Publications by authors named "Arnau Cordomí"

65 Publications

TMSNP: a web server to predict pathogenesis of missense mutations in the transmembrane region of membrane proteins.

NAR Genom Bioinform 2021 Mar 23;3(1):lqab008. Epub 2021 Feb 23.

Bioinformatics and Medical Statistics Group, Facultat de Ciències i Tecnologia, UVIC-UCC, 08500 Vic, Barcelona, Spain.

The massive amount of data generated from genome sequencing brings tons of newly identified mutations, whose pathogenic/non-pathogenic effects need to be evaluated. This has given rise to several mutation predictor tools that, in general, do not consider the specificities of the various protein groups. We aimed to develop a predictor tool dedicated to membrane proteins, under the premise that their specific structural features and environment would give different responses to mutations compared to globular proteins. For this purpose, we created TMSNP, a database that currently contains information from 2624 pathogenic and 196 705 non-pathogenic reported mutations located in the transmembrane region of membrane proteins. By computing various conservation parameters on these mutations in combination with annotations, we trained a machine-learning model able to classify mutations as pathogenic or not. TMSNP (freely available at http://lmc.uab.es/tmsnp/) improves considerably the prediction power of commonly used mutation predictors trained with globular proteins.
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http://dx.doi.org/10.1093/nargab/lqab008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7902201PMC
March 2021

Structure and function of adenosine receptor heteromers.

Cell Mol Life Sci 2021 Feb 12. Epub 2021 Feb 12.

Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Campus Universitari, 08193, Bellaterra (Barcelona), Spain.

Adenosine is one of the most ancient signaling molecules and has receptors in both animals and plants. In mammals there are four specific receptors, A, A, A, and A, which belong to the superfamily of G-protein-coupled receptors (GPCRs). Evidence accumulated in the last 20 years indicates that GPCRs are often expressed as oligomeric complexes formed by a number of equal (homomers) or different (heteromers) receptors. This review presents the data showing the occurrence of heteromers formed by A and A, A and A, and A and A receptors highlighting (i) their tetrameric structural arrangements, and (ii) the functional diversity that those heteromers provide to adenosinergic signaling.
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http://dx.doi.org/10.1007/s00018-021-03761-6DOI Listing
February 2021

Discovery of a macromolecular complex mediating the hunger suppressive actions of cocaine: Structural and functional properties.

Addict Biol 2021 Feb 8:e13017. Epub 2021 Feb 8.

Department of Biochemistry and Molecular Biomedicine, School of Biology, University of Barcelona, Barcelona, Spain.

Cocaine not only increases brain dopamine levels but also activates the sigma receptor (σ R) that in turn regulates orexigenic receptor function. Identification of interactions involving dopamine D (D R), ghrelin (GHS-R ), and σ receptors have been addressed by biophysical techniques and a complementation approach using interfering peptides. The effect of cocaine on receptor functionality was assayed by measuring second messenger, cAMP and Ca , levels. The effect of acute or chronic cocaine administration on receptor complex expression was assayed by in situ proximity ligation assay. In silico procedures were used for molecular model building. σ R KO mice were used for confirming involvement of this receptor. Upon identification of protomer interaction and receptor functionality, a unique structural model for the macromolecular complex formed by σ R, D R, and GHS-R is proposed. The functionality of the complex, able to couple to both Gs and Gq proteins, is affected by cocaine binding to the σ R, as confirmed using samples from σ R mice. The expression of the macromolecular complex was differentially affected upon acute and chronic cocaine administration to rats. The constructed 3D model is consistent with biochemical, biophysical, and available structural data. The σ R, D R, and GHS-R complex constitutes a functional unit that is altered upon cocaine binding to the σ R. Remarkably, the heteromer can simultaneously couple to two G proteins, thus allowing dopamine to signal via Ca and ghrelin via cAMP. The anorexic action of cocaine is mediated by such complex whose expression is higher after acute than after chronic administration regimens.
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http://dx.doi.org/10.1111/adb.13017DOI Listing
February 2021

Experimental and computational analysis of biased agonism on full-length and a C-terminally truncated adenosine A receptor.

Comput Struct Biotechnol J 2020 24;18:2723-2732. Epub 2020 Sep 24.

Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas. Instituto de Salud Carlos III, Madrid, Spain.

