti-cancer and cancer-preventive agents. Full article
(This article belongs to the Special Issue Structure-Property/Activity Modeling of Polyphenols)
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390 KiB  
Article
3D-QSAR Investigation of Synthetic Antioxidant Chromone Derivatives by Molecular Field Analysis
by Weerasak Samee, Patcharawee Nunthanavanit and Jiraporn Ungwitayatorn
Int. J. Mol. Sci. 2008, 9(3), 235-246; https://doi.org/10.3390/ijms9030235 - 29 Feb 2008
Cited by 24 | Viewed by 9109
Abstract
A series of 7-hydroxy, 8-hydroxy and 7,8-dihydroxy synthetic chromone derivatives was evaluated for their DPPH free radical scavenging activities. A training set of 30 synthetic chromone derivatives was subject to three-dimensional quantitative structure-activity relationship (3D-QSAR) studies using molecular field analysis (MFA). The substitutional [...] Read more.
A series of 7-hydroxy, 8-hydroxy and 7,8-dihydroxy synthetic chromone derivatives was evaluated for their DPPH free radical scavenging activities. A training set of 30 synthetic chromone derivatives was subject to three-dimensional quantitative structure-activity relationship (3D-QSAR) studies using molecular field analysis (MFA). The substitutional requirements for favorable antioxidant activity were investigated and a predictive model that could be used for the design of novel antioxidants was derived. Regression analysis was carried out using genetic partial least squares (G/PLS) method. A highly predictive and statistically significant model was generated. The predictive ability of the developed model was assessed using a test set of 5 compounds (r2pred = 0.924). The analyzed MFA model demonstrated a good fit, having r2 value of 0.868 and crossvalidated coefficient r2cv value of 0.771. Full article
(This article belongs to the Special Issue Structure-Property/Activity Modeling of Polyphenols)
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