title: Fragment growing induces conformational changes in acetylcholine-binding protein: a structural and thermodynamic analysis.
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.
authors.affiliation: Leiden/Amsterdam Center of Drug Research (LACDR), Division of Medicinal Chemistry, Faculty of Sciences, VU University Amsterdam, The Netherlands.
authors.forename: Ewald
authors.initials: E
authors.lastname: Edink
authors.forename: Prakash
authors.initials: P
authors.lastname: Rucktooa
authors.forename: Kim
authors.initials: K
authors.lastname: Retra
authors.forename: Atilla
authors.initials: A
authors.lastname: Akdemir
authors.forename: Tariq
authors.initials: T
authors.lastname: Nahar
authors.forename: Obbe
authors.initials: O
authors.lastname: Zuiderveld
authors.forename: René
authors.initials: R
authors.lastname: van Elk
authors.forename: Elwin
authors.initials: E
authors.lastname: Janssen
authors.forename: Pim
authors.initials: P
authors.lastname: van Nierop
authors.forename: Jacqueline
authors.initials: J
authors.lastname: van Muijlwijk-Koezen
authors.forename: August B
authors.initials: AB
authors.lastname: Smit
authors.forename: Titia K
authors.initials: TK
authors.lastname: Sixma
authors.forename: Rob
authors.initials: R
authors.lastname: Leurs
authors.forename: Iwan J P
authors.initials: IJ
authors.lastname: de Esch
mesh_terms: D002151:Calorimetry; D002352:Carrier Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D018360:Crystallography, X-Ray; D055808:Drug Discovery / Q000379:methods*; D008024:Ligands; D008958:Models, Molecular; D016297:Mutagenesis, Site-Directed; D011487:Protein Conformation / Q000187:drug effects; D055550:Protein Stability / Q000187:drug effects; D015203:Reproducibility of Results; D013045:Species Specificity; D020349:Surface Plasmon Resonance; D013816:Thermodynamics; D014443:Tyrosine
chemical_list: C428944:AChBP protein, Lymnaea; D002352:Carrier Proteins; D008024:Ligands; D014443:Tyrosine