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Wang J, Wang D, Huang M, Sun B, Ren F, Wu J, Zhang J, Li H, Sun X. Decoding Molecular Mechanism Underlying Human Olfactory Receptor OR8D1 Activation by Sotolone Enantiomers. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5403-5415. [PMID: 38386648 DOI: 10.1021/acs.jafc.3c09142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Sotolone, a chiral compound, plays an important role in the food industry. Herein, (R)-/(S)-sotolone were separated to determine their odor characteristics and thresholds in air (R-form: smoky, burned, herb, and green aroma, 0.0514 μg/m3; S-form: sweet, milk, acid, and nutty aroma, 0.0048 μg/m3). OR8D1 responses to (R)-/(S)-sotolone were detected in a HEK293 cell-based luminescence assay. (S)-Sotolone was a more potent agonist than (R)-sotolone (EC50 values of 84.98 ± 1.05 and 167.20 ± 0.25 μmol/L, respectively). Molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area analyses confirmed that the combination of (S)-sotolone and OR8D1 was more stable than that of (R)-sotolone. Odorant docking, multiple sequence alignments, site-directed mutagenesis, and functional studies with recombinant odorant receptors (ORs) in a cell-based luminescence assay identified 11 amino-acid residues that influence the enantioselectivity of OR8D1 toward sotolone significantly and that N2065.46 was indispensable to the activation of OR8D1 by (S)-sotolone.
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Affiliation(s)
- Juan Wang
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Danqing Wang
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China
| | - Mingquan Huang
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China
| | - Baoguo Sun
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Fazheng Ren
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Jihong Wu
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China
| | - Jinglin Zhang
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China
| | - Hehe Li
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China
| | - Xiaotao Sun
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology & Business University (BTBU), Beijing 100048, China
- Key Laboratory of Geriatric Nutrition and Health, Beijing Technology and Business University, Ministry of Education, Beijing 100048, China
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Pacalon J, Audic G, Magnat J, Philip M, Golebiowski J, Moreau CJ, Topin J. Elucidation of the structural basis for ligand binding and translocation in conserved insect odorant receptor co-receptors. Nat Commun 2023; 14:8182. [PMID: 38081900 PMCID: PMC10713630 DOI: 10.1038/s41467-023-44058-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
In numerous insects, the olfactory receptor family forms a unique class of heteromeric cation channels. Recent progress in resolving the odorant receptor structures offers unprecedented opportunities for deciphering their molecular mechanisms of ligand recognition. Unexpectedly, these structures in apo or ligand-bound states did not reveal the pathway taken by the ligands between the extracellular space and the deep internal cavities. By combining molecular modeling with electrophysiological recordings, we identified amino acids involved in the dynamic entry pathway and the binding of VUAA1 to Drosophila melanogaster's odorant receptor co-receptor (Orco). Our results provide evidence for the exact location of the agonist binding site and a detailed and original mechanism of ligand translocation controlled by a network of conserved residues. These findings would explain the particularly high selectivity of Orcos for their ligands.
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Affiliation(s)
- Jody Pacalon
- Université Côte d'Azur, Institut de Chimie de Nice UMR7272, CNRS, Nice, France
| | | | | | - Manon Philip
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Jérôme Golebiowski
- Department of Brain & Cognitive Sciences, DGIST, 333, Techno JungAng, Daero, HyeongPoong Myeon, Daegu, Republic of Korea
| | | | - Jérémie Topin
- Université Côte d'Azur, Institut de Chimie de Nice UMR7272, CNRS, Nice, France.
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Zeng S, Zhang L, Li P, Pu D, Fu Y, Zheng R, Xi H, Qiao K, Wang D, Sun B, Sun S, Zhang Y. Molecular mechanisms of caramel-like odorant-olfactory receptor interactions based on a computational chemistry approach. Food Res Int 2023; 171:113063. [PMID: 37330856 DOI: 10.1016/j.foodres.2023.113063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/19/2023]
Abstract
Molecular mechanisms of caramel-like odorant-olfactory receptor interactions were investigated based on molecular docking and molecular dynamics simulations. The transmembrane regions TM-3, TM-5 and TM-6 of receptors were main contributors of amino acid residues in the docking. Molecular docking results showed that hydrogen bonding and pi-pi stacking were the key forces for the stabilization of caramel-like odorants. The binding energies were positively correlated with the molecular weight of caramel-like odorants. Residues Asn155 (84%, OR2W1), Asn206 (86%, OR8D1), Ser155 (77%, OR8D1), Asp179 (87%, OR5M3), Val182 (84%, OR2J2) and Tyr260 (94%, OR2J2) with high frequencies played an important role in the complexes formation. Odorants 4-hydroxy-5-methylfuran-3(2H)-one (16#) and methylglyoxal (128#) were screened by molecular field-based similarity analysis, which tended to bind to the receptors OR1G1 and OR52H1 respectively, resulting a caramel-like aroma perception. The obtained results are useful for better understanding the perception of caramel-like odorants and their high-throughput screening.
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Affiliation(s)
- Shitong Zeng
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China; Key Laboratory of Flavor Science of China General Chamber of Commerce, Beijing Technology and Business University, Beijing 100048, China
| | - Lili Zhang
- Key Laboratory of Flavor Science of China General Chamber of Commerce, Beijing Technology and Business University, Beijing 100048, China; Food Laboratory of Zhongyuan, Beijing Technology and Business University, Beijing 100048, China
| | - Peng Li
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Dandan Pu
- Key Laboratory of Flavor Science of China General Chamber of Commerce, Beijing Technology and Business University, Beijing 100048, China; Food Laboratory of Zhongyuan, Beijing Technology and Business University, Beijing 100048, China
| | - Yingjie Fu
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Ruiyi Zheng
- Key Laboratory of Flavor Science of China General Chamber of Commerce, Beijing Technology and Business University, Beijing 100048, China; Food Laboratory of Zhongyuan, Beijing Technology and Business University, Beijing 100048, China
| | - Hui Xi
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Kaina Qiao
- Key Laboratory of Flavor Science of China General Chamber of Commerce, Beijing Technology and Business University, Beijing 100048, China; Food Laboratory of Zhongyuan, Beijing Technology and Business University, Beijing 100048, China
| | - Dingzhong Wang
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China
| | - Baoguo Sun
- Key Laboratory of Flavor Science of China General Chamber of Commerce, Beijing Technology and Business University, Beijing 100048, China; Food Laboratory of Zhongyuan, Beijing Technology and Business University, Beijing 100048, China
| | - Shihao Sun
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China.
| | - Yuyu Zhang
- Key Laboratory of Flavor Science of China General Chamber of Commerce, Beijing Technology and Business University, Beijing 100048, China; Food Laboratory of Zhongyuan, Beijing Technology and Business University, Beijing 100048, China.
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Rugard M, Audouze K, Tromelin A. Combining the Classification and Pharmacophore Approaches to Understand Homogeneous Olfactory Perceptions at Peripheral Level: Focus on Two Aroma Mixtures. Molecules 2023; 28:molecules28104028. [PMID: 37241770 DOI: 10.3390/molecules28104028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/20/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
The mechanisms involved in the homogeneous perception of odorant mixtures remain largely unknown. With the aim of enhancing knowledge about blending and masking mixture perceptions, we focused on structure-odor relationships by combining the classification and pharmacophore approaches. We built a dataset of about 5000 molecules and their related odors and reduced the multidimensional space defined by 1014 fingerprints representing the structures to a tridimensional 3D space using uniform manifold approximation and projection (UMAP). The self-organizing map (SOM) classification was then performed using the 3D coordinates in the UMAP space that defined specific clusters. We explored the allocating in these clusters of the components of two aroma mixtures: a blended mixture (red cordial (RC) mixture, 6 molecules) and a masking binary mixture (isoamyl acetate/whiskey-lactone [IA/WL]). Focusing on clusters containing the components of the mixtures, we looked at the odor notes carried by the molecules belonging to these clusters and also at their structural features by pharmacophore modeling (PHASE). The obtained pharmacophore models suggest that WL and IA could have a common binding site(s) at the peripheral level, but that would be excluded for the components of RC. In vitro experiments will soon be carried out to assess these hypotheses.
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Affiliation(s)
- Marylène Rugard
- T3S, Inserm UMR S-1124, Université Paris Cité, F-75006 Paris, France
| | - Karine Audouze
- T3S, Inserm UMR S-1124, Université Paris Cité, F-75006 Paris, France
| | - Anne Tromelin
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Institut Agro, Université de Bourgogne, F-21000 Dijon, France
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Nicoli A, Haag F, Marcinek P, He R, Kreißl J, Stein J, Marchetto A, Dunkel A, Hofmann T, Krautwurst D, Di Pizio A. Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K1. J Chem Inf Model 2023; 63:2014-2029. [PMID: 36696962 PMCID: PMC10091413 DOI: 10.1021/acs.jcim.2c00752] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
With approximately 400 encoding genes in humans, odorant receptors (ORs) are the largest subfamily of class A G protein-coupled receptors (GPCRs). Despite its high relevance and representation, the odorant-GPCRome is structurally poorly characterized: no experimental structures are available, and the low sequence identity of ORs to experimentally solved GPCRs is a significant challenge for their modeling. Moreover, the receptive range of most ORs is unknown. The odorant receptor OR5K1 was recently and comprehensively characterized in terms of cognate agonists. Here, we report two additional agonists and functional data of the most potent compound on two mutants, L1043.32 and L2556.51. Experimental data was used to guide the investigation of the binding modes of OR5K1 ligands into the orthosteric binding site using structural information from AI-driven modeling, as recently released in the AlphaFold Protein Structure Database, and from homology modeling. Induced-fit docking simulations were used to sample the binding site conformational space for ensemble docking. Mutagenesis data guided side chain residue sampling and model selection. We obtained models that could better rationalize the different activity of active (agonist) versus inactive molecules with respect to starting models and also capture differences in activity related to minor structural differences. Therefore, we provide a model refinement protocol that can be applied to model the orthosteric binding site of ORs as well as that of GPCRs with low sequence identity to available templates.