Biased agonism, the ability of agonists to differentially activate downstream signaling pathways by stabilizing specific receptor conformations, is a key issue for G protein-coupled receptor (GPCR) signaling. The C-terminal domain might influence this functional selectivity of GPCRs as it engages G proteins, GPCR kinases, β-arrestins, and several other proteins. Thus, the aim of this paper is to compare the agonist-dependent selectivity for intracellular pathways in a heterologous system expressing the full-length (AR) and a C-tail truncated (AR lacking the last 40 amino acids) adenosine A receptor, a GPCR that is already targeted in Parkinson's disease using a first-in-class drug. Experimental data such as ligand binding, cAMP production, β-arrestin recruitment, ERK1/2 phosphorylation and dynamic mass redistribution assays, which correspond to different aspects of signal transduction, were measured upon the action of structurally diverse compounds (the agonists adenosine, NECA, CGS-21680, PSB-0777 and LUF-5834 and the SCH-58261 antagonist) in cells expressing AR and AR. The results show that taking cAMP levels and the endogenous adenosine agonist as references, the main difference in bias was obtained with PSB-0777 and LUF-5834. The C-terminus is dispensable for both G-protein and β-arrestin recruitment and also for MAPK activation. Unrestrained molecular dynamics simulations, at the μs timescale, were used to understand the structural arrangements of the binding cavity, triggered by these chemically different agonists, facilitating G protein binding with different efficacy.
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http://dx.doi.org/10.1016/j.csbj.2020.09.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7550916PMC
September 2020

Discovery of Homobivalent Bitopic Ligands of the Cannabinoid CB Receptor*.

Chemistry 2020 Dec 9;26(68):15839-15842. Epub 2020 Nov 9.

Medicinal Chemistry Institute, Spanish Research Council, Madrid, Spain.

Single chemical entities with potential to simultaneously interact with two binding sites are emerging strategies in medicinal chemistry. We have designed, synthesized and functionally characterized the first bitopic ligands for the CB receptor. These compounds selectively target CB versus CB receptors. Their binding mode was studied by molecular dynamic simulations and site-directed mutagenesis.
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http://dx.doi.org/10.1002/chem.202003389DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7756656PMC
December 2020

GPCRmd uncovers the dynamics of the 3D-GPCRome.

Nat Methods 2020 08 13;17(8):777-787. Epub 2020 Jul 13.

Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute-Department of Experimental and Health Sciences, Pompeu Fabra University, Barcelona, Spain.

G-protein-coupled receptors (GPCRs) are involved in numerous physiological processes and are the most frequent targets of approved drugs. The explosion in the number of new three-dimensional (3D) molecular structures of GPCRs (3D-GPCRome) over the last decade has greatly advanced the mechanistic understanding and drug design opportunities for this protein family. Molecular dynamics (MD) simulations have become a widely established technique for exploring the conformational landscape of proteins at an atomic level. However, the analysis and visualization of MD simulations require efficient storage resources and specialized software. Here we present GPCRmd (http://gpcrmd.org/), an online platform that incorporates web-based visualization capabilities as well as a comprehensive and user-friendly analysis toolbox that allows scientists from different disciplines to visualize, analyze and share GPCR MD data. GPCRmd originates from a community-driven effort to create an open, interactive and standardized database of GPCR MD simulations.
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http://dx.doi.org/10.1038/s41592-020-0884-yDOI Listing
August 2020

Adenosine/A2B Receptor Signaling Ameliorates the Effects of Aging and Counteracts Obesity.

Cell Metab 2020 Jul 25;32(1):56-70.e7. Epub 2020 Jun 25.

Institute of Pharmacology and Toxicology, University Hospital, University of Bonn, 53127 Bonn, Germany. Electronic address:

The combination of aging populations with the obesity pandemic results in an alarming rise in non-communicable diseases. Here, we show that the enigmatic adenosine A2B receptor (A2B) is abundantly expressed in skeletal muscle (SKM) as well as brown adipose tissue (BAT) and might be targeted to counteract age-related muscle atrophy (sarcopenia) as well as obesity. Mice with SKM-specific deletion of A2B exhibited sarcopenia, diminished muscle strength, and reduced energy expenditure (EE), whereas pharmacological A2B activation counteracted these processes. Adipose tissue-specific ablation of A2B exacerbated age-related processes and reduced BAT EE, whereas A2B stimulation ameliorated obesity. In humans, A2B expression correlated with EE in SKM, BAT activity, and abundance of thermogenic adipocytes in white fat. Moreover, A2B agonist treatment increased EE from human adipocytes, myocytes, and muscle explants. Mechanistically, A2B forms heterodimers required for adenosine signaling. Overall, adenosine/A2B signaling links muscle and BAT and has both anti-aging and anti-obesity potential.
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http://dx.doi.org/10.1016/j.cmet.2020.06.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7437516PMC
July 2020

HomolWat: a web server tool to incorporate 'homologous' water molecules into GPCR structures.

Nucleic Acids Res 2020 07;48(W1):W54-W59

Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.

Internal water molecules play an essential role in the structure and function of membrane proteins including G protein-coupled receptors (GPCRs). However, technical limitations severely influence the number and certainty of observed water molecules in 3D structures. This may compromise the accuracy of further structural studies such as docking calculations or molecular dynamics simulations. Here we present HomolWat, a web application for incorporating water molecules into GPCR structures by using template-based modelling of homologous water molecules obtained from high-resolution structures. While there are various tools available to predict the positions of internal waters using energy-based methods, the approach of borrowing lacking water molecules from homologous GPCR structures makes HomolWat unique. The tool can incorporate water molecules into a protein structure in about a minute with around 85% of water recovery. The web server is freely available at http://lmc.uab.es/homolwat.
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http://dx.doi.org/10.1093/nar/gkaa440DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7319549PMC
July 2020

Altered Signaling in CB1R-5-HT2AR Heteromers in Olfactory Neuroepithelium Cells of Schizophrenia Patients is Modulated by Cannabis Use.

