In silico design of peptidic inhibitors targeting estrogen receptor alpha dimer interface

Molecular Diversity

Volumn 16, Issue 3, 2012, Pages 441-451

  Chakraborty, Sandipan ^a   Cole, Shawn ^a   Rader, Nicholas ^a   King, Candace ^a   Rajnarayanan, R ^b   Biswas, P K ^a  

^a TOUGALOO COLLEGE   (United States)

^b UNIVERSITY AT BUFFALO   (United States)

Author keywords

Bio molecular modeling and simulations; Estrogen receptor alpha; Helical stability; Peptidic inhibitors; Selective estrogen receptor modulators; Sequence motif

Indexed keywords

AFIMOXIFENE; ASPARTIC ACID DERIVATIVE; ASPARTYLLYSYLISOLEUCYLTHREONYLASPARTIC ACID; DIETHYLSTILBESTROL; DIMER; ESTROGEN RECEPTOR ALPHA; GLUTAMINE DERIVATIVE; GLUTAMINYLGLUTAMINYLGLUTAMINYLHISTIDYLGLUTAMINYLARGINYLLEUCYLALANYLGLUTAMINE; HYDROGEN; LEUCYLGLUTAMINYLGLUTAMINYLGLUTAMINYLHISTIDYLGLUTAMINYLGLUTAMINYLLEUCYLALANYLGLUTAMINE; LEUCYLSERYLHISTIDYLISOLEUCYLARGINYLHISTIDYLMETHIONYLSERYLASPARAGINYLLYSINE; LIGAND; LYSINE DERIVATIVE; MONOMER; PEPTIDE DERIVATIVE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER MODEL; CONTROLLED STUDY; DIMERIZATION; DRUG ACTIVITY; DRUG DESIGN; GENE MUTATION; GROWTH INHIBITION; HUMAN; HYDROGEN BOND; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN MOTIF; PROTEIN STABILITY; PROTEIN TARGETING; TRANSACTIVATION;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; DIETHYLSTILBESTROL; DRUG DESIGN; ESTROGEN RECEPTOR ALPHA; LIGANDS; MOLECULAR DYNAMICS SIMULATION; OLIGOPEPTIDES; PROTEIN MULTIMERIZATION; PROTEIN STABILITY; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; TAMOXIFEN;

EID: 84869501807     PISSN: 13811991     EISSN: 1573501X     Source Type: Journal    
DOI: 10.1007/s11030-012-9378-x     Document Type: Article

References (37)

