Le pharmacorephore nicotinique : structures et interactions de liaison hydrogène d'agonistes de l'acetylcholine

La liaison hydrogène (liaison H) occupe un rôle central dans le processus de reconnaissance moléculaire des agonistes nicotiniques par les récepteurs nicotiniques de l'acétylcholine (nAChRs). Nous avons mesuré la basicité de liaison H d'une vingtaine de ligands neutres et/ou protonés caractérisés par une très large gamme d'affinité pour les sous unités 4 2 du système nerveux central. Les aspects biologiques et structuraux des nAChRs sont analysés à partir des résultats de la littérature pour acquérir toutes les informations nécessaires sur les interactions des agonistes avec les résidus du site de reconnaissance de la protéine. La méthodologie expérimentale utilisée pour l'analyse structurale des ligands et l'évaluation de leur basicité de liaison H fait appel à la spectroscopie IRTF et à la dipolemétrie. Les résultats sont systématiquement validés par des calculs théoriques réalisés sur les bases et sur les complexes par une méthode de la fonctionnelle de la densité. Les ligands neutres (nicotine nornicotine anabasine, cotinine, myosmine ...) qui possèdent des sites carbonyle, pyridine ou amine sont des composés polyfonctionnels et la basicité individuelle de chacun des sites a été mesurée ou calculée. Notre étude révèle l'existence d'une relation entre la basicité de liaison H du site protonable des ligands et leur affinité pour le récepteur. Les formes actives chargées de certains ligands peuvent également être analysées en solution sous forme de sels de l'acide picrique. Le degré de substitution de la tête ammonium apparaît comme un paramètre clef de l'affinité. Nos résultats montrent que l'une des raisons de la meilleure affinité de la nicotine pour les 4 2 nAChRs par rapport à l'acétylcholine pourrait résider dans le fait qu'un ammonium tertiaire possède un plus grand pouvoir donneur de liaison H qu'un ammonium quaternaire.The hydrogen bond (HB) is an essential feature of the molecular recognition process of nicotinic agonists by the nicotinic Acetylcholine receptors (nAChRs). We have measured the HB basicity of about twenty neutral and/or protonated ligands spanning a very large range of affinity for the 4 2 subunits of the central nervous system. The biological and structural aspects of the nAChRs are analysed from the iterature in order to get the necessary informations on the interactions between the agonists and the amino acid residues of the protein. The experimental method used for the structural analysis of the ligands and the HB basicity measurements are carried out by FTIR and dipolmetry. The results are systematically validated by theoretical calculations on the free bases and the complexes using a functional density method. Neutral ligands (nicotine nornicotine anabasine, cotinine, myosmine ...) bearing carbonyl, pyridine and amine sites are polyfunctional molecules and the basicity of all individual sites has been either measured or calculated. Our study shows that a relationship holds between the HB basicity of the amine protonable site and the receptor affinity. The charged active forms of some ligands have also been analysed in solution as picrate salts. The level of alkyl substitution of the cationic head appears as a key parameter for a good affinity. Our results show that one of the reasons of the best affinity for the 4 2 nAChRs of nicotine by comparison to acetylcholine could stem from the fact that a tertiary ammonium has a greater HB donating strength than a quaternary ammonium.NANTES-BU Sciences (441092104) / SudocSudocFranceF

New insights on the structural and molecular recognition properties of insecticides through computational chemistry: The challenging case of sulfoxaflor

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Structure et interactions moléculaires d agonistes et de modulateurs allostériques des récepteurs nicotiniques de l acétylcholine