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Affiliation(s)
- Alessandro Nicoli
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Franziska Haag
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Patrick Marcinek
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Ruiming He
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany.,Department of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Johanna Kreißl
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Jörg Stein
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Alessandro Marchetto
- Computational Biomedicine, Institute for Advanced Simulations (IAS)-5/Institute for Neuroscience and Medicine (INM)-9, Forschungszentrum Jülich, 52428 Jülich, Germany.,Department of Biology, Faculty of Mathematics, Computer Science and Natural Sciences, RWTH Aachen University, 52074 Aachen, Germany
| | - Andreas Dunkel
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Thomas Hofmann
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, 85354 Freising, Germany
| | - Dietmar Krautwurst
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Antonella Di Pizio
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
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The Third Extracellular Loop of Mammalian Odorant Receptors Is Involved in Ligand Binding. Int J Mol Sci 2022; 23:ijms232012501. [PMID: 36293357 PMCID: PMC9604345 DOI: 10.3390/ijms232012501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/22/2022] [Accepted: 10/06/2022] [Indexed: 12/30/2022] Open
Abstract
Mammals recognize chemicals in the air via G protein-coupled odorant receptors (ORs). In addition to their orthosteric binding site, other segments of these receptors modulate ligand recognition. Focusing on human hOR1A1, which is considered prototypical of class II ORs, we used a combination of molecular modeling, site-directed mutagenesis, and in vitro functional assays. We showed that the third extracellular loop of ORs (ECL3) contributes to ligand recognition and receptor activation. Indeed, site-directed mutations in ECL3 showed differential effects on the potency and efficacy of both carvones, citronellol, and 2-nonanone.
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7
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Extracellular loop 2 of G protein-coupled olfactory receptors is critical for odorant recognition. J Biol Chem 2022; 298:102331. [PMID: 35926708 PMCID: PMC9442423 DOI: 10.1016/j.jbc.2022.102331] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/27/2022] Open
Abstract
G protein–coupled olfactory receptors (ORs) enable us to detect innumerous odorants. They are also ectopically expressed in nonolfactory tissues and emerging as attractive drug targets. ORs can be promiscuous or highly specific, which is part of a larger mechanism for odor discrimination. Here, we demonstrate that the OR extracellular loop 2 (ECL2) plays critical roles in OR promiscuity and specificity. Using site-directed mutagenesis and molecular modeling, we constructed 3D OR models in which ECL2 forms a lid over the orthosteric pocket. We demonstrate using molecular dynamics simulations that ECL2 controls the shape and volume of the odorant-binding pocket, maintains the pocket hydrophobicity, and acts as a gatekeeper of odorant binding. Therefore, we propose the interplay between the specific orthosteric pocket and the variable, less specific ECL2 controls OR specificity and promiscuity. Furthermore, the 3D models created here enabled virtual screening of new OR agonists and antagonists, which exhibited a 70% hit rate in cell assays. Our approach can potentially be generalized to structure-based ligand screening for other G protein–coupled receptors that lack high-resolution 3D structures.
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Functional analysis of human olfactory receptors with a high basal activity using LNCaP cell line. PLoS One 2022; 17:e0267356. [PMID: 35446888 PMCID: PMC9022881 DOI: 10.1371/journal.pone.0267356] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/06/2022] [Indexed: 11/19/2022] Open
Abstract
Humans use a family of more than 400 olfactory receptors (ORs) to detect odorants. However, deorphanization of ORs is a critical issue because the functional properties of more than 80% of ORs remain unknown, thus, hampering our understanding of the relationship between receptor function and perception. HEK293 cells are the most commonly used heterologous expression system to determine the function of a given OR; however, they cannot functionally express a majority of ORs probably due to a lack of factor(s) required in cells in which ORs function endogenously. Interestingly, ORs have been known to be expressed in a variety of cells outside the nose and play critical physiological roles. These findings prompted us to test the capacity of cells to functionally express a specific repertoire of ORs. In this study, we selected three cell lines that endogenously express functional ORs. We demonstrated that human prostate carcinoma (LNCaP) cell lines successfully identified novel ligands for ORs that were not recognized when expressed in HEK293 cells. Further experiments suggested that the LNCaP cell line was effective for functional expression of ORs, especially with a high basal activity, which impeded the sensitive detection of ligand-mediated activity of ORs. This report provides an efficient functional assay system for a specific repertoire of ORs that cannot be characterized in current cell systems.
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Topin J, Bouysset C, Pacalon J, Kim Y, Rhyu MR, Fiorucci S, Golebiowski J. Functional molecular switches of mammalian G protein-coupled bitter-taste receptors. Cell Mol Life Sci 2021; 78:7605-7615. [PMID: 34687318 PMCID: PMC11073308 DOI: 10.1007/s00018-021-03968-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/20/2021] [Accepted: 09/26/2021] [Indexed: 10/20/2022]
Abstract
Bitter taste receptors (TAS2Rs) are a poorly understood subgroup of G protein-coupled receptors (GPCRs). The experimental structure of these receptors has yet to be determined, and key-residues controlling their function remain mostly unknown. We designed an integrative approach to improve comparative modeling of TAS2Rs. Using current knowledge on class A GPCRs and existing experimental data in the literature as constraints, we pinpointed conserved motifs to entirely re-align the amino-acid sequences of TAS2Rs. We constructed accurate homology models of human TAS2Rs. As a test case, we examined the accuracy of the TAS2R16 model with site-directed mutagenesis and in vitro functional assays. This combination of in silico and in vitro results clarifies sequence-function relationships and proposes functional molecular switches that encode agonist sensing and downstream signaling mechanisms within mammalian TAS2Rs sequences.
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Affiliation(s)
- Jérémie Topin
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France.
| | - Cédric Bouysset
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France
| | - Jody Pacalon
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France
| | - Yiseul Kim
- Korea Food Research Institute, 245 Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Mee-Ra Rhyu
- Korea Food Research Institute, 245 Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Sébastien Fiorucci
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France.
| | - Jérôme Golebiowski
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France
- Department of Brain and Cognitive Sciences, DGIST, 333, Techno JungAng, Daero, HyeongPoong Myeon, Daegu, 711-873, Republic of Korea
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Del Mármol J, Yedlin MA, Ruta V. The structural basis of odorant recognition in insect olfactory receptors. Nature 2021; 597:126-131. [PMID: 34349260 PMCID: PMC8410599 DOI: 10.1038/s41586-021-03794-8] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023]
Abstract
Olfactory systems must detect and discriminate amongst an enormous variety of odorants1. To contend with this challenge, diverse species have converged on a common strategy in which odorant identity is encoded through the combinatorial activation of large families of olfactory receptors1-3, thus allowing a finite number of receptors to detect a vast chemical world. Here we offer structural and mechanistic insight into how an individual olfactory receptor can flexibly recognize diverse odorants. We show that the olfactory receptor MhOR5 from the jumping bristletail4 Machilis hrabei assembles as a homotetrameric odorant-gated ion channel with broad chemical tuning. Using cryo-electron microscopy, we elucidated the structure of MhOR5 in multiple gating states, alone and in complex with two of its agonists-the odorant eugenol and the insect repellent DEET. Both ligands are recognized through distributed hydrophobic interactions within the same geometrically simple binding pocket located in the transmembrane region of each subunit, suggesting a structural logic for the promiscuous chemical sensitivity of this receptor. Mutation of individual residues lining the binding pocket predictably altered the sensitivity of MhOR5 to eugenol and DEET and broadly reconfigured the receptor's tuning. Together, our data support a model in which diverse odorants share the same structural determinants for binding, shedding light on the molecular recognition mechanisms that ultimately endow the olfactory system with its immense discriminatory capacity.
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Affiliation(s)
- Josefina Del Mármol
- Laboratory of Neurophysiology and Behavior, The Rockefeller University, New York, NY, USA
| | - Mackenzie A Yedlin
- Laboratory of Neurophysiology and Behavior, The Rockefeller University, New York, NY, USA
| | - Vanessa Ruta
- Laboratory of Neurophysiology and Behavior, The Rockefeller University, New York, NY, USA.
