Skip to main content

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


A series of 51 5-HT2A partial agonistic arylethylamines (primary or benzylamines) from different structural classes (indoles, methoxybenzenes, quinazolinediones) was investigated by fragment regression analysis (FRA), docking and 3D-QSAR approaches. The data, pEC50 values and intrinsic activities (Emax) on rat arteries, show high variability of pEC50 from 4 to 10 and of Emax from 15 to 70%. FRA indicates which substructures affect potency or intrinsic activity. The high contribution of halogens in para position of phenethylamines to pEC50 points to a specific hydrophobic pocket. Other results suggest the significance of hydrogen bonds of the aryl moiety for activation and the contrary effect of benzyl groups on affinity (increasing) and intrinsic activity (decreasing). Results from fragment regression and data on all available mutants were considered to derive a common binding site at the rat 5-HT2A receptor. After generation and MD simulations of a receptor model based on the β2-adrenoceptor structure, typical derivatives were docked, leading to the suggestion of common interactions, e.g., with serines in TM3 and TM5 and with a cluster of aromatic amino acids in TM5 and TM6. The whole series was aligned by docking and minimization of the complexes. The pEC50 values correlate well with Sybyl docking energies and hydrophobicity of the aryl moieties. With this alignment, CoMFA and CoMSIA approaches based on a training set of 36 and a test set of 15 compounds were performed. The correlation of pEC50 with steric, electrostatic, hydrophobic and H-bond acceptor fields resulted in sufficient fit (q 2: 0.75–0.8, r 2: 0.92–0.95) and predictive power (r 2pred : 0.85–0.88). The important interaction regions largely reflect the patterns provided by the putative binding site. In particular, the fit of the aryl moieties and benzyl substituents to two hydrophobic pockets is evident.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4



Human 5-HT2A receptor


Rat 5-HT2A receptor


Human β2 adrenoceptor


G-protein coupled receptor


Transmembranous segment


Fragment regression analysis


Comparative molecular field analysis


Comparative molecular similarity index analysis


Partial least squares analysis


Principal component


Three-dimensional quantitative structure–activity relationships


  1. 1.

    Peroutka SJ (1990) 5-Hydroxytryptamine receptor subtypes. Pharmacol Toxicol 67:373–383

    CAS  Article  Google Scholar 

  2. 2.

    Rapport MM, Green AA, Page IH (1947) Purification of the substance which is responsible for vasoconstrictor activity of serum. Fed Proc 6:184

    CAS  Google Scholar 

  3. 3.

    Rapport MM, Green AA, Page IH (1948) Serum vasoconstrictor (serotonin): isolation and characterization. J Biol Chem 176:1243–1251

    CAS  Google Scholar 

  4. 4.

    Roth BL, Willins DL, Kristiansen K, Kroeze WK (1998) 5-Hydroxytryptamine2-family receptors (5-hydroxytryptamine2A, 5-hydroxytryptamine2B, 5-hydroxytryptamine2C): where structure meets function. Pharmacol Ther 79:231–257

    CAS  Article  Google Scholar 

  5. 5.

    Zifa E, Fillion G (1992) 5-Hydroxytryptamine Receptors. Pharmacol Rev 44:401–457

    CAS  Google Scholar 

  6. 6.

    Nichols DE, Nichols CD (2008) Serotonin receptors. Chem Rev 108:1614–1641

    CAS  Article  Google Scholar 

  7. 7.

    Braden MR, Parrish JC, Naylor JC, Nichols DE (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

    CAS  Article  Google Scholar 

  8. 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. 9.

    Elz S, Kläß T, Warnke U, Pertz HH (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

    Article  Google Scholar 

  10. 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. 11.

    Heim R, Pertz HH, Walther I, Elz S (1998) Congeners of 3-(2-Benzylaminoethyl)-2, 4-quinazolindione: partial agonists for rat vascular 5-HT2A receptors. Naunyn-Schmiedeberg’s Arch Pharmacol 358:R105

    Google Scholar 

  12. 12.

