1
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He M, Liu W, Zhang C, Liu Y, Zhuang H, O'Hagan D. Selectively Fluorinated Citronellol Analogues Support a Hydrogen Bonding Donor Interaction with the Human OR1A1 Olfactory Receptor. Org Lett 2022; 24:4415-4420. [PMID: 35686936 PMCID: PMC9237825 DOI: 10.1021/acs.orglett.2c01635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
C-2 fluorinated and
methylated stereoisomers of the fragrance citronellol 1 and its oxalate esters were prepared from (R)-pulegone 11 and explored as agonists of the human
olfactory receptor OR1A1 and assayed also against site-specific mutants.
There were clear isomer preferences and C-2 difluorination as in 18 led to the most active compound suggesting an important
hydrogen bond donor role for citronellol 1. C-2 methylation
and the corresponding oxalate ester analogues were less active.
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Affiliation(s)
- Mengfan He
- School of Chemistry, University of St. Andrews, St. Andrews, KY16 9ST, U.K
| | - Weihong Liu
- Intelligent Perception Lab, Hanwang Technology Co., Ltd., Beijing, 100193, China
| | - Chen Zhang
- Intelligent Perception Lab, Hanwang Technology Co., Ltd., Beijing, 100193, China
| | - Yingjian Liu
- Intelligent Perception Lab, Hanwang Technology Co., Ltd., Beijing, 100193, China
| | - Hanyi Zhuang
- Intelligent Perception Lab, Hanwang Technology Co., Ltd., Beijing, 100193, China
| | - David O'Hagan
- School of Chemistry, University of St. Andrews, St. Andrews, KY16 9ST, U.K
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2
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Zhang S, Li L, Li H. Role of ectopic olfactory receptors in glucose and lipid metabolism. Br J Pharmacol 2021; 178:4792-4807. [PMID: 34411276 DOI: 10.1111/bph.15666] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 05/25/2021] [Accepted: 08/11/2021] [Indexed: 12/25/2022] Open
Abstract
The metabolic syndrome has become one of the major public health challenges in the world, and adjusting glucose and lipid levels to their normal values is crucial for treating the metabolic syndrome. Olfactory receptors (ORs) expressed in extra-nasal tissues participate in diverse biological processes, including the regulation of glucose and lipid metabolism. Ectopic ORs can regulate a variety of metabolic events including insulin secretion, glucagon secretion, fatty acid oxidation, lipogenesis and thermogenesis. Understanding the physiological function and deciphering the olfactory recognition code by suitable ligands make ectopic ORs potential targets for the treatment of the metabolic syndrome. In this review, we delineate the roles and mechanisms of ectopic ORs in the regulation of glucose and lipid metabolism, summarize the corresponding natural ligands, and discuss existing problems and the therapeutic potential of targeting ORs in the metabolic syndrome.
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Affiliation(s)
- Siyu Zhang
- Institute of Pharmacology, Department of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Linghuan Li
- Institute of Pharmacology, Department of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
| | - Hanbing Li
- Institute of Pharmacology, Department of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China.,Section of Endocrinology, School of Medicine, Yale University, New Haven, Connecticut, USA
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3
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Koenis MAJ, Xia Y, Domingos SR, Visscher L, Buma WJ, Nicu VP. Taming conformational heterogeneity in and with vibrational circular dichroism spectroscopy. Chem Sci 2019; 10:7680-7689. [PMID: 31803406 PMCID: PMC6844231 DOI: 10.1039/c9sc02866h] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/08/2019] [Indexed: 01/19/2023] Open
Abstract
Genetic fitting algorithm accounting for the uncertainty in computed energies allows a significantly more reliable assignment of stereochemistry and conformational heterogeneity of chiral compounds using vibrational circular dichroism.