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Ectopic Odorant Receptor Responding to Flavor Compounds: Versatile Roles in Health and Disease. Pharmaceutics 2021; 13:pharmaceutics13081314. [PMID: 34452275 PMCID: PMC8402194 DOI: 10.3390/pharmaceutics13081314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/11/2021] [Accepted: 08/17/2021] [Indexed: 12/23/2022] Open
Abstract
Prompted by the ground-breaking discovery of the rodent odorant receptor (OR) gene family within the olfactory epithelium nearly 30 years ago, followed by that of OR genes in cells of the mammalian germ line, and potentiated by the identification of ORs throughout the body, our appreciation for ORs as general chemoreceptors responding to odorant compounds in the regulation of physiological or pathophysiological processes continues to expand. Ectopic ORs are now activated by a diversity of flavor compounds and are involved in diverse physiological phenomena varying from adipogenesis to myogenesis to hepatic lipid accumulation to serotonin secretion. In this review, we outline the key biological functions of the ectopic ORs responding to flavor compounds and the underlying molecular mechanisms. We also discuss research opportunities for utilizing ectopic ORs as therapeutic strategies in the treatment of human disease as well as challenges to be overcome in the future. The recognition of the potent function, signaling pathway, and pharmacology of ectopic ORs in diverse tissues and cell types, coupled with the fact that they belong to G protein-coupled receptors, a highly druggable protein family, unequivocally highlight the potential of ectopic ORs responding to flavor compounds, especially food-derived odorant compounds, as a promising therapeutic strategy for various diseases.
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Ben Khemis I, Sagaama A, Issaoui N, Ben Lamine A. Steric and energetic characterizations of mouse and human musk receptors activated by nitro musk smelling compounds at molecular level: Statistical physics treatment and molecular docking analysis. Int J Biol Macromol 2021; 188:333-342. [PMID: 34389381 DOI: 10.1016/j.ijbiomac.2021.08.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/12/2021] [Accepted: 08/05/2021] [Indexed: 01/18/2023]
Abstract
Understanding olfaction process at a microscopic or molecular level needs more elucidation of the multiple stages involved in the olfaction mechanism. A worth full elucidation and a better understanding of this molecular mechanism, a necessary preamble should be achieved. The content of this work is a preamble for that. A study of the mouse and human olfactory receptors activation in response to two nitro musks stimuli, which are the musk xylol and the musk ketone, are considered here, first, for their wide expanded use in perfumery, but also to show some particular aspects of this process in the case of these two stimuli, which could help to deduce more details and more general aspects in the global olfactory mechanism. A statistical physics modeling using the monolayer model with two independent types of receptor binding sites of the response of the mouse olfactory receptor MOR215-1 and the human olfactory receptor OR5AN1, which are identified as specifically responding to musk compounds, is used to characterize the interaction between the two nitro musk molecules, the mouse and the human olfactory receptors and to determine the olfactory band of these two odorants through the determination of the molar adsorption energies and the adsorption energy distributions. The physico-chemical model parameters can be used for the steric characterization via the calculation of the receptor site size distributions. The docking computation between these two nitro musks and the human olfactory receptor OR5AN1 is performed demonstrating a large similarity in receptor-ligand detection process. Thus, docking finding results prove that the calculated binding affinities were belonging to the spectrum of adsorption energies.
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Affiliation(s)
- Ismahene Ben Khemis
- Laboratory of Quantum and Statistical Physics LR 18 ES 18, Faculty of Sciences of Monastir, Environnement Street, 5019 Monastir, Tunisia.
| | - Abir Sagaama
- Laboratory of Quantum and Statistical Physics LR 18 ES 18, Faculty of Sciences of Monastir, Environnement Street, 5019 Monastir, Tunisia
| | - Noureddine Issaoui
- Laboratory of Quantum and Statistical Physics LR 18 ES 18, Faculty of Sciences of Monastir, Environnement Street, 5019 Monastir, Tunisia
| | - Abdelmottaleb Ben Lamine
- Laboratory of Quantum and Statistical Physics LR 18 ES 18, Faculty of Sciences of Monastir, Environnement Street, 5019 Monastir, Tunisia.
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Manzini I, Schild D, Di Natale C. Principles of odor coding in vertebrates and artificial chemosensory systems. Physiol Rev 2021; 102:61-154. [PMID: 34254835 DOI: 10.1152/physrev.00036.2020] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The biological olfactory system is the sensory system responsible for the detection of the chemical composition of the environment. Several attempts to mimic biological olfactory systems have led to various artificial olfactory systems using different technical approaches. Here we provide a parallel description of biological olfactory systems and their technical counterparts. We start with a presentation of the input to the systems, the stimuli, and treat the interface between the external world and the environment where receptor neurons or artificial chemosensors reside. We then delineate the functions of receptor neurons and chemosensors as well as their overall I-O relationships. Up to this point, our account of the systems goes along similar lines. The next processing steps differ considerably: while in biology the processing step following the receptor neurons is the "integration" and "processing" of receptor neuron outputs in the olfactory bulb, this step has various realizations in electronic noses. For a long period of time, the signal processing stages beyond the olfactory bulb, i.e., the higher olfactory centers were little studied. Only recently there has been a marked growth of studies tackling the information processing in these centers. In electronic noses, a third stage of processing has virtually never been considered. In this review, we provide an up-to-date overview of the current knowledge of both fields and, for the first time, attempt to tie them together. We hope it will be a breeding ground for better information, communication, and data exchange between very related but so far little connected fields.
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Affiliation(s)
- Ivan Manzini
- Animal Physiology and Molecular Biomedicine, Justus-Liebig-University Gießen, Gießen, Germany
| | - Detlev Schild
- Institute of Neurophysiology and Cellular Biophysics, University Medical Center, University of Göttingen, Göttingen, Germany
| | - Corrado Di Natale
- Department of Electronic Engineering, University of Rome Tor Vergata, Rome, Italy
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14
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Alfonso-Prieto M. Bitter Taste and Olfactory Receptors: Beyond Chemical Sensing in the Tongue and the Nose. J Membr Biol 2021; 254:343-352. [PMID: 34173018 PMCID: PMC8231087 DOI: 10.1007/s00232-021-00182-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/29/2021] [Indexed: 11/24/2022]
Abstract
Abstract The Up-and-Coming-Scientist section of the current issue of the Journal of Membrane Biology features the invited essay by Dr. Mercedes Alfonso-Prieto, Assistant Professor at the Forschungszentrum Jülich (FZJ), Germany, and the Heinrich-Heine University Düsseldorf, Vogt Institute for Brain Research.
Dr. Alfonso-Prieto completed her doctoral degree in chemistry at the Barcelona Science Park, Spain, in 2009, pursued post-doctoral research in computational molecular sciences at Temple University, USA, and then, as a Marie Curie post-doctoral fellow at the University of Barcelona, worked on computations of enzyme reactions and modeling of photoswitchable ligands targeting neuronal receptors. In 2016, she joined the Institute for Advanced Science and the Institute for Computational Biomedicine at the FZJ, where she pursues research on modeling and simulation of chemical senses.
The invited essay by Dr. Alfonso-Prieto discusses state-of-the-art modeling of molecular receptors involved in chemical sensing – the senses of taste and smell. These receptors, and computational methods to study them, are the focus of Dr. Alfonso-Prieto’s research. Recently, Dr. Alfonso-Prieto and colleagues have presented a new methodology to predict ligand binding poses for GPCRs, and extensive computations that deciphered the ligand selectivity determinants of bitter taste receptors. These developments inform our current understanding of how taste occurs at the molecular level. Graphic Abstract ![]()
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Affiliation(s)
- Mercedes Alfonso-Prieto
- Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich GmbH, Jülich, Germany. .,Medical Faculty, Cécile and Oskar Vogt Institute for Brain Research, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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15
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Smell compounds classification using UMAP to increase knowledge of odors and molecular structures linkages. PLoS One 2021; 16:e0252486. [PMID: 34048487 PMCID: PMC8162648 DOI: 10.1371/journal.pone.0252486] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/15/2021] [Indexed: 12/17/2022] Open
Abstract
This study aims to highlight the relationships between the structure of smell compounds and their odors. For this purpose, heterogeneous data sources were screened, and 6038 odorant compounds and their known associated odors (162 odor notes) were compiled, each individual molecule being represented with a set of 1024 structural fingerprint. Several dimensional reduction techniques (PCA, MDS, t-SNE and UMAP) with two clustering methods (k-means and agglomerative hierarchical clustering AHC) were assessed based on the calculated fingerprints. The combination of UMAP with k-means and AHC methods allowed to obtain a good representativeness of odors by clusters, as well as the best visualization of the proximity of odorants on the basis of their molecular structures. The presence or absence of molecular substructures has been calculated on odorant in order to link chemical groups to odors. The results of this analysis bring out some associations for both the odor notes and the chemical structures of the molecules such as "woody" and "spicy" notes with allylic and bicyclic structures, "balsamic" notes with unsaturated rings, both "sulfurous" and "citrus" with aldehydes, alcohols, carboxylic acids, amines and sulfur compounds, and "oily", "fatty" and "fruity" characterized by esters and with long carbon chains. Overall, the use of UMAP associated to clustering is a promising method to suggest hypotheses on the odorant structure-odor relationships.