Schizophr Bull 2020 12;46(6):1547-1557

Integrative Pharmacology and Systems Neuroscience, IMIM-Hospital del Mar Research Institute, Barcelona, Spain.

Schizophrenia (SCZ) has been associated with serotonergic and endocannabinoid systems dysregulation, but difficulty in obtaining in vivo neurological tissue has limited its exploration. We investigated CB1R-5-HT2AR heteromer expression and functionality via intracellular pERK and cAMP quantification in olfactory neuroepithelium (ON) cells of SCZ patients non-cannabis users (SCZ/nc), and evaluated whether cannabis modulated these parameters in patients using cannabis (SCZ/c). Results were compared vs healthy controls non-cannabis users (HC/nc) and healthy controls cannabis users (HC/c). Further, antipsychotic effects on heteromer signaling were tested in vitro in HC/nc and HC/c. Results indicated that heteromer expression was enhanced in both SCZ groups vs HC/nc. Additionally, pooling all 4 groups together, heteromer expression correlated with worse attentional performance and more neurological soft signs (NSS), indicating that these changes may be useful markers for neurocognitive impairment. Remarkably, the previously reported signaling properties of CB1R-5-HT2AR heteromers in ON cells were absent, specifically in SCZ/nc treated with clozapine. These findings were mimicked in cells from HC/nc exposed to clozapine, suggesting a major role of this antipsychotic in altering the quaternary structure of the CB1R-5-HT2AR heteromer in SCZ/nc patients. In contrast, cells from SCZ/c showed enhanced heteromer functionality similar to HC/c. Our data highlight a molecular marker of the interaction between antipsychotic medication and cannabis use in SCZ with relevance for future studies evaluating its association with specific neuropsychiatric alterations.
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http://dx.doi.org/10.1093/schbul/sbaa038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7846100PMC
December 2020

DIMERBOW: exploring possible GPCR dimer interfaces.

Bioinformatics 2020 05;36(10):3271-3272

Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.

Motivation: G protein-coupled receptors (GPCRs) can form homo-, heterodimers and larger order oligomers that exert different functions than monomers. The pharmacological potential of such complexes is hampered by the limited information available on the type of complex formed and its quaternary structure. Several GPCR structures in the Protein Data Bank display crystallographic interfaces potentially compatible with physiological interactions.

Results: Here, we present DIMERBOW, a database and web application aimed to visually browse the complete repertoire of potential GPCR dimers present in solved structures. The tool is suited to help finding the best possible structural template to model GPCR homomers.

Availability And Implementation: DIMERBOW is available at http://lmc.uab.es/dimerbow/.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btaa117DOI Listing
May 2020

Control of glutamate release by complexes of adenosine and cannabinoid receptors.

BMC Biol 2020 01 23;18(1). Epub 2020 Jan 23.

Integrative Neurobiology Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA.

Background: It has been hypothesized that heteromers of adenosine A receptors (A2AR) and cannabinoid CB receptors (CB1R) localized in glutamatergic nerve terminals mediate the integration of adenosine and endocannabinoid signaling involved in the modulation of striatal excitatory neurotransmission. Previous studies have demonstrated the existence of A2AR-CB1R heteromers in artificial cell systems. A dependence of A2AR signaling for the Gi protein-mediated CB1R signaling was described as one of its main biochemical characteristics. However, recent studies have questioned the localization of functionally significant A2AR-CB1R heteromers in striatal glutamatergic terminals.

Results: Using a peptide-interfering approach combined with biophysical and biochemical techniques in mammalian transfected cells and computational modeling, we could establish a tetrameric quaternary structure of the A2AR-CB1R heterotetramer. This quaternary structure was different to the also tetrameric structure of heteromers of A2AR with adenosine A receptors or dopamine D receptors, with different heteromeric or homomeric interfaces. The specific quaternary structure of the A2A-CB1R, which depended on intermolecular interactions involving the long C-terminus of the A2AR, determined a significant A2AR and Gs protein-mediated constitutive activation of adenylyl cyclase. Using heteromer-interfering peptides in experiments with striatal glutamatergic terminals, we could then demonstrate the presence of functionally significant A2AR-CB1R heteromers with the same biochemical characteristics of those studied in mammalian transfected cells. First, either an A2AR agonist or an A2AR antagonist allosterically counteracted Gi-mediated CB1R agonist-induced inhibition of depolarization-induced glutamate release. Second, co-application of both an A2AR agonist and an antagonist cancelled each other effects. Finally, a CB1R agonist inhibited glutamate release dependent on a constitutive activation of A2AR by a canonical Gs-Gi antagonistic interaction at the adenylyl cyclase level.