    Heim R, Pertz HH, Zabel M, Elz S (2002) Stereoselective synthesis, absolute configuration and 5-HT2A agonism of chiral 2-methoxybenzylamines. Arch Pharm Pharm Med Chem 335:82

    Google Scholar 

  13. 13.

    Pertz HH, Heim R, Elz S (2000) N-benzylated phenylethanamines are highly potent partial agonists at 5-HT2A receptors. Arch Pharm Pharm Med Chem 333:30

    Google Scholar 

  14. 14.

    Ratzeburg K, Heim R, Mahboobi S, Henatsch J, Pertz HH, Elz S (2003) Potent partial 5-HT2A-receptor agonism of phenylethamines related to mescaline in the rat tail artery model. Naunyn-Schmiedeberg’s Arch Pharmacol 367:R31

    Google Scholar 

  15. 15.

    Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SG, Thian FS, Kobilka TS, Choi HJ, Kuhn P, Weis WI, Kobilka BK, Stevens RC (2007) High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor. Science 318:1258–1265

    CAS  Article  Google Scholar 

  16. 16.

    Rasmussen SG, Choi HJ, Rosenbaum DM, Kobilka TS, Thian FS, Edwards PC, Burghammer M, Ratnala VR, Sanishvili R, Fischetti RF, Schertler GF, Weis WI, Kobilka BK (2007) Crystal structure of the human beta2 adrenergic G-protein-coupled receptor. Nature 450:383–387

    CAS  Article  Google Scholar 

  17. 17.

    Gasteiger E, Gattiker A, Hoogland C, Ivanyi I, Appel RD, Bairoch A (2003) ExPASy: the proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res 31:3784–3788

    CAS  Article  Google Scholar 

  18. 18.

    Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25:1157–1174

    CAS  Article  Google Scholar 

  19. 19.

    Lovell SC, Word JM, Richardson JS, Richardson DC (2000) The penultimate rotamer library. Proteins 40:389–408

    CAS  Article  Google Scholar 

  20. 20.

    Strasser A, Striegl B, Wittmann HJ, Seifert R (2008) Pharmacological profile of histaprodifens at four recombinant histamine H-1 receptor species isoforms. J Pharmacol Exp Ther 324:60–71

    CAS  Article  Google Scholar 

  21. 21.

    Van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701–1718

    Article  Google Scholar 

  22. 22.

    Oostenbrink C, Villa A, Mark AE, Van Gunsteren WF (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

    CAS  Article  Google Scholar 

  23. 23.

    Sealfon SC, Chi L, Ebersole BJ, Rodic V, Zhang D, Ballesteros J, Weinstein H (1995) Related contribution of specific helix 2 and 7 residues to conformational activation of the serotonin 5-HT2A receptor. J Biol Chem 28:16683–16688

    Google Scholar 

  24. 24.

    Wang CD, Gallaher TK, Shih JC (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

    CAS  Google Scholar 

  25. 25.

    Almaula N, Ebersole BJ, Zhang D, Weinstein H, Sealfon SC (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

    CAS  Article  Google Scholar 

  26. 26.

    Johnson MP, Loncharich RJ, Baez M, Nelson DL (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

    CAS  Google Scholar 

  27. 27.

    Johnson MP, Wainscott DB, Lucaites VL, Baez M, Nelson DL (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

    CAS  Article  Google Scholar 

  28. 28.

    Shapiro DA, Kristiansen K, Kroeze WK, Roth BL (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

    CAS  Google Scholar 

  29. 29.

    Choudhary MS, Craigo S, Roth BL (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

    CAS  Google Scholar 

  30. 30.

    Choudhary MS, Sachs N, Uluer A, Glennon RA, Westkaemper RB, Roth BL (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

    CAS  Google Scholar 

  31. 31.

    Ballesteros JA, Weinstein H (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

    CAS  Article  Google Scholar 

  32. 32.