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16
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Ben Khemis I, Bouzid M, Mechi N, Ben Lamine A. Statistical physics modeling and interpretation of the adsorption of enantiomeric terpenes onto the human olfactory receptor OR1A1. Int J Biol Macromol 2021; 171:428-434. [PMID: 33412204 DOI: 10.1016/j.ijbiomac.2020.12.209] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/24/2020] [Accepted: 12/29/2020] [Indexed: 12/16/2022]
Abstract
The statistical physics approach has been well studied by our research team for liquid and gaseous adsorption systems. This treatment is based on the grand canonical partition function to give new interpretations of the adsorption process at molecular level for chemical senses: olfaction and taste. This work represents a contribution to understand the olfaction mechanism of four of enantiomeric terpenes by applying a statistical physics treatment that allows giving a physico-chemical meaning to parameters involved in the analytical model. It is possible to estimate the number of adsorbed molecules per site, the anchorage number, the receptor density, the concentration at half saturation and the molar adsorption energy. Through this selection of the best fitting model and through fitted values of these parameters, we showed that the adsorption of carvone and limonene enantiomers is not a multilayer process but a monolayer monosite process (monolayer adsorption model with identical and independent sites (n ≠ 1)). The physico-chemical model parameters can be used for the energetic characterization of the interactions between the carvone and the limonene enantiomers and the human olfactory receptor OR1A1 and the determination of an olfactory band of order of 14 kJ/mol, 7 kJ/mol, 9 kJ/mol, 8 kJ/mol for (R)-(-)-carvone, (S)-(+)-carvone, (R)-(+)-limonene and (S)-(-)-limonene, respectively, through the determination of the adsorption energy values and the adsorption energy distributions (AEDs). Thanks to the grand canonical formalism in statistical physics, the negative values of the Gibbs free enthalpy indicate that the adsorption process of the four enantiomeric terpenes onto the human olfactory receptor OR1A1 was spontaneous. The exothermic adsorption mechanism involved in the olfactory perception was explained via the negative values of the internal energy.
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Affiliation(s)
- Ismahene Ben Khemis
- Laboratory of Quantum and Statistical Physics LR18 ES18, Faculty of Sciences of Monastir, Environnement Street, 5019 Monastir, Tunisia.
| | - Mohamed Bouzid
- Laboratory of Quantum and Statistical Physics LR18 ES18, Faculty of Sciences of Monastir, Environnement Street, 5019 Monastir, Tunisia
| | - Nesrine Mechi
- Laboratory of Quantum and Statistical Physics LR18 ES18, Faculty of Sciences of Monastir, Environnement Street, 5019 Monastir, Tunisia
| | - Abdelmottaleb Ben Lamine
- Laboratory of Quantum and Statistical Physics LR18 ES18, Faculty of Sciences of Monastir, Environnement Street, 5019 Monastir, Tunisia.
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17
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Interpretations of key food odorant dose-olfactory response curves using statistical physics method. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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18
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Ben Khemis I, Mechi N, Ben Lamine A. Investigation of mouse eugenol olfactory receptor activated by eugenol, vanillin and ethyl vanillin: Steric and energetic characterizations. Int J Biol Macromol 2020; 163:2325-2333. [DOI: 10.1016/j.ijbiomac.2020.09.119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 09/16/2020] [Indexed: 11/30/2022]
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19
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Kowalewski J, Ray A. Predicting Human Olfactory Perception from Activities of Odorant Receptors. iScience 2020; 23:101361. [PMID: 32731170 PMCID: PMC7393469 DOI: 10.1016/j.isci.2020.101361] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 05/31/2020] [Accepted: 07/09/2020] [Indexed: 11/30/2022] Open
Abstract
Odor perception in humans is initiated by activation of odorant receptors (ORs) in the nose. However, the ORs linked to specific olfactory percepts are unknown, unlike in vision or taste where receptors are linked to perception of different colors and tastes. The large family of ORs (~400) and multiple receptors activated by an odorant present serious challenges. Here, we first use machine learning to screen ~0.5 million compounds for new ligands and identify enriched structural motifs for ligands of 34 human ORs. We next demonstrate that the activity of ORs successfully predicts many of the 146 different perceptual qualities of chemicals. Although chemical features have been used to model odor percepts, we show that biologically relevant OR activity is often superior. Interestingly, each odor percept could be predicted with very few ORs, implying they contribute more to each olfactory percept. A similar model is observed in Drosophila where comprehensive OR-neuron data are available. Machine learning predicted activity of 34 human ORs for ~0.5 million chemicals Activities of human ORs could predict odor character using machine learning Few OR activities were needed to optimize predictions of each odor percept Behavior predictions in Drosophila also need few olfactory receptor activities
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Affiliation(s)
- Joel Kowalewski
- Interdepartmental Neuroscience Program, University of California, Riverside, CA 92521, USA
| | - Anandasankar Ray
- Interdepartmental Neuroscience Program, University of California, Riverside, CA 92521, USA; Department of Molecular, Cell and Systems Biology, University of California, 3401 Watkins Drive, Riverside, CA 92521, USA.
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20
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Haag F, Ahmed L, Reiss K, Block E, Batista VS, Krautwurst D. Copper-mediated thiol potentiation and mutagenesis-guided modeling suggest a highly conserved copper-binding motif in human OR2M3. Cell Mol Life Sci 2020; 77:2157-2179. [PMID: 31435697 PMCID: PMC7256108 DOI: 10.1007/s00018-019-03279-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 08/07/2019] [Accepted: 08/12/2019] [Indexed: 12/20/2022]
Abstract
Sulfur-containing compounds within a physiological relevant, natural odor space, such as the key food odorants, typically constitute the group of volatiles with the lowest odor thresholds. The observation that certain metals, such as copper, potentiate the smell of sulfur-containing, metal-coordinating odorants led to the hypothesis that their cognate receptors are metalloproteins. However, experimental evidence is sparse-so far, only one human odorant receptor, OR2T11, and a few mouse receptors, have been reported to be activated by sulfur-containing odorants in a copper-dependent way, while the activation of other receptors by sulfur-containing odorants did not depend on the presence of metals. Here we identified an evolutionary conserved putative copper interaction motif CC/CSSH, comprising two copper-binding sites in TMH5 and TMH6, together with the binding pocket for 3-mercapto-2-methylpentan-1-ol in the narrowly tuned human receptor OR2M3. To characterize the copper-binding motif, we combined homology modeling, docking studies, site-directed mutagenesis, and functional expression of recombinant ORs in a cell-based, real-time luminescence assay. Ligand activation of OR2M3 was potentiated in the presence of copper. This effect of copper was mimicked by ionic and colloidal silver. In two broadly tuned receptors, OR1A1 and OR2W1, which did not reveal a putative copper interaction motif, activation by their most potent, sulfur-containing key food odorants did not depend on the presence of copper. Our results suggest a highly conserved putative copper-binding motif to be necessary for a copper-modulated and thiol-specific function of members from three subfamilies of family 2 ORs.
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Affiliation(s)
- Franziska Haag
- Leibniz-Institute for Food Systems Biology, Technical University of Munich, Lise-Meitner-Str. 34, 85354, Freising, Germany
| | - Lucky Ahmed
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Krystle Reiss
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Eric Block
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Dietmar Krautwurst
- Leibniz-Institute for Food Systems Biology, Technical University of Munich, Lise-Meitner-Str. 34, 85354, Freising, Germany.
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21
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Jeong P, Kim SK, Li Q, Oh SJ, Son S, Chen G, Tan H, Kim S, Park JH, Park KD, Kim YO, Yoon MH, Kim YC, Goddard WA. Discovery of Novel Biased Opioid Receptor Ligands through Structure-Based Pharmacophore Virtual Screening and Experiment. ChemMedChem 2019; 14:1783-1794. [PMID: 31359587 DOI: 10.1002/cmdc.201900418] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Indexed: 11/08/2022]
Abstract
Gi -protein-biased agonists with minimal β-arrestin recruitment represent opportunities to overcome the serious adverse effects of human mu opioid receptor (μ-OR) agonists and developing alternative and safe treatments for pain. In order to discover novel non-morphinan opioid receptor agonists, we applied hierarchical virtual screening of our in-house database against a pharmacophore based on modeling the active conformations of opioid receptors. We discovered an initial hit compound, a novel μ-OR agonist with a pyrazoloisoquinoline scaffold. We applied computational R-group screening to this compound and synthesized 14 derivatives predicted to be the best. Of these, a new Gi -protein-biased compound, 1-{5-(3-chlorophenyl)-7,8-dimethoxy-3-[4-(methylsulfonyl)benzyl]-3H-pyrazolo[3,4-c]isoquinolin-1-yl}-N,N-dimethylmethanamine, showed an EC50 value of 179 nm against the μ-OR. This resulted in significant pain relief for mice in the phase II period of formalin response tests. This study provides a new strategy to identify diverse sets of promising compounds that might prove useful for the development of drugs that target other G-protein-coupled receptors.
