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Ferri F, Cannariato M, Deriu MA, Pallante L. Machine learning approaches to predict TAS2R receptors for bitterants. Biotechnol Bioeng 2024; 121:1755-1758. [PMID: 38587175 DOI: 10.1002/bit.28709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/08/2024] [Accepted: 03/21/2024] [Indexed: 04/09/2024]
Abstract
Bitter taste involves the detection of diverse chemical compounds by a family of G protein-coupled receptors, known as taste receptor type 2 (TAS2R). It is often linked to toxins and harmful compounds and in particular bitter taste receptors participate in the regulation of glucose homeostasis, modulation of immune and inflammatory responses, and may have implications for various diseases. Human TAS2Rs are characterized by their polymorphism and differ in localization and function. Different receptors can activate various signaling pathways depending on the tissue and the ligand. However, in vitro screening of possible TAS2R ligands is costly and time-consuming. For this reason, in silico methods to predict bitterant-TAS2R interactions could be powerful tools to help in the selection of ligands and targets for experimental studies and improve our knowledge of bitter receptor roles. Machine learning (ML) is a branch of artificial intelligence that applies algorithms to large datasets to learn from patterns and make predictions. In recent years, there has been a record of numerous taste classifiers in literature, especially on bitter/non-bitter or bitter/sweet classification. However, only a few of them exploit ML to predict which TAS2R receptors could be targeted by bitter molecules. Indeed, the shortage and incompleteness of data on receptor-ligand associations in literature make this task non-trivial. In this work, we provide an overview of the state of the art dealing with this specific investigation, focusing on three ML-based models, namely BitterX (2016), BitterSweet (2019) and BitterMatch (2022). This review aims to establish the foundation for future research endeavours focused on addressing the limitations and drawbacks of existing models.
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Affiliation(s)
- Francesco Ferri
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Marco Cannariato
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Marco Agostino Deriu
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
| | - Lorenzo Pallante
- PolitoBIOMed Lab, Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Turin, Italy
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2
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Schaefer S, Ziegler F, Lang T, Steuer A, Di Pizio A, Behrens M. Membrane-bound chemoreception of bitter bile acids and peptides is mediated by the same subset of bitter taste receptors. Cell Mol Life Sci 2024; 81:217. [PMID: 38748186 PMCID: PMC11096235 DOI: 10.1007/s00018-024-05202-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 05/18/2024]
Abstract
The vertebrate sense of taste allows rapid assessment of the nutritional quality and potential presence of harmful substances prior to ingestion. Among the five basic taste qualities, salty, sour, sweet, umami, and bitter, bitterness is associated with the presence of putative toxic substances and elicits rejection behaviors in a wide range of animals including humans. However, not all bitter substances are harmful, some are thought to be health-beneficial and nutritious. Among those compound classes that elicit a bitter taste although being non-toxic and partly even essential for humans are bitter peptides and L-amino acids. Using functional heterologous expression assays, we observed that the 5 dominant human bitter taste receptors responsive to bitter peptides and amino acids are activated by bile acids, which are notorious for their extreme bitterness. We further demonstrate that the cross-reactivity of bitter taste receptors for these two different compound classes is evolutionary conserved and can be traced back to the amphibian lineage. Moreover, we show that the cross-detection by some receptors relies on "structural mimicry" between the very bitter peptide L-Trp-Trp-Trp and bile acids, whereas other receptors exhibit a phylogenetic conservation of this trait. As some bile acid-sensitive bitter taste receptor genes fulfill dual-roles in gustatory and non-gustatory systems, we suggest that the phylogenetic conservation of the rather surprising cross-detection of the two substance classes could rely on a gene-sharing-like mechanism in which the non-gustatory function accounts for the bitter taste response to amino acids and peptides.
