Crystal structure of the M5 muscarinic acetylcholine receptor (original) (raw)
Related papers
Homology Modeling and Validation of the Human M1 Muscarinic Acetylcholine Receptor
Molecular Informatics, 2012
In practice 14 % (earlier 30 % ) of the available pharmaceutical compounds develops its effect on this site of action. Although these receptors themselves are important targets, drugs developed with other therapeutic aim can also act on these receptors and cause adverse side effects. Therefore these targets are antitargets as well and the screening for the possible side effects is very important in the early phase of drug development. From the point of view of the GPCRs, the main antitargets are as follows (in paranthesis the action of the compounds and their main adverse effect is enumerated): adrenergic a 1a (antagonist, orthostatic hypotension, dizziness and fainting spells), dopaminergic D 2 (antagonist, extrapyramidal syndrome, tardive dyskinesia), serotonin 5-HT 2C (antagonist, weight gain, obesity), serotonin 5-HT 2B (agonist, valvular heart disease) and muscarinic M1 (antagonist, attention deficits, hallucinations and memory deficits). Nowadays the accurate structure-based description of the GPCRÀligand interaction is more feasible due to the increased number of available crystal structures. Experimental structures of the aforementioned GPCRs are not available, therefore the initial structure has to be built up using a homology modeling (HM) approach and the structure obtained should be submitted for validation (structural and ligand recognition). In the past several years a few 3D structures of the human M1 muscarinic acetylcholine receptor (hM1acr) have been developed using various methods. Recently Haga et al. solved the crystal structure of the human M2 muscarinic acetylcholine receptor (hM2acr), which can be used as the most appropriate template for the 3D structure generation of other muscarinic receptors. The aim of our study was to build a relevant 3D structure (Model#1) of the hM1acr using the most appropriate reference structure, the crystallographic structure of hM2acr as a template. This model was compared to the model developed by McRobb et al. [6b] (a b 2 adrenergic receptor based structure, Model#2) from structural and enrichment factor point of views (using the recently developed GPCR ligand library (GLL) and GPCR decoy database (GDD) set ). These sets of active and decoy compounds were prepared in order to obtain chemically diverse molecules with similar physical properties (molecular weight, formal charge, number of rotatable bonds, number of hy-drogen bond acceptors and donors, octanol-water partition coefficient, and topological polar surface area) which resulted in unbiased enrichment compared to random selection. The structure obtained from HM was analyzed in order to verify its 3D structure from structural points of view. On the Ramachandran surface we did not find any residue in the disallowed region (see Supporting Information, Figure S1) and outliers were not found in the angle and torsional angle space either.
Structural insights into the subtype-selective antagonist binding to the M2 muscarinic receptor
Nature Chemical Biology, 2018
Human muscarinic receptor, M 2 is one of the five subtypes of muscarinic receptors belonging to the family of G protein-coupled receptors. Muscarinic receptors are targets for multiple neurodegenerative diseases. The challenge has been designing subtype selective ligands against one of the five muscarinic receptors. We report high resolution structures of a thermostabilized mutant M 2 receptor bound to a subtype selective antagonist AF-DX 384 and a non-selective antagonist NMS. The thermostabilizing mutation S110R in M 2 was predicted using a theoretical strategy previously developed in our group. Comparison of the crystal structures and pharmacological properties of the M 2 receptor shows that the Arg in the S110R mutant mimics the stabilizing role of the sodium cation, that is known to allosterically stabilize inactive state(s) of class A GPCRs. Molecular Dynamics simulations reveal that tightening of the ligand-residue contacts in M 2 receptor compared to M 3 receptor leads to subtype selectivity of AF-DX 384.
Toward activated homology models of the human M1 muscarinic acetylcholine receptor
Journal of Molecular Graphics and Modelling, 2014
Structure-based virtual screening offers a good opportunity for the discovery of selective M 1 muscarinic acetylcholine receptor (mAChR) agonists for the treatment of Alzheimer's disease. However, no 3-D structure of an M 1 mAChR is yet available and the homology models that have been previously reported are only able to identify antagonists in virtual screening experiments. In this study, we generated a homology model of the human M 1 mAChR, based on the crystal structure of an M 3 mAChR as the template. This initial model was modified, using the agonist-bound crystal structure of a ˇ2-adrenergic receptor as a guide, to give two possible activated structures. The T192 side chain was adjusted in both structures and one of the structures also had the whole of transmembrane (TM) 5 rotated and tilted toward the inner channel of the transmembrane region. The binding sites of all three structures were then refined by induced-fit docking (IFD) with acetylcholine. Virtual screening experiments showed that all three refined models could efficiently differentiate agonists from decoy molecules, with the TM5-modified models also giving good agonist/antagonist selectivity. The whole range of agonists and antagonists was observed to bind within the orthosteric site of the structure obtained by IFD refinement alone, implying that it has inactive state character. In contrast, the two TM5-modified structures were unable to accommodate the antagonists, supporting the proposition that they possess activated state character.
Antagonist binding in the rat muscarinic receptor: A study by docking and X-ray crystallography
2004
A series of agonists to the rat muscarinic receptor have been docked computationally to the active site of a homology model of rat M1 muscarinic receptor. The agonists were modelled on the X-ray crystal structure of atropine, which is reported here and the docking studies are shown to reproduce correctly the order of experimental binding affinities for the agonists as well as indicate where there appear to be inconsistencies in the experimental data. The crystal and molecular structure of atropine (tropine tropate; ␣-[hydroxymethyl]benzeneacetic acid 8-methyl[3.2.1]oct-3-yl ester C 17 H 23 NO 3 ) has been determined by X-ray crystallography using an automated Patterson search method, and refined by full-matrix least-squares to a final R of 0.0452 for 2701 independent observed reflections and 192 parameters using Mo K␣ radiation, λ = 0.71073Å at 150 K. The compound crystallises in space group Fdd2 with Z = 16 molecules per unit cell.
On homology modeling of the M2 muscarinic acetylcholine receptor subtype
Journal of Computer-Aided Molecular Design, 2013
Twelve homology models of the human M 2 muscarinic receptor using different sets of templates have been designed using the Prime program or the modeller program and compared to crystallographic structure (PDB:3UON). The best models were obtained using single template of the closest published structure, the M 3 muscarinic receptor (PDB:4DAJ). Adding more (structurally distant) templates led to worse models. Data document a key role of the template in homology modeling. The models differ substantially. The quality checks built into the programs do not correlate with the RMSDs to the crystallographic structure and cannot be used to select the best model. Re-docking of the antagonists present in crystallographic structure and relative binding energy estimation by calculating MM/GBSA in Prime and the binding energy function in YASARA suggested it could be possible to evaluate the quality of the orthosteric binding site based on the prediction of relative binding energies. Although estimation of relative binding energies distinguishes between relatively good and bad models it does not indicate the best one. On the other hand, visual inspection of the models for known features and knowledge-based analysis of the intramolecular interactions allows an experimenter to select overall best models manually.
Molecular Modeling of the M3 Acetylcholine Muscarinic Receptor and Its Binding Site
Journal of Biomedicine and Biotechnology, 2012
The present study reports the results of a combined computational and site mutagenesis study designed to provide new insights into the orthosteric binding site of the human M3 muscarinic acetylcholine receptor. For this purpose a three-dimensional structure of the receptor at atomic resolution was built by homology modeling, using the crystallographic structure of bovine rhodopsin as a template. Then, the antagonist N-methylscopolamine was docked in the model and subsequently embedded in a lipid bilayer for its refinement using molecular dynamics simulations. Two different lipid bilayer compositions were studied: one component palmitoyl-oleyl phosphatidylcholine (POPC) and two-component palmitoyl-oleyl phosphatidylcholine/palmitoyloleyl phosphatidylserine (POPC-POPS). Analysis of the results suggested that residues F222 and T235 may contribute to the ligand-receptor recognition. Accordingly, alanine mutants at positions 222 and 235 were constructed, expressed, and their binding properties determined. The results confirmed the role of these residues in modulating the binding affinity of the ligand.
The Journal of biological chemistry, 2014
Background: Selective and potent positive allosteric modulators (PAMs) of the M 1 mAChR have been recently described. Results: Use of structural analogues and mutagenic mapping identified the mechanistic basis for increased PAM activity. Conclusion: Combined analytical, structure-function, and modeling approaches uncover allosteric mechanisms at the M 1 mAChR. Significance: New chemical space can be explored in the development of tailored M 1 mAChR PAMs.
Structure-guided development of selective M3 muscarinic acetylcholine receptor antagonists
Proceedings of the National Academy of Sciences
Drugs that treat chronic obstructive pulmonary disease by antagonizing the M3 muscarinic acetylcholine receptor (M3R) have had a significant effect on health, but can suffer from their lack of selectivity against the M2R subtype, which modulates heart rate. Beginning with the crystal structures of M2R and M3R, we exploited a single amino acid difference in their orthosteric binding pockets using molecular docking and structure-based design. The resulting M3R antagonists had up to 100-fold selectivity over M2R in affinity and over 1,000-fold selectivity in vivo. The crystal structure of the M3R-selective antagonist in complex with M3R corresponded closely to the docking-predicted geometry, providing a template for further optimization.
Chemistry & Biodiversity, 2006
Three-dimensional models of the five human muscarinic receptors were obtained from their known sequences. Homology modelling based on the crystallographic structure of bovine rhodopsin yielded models compatible with known results from site-directed mutagenesis studies. The only exceptions were the cytoplasmic loop 3 (CL3) in the five receptors, and the large C-terminal domain in M 1. Here, homology modelling with other closely related proteins allowed to solve these gaps. A detailed comparative discussion of the five models is given. The second part of the work involved docking experiments with the physiological ligand acetylcholine, again yielding results entirely compatible with results from mutagenesis experiments. The study revealed analogies and differences between the five receptors in the residues, and interactions leading to the recognition and binding of acetylcholine.