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Affiliation(s)
- Pyeonghwa Jeong
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, 61005, South Korea
| | - Soo-Kyung Kim
- Materials and Process Simulation Center (MC-139-74), California Institute of Technology, Pasadena, California, 91125, USA
| | - Quanjie Li
- Materials and Process Simulation Center (MC-139-74), California Institute of Technology, Pasadena, California, 91125, USA.,College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China.,Institute of Medicinal Biotechnology, Chinese Academy of Medical Science, Beijing, 100050, P. R. China
| | - Su-Jin Oh
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, 61005, South Korea
| | - Seonil Son
- School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, 61005, South Korea
| | - Guangju Chen
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Hongwei Tan
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Siwon Kim
- Convergence Research Center for Diagnosis, Treatment, and Care system of Dementia, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea.,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, South Korea
| | - Jong-Hyun Park
- Convergence Research Center for Diagnosis, Treatment, and Care system of Dementia, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea
| | - Ki Duk Park
- Convergence Research Center for Diagnosis, Treatment, and Care system of Dementia, Korea Institute of Science and Technology (KIST), Seoul, 02792, South Korea.,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul, 02792, South Korea.,KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul, 02447, South Korea
| | - Yeo Ok Kim
- Department of Anesthesiology and Pain Medicine, Medical School, Chonnam National University, Gwangju, 501-757, South Korea
| | - Myung Ha Yoon
- Department of Anesthesiology and Pain Medicine, Medical School, Chonnam National University, Gwangju, 501-757, South Korea
| | - Yong-Chul Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, 61005, South Korea.,School of Life Sciences, Gwangju Institute of Science and Technology, 123 Cheomdan-gwagiro, Buk-gu, 61005, South Korea
| | - William A Goddard
- Materials and Process Simulation Center (MC-139-74), California Institute of Technology, Pasadena, California, 91125, USA
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22
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Jabeen A, Ranganathan S. Applications of machine learning in GPCR bioactive ligand discovery. Curr Opin Struct Biol 2019; 55:66-76. [PMID: 31005679 DOI: 10.1016/j.sbi.2019.03.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/14/2019] [Accepted: 03/14/2019] [Indexed: 12/17/2022]
Abstract
GPCRs constitute the largest druggable family having targets for 475 Food and Drug Administration (FDA) approved drugs. As GPCRs are of great interest to pharmaceutical industry, enormous efforts are being expended to find relevant and potent GPCR ligands as lead compounds. There are tens of millions of compounds present in different chemical databases. In order to scan this immense chemical space, computational methods, especially machine learning (ML) methods, are essential components of GPCR drug discovery pipelines. ML approaches have applications in both ligand-based and structure-based virtual screening. We present here a cheminformatics overview of ML applications to different stages of GPCR drug discovery. Focusing on olfactory receptors, which are the largest family of GPCRs, a case study for predicting agonists for an ectopic olfactory receptor, OR1G1, compares four classical ML methods.
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Affiliation(s)
- Amara Jabeen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia.
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23
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Cong X, Zheng Q, Ren W, Chéron JB, Fiorucci S, Wen T, Zhang C, Yu H, Golebiowski J, Yu Y. Zebrafish olfactory receptors ORAs differentially detect bile acids and bile salts. J Biol Chem 2019; 294:6762-6771. [PMID: 30833327 DOI: 10.1074/jbc.ra118.006483] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/20/2019] [Indexed: 11/06/2022] Open
Abstract
The fish olfactory receptor ORA family is orthologous to the mammalian vomeronasal receptors type 1. It consists of six highly conserved chemosensory receptors expected to be essential for survival and communication. We deorphanized the zebrafish ORA family in a heterologous cell system. The six receptors responded specifically to lithocholic acid (LCA) and closely related C24 5β-bile acids/salts. LCA attracted zebrafish as strongly as food in behavioral tests, whereas the less potent cholanic acid elicited weaker attraction, consistent with the in vitro results. The ORA-ligand recognition patterns were probed with site-directed mutagenesis guided by in silico modeling. We revealed the receptors' structure-function relationship underlying their specificity and selectivity for these compounds. Bile acids/salts are putative fish semiochemicals or pheromones sensed by the olfactory system with high specificity. This work identified their receptors and provided the basis for probing the roles of ORAs and bile acids/salts in fish chemosensation.
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Affiliation(s)
- Xiaojing Cong
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice 06108 France
| | - Qian Zheng
- From the School of Life Sciences, Shanghai University, Shanghai 200444 China
| | - Wenwen Ren
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200031 China, and
| | - Jean-Baptiste Chéron
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice 06108 France
| | - Sébastien Fiorucci
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice 06108 France
| | - Tieqiao Wen
- From the School of Life Sciences, Shanghai University, Shanghai 200444 China
| | - Chunbo Zhang
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois 60616
| | - Hongmeng Yu
- Department of Otolaryngology, Eye, Ear, Nose and Throat Hospital, Shanghai Key Clinical Disciplines of Otorhinolaryngology, Fudan University, Shanghai 200031 China,
| | - Jérôme Golebiowski
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice 06108 France, .,Department of Brain and Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology, Daegu 711-873 South Korea
| | - Yiqun Yu
- From the School of Life Sciences, Shanghai University, Shanghai 200444 China, .,Department of Otolaryngology, Eye, Ear, Nose and Throat Hospital, Shanghai Key Clinical Disciplines of Otorhinolaryngology, Fudan University, Shanghai 200031 China
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24
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Bushdid C, de March CA, Topin J, Do M, Matsunami H, Golebiowski J. Mammalian class I odorant receptors exhibit a conserved vestibular-binding pocket. Cell Mol Life Sci 2019; 76:995-1004. [PMID: 30599066 PMCID: PMC7313674 DOI: 10.1007/s00018-018-2996-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 12/22/2022]
Abstract
Odorant receptors represent the largest family of mammalian G protein-coupled receptors. Phylogenetically, they are split into two classes (I and II). By analyzing the entire subclass I odorant receptors sequences, we identified two class I-specific and highly conserved motifs. These are predicted to face each other at the extra-cellular portion of the transmembrane domain, forming a vestibular site at the entrance to the orthosteric-binding cavity. Molecular dynamics simulation combined with site-directed mutagenesis and in vitro functional assays confirm the functional role of this vestibular site in ligand-driven activation. Mutations at this part of the receptor differentially affect the receptor response to four agonists. Since this vestibular site is involved in ligand recognition, it could serve ligand design that targets specifically this sub-genome of mammalian odorant receptors.
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Affiliation(s)
- Caroline Bushdid
- Institute of Chemistry - Nice, UMR CNRS 7272, Université Côte d'Azur, Nice, France
| | - Claire A de March
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Jérémie Topin
- Institute of Chemistry - Nice, UMR CNRS 7272, Université Côte d'Azur, Nice, France
| | - Matthew Do
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA.
- Department of Neurobiology, Duke Institute for Brain Sciences, Duke University, Durham, NC, 27710, USA.
| | - Jérôme Golebiowski
- Institute of Chemistry - Nice, UMR CNRS 7272, Université Côte d'Azur, Nice, France.
- Department of Brain and Cognitive Sciences, DGIST, Daegu, Republic of Korea.
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25
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Wu C, Thach TT, Kim YJ, Lee SJ. Olfactory receptor 43 reduces hepatic lipid accumulation and adiposity in mice. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:489-499. [PMID: 30639733 DOI: 10.1016/j.bbalip.2019.01.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 12/30/2018] [Accepted: 01/05/2019] [Indexed: 12/14/2022]
Abstract
Olfactory receptors are primarily expressed in nasal olfactory epithelium, but these receptors are also ectopically expressed in diverse tissues. In this study, we investigated the biological functions of Olfr43, a mouse homolog of human OR1A1, in cultured hepatocytes and mice to assess its functionality in lipid metabolism. Olfr43 was expressed in mouse hepatocytes, and Olfr43 activation by a known ligand, (-)-carvone, stimulated cAMP response element-binding protein (CREB) activity. In ligand-receptor binding studies using site-directed mutagenesis, (-)-carvone binding required two residues, M257 and Y258, in Olfr43. In the mouse study, oral administration of (-)-carvone for 5 weeks in high-fat diet-fed mice improved energy metabolism, including reductions in hepatic steatosis and adiposity, and improved glucose and insulin tolerance. In mouse livers and cultured mouse hepatocytes, Olfr43 activation simulated the CREB-hairy and enhancer of split 1 (HES1)-peroxisome proliferator-activated receptor (PPAR)-γ signaling axis, leading to a reduction in hepatic triglyceride accumulation in the mouse liver. Thus, long-term administration of (-)-carvone reduces hepatic steatosis. The knockdown of Olfr43 gene expression in cultured hepatocytes negated these effects of (-)-carvone. In conclusion, an ectopic olfactory receptor, hepatic Olfr43, regulates energy metabolism via the CREB-HES1-PPARγ signaling axis.
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Affiliation(s)
- Chunyan Wu
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Korea University, Seoul 02841, Republic of Korea
| | - Trung Thanh Thach
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Korea University, Seoul 02841, Republic of Korea
| | - Yeon-Ji Kim
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Korea University, Seoul 02841, Republic of Korea
| | - Sung-Joon Lee
- Department of Biotechnology, School of Life Sciences and Biotechnology for BK21 PLUS, Korea University, Seoul 02841, Republic of Korea.
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26
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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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27
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Maßberg D, Hatt H. Human Olfactory Receptors: Novel Cellular Functions Outside of the Nose. Physiol Rev 2018; 98:1739-1763. [PMID: 29897292 DOI: 10.1152/physrev.00013.2017] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Olfactory receptors (ORs) are not exclusively expressed in the olfactory sensory neurons; they are also observed outside of the olfactory system in all other human tissues tested to date, including the testis, lung, intestine, skin, heart, and blood. Within these tissues, certain ORs have been determined to be exclusively expressed in only one tissue, whereas other ORs are more widely distributed in many different tissues throughout the human body. For most of the ectopically expressed ORs, limited data are available for their functional roles. They have been shown to be involved in the modulation of cell-cell recognition, migration, proliferation, the apoptotic cycle, exocytosis, and pathfinding processes. Additionally, there is a growing body of evidence that they have the potential to serve as diagnostic and therapeutic tools, as ORs are highly expressed in different cancer tissues. Interestingly, in addition to the canonical signaling pathways activated by ORs in olfactory sensory neurons, alternative pathways have been demonstrated in nonolfactory tissues. In this review, the existing data concerning the expression, as well as the physiological and pathophysiological functions, of ORs outside of the nose are highlighted to provide insights into future lines of research.
