Theoretical studies on the interaction of partial agonists with the 5-HT2A receptor

Journal of Computer-Aided Molecular Design

Volumn 25, Issue 1, 2011, Pages 51-66

  Silva, Maria Elena ^a,b   Heim, Ralf ^a   Strasser, Andrea ^a   Elz, Sigurd ^a   Dove, Stefan ^a  

^a UNIVERSITY OF REGENSBURG   (Germany)

^b PARACELSUS MEDICAL UNIVERSITY   (Austria)

Author keywords

3D QSAR; Docking; GPCR modeling; Partial agonists

Indexed keywords

AMINO ACIDS; BINDING ENERGY; COMPUTATIONAL CHEMISTRY; HYDROGEN BONDS; HYDROPHOBICITY; RATS;

3D-QSAR; BENZYLAMINES; DOCKING; GPCR MODELING; HYDROPHOBIC POCKETS; INTRINSIC ACTIVITIES; METHOXYBENZENE; PARTIAL AGONIST; STRUCTURAL CLASS; THEORETICAL STUDY;

REGRESSION ANALYSIS;

BETA 2 ADRENERGIC RECEPTOR; PHENETHYLAMINE DERIVATIVE; SEROTONIN 2A AGONIST; SEROTONIN 2A RECEPTOR;

ACCURACY; AMINO ACID SEQUENCE; ANIMAL TISSUE; ARTICLE; BINDING AFFINITY; BINDING SITE; COMPARATIVE MOLECULAR SIMILARITY INDICES ANALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; DRUG POTENCY; DRUG RECEPTOR BINDING; DRUG STRUCTURE; HYDROGEN BOND; HYDROPHOBICITY; INTERMETHOD COMPARISON; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; RAT; REGRESSION ANALYSIS; SEQUENCE ALIGNMENT; THREE DIMENSIONAL IMAGING;

EID: 78651228983     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-010-9400-2     Document Type: Article

References (49)

