The Quantum Nature of Drug-Receptor Interactions: Deuteration Changes Binding Affinities for Histamine Receptor Ligands

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.

Experimental evaluation of the generalized vibrational theory of G protein-coupled receptor activation

“…These findings do not argue for the irrelevancy of isotopic exchange, but do relegate the majority of this concern to binding. Isotope effects on the binding of a ligand with a protein have been examined extensively (85,86) and were the subject of a recent paper on the H2 histamine receptor (58). Whereas Kržan et al (58) detected small alterations in the binding of ligand to receptor due to isotope exchange and conclude with possibly relevant comments concerning the VTO, we considered both the affinity and the functional activity.…”

“…Isotope effects on the binding of a ligand with a protein have been examined extensively (85,86) and were the subject of a recent paper on the H2 histamine receptor (58). Whereas Kržan et al (58) detected small alterations in the binding of ligand to receptor due to isotope exchange and conclude with possibly relevant comments concerning the VTO, we considered both the affinity and the functional activity. By considering both aspects, we are able to draw conclusions regarding the activation of the proteinaddressing the VTO directly-while retaining knowledge of possible binding effects.…”

“…Turin-within the contemporary VTO-hypothesized that the active site of the GPCR [specifically an OR, although later works considered generalizing this hypothesis (18,36,58)] acts as an ET junction (11). According to the theory, an electron emerges from a donation site-likely a metal atom acting as a cofactor (11,31), redox chemistry (59), or peptide sidechain (11,60) capable of oxidation-and traverses the active site to an acceptor site, which is likely a specific motif or residue sidechain.…”

Arginine side chain stacking with peptide plane stabilizes the protein helix conformation in a cooperative way

“…Potentially, one can use this chemical shift to monitor the R – PP stacking effect on the h‐bond. Recently, it has also been shown that deuteration can affect the binding of small molecules to a protein presumably through perturbing h‐bonds . This isotope effect may provide new insight into h‐bond interactions and some hint in the cooperativity study.…”

Molecule‐Membrane Interactions in Biological Cells Studied with Second Harmonic Light Scattering

“…Furthermore, the patch clamp technique cannot be used as the basis of an imaging modality. Fluorescence based techniques, on the other hand, are plagued by concerns over the relative inertness of the molecular label and are generally ill‐equipped for dynamically resolving surface specific interactions in multi‐membrane cells.…”