Conclusions: We demonstrate that the well-established cannabinoid-induced inhibition of striatal glutamate release can mostly be explained by a CB1R-mediated counteraction of the A2AR-mediated constitutive activation of adenylyl cyclase in the A2AR-CB1R heteromer.
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http://dx.doi.org/10.1186/s12915-020-0739-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6979073PMC
January 2020

GIP receptor: Expression in neuroendocrine tumours, internalization, signalling from endosomes and structure-function relationship studies.

Peptides 2020 03 16;125:170229. Epub 2019 Dec 16.

LPCNO, ERL 1226 INSERM, Université De Toulouse, CNRS, INSA, UPS, 135 Avenue De RAngueil, 31077 Toulouse, France. Electronic address:

GIP is well known as a peptide regulating metabolic functions. In this review paper, we summarize a series of data on GIP receptor (GIPR). First, expression study of GIPR in human neuroendocrine tumours showed a very high incidence (nearly 100%) and a high density in both functional and non functional pancreatic tumours, ileal tumours, bronchial tumours and medullary thyroid carcinomas. Then, data on internalization of GIPR following stimulation by GIP are reported. Rapid and abundant internalization of GIPR also found in tumor pancreatic endocrine cells opens the possibility of tumor imaging and eradication using radiolabeled GIP. Interestingly, internalized GIPR continues to signal in early endosomes stimulating production of cAMP and activation of PKA, thus, supporting the view that GIPR signals from both plasma membrane and vesicles of internalization. At last, we summarize data from studies using in synergy molecular modeling and site-directed mutagenesis, which identified crucial amino acids of transmembrane domains of GIPR involved in GIPR binding site of GIP and/or in its activation and coupling to Gs protein. All together, these last molecular data may help to better understand structure-activity relationship data on GIP and GIPR.
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http://dx.doi.org/10.1016/j.peptides.2019.170229DOI Listing
March 2020

Ligand Binding Mechanisms in Human Cone Visual Pigments.

Trends Biochem Sci 2019 07 7;44(7):629-639. Epub 2019 Mar 7.

Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya-Barcelona Tech, Rambla de Sant Nebridi 22, 08222 Terrassa, Spain. Electronic address:

Vertebrate vision starts with light absorption by visual pigments in rod and cone photoreceptor cells of the retina. Rhodopsin, in rod cells, responds to dim light, whereas three types of cone opsins (red, green, and blue) function under bright light and mediate color vision. Cone opsins regenerate with retinal much faster than rhodopsin, but the molecular mechanism of regeneration is still unclear. Recent advances in the area pinpoint transient intermediate opsin conformations, and a possible secondary retinal-binding site, as determinant factors for regeneration. In this Review, we compile previous and recent findings to discuss possible mechanisms of ligand entry in cone opsins, involving a secondary binding site, which may have relevant functional and evolutionary implications.
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http://dx.doi.org/10.1016/j.tibs.2019.02.001DOI Listing
July 2019

Inter-residue interactions in alpha-helical transmembrane proteins.

Bioinformatics 2019 08;35(15):2578-2584

Bioinformatics Area, School of International Studies, ESCI-UPF, Barcelona, Spain.

Motivation: The number of available membrane protein structures has markedly increased in the last years and, in parallel, the reliability of the methods to detect transmembrane (TM) segments. In the present report, we characterized inter-residue interactions in α-helical membrane proteins using a dataset of 3462 TM helices from 430 proteins. This is by far the largest analysis published to date.

Results: Our analysis of residue-residue interactions in TM segments of membrane proteins shows that almost all interactions involve aliphatic residues and Phe. There is lack of polar-polar, polar-charged and charged-charged interactions except for those between Thr or Ser sidechains and the backbone carbonyl of aliphatic and Phe residues. The results are discussed in the context of the preferences of amino acids to be in the protein core or exposed to the lipid bilayer and to occupy specific positions along the TM segment. Comparison to datasets of β-barrel membrane proteins and of α-helical globular proteins unveils the specific patterns of interactions and residue composition characteristic of α-helical membrane proteins that are the clue to understanding their structure.

Availability And Implementation: Results data and datasets used are available at http://lmc.uab.cat/TMalphaDB/interactions.php.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/bty978DOI Listing
August 2019

Design of a True Bivalent Ligand with Picomolar Binding Affinity for a G Protein-Coupled Receptor Homodimer.

J Med Chem 2018 10 11;61(20):9335-9346. Epub 2018 Oct 11.

Biomaterials and Nanomedicine , Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN) , Barcelona Science Park , 08028 Barcelona , Spain.