The flexibility of a molecule has important consequences on its function and application. Vibrational Circular Dichroism (VCD) is intrinsically an excellent experimental technique to get a hold on this flexibility as it is highly sensitive to key conformational details and able to distinguish rapidly interconverting conformers. One of the major challenges in analyzing the spectra by comparison to theoretical predictions is the uncertainty in the computed energies of the multitude of conformations. This uncertainty also affects the reliability of the stereochemical assignment it is normally used for. We present here a novel approach that explicitly takes the energy uncertainties into account in a genetic algorithm based method that fits calculated to the experimental spectra. We show that this approach leads to significant improvements over previously used methodologies. Importantly, statistical validation studies provide quantitative measures for the reliability of relevant parameters used such as the energy uncertainty and the extent to which conformational heterogeneity can be determined. Similarly, quantitative measures can be obtained for the possibility that the flexibility that is introduced in the fit might lead to an incorrect assignment of the stereochemistry. These results break new ground for different techniques based on VCD to elucidate conformational flexibility.
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Affiliation(s)
- Mark A J Koenis
- Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH Amsterdam , The Netherlands .
| | - Yiyin Xia
- Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH Amsterdam , The Netherlands .
| | - Sérgio R Domingos
- Deutsches Elektronen-Synchrotron DESY , Notkestraße 85 , 22607 Hamburg , Germany
| | - Lucas Visscher
- Amsterdam Center for Multiscale Modeling , Division Theoretical Chemistry , Faculty of Sciences , Vrije Universiteit Amsterdam , De Boelelaan 1083 , 1081 HV Amsterdam , The Netherlands
| | - Wybren Jan Buma
- Van't Hoff Institute for Molecular Sciences , University of Amsterdam , Science Park 904 , 1098 XH Amsterdam , The Netherlands . .,Radboud University , Institute for Molecules and Materials , FELIX Laboratory , Toernooiveld 7c , 6525 ED Nijmegen , The Netherlands
| | - Valentin P Nicu
- Department of Environmental Science, Physics, Physical Education and Sport , Lucian Blaga University of Sibiu , loan Ratiu Street Nr. 7-9 , 550012 Sibiu , Romania .
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4
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Block E. Molecular Basis of Mammalian Odor Discrimination: A Status Report. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:13346-13366. [PMID: 30453735 DOI: 10.1021/acs.jafc.8b04471] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Humans have 396 unique, intact olfactory receptors (ORs), G-protein coupled receptors (GPCRs) containing receptor-specific binding sites; other mammals have more. Activation of these transmembrane proteins by an odorant initiates a signaling cascade, evoking an action potential leading to perception of a smell. Because the number of distinguishable odorants vastly exceeds the number of ORs, research has focused on mechanisms of recognition and signaling processes for classes of odorants. In this review, selected recent examples will be presented of "deorphaned" mammalian receptors, where the OR ligands (odorants) as well as key aspects of receptor-odorant interactions were identified using odorant-mediated receptor activation data together with site-directed mutagenesis and molecular modeling. Based on cumulative evidence from OR deorphaning and olfactory receptor neuron activation studies, a receptor-ligand docking model rather than an alternative bond vibration model is suggested to best explain the molecular basis of the exquisitely sensitive odor discrimination in mammals.
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Affiliation(s)
- Eric Block
- Department of Chemistry , University at Albany, SUNY , Albany , New York 12222 , United States
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5
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Domingos SR, Pérez C, Medcraft C, Pinacho P, Schnell M. Flexibility unleashed in acyclic monoterpenes: conformational space of citronellal revealed by broadband rotational spectroscopy. Phys Chem Chem Phys 2018; 18:16682-9. [PMID: 27298210 DOI: 10.1039/c6cp02876d] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Conformational flexibility is intrinsically related to the functionality of biomolecules. Elucidation of the potential energy surface is thus a necessary step towards understanding the mechanisms for molecular recognition such as docking of small organic molecules to larger macromolecular systems. In this work, we use broadband rotational spectroscopy in a molecular jet experiment to unravel the complex conformational space of citronellal. We observe fifteen conformations in the experimental conditions of the molecular jet, the highest number of conformers reported to date for a chiral molecule of this size using microwave spectroscopy. Studies of relative stability using different carrier gases in the supersonic expansion reveal conformational relaxation pathways that strongly favour ground-state structures with globular conformations. This study provides a blueprint of the complex conformational space of an important biosynthetic precursor and gives insights on the relation between its structure and biological functionality.