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Affiliation(s)
- Silvia Schaefer
- TUM Graduate School, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, 85354, Freising, Germany
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Strasse 34, 85354, Freising, Germany
| | - Florian Ziegler
- TUM Graduate School, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, 85354, Freising, Germany
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Strasse 34, 85354, Freising, Germany
| | - Tatjana Lang
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Strasse 34, 85354, Freising, Germany
| | - Alexandra Steuer
- TUM Graduate School, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Alte Akademie 8, 85354, Freising, Germany
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Strasse 34, 85354, Freising, Germany
| | - Antonella Di Pizio
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Strasse 34, 85354, Freising, Germany
- Chemoinformatics and Protein Modelling, Technical University of Munich, Freising, Germany
| | - Maik Behrens
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Strasse 34, 85354, Freising, Germany.
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3
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Ziaikin E, Tello E, Peterson DG, Niv MY. BitterMasS: Predicting Bitterness from Mass Spectra. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10537-10547. [PMID: 38685906 PMCID: PMC11082931 DOI: 10.1021/acs.jafc.3c09767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/02/2024]
Abstract
Bitter compounds are common in nature and among drugs. Previously, machine learning tools were developed to predict bitterness from the chemical structure. However, known structures are estimated to represent only 5-10% of the metabolome, and the rest remain unassigned or "dark". We present BitterMasS, a Random Forest classifier that was trained on 5414 experimental mass spectra of bitter and nonbitter compounds, achieving precision = 0.83 and recall = 0.90 for an internal test set. Next, the model was tested against spectra newly extracted from the literature 106 bitter and nonbitter compounds and for additional spectra measured for 26 compounds. For these external test cases, BitterMasS exhibited 67% precision and 93% recall for the first and 58% accuracy and 99% recall for the second. The spectrum-bitterness prediction strategy was more effective than the spectrum-structure-bitterness prediction strategy and covered more compounds. These encouraging results suggest that BitterMasS can be used to predict bitter compounds in the metabolome without the need for structural assignment of individual molecules. This may enable identification of bitter compounds from metabolomics analyses, for comparing potential bitterness levels obtained by different treatments of samples and for monitoring bitterness changes overtime.
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Affiliation(s)
- Evgenii Ziaikin
- Food
Science and Nutrition, The Robert H. Smith Faculty of Agriculture,
Food and Environment, The Institute of Biochemistry, Food and Nutrition, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Edisson Tello
- Department
of Food Science and Technology, College of Food, Agriculture, and
Environmental Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Devin G. Peterson
- Department
of Food Science and Technology, College of Food, Agriculture, and
Environmental Sciences, The Ohio State University, Columbus, Ohio 43210, United States
| | - Masha Y. Niv
- Food
Science and Nutrition, The Robert H. Smith Faculty of Agriculture,
Food and Environment, The Institute of Biochemistry, Food and Nutrition, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
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4
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Chu X, Zhu W, Li X, Su E, Wang J. Bitter flavors and bitter compounds in foods: identification, perception, and reduction techniques. Food Res Int 2024; 183:114234. [PMID: 38760147 DOI: 10.1016/j.foodres.2024.114234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 03/09/2024] [Accepted: 03/12/2024] [Indexed: 05/19/2024]
Abstract
Bitterness is one of the five basic tastes generally considered undesirable. The widespread presence of bitter compounds can negatively affect the palatability of foods. The classification and sensory evaluation of bitter compounds have been the focus in recent research. However, the rigorous identification of bitter tastes and further studies to effectively mask or remove them have not been thoroughly evaluated. The present paper focuses on identification of bitter compounds in foods, structural-based activation of bitter receptors, and strategies to reduce bitter compounds in foods. It also discusses the roles of metabolomics and virtual screening analysis in bitter taste. The identification of bitter compounds has seen greater success through metabolomics with multivariate statistical analysis compared to conventional chromatography, HPLC, LC-MS, and NMR techniques. However, to avoid false positives, sensory recognition should be combined. Bitter perception involves the structural activation of bitter taste receptors (TAS2Rs). Only 25 human TAS2Rs have been identified as responsible for recognizing numerous bitter compounds, showcasing their high structural diversity to bitter agonists. Thus, reducing bitterness can be achieved through several methods. Traditionally, the removal or degradation of bitter substances has been used for debittering, while the masking of bitterness presents a new effective approach to improving food flavor. Future research in food bitterness should focus on identifying unknown bitter compounds in food, elucidating the mechanisms of activation of different receptors, and developing debittering techniques based on the entire food matrix.
