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Pallante L, Cannariato M, Androutsos L, Zizzi EA, Bompotas A, Hada X, Grasso G, Kalogeras A, Mavroudi S, Di Benedetto G, Theofilatos K, Deriu MA. VirtuousPocketome: a computational tool for screening protein-ligand complexes to identify similar binding sites. Sci Rep 2024; 14:6296. [PMID: 38491261 PMCID: PMC10943019 DOI: 10.1038/s41598-024-56893-7] [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: 01/09/2024] [Accepted: 03/12/2024] [Indexed: 03/18/2024] Open
Abstract
Protein residues within binding pockets play a critical role in determining the range of ligands that can interact with a protein, influencing its structure and function. Identifying structural similarities in proteins offers valuable insights into their function and activation mechanisms, aiding in predicting protein-ligand interactions, anticipating off-target effects, and facilitating the development of therapeutic agents. Numerous computational methods assessing global or local similarity in protein cavities have emerged, but their utilization is impeded by complexity, impractical automation for amino acid pattern searches, and an inability to evaluate the dynamics of scrutinized protein-ligand systems. Here, we present a general, automatic and unbiased computational pipeline, named VirtuousPocketome, aimed at screening huge databases of proteins for similar binding pockets starting from an interested protein-ligand complex. We demonstrate the pipeline's potential by exploring a recently-solved human bitter taste receptor, i.e. the TAS2R46, complexed with strychnine. We pinpointed 145 proteins sharing similar binding sites compared to the analysed bitter taste receptor and the enrichment analysis highlighted the related biological processes, molecular functions and cellular components. This work represents the foundation for future studies aimed at understanding the effective role of tastants outside the gustatory system: this could pave the way towards the rationalization of the diet as a supplement to standard pharmacological treatments and the design of novel tastants-inspired compounds to target other proteins involved in specific diseases or disorders. The proposed pipeline is publicly accessible, can be applied to any protein-ligand complex, and could be expanded to screen any database of protein structures.
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Affiliation(s)
- Lorenzo Pallante
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, PolitoBIOMedLab, 10129, Torino, Italy
| | - Marco Cannariato
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, PolitoBIOMedLab, 10129, Torino, Italy
| | | | - Eric A Zizzi
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, PolitoBIOMedLab, 10129, Torino, Italy
| | - Agorakis Bompotas
- Industrial Systems Institute, Athena Research Center, 265 04, Patras, Greece
| | - Xhesika Hada
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, PolitoBIOMedLab, 10129, Torino, Italy
| | - Gianvito Grasso
- Dalle Molle Institute for Artificial Intelligence IDSIA USI-SUPSI, 6962, Lugano-Viganello, Switzerland
| | | | - Seferina Mavroudi
- Department of Nursing, School of Health Rehabilitation Sciences, University of Patras, 265 04, Patras, Greece
| | | | | | - Marco A Deriu
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, PolitoBIOMedLab, 10129, Torino, Italy.
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2
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Bloxham CJ, Hulme KD, Fierro F, Fercher C, Pegg CL, O'Brien SL, Foster SR, Short KR, Furness SGB, Reichelt ME, Niv MY, Thomas WG. Cardiac human bitter taste receptors contain naturally occurring variants that alter function. Biochem Pharmacol 2024; 219:115932. [PMID: 37989413 DOI: 10.1016/j.bcp.2023.115932] [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: 07/13/2023] [Revised: 10/26/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023]
Abstract
Bitter taste receptors (T2R) are a subfamily of G protein-coupled receptors that enable humans to detect aversive and toxic substances. The ability to discern bitter compounds varies between individuals and is attributed mainly to naturally occurring T2R polymorphisms. T2Rs are also expressed in numerous non-gustatory tissues, including the heart, indicating potential contributions to cardiovascular physiology. In this study. T2Rs that have previously been identified in human cardiac tissues (T2Rs - 10, 14, 30, 31, 46 and 50) and their naturally occurring polymorphisms were functionally characterised. The ligand-dependent signaling responses of some T2R variants were completely abolished (T2R30 Leu252 and T2R46 Met228), whereas other receptor variants had moderate changes in their maximal response, but not potency, relative to wild type. Using a cAMP fluorescent biosensor, we reveal the productive coupling of T2R14, but not the T2R14 Phe201 variant, to endogenous Gαi. Modeling revealed that these variants resulted in altered interactions that generally affected ligand binding (T2R30 Leu252) or Gα protein interactions (T2R46 Met228 and T2R14 Phe201), rather than receptor structural stability. Interestingly, this study is the first to show a difference in signaling for T2R50 Tyr203 (rs1376251) which has been associated with cardiovascular disease. The observation of naturally occurring functional variation in the T2Rs with the greatest expression in the heart is important, as their discovery should prove useful in deciphering the role of T2Rs within the cardiovascular system.