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Affiliation(s)
- Désirée Maßberg
- Ruhr-University Bochum, Department of Cell Physiology , Bochum , Germany
| | - Hanns Hatt
- Ruhr-University Bochum, Department of Cell Physiology , Bochum , Germany
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28
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Molecular mechanism of activation of human musk receptors OR5AN1 and OR1A1 by ( R)-muscone and diverse other musk-smelling compounds. Proc Natl Acad Sci U S A 2018; 115:E3950-E3958. [PMID: 29632183 DOI: 10.1073/pnas.1713026115] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Understanding olfaction at the molecular level is challenging due to the lack of crystallographic models of odorant receptors (ORs). To better understand the molecular mechanism of OR activation, we focused on chiral (R)-muscone and other musk-smelling odorants due to their great importance and widespread use in perfumery and traditional medicine, as well as environmental concerns associated with bioaccumulation of musks with estrogenic/antiestrogenic properties. We experimentally and computationally examined the activation of human receptors OR5AN1 and OR1A1, recently identified as specifically responding to musk compounds. OR5AN1 responds at nanomolar concentrations to musk ketone and robustly to macrocyclic sulfoxides and fluorine-substituted macrocyclic ketones; OR1A1 responds only to nitromusks. Structural models of OR5AN1 and OR1A1 based on quantum mechanics/molecular mechanics (QM/MM) hybrid methods were validated through direct comparisons with activation profiles from site-directed mutagenesis experiments and analysis of binding energies for 35 musk-related odorants. The experimentally found chiral selectivity of OR5AN1 to (R)- over (S)-muscone was also computationally confirmed for muscone and fluorinated (R)-muscone analogs. Structural models show that OR5AN1, highly responsive to nitromusks over macrocyclic musks, stabilizes odorants by hydrogen bonding to Tyr260 of transmembrane α-helix 6 and hydrophobic interactions with surrounding aromatic residues Phe105, Phe194, and Phe207. The binding of OR1A1 to nitromusks is stabilized by hydrogen bonding to Tyr258 along with hydrophobic interactions with surrounding aromatic residues Tyr251 and Phe206. Hydrophobic/nonpolar and hydrogen bonding interactions contribute, respectively, 77% and 13% to the odorant binding affinities, as shown by an atom-based quantitative structure-activity relationship model.
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29
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Predicting glycosaminoglycan surface protein interactions and implications for studying axonal growth. Proc Natl Acad Sci U S A 2017; 114:13697-13702. [PMID: 29229841 DOI: 10.1073/pnas.1715093115] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Cell-surface carbohydrates play important roles in numerous biological processes through their interactions with various protein-binding partners. These interactions are made possible by the vast structural diversity of carbohydrates and the diverse array of carbohydrate presentations on the cell surface. Among the most complex and important carbohydrates are glycosaminoglycans (GAGs), which display varied stereochemistry, chain lengths, and patterns of sulfation. GAG-protein interactions participate in neuronal development, angiogenesis, spinal cord injury, viral invasion, and immune response. Unfortunately, little structural information is available for these complexes; indeed, for the highly sulfated chondroitin sulfate motifs, CS-E and CS-D, there are no structural data. We describe here the development and validation of the GAG-Dock computational method to predict accurately the binding poses of protein-bound GAGs. We validate that GAG-Dock reproduces accurately (<1-Å rmsd) the crystal structure poses for four known heparin-protein structures. Further, we predict the pose of heparin and chondroitin sulfate derivatives bound to the axon guidance proteins, protein tyrosine phosphatase σ (RPTPσ), and Nogo receptors 1-3 (NgR1-3). Such predictions should be useful in understanding and interpreting the role of GAGs in neural development and axonal regeneration after CNS injury.
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30
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Geithe C, Protze J, Kreuchwig F, Krause G, Krautwurst D. Structural determinants of a conserved enantiomer-selective carvone binding pocket in the human odorant receptor OR1A1. Cell Mol Life Sci 2017; 74:4209-4229. [PMID: 28656349 PMCID: PMC11107518 DOI: 10.1007/s00018-017-2576-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 05/29/2017] [Accepted: 06/16/2017] [Indexed: 12/17/2022]
Abstract
Chirality is a common phenomenon within odorants. Most pairs of enantiomers show only moderate differences in odor quality. One example for enantiomers that are easily discriminated by their odor quality is the carvones: humans significantly distinguish between the spearmint-like (R)-(-)-carvone and caraway-like (S)-(+)-carvone enantiomers. Moreover, for the (R)-(-)-carvone, an anosmia is observed in about 8% of the population, suggesting enantioselective odorant receptors (ORs). With only about 15% de-orphaned human ORs, the lack of OR crystal structures, and few comprehensive studies combining in silico and experimental approaches to elucidate structure-function relations of ORs, knowledge on cognate odorant/OR interactions is still sparse. An adjusted homology modeling approach considering OR-specific proline-caused conformations, odorant docking studies, single-nucleotide polymorphism (SNP) analysis, site-directed mutagenesis, and subsequent functional studies with recombinant ORs in a cell-based, real-time luminescence assay revealed 11 amino acid positions to constitute an enantioselective binding pocket necessary for a carvone function in human OR1A1 and murine Olfr43, respectively. Here, we identified enantioselective molecular determinants in both ORs that discriminate between minty and caraway odor. Comparison with orthologs from 36 mammalian species demonstrated a hominid-specific carvone binding pocket with about 100% conservation. Moreover, we identified loss-of-function SNPs associated with the carvone binding pocket of OR1A1. Given carvone enantiomer-specific receptor activation patterns including OR1A1, our data suggest OR1A1 as a candidate receptor for constituting a carvone enantioselective phenotype, which may help to explain mechanisms underlying a (R)-(-)-carvone-specific anosmia in humans.
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Affiliation(s)
- Christiane Geithe
- Deutsche Forschungsanstalt für Lebensmittelchemie Leibniz Institut (DFA), Freising, Germany
| | - Jonas Protze
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Franziska Kreuchwig
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Gerd Krause
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin, Germany.
| | - Dietmar Krautwurst
- Deutsche Forschungsanstalt für Lebensmittelchemie Leibniz Institut (DFA), Freising, Germany.
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31
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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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32
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Affiliation(s)
- Anne Tromelin
- CNRS; UMR6265 Centre des Sciences du Goût et de l'Alimentation; F-21000 Dijon France
- INRA; UMR1324 Centre des Sciences du Goût et de l'Alimentation; F-21000 Dijon France
- Université de Bourgogne; UMR Centre des Sciences du Goût et de l'Alimentation; F-21000 Dijon France
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33
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Responsiveness of G protein-coupled odorant receptors is partially attributed to the activation mechanism. Proc Natl Acad Sci U S A 2015; 112:14966-71. [PMID: 26627247 DOI: 10.1073/pnas.1517510112] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Mammals detect and discriminate numerous odors via a large family of G protein-coupled odorant receptors (ORs). However, little is known about the molecular and structural basis underlying OR response properties. Using site-directed mutagenesis and computational modeling, we studied ORs sharing high sequence homology but with different response properties. When tested in heterologous cells by diverse odorants, MOR256-3 responded broadly to many odorants, whereas MOR256-8 responded weakly to a few odorants. Out of 36 mutant MOR256-3 ORs, the majority altered the responses to different odorants in a similar manner and the overall response of an OR was positively correlated with its basal activity, an indication of ligand-independent receptor activation. Strikingly, a single mutation in MOR256-8 was sufficient to confer both high basal activity and broad responsiveness to this receptor. These results suggest that broad responsiveness of an OR is at least partially attributed to its activation likelihood.
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34
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Harini K, Sowdhamini R. Computational Approaches for Decoding Select Odorant-Olfactory Receptor Interactions Using Mini-Virtual Screening. PLoS One 2015. [PMID: 26221959 PMCID: PMC4519343 DOI: 10.1371/journal.pone.0131077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Olfactory receptors (ORs) belong to the class A G-Protein Coupled Receptor superfamily of proteins. Unlike G-Protein Coupled Receptors, ORs exhibit a combinatorial response to odors/ligands. ORs display an affinity towards a range of odor molecules rather than binding to a specific set of ligands and conversely a single odorant molecule may bind to a number of olfactory receptors with varying affinities. The diversity in odor recognition is linked to the highly variable transmembrane domains of these receptors. The purpose of this study is to decode the odor-olfactory receptor interactions using in silico docking studies. In this study, a ligand (odor molecules) dataset of 125 molecules was used to carry out in silico docking using the GLIDE docking tool (SCHRODINGER Inc Pvt LTD). Previous studies, with smaller datasets of ligands, have shown that orthologous olfactory receptors respond to similarly-tuned ligands, but are dramatically different in their efficacy and potency. Ligand docking results were applied on homologous pairs (with varying sequence identity) of ORs from human and mouse genomes and ligand binding residues and the ligand profile differed among such related olfactory receptor sequences. This study revealed that homologous sequences with high sequence identity need not bind to the same/ similar ligand with a given affinity. A ligand profile has been obtained for each of the 20 receptors in this analysis which will be useful for expression and mutation studies on these receptors.