    Clark M, Cramer I RD, Van Opdenbosch N (1989) Validation of the general purpose tripos 5.2 force field. J Comp Chem 10:982–1012

    CAS  Article  Google Scholar 

  33. 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

    Google Scholar 

  34. 34.

    Giger R (1989) Actual Chim Ther 16:151–186

    CAS  Google Scholar 

  35. 35.

    Cramer I RD, Patterson DE, Buce JD (1988) Comparative molecular field analysis (CoMFA): effect of shape on binding of steroids to carrier protein. J Am Chem Soc 110:5959–5967

    Article  Google Scholar 

  36. 36.

    Klebe G, Abraham U, Mietzner T (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

    CAS  Article  Google Scholar 

  37. 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

    Google Scholar 

  38. 38.

    Wold S, Ruhe A, Wold H, Dunn WJ (1984) The covariance problem in linear regression. The partial least squares (PLS) approach to generalized inverses. SIAM J Sci Stat Comp 5:735–743

    Article  Google Scholar 

  39. 39.

    Cramer I RD, Buce JD, Petterson DE (1988) Crossvalidation, bootstrapping, and partial least squares compared with multiple regression in conventional QSAR studies. Quant Struct-Act Relat 7:18–25

    Article  Google Scholar 

  40. 40.

    Clark RD, Fox PC (2004) Statistical variation in progressive scrambling. J Comput Aided Mol Des 18:563–576

    CAS  Article  Google Scholar 

  41. 41.

    Golbraikh A, Tropsha A (2002) Beware of q(2)!. J Mol Graph Model 20:269–276

    CAS  Article  Google Scholar 

  42. 42.

    Doweyko AM (2004) 3D-QSAR illusions. J Comput Aided Mol Des 18:587–596

    CAS  Article  Google Scholar 

  43. 43.

    Roth BL, Choudhary MS, Khan N, Uluer AZ (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

    CAS  Google Scholar 

  44. 44.

    Roth BL, Shoham M, Choudhary MS, Khan N (1997) Identification of conserved aromatic residues essential for agonist binding and second messenger production at 5-hydroxytryptamine2A receptors. Mol Pharmacol 52:259–266

    CAS  Google Scholar 

  45. 45.

    Warne T, Serrano-Vega MJ, Baker JG, Moukhametzianov R, Edwards PC, Henderson R, Leslie AGW, Tate CG, Schertler GFX (2008) Structure of a β1-adrenergic G-protein-coupled receptor. Nature 454:U482–U486

    Article  Google Scholar 

  46. 46.

    Scheerer P, Park JH, Hildebrand PW, Kim YJ, Krauss N, Choe HW, Hofmann KP, Ernst OP (2008) Crystal structure of opsin in its G-protein-interacting conformation. Nature 455:497–503

    CAS  Article  Google Scholar 

  47. 47.

    Kubinyi H, Hamprecht FA, Mietzner T (1998) Three-dimensional quantitative similarity-activity relationships (3D QSiAR) from SEAL similarity matrices. J Med Chem 41:2553–2564

    CAS  Article  Google Scholar 

  48. 48.

    Ghose AK, Viswanadhan VN, Wendoloski JJ (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

    CAS  Google Scholar 

  49. 49.

    Heiden W, Moeckel G, Brickmann J (1993) A new approach to analysis and display of local lipophilicity/hydrophilicity mapped on molecular surfaces. J Comput Aided Mol Des 7:503–514

    CAS  Article  Google Scholar 

Download references


This work was supported by the Graduate Training Program (Graduiertenkolleg) GRK 760, “Medicinal Chemistry: Molecular Recognition - Ligand-Receptor Interactions”, of the Deutsche Forschungsgemeinschaft.

Author information



Corresponding author

Correspondence to Stefan Dove.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Silva, M.E., Heim, R., Strasser, A. et al. Theoretical studies on the interaction of partial agonists with the 5-HT2A receptor. J Comput Aided Mol Des 25, 51–66 (2011).

Download citation


  • 5-HT2A receptor
  • Partial agonists
  • GPCR modeling
  • Docking
  • 3D-QSAR