1. Beato M, Herrlich P, Schutz G (1995) Steroid hormone receptors: many actors in search of a plot. Cell 83:851-857. doi:10.1016/0092-8674(95)90201-5 (Pubitemid 26006527)
2. Levin ER (2001) Cell localization, physiology, and nongenomic actions of estrogen receptors. J Appl Physiol 91:1860-1867 (Pubitemid 32900382)
3. Vidal O, Lindberg M, Sävendahl L, Lubahn DB, Ritzen EM, Gustafsson JÅ, Ohlsson C (1999) Disproportional body growth in female estrogen receptor-α-inactivated mice. Biochem Biophys Res Commun 19: 569-571. doi:10.1006/bbrc.1999.1711
4. Stender JD, Kim K, Charn TH, Komm B, Chang KCN, Kraus WL, Benner C, Glass CK, Katzenellenbogen BS (2010) Genomewide analysis of estrogen receptor α DNA binding and tethering mechanisms identifies runx1 as a novel tethering factor in receptormediated transcriptional activation. Mol Cell Biol 30: 3943-3955. doi:10.1128/MCB.00118-10
5. Hall JM, Couse JF, Korach KS (2001) The multifaceted mechanisms of estradiol and estrogen receptor signaling. J Biol Chem 276: 36869-36872. doi:10.1074/jbc.R100029200
6. Nadal A, Diaz M, Valverde MA (2001) The estrogen trinity:membrane, cytosolic, and nuclear effects. News Physiol Sci 16:251-255 (Pubitemid 33575264)
7. Bjornstrom L, Sjoberg M (2005) Mechanisms of estrogen receptor signaling: convergence of genomic and nongenomic actions on target genes. Mol Endocrinol 19: 833-842. doi:10.1210/me.2004-0486 (Pubitemid 40397050)
8. Horwitz KB (1999) Bringing estrogen receptors under control. Breast Cancer Res 1: 5-7. doi:10.1186/bcr3 (Pubitemid 32223526)
9. Shiau AK, Barstad D, Loria PM, Cheng L, Kushner PJ, Agard DA, GreeneGL (1998) The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell 95: 927-937. doi:10.1016/S0092-8674(00)81717-1 (Pubitemid 29019045)
10. Gottardis MM, Robinson SP, Satyaswaroop PG, Jordan VC (1988) Contrasting actions of tamoxifen on endometrial and breast tumor growth in the athymic mouse. Cancer Res 48:812-815 (Pubitemid 18061868)
11. Jordan VC (1998) Antiestrogenic action of raloxifene and tamoxifen: today and tomorrow. J Natl Cancer Inst 90: 967-971. doi:10.1093/jnci/90.13.967 (Pubitemid 28340436)
12. Ruff M, GangloffM,Wurtz JM, MorasD (2000) Estrogen receptor transcription and transactivation Structure-function relationship in DNA-and ligand-binding domains of estrogen receptors. Breast Cancer Res 2: 353-359. doi:10.1186/bcr80 (Pubitemid 32223618)
13. Kumar V, Green S, Stack G, Berry M, Jim JR, Chambon P (1987) Functional domains of the human estrogen receptor. Cell 51: 941-951. doi:10.1016/0092- 8674(87)90581-2
14. Kraus WL, McInerney EM, Katzenellenbogen BS (1995) Ligand dependent transcriptionally productive association of the aminoand carboxyl-terminal regions of a steroid hormone nuclear receptor. Proc Natl Acad Sci USA 92:12314-12318 (Pubitemid 26014061)
15. Gandini O, Kohno H, Curtis S, Korach KS (1997) Two transcription activation functions in the amino terminus of the mouse estrogen receptor that are affected by the carboxy terminus. Steroids 62: 508-515. doi:10.1016/S0039- 128X(97)00001-9 (Pubitemid 27319199)
16. Warnmark A, Treuter E, Wright PHA, Gustafsson J (2003) Activation functions 1 and 2 of nuclear receptors: molecular strategies for transcriptional activation. Mol Endocr 17: 1901-1909. doi:10.1210/me.2002-0384 (Pubitemid 37287610)
17. Wansa KDSA, Harris JM, Muscat GEO (2002) The activation function-1 domain of Nur77/NR4A1 mediates transactivation, cell specificity and coactivator recruitment. J Biol Chem 277: 33001-33011. doi:10.1074/jbc.M203572200 (Pubitemid 34984815)
18. Meegan MJ, Lloyd DG (2003) Advances in the science of estrogen receptor modulation. Curr Med Chem 10:181-210 (Pubitemid 36131653)
19. Schwabe JWR, Chapman L, Finch JT, Rhodes D (1993) The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements. Cell 75: 567-578. doi:10.1016/0092-8674(93)90390-C (Pubitemid 23335081)
20. Bourguet W, Ruff M, Chambon P, Gronemeyer H, Moras D (1995) Crystal structure of the ligand-binding domain of the human nuclear receptor RXR-a. Nature 375: 377-382. doi:10.1038/375377a0
21. Wurtz JM, Bourguet W,Renaud JP, Vivat V, Chambon P, Moras D, Gronemeyer H (1996) Acanonical structure for the ligand-binding domain of nuclear receptors.Nat Struct Biol 3: 87-94. doi:10.1038/nsb0196-87 (Pubitemid 26023915)
22. Shiau AK, Barstad D, Loria PM, Cheng L, Kushner PJ, Agard DA, GreeneGL (1998) The structural basis of estrogen receptor/coactivator recognition and the antagonism of this interaction by tamoxifen. Cell 95: 927-937. doi:10.1016/S0092-8674(00)81717-1 (Pubitemid 29019045)
23. Brzozowski AM, Pike AC, Dauter Z, Hubbard RE, Bonn T, Engstrom O, Ohman L, Greene G L, Gustafsson JA, Carlquist M (1997) Molecular basis of agonism and antagonism in the estrogen receptor. Nature 389: 753-758. doi:10.1038/39645 (Pubitemid 27458965)
24. Dutia BM, Frame MC, Subak-Sharpe JH, Clark WN, Marsden HS (1986) Specific inhibition of herpesvirus ribonucleotide reductase by synthetic peptides. Nature 321: 439-441. doi:10.1038/321439a0 (Pubitemid 16055497)
25. Divita G, Restle T, Goody RS, Chermann JC, Baillon JG (1994) Inhibition of HIV1 reverse transcriptase dimerization using synthetic peptides derived from the connection domain. J Biol Chem 269:13080-13083 (Pubitemid 24206066)
26. Yudt MR, Koide S (2001) Preventing estrogen receptor action with dimer-interface peptides. Steroids 66: 549-558. doi:10.1016/S0039-128X(00)00224- 5 (Pubitemid 32372660)
27. Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234: 779-815. doi:10.1006/jmbi.1993.1626 (Pubitemid 24007801)
28. Humphrey W, Dalke A, Schulten K (1996) VMD - visual molecular dynamics. J Mol Graphics 14: 33-38. doi:10.1016/0263-7855(96)00018-5 (Pubitemid 26152973)
29. Berendsen HJC, Spoel DVD, Drunen RV (1995) GROMACS: a message-passing parallel molecular dynamics implementation. Comput Phys Commun 91:45-56. doi:10.1016/0010-4655(95)00042-E
30. Lindahl E, Hess B, Spoel DVD (2001) GROMACS 3.0 a package for molecular simulation and trajectory analysis. J Mol Model 7: 306-317. doi:10.1007/ s008940100045 (Pubitemid 36153547)
31. Jorgensen WL, Rives T (1988) Development and testing of the OPLS all-atom force field on conformational energetic and properties of organic liquids. J Am Chem Soc 110: 1657-1666. doi:10.1021/ja00214a001
32. Hess B, Bekker H, Berendsen HJC, Fraaije JGEM (1997) LINCS: A linear constraint solver for molecular simulations. J Comp Chem 18: 1463-1472. doi:10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H (Pubitemid 127637344)
33. DeLano WL (2002) The PyMOL molecular graphics system. DeLano Scientific, Palo Alto
34. Bryson K, McGuffin LJ, Marsden RL, Ward JJ, Sodhi JS, Jones DT (2005) Protein structure prediction servers at University College London. Nucl Acids Res 33 (Web server issue):W36-W38. doi:10.1093/nar/gki410 (Pubitemid 44529876)
35. Capriotti E, Fariselli P, Casadio R (2005) I-Mutant 2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucl Acids Res 33 (Web server issue):W306-W310. doi:10.1093/nar/gki375 (Pubitemid 44529932)
36. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc Natl Acad SciUSA98: 10037-10041. doi:10.1073/pnas.181342398 (Pubitemid 32802969)
37. Tamrazi A, Carlson KE, Daniels JR, Hurth KM, Katzenellenbogen JA (2002) Estrogen receptor dimerization: ligand binding regulates dimer affinity and dimer dissociation rate. Mol Endocrinol 16: 2706-2719. doi:10.1210/me.2002-0250 (Pubitemid 36020652)