Identification by molecular docking of homoisoflavones from leopoldia comosa as ligands of estrogen receptors

Molecules

Volumn 23, Issue 4, 2018, Pages

  Grande, Fedora ^a   Rizzuti, Bruno ^a   Occhiuzzi, Maria A ^a   Ioele, Giuseppina ^a   Casacchia, Teresa ^a   Gelmini, Fabrizio ^b   Guzzi, Rita ^a   Garofalo, Antonio ^a   Statti, Giancarlo ^a  

^a UNIVERSITY OF CALABRIA   (Italy)

^b UNIVERSITY OF MILAN   (Italy)

Author keywords

Estrogen receptors; Ligand interactions; Molecular docking; Natural compounds

Indexed keywords

ESTROGEN RECEPTOR; ISOFLAVONE DERIVATIVE; PLANT EXTRACT;

CHEMICAL STRUCTURE; CHEMISTRY; DRUG EFFECT; ENZYME ACTIVE SITE; HYACINTHUS; METABOLISM; MOLECULAR DOCKING; MOLECULAR MODEL;

CATALYTIC DOMAIN; HYACINTHUS; ISOFLAVONES; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; MOLECULAR STRUCTURE; PLANT EXTRACTS; RECEPTORS, ESTROGEN;

EID: 85045235552     PISSN: None     EISSN: 14203049     Source Type: Journal    
DOI: 10.3390/molecules23040894     Document Type: Article

References (55)