Bivalent ligands have emerged as chemical tools to study G protein-coupled receptor dimers. Using a combination of computational, chemical, and biochemical tools, here we describe the design of bivalent ligand 13 with high affinity ( K = 21 pM) for the dopamine D receptor (DR) homodimer. Bivalent ligand 13 enhances the binding affinity relative to monovalent compound 15 by 37-fold, indicating simultaneous binding at both protomers. Using synthetic peptides with amino acid sequences of transmembrane (TM) domains of DR, we provide evidence that TM6 forms the interface of the homodimer. Notably, the disturber peptide TAT-TM6 decreased the binding of bivalent ligand 13 by 52-fold and had no effect on monovalent compound 15, confirming the DR homodimer through TM6 ex vivo. In conclusion, by using a versatile multivalent chemical platform, we have developed a precise strategy to generate a true bivalent ligand that simultaneously targets both orthosteric sites of the DR homodimer.
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http://dx.doi.org/10.1021/acs.jmedchem.8b01249DOI Listing
October 2018

GPCR-SAS: A web application for statistical analyses on G protein-coupled receptors sequences.

PLoS One 2018 25;13(7):e0199843. Epub 2018 Jul 25.

Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain.

G protein-coupled receptors (GPCRs) are one of the largest protein families in mammals. They mediate signal transduction across cell membranes and are important targets for the pharmaceutical industry. The G Protein-Coupled Receptors-Sequence Analysis and Statistics (GPCR-SAS) web application provides a set of tools to perform comparative analysis of sequence positions between receptors, based on a curated structural-informed multiple sequence alignment. The analysis tools include: (i) percentage of occurrence of an amino acid or motif and entropy at a position or range of positions, (ii) covariance of two positions, (iii) correlation between two amino acids in two positions (or two sequence motifs in two ranges of positions), and (iv) snake-plot representation for a specific receptor or for the consensus sequence of a group of selected receptors. The analysis of conservation of residues and motifs across transmembrane (TM) segments may guide the design of more selective ligands or help to rationalize activation mechanisms, among others. As an example, here we analyze the amino acids of the "transmission switch", that initiates receptor activation following ligand binding. The tool is freely accessible at http://lmc.uab.cat/gpcrsas/.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0199843PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6059404PMC
December 2018

Cocaine Blocks Effects of Hunger Hormone, Ghrelin, Via Interaction with Neuronal Sigma-1 Receptors.

Mol Neurobiol 2019 Feb 7;56(2):1196-1210. Epub 2018 Jun 7.

Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain.

Despite ancient knowledge on cocaine appetite-suppressant action, the molecular basis of such fact remains unknown. Addiction/eating disorders (e.g., binge eating, anorexia, bulimia) share a central control involving reward circuits. However, we here show that the sigma-1 receptor (σR) mediates cocaine anorectic effects by interacting in neurons with growth/hormone/secretagogue (ghrelin) receptors. Cocaine increases colocalization of σR and GHS-R1a at the cell surface. Moreover, in transfected HEK-293T and neuroblastoma SH-SY5Y cells, and in primary neuronal cultures, pretreatment with cocaine or a σR agonist inhibited ghrelin-mediated signaling, in a similar manner as the GHS-R1a antagonist YIL-781. Results were similar in G protein-dependent (cAMP accumulation and calcium release) and in partly dependent or independent (ERK1/2 phosphorylation and label-free) assays. We provide solid evidence for direct interaction between receptors and the functional consequences, as well as a reliable structural model of the macromolecular σR-GHS-R1a complex, which arises as a key piece in the puzzle of the events linking cocaine consumption and appetitive/consummatory behaviors.
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http://dx.doi.org/10.1007/s12035-018-1140-7DOI Listing
February 2019

The size matters? A computational tool to design bivalent ligands.

Bioinformatics 2018 11;34(22):3857-3863

Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.

Motivation: Bivalent ligands are increasingly important such as for targeting G protein-coupled receptor (GPCR) dimers or proteolysis targeting chimeras (PROTACs). They contain two pharmacophoric units that simultaneously bind in their corresponding binding sites, connected with a spacer chain. Here, we report a molecular modelling tool that links the pharmacophore units via the shortest pathway along the receptors van der Waals surface and then scores the solutions providing prioritization for the design of new bivalent ligands.

Results: Bivalent ligands of known dimers of GPCRs, PROTACs and a model bivalent antibody/antigen system were analysed. The tool could rapidly assess the preferred linker length for the different systems and recapitulated the best reported results. In the case of GPCR dimers the results suggest that in some cases these ligands might bind to a secondary binding site at the extracellular entrance (vestibule or allosteric site) instead of the orthosteric binding site.

Availability And Implementation: Freely accessible from the Molecular Operating Environment svl exchange server (https://svl.chemcomp.com/).

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/bty422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6223368PMC
November 2018

Essential Control of the Function of the Striatopallidal Neuron by Pre-coupled Complexes of Adenosine A-Dopamine D Receptor Heterotetramers and Adenylyl Cyclase.

Front Pharmacol 2018 9;9:243. Epub 2018 Apr 9.

Circuit Therapeutics, Inc., Menlo Park, CA, United States.