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Affiliation(s)
- K. Harini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (TIFR), GKVK Campus, Bellary Road, Bangalore, India
- * E-mail:
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35
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de March CA, Yu Y, Ni MJ, Adipietro KA, Matsunami H, Ma M, Golebiowski J. Conserved Residues Control Activation of Mammalian G Protein-Coupled Odorant Receptors. J Am Chem Soc 2015; 137:8611-8616. [PMID: 26090619 PMCID: PMC4497840 DOI: 10.1021/jacs.5b04659] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Odorant receptor (OR) genes and proteins represent more than 2% of our genome and 4% of our proteome and constitute the largest subgroup of G protein-coupled receptors (GPCRs). The mechanism underlying OR activation remains poorly understood, as they do not share some of the highly conserved motifs critical for activation of non-olfactory GPCRs. By combining site-directed mutagenesis, heterologous expression, and molecular dynamics simulations that capture the conformational change of constitutively active mutants, we tentatively identified crucial residues for the function of these receptors using the mouse MOR256-3 (Olfr124) as a model. The toggle switch for sensing agonists involves a highly conserved tyrosine residue in helix VI. The ionic lock is located between the "DRY" motif in helix III and a positively charged "R/K" residue in helix VI. This study provides an unprecedented model that captures the main mechanisms of odorant receptor activation.
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Affiliation(s)
- Claire A. de March
- Institute of Chemistry - Nice, UMR 7272 CNRS - University Nice - Sophia Antipolis, 06108 Nice cedex 2, France
| | - Yiqun Yu
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Mengjue J. Ni
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Kaylin A. Adipietro
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Minghong Ma
- Department of Neuroscience, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jérôme Golebiowski
- Institute of Chemistry - Nice, UMR 7272 CNRS - University Nice - Sophia Antipolis, 06108 Nice cedex 2, France
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36
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de March CA, Ryu S, Sicard G, Moon C, Golebiowski J. Structure-odour relationships reviewed in the postgenomic era. FLAVOUR FRAG J 2015. [DOI: 10.1002/ffj.3249] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Claire A. de March
- Institut de Chimie de Nice; Université Nice Sophia Antipolis; UMR CNRS 7272, parc Valrose 06108 Nice cedex 02 France
| | - SangEun Ryu
- Laboratory of Chemical Senses, Department of Brain and Cognitive Science; DGIST (Daegu Gyeongbuk Institute of Science & Technology); 50-1 Sang-Ri, Hyeonpung-Myeon, Dalseong-Gun Daegu 711-873 Korea
| | - Gilles Sicard
- Neurobiology of Cellular Interactions and Neurophysiopathology; Aix-Marseille Université; UMR CNRS 7259 13331 Marseille cedex 03 France
| | - Cheil Moon
- Laboratory of Chemical Senses, Department of Brain and Cognitive Science; DGIST (Daegu Gyeongbuk Institute of Science & Technology); 50-1 Sang-Ri, Hyeonpung-Myeon, Dalseong-Gun Daegu 711-873 Korea
| | - Jérôme Golebiowski
- Institut de Chimie de Nice; Université Nice Sophia Antipolis; UMR CNRS 7272, parc Valrose 06108 Nice cedex 02 France
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37
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Dong SS, Abrol R, Goddard WA. The predicted ensemble of low-energy conformations of human somatostatin receptor subtype 5 and the binding of antagonists. ChemMedChem 2015; 10:650-61. [PMID: 25772628 DOI: 10.1002/cmdc.201500023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Indexed: 12/17/2022]
Abstract
Human somatostatin receptor subtype 5 (hSSTR5) regulates cell proliferation and hormone secretion. However, the identification of effective therapeutic small-molecule ligands is impeded because experimental structures are not available for any SSTR subtypes. Here, we predict the ensemble of low-energy 3D structures of hSSTR5 using a modified GPCR Ensemble of Structures in Membrane BiLayer Environment (GEnSeMBLE) complete sampling computational method. We find that this conformational ensemble displays most interhelical interactions conserved in class A G protein-coupled receptors (GPCRs) plus seven additional interactions (e.g., Y2.43-D3.49, T3.38-S4.53, K5.64-Y3.51) likely conserved among SSTRs. We then predicted the binding sites for a series of five known antagonists, leading to predicted binding energies consistent with experimental results reported in the literature. Molecular dynamics (MD) simulation of 50 ns in explicit water and lipid retained the predicted ligand-bound structure and formed new interaction patterns (e.g. R3.50-T6.34) consistent with the inactive μ-opioid receptor X-ray structure. We suggest more than six mutations for experimental validation of our prediction. The final predicted receptor conformations and antagonist binding sites provide valuable insights for designing new small-molecule drugs targeting SSTRs.
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Affiliation(s)
- Sijia S Dong
- Materials & Process Simulation Center (MC 139-74), California Institute of Technology, Pasadena, CA 91125 (USA)
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38
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Li Q, Kim SK, Goddard WA, Chen G, Tan H. Predicted structures for kappa opioid G-protein coupled receptor bound to selective agonists. J Chem Inf Model 2015; 55:614-27. [PMID: 25642595 DOI: 10.1021/ci500523z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Human kappa opioid receptor (κ-OR), a G protein-coupled receptor (GPCR), has been identified as a drug target for treatment of such human disorders as pain perception, neuroendocrine physiology, affective behavior, and cognition. In order to find more selective and active agonists, one would like to do structure based drug design. Indeed, there is an X-ray structure for an antagonist bound to κ-OR, but structures for activated GPCRs are quite different from those for the inactive GPCRs. Here we predict the ensemble of 24 low-energy structures of human kappa opioid receptor (κ-OR), obtained by application of the GEnSeMBLE (GPCR Ensemble of Structures in Membrane Bilayer Environment) complete sampling method, which evaluates 13 trillion combinations of tilt and rotation angles for κ-OR to select the best 24. To validate these structures, we used the DarwinDock complete sampling method to predict the binding sites for five known agonists (ethylketocyclazocine, bremazocine, pentazocine, nalorphine, and morphine) bound to all 24 κ-OR conformations. We find that some agonists bind selectively to receptor conformations that lack the salt bridge between transmembrane domains 3 and 6 as expected for active conformations. These 3D structures for κ-OR provide a structural basis for understanding ligand binding and activation of κ-OR, which should be useful for guiding subtype specific drug design.
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Affiliation(s)
- Quanjie Li
- †Materials and Process Simulation Center (MC-139-74), California Institute of Technology, Pasadena, California 91125, United States.,‡College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Soo-Kyung Kim
- †Materials and Process Simulation Center (MC-139-74), California Institute of Technology, Pasadena, California 91125, United States
| | - William A Goddard
- †Materials and Process Simulation Center (MC-139-74), California Institute of Technology, Pasadena, California 91125, United States
| | - Guangju Chen
- ‡College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Hongwei Tan
- ‡College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
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Li Y, Peterlin Z, Ho J, Yarnitzky T, Liu MT, Fichman M, Niv MY, Matsunami H, Firestein S, Ryan K. Aldehyde recognition and discrimination by mammalian odorant receptors via functional group-specific hydration chemistry. ACS Chem Biol 2014; 9:2563-71. [PMID: 25181321 PMCID: PMC4245160 DOI: 10.1021/cb400290u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
![]()
The mammalian odorant
receptors (ORs) form a chemical-detecting
interface between the atmosphere and the nervous system. This large
gene family is composed of hundreds of membrane proteins predicted
to form as many unique small molecule binding niches within their
G-protein coupled receptor (GPCR) framework, but very little is known
about the molecular recognition strategies they use to bind and discriminate
between small molecule odorants. Using rationally designed synthetic
analogs of a typical aliphatic aldehyde, we report evidence that among
the ORs showing specificity for the aldehyde functional group, a significant
percentage detect the aldehyde through its ability to react with water
to form a 1,1-geminal (gem)-diol.
Evidence is presented indicating that the rat OR-I7, an often-studied
and modeled OR known to require the aldehyde function of octanal for
activation, is likely one of the gem-diol activated
receptors. A homology model based on an activated GPCR X-ray structure
provides a structural hypothesis for activation of OR-I7 by the gem-diol of octanal.