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Affiliation(s)
- Conor J Bloxham
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, QLD, Australia; Regenerative Medicine in Cardiovascular Diseases, First Department of Medicine, Klinikum rechts der Isar, Technical University of Munich, Germany
| | - Katina D Hulme
- School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, QLD, Australia; Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Fabrizio Fierro
- Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Israel
| | - Christian Fercher
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, QLD, Australia
| | - Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, QLD, Australia
| | - Shannon L O'Brien
- Institute of Metabolism and Systems Research, University of Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Simon R Foster
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, QLD, Australia; QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, QLD, Australia
| | - Sebastian G B Furness
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, QLD, Australia; Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Melissa E Reichelt
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, QLD, Australia
| | - Masha Y Niv
- Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Israel
| | - Walter G Thomas
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, QLD, Australia.
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3
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Soh R, Fu L, Guo WM, Seetoh WG, Koay A. Inhibitors of human bitter taste receptors from the five-flavour berry, Schisandra chinensis. Food Funct 2023; 14:10700-10708. [PMID: 37986606 DOI: 10.1039/d3fo02303f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The human bitter taste 2 receptor member 16 (TAS2R16) is one of 25 class A G-protein-coupled receptors (GPCRs) and responds to a variety of molecules responsible for the bitter taste sensation perceived in humans. TAS2R16 can be activated by β-glucopyranosides, and its activation can be inhibited by probenecid, a synthetic drug compound used to treat gout. In this study we describe naturally derived compounds which can inhibit the activation of TAS2R16 by salicin in vitro. These compounds belong to the lignan class derived from the fruit of Schisandra chinensis, which is commonly known as the five-flavour berry. We further tested other analogs with this lignan scaffold, found their differential inhibitory activities towards TAS2R16 in vitro, and sought to rationalize the activity using molecular docking of these lignans on a computationally modelled structure of TAS2R16. Selected lignans with inhibitory activity against other TAS2Rs reveal sub-millimolar inhibitory activity towards TAS2R10, TAS2R14, and TAS2R43 in cell-based assays. These compounds with demonstrated in vitro inhibition of bitter taste receptors may serve as tool compounds to investigate the molecular mechanisms of hTAS2Rs biology in gustatory and non-gustatory tissues.
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Affiliation(s)
- Ryan Soh
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #02-01 Nanos, Singapore 138669, Singapore.
| | - Lin Fu
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #02-01 Nanos, Singapore 138669, Singapore.
| | - Wei Mei Guo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #02-01 Nanos, Singapore 138669, Singapore.
| | - Wei-Guang Seetoh
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #02-01 Nanos, Singapore 138669, Singapore.
| | - Ann Koay
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, #02-01 Nanos, Singapore 138669, Singapore.
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4
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Fiorentini R, Tarenzi T, Potestio R. Fast, Accurate, and System-Specific Variable-Resolution Modeling of Proteins. J Chem Inf Model 2023; 63:1260-1275. [PMID: 36735551 PMCID: PMC9976289 DOI: 10.1021/acs.jcim.2c01311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Indexed: 02/04/2023]
Abstract
In recent years, a few multiple-resolution modeling strategies have been proposed, in which functionally relevant parts of a biomolecule are described with atomistic resolution, with the remainder of the system being concurrently treated using a coarse-grained model. In most cases, the parametrization of the latter requires lengthy reference all-atom simulations and/or the usage of off-shelf coarse-grained force fields, whose interactions have to be refined to fit the specific system under examination. Here, we overcome these limitations through a novel multiresolution modeling scheme for proteins, dubbed coarse-grained anisotropic network model for variable resolution simulations, or CANVAS. This scheme enables a user-defined modulation of the resolution level throughout the system structure; a fast parametrization of the potential without the necessity of reference simulations; and the straightforward usage of the model on the most commonly used molecular dynamics platforms. The method is presented and validated with two case studies, the enzyme adenylate kinase and the therapeutic antibody pembrolizumab, by comparing the results obtained with the CANVAS model against fully atomistic simulations. The modeling software, implemented in Python, is made freely available for the community on a collaborative github repository.