1. Wang, P.; McInnes, C.; Zhu, B.T. Structural characterization of the binding interactions of various endogenous estrogen metabolites with human estrogen receptor α and β subtypes: A molecular modeling study. PLoS ONE 2013, 8, e74615.
2. Sukocheva, O.A. Estrogen, estrogen receptors, and hepatocellular carcinoma: Are we there yet? World J. Gastroenterol. 2018, 24, 1–4.
3. Guillaume, M.; Montagner, A.; Fontaine, C.; Lenfant, F.; Arnal, J.F.; Gourdy, P. Nuclear and membrane actions of estrogen receptor alpha: contribution to the regulation of energy and glucose homeostasis. Adv. Exp. Med. Biol. 2017, 1043, 401–426.
4. Jia, M.; Dahlman-Wright, K.; Gustafsson, J.A. Estrogen receptor alpha and beta in health and disease. Best Pract. Res. Clin. Endoc. Metab. 2015, 29, 557–568.
5. Pettersson, K.; Delaunay, F.; Gustafsson, J.A. Estrogen receptor beta acts as a dominant regulator of estrogen signaling. Oncogene 2000, 19, 4970–4978.
6. Paech, K.; Webb, P.; Kuiper, G.G.; Nilsson, S.; Gustafsson, J.; Kushner, P.J.; Scanlan, T.S. Differential ligand activation of estrogen receptors ERalpha and ERbeta at AP1 sites. Science 1997, 277, 1508–1510.
7. Cowley, S.M.; Parker, M.G. A comparison of transcriptional activation by ER alpha and ER beta. J. Steroid Biochem. Mol. Biol. 1999, 69, 165–175.
8. Chakraborty, S.; Willett, H.; Biswas, P.K. Insight into estrogen receptor beta-beta and alpha-beta homo- and heterodimerization: A combined molecular dynamics and sequence analysis study. Biophys. Chem. 2012, 170, 42–50.
9. Farzaneh, S.; Zarghi, A. Estrogen Receptor Ligands: A Review (2013–2015). Sci. Pharm. 2016, 84, 409–427.
10. Paterni, I.; Granchi, C.; Katzenellenbogen, J.A.; Minutolo, F. Estrogen receptors alpha (ERalpha) and beta (ERbeta): Subtype-selective ligands and clinical potential. Steroids 2014, 90, 13–29.
11. Kumar, R.; Zakharov, M.N.; Khan, S.H.; Miki, R.; Jang, H.; Toraldo, G.; Singh, R.; Bhasin, S.; Jasuja, R. The dynamic structure of the estrogen receptor. J. Amino Acids 2011, 2011, 812540.
12. Traboulsi, T.; El Ezzy, M.; Gleason, J.L.; Mader, S. Antiestrogens: Structure-activity relationships and use in breast cancer treatment. J. Mol. Endocrinol. 2017, 58, R15–R31.
13. Ascenzi, P.; Bocedi, A.; Marino, M. Structure-function relationship of estrogen receptor alpha and beta: Impact on human health. Mol. Asp. Med. 2006, 27, 299–402.
14. Huang, B.; Omoto, Y.; Iwase, H.; Yamashita, H.; Toyama, T.; Coombes, R.C.; Filipovic, A.; Warner, M.; Gustafsson, J.A. Differential expression of estrogen receptor α, β1, and β2 in lobular and ductal breast cancer. Proc. Natl. Acad. Sci. USA 2014, 111, 1933–1938.
15. Zhao, C.; Lam, E.W.; Sunters, A.; Enmark, E.; de Bella, M.T.; Coombes, R.C.; Gustafsson, J.A.; Dahlman-Wright, K. Expression of estrogen receptor beta isoforms in normal breast epithelial cells and breast cancer: Regulation by methylation. Oncogene 2003, 22, 7600–7606.
16. Lee, J.Y.; Kim, H.S.; Song, Y.S. Genistein as a potential anticancer agent against ovarian cancer. J. Tradit. Complement. Med. 2012, 2, 96–104.
17. Zhang, L.L.; Li, L.; Wu, D.P.; Fan, J.H.; Li, X.; Wu, K.J.; Wang, X.Y.; He, D.L. A novel anti-cancer effect of genistein: Reversal of epithelial mesenchymal transition in prostate cancer cells. Acta Pharmacol. Sin. 2008, 29, 1060–1068.
18. Peterson, G.; Barnes, S. Genistein inhibition of the growth of human breast cancer cells: independence from estrogen receptors and the multi-drug resistance gene. Biochem. Biophys. Res. Commun. 1991, 179, 661–667.
19. Lentini, F.; Venza, F. Wild food plants of popular use in Sicily. J. Ethnobiol. Ethnomed. 2007, 3, 15.
20. Pieroni, A.; Nebel, S.; Santoro, R.F.; Heinrich, M. Food for two seasons: culinary uses of non-cultivated local vegetables and mushrooms in a south Italian village. Int. J. Food Sci. Nutr. 2005, 56, 245–272.
