Exploring the molecular basis of action of ring D aromatic steroidal antiestrogens

Proteins: Structure, Function and Bioinformatics

Volumn 83, Issue 7, 2015, Pages 1297-1306

  Alvarez, Lautaro D ^a   Veleiro, Adriana S ^a   Burton, Gerardo ^a  

^a UNIVERSIDAD DE BUENOS AIRES   (Argentina)

Author keywords

Antiestrogenic; Estrogen receptor; Molecular dynamics; Salpichrolide; Withanolide

Indexed keywords

ANTIESTROGEN; ESTRADIOL; ESTROGEN RECEPTOR ALPHA; PHYTOSTEROL; PROTEIN; PROTEIN HIS524; SALPICHROLIDE A; UNCLASSIFIED DRUG; ERGOSTEROL; LIGAND; PROTEIN BINDING; SELECTIVE ESTROGEN RECEPTOR MODULATOR;

ARTICLE; BREAST CANCER; CANCER HORMONE THERAPY; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTAL STRUCTURE; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN INTERACTION; TRANSCRIPTION INITIATION; ANALOGS AND DERIVATIVES; ANTAGONISTS AND INHIBITORS; BINDING SITE; CHEMISTRY; COMPUTER INTERFACE; HUMAN; MOLECULAR DOCKING; MOLECULAR GENETICS; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; STRUCTURE ACTIVITY RELATION; SYNTHESIS; THERMODYNAMICS;

AMINO ACID MOTIFS; BINDING SITES; ERGOSTEROL; ESTRADIOL; ESTROGEN RECEPTOR ALPHA; ESTROGEN RECEPTOR MODULATORS; HUMANS; LIGANDS; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS; USER-COMPUTER INTERFACE;

EID: 84931006883     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24820     Document Type: Article

References (39)