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Affiliation(s)
- Raffaele Fiorentini
- Department
of Physics, University of Trento, via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento
Institute for Fundamental Physics and Applications, via Sommarive 14, I-38123 Trento, Italy
| | - Thomas Tarenzi
- Department
of Physics, University of Trento, via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento
Institute for Fundamental Physics and Applications, via Sommarive 14, I-38123 Trento, Italy
| | - Raffaello Potestio
- Department
of Physics, University of Trento, via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento
Institute for Fundamental Physics and Applications, via Sommarive 14, I-38123 Trento, Italy
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5
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Ke X, Ma H, Yang J, Qiu M, Wang J, Han L, Zhang D. New strategies for identifying and masking the bitter taste in traditional herbal medicines: The example of Huanglian Jiedu Decoction. Front Pharmacol 2022; 13:843821. [PMID: 36060004 PMCID: PMC9431955 DOI: 10.3389/fphar.2022.843821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Suppressing the bitter taste of traditional Chinese medicine (TCM) largely has been a major clinical challenge due to complex and diverse metabolites and high dispersion of bitter metabolites in liquid preparations. In this work, we developed a novel strategy for recognizing bitter substances, hiding their bitter taste, and elucidated the mechanism of flavor masking in TCM. Huanglian Jie-Du Decoction (HLJDD) with an intense bitter taste was studied as a typical case. UHPLC-MS/MS was used to analyze the chemical components in HLJDD, whereas the bitter substances were identified by pharmacophores. Additionally, the screening results of the pharmacophores were further validated by using experimental assays. The mask formula of HLJDD was effectively screened under the condition of clear bitter substances. Subsequently, computational chemistry, molecular docking, and infrared characterization (IR) techniques were then used to explicate the mechanism of flavor masking. Consequently, neotame, γ-CD, and mPEG2000-PLLA2000 significantly reduced the bitterness of HLJDD. Specifically, mPEG2000-PLLA2000 increased the colloid proportion in the decoction system and minimized the distribution of bitter components in the real solution. Sweetener neotame suppressed the perception of bitter taste and inhibited bitter taste receptor activation to eventually reduce the bitter taste. The γ-CD included in the decoction bound the hydrophobic groups of the bitter metabolites in real solution and “packed” all or part of the bitter metabolites into the “cavity”. We established a novel approach for screening bitter substances in TCM by integrating virtual screening and experimental assays. Based on this strategy, the bitter taste masking of TCM was performed from three different aspects, namely, changing the drug phase state, component distribution, and interfering with bitter taste signal transduction. Collectively, the methods achieved a significant effect on bitter taste suppression and taste masking. Our findings will provide a novel strategy for masking the taste of TCM liquid preparation/decoction, which will in return help in improving the clinical efficacy of TCM.
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Affiliation(s)
- Xiumei Ke
- College of Pharmacy, Chongqing Medical University, Chongqing, China
- *Correspondence: Xiumei Ke, ; Jianwei Wang, ; Li Han, ; Dingkun Zhang,
| | - Hongyan Ma
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Junxuan Yang
- College of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Min Qiu
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jianwei Wang
- College of Pharmacy, Chongqing Medical University, Chongqing, China
- *Correspondence: Xiumei Ke, ; Jianwei Wang, ; Li Han, ; Dingkun Zhang,
| | - Li Han
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Xiumei Ke, ; Jianwei Wang, ; Li Han, ; Dingkun Zhang,
| | - Dingkun Zhang
- State Key Laboratory Breeding Base of Systematic Research, Development and Utilization of Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Xiumei Ke, ; Jianwei Wang, ; Li Han, ; Dingkun Zhang,
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6
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Margulis E, Slavutsky Y, Lang T, Behrens M, Benjamini Y, Niv MY. BitterMatch: recommendation systems for matching molecules with bitter taste receptors. J Cheminform 2022; 14:45. [PMID: 35799226 PMCID: PMC9261901 DOI: 10.1186/s13321-022-00612-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/14/2022] [Indexed: 11/10/2022] Open
Abstract
Bitterness is an aversive cue elicited by thousands of chemically diverse compounds. Bitter taste may prevent consumption of foods and jeopardize drug compliance. The G protein-coupled receptors for bitter taste, TAS2Rs, have species-dependent number of subtypes and varying expression levels in extraoral tissues. Molecular recognition by TAS2R subtypes is physiologically important, and presents a challenging case study for ligand-receptor matchmaking. Inspired by hybrid recommendation systems, we developed a new set of similarity features, and created the BitterMatch algorithm that predicts associations of ligands to receptors with ~ 80% precision at ~ 50% recall. Associations for several compounds were tested in-vitro, resulting in 80% precision and 42% recall. The encouraging performance was achieved by including receptor properties and integrating experimentally determined ligand-receptor associations with chemical ligand-to-ligand similarities. BitterMatch can predict off-targets for bitter drugs, identify novel ligands and guide flavor design. The novel features capture information regarding the molecules and their receptors, which could inform various chemoinformatic tasks. Inclusion of neighbor-informed similarities improves as experimental data mounts, and provides a generalizable framework for molecule-biotarget matching.