21. Pieroni, A.; Nebel, S.; Quave, C.; Munz, H.; Heinrich, M. Ethnopharmacology of liakra: Traditional weedy vegetables of the Arbereshe of the Vulture area in southern Italy. J. Ethnopharmacol. 2002, 81, 165–185.
22. Lin, L.G.; Liu, Q.Y.; Ye, Y. Naturally occurring homoisoflavonoids and their pharmacological activities. Planta Med. 2014, 80, 1053–1066.
23. Casacchia, T.; Scavello, F.; Rocca, C.; Granieri, M.C.; Beretta, G.; Amelio, D.; Gelmini, F.; Spena, A.; Mazza, R.; Toma, C.C.; et al. Leopoldia comosa prevents metabolic disorders in rats with high-fat diet-induced obesity. Eur. J. Nutr. 2018, 1–15, doi:org/10.1007/s00394-018-1609-1.
24. Nirmal, N.P.; Rajput, M.S.; Prasad, R.G.; Ahmad, M. Brazilin from Caesalpinia sappan heartwood and its pharmacological activities: A review. Asian Pac. J. Trop. Med. 2015, 8, 421–430.
25. Loizzo M.R.; Tundis, R.; Menichini, F.; Pugliese, A.; Bonesi, M.; Solimene, U.; Menichini, F. Chelating, antioxidant and hypoglycaemic potential of Muscari comosum (L.) Mill. bulb extracts. Int. J. Food Sci. Nutr. 2010, 61, 780–791.
26. Dai, Y.; Harinantenaina, L.; Brodie, P.J.; Goetz, M.; Shen, Y.; TenDyke, K.; Kingston, D.G. Antiproliferative homoisoflavonoids and bufatrienolides from Urginea depressa. J. Nat. Prod. 2013, 76, 865–872.
27. Mulholland, D.A.; Schwikkard, S.L.; Crouch, N.R. The chemistry and biological activity of the Hyacinthaceae. Nat. Prod. Rep. 2013, 30, 1165–1210.
28. Du Toit, K.; Elgorashi, E.E.; Malan, S.F.; Drewes, S.E.; van Staden, J.; Crouch, N.R.; Mulholland, D.A. Anti-inflammatory activity and QSAR studies of compounds isolated from Hyacinthaceae species and Tachiadenus longiflorus Griseb. (Gentianaceae). Bioorg. Med. Chem. 2005, 13, 2561–2568.
29. Abegaz, B.M.; Mutanyatta-Comar J.N. Naturally occurring homoisoflavonoids: Phytochemistry, biological activities and synthesis. Nat. Prod. Commun. 2007, 2, 475–498.
30. Castelli, M.V.; López, S.N. Homoisoflavonoids: Occurrence, biosynthesis, and biological activity. In Studies in Natural Products Chemistry; Elsevier: Amsterdam, Netherlands, 2017, Volume 54, pp. 315–354.
31. Mann, J.; Davidson, R.S.; Hobbs, J.B.; Banthorpe, D.V.; Harbome, J. B. Natural products: Their chemistry and biological significance. In Longman Scientific and Technical; Harlow, E., Ed; Longman Group UK Ltd.: Harlow, UK, 1994, p. 372.
32. De Vincenzi, S.; Lupattelli, M.; Cestola, E.; Liponi, G.B. Effect of variety and agronomical conditions on the level of polyphenols and antinutritional factors of Vicia Faba Minor. Vet. Res. Commun. 2006, 30, 371–374.
33. Casacchia, T.; Sofo, A.; Casaburi, I.; Marrelli, M.; Conforti, F.; Statti, G.A. Antioxidant, enzyme-inhibitory and antitumor activity of the wild dietary plant Muscari comosum (L.). Int. J. Plant Biol. 2017, 8, 6895.
34. Marrelli, M.; Cristaldi, B.; Menichini, F.; Conforti, F. Inhibitory effects of wild dietary plants on lipid peroxidation and on the proliferation of human cancer cells. Food Chem. Toxicol. 2015, 86, 16–24.
35. Martinez-Archundia, M.; Garcia-Vazquez, J.B.; Colin-Astudillo, B.; Bello, M.; Prestegui-Martel, B.; Chavez-Blanco, A.; Duenas-Gonzalez, A.; Fragoso-Vazquez, M.J.; Mendieta-Wejebe, J.; Abarca-Rojano, E.; et al. Computational study of the binding modes of diverse DPN analogues on estrogen receptors (ER) and the biological evaluation of a new potential antiestrogenic ligand. Anticancer Agents Med. Chem. 2018, doi:10.2174/1871520618666171129152953.
36. Yugandhar, P.; Kumar, K.K.; Neeraja, P.; Savithramma, N. Isolation, characterization and in silico docking studies of synergistic estrogen receptor a anticancer polyphenols from Syzygium alternifolium (Wt.) Walp. J. Intercult. Ethnopharmacol. 2017, 6, 296–310.