1. SJ Peroutka 1990 5-Hydroxytryptamine receptor subtypes Pharmacol Toxicol 67 373 383 1:CAS:528:DyaK3MXlsFWlug%3D%3D 10.1111/j.1600-0773.1990.tb00848.x
2. MM Rapport AA Green IH Page 1947 Purification of the substance which is responsible for vasoconstrictor activity of serum Fed Proc 6 184 1:STN:280:DyaH2s%2FmtFyntA%3D%3D
3. MM Rapport AA Green IH Page 1948 Serum vasoconstrictor (serotonin): isolation and characterization J Biol Chem 176 1243 1251 1:CAS:528: DyaH1MXhtFWlug%3D%3D
4. BL Roth DL Willins K Kristiansen WK Kroeze 1998 5-Hydroxytryptamine2- family receptors (5-hydroxytryptamine2A, 5-hydroxytryptamine2B, 5-hydroxytryptamine2C): where structure meets function Pharmacol Ther 79 231 257 1:CAS:528:DyaK1cXlsFCrsLo%3D 10.1016/S0163-7258(98)00019-9 (Pubitemid 28393877)
5. E Zifa G Fillion 1992 5-Hydroxytryptamine Receptors Pharmacol Rev 44 401 457 1:CAS:528:DyaK3sXovVQ%3D
6. DE Nichols CD Nichols 2008 Serotonin receptors Chem Rev 108 1614 1641 1:CAS:528:DC%2BD1cXlslOisL8%3D 10.1021/cr078224o (Pubitemid 351796401)
7. MR Braden JC Parrish JC Naylor DE Nichols 2006 Molecular interaction of serotonin 5-HT2A receptor residues Phe339(6.51) and Phe340(6.52) with superpotent N-benzyl phenethylamine agonists Mol Pharmacol 70 1956 1964 1:CAS:528:DC%2BD28Xht1ylt7rK 10.1124/mol.106.028720 (Pubitemid 44771911)
8. Heim R (2003) Synthesis and pharmacology of potent 5-HT2A receptor agonists with N-2-methoxybenzyl partial structure. Dr. rer. nat. PhD Thesis, Free University, Berlin
9. S Elz T Klä U Warnke HH Pertz 2002 Development of highly potent partial agonists and chiral antagonists as tool for the study of 5-HT2A-receptor mediated function Naunyn-Schmiedeberg's Arch Pharmacol 365 R29 10.1007/s00210-001-0490-1 (Pubitemid 34045237)
10. Halter CC (2004) Mescaline analogs as partial 5-HT2A receptor agonists: Synthesis and pharmacological in vitro testing. Dipl. chem. Diploma thesis, University Regensburg, Regensburg
11. R Heim HH Pertz I Walther S Elz 1998 Congeners of 3-(2-Benzylaminoethyl)- 2, 4-quinazolindione: partial agonists for rat vascular 5-HT2A receptors Naunyn-Schmiedeberg's Arch Pharmacol 358 R105
12. 2A agonism of chiral 2-methoxybenzylamines Arch Pharm Pharm Med Chem 335 82
13. 2A receptors Arch Pharm Pharm Med Chem 333 30
14. 2A-receptor agonism of phenylethamines related to mescaline in the rat tail artery model Naunyn-Schmiedeberg's Arch Pharmacol 367 R31
15. V Cherezov DM Rosenbaum MA Hanson SG Rasmussen FS Thian TS Kobilka HJ Choi P Kuhn WI Weis BK Kobilka RC Stevens 2007 High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor Science 318 1258 1265 1:CAS:528:DC%2BD2sXhtlGmur7I 10.1126/science.1150577 (Pubitemid 350172884)
16. SG Rasmussen HJ Choi DM Rosenbaum TS Kobilka FS Thian PC Edwards M Burghammer VR Ratnala R Sanishvili RF Fischetti GF Schertler WI Weis BK Kobilka 2007 Crystal structure of the human beta2 adrenergic G-protein-coupled receptor Nature 450 383 387 1:CAS:528:DC%2BD2sXhtlajs77N 10.1038/nature06325 (Pubitemid 350126755)
17. E Gasteiger A Gattiker C Hoogland I Ivanyi RD Appel A Bairoch 2003 ExPASy: the proteomics server for in-depth protein knowledge and analysis Nucleic Acids Res 31 3784 3788 1:CAS:528:DC%2BD3sXltVWjtLc%3D 10.1093/nar/gkg563 (Pubitemid 37442246)
18. J Wang RM Wolf JW Caldwell PA Kollman DA Case 2004 Development and testing of a general amber force field J Comput Chem 25 1157 1174 1:CAS:528:DC%2BD2cXksFakurc%3D 10.1002/jcc.20035
19. SC Lovell JM Word JS Richardson DC Richardson 2000 The penultimate rotamer library Proteins 40 389 408 1:CAS:528:DC%2BD3cXlsFCrtLc%3D 10.1002/1097-0134(20000815)40:3<389::AID-PROT50>3.0.CO;2-2 (Pubitemid 30624447)
20. A Strasser B Striegl HJ Wittmann R Seifert 2008 Pharmacological profile of histaprodifens at four recombinant histamine H-1 receptor species isoforms J Pharmacol Exp Ther 324 60 71 1:CAS:528:DC%2BD1cXhsF2isg%3D%3D 10.1124/jpet.107.129601 (Pubitemid 350294157)
21. D Van der Spoel E Lindahl B Hess G Groenhof AE Mark HJC Berendsen 2005 GROMACS: fast, flexible, and free J Comput Chem 26 1701 1718 10.1002/jcc.20291 (Pubitemid 43076182)
22. C Oostenbrink A Villa AE Mark WF Van Gunsteren 2004 A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6 J Comput Chem 25 1656 1676 1:CAS:528:DC%2BD2cXmvVOhtr4%3D 10.1002/jcc.20090
23. 2A receptor J Biol Chem 28 16683 16688
24. CD Wang TK Gallaher JC Shih 1993 Site-directed mutagenesis of the serotonin 5-hydroxytrypamine2 receptor: identification of amino acids necessary for ligand binding and receptor activation Mol Pharmacol 43 931 940 1:CAS:528:DyaK3sXltlWktbo%3D
25. N Almaula BJ Ebersole D Zhang H Weinstein SC Sealfon 1996 Mapping the binding site pocket of the serotonin 5-Hydroxytryptamine2A receptor. Ser3.36(159) provides a second interaction site for the protonated amine of serotonin but not of lysergic acid diethylamide or bufotenin J Biol Chem 271 14672 14675 1:CAS:528:DyaK28XjvVWms7Y%3D 10.1074/jbc.271.25.14672 (Pubitemid 26194940)