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Affiliation(s)
- Eitan Margulis
- The Institute of Biochemistry, Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yuli Slavutsky
- Department of Statistics and Data Science, Faculty of Social Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tatjana Lang
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Maik Behrens
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Yuval Benjamini
- Department of Statistics and Data Science, Faculty of Social Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Masha Y Niv
- The Institute of Biochemistry, Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
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7
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Itoigawa A, Hayakawa T, Zhou Y, Manning AD, Zhang G, Grutzner F, Imai H. Functional Diversity and Evolution of Bitter Taste Receptors in Egg-Laying Mammals. Mol Biol Evol 2022; 39:6591311. [PMID: 35652727 PMCID: PMC9161717 DOI: 10.1093/molbev/msac107] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Egg-laying mammals (monotremes) are a sister clade of therians (placental mammals and marsupials) and a key clade to understand mammalian evolution. They are classified into platypus and echidna, which exhibit distinct ecological features such as habitats and diet. Chemosensory genes, which encode sensory receptors for taste and smell, are believed to adapt to the individual habitats and diet of each mammal. In this study, we focused on the molecular evolution of bitter taste receptors (TAS2Rs) in monotremes. The sense of bitter taste is important to detect potentially harmful substances. We comprehensively surveyed agonists of all TAS2Rs in platypus (Ornithorhynchus anatinus) and short-beaked echidna (Tachyglossus aculeatus) and compared their functions with orthologous TAS2Rs of marsupial and placental mammals (i.e., therians). As results, the agonist screening revealed that the deorphanized monotreme receptors were functionally diversified. Platypus TAS2Rs had broader receptive ranges of agonists than those of echidna TAS2Rs. While platypus consumes a variety of aquatic invertebrates, echidna mainly consumes subterranean social insects (ants and termites) as well as other invertebrates. This result indicates that receptive ranges of TAS2Rs could be associated with feeding habits in monotremes. Furthermore, some orthologous receptors in monotremes and therians responded to β-glucosides, which are feeding deterrents in plants and insects. These results suggest that the ability to detect β-glucosides and other substances might be shared and ancestral among mammals.
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Affiliation(s)
- Akihiro Itoigawa
- Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, Inuyama, Aichi, Japan.,Department of Agricultural Chemistry, School of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Hokkaido, Japan.,Japan Monkey Centre, Inuyama, Aichi, Japan
| | | | - Adrian D Manning
- Fenner School of Environment and Society, The Australian National University, Canberra, ACT, Australia
| | - Guojie Zhang
- Department of Biology, University of Copenhagen, Kobenhavn, Denmark
| | - Frank Grutzner
- School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Hiroo Imai
- Molecular Biology Section, Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi, Japan
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8
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Bayer S, Mayer AI, Borgonovo G, Morini G, Di Pizio A, Bassoli A. Chemoinformatics View on Bitter Taste Receptor Agonists in Food. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:13916-13924. [PMID: 34762411 PMCID: PMC8630789 DOI: 10.1021/acs.jafc.1c05057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Food compounds with a bitter taste have a role in human health, both for their capability to influence food choice and preferences and for their possible systemic effect due to the modulation of extra-oral bitter taste receptors (TAS2Rs). Investigating the interaction of bitter food compounds with TAS2Rs is a key step to unravel their complex effects on health and to pave the way to rationally design new additives for food formulation or drugs. Here, we propose a collection of food bitter compounds, for which in vitro activity data against TAS2Rs are available. The patterns of TAS2R subtype-specific agonists were analyzed using scaffold decomposition and chemical space analysis, providing a detailed characterization of the associations between food bitter tastants and TAS2Rs.
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Affiliation(s)
- Sebastian Bayer
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner Str. 34, D-85354 Freising, Germany
- Faculty
of Life Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Ariane Isabell Mayer
- Department
of Food, Environmental and Nutritional Sciences-DeFENS, University of Milan, via Celoria 2, 20147 Milano, Italy
| | - Gigliola Borgonovo
- Department
of Food, Environmental and Nutritional Sciences-DeFENS, University of Milan, via Celoria 2, 20147 Milano, Italy
| | - Gabriella Morini
- University
of Gastronomic Sciences, piazza Vittorio Emanuele 9, 12042 Pollenzo, (Bra, CN), Italy
| | - Antonella Di Pizio
- Leibniz
Institute for Food Systems Biology at the Technical University of
Munich, Lise-Meitner Str. 34, D-85354 Freising, Germany
- . Phone: +49(0)8161716516
| | - Angela Bassoli
- Department
of Food, Environmental and Nutritional Sciences-DeFENS, University of Milan, via Celoria 2, 20147 Milano, Italy
- . Phone: +39(0)250316815
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9
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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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10
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Giulini M, Rigoli M, Mattiotti G, Menichetti R, Tarenzi T, Fiorentini R, Potestio R. From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules. Front Mol Biosci 2021; 8:676976. [PMID: 34164432 PMCID: PMC8215203 DOI: 10.3389/fmolb.2021.676976] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/06/2021] [Indexed: 12/18/2022] Open
Abstract
The ever increasing computer power, together with the improved accuracy of atomistic force fields, enables researchers to investigate biological systems at the molecular level with remarkable detail. However, the relevant length and time scales of many processes of interest are still hardly within reach even for state-of-the-art hardware, thus leaving important questions often unanswered. The computer-aided investigation of many biological physics problems thus largely benefits from the usage of coarse-grained models, that is, simplified representations of a molecule at a level of resolution that is lower than atomistic. A plethora of coarse-grained models have been developed, which differ most notably in their granularity; this latter aspect determines one of the crucial open issues in the field, i.e. the identification of an optimal degree of coarsening, which enables the greatest simplification at the expenses of the smallest information loss. In this review, we present the problem of coarse-grained modeling in biophysics from the viewpoint of system representation and information content. In particular, we discuss two distinct yet complementary aspects of protein modeling: on the one hand, the relationship between the resolution of a model and its capacity of accurately reproducing the properties of interest; on the other hand, the possibility of employing a lower resolution description of a detailed model to extract simple, useful, and intelligible information from the latter.