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Affiliation(s)
- Sérgio R Domingos
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany. and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany and The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Cristóbal Pérez
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany. and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany and The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Chris Medcraft
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany.
| | - Pablo Pinacho
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany. and Department of Physical Chemistry and Inorganic Chemistry, Universidad de Valladolid, Valladolid, Spain
| | - Melanie Schnell
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany. and Center for Free-Electron Laser Science, Luruper Chaussee 149, 22761 Hamburg, Germany and The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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6
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Activation of intestinal olfactory receptor stimulates glucagon-like peptide-1 secretion in enteroendocrine cells and attenuates hyperglycemia in type 2 diabetic mice. Sci Rep 2017; 7:13978. [PMID: 29070885 PMCID: PMC5656655 DOI: 10.1038/s41598-017-14086-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 09/27/2017] [Indexed: 12/01/2022] Open
Abstract
Odorants are non-nutrients. However, they exist abundantly in foods, wines, and teas, and thus can be ingested along with the other nutrients during a meal. Here, we have focused on the chemical-recognition ability of these ORs and hypothesized that the odorants ingested during a meal may play a physiological role by activating the gut-expressed ORs. Using a human-derived enteroendocrine L cell line, we discovered the geraniol- and citronellal-mediated stimulation of glucagon-like peptide-1 (GLP-1) secretion and elucidated the corresponding cellular downstream signaling pathways. The geraniol-stimulated GLP-1 secretion event in the enteroendocrine cell line was mediated by the olfactory-type G protein, the activation of adenylyl cyclase, increased intracellular cAMP levels, and extracellular calcium influx. TaqMan qPCR demonstrated that two ORs corresponding to geraniol and citronellal were expressed in the human enteroendocrine cell line and in mouse intestinal specimen. In a type 2 diabetes mellitus mouse model (db/db), oral administration of geraniol improved glucose homeostasis by increasing plasma GLP-1 and insulin levels. This insulinotropic action of geraniol was GLP-1 receptor-mediated, and also was glucose-dependent. This study demonstrates that odor compounds can be recognized by gut-expressed ORs during meal ingestion and therefore, participate in the glucose homeostasis by inducing the secretion of gut-peptides.
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7
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Fierro F, Suku E, Alfonso-Prieto M, Giorgetti A, Cichon S, Carloni P. Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis. Front Mol Biosci 2017; 4:63. [PMID: 28932739 PMCID: PMC5592726 DOI: 10.3389/fmolb.2017.00063] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/22/2017] [Indexed: 12/17/2022] Open
Abstract
Human G-protein coupled receptors (hGPCRs) constitute a large and highly pharmaceutically relevant membrane receptor superfamily. About half of the hGPCRs' family members are chemosensory receptors, involved in bitter taste and olfaction, along with a variety of other physiological processes. Hence these receptors constitute promising targets for pharmaceutical intervention. Molecular modeling has been so far the most important tool to get insights on agonist binding and receptor activation. Here we investigate both aspects by bioinformatics-based predictions across all bitter taste and odorant receptors for which site-directed mutagenesis data are available. First, we observe that state-of-the-art homology modeling combined with previously used docking procedures turned out to reproduce only a limited fraction of ligand/receptor interactions inferred by experiments. This is most probably caused by the low sequence identity with available structural templates, which limits the accuracy of the protein model and in particular of the side-chains' orientations. Methods which transcend the limited sampling of the conformational space of docking may improve the predictions. As an example corroborating this, we review here multi-scale simulations from our lab and show that, for the three complexes studied so far, they significantly enhance the predictive power of the computational approach. Second, our bioinformatics analysis provides support to previous claims that several residues, including those at positions 1.50, 2.50, and 7.52, are involved in receptor activation.
