Abstract
In this article we report a combined experimental and computational study concerning the effects of deuteration on the binding of histamine and two other histaminergic agonists to 3H-tiotidine-labeled histamine H2 receptor in neonatal rat astrocytes. Binding affinities were measured by displacing radiolabeled tiotidine from H2 receptor binding sites present on cultured neonatal rat astrocytes. Quantum-chemical calculations were performed by employing the empirical quantization of nuclear motion within a cluster model of the receptor binding site extracted from the homology model of the entire H2 receptor. Structure of H2 receptor built by homology modelling is attached in the supporting information (S1 Table) Experiments clearly demonstrate that deuteration affects the binding by increasing the affinity for histamine and reducing it for 2-methylhistamine, while basically leaving it unchanged for 4-methylhistamine. Ab initio quantum-chemical calculations on the cluster system extracted from the homology H2 model along with the implicit quantization of the acidic N–H and O–H bonds demonstrate that these changes in the binding can be rationalized by the altered strength of the hydrogen bonding upon deuteration known as the Ubbelohde effect. Our computational analysis also reveals a new mechanism of histamine binding, which underlines an important role of Tyr250 residue. The present work is, to our best knowledge, the first study of nuclear quantum effects on ligand receptor binding. The ligand H/D substitution is relevant for therapy in the context of perdeuterated and thus more stable drugs that are expected to enter therapeutic practice in the near future. Moreover, presented approach may contribute towards understanding receptor activation, while a distant goal remains in silico discrimination between agonists and antagonists based on the receptor structure.
Highlights
G-protein coupled receptors (GPCR) are a family of septahelix transmembrane (TM) proteins found in eukaryotic organisms, which represent one of the main targets for drug action
In order to initiate downstream signal transduction leading to a receptor-mediated effect, a ligand-induced or a ligand-stabilized conformational change in the GPRC, which interacts with guanine nucleotide–binding proteins (G-proteins), is necessary
After building a homology model of the histamine H2 receptor and performing molecular dynamics simulations with bound histamine, we identified three residues crucial for histamine binding as Asp98, Asp186 and Tyr250, which bind histamine to its ethylamino group, N–H moiety on the imidazole ring and imino nitrogen atom of the same group, respectively (Fig 4)
Summary
G-protein coupled receptors (GPCR) are a family of septahelix transmembrane (TM) proteins found in eukaryotic organisms, which represent one of the main targets for drug action. GPCR have two main functions: ligand binding and signal propagation. In order to initiate downstream signal transduction leading to a receptor-mediated effect, a ligand-induced or a ligand-stabilized conformational change in the GPRC, which interacts with guanine nucleotide–binding proteins (G-proteins), is necessary. Most GPCR show some constitutive activity even in the absence of the ligand bound to them; ligands are described as agonists if they are capable of showing full efficacy, partial agonists show only partial biological response, antagonists if their binding to receptor does not involve any change of basal receptor activity, or inverse agonist, a ligand with negative efficacy. From the thermodynamic point of view, the binding of antagonists to their targets is usually associated with more favorable interaction free energy (affinity) with the receptor than agonists
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