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Affiliation(s)
- Marco Giulini
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Marta Rigoli
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Giovanni Mattiotti
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Roberto Menichetti
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Thomas Tarenzi
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Raffaele Fiorentini
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
| | - Raffaello Potestio
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
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11
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Montoro P, D’Urso G, Kowalczyk A, Tuberoso CIG. LC-ESI/LTQ-Orbitrap-MS Based Metabolomics in Evaluation of Bitter Taste of Arbutus unedo Honey. Molecules 2021; 26:molecules26092765. [PMID: 34066670 PMCID: PMC8125850 DOI: 10.3390/molecules26092765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 11/29/2022] Open
Abstract
Strawberry tree honey is a high-value honey from the Mediterranean area and it is characterised by a typical bitter taste. To possibly identify the secondary metabolites responsible for the bitter taste, the honey was fractionated on a C18 column and the individual fractions were subjected to sensory analysis and then analysed by liquid chromatography coupled with high-resolution tandem mass spectrometry in negative ion mode, using a mass spectrometer with an electrospray source coupled to a hybrid high resolution mass analyser (LC-ESI/LTQ-Orbitrap-MS). A chemometric model obtained by preliminary principal component analysis (PCA) of LC-ESI/LTQ-Orbitrap-MS data allowed the identification of the fractions that caused the perception of bitterness. Subsequently, a partial least squares (PLS) regression model was built. The studies carried out with multivariate analysis showed that unedone (2-(1,2-dihydroxypropyl)-4,4,8-trimethyl-1-oxaspiro [2.5] oct-7-en-6-one) can be considered responsible for the bitter taste of strawberry tree honey. Confirmation of the bitter taste of unedone was obtained by sensory evaluation of a pure standard, allowing it to be added to the list of natural compounds responsible for giving the sensation of bitterness to humans.
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Affiliation(s)
- Paola Montoro
- Department of Pharmacy, University of Salerno, via Giovanni Paolo II, 132, 84084 Fisciano, Italy; (P.M.); (G.D.)
| | - Gilda D’Urso
- Department of Pharmacy, University of Salerno, via Giovanni Paolo II, 132, 84084 Fisciano, Italy; (P.M.); (G.D.)
| | - Adam Kowalczyk
- Department of Pharmacognosy and Herbal Medicines, Wrocław Medical University, ul. Borowska, 211, 50-556 Wrocław, Poland;
| | - Carlo Ignazio Giovanni Tuberoso
- Department of Life and Environmental Sciences, University of Cagliari, University Campus, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato, Italy
- Correspondence: ; Tel.: +39-070-675-8644
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12
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Itoigawa A, Fierro F, Chaney ME, Lauterbur ME, Hayakawa T, Tosi AJ, Niv MY, Imai H. Lowered sensitivity of bitter taste receptors to β-glucosides in bamboo lemurs: an instance of parallel and adaptive functional decline in TAS2R16? Proc Biol Sci 2021; 288:20210346. [PMID: 33849315 PMCID: PMC8059561 DOI: 10.1098/rspb.2021.0346] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Bitter taste facilitates the detection of potentially harmful substances and is perceived via bitter taste receptors (TAS2Rs) expressed on the tongue and oral cavity in vertebrates. In primates, TAS2R16 specifically recognizes β-glucosides, which are important in cyanogenic plants' use of cyanide as a feeding deterrent. In this study, we performed cell-based functional assays for investigating the sensitivity of TAS2R16 to β-glucosides in three species of bamboo lemurs (Prolemur simus, Hapalemur aureus and H. griseus), which primarily consume high-cyanide bamboo. TAS2R16 receptors from bamboo lemurs had lower sensitivity to β-glucosides, including cyanogenic glucosides, than that of the closely related ring-tailed lemur (Lemur catta). Ancestral reconstructions of TAS2R16 for the bamboo-lemur last common ancestor (LCA) and that of the Hapalemur LCA showed an intermediate sensitivity to β-glucosides between that of the ring-tailed lemurs and bamboo lemurs. Mutagenetic analyses revealed that P. simus and H. griseus had separate species-specific substitutions that led to reduced sensitivity. These results indicate that low sensitivity to β-glucosides at the cellular level—a potentially adaptive trait for feeding on cyanogenic bamboo—evolved independently after the Prolemur–Hapalemur split in each species.