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Affiliation(s)
- Fabrizio Fierro
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany
| | - Eda Suku
- Department of Biotechnology, University of VeronaVerona, Italy
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany.,Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University DüsseldorfDüsseldorf, Germany
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany.,Department of Biotechnology, University of VeronaVerona, Italy
| | - Sven Cichon
- Institute of Neuroscience and Medicine INM-1, Forschungszentrum JülichJülich, Germany.,Institute for Human Genetics, Department of Genomics, Life&Brain Center, University of BonnBonn, Germany.,Division of Medical Genetics, Department of Biomedicine, University of BaselBasel, Switzerland
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany.,Department of Physics, Rheinisch-Westfälische Technische Hochschule AachenAachen, Germany.,VNU Key Laboratory "Multiscale Simulation of Complex Systems", VNU University of Science, Vietnam National UniversityHanoi, Vietnam
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8
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Belloir C, Miller-Leseigneur ML, Neiers F, Briand L, Le Bon AM. Biophysical and functional characterization of the human olfactory receptor OR1A1 expressed in a mammalian inducible cell line. Protein Expr Purif 2017; 129:31-43. [DOI: 10.1016/j.pep.2016.09.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/07/2016] [Accepted: 09/15/2016] [Indexed: 10/21/2022]
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9
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Wailzer B, Klocker J, Wolschann P, Buchbauer G. Structural Features for Furan-Derived Fruity and Meaty Aroma Impressions. Nat Prod Commun 2016. [DOI: 10.1177/1934578x1601101014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Furan derivatives are part of nearly all food aromas. They are mainly formed by thermal degradation of carbohydrates and ascorbic acid and from sugar-amino acid interactions during food processing. Caramel-like, sweet, fruity, nutty, meaty, and burnt odor impressions are associated with this class of compounds. In the presented work, structure-activity relationship (SAR) investigations are performed on a series of furan derivatives in order to find structural subunits, which are responsible for the particular characteristic flavors. Therefore, artificial neural networks are applied on a set of 35 furans with the aroma categories “meaty” or “fruity” to calculate a classification rule and class boundaries for these two aroma impressions. By training a multilayer perceptron network architecture with a backpropagation algorithm, a correct classification rate of 100% is obtained. The neural network is able to distinguish between the two studied groups by using the following significant descriptors as inputs: number of sulfur atoms, Looping Centric Information Index, Folding Degree Index and Petitjean Shape Indices. Finally, the results clearly demonstrate that artificial neural networks are successful tools to investigate non-linear qualitative structure-odor relationships of aroma compounds.
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Affiliation(s)
- Bettina Wailzer
- Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Johanna Klocker
- Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Peter Wolschann
- Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria
- Department of Pharmaceutical Technology and Biopharmaceutics, University of Vienna, Vienna, Austria
| | - Gerhard Buchbauer
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
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10
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El Mountassir F, Belloir C, Briand L, Thomas-Danguin T, Le Bon AM. Encoding odorant mixtures by human olfactory receptors. FLAVOUR FRAG J 2016. [DOI: 10.1002/ffj.3331] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fouzia El Mountassir
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRA; Univ. Bourgogne Franche-Comté; F-21000 Dijon France
| | - Christine Belloir
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRA; Univ. Bourgogne Franche-Comté; F-21000 Dijon France
| | - Loïc Briand
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRA; Univ. Bourgogne Franche-Comté; F-21000 Dijon France
| | - Thierry Thomas-Danguin
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRA; Univ. Bourgogne Franche-Comté; F-21000 Dijon France
| | - Anne-Marie Le Bon
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRA; Univ. Bourgogne Franche-Comté; F-21000 Dijon France
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11
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12
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Audouze K, Tromelin A, Le Bon AM, Belloir C, Petersen RK, Kristiansen K, Brunak S, Taboureau O. Identification of odorant-receptor interactions by global mapping of the human odorome. PLoS One 2014; 9:e93037. [PMID: 24695519 PMCID: PMC3973694 DOI: 10.1371/journal.pone.0093037] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 02/27/2014] [Indexed: 12/14/2022] Open
Abstract
The human olfactory system recognizes a broad spectrum of odorants using approximately 400 different olfactory receptors (hORs). Although significant improvements of heterologous expression systems used to study interactions between ORs and odorant molecules have been made, screening the olfactory repertoire of hORs remains a tremendous challenge. We therefore developed a chemical systems level approach based on protein-protein association network to investigate novel hOR-odorant relationships. Using this new approach, we proposed and validated new bioactivities for odorant molecules and OR2W1, OR51E1 and OR5P3. As it remains largely unknown how human perception of odorants influence or prevent diseases, we also developed an odorant-protein matrix to explore global relationships between chemicals, biological targets and disease susceptibilities. We successfully experimentally demonstrated interactions between odorants and the cannabinoid receptor 1 (CB1) and the peroxisome proliferator-activated receptor gamma (PPARγ). Overall, these results illustrate the potential of integrative systems chemical biology to explore the impact of odorant molecules on human health, i.e. human odorome.