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Affiliation(s)
- Yadi Li
- Department
of Chemistry, The City College of New York, and Biochemistry Program, The City University of New York Graduate Center, New York, New York 10031, United States
| | - Zita Peterlin
- Department
of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Jianghai Ho
- Department
of Molecular Genetics and Microbiology, and Neurobiology, Duke University Medical Center, Durham, North Carolina 27710 United States
| | - Tali Yarnitzky
- Institute
of Biochemistry, Food Science, and Nutrition, The Robert H. Smith
Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot 76100, Israel
| | - Min Ting Liu
- Department
of Chemistry, The City College of New York, and Biochemistry Program, The City University of New York Graduate Center, New York, New York 10031, United States
| | - Merav Fichman
- Institute
of Biochemistry, Food Science, and Nutrition, The Robert H. Smith
Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot 76100, Israel
| | - Masha Y. Niv
- Institute
of Biochemistry, Food Science, and Nutrition, The Robert H. Smith
Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot 76100, Israel
| | - Hiroaki Matsunami
- Department
of Molecular Genetics and Microbiology, and Neurobiology, Duke University Medical Center, Durham, North Carolina 27710 United States
| | - Stuart Firestein
- Department
of Biological Sciences, Columbia University, New York, New York 10027, United States
| | - Kevin Ryan
- Department
of Chemistry, The City College of New York, and Biochemistry Program, The City University of New York Graduate Center, New York, New York 10031, United States
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40
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Don CG, Riniker S. Scents and sense:In silicoperspectives on olfactory receptors. J Comput Chem 2014; 35:2279-87. [DOI: 10.1002/jcc.23757] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/23/2014] [Accepted: 09/27/2014] [Indexed: 11/12/2022]
Affiliation(s)
- Charleen G. Don
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich; 8093 Zurich Switzerland
| | - Sereina Riniker
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich; 8093 Zurich Switzerland
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41
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Kim SK, Goddard WA. Predicted 3D structures of olfactory receptors with details of odorant binding to OR1G1. J Comput Aided Mol Des 2014; 28:1175-90. [PMID: 25224127 DOI: 10.1007/s10822-014-9793-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 09/02/2014] [Indexed: 11/24/2022]
Abstract
Olfactory receptors (ORs) are responsible for mediating the sense of smell; they allow humans to recognize an enormous number of odors but the connection between binding and perception is not known. We predict the ensemble of low energy structures for the human OR1G1 (hOR1G1) and also for six other diverse ORs, using the G protein-coupled receptor Ensemble of Structures in Membrane BiLayer Environment complete sampling method that samples 13 trillion different rotations and tilts using four different templates to predict the 24 structures likely to be important in binding and activation. Our predicted most stable structures of hOR1G1 have a salt-bridge between the conserved D3.49 and K6.30 in the D(E)RY region, that we expect to be associated with an inactive form. The hOR1G1 structure also has specific interaction in transmembrane domains (TMD) 3-6 (E3.39 and H6.40), which is likely an important conformational feature for all hORs because of the ~94 to 98 % conservation among all hOR sequences. Of the five ligands studied (nonanal, 9-decen-1-ol, 1-nonanol, camphor, and n-butanal), we find that the 4 expected to bind lead to similar binding energies with nonanol the strongest.
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Affiliation(s)
- Soo-Kyung Kim
- Materials and Process Simulation Center (MC139-74), California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA,
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43
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Topin J, de March CA, Charlier L, Ronin C, Antonczak S, Golebiowski J. Discrimination between olfactory receptor agonists and non-agonists. Chemistry 2014; 20:10227-30. [PMID: 25043138 DOI: 10.1002/chem.201402486] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Indexed: 01/27/2023]
Abstract
A joint approach combining free-energy calculations and calcium-imaging assays on the broadly tuned human 1G1 olfactory receptor is reported. The free energy of binding of ten odorants was computed by means of molecular-dynamics simulations. This state function allows separating the experimentally determined eight agonists from the two non-agonists. This study constitutes a proof-of-principle for the computational deorphanization of olfactory receptors.
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Affiliation(s)
- Jérémie Topin
- Université de Nice - Sophia Antipolis, Institut de Chimie de Nice UMR 7272, Parc Valrose 28, Avenue Valrose 06108, Nice, Cedex 2 (France)
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A computational microscope focused on the sense of smell. Biochimie 2014; 107 Pt A:3-10. [PMID: 24952349 DOI: 10.1016/j.biochi.2014.06.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 06/07/2014] [Indexed: 11/24/2022]
Abstract
In this article, we review studies of the protagonists of the perception of smell focusing on Odorant-Binding Proteins and Olfactory Receptors. We notably put forward studies performed by means of molecular modeling, generally combined with experimental data. Those works clearly emphasize that computational approaches are now a force to reckon with. In the future, they will certainly be more and more used, notably in the framework of a computational microscope meant to observe how the laws of physics govern the biomolecular systems originating our sense of smell.
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Teixeira MA, Rodrigues AE. Coupled Extraction and Dynamic Headspace Techniques for the Characterization of Essential Oil and Aroma Fingerprint of Thymus Species. Ind Eng Chem Res 2014. [DOI: 10.1021/ie501301u] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Miguel A. Teixeira
- LSRE—Laboratory
of
Separation and Reaction Engineering, Associate Laboratory LSRE/LCM,
Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Alírio E. Rodrigues
- LSRE—Laboratory
of
Separation and Reaction Engineering, Associate Laboratory LSRE/LCM,
Department of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
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Teixeira MA, Barrault L, Rodríguez O, Carvalho CC, Rodrigues AE. Perfumery Radar 2.0: A Step toward Fragrance Design and Classification. Ind Eng Chem Res 2014. [DOI: 10.1021/ie403968w] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Miguel A. Teixeira
- Laboratory of Separation
and Reaction Engineering (LSRE), Associate Laboratory LSRE/LCM, Department
of Chemical Engineering, Faculty of Engineering of University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Lucas Barrault
- Laboratory of Separation
and Reaction Engineering (LSRE), Associate Laboratory LSRE/LCM, Department
of Chemical Engineering, Faculty of Engineering of University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Oscar Rodríguez
- Laboratory of Separation
and Reaction Engineering (LSRE), Associate Laboratory LSRE/LCM, Department
of Chemical Engineering, Faculty of Engineering of University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Cindy C. Carvalho
- Laboratory of Separation
and Reaction Engineering (LSRE), Associate Laboratory LSRE/LCM, Department
of Chemical Engineering, Faculty of Engineering of University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Alírio E. Rodrigues
- Laboratory of Separation
and Reaction Engineering (LSRE), Associate Laboratory LSRE/LCM, Department
of Chemical Engineering, Faculty of Engineering of University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
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Peterlin Z, Firestein S, Rogers ME. The state of the art of odorant receptor deorphanization: a report from the orphanage. ACTA ACUST UNITED AC 2014; 143:527-42. [PMID: 24733839 PMCID: PMC4003190 DOI: 10.1085/jgp.201311151] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The odorant receptors (ORs) provide our main gateway to sensing the world of volatile chemicals. This involves a complex encoding process in which multiple ORs, each of which detects its own set of odorants, work as an ensemble to produce a distributed activation code that is presumably unique to each odorant. One marked challenge to decoding the olfactory code is OR deorphanization, the identification of a set of activating odorants for a particular receptor. Here, we survey various methods used to try to express defined ORs of interest. We also suggest strategies for selecting odorants for test panels to evaluate the functional expression of an OR. Integrating these tools, while retaining awareness of their idiosyncratic limitations, can provide a multi-tiered approach to OR deorphanization, spanning the initial discovery of a ligand to vetting that ligand in a physiologically relevant setting.
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Affiliation(s)
- Zita Peterlin
- Corporate Research and Development, Firmenich Incorporated, Plainsboro, NJ 08536
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48
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Bavan S, Sherman B, Luetje CW, Abaffy T. Discovery of novel ligands for mouse olfactory receptor MOR42-3 using an in silico screening approach and in vitro validation. PLoS One 2014; 9:e92064. [PMID: 24637889 PMCID: PMC3956865 DOI: 10.1371/journal.pone.0092064] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 02/17/2014] [Indexed: 11/19/2022] Open
Abstract
The ligands for many olfactory receptors remain largely unknown despite successful heterologous expression of these receptors. Understanding the molecular receptive range of olfactory receptors and deciphering the olfactory recognition code are hampered by the huge number of odorants and large number of olfactory receptors, as well as the complexity of their combinatorial coding. Here, we present an in silico screening approach to find additional ligands for a mouse olfactory receptor that allows improved definition of its molecular receptive range. A virtual library of 574 odorants was screened against a mouse olfactory receptor MOR42-3. We selected the top 20 candidate ligands using two different scoring functions. These 40 odorant candidate ligands were then tested in vitro using the Xenopus oocyte heterologous expression system and two-electrode voltage clamp electrophysiology. We experimentally confirmed 22 of these ligands. The candidate ligands were screened for both agonist and antagonist activity. In summary, we validated 19 agonists and 3 antagonists. Two of the newly identified antagonists were of low potency. Several previously known ligands (mono- and dicarboxylic acids) are also confirmed in this study. However, some of the newly identified ligands were structurally dissimilar compounds with various functional groups belonging to aldehydes, phenyls, alkenes, esters and ethers. The high positive predictive value of our in silico approach is promising. We believe that this approach can be used for initial deorphanization of olfactory receptors as well as for future comprehensive studies of molecular receptive range of olfactory receptors.
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Affiliation(s)
- Selvan Bavan
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Benjamin Sherman
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Charles W Luetje
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
| | - Tatjana Abaffy
- Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
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Abstract
Providing a rationale that associates a chemical structure of an odorant to its induced perception has been sought for a long time. To achieve this, a detailed atomic structure of both the odorant and the olfactory receptor must be known. State-of-the-art techniques to model the 3D structure of an olfactory receptor in complex with various odorants are presented here. These range from sequence alignment with known structures to molecular dynamics simulations in a realistic environment.
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Park JH, Morizumi T, Li Y, Hong JE, Pai EF, Hofmann KP, Choe HW, Ernst OP. Opsin, a structural model for olfactory receptors? Angew Chem Int Ed Engl 2013; 52:11021-4. [PMID: 24038729 DOI: 10.1002/anie.201302374] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 07/30/2013] [Indexed: 11/11/2022]
Abstract
Receptor-ligand interaction: Olfactory receptors (ORs) are G-protein-coupled receptors (GPCRs), which detect signaling molecules such as hormones and odorants. The structure of opsin, the GPCR employed in vision, with a detergent molecule bound deep in its orthosteric ligand-binding pocket provides a template for OR homology modeling, thus enabling investigation of the structural basis of the mechanism of odorant-receptor recognition.
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Affiliation(s)
- Jung Hee Park
- Division of Biotechnology, Advanced Institute of Environment and Bioscience, College of Environmental & Bioresources Sciences, Chonbuk National University, 570-752 Iksan (Republic of Korea).
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