1. Gronemeyer H, Gustafsson JA, Laudet V. Principles for modulation of the nuclear receptor superfamily. Nat Rev Drug Discov 2004;3:950-964.
2. D'Auria MV, Sepe V, Zampella A. Natural ligands for nuclear receptors: biology and potential therapeutic applications. Curr Top Med Chem 2012;12:637-669.
3. Moore JT, Collins JL, Pearce KH. The nuclear receptor superfamily and drug discovery. ChemMedChem 2006;1:504-523.
4. Yang G, Nowsheen S, Aziz K, Georgakilas AG. Toxicity and adverse effects of tamoxifen and other anti-estrogen drugs. Pharmacol Ther 2013;139:392-404.
5. Brelivet Y, Rochel N, Moras D. Structural analysis of nuclear receptors: from isolated domains to integral proteins. Mol Cell Endocrinol 2012;348:466-473.
6. Tanenbaum DM, Wang Y, Williams SP, Sigler PB. Crystallographic comparison of the estrogen and progesterone receptor's ligand binding domains. Proc Natl Acad Sci USA 1998;95:5998-6003.
7. Gangloff M, Ruff M, Eiler S, Duclaud S, Wurtz JM, Moras D. Crystal structure of a mutant hERalpha ligand-binding domain reveals key structural features for the mechanism of partial agonism. J Biol Chem 2001;276:15059-15065.
8. Brzozowski AM, Pike AC, Dauter Z, Hubbard RE, Bonn T, Engström O, Ohman L, Greene GL, Gustafsson JA, Carlquist M. Molecular basis of agonism and antagonism in the oestrogen receptor. Nature 1997;389:753-758.
9. Ekena K, Weis KE, Katzenellenbogen JA, Katzenellenbogen BS. Different residues of the human estrogen receptor are involved in the recognition of structurally diverse estrogens and antiestrogens. J Biol Chem 1997;272:5069-5075.
10. Ekena K, Weis KE, Katzenellenbogen JA, Katzenellenbogen BS. Identification of amino acids in the hormone binding domain of the human estrogen receptor important in estrogen binding. J Biol Chem 1996;271:20053-20059.
11. Bolli A, Marino M. Current and future development of estrogen receptor ligands: applications in estrogen-related cancers. Recent Pat Endocr Metab Immune Drug Discov 2011;5:210-229.
12. Shiau AK, Barstad D, Loria PM, Cheng L, Kushner PJ, Agard DA, Greene GL. The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell 1998;95:927-937.
13. Shiau AK, Barstad D, Radek JT, Meyers MJ, Nettles KW, Katzenellenbogen BS, Katzenellenbogen JA, Agard DA, Greene GL. Structural characterization of a subtype-selective ligand reveals a novel mode of estrogen receptor antagonism. Nat Struct Biol 2002;9:359-364.
14. Michel T, Halabalaki M, Skaltsounis AL. New concepts, experimental approaches, and dereplication strategies for the discovery of novel phytoestrogens from natural sources. Planta Med 2013;79:514-532.
15. Castelo-Branco C, Soveral I. Phytoestrogens and bone health at different reproductive stages. Gynecol Endocrinol 2013;29:735-743.
16. Cassidy A. Dietary phytoestrogens and bone health. J Br Menopause Soc 2003;9:17-21.
17. Patisaul HB, Jefferson W. The pros and cons of phytoestrogens. Front Neuroendocrinol 2010;31:400-419.
18. Misico RI, Nicotra VE, Oberti JC, Barboza G, Gil RR, Burton G. Withanolides and related steroids. Prog Chem Org Nat Prod 2011;94:127-229.
19. Veleiro AS, Oberti JC, Burton G. Chemistry and bioactivity of withanolides from South American solanaceae. Studies in natural products chemistry. Bioactive Nat Prod 2005;32:1019-1052.
20. Veleiro AS, Oberti JC, Burton G. A Ring-D aromatic withanolide from Salpichroa origanifolia. Phytochemistry 1992;31:935-937.
21. Tettamanzi MC, Veleiro AS, de la Fuente JR, Burton G. Withanolides from Salpichroa origanifolia. J Nat Prod 2001;64:783-786.
22. Machin RP, Veleiro AS, Nicotra VE, Oberti JC, M Padrón J. Antiproliferative activity of withanolides against human breast cancer cell lines. J Nat Prod 2010;73:966-968.
23. Sonego JM, Rivero EM, Gargiulo L, Lüthy I, Alvarez LD, Veleiro AS, Burton G. Synthesis and biological evaluation of salpichrolide analogs as antiestrogenic agents. Eur J Med Chem 2014;82:233-241.
24. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA. Gaussian, version 03, revision C. Wallingford: Gaussian Inc.; 2004.
25. Case DA, Cheatham TA, III, Simmerling CL, Wang J, Duke RE, Luo R, Walker RC, Zhang W, Merz KM, Roberts B, Hayik S, Roitberg A, Seabra A, Swails J, Goetz AW, Kolossváry I, Wong KF, Paesani F, Vanicek J, Wolf RM, Liu J, Wu X, Brozell SR, Steinbrecher T, Gohlke H, Cai Q, Ye X, Wang J, Cui G, Roe DR, Mathews DH, Seetin MG, Salomon-Ferrer R, Sagui C, Babin V, Luchko T, Gusarov S, Kovalenko A, Kollman PA. AMBER 12. San Francisco, CA: University of California; 2012.
26. Cheatham TE, III, Cieplak P, Kollman PA. A modified version of the Cornell et al. Force field with improved sugar pucker phases and helical repeat. J Biomol Struct Dyn 1999;16:845-862.
27. Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph 1996;14:33-38.
28. Anisimov VM, Cavasotto CN. Quantum mechanical binding free energy calculation for phosphopeptide inhibitors of the lck sh2 domain. J Comput Chem 2011;32:2254-2263.
29. MOPAC2009. JJPS, Stewart Computational Chemistry, Colorado Springs, CO, 2008.
30. Stewart JJ. Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements. J Mol Model 2007;13:1173-1213.
31. Chovancová E, Pavelka A, Beneš P, Strnad O, Brezovský J, Kozlíková B, Gora A, Šustr V, Klvaňa M, Medek P, Biedermannová L, Sochor J, Damborský J. CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures. PLoS Comp Biol 2012;8:e1002708.
32. Celik L, Lund JD, Schiott B. Conformational dynamics of the estrogen receptor alpha: molecular dynamics simulations of the influence of binding site structure on protein dynamics. Biochemistry 2007;46:1743-1758.
33. Gao L, Tu Y, Ågren H, Eriksson LA. Characterization of agonist binding to his524 in the estrogen receptor alpha ligand binding domain. J Phys Chem B 2012;116:4823-4830.
34. Petrek M, Otyepka M, Banáš P, Kosinová P, Koča J, Damborský J. CAVER: a new tool to explore routes from protein clefts, pockets and cavities. BMC Bioinformatics 2006;7:316.
35. Kosztin D, Izrailev S, Schulten K. Unbinding of retinoic acid from its receptor studied by steered molecular dynamics. Biophys J 1999;76:188-197.
36. Burendahl S, Danciulescu C, Nilsson L. Ligand unbinding from the estrogen receptor: a computational study of pathways and ligand specificity. Proteins 2009;77:842-856.
37. Perakyla M. Ligand unbinding pathways from the vitamin D receptor studied by molecular dynamics simulations. Eur Biophys J 2009;38:185-198.
38. Martinez L, Polikarpov I, Skaf MS. Only subtle protein conformational adaptations are required for ligand binding to thyroid hormone receptors: simulations using a novel multipoint steered molecular dynamics approach. J Phys Chem B 2008;112:10741-10751.
39. Capelli AM, Bruno A, Entrena Guadix A, Costantino G. Unbinding pathways from the glucocorticoid receptor shed light on the reduced sensitivity of glucocorticoid ligands to a naturally occurring, clinically relevant mutant receptor. J Med Chem 2013;56:7003-7014.