The central adenosine system and adenosine receptors play a fundamental role in the modulation of dopaminergic neurotransmission. This is mostly achieved by the strategic co-localization of different adenosine and dopamine receptor subtypes in the two populations of striatal efferent neurons, striatonigral and striatopallidal, that give rise to the direct and indirect striatal efferent pathways, respectively. With optogenetic techniques it has been possible to dissect a differential role of the direct and indirect pathways in mediating "Go" responses upon exposure to reward-related stimuli and "NoGo" responses upon exposure to non-rewarded or aversive-related stimuli, respectively, which depends on their different connecting output structures and their differential expression of dopamine and adenosine receptor subtypes. The striatopallidal neuron selectively expresses dopamine D receptors (D2R) and adenosine A receptors (A2AR), and numerous experiments using multiple genetic and pharmacological and approaches, demonstrate they can form A2AR-D2R heteromers. It was initially assumed that different pharmacological interactions between dopamine and adenosine receptor ligands indicated the existence of different subpopulations of A2AR and D2R in the striatopallidal neuron. However, as elaborated in the present essay, most evidence now indicates that all interactions can be explained with a predominant population of striatal A2AR-D2R heteromers forming complexes with adenylyl cyclase subtype 5 (AC5). The A2AR-D2R heteromer has a tetrameric structure, with two homodimers, which allows not only multiple allosteric interactions between different orthosteric ligands, agonists, and antagonists, but also the canonical Gs-Gi antagonistic interaction at the level of AC5. We present a model of the function of the A2AR-D2R heterotetramer-AC5 complex, which acts as an integrative device of adenosine and dopamine signals that determine the excitability and gene expression of the striatopallidal neurons. The model can explain most behavioral effects of A2AR and D2R ligands, including the psychostimulant effects of caffeine. The model is also discussed in the context of different functional striatal compartments, mainly the dorsal and the ventral striatum. The current accumulated knowledge of the biochemical properties of the A2AR-D2R heterotetramer-AC5 complex offers new therapeutic possibilities for Parkinson's disease, schizophrenia, SUD and other neuropsychiatric disorders with dysfunction of dorsal or ventral striatopallidal neurons.
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http://dx.doi.org/10.3389/fphar.2018.00243DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5900444PMC
April 2018

Ligand-Triggered Structural Changes in the M Muscarinic Acetylcholine Receptor.

J Chem Inf Model 2018 05 2;58(5):1074-1082. Epub 2018 May 2.

Laboratori de Medicina Computacional, Unitat de Bioestadística , Facultat de Medicina, Universitat Autònoma de Barcelona , 08193 Bellaterra , Spain.

The muscarinic M acetylcholine receptor, one of the few G-protein coupled receptors that has not only been crystallized in both active and inactive conformations but also in the presence of a positive allosteric modulator, is an interesting system to study the molecular mechanisms of GPCR activation and ligand allosterism. Here, we have employed molecular dynamics (MD) simulations (adding to 14 μs in total) to study conformational changes triggered by the inverse agonist R-(-)-3-quinuclidinyl-benzilate (QNB) in the structure of the active M receptor (PBD ID 4MQS ) after replacement of the agonist iperoxo by the inverse agonist QNB. This permitted us to identify the sequence of events in the deactivation mechanism of the M acetylcholine receptor, which results first in the rearrangement of the transmission switch, the subsequent opening of the extracellular portion of the receptor and finally, the closure of the intracellular part. We also evaluate the effect of the positive allosteric modulator LY2119620 when bound simultaneously with the orthosteric agonist iperoxo and find that it restricts the conformation of Trp422 in a position that modulates the orientation of the Tyr426 at the orthosteric-binding pocket.
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http://dx.doi.org/10.1021/acs.jcim.8b00108DOI Listing
May 2018

Evidence for functional pre-coupled complexes of receptor heteromers and adenylyl cyclase.

Nat Commun 2018 03 28;9(1):1242. Epub 2018 Mar 28.

Integrative Neurobiology Section, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA.

G protein-coupled receptors (GPCRs), G proteins and adenylyl cyclase (AC) comprise one of the most studied transmembrane cell signaling pathways. However, it is unknown whether the ligand-dependent interactions between these signaling molecules are based on random collisions or the rearrangement of pre-coupled elements in a macromolecular complex. Furthermore, it remains controversial whether a GPCR homodimer coupled to a single heterotrimeric G protein constitutes a common functional unit. Using a peptide-based approach, we here report evidence for the existence of functional pre-coupled complexes of heteromers of adenosine A receptor and dopamine D receptor homodimers coupled to their cognate Gs and Gi proteins and to subtype 5 AC. We also demonstrate that this macromolecular complex provides the necessary frame for the canonical Gs-Gi interactions at the AC level, sustaining the ability of a Gi-coupled GPCR to counteract AC activation mediated by a Gs-coupled GPCR.
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http://dx.doi.org/10.1038/s41467-018-03522-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5871782PMC
March 2018

Human Blue Cone Opsin Regeneration Involves Secondary Retinal Binding with Analog Specificity.

