Fragment growing induces conformational changes in acetylcholine-binding protein: a structural and thermodynamic analysis

E.S. Edink, P. Rucktooa, K. Retra, A. Akdemir, T.T. Nahar, O.P. Zuiderveld, R. van Elk, E. Janssen, P. van Nierop, J.E. van Muijlwijk-Koezen, A.B. Smit, T.K. Sixma, R. Leurs, I.J.P. de Esch

Research output: Contribution to JournalArticleAcademicpeer-review

Abstract

Optimization of fragment hits toward high-affinity lead compounds is a crucial aspect of fragment-based drug discovery (FBDD). In the current study, we have successfully optimized a fragment by growing into a ligand-inducible subpocket of the binding site of acetylcholine-binding protein (AChBP). This protein is a soluble homologue of the ligand binding domain (LBD) of Cys-loop receptors. The fragment optimization was monitored with X-ray structures of ligand complexes and systematic thermodynamic analyses using surface plasmon resonance (SPR) biosensor analysis and isothermal titration calorimetry (ITC). Using site-directed mutagenesis and AChBP from different species, we find that specific changes in thermodynamic binding profiles, are indicative of interactions with the ligand-inducible subpocket of AChBP. This study illustrates that thermodynamic analysis provides valuable information on ligand binding modes and is complementary to affinity data when guiding rational structure- and fragment-based discovery approaches.

Original languageEnglish
Pages (from-to)5363-5371
Number of pages9
JournalJournal of the American Chemical Society
Volume133
Issue number14
DOIs
Publication statusPublished - 15 Feb 2011

Keywords

  • Calorimetry
  • Carrier Proteins/chemistry
  • Crystallography, X-Ray
  • Drug Discovery/methods
  • Ligands
  • Models, Molecular
  • Mutagenesis, Site-Directed
  • Protein Conformation/drug effects
  • Protein Stability/drug effects
  • Reproducibility of Results
  • Species Specificity
  • Surface Plasmon Resonance
  • Thermodynamics
  • Tyrosine

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