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Affiliation(s)
- Karine Audouze
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Anne Tromelin
- Centre des Sciences du Goût et de l'Alimentation, UMR6265 CNRS, UMR1324 INRA, Bourgogne University, Dijon, France
| | - Anne Marie Le Bon
- Centre des Sciences du Goût et de l'Alimentation, UMR6265 CNRS, UMR1324 INRA, Bourgogne University, Dijon, France
| | - Christine Belloir
- Centre des Sciences du Goût et de l'Alimentation, UMR6265 CNRS, UMR1324 INRA, Bourgogne University, Dijon, France
| | | | | | - Søren Brunak
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Olivier Taboureau
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- INSERM UMR-S973, Molecules Thérapeutiques In Silico, Paris Diderot University, Paris, France
- * E-mail:
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13
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Launay G, Sanz G, Pajot-Augy E, Gibrat JF. Modeling of mammalian olfactory receptors and docking of odorants. Biophys Rev 2012; 4:255-269. [PMID: 28510073 DOI: 10.1007/s12551-012-0080-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Accepted: 05/24/2012] [Indexed: 11/29/2022] Open
Abstract
Olfactory receptors (ORs) belong to the superfamily of G protein-coupled receptors (GPCRs), the second largest class of genes after those related to immunity, and account for about 3 % of mammalian genomes. ORs are present in all multicellular organisms and represent more than half the GPCRs in mammalian species (e.g., the mouse OR repertoire contains >1,000 functional genes). ORs are mainly expressed in the olfactory epithelium where they detect odorant molecules, but they are also expressed in a number of other cells, such as sperm cells, although their functions in these cells remain mostly unknown. It has recently been reported that ORs are present in tumoral tissues where they are expressed at different levels than in healthy tissues. A specific OR is over-expressed in prostate cancer cells, and activation of this OR has been shown to inhibit the proliferation of these cells. Odorant stimulation of some of these receptors results in inhibition of cell proliferation. Even though their biological role has not yet been elucidated, these receptors might constitute new targets for diagnosis and therapeutics. It is important to understand the activation mechanism of these receptors at the molecular level, in particular to be able to predict which ligands are likely to activate a particular receptor ('deorphanization') or to design antagonists for a given receptor. In this review, we describe the in silico methodologies used to model the three-dimensional (3D) structure of ORs (in the more general framework of GPCR modeling) and to dock ligands into these 3D structures.