37. Muchtaridi, M.; Syahidah, H.N.; Subarnas, A.; Yusuf, M.; Bryant, S.D.; Langer, T. Molecular docking and 3D-pharmacophore modeling to study the interactions of chalcone derivatives with estrogen receptor alpha. Pharmaceuticals 2017, 10, 81.
38. Manas, E.S.; Unwalla, R.J.; Xu, Z.B.; Malamas, M.S.; Miller, C.P.; Harris, H.A.; Hsiao, C.; Akopian, T.; Hum, W.T.; Malakian, K.; et al. Structure-based design of estrogen receptor-beta selective ligands. J. Am. Chem. Soc. 2004, 126, 15106–15119.
39. Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne, P.E. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235–242.
40. Manas, E.S.; Xu, Z.B.; Unwalla, R.J.; Somers, W.S. Understanding the selectivity of genistein for human estrogen receptor-beta using X-ray crystallography and computational methods. Structure 2004, 12, 2197–2207.
41. Koide, A.; Abbatiello, S.; Rothgery, L.; Koide, S. Probing protein conformational changes in living cells by using designer binding proteins: application to the estrogen receptor. Proc. Natl. Acad. Sci. USA 2002, 99, 1253–1258.
42. Pike, A.C.; Brzozowski, A.M.; Hubbard, R.E.; Bonn, T.; Thorsell, A.G.; Engstrom, O.; Ljunggren, J.; Gustafsson, J.A.; Carlquist, M. Structure of the ligand-binding domain of oestrogen receptor beta in the presence of a partial agonist and a full antagonist. Embo J. 1999, 18, 4608–4618.
43. Nettles, K.W.; Bruning, J.B.; Gil, G.; Nowak, J.; Sharma, S.K.; Hahm, J.B.; Kulp, K.; Hochberg, R.B.; Zhou, H.; Katzenellenbogen, J.A.; et al. NFkB selectivity of estrogen receptor ligands revealed by comparative crystallographic analyses. Nat. Chem. Biol. 2008, 4, 241–247.
44. Tanenbaum, D.M.; Wang, Y.; Williams, S.P.; Sigler, P.B. Crystallographic comparison of the estrogen and progesterone receptor's ligand binding domains. Proc. Natl. Acad. Sci. USA 1998, 95, 5998–6003.
45. Warnmark, A.; Treuter, E.; Gustafsson, J.A.; Hubbard, R.E.; Brzozowski, A.M.; Pike, A.C. Interaction of transcriptional intermediary factor 2 nuclear receptor box peptides with the coactivator binding site of estrogen receptor alpha. J. Biol. Chem. 2002, 277, 21862–21868.
46. Souza, P.C.T.; Textor, L.C.; Melo, D.C.; Nascimento, A.S.; Skaf, M.S.; Polikarpov, I. An alternative conformation of ERbeta bound to estradiol reveals H12 in a stable antagonist position. Sci. Rep. 2017, 7, 3509.
47. Trott, O.; Olson, A.J. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 2010, 31, 455–461.
48. Labbè, C.M.; Pencheva, T.; Jereva, D.; Desvillechabrol, D.; Becot, J.; Villoutreix, B.O.; Pajeva, I.; Miteva, M.A. AMMOS2: A web server for protein-ligand-water complexes refinement via molecular mechanics. Nucleic Acids Res. 2017, 45, W350–W355.
49. Summa, C.M.; Levitt, M. Near-native structure refinement using in vacuo energy minimization. Proc. Natl. Acad. Sci. USA 2007, 104, 3177–3182.
50. Rizzuti, B.; Daggett, V. Using simulations to provide the framework for experimental protein folding studies. Arch. Biochem. Biophys. 2013, 531, 128–135.
51. Salentin, S.; Schreiber, S.; Haupt, V.J.; Adasme, M.F.; Schroeder, M. PLIP: Fully automated protein-ligand interaction profiler. Nucleic Acids Res. 2015, 43, W443–W447.
52. Hanwell, M.D.; Curtis, D.E.; Lonie, D.C.; Vandermeersch, T.; Zurek, E.; Hutchison, G.R. Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. J. Cheminform. 2012, 4, 17.
53. Morris, G.M.; Goodsell, D.S.; Halliday, R.S.; Huey, R.; Hart, W.E.; Belew, R.K.; Olson, A.J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 1998, 19, 1639–1662.
54. Rappé, A.K.; Casewit, C.J.; Colwell, K.S.; Goddard, W.A. UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J. Am. Chem. Soc. 1992, 114, 10024–10035.
55. Weiner, S.J.; Kollman, P.A.; Nguyen, D.T.; Case, D.A. An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem. 1986, 7, 230–252.