Conformational changes induced by fragment growing: A structural and thermodynamic analysis

Abstract

Neuronal nicotinic acetylcholine receptors (nAChRs) are potential therapeutic targets for the treatment of pain, epilepsy and a wide variety of neurodegenerative and psychiatric disorders e.g. Alzheimer's disease, Parkinson's disease, schizophrenia and depression. Several important physiological processes appear to be regulated by a single or a few nAChR subtypes.1 Subtype selective ligands are needed to aid target validation for the development of safe and selective drugs. However, due to high homology between the binding sites of the different subtypes, the design of selective ligands poses an interesting challenge. Recently, high-quality X-ray structures of several acetylcholinebinding proteins (AChBPs) co-crystallized with ligands, have become available.2,3 These proteins are water soluble homologs of the ligand-binding domain of nAChRs.4 Fragment library screening using a variety of orthogonal biochemical and biophysical approaches has resulted in the identification of novel hit fragments. Several of these fragments have been co-crystallized with AChBP. We here describe the growing of one of these fragments into a sub-pocket of the binding site that becomes accessible upon a ligand-induced change in rotameric state of a gatekeeper tyrosine residue. These studies were guided by pharmacological, structural and thermodynamic data and illustrate the detailed insights and molecular understanding that can be obtained by fragment-based design approaches.