26. MP Johnson RJ Loncharich M Baez DL Nelson 1994 Species variations in transmembrane region V of the 5-hydroxytryptamine type 2A receptor alter the structure-activity relationship of certain ergolines and tryptamines Mol Pharmacol 45 277 286 1:CAS:528:DyaK2cXitlGnsL4%3D
27. MP Johnson DB Wainscott VL Lucaites M Baez DL Nelson 1997 Mutations of transmembrane IV and V serines indicate that all tryptamines do not bind to the rat 5-HT2A receptor in the same manner Molecular Brain Research 49 1 6 1:CAS:528:DyaK2sXlsleqsb0%3D 10.1016/S0169-328X(97)00115-0 (Pubitemid 27453108)
28. DA Shapiro K Kristiansen WK Kroeze BL Roth 2000 Differential modes of agonist binding to 5-hydroxytryptamine(2A) serotonin receptors revealed by mutation and molecular modeling of conserved residues in transmembrane region 5 Mol Pharmacol 58 877 886 1:CAS:528:DC%2BD3cXnslKgsbo%3D
29. MS Choudhary S Craigo BL Roth 1993 A single point mutation (Phe340 - >Leu340) of a conserved phenylalanine abolishes 4-[125I]iodo-(2, 5-dimethoxy)phenylisopropylamine and [3H]mesulergine but not [3H]ketanserin binding to 5-hydroxytryptamine2 receptors Mol Pharmacol 43 755 761 1:CAS:528:DyaK3sXks1egt7o%3D
30. MS Choudhary N Sachs A Uluer RA Glennon RB Westkaemper BL Roth 1995 Differential ergoline and ergopeptine binding to 5-hydroxytryptamine2A receptors: ergolines require an aromatic residue at position 340 for high affinity binding Mol Pharmacol 47 450 457 1:STN:280:DyaK2M3hsVKgsg%3D%3D
31. JA Ballesteros H Weinstein 1995 Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors Methods Neurosci 25 366 428 1:CAS:528:DyaK2MXmt1Kmtrk%3D 10.1016/S1043-9471(05)80049-7
32. M Clark RD Cramer I N Van Opdenbosch 1989 Validation of the general purpose tripos 5.2 force field J Comp Chem 10 982 1012 1:CAS:528: DyaK3cXhtlygsbk%3D 10.1002/jcc.540100804
33. Glennon RA, Westkaemper RB, Bartyzel P (1991) Serotonin receptor subtypes: basic and clinical aspects. In: Venter CJ, Harrison LC, Peroutka SJ (eds) Receptor biochemistry and methodology. Wiley-Liss, New York, pp 19-64
34. R Giger 1989 Actual Chim Ther 16 151 186 1:CAS:528:DyaL1MXlvVOltrY%3D
35. RD Cramer I DE Patterson JD Buce 1988 Comparative molecular field analysis (CoMFA): effect of shape on binding of steroids to carrier protein J Am Chem Soc 110 5959 5967 10.1021/ja00226a005
36. G Klebe U Abraham T Mietzner 1994 Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity J Med Chem 37 4130 4146 1:CAS:528:DyaK2cXmslWhu7Y%3D 10.1021/jm00050a010 (Pubitemid 24379702)
37. Folkers G, Merz A, Rognan D (1993) CoMFA: Scope and Limitations. In: Kubinyi H (ed) 3D QSAR in drug design: theory, methods and applications. ESCOM, Leiden, pp 583-618
38. S Wold A Ruhe H Wold WJ Dunn 1984 The covariance problem in linear regression. The partial least squares (PLS) approach to generalized inverses SIAM J Sci Stat Comp 5 735 743 10.1137/0905052
39. RD Cramer I JD Buce DE Petterson 1988 Crossvalidation, bootstrapping, and partial least squares compared with multiple regression in conventional QSAR studies Quant Struct-Act Relat 7 18 25 10.1002/qsar.19880070105
40. RD Clark PC Fox 2004 Statistical variation in progressive scrambling J Comput Aided Mol Des 18 563 576 1:CAS:528:DC%2BD2MXltVaktg%3D%3D 10.1007/s10822-004-4077-z
41. A Golbraikh A Tropsha 2002 Beware of q(2)! J Mol Graph Model 20 269 276 1:CAS:528:DC%2BD3MXpt1art7o%3D 10.1016/S1093-3263(01)00123-1 (Pubitemid 34017544)
42. AM Doweyko 2004 3D-QSAR illusions J Comput Aided Mol Des 18 587 596 1:CAS:528:DC%2BD2MXltVarsw%3D%3D 10.1007/s10822-004-4068-0
43. BL Roth MS Choudhary N Khan AZ Uluer 1997 High-affinity agonist binding is not sufficient for agonist efficacy at 5-hydroxytryptamine2A receptors: evidence in favor of a modified ternary complex model J Pharmacol Exp Ther 280 576 583 1:CAS:528:DyaK2sXivVWlsLY%3D
44. BL Roth M Shoham MS Choudhary N Khan 1997 Identification of conserved aromatic residues essential for agonist binding and second messenger production at 5-hydroxytryptamine2A receptors Mol Pharmacol 52 259 266 1:CAS:528: DyaK2sXlvVeis7Y%3D
45. 1- adrenergic G-protein-coupled receptor Nature 454 U482 U486 10.1038/nature07101
46. P Scheerer JH Park PW Hildebrand YJ Kim N Krauss HW Choe KP Hofmann OP Ernst 2008 Crystal structure of opsin in its G-protein-interacting conformation Nature 455 497 503 1:CAS:528:DC%2BD1cXhtFKhtbzF 10.1038/nature07330
47. H Kubinyi FA Hamprecht T Mietzner 1998 Three-dimensional quantitative similarity-activity relationships (3D QSiAR) from SEAL similarity matrices J Med Chem 41 2553 2564 1:CAS:528:DyaK1cXkt12jtb8%3D 10.1021/jm970732a (Pubitemid 28321904)
48. AK Ghose VN Viswanadhan JJ Wendoloski 1998 Prediction of Hydrophobic (Lipophilic) Properties of Small Organic Molecules Using Fragmental Methods: An Analysis of ALOGP and CLOGP Methods J Phys Chem 102 3762 3772 1:CAS:528:DyaK1cXis12rsrY%3D
49. W Heiden G Moeckel J Brickmann 1993 A new approach to analysis and display of local lipophilicity/hydrophilicity mapped on molecular surfaces J Comput Aided Mol Des 7 503 514 1:CAS:528:DyaK2cXivFent7c%3D 10.1007/BF00124359