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Affiliation(s)
- Guillaume Launay
- Equipe interactions hôte-pathogène, Bases Moléculaires et Structurales des Systèmes Infectieux, UMR5086 CNRS/Université de Lyon1, 7 Passage du Vercors, Lyon cedex 07, France
| | - Guenhaël Sanz
- Neurobiologie de l'Olfaction et Modélisation en Imagerie UR1197, INRA, 78350, Jouy-en-Josas, France
| | - Edith Pajot-Augy
- Neurobiologie de l'Olfaction et Modélisation en Imagerie UR1197, INRA, 78350, Jouy-en-Josas, France
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14
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Maffei ME, Gertsch J, Appendino G. Plant volatiles: Production, function and pharmacology. Nat Prod Rep 2011; 28:1359-80. [DOI: 10.1039/c1np00021g] [Citation(s) in RCA: 216] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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15
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Cometto-Muñiz JE, Abraham MH. Odor detection by humans of lineal aliphatic aldehydes and helional as gauged by dose-response functions. Chem Senses 2010; 35:289-99. [PMID: 20190010 DOI: 10.1093/chemse/bjq018] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have measured concentration detection (i.e., psychometric) functions to determine the odor detectability of homologous aliphatic aldehydes (propanal, butanal, hexanal, octanal, and nonanal) and helional. Subjects (16 < or = n < or = 18) used a 3-alternative forced-choice procedure against carbon-filtered air (blanks), under an ascending concentration approach. Generation, delivery, and control of each vapor were achieved via an 8-station vapor delivery device. Gas chromatography served to quantify the concentrations presented. Group and individual functions were modeled by a sigmoid (logistic) equation. Odor detection thresholds (ODTs) were defined as the concentration producing a detectability (P) halfway (P = 0.5) between chance (P = 0.0) and perfect detection (P = 1.0). ODTs decreased with carbon chain length: 2.0, 0.46, 0.33, and 0.17 ppb, respectively, from propanal to octanal, but the threshold increased for nonanal (0.53 ppb), revealing maximum sensitivity for the 8-carbon member. The strong olfactory receptor (OR) ligands octanal and helional (0.14 ppb) showed the lowest thresholds. ODTs fell at the lower end of previously reported values. Interindividual variability (ODT ratios) amounted to a factor ranging from 10 to 50, lower than typically reported, and was highest for octanal and hexanal. The behavioral dose-response functions emerge at concentrations 2-5 orders of magnitude lower than those required for functions tracing the activation of specific human ORs by the same aldehydes in cell/molecular studies, after all functions were expressed as vapor concentrations.
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Affiliation(s)
- J Enrique Cometto-Muñiz
- Chemosensory Perception Laboratory, Department of Surgery (Otolaryngology), 9500 Gilman Drive-Mail Code 0957, University of California, San Diego, La Jolla, CA 92093-0957, USA.
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16
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Guo S, Kim J. Dissecting the molecular mechanism of drosophila odorant receptors through activity modeling and comparative analysis. Proteins 2010; 78:381-99. [PMID: 19714770 DOI: 10.1002/prot.22556] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
To gain insight into the molecular mechanism of odorant receptors (ORs) in Drosophila species, we developed a Quantitative Structure Activity Relationship (QSAR) model that predicts experimentally measured electrophysiological activities between 24 D. melanogaster ORs and 108 odorants. Although the model is limited by the tested odorants,analyzing the model allowed dissection of specific topological and chemical properties necessary for an odorant to elicit excitatory or inhibitory receptor response. Linear odorants with five to eight nonhydrogen atoms at the main chain and hydrogen-bond acceptor and/or hydrogen-bond donor at its ends were found to stimulate strong excitatory response. A comparative sequence analysis of 90 ORs in 15 orthologous groups identified 15 putative specificity-determining residues (SDRs) and 15 globally conserved residues that we postulate as functionally key residues. Mapping to a model of secondary structure resulted in 14 out of 30 key residues locating to the transmembrane (TM) domains. Twelve residues, including six SDRs and six conserved residues, are located at the extracellular halves of the TM domains. Combining the evidence from the QSAR modeling and the comparative sequence analysis, we hypothesize that the Drosophila ORs accept odorants into a binding pocket located on the extracellular halves of its TM domains. The QSAR modeling suggests that the binding pocket is around 15 A in depth and about 6 A in width. Twelve mainly polar or charged key residues, both SDRs and conserved, are located in this pocket and postulated to distinguish docked odorants via primarily geometry fitting and hydrogen-bond interaction.