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Affiliation(s)
- Xinyu Chu
- Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Wangsheng Zhu
- Engineering Technology Research Center for Plant Cell of Anhui Province, West Anhui University, Anhui 237012, China
| | - Xue Li
- Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Erzheng Su
- Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China; Co-innovation Center for the Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; Co-Innovation Center of Efficient Procession of Forest Resources, Nanjing Forestry University, Nanjing 210037, China
| | - Jiahong Wang
- Department of Food Science and Technology, College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, China; Co-innovation Center for the Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China; Co-Innovation Center of Efficient Procession of Forest Resources, Nanjing Forestry University, Nanjing 210037, China.
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5
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Scharf MM, Humphrys LJ, Berndt S, Di Pizio A, Lehmann J, Liebscher I, Nicoli A, Niv MY, Peri L, Schihada H, Schulte G. The dark sides of the GPCR tree - research progress on understudied GPCRs. Br J Pharmacol 2024. [PMID: 38339984 DOI: 10.1111/bph.16325] [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: 08/25/2023] [Revised: 11/24/2023] [Accepted: 01/08/2024] [Indexed: 02/12/2024] Open
Abstract
A large portion of the human GPCRome is still in the dark and understudied, consisting even of entire subfamilies of GPCRs such as odorant receptors, class A and C orphans, adhesion GPCRs, Frizzleds and taste receptors. However, it is undeniable that these GPCRs bring an untapped therapeutic potential that should be explored further. Open questions on these GPCRs span diverse topics such as deorphanisation, the development of tool compounds and tools for studying these GPCRs, as well as understanding basic signalling mechanisms. This review gives an overview of the current state of knowledge for each of the diverse subfamilies of understudied receptors regarding their physiological relevance, molecular mechanisms, endogenous ligands and pharmacological tools. Furthermore, it identifies some of the largest knowledge gaps that should be addressed in the foreseeable future and lists some general strategies that might be helpful in this process.
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Affiliation(s)
- Magdalena M Scharf
- Karolinska Institutet, Dept. Physiology & Pharmacology, Sec. Receptor Biology & Signaling, Stockholm, Sweden
| | - Laura J Humphrys
- Institute of Pharmacy, University of Regensburg, Regensburg, Germany
| | - Sandra Berndt
- Rudolf Schönheimer Institute for Biochemistry, Molecular Biochemistry, University of Leipzig, Leipzig, Germany
| | - Antonella Di Pizio
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Chemoinformatics and Protein Modelling, Department of Molecular Life Science, School of Life Science, Technical University of Munich, Freising, Germany
| | - Juliane Lehmann
- Rudolf Schönheimer Institute for Biochemistry, Molecular Biochemistry, University of Leipzig, Leipzig, Germany
| | - Ines Liebscher
- Rudolf Schönheimer Institute for Biochemistry, Molecular Biochemistry, University of Leipzig, Leipzig, Germany
| | - Alessandro Nicoli
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Chemoinformatics and Protein Modelling, Department of Molecular Life Science, School of Life Science, Technical University of Munich, Freising, Germany
| | - Masha Y Niv
- The Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Lior Peri
- The Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Hannes Schihada
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Gunnar Schulte
- Karolinska Institutet, Dept. Physiology & Pharmacology, Sec. Receptor Biology & Signaling, Stockholm, Sweden
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6
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Song Y, Chang S, Tian J, Pan W, Feng L, Ji H. A Comprehensive Comparative Analysis of Deep Learning Based Feature Representations for Molecular Taste Prediction. Foods 2023; 12:3386. [PMID: 37761095 PMCID: PMC10529232 DOI: 10.3390/foods12183386] [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: 07/26/2023] [Revised: 08/30/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Taste determination in small molecules is critical in food chemistry but traditional experimental methods can be time-consuming. Consequently, computational techniques have emerged as valuable tools for this task. In this study, we explore taste prediction using various molecular feature representations and assess the performance of different machine learning algorithms on a dataset comprising 2601 molecules. The results reveal that GNN-based models outperform other approaches in taste prediction. Moreover, consensus models that combine diverse molecular representations demonstrate improved performance. Among these, the molecular fingerprints + GNN consensus model emerges as the top performer, highlighting the complementary strengths of GNNs and molecular fingerprints. These findings have significant implications for food chemistry research and related fields. By leveraging these computational approaches, taste prediction can be expedited, leading to advancements in understanding the relationship between molecular structure and taste perception in various food components and related compounds.