Biophys J 2018 03;114(6):1285-1294

Universitat Politècnica de Catalunya, Terrassa, Spain. Electronic address:

Human color vision is mediated by the red, green, and blue cone visual pigments. Cone opsins are G-protein-coupled receptors consisting of an opsin apoprotein covalently linked to the 11-cis-retinal chromophore. All visual pigments share a common evolutionary origin, and red and green cone opsins exhibit a higher homology, whereas blue cone opsin shows more resemblance to the dim light receptor rhodopsin. Here we show that chromophore regeneration in photoactivated blue cone opsin exhibits intermediate transient conformations and a secondary retinoid binding event with slower binding kinetics. We also detected a fine-tuning of the conformational change in the photoactivated blue cone opsin binding site that alters the retinal isomer binding specificity. Furthermore, the molecular models of active and inactive blue cone opsins show specific molecular interactions in the retinal binding site that are not present in other opsins. These findings highlight the differential conformational versatility of human cone opsin pigments in the chromophore regeneration process, particularly compared to rhodopsin, and point to relevant functional, unexpected roles other than spectral tuning for the cone visual pigments.
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http://dx.doi.org/10.1016/j.bpj.2018.01.032DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5883618PMC
March 2018

Cross-communication between G and G in a G-protein-coupled receptor heterotetramer guided by a receptor C-terminal domain.

BMC Biol 2018 02 28;16(1):24. Epub 2018 Feb 28.

Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.

Background: G-protein-coupled receptor (GPCR) heteromeric complexes have distinct properties from homomeric GPCRs, giving rise to new receptor functionalities. Adenosine receptors (AR or AR) can form AR-AR heteromers (A-AHet), and their activation leads to canonical G-protein-dependent (adenylate cyclase mediated) and -independent (β-arrestin mediated) signaling. Adenosine has different affinities for AR and AR, allowing the heteromeric receptor to detect its concentration by integrating the downstream G- and G-dependent signals. cAMP accumulation and β-arrestin recruitment assays have shown that, within the complex, activation of AR impedes signaling via AR.

Results: We examined the mechanism by which A-AHet integrates G- and G-dependent signals. AR blockade by AR in the A-AHet is not observed in the absence of AR activation by agonists, in the absence of the C-terminal domain of AR, or in the presence of synthetic peptides that disrupt the heteromer interface of A-AHet, indicating that signaling mediated by AR and AR is controlled by both G and G proteins.

Conclusions: We identified a new mechanism of signal transduction that implies a cross-communication between G and G proteins guided by the C-terminal tail of the AR. This mechanism provides the molecular basis for the operation of the A-AHet as an adenosine concentration-sensing device that modulates the signals originating at both AR and AR.
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http://dx.doi.org/10.1186/s12915-018-0491-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6389107PMC
February 2018

Molecular Switches of Allosteric Modulation of the Metabotropic Glutamate 2 Receptor.

Structure 2017 07 22;25(7):1153-1162.e4. Epub 2017 Jun 22.

Computational Chemistry, Janssen Research and Development, Calle Jarama 75A, 45007 Toledo, Spain; Janssen Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium. Electronic address:

Metabotropic glutamate (mGlu) receptors are class C G protein-coupled receptors (GPCRs) crucial for CNS function and important drug discovery targets. Glutamate triggers receptor activation from an extracellular domain binding site while allosteric modulators bind in the seven-transmembrane domain. Little is known about how allosteric modulators produce their functional effects at the molecular level. Here we address this topic with combined experimental and computational approaches and reveal that mGlu receptor allosteric modulators interact with the homologous "trigger switch" and "transmission switch" amino acids as seen in class A GPCRs, in short, the characteristic hallmarks of class A agonist activation translate to the mGlu allosteric modulator. The proposed "trigger switch" for the mGlu involves the side chains of F643, N735, and W773, whereas the "transmission switch" involves the Y647, L738, and T769 amino acids. The work has wide impact on understanding mGlu GPCR function and for future allosteric modulator drugs.
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http://dx.doi.org/10.1016/j.str.2017.05.021DOI Listing
July 2017

Understanding Corticotropin Releasing Factor Receptor (CRFR) Activation Using Structural Models.

Curr Mol Pharmacol 2017 ;10(4):325-333

Laboratori de Medicina Computacional, Unitat de Bioestadistica, Facultat de Medicina, Universitat Autonoma de Barcelona, 08193, Bellaterra (Barcelona). Spain.

