Advertisement

Structure-based exploration of an allosteric binding pocket in the NTS1 receptor using bitopic NT(8-13) derivatives and molecular dynamics simulations

  • Ralf Christian Kling
  • Carolin Burchardt
  • Jürgen Einsiedel
  • Harald Hübner
  • Peter GmeinerEmail author
Original Paper
Part of the following topical collections:
  1. Tim Clark 70th Birthday Festschrift

Abstract

Crystal structures of neurotensin receptor subtype 1 (NTS1) allowed us to visualize the binding mode of the endogenous peptide hormone neurotensin and its pharmacologically active C-terminal fragment NT(8-13) within the orthosteric binding pocket of NTS1. Beneath the orthosteric binding pocket, we detected a cavity that exhibits different sequences in the neurotensin receptor subtypes NTS1 and NTS2. In this study, we explored this allosteric binding pocket using bitopic test peptides of type NT(8-13)-Xaa, in which the C-terminal part of NT(8-13) is connected to different amino acids that extend into the newly discovered pocket. Our test compounds showed nanomolar affinities for NTS1, a measurable increase in subtype selectivity compared to the parent peptide NT(8-13), and the capacity to activate the receptor in an IP accumulation assay. Computational investigation of the selected test compounds at NTS1 showed a conserved binding mode within the orthosteric binding pocket, whereas the allosteric cavity was able to adapt to different residues, which suggests a high degree of structural plasticity within that cavity of NTS1.

Keywords

Structure-based drug design Allosteric binding pocket Neurotensin receptor GPCR ligands Peptide Subtype selectivity Molecular dynamics simulations SPPS 

Notes

Supplementary material

894_2019_4064_MOESM1_ESM.docx (10 mb)
ESM 1 (DOCX 10271 kb)

References

  1. 1.
    Carraway R, Leeman SE (1975) The amino acid sequence of a hypothalamic peptide, neurotensin. J Biol Chem 250:1907–1911Google Scholar
  2. 2.
    Binder EB, Kinkead B, Owens MJ, Nemeroff CB (2001) Neurotensin and dopamine interactions. Pharmacol Rev 53:453–486PubMedGoogle Scholar
  3. 3.
    Kasckow J, Nemeroff CB (1991) The neurobiology of neurotensin: focus on neurotensin-dopamine interactions. Regul Pept 36:153–164Google Scholar
  4. 4.
    Fuxe K, Von Euler G, Agnati LF et al (1992) Intramembrane interactions between neurotensin receptors and dopamine D2 receptors as a major mechanism for the neuroleptic-like action of neurotensin. Ann New York Acad Sci 668:186–204CrossRefGoogle Scholar
  5. 5.
    Clineschmidt BV, McGuffin JC, Bunting PB (1979) Neurotensin: antinocisponsive action in rodents. Eur J Pharmacol 54:129–139CrossRefGoogle Scholar
  6. 6.
    Boules M, Liang Y, Briody S et al (2010) NT79: a novel neurotensin analog with selective behavioral effects. Brain Res 1308:35–46.  https://doi.org/10.1016/j.brainres.2009.10.050
  7. 7.
    Schaab C, Kling RC, Einsiedel J et al (2014) Structure-based evolution of subtype-selective neurotensin receptor ligands. Chem Open 3:206–218.  https://doi.org/10.1002/open.201402031 CrossRefGoogle Scholar
  8. 8.
    Einsiedel J, Held C, Hervet M et al (2011) Discovery of highly potent and neurotensin receptor 2 selective neurotensin mimetics. J Med Chem 54:2915–2923.  https://doi.org/10.1021/jm200006c CrossRefPubMedGoogle Scholar
  9. 9.
    Harterich S, Koschatzky S, Einsiedel J, Gmeiner P (2008) Novel insights into GPCR–peptide interactions: mutations in extracellular loop 1, ligand backbone methylations and molecular modeling of neurotensin receptor 1. Bioorg Med Chem 16:9359–9368.  https://doi.org/10.1016/j.bmc.2008.08.051
  10. 10.
    Held C, Hübner H, Kling R et al (2013) Impact of the proline residue on ligand binding of neurotensin receptor 2 (NTS2)-selective peptide-peptoid hybrids. ChemMedChem 8:772–778.  https://doi.org/10.1002/cmdc.201300054 CrossRefPubMedGoogle Scholar
  11. 11.
    Pratsch G, Unfried JF, Einsiedel J et al (2011) Radical arylation of tyrosine and its application in the synthesis of a highly selective neurotensin receptor 2 ligand. Org Biomol Chem 9:3746–3752.  https://doi.org/10.1039/C1ob05292f CrossRefPubMedGoogle Scholar
  12. 12.
    Einsiedel J, Hubner H, Hervet M et al (2008) Peptide backbone modifications on the C-terminal hexapeptide of neurotensin. Bioorg Med Chem Lett 18:2013–2018.  https://doi.org/10.1016/j.bmcl.2008.01.110 CrossRefPubMedGoogle Scholar
  13. 13.
    Richelson E, McCormick DJ, Pang Y-P, Phillips KS (2009) Peptide analogs that are potent and selective for human neurotensin preceptor subtype 2. US Patent US20110263507A1Google Scholar
  14. 14.
    Cusack B, McCormick DJ, Pang YP et al (1995) Pharmacological and biochemical profiles of unique neurotensin 8-13 analogs exhibiting species selectivity, stereoselectivity, and superagonism. J Biol Chem 270:18359–18366CrossRefGoogle Scholar
  15. 15.
    Tourwe D, Iterbeke K, Török G, et al (2002) Pro10-Tyr11 substitutions provide potent or selective NT(8-13) analogs. In: Benedetti E, Pedone C (eds) Peptides 2002, Proc 27th European Peptide Symposium, Napoli, Italy, 31 Aug–6 Sept 2002, pp 304–305Google Scholar
  16. 16.
    Valant C, Robert Lane J, Sexton PM, Christopoulos A (2012) The best of both worlds? Bitopic orthosteric/allosteric ligands of g protein-coupled receptors. Ann Rev Pharmacol Toxicol 52:153–178.  https://doi.org/10.1146/annurev-pharmtox-010611-134514 CrossRefGoogle Scholar
  17. 17.
    Kruse AC, Ring AM, Manglik A et al (2013) Activation and allosteric modulation of a muscarinic acetylcholine receptor. Nature 504:101–106.  https://doi.org/10.1038/nature12735 CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Tan Q, Zhu Y, Li J et al (2013) Structure of the CCR5 chemokine receptor-HIV entry inhibitor maraviroc complex. Science 341:1387–1390.  https://doi.org/10.1126/science.1241475 CrossRefPubMedGoogle Scholar
  19. 19.
    Wu B, Chien EY, Mol CD et al (2010) Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science 330:1066–1071.  https://doi.org/10.1126/science.1194396 CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Egloff P, Hillenbrand M, Klenk C et al (2014) Structure of signaling-competent neurotensin receptor 1 obtained by directed evolution in Escherichia coli. Proc Natl Acad Sci USA 111:655–662.  https://doi.org/10.1073/pnas.1317903111
  21. 21.
    White JF, Noinaj N, Shibata Y et al (2012) Structure of the agonist-bound neurotensin receptor. Nature 490:508–513.  https://doi.org/10.1038/nature11558 CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Hubner H, Haubmann C, Utz W, Gmeiner P (2000) Conjugated enynes as nonaromatic catechol bioisosteres: synthesis, binding experiments, and computational studies of novel dopamine receptor agonists recognizing preferentially the D(3) subtype. J Med Chem 43:756–762CrossRefGoogle Scholar
  23. 23.
    Jordan M, Schallhorn A, Wurm FM (1996) Transfecting mammalian cells: optimization of critical parameters affecting calcium-phosphate precipitate formation. Nucleic Acids Res 24:596–601CrossRefGoogle Scholar
  24. 24.
    Lowry OH, Rosebrough NJ, Farr AL, Randall RJ (1951) Protein measurement with the Folin phenol reagent. J Biol Chem 193:265–275PubMedPubMedCentralGoogle Scholar
  25. 25.
    Cheng Y, Prusoff WH (1973) Relationship between the inhibition constant (K1) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction. Biochem Pharmacol 22:3099–3108CrossRefGoogle Scholar
  26. 26.
    Liu H, Hofmann J, Fish I et al (2018) Structure-guided development of selective M3 muscarinic acetylcholine receptor antagonists. Proc Natl Acad Sci 115:12046–12050.  https://doi.org/10.1073/pnas.1813988115 CrossRefPubMedGoogle Scholar
  27. 27.
    Weichert D, Kruse AC, Manglik A et al (2014) Covalent agonists for studying G protein-coupled receptor activation. Proc Natl Acad Sci USA 111:10744–10748.  https://doi.org/10.1073/pnas.1410415111 CrossRefPubMedGoogle Scholar
  28. 28.
    Šali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Molec Biol 234:779–815.  https://doi.org/10.1006/jmbi.1993.1626
  29. 29.
    Hiller C, Kling RC, Heinemann FW et al (2013) Functionally selective dopamine D2/D3 receptor agonists comprising an enyne moiety. J Med Chem 56:5130–5141.  https://doi.org/10.1021/jm400520c CrossRefPubMedGoogle Scholar
  30. 30.
    Hornak V, Abel R, Okur A et al (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65:712–725.  https://doi.org/10.1002/prot.21123
  31. 31.
    van der Spoel D, Lindahl E, Hess B et al (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701–1718.  https://doi.org/10.1002/jcc.20291
  32. 32.
    Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theor Comput 4:435–447.  https://doi.org/10.1021/ct700301q
  33. 33.
    Möller D, Kling RC, Skultety M et al (2014) Functionally selective dopamine D2, D3 receptor partial agonists. J Med Chem 57:4861–4875.  https://doi.org/10.1021/jm5004039 CrossRefPubMedGoogle Scholar
  34. 34.
    Goetz A, Lanig H, Gmeiner P, Clark T (2011) Molecular dynamics simulations of the effect of the G-protein and diffusible ligands on the β2-adrenergic receptor. J Molec Biol 414:611–623.  https://doi.org/10.1016/j.jmb.2011.10.015
  35. 35.
    Schrodinger, LLC (2010) The PyMOL molecular graphics system, version 1.3r1. Schrodinger, LLC, New YorkGoogle Scholar
  36. 36.
    Pettersen EF, Goddard TD, Huang CC et al (2004) UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612.  https://doi.org/10.1002/jcc.20084

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Ralf Christian Kling
    • 1
    • 2
  • Carolin Burchardt
    • 1
  • Jürgen Einsiedel
    • 1
  • Harald Hübner
    • 1
  • Peter Gmeiner
    • 1
    Email author
  1. 1.Department of Chemistry and PharmacyFriedrich Alexander UniversityErlangenGermany
  2. 2.ABF-Pharmazie GmbHFürthGermany

Personalised recommendations