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Affiliation(s)
- Akihiro Itoigawa
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, 41-2 Kanrin, Inuyama, Aichi 484-8506, Japan.,Japan Society for the Promotion of Science, Kojimachi, Chiyoda-ku, Tokyo 102-0083, Japan
| | - Fabrizio Fierro
- The Institute of Biochemistry, Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Morgan E Chaney
- Department of Anthropology, Kent State University, Kent, OH 44242, USA
| | - M Elise Lauterbur
- Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ 85721, USA
| | - Takashi Hayakawa
- Faculty of Environmental Earth Science, Hokkaido University, N10W5, Kita-ku, Sapporo, Hokkaido 060-0810, Japan.,Japan Monkey Centre, 26 Inuyamakanrin, Inuyama, Aichi 484-0081, Japan
| | - Anthony J Tosi
- Department of Anthropology, Kent State University, Kent, OH 44242, USA
| | - Masha Y Niv
- The Institute of Biochemistry, Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100 Rehovot, Israel
| | - Hiroo Imai
- Molecular Biology Section, Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, 41-2 Kanrin, Inuyama, Aichi 484-8506, Japan
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13
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Bitter taste in silico: A review on virtual ligand screening and characterization methods for TAS2R-bitterant interactions. Int J Pharm 2021; 600:120486. [PMID: 33744445 DOI: 10.1016/j.ijpharm.2021.120486] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/21/2021] [Accepted: 03/09/2021] [Indexed: 11/21/2022]
Abstract
The growing pharmaceutical interest in the human bitter taste receptors (hTAS2Rs) has two dimensions; i) evaluation of the bitterness of active pharmaceutical compounds, in order to develop strategies for improving patients' adherence to medication, and ii) application of ligands for extra-cellular hTAS2Rs for potential preventive therapeutic achievements. The result is an increasing demand on robust tools for bitterness assessment and screening the receptor-ligand affinity. In silico tools are useful for aiding experimental-screening, as well as to elucide ligand-receptor interactions. In this review, the ligand-based and structure-based approaches are described as the two main in silico tools for bitter taste analysis. The strengths and weaknesses of each approach are discussed. Both approaches provide key tools for understanding and exploiting bitter taste for human health applications.
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14
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Sena DM, Cong X, Giorgetti A. Ligand based conformational space studies of the μ-opioid receptor. Biochim Biophys Acta Gen Subj 2020; 1865:129838. [PMID: 33373630 DOI: 10.1016/j.bbagen.2020.129838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 01/25/2023]
Abstract
BACKGROUND G protein-coupled receptors (GPCRs) comprise a family of membrane proteins that can be activated by a variety of external factors. The μ-opioid receptor (MOR), a class A GPCR, is the main target of morphine. Recently, enhanced sampling molecular dynamics simulations of a constitutively active mutant of MOR in its apo form allowed us to capture the novel intermediate states of activation, as well as the active state. This prompted us to apply the same techniques to wild type MOR in complex with ligands, in order to explore their contributions to the receptor conformational changes in the activation process. METHODS MOR was modeled in complex with agonists (morphine, BU72), a partial agonist (naloxone benzoylhydrazone) and an antagonist (naloxone). Replica exchange with solute tempering (REST2) molecular dynamics simulations were carried out for all systems. Trajectory frames were clustered, and the activation state of each cluster was assessed by two different methods. RESULTS Cluster sizes and activation indices show that while agonists stabilized structures in a higher activation state, the antagonist behaved oppositely. Morphine tends to drive the receptor towards increasing R165-T279 distances, while naloxone tends to increase the NPxxYA motif conformational change. CONCLUSIONS Despite not observing a full transition between inactive and active states, an important conformational change of transmembrane helix 5 was observed and associated with a ligand-driven step of the process. GENERAL SIGNIFICANCE The activation process of GPCRs is widely studied but still not fully understood. Here we carried out a step forward in the direction of gaining more details of this process.
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Affiliation(s)
- Diniz M Sena
- Universidade Regional do Cariri - URCA, Biological Chemistry Dept., Crato, CE 63105-000, Brazil.
| | - Xiaojing Cong
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice UMR7272, Nice 06108, France
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany; Department of Biotechnology, University of Verona, Verona, Italy.