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Affiliation(s)
- Yu Song
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China;
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518120, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Sihao Chang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518120, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jing Tian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518120, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Weihua Pan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518120, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lu Feng
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China;
| | - Hongchao Ji
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518120, China
- Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
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7
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Rojas C, Ballabio D, Consonni V, Suárez-Estrella D, Todeschini R. Classification-based machine learning approaches to predict the taste of molecules: A review. Food Res Int 2023; 171:113036. [PMID: 37330849 DOI: 10.1016/j.foodres.2023.113036] [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: 05/02/2023] [Accepted: 05/22/2023] [Indexed: 06/19/2023]
Abstract
The capacity to discriminate safe from dangerous compounds has played an important role in the evolution of species, including human beings. Highly evolved senses such as taste receptors allow humans to navigate and survive in the environment through information that arrives to the brain through electrical pulses. Specifically, taste receptors provide multiple bits of information about the substances that are introduced orally. These substances could be pleasant or not according to the taste responses that they trigger. Tastes have been classified into basic (sweet, bitter, umami, sour and salty) or non-basic (astringent, chilling, cooling, heating, pungent), while some compounds are considered as multitastes, taste modifiers or tasteless. Classification-based machine learning approaches are useful tools to develop predictive mathematical relationships in such a way as to predict the taste class of new molecules based on their chemical structure. This work reviews the history of multicriteria quantitative structure-taste relationship modelling, starting from the first ligand-based (LB) classifier proposed in 1980 by Lemont B. Kier and concluding with the most recent studies published in 2022.
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Affiliation(s)
- Cristian Rojas
- Grupo de Investigación en Quimiometría y QSAR, Facultad de Ciencia y Tecnología, Universidad del Azuay, Av. 24 de Mayo 7-77 y Hernán Malo, Cuenca 010107, Ecuador.
| | - Davide Ballabio
- Milano Chemometrics and QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, P.za della Scienza 1-20126, Milano, Italy
| | - Viviana Consonni
- Milano Chemometrics and QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, P.za della Scienza 1-20126, Milano, Italy
| | - Diego Suárez-Estrella
- Grupo de Investigación en Quimiometría y QSAR, Facultad de Ciencia y Tecnología, Universidad del Azuay, Av. 24 de Mayo 7-77 y Hernán Malo, Cuenca 010107, Ecuador
| | - Roberto Todeschini
- Milano Chemometrics and QSAR Research Group, Department of Earth and Environmental Sciences, University of Milano-Bicocca, P.za della Scienza 1-20126, Milano, Italy
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8
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Margulis E, Lang T, Tromelin A, Ziaikin E, Behrens M, Niv MY. Bitter Odorants and Odorous Bitters: Toxicity and Human TAS2R Targets. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37263600 DOI: 10.1021/acs.jafc.3c00592] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Flavor is perceived through the olfactory, taste, and trigeminal systems, mediated by designated GPCRs and channels. Signal integration occurs mainly in the brain, but some cross-reactivities occur at the receptor level. Here, we predict potential bitterness and taste receptors targets for thousands of odorants. BitterPredict and BitterIntense classifiers suggest that 3-9% of flavor and food odorants have bitter taste, but almost none are intensely bitter. About 14% of bitter molecules are expected to have an odor. Bitterness is more common for unpleasant smells such as fishy, amine, and ammoniacal, while non-bitter odorants often have pleasant smells. Experimental toxicity values suggest that fishy ammoniac smells are more toxic than pleasant smells, regardless of bitterness. TAS2R14 is predicted as the main bitter receptor for odorants, confirmed by in vitro profiling of 10 odorants. The activity of bitter odorants may have implications for physiology due to ectopic expression of taste and smell receptors.
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Affiliation(s)
- Eitan Margulis
- Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Institute of Biochemistry, Food and Nutrition, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Tatjana Lang
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Anne Tromelin
- Centre des Sciences du Goût et de l'Alimentation, CNRS, INRAE, Institut Agro, Université de Bourgogne Franche-Comté, F-21000 Dijon, France
| | - Evgenii Ziaikin
- Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Institute of Biochemistry, Food and Nutrition, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Maik Behrens
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, 85354 Freising, Germany
| | - Masha Y Niv
- Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Institute of Biochemistry, Food and Nutrition, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
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9
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Fierro F, Peri L, Hübner H, Tabor-Schkade A, Waterloo L, Löber S, Pfeiffer T, Weikert D, Dingjan T, Margulis E, Gmeiner P, Niv MY. Inhibiting a promiscuous GPCR: iterative discovery of bitter taste receptor ligands. Cell Mol Life Sci 2023; 80:114. [PMID: 37012410 PMCID: PMC11072104 DOI: 10.1007/s00018-023-04765-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/09/2023] [Accepted: 03/21/2023] [Indexed: 04/05/2023]
Abstract
The human GPCR family comprises circa 800 members, activated by hundreds of thousands of compounds. Bitter taste receptors, TAS2Rs, constitute a large and distinct subfamily, expressed orally and extra-orally and involved in physiological and pathological conditions. TAS2R14 is the most promiscuous member, with over 150 agonists and 3 antagonists known prior to this study. Due to the scarcity of inhibitors and to the importance of chemical probes for exploring TAS2R14 functions, we aimed to discover new ligands for this receptor, with emphasis on antagonists. To cope with the lack of experimental structure of the receptor, we used a mixed experimental/computational methodology which iteratively improved the performance of the predicted structure. The increasing number of active compounds, obtained here through experimental screening of FDA-approved drug library, and through chemically synthesized flufenamic acid derivatives, enabled the refinement of the binding pocket, which in turn improved the structure-based virtual screening reliability. This mixed approach led to the identification of 10 new antagonists and 200 new agonists of TAS2R14, illustrating the untapped potential of rigorous medicinal chemistry for TAS2Rs. 9% of the ~ 1800 pharmaceutical drugs here tested activate TAS2R14, nine of them at sub-micromolar concentrations. The iterative framework suggested residues involved in the activation process, is suitable for expanding bitter and bitter-masking chemical space, and is applicable to other promiscuous GPCRs lacking experimental structures.
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Affiliation(s)
- Fabrizio Fierro
- The Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Lior Peri
- The Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Alina Tabor-Schkade
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Lukas Waterloo
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Stefan Löber
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Tara Pfeiffer
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Dorothee Weikert
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany
| | - Tamir Dingjan
- The Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Eitan Margulis
- The Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Nikolaus-Fiebiger-Str. 10, 91058, Erlangen, Germany.
| | - Masha Y Niv
- The Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
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10
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Dubovski N, Fierro F, Margulis E, Ben Shoshan-Galeczki Y, Peri L, Niv MY. Taste GPCRs and their ligands. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 193:177-193. [PMID: 36357077 DOI: 10.1016/bs.pmbts.2022.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Taste GPCRs are expressed in taste buds on the tongue and play a key role in food choice and consumption. They are also expressed extra-orally, with various physiological roles that are currently under study. Unraveling the roles of these receptors relies on the knowledge of their ligands. Combining sensory, cell-based and computational approaches enabled the discovery of numerous agonists and several antagonists. Here we provide a short overview of taste receptor families, main recent methods for ligands discovery, and current sources of information about known ligands. The future directions that are likely to impact the taste GPCR field include focus on ligand interactions with naturally occurring polymorphisms, as well as harnessing the power of CryoEM and of multiple signaling readout techniques.
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Affiliation(s)
- Nitzan Dubovski
- The Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Fabrizio Fierro
- The Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Eitan Margulis
- The Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yaron Ben Shoshan-Galeczki
- The Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Lior Peri
- The Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Masha Y Niv
- The Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
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