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Affiliation(s)
- Sheng Guo
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
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17
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Knape K, Beyer A, Stary A, Buchbauer G, Wolschann P. Evolutionary trace of human odorant receptors of chromosome 17. FLAVOUR FRAG J 2009. [DOI: 10.1002/ffj.1933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Knape K, Beyer A, Stary A, Buchbauer G, Wolschann P. Genomics of selected human odorant receptors. MONATSHEFTE FUR CHEMIE 2008. [DOI: 10.1007/s00706-008-0957-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sanz G, Thomas-Danguin T, Hamdani EH, Le Poupon C, Briand L, Pernollet JC, Guichard E, Tromelin A. Relationships between molecular structure and perceived odor quality of ligands for a human olfactory receptor. Chem Senses 2008; 33:639-53. [PMID: 18603653 DOI: 10.1093/chemse/bjn032] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Perception of thousands of odors by a few hundreds of olfactory receptors (ORs) results from a combinatorial coding, in which one OR recognizes multiple odorants and an odorant is recognized by a specific group of ORs. Moreover, odorants could act both as agonists or antagonists depending on the OR. This dual agonist-antagonist combinatorial coding is in good agreement with behavioral and psychophysical observations of mixture perception. We previously described the odorant repertoire of a human OR, OR1G1, identifying both agonists and antagonists. In this paper, we performed a 3D-quantitative structure-activity relationship (3D-QSAR) study of these ligands. We obtained a double-alignment model explaining previously reported experimental activities and permitting to predict novel agonists and antagonists for OR1G1. These model predictions were experimentally validated. Thereafter, we evaluated the statistical link between OR1G1 response to odorants, 3D-QSAR categorization of OR1G1 ligands, and their olfactory description. We demonstrated that OR1G1 recognizes a group of odorants that share both 3D structural and perceptual qualities. We hypothesized that OR1G1 contributes to the coding of waxy, fatty, and rose odors in humans.
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Affiliation(s)
- Guenhaël Sanz
- Institut National de la Recherche Agronomique, Unité Minte de Recherche 1197 Neurobiologie de l'Olfaction et de la Prise Alimentaire, F-78352 Jouy-en-Josas, France.
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Grus WE, Zhang J. Distinct evolutionary patterns between chemoreceptors of 2 vertebrate olfactory systems and the differential tuning hypothesis. Mol Biol Evol 2008; 25:1593-601. [PMID: 18460446 DOI: 10.1093/molbev/msn107] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Most tetrapod vertebrates have 2 olfactory systems, the main olfactory system (MOS) and the vomeronasal system (VNS). According to the dual olfactory hypothesis, the MOS detects environmental odorants, whereas the VNS recognizes intraspecific pheromonal cues. However, this strict functional distinction has been blurred by recent reports that both systems can perceive both types of signals. Studies of a limited number of receptors suggest that MOS receptors are broadly tuned generalists, whereas VNS receptors are narrowly tuned specialists. However, whether this distinction applies to all MOS and VNS receptors remains unknown. The differential tuning hypothesis predicts that generalist MOS receptors detect an overlapping set of ligands and thus are more likely to be conserved over evolutionary time than specialist VNS receptors, which would evolve in a more lineage-specific manner. Here we test this prediction for all olfactory chemoreceptors by examining the evolutionary patterns of MOS-expressed odorant receptors (ORs) and trace amine-associated receptors (TAARs) and VNS-expressed vomeronasal type 1 receptors (V1Rs) and vomeronasal type 2 receptors (V2Rs) in 7 tetrapods (mouse, rat, dog, opossum, platypus, chicken, and frog). The phylogenies of V1Rs and V2Rs show abundant lineage-specific gene gains/losses and virtually no one-to-one orthologs between species. Opposite patterns are found for ORs and TAARs. Analysis of functional data and ligand-binding sites of ORs confirms that paralogous chemoreceptors are more likely than orthologs to have different ligands and that functional divergence between paralogous chemoreceptors is established relatively quickly following gene duplication. Together, these results strongly suggest that the functional profile of the VNS chemoreceptor repertoire evolves much faster than that of the MOS chemoreceptor repertoire and that the differential tuning hypothesis applies to the majority, if not all, of MOS and VNS receptors.
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Affiliation(s)
- Wendy E Grus
- Department of Ecology and Evolutionary Biology, University of Michigan, USA
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