La découverte de l acétylcholine binding protein (AChBP) a permis des avancées majeures dans la caractérisation des récepteurs nicotiniques de l acétylcholine (nAChRs). Dans le cadre de ce travail, une approche combinant la mise en oeuvre de méthodes expérimentales et de calculs quantiques issus de la théorie de la fonctionnelle de la densité (DFT) a été utilisée pour (i) déterminer les conformations de basse énergie et les interactions d une série de ligands des nAChRs (l ACh, la nicotine, l épibatidine, la galanthamine et la codéine) (ii) mettre à jour un motif structural de l AChBP jouant un rôle majeur dans l interaction avec les agonistes (iii) étudier la complexation de trois ligands avec un modèle tridimensionnel du site de fixation par une méthode mixte QM/QM . Ainsi, malgré l importante similitude structurale de la galanthamine et de la codéine, la confrontation des résultats obtenus au cours de ce travail révèle des différences d interactions par liaison H significatives entre les deux composés. Par ailleurs, le motif structural mis à jour, qui comprend le Trp 143, impliqué dans la fixation des agonistes, et l Asp 85, hautement conservé dans la famille des canaux ioniques, a été caractérisé de façon approfondie, l influence d un effet coopératif sur le réseau de liaison H formé étant démontrée. Enfin, l ordre énergétique d interaction ACh<Nicotine<Epibatidine rapporté dans la littérature a été reproduit par nos simulations, validées par le bon accord des résultats obtenus avec les données expérimentales disponibles. Cette séquence d affinité a été rationalisée par une analyse fine de paramètres géométriques clés des interactions agonistes-AChBP.The discovery of the Acetylcholine Binding Protein (AChBP) has allowed major breakthroughs in the characterization of nicotinic acetylcholine receptors (nAChRs). In this work, a combined approach based on the use of various experimental methods and of theoretical calculations from density functional theory (DFT) has allowed to (i) determine the conformations and interactions of five nAChRs ligands (ACh, nicotine, epibatidine, galanthamine and codeine) in various environments (ii) shed light on a structural motif of AChBP playing a key role in the agonist binding (iii) study the complexation of ACh, nicotine and epibatidine with a three dimensional model of the AChBP binding site through a mixed QM/QM approach. Thus, despite the important similarities of galanthamine and codeine, the confrontation of the results obtained from the various approaches used in this work reveals significant differences of hydrogen-bond interactions of the two compounds. Furthermore, the structural motif we have found, which includes the Trp 143, involved in the agonists binding, and the Asp 85, highly conserved in the ion channels family, has been deeply characterized, the influence of a cooperative effect on the H-bond network formed being demonstrated. Finally, the energetic ranking of interaction of the three ligands ACh<Nicotine<Epibatidine reported in the literature has been reproduced by our simulations, the results obtained being validated by their good agreement with the experimental data available. This affinity sequence has been rationalized by a comprehensive analysis of key geometric parameters of agonists-AChBP interactions.NANTES-BU Sciences (441092104) / SudocSudocFranceF

Mapping of the interaction sites of galanthamine: a quantitative analysis through pairwise potentials and quantum chemistry

A quantitative analysis of the interaction sites of the anti-Alzheimer drug galanthamine with molecular probes (water and benzene molecules) representative of its surroundings in the binding site of acetylcholinesterase (AChE) has been realized through pairwise potentials calculations and quantum chemistry. This strategy allows a full and accurate exploration of the galanthamine potential energy surface of interaction. Significantly different results are obtained according to the distances of approaches between the various molecular fragments and the conformation of the galanthamine N-methyl substituent. The geometry of the most relevant complexes has then been fully optimized through MPWB1K/6-31 + G(d,p) calculations, final energies being recomputed at the LMP2/aug-cc-pVTZ(-f) level of theory. Unexpectedly, galanthamine is found to interact mainly from its hydrogen-bond donor groups. Among those, CH groups in the vicinity of the ammonium group are prominent. The trends obtained provide rationales to the predilection of the equatorial orientation of the galanthamine N-methyl substituent for binding to AChE. The analysis of the interaction energies pointed out the independence between the various interaction sites and the rigid character of galanthamine. The comparison between the cluster calculations and the crystallographic observations in galanthamine-AChE co-crystals allows the validation of the theoretical methodology. In particular, the positions of several water molecules appearing as strongly conserved in galanthamine-AChE co-crystals are predicted by the calculations. Moreover, the experimental position and orientation of lateral chains of functionally important aminoacid residues are in close agreement with the ones predicted theoretically. Our study provides relevant information for a rational drug design of galanthamine based AChE inhibitors

Insights into a highly conserved network of hydrogen bonds in the agonist binding site of nicotinic acetylcholine receptors: A structural and theoretical study

Structural and theoretical studies on the geometrical features of a hydrogen-bond network occurring in the binding site of nicotinic acetylcholine receptors (nAChRs) and composed of interconnected WxPD (Trp-x-Pro-Asp) and SWyz (Ser-Trp-yz) sequences from loops A and B, respectively, have been carried out. Multiple sequence alignments using as template the sequence of the apoform of Aplysia californica acetylcholine binding protein (Ac-AChBP) show the strict conservation of serine and tryptophan residues of the loop B SWyz sequence. Considering a sample of 19 high resolution AChBP structures, the strong conformational preferences of the key tryptophan residue has been pointing out, whatever the form, free or bounded, of AChBP. The geometry of the motif hydrogen-bond network has been characterized through the analyses of seven distances. The robustness of the various hydrogen-bond interactions is pointed out, the one involving the aspartate carboxylate group and the serine residue being the shortest of the network. The role of a cooperative effect involving a NH(His145)center dot center dot center dot OH (Ser142) hydrogen bond is highlighted. Density functional theory calculations on several simplified models based on the motif hydrogen-bond network allow probing the importance of the various hydrogen-bond interactions. The removal of the Ser142 hydroxyl group induces strong structural rearrangements, in agreement with the structural observations. Molecular electrostatic potential calculations on model systems highlight the importance of a cooperative effect in the whole hydrogen-bond network. More precisely, the key role of the Ser142 hydroxyl group, involved in several hydrogen bonds, is underlined. (C) 2014 Wiley Periodicals, Inc