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15
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Margulis E, Dagan-Wiener A, Ives RS, Jaffari S, Siems K, Niv MY. Intense bitterness of molecules: Machine learning for expediting drug discovery. Comput Struct Biotechnol J 2020; 19:568-576. [PMID: 33510862 PMCID: PMC7807207 DOI: 10.1016/j.csbj.2020.12.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/17/2020] [Accepted: 12/20/2020] [Indexed: 12/16/2022] Open
Abstract
Drug development is a long, expensive and multistage process geared to achieving safe drugs with high efficacy. A crucial prerequisite for completing the medication regimen for oral drugs, particularly for pediatric and geriatric populations, is achieving taste that does not hinder compliance. Currently, the aversive taste of drugs is tested in late stages of clinical trials. This can result in the need to reformulate, potentially resulting in the use of more animals for additional toxicity trials, increased financial costs and a delay in release to the market. Here we present BitterIntense, a machine learning tool that classifies molecules into "very bitter" or "not very bitter", based on their chemical structure. The model, trained on chemically diverse compounds, has above 80% accuracy on several test sets. Our results suggest that about 25% of drugs are predicted to be very bitter, with even higher prevalence (~40%) in COVID19 drug candidates and in microbial natural products. Only ~10% of toxic molecules are predicted to be intensely bitter, and it is also suggested that intense bitterness does not correlate with hepatotoxicity of drugs. However, very bitter compounds may be more cardiotoxic than not very bitter compounds, possessing significantly lower QPlogHERG values. BitterIntense allows quick and easy prediction of strong bitterness of compounds of interest for food, pharma and biotechnology industries. We estimate that implementation of BitterIntense or similar tools early in drug discovery process may lead to reduction in delays, in animal use and in overall financial burden.
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Affiliation(s)
- Eitan Margulis
- The Institute of Biochemistry, Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ayana Dagan-Wiener
- The Institute of Biochemistry, Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Robert S Ives
- Comparative & Translational Sciences, GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, United Kingdom
| | - Sara Jaffari
- Product Development & Supply, GlaxoSmithKline, Park Road, Ware, SG12 0DP, United Kingdom
| | | | - Masha Y Niv
- The Institute of Biochemistry, Food Science and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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16
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Di Pizio A, Nicoli A. In Silico Molecular Study of Tryptophan Bitterness. Molecules 2020; 25:molecules25204623. [PMID: 33050648 PMCID: PMC7587216 DOI: 10.3390/molecules25204623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/06/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022] Open
Abstract
Tryptophan is an essential amino acid, required for the production of serotonin. It is the most bitter amino acid and its bitterness was found to be mediated by the bitter taste receptor TAS2R4. Di-tryptophan has a different selectivity profile and was found to activate three bitter taste receptors, whereas tri-tryptophan activated five TAS2Rs. In this work, the selectivity/promiscuity profiles of the mono-to-tri-tryptophans were explored using molecular modeling simulations to provide new insights into the molecular recognition of the bitter tryptophan. Tryptophan epitopes were found in all five peptide-sensitive TAS2Rs and the best tryptophan epitope was identified and characterized at the core of the orthosteric binding site of TAS2R4.
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17
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Structure-Function Analyses of Human Bitter Taste Receptors-Where Do We Stand? Molecules 2020; 25:molecules25194423. [PMID: 32993119 PMCID: PMC7582848 DOI: 10.3390/molecules25194423] [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: 08/31/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
The finding that bitter taste receptors are expressed in numerous tissues outside the oral cavity and fulfill important roles in metabolic regulation, innate immunity and respiratory control, have made these receptors important targets for drug discovery. Efficient drug discovery depends heavily on detailed knowledge on structure-function-relationships of the target receptors. Unfortunately, experimental structures of bitter taste receptors are still lacking, and hence, the field relies mostly on structures obtained by molecular modeling combined with functional experiments and point mutageneses. The present article summarizes the current knowledge on the structure–function relationships of human bitter taste receptors. Although these receptors are difficult to express in heterologous systems and their homology with other G protein-coupled receptors is very low, detailed information are available at least for some of these receptors.
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18
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Dunkel A, Hofmann T, Di Pizio A. In Silico Investigation of Bitter Hop-Derived Compounds and Their Cognate Bitter Taste Receptors. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10414-10423. [PMID: 32027492 DOI: 10.1021/acs.jafc.9b07863] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The typical bitter taste of beer is caused by adding hops (Humulus lupulus L.) during the wort boiling process. The bitter taste of hop-derived compounds was found to be mediated by three bitter taste receptors: TAS2R1, TAS2R14, and TAS2R40. In this work, structural bioinformatics analyses were used to characterize the binding modes of trans-isocohumulone, trans-isohumulone, trans-isoadhumulone, cis-isocohumulone, cis-isohumulone, cis-isoadhumulone, cohumulone, humulone, adhumulone, and 8-prenylnaringenin into the orthosteric binding site of their cognate receptors. A conserved asparagine in transmembrane 3 was found to be essential for the recognition of hop-derived compounds, whereas the surrounding residues in the binding site of the three receptors encode the ligand specificity. Hop-derived compounds are renowned bioactive molecules and are considered as potential hit molecules for drug discovery to treat metabolic diseases. A chemoinformatics analysis revealed that hop-derived compounds cluster in a different region of the chemical space compared to known bitter food-derived compounds, pinpointing hop-derived compounds as a very peculiar class of bitter compounds.
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Affiliation(s)
- Andreas Dunkel
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner Straße 34, D-85354 Freising, Germany
| | - Thomas Hofmann
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, D-85354 Freising, Germany
| | - Antonella Di Pizio
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner Straße 34, D-85354 Freising, Germany
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19
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Schneider J, Ribeiro R, Alfonso-Prieto M, Carloni P, Giorgetti A. Hybrid MM/CG Webserver: Automatic Set Up of Molecular Mechanics/Coarse-Grained Simulations for Human G Protein-Coupled Receptor/Ligand Complexes. Front Mol Biosci 2020; 7:576689. [PMID: 33102525 PMCID: PMC7500467 DOI: 10.3389/fmolb.2020.576689] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022] Open
Abstract
Hybrid Molecular Mechanics/Coarse-Grained (MM/CG) simulations help predict ligand poses in human G protein-coupled receptors (hGPCRs), the most important protein superfamily for pharmacological applications. This approach allows the description of the ligand, the binding cavity, and the surrounding water molecules at atomistic resolution, while coarse-graining the rest of the receptor. Here, we present the Hybrid MM/CG Webserver (mmcg.grs.kfa-juelich.de) that automatizes and speeds up the MM/CG simulation setup of hGPCR/ligand complexes. Initial structures for such complexes can be easily and efficiently generated with other webservers. The Hybrid MM/CG server also allows for equilibration of the systems, either fully automatically or interactively. The results are visualized online (using both interactive 3D visualizations and analysis plots), helping the user identify possible issues and modify the setup parameters accordingly. Furthermore, the prepared system can be downloaded and the simulation continued locally.
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Affiliation(s)
- Jakob Schneider
- Computational Biomedicine, Institute for Advanced Simulation IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany.,JARA-Institute: Molecular Neuroscience and Neuroimaging, Institute for Neuroscience and Medicine INM-11/JARA-BRAIN Institute JBI-2, Forschungszentrum Jülich GmbH, Jülich, Germany.,Department of Physics, RWTH Aachen University, Aachen, Germany
| | - Rui Ribeiro
- Department of Biotechnology, University of Verona, Verona, Italy
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulation IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany.,Medical Faculty, Cécile and Oskar Vogt Institute for Brain Research, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany.,JARA-Institute: Molecular Neuroscience and Neuroimaging, Institute for Neuroscience and Medicine INM-11/JARA-BRAIN Institute JBI-2, Forschungszentrum Jülich GmbH, Jülich, Germany.,Department of Physics, RWTH Aachen University, Aachen, Germany
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany.,Department of Biotechnology, University of Verona, Verona, Italy
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20
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Schneider J, Korshunova K, Si Chaib Z, Giorgetti A, Alfonso-Prieto M, Carloni P. Ligand Pose Predictions for Human G Protein-Coupled Receptors: Insights from the Amber-Based Hybrid Molecular Mechanics/Coarse-Grained Approach. J Chem Inf Model 2020; 60:5103-5116. [PMID: 32786708 DOI: 10.1021/acs.jcim.0c00661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Human G protein-coupled receptors (hGPCRs) are the most frequent targets of Food and Drug Administration (FDA)-approved drugs. Structural bioinformatics, along with molecular simulation, can support structure-based drug design targeting hGPCRs. In this context, several years ago, we developed a hybrid molecular mechanics (MM)/coarse-grained (CG) approach to predict ligand poses in low-resolution hGPCR models. The approach was based on the GROMOS96 43A1 and PRODRG united-atom force fields for the MM part. Here, we present a new MM/CG implementation using, instead, the Amber 14SB and GAFF all-atom potentials for proteins and ligands, respectively. The new implementation outperforms the previous one, as shown by a variety of applications on models of hGPCR/ligand complexes at different resolutions, and it is also more user-friendly. Thus, it emerges as a useful tool to predict poses in low-resolution models and provides insights into ligand binding similarly to all-atom molecular dynamics, albeit at a lower computational cost.
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Affiliation(s)
- Jakob Schneider
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52074 Aachen, Germany.,JARA-Institute: Molecular Neuroscience and Neuroimaging, Institute for Neuroscience and Medicine INM-11/JARA-BRAIN Institute JBI-2, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Ksenia Korshunova
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52074 Aachen, Germany
| | - Zeineb Si Chaib
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,RWTH Aachen University, 52062 Aachen, Germany
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Biotechnology, University of Verona, 37314 Verona, Italy.,JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Cecile and Oskar Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52074 Aachen, Germany.,JARA-Institute: Molecular Neuroscience and Neuroimