Induced-fit docking of mometasone furoate and further evidence for glucocorticoid receptor 17α pocket flexibility

Journal of Molecular Graphics and Modelling

Volumn 27, Issue 4, 2008, Pages 512-521

  Wang, Hongwu ^a   Aslanian, Robert ^a   Madison, Vincent S ^a  

^a MERCK RESEARCH LABORATORIES   (United States)

Author keywords

Glucocorticoid receptor; Glucocorticoids; Induced fit docking; Ligand protein interaction; Mometasone furoate; Protein flexibility

Indexed keywords

BINDING SITES; BIOCHEMISTRY; DOCKING; ESTERS; HYDROGEN; HYDROGEN BONDS; HYDROPHOBICITY; LIGANDS; ORGANIC COMPOUNDS; TRANSCRIPTION FACTORS;

GLUCOCORTICOID RECEPTOR; GLUCOCORTICOIDS; INDUCED-FIT DOCKING; MOMETASONE FUROATE; PROTEIN FLEXIBILITY;

FLOW INTERACTIONS;

CELL NUCLEUS RECEPTOR; CICLESONIDE; DESISOBUTYRYL CICLESONIDE; DEXAMETHASONE; GLUCOCORTICOID RECEPTOR 17 ALPHA; GLUCOCORTICOID RECEPTOR ALPHA; MOMETASONE FUROATE; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL REACTION; CHEMICAL STRUCTURE; CRYSTAL STRUCTURE; DRUG BINDING SITE; DRUG BIOAVAILABILITY; DRUG MECHANISM; DRUG STRUCTURE; HYDROGEN BOND; LIGAND BINDING; PRIORITY JOURNAL; VALIDATION STUDY;

BINDING SITES; CARBON; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PREGNADIENEDIOLS; RECEPTORS, GLUCOCORTICOID;

EID: 55949116957     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2008.09.002     Document Type: Article

References (46)

1. Global Initiative for Asthma, Global strategy for asthma management and prevention, NHLBI/WHO Workshop Report, 2006, pp. 1-96, Available at: www.ginasthma.com.
2. Dykewicz M.S., and Fineman S. Executive summary of joint task force practice parameters on diagnosis and management of rhinitis. Ann. Allergy Asth. Immunol. 81 (1998) 463-468
3. van Cauwenberge P., Bachert C., Passalacqua G., Bousquet J., Canonica G.W., Durham S.R., Fokkens W.J., Howarth P.H., Lund V., Malling H.J., Mygind N., Passali D., Scadding G.K., and Wang D.Y. Consensus statement on the treatment of allergic rhinitis. Eur. Acad. Allergol. Clin. Immunol., Allergy 55 (2000) 116-134
4. Bousquet J., Van Cauwenberge P., Khaltaev N., Aria Workshop Group, and World Health Organization. Allergic rhinitis and its impact on asthma. J. Allergy Clin. Immunol. 108 (2001) S147-S334
5. Umland S.P., Schleimer R.P., and Johnston S.L. Review of the molecular and cellular mechanisms of action of glucocorticoids for use in asthma. Pulm. Pharmacol. Ther. 15 (2002) 35-50
6. Schacke H., Docke W.D., and Asadullah K. Mechanisms involved in the side effects of glucocorticoids. Pharmacol. Ther. 96 (2002) 23-43
7. Ramamurthy L., and Trump R.P. Nuclear receptor ligands in inflammatory lung diseases. Drug Dis. Today: Dis. Mech. 3 (2006) 85-90
8. Bledsoe R.K., Montana V.G., Stanley T.B., Delves C.J., Apolito C.J., McKee D.D., Consler T.G., Parks D.J., Stewart E.L., Willson T.M., Lambert M.H., Moore J.T., Pearce K.H., and Xu H.E. Crystal structure of the glucocorticoid receptor ligand binding domain reveals a novel mode of receptor dimerization and coactivator recognition. Cell 110 (2002) 93-105
9. Kauppi B., Jakob C., Farnegardh M., Yang J., Ahola H., Alarcon M., Calles K., Engstrom O., Harlan J., Muchmore S., Ramqvist A.K., Thorell S., Ohman L., Greer J., Gustafsson J.A., Carlstedt-Duke J., and Carlquist M. The three-dimensional structures of antagonistic and agonistic forms of the glucocorticoid receptor ligand-binding domain: RU-486 induces a transconformation that leads to active antagonism. J. Biol. Chem. 278 (2003) 22748-22754
10. Suino-Powell K., Xu Y., Zhang C., Tao Y.-G., Tolbert W.D., Simons Jr. S.S., and Xu H.E. Doubling the size of the glucocorticoid receptor ligand binding pocket by deacylcortivazol. Mol. Cell. Biol. 28 (2008) 1915-1923
11. Leach A.R., Shoichet B.K., and Peishoff C.E. Prediction of protein-ligand interactions. Docking and scoring: successes and gaps. J. Med. Chem. 49 (2006) 5851-5855
12. Sousa S.F., Fernandes P.A., and Ramos M.J. Protein-ligand docking: current status and future challenges. Proteins 65 (2006) 15-26
13. Boström J., Hogner A., and Schmitt S. Do structurally similar ligands bind in a similar fashion?. J. Med. Chem. 49 (2006) 6716-6725
14. Cavasotto C.N., and Abagyan R.A. Protein flexibility in ligand docking and virtual screening to protein kinases. J. Mol. Biol. 337 (2004) 209-225
15. Moitessier N., Therrien E., and Hanessian S. A method for induced-fit docking, scoring, and ranking of flexible ligands. Application to peptidic and pseudopeptidic beta-secretase (BACE 1) inhibitors. J. Med. Chem. 49 (2006) 5885-5894
16. Sherman W., Day T., Jacobson M.P., Friesner R.A., and Farid R. Novel procedure for modeling ligand/receptor induced fit effects. J. Med. Chem. 49 (2006) 534-553
17. Friesner R.A., Banks J.L., Murphy R.B., Halgren T.A., Klicic J.J., Mainz D.T., Repasky M.P., Knoll E.H., Shelley M., Perry J.K., Shaw D.E., Francis P., and Shenkin P.S. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 47 (2004) 1739-1749
18. Claussen H., Buning C., Rarey M., and Lengauer T. FlexE: efficient molecular docking considering protein structure variations. J. Mol. Biol. 308 (2001) 377-395
19. Carlson H.A. Protein flexibility and drug design: how to hit a moving target. Curr. Opin. Chem. Biol. 6 (2002) 447-452
20. Zhu K., Shirts M.R., and Friesner R.A. Improved methods for side chain and loop predictions via the protein local optimization program: variable dielectric model for implicitly improving the treatment of polarization effects. J. Chem. Theory Comput. 3 (2007) 2108-2119
21. Avery M.A., and Woolfrey J.R. Anti-inflammatory steroids. In: Abraham D.J. (Ed). Burger's Medicinal Chemistry & Drug Discovery (2003), John Wiley and Sons, Hoboken, NJ 747-851
22. Bikowski J., Pillai R., and Shroot B. The position not the presence of the halogen in corticosteroids influences potency and side effects. J. Drugs Dermatol. 5 (2006) 125-130
23. Hogger P. Current concepts for optimizing the therapeutic index of glucocorticoid receptor ligands for oral and inhalative use: basic considerations and clinical reality. Curr. Med. Chem.-Anti-Inflam. Anti-Allergy Agents 2 (2003) 395-408
24. Valotis A., and Hogger P. Human receptor kinetics and lung tissue retention of the enhanced-affinity glucocorticoid fluticasone furoate. Respir. Res. 8 (2007) 54
25. Smith C.L., and Kreutner W. In vitro glucocorticoid receptor binding and transcriptional activation by topically active glucocorticoids. Arzneim. Forsch. 48 (1998) 956-960
26. Issar M., Sahasranaman S., Buchwald P., and Hochhaus G. Differences in the glucocorticoid to progesterone receptor selectivity of inhaled glucocorticoids. Eur. Respir. J. 27 (2006) 511-516
27. Stoeck M., Riedel R., Hochhaus G., Hafner D., Masso J.M., Schmidt B., Hatzelmann A., Marx D., and Bundschuh D.S. In vitro and in vivo anti-inflammatory activity of the new glucocorticoid ciclesonide. J. Pharmacol. Exp. Ther. 309 (2004) 249-258
28. Mutch E., Nave R., McCracken N., Zech K., and Williams F.M. The role of esterases in the metabolism of ciclesonide to desisobutyryl-ciclesonide in human tissue. Biochem. Pharmacol. 73 (2007) 1657-1664
29. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 28 (2000) 235-242
30. Williams S.P., and Sigler P.B. Atomic structure of progesterone complexed with its receptor. Nature 393 (1998) 392-396
31. Madauss K.P., Deng S.J., Austin R.J., Lambert M.H., McLay I., Pritchard J., Short S.A., Stewart E.L., Uings I.J., and Williams S.P. Progesterone receptor ligand binding pocket flexibility: crystal structures of the norethindrone and mometasone furoate complexes. J. Med. Chem. 47 (2004) 3381-3387
32. Kleywegt G.J. Experimental assessment of differences between related protein crystal structures. Acta Crystallogr., Sect. B 55 (1999) 1878-1884
33. R.K. Bledsoe, M.H. Lambert, V.G. Montana, E.L. Stewart, E.H. Xu, Structure of a glucocorticoid receptor ligand binding domain comprising an expanded binding pocket, and methods using nuclear receptors structure for drug design, Eur. Pat. Appl. 1375517 (2004).
34. Maestro Software, Scherödinger, LLC, 120 West 45th Street, New York, NY 10036, USA.
35. Kleywegt G.J., and Jones T.A. Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr., Sect. D 50 (1994) 178-185
36. Concord Software Distributed by Tripos Inc., St. Louis, Missouri, MO 63144, USA.
37. MacroModel Software, Scherödinger, LLC, 120 West 45th Street, New York, NY 10036, USA.
38. Salter M., Biggadike K., Matthews J.L., West M.R., Haase M.V., Farrow S.N., Uings I.J., and Gray D.W. Pharmacological properties of the enhanced-affinity glucocorticoid fluticasone furoate in vitro and in an in vivo model of respiratory inflammatory disease. Am. J. Physiol. Lung Cell. Mol. Physiol. 293 (2007) L660-L667
39. Huyet J., Pinon G.M., Fay M.R., Fagart J., and Rafestin-Oblin M.-E. Structural basis of spirolactone recognition by the mineralocorticoid receptor. Mol. Pharmacol. 72 (2007) 563-571
40. Bohl C.E., Wu Z., Miller D.D., Bell C.E., and Dalton J.T. Crystal structure of the T877A human androgen receptor ligand-binding domain complexed to cyproterone acetate provides insight for ligand-induced conformational changes and structure-based drug design. J. Biol. Chem. 282 (2007) 13648-13655
41. Cantin L., Faucher F., Couture J.-F., de Jesus-Tran K.P., Legrand P., Ciobanu L.C., Frechette Y., Labrecque R., Singh S.M., Labrie F., and Breton R. Structural characterization of the human androgen receptor ligand-binding domain complexed with EM5744, a rationally designed steroidal ligand bearing a bulky chain directed toward helix 12. J. Biol. Chem. 282 (2007) 30910-30919
42. Roumestan C., Henriquet C., Bousquet J., and Mathieu M. Fluticasone propionate and mometasone furoate have equivalent transcriptional potencies. Clin. Exp. Allergy 33 (2003) 895-901
43. Crim C., Pierre L.N., and Daley-Yates P.T. A review of the pharmacology and pharmacokinetics of inhaled fluticasone propionate and mometasone furoate. Clin. Ther. 23 (2001) 1339-1354
44. Biggadike K., Bledsoe R., Hassell A., Hughes S., and Shewchuk L. GW685698X-enhanced affinity for the glucocorticoid receptor: receptor crystal structure and route of metabolic inactivation. Proceedings of the XXVth Congress of the European Academy of Allergology and Clinical Immunology. Vienna, Austria (2006)
45. van Drunen C., Meltzer E.O., Bachert C., Bousquet J., and Fokkens W.J. Nasal allergies and beyond: a clinical review of the pharmacology, efficacy, and safety of mometasone furoate. Allergy 80 (2005) 5-19
46. Brannan M.D., Seiberling M., Cutler D.L., Cuss F.M., and Affrime M.B. Lack of systemic activity with intranasal mometasone furoate. J. Allergy Clin. Immunol. 97 (1996) 198