Functional Probes of Drug–Receptor Interactions Implicated by Structural Studies: Cys-Loop Receptors Provide a Fertile Testing Ground

Abstract

Structures of integral membrane receptors provide valuable models for drug–receptor interactions across many important classes of drug targets and have become much more widely available in recent years. However, it remains to be determined to what extent these images are relevant to human receptors in their biological context and how subtle issues such as subtype selectivity can be informed by them. The high precision structural modifications enabled by unnatural amino acid mutagenesis on mammalian receptors expressed in vertebrate cells allow detailed tests of predictions from structural studies. Using the Cys-loop superfamily of ligand-gated ion channels, we show that functional studies lead to detailed binding models that, at times, are significantly at odds with the structural studies on related invertebrate proteins. Importantly, broad variations in binding interactions are seen for very closely related receptor subtypes and for varying drugs at a given binding site. These studies highlight the essential interplay between structural studies and functional studies that can guide efforts to develop new pharmaceuticals.

Cation–π interactions: computational analyses of the aromatic box motif and the fluorination strategy for experimental evaluation

“…The largest contribution comes from TrpB, the residue that has been shown experimentally to make a functionally important cation-π interaction in most nAChRs. 4 …”

“…In our experimental studies of a possible cation-π interaction to a Phe or a Tyr, 4 we have used 4-F-Phe, 3,5-F 2 -Phe, and 3,4,5-F 3 -Phe as our cation-π interaction probes, while for Trp we use the 5-, 5,7-, 5,6,7-, and 4,5,6,7-fluorotryptophans. As such, we have focused on the analogous benzenes and indoles for our computational studies (Tables 2 and 5).…”

“…4 We can now preform more realistic comparisons. For primary amines, the previously described cation-π interaction between glycine and fluorinated phenylalanine residues in the glycine receptor 46 was re-evaluated using the results for the binding of an ammonium ion to fluorinated benzenes.…”

“…Over the past 20 years we have addressed this issue using non-canonical amino acid mutagenesis. 4, 8 The aromatic of interest (the side chain of a phenylalanine (Phe), tyrosine (Tyr), or tryptophan (Trp)) is progressively fluorinated. Fluorine is well known to be deactivating in a cation-π interaction, and its effects are typically additive.…”

Biomolecular recognition of antagonists by α7 nicotinic acetylcholine receptor: Antagonistic mechanism and structure–activity relationships studies

“…Nevertheless, neuronal nAChRs are also confirmed to be connected intimately with many kinds of diseases, e.g. Alzheimer's disease, epilepsy, neurodegeneration and cognitive deficits in Parkinson's disease, and schizophrenia (Changeux and Edelstein, 2005;Zhang et al, 2012;van Arnam and Dougherty, 2014). Normally, it has yielded the viewpoint that neuronal nAChRs exercise a principally regulative effect in the CNS, and this notion has been ratified by several biological proofs (van Arnam et al, 2013;Schaaf, 2014).…”