The corticotropin-releasing factor type 1 and 2 receptors (CRF1R and CRF2R) belong to the secretin-like family, also known as class B1, of G protein-coupled receptors (GPCRs). Several endogenous hormones mediate their responses through the CRF receptors, such as CRF and the urocortins. The structures for the N-terminus extracellular domain of both CRF1R and CRF2R in complex with peptidic ligands were released a few years ago and permitted the study of hormone binding to the orthosteric binding site. Until the crystal structure of the transmembrane domain of human CRF1R in its inactive state bound to an allosteric antagonist became available. Together with the crystal structures of the transmembrane domain of the glucagon receptor (GCGR), they have enabled the structural alignment between the rhodopsin and secretin-like families, which permits the direct comparison of the functional domains in both classes. In this report, we review the current structural landscape, in addition to the knowledge regarding activation of both CRF receptors and the generalization to secretin-like GPCRs in general. Thus, significant effort was put in trying to identify possible analogous microswitches in the class B1, with the hypothesis that both families could maintain a similar arrangement of their functional domain.
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http://dx.doi.org/10.2174/1874467210666170110122939DOI Listing
June 2018

Gut hormone GPCRs: structure, function, drug discovery.

Curr Opin Pharmacol 2016 12 16;31:63-67. Epub 2016 Sep 16.

Molecular Modelling Laboratory, School of Pharmacy, Queen's University Belfast, Northern Ireland, UK.

Crystallization and determination of the high resolution three-dimensional structure of the β2-adrenergic receptor in 2007 was followed by structure elucidation of a number of other receptors, including those for neurotensin and glucagon. These major advances foster the understanding of structure-activity relationship of these receptors and structure-based rational design of new ligands having more predictable activity. At present, structure determination of gut hormone receptors in complex with their ligands (natural, synthetic) and interacting signalling proteins, for example, G-proteins, arrestins, represents a challenge which promises to revolutionize gut hormone endocrinonology.
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http://dx.doi.org/10.1016/j.coph.2016.09.001DOI Listing
December 2016

Analysis of the interactions of sulfur-containing amino acids in membrane proteins.

Protein Sci 2016 08 8;25(8):1517-24. Epub 2016 Jun 8.

Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, Barcelona, E-08193, Bellaterra, Spain.

The interactions of Met and Cys with other amino acid side chains have received little attention, in contrast to aromatic-aromatic, aromatic-aliphatic or/and aliphatic-aliphatic interactions. Precisely, these are the only amino acids that contain a sulfur atom, which is highly polarizable and, thus, likely to participate in strong Van der Waals interactions. Analysis of the interactions present in membrane protein crystal structures, together with the characterization of their strength in small-molecule model systems at the ab-initio level, predicts that Met-Met interactions are stronger than Met-Cys ≈ Met-Phe ≈ Cys-Phe interactions, stronger than Phe-Phe ≈ Phe-Leu interactions, stronger than the Met-Leu interaction, and stronger than Leu-Leu ≈ Cys-Leu interactions. These results show that sulfur-containing amino acids form stronger interactions than aromatic or aliphatic amino acids. Thus, these amino acids may provide additional driving forces for maintaining the 3D structure of membrane proteins and may provide functional specificity.
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http://dx.doi.org/10.1002/pro.2955DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4972207PMC
August 2016

Quaternary structure of a G-protein-coupled receptor heterotetramer in complex with Gi and Gs.

BMC Biol 2016 Apr 5;14:26. Epub 2016 Apr 5.

Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.

Background: G-protein-coupled receptors (GPCRs), in the form of monomers or homodimers that bind heterotrimeric G proteins, are fundamental in the transfer of extracellular stimuli to intracellular signaling pathways. Different GPCRs may also interact to form heteromers that are novel signaling units. Despite the exponential growth in the number of solved GPCR crystal structures, the structural properties of heteromers remain unknown.

Results: We used single-particle tracking experiments in cells expressing functional adenosine A1-A2A receptors fused to fluorescent proteins to show the loss of Brownian movement of the A1 receptor in the presence of the A2A receptor, and a preponderance of cell surface 2:2 receptor heteromers (dimer of dimers). Using computer modeling, aided by bioluminescence resonance energy transfer assays to monitor receptor homomerization and heteromerization and G-protein coupling, we predict the interacting interfaces and propose a quaternary structure of the GPCR tetramer in complex with two G proteins.

Conclusions: The combination of results points to a molecular architecture formed by a rhombus-shaped heterotetramer, which is bound to two different interacting heterotrimeric G proteins (Gi and Gs). These novel results constitute an important advance in understanding the molecular intricacies involved in GPCR function.
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http://dx.doi.org/10.1186/s12915-016-0247-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4822319PMC
April 2016

Structures for G-Protein-Coupled Receptor Tetramers in Complex with G Proteins.

Trends Biochem Sci 2015 Oct;40(10):548-551

Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain; Centro de Investigación Biomédica en Red: Enfermedades neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Valderrebollo 5 28031, Madrid, Spain.

G-Protein-coupled receptors (GPCRs) were classically described as monomers. We now appreciate that they also function as homo- and hetero-oligomers, for which structural information is lacking. Here, we use available 3D structures and biochemical considerations to present and evaluate experimentally testable structural models for GPCR oligomers and associated G proteins.
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http://dx.doi.org/10.1016/j.tibs.2015.07.007DOI Listing
October 2015