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

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Thermodynamics
Acetylcholine
Carrier Proteins
Ligands
Cysteine Loop Ligand-Gated Ion Channel Receptors
Calorimetry
Surface Plasmon Resonance
Biosensing Techniques
Drug Discovery
Site-Directed Mutagenesis
Binding Sites
X-Rays
Proteins

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

Cite this

Edink, E.S. ; Rucktooa, P. ; Retra, K. ; Akdemir, A. ; Nahar, T.T. ; Zuiderveld, O.P. ; van Elk, R. ; Janssen, E. ; van Nierop, P. ; van Muijlwijk-Koezen, J.E. ; Smit, A.B. ; Sixma, T.K. ; Leurs, R. ; de Esch, I.J.P. / Fragment growing induces conformational changes in acetylcholine-binding protein : a structural and thermodynamic analysis. In: Journal of the American Chemical Society. 2011 ; Vol. 133, No. 14. pp. 5363-5371.
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author = "E.S. Edink and P. Rucktooa and K. Retra and A. Akdemir and T.T. Nahar and O.P. Zuiderveld and {van Elk}, R. and E. Janssen and {van Nierop}, P. and {van Muijlwijk-Koezen}, J.E. and A.B. Smit and T.K. Sixma and R. Leurs and {de Esch}, I.J.P.",
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Fragment growing induces conformational changes in acetylcholine-binding protein : a structural and thermodynamic analysis. / Edink, E.S.; Rucktooa, P.; Retra, K.; Akdemir, A.; Nahar, T.T.; Zuiderveld, O.P.; van Elk, R.; Janssen, E.; van Nierop, P.; van Muijlwijk-Koezen, J.E.; Smit, A.B.; Sixma, T.K.; Leurs, R.; de Esch, I.J.P.

In: Journal of the American Chemical Society, Vol. 133, No. 14, 15.02.2011, p. 5363-5371.

Research output: Contribution to JournalArticleAcademicpeer-review

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T2 - a structural and thermodynamic analysis

AU - Edink, E.S.

AU - Rucktooa, P.

AU - Retra, K.

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AU - Nahar, T.T.

AU - Zuiderveld, O.P.

AU - van Elk, R.

AU - Janssen, E.

AU - van Nierop, P.

AU - van Muijlwijk-Koezen, J.E.

AU - Smit, A.B.

AU - Sixma, T.K.

AU - Leurs, R.

AU - de Esch, I.J.P.

N1 - © 2011 American Chemical Society

PY - 2011/2/15

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N2 - 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.

AB - 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.

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KW - Carrier Proteins/chemistry

KW - Crystallography, X-Ray

KW - Drug Discovery/methods

KW - Ligands

KW - Models, Molecular

KW - Mutagenesis, Site-Directed

KW - Protein Conformation/drug effects

KW - Protein Stability/drug effects

KW - Reproducibility of Results

KW - Species Specificity

KW - Surface Plasmon Resonance

KW - Thermodynamics

KW - Tyrosine

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DO - 10.1021/ja110571r

M3 - Article

VL - 133

SP - 5363

EP - 5371

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

SN - 0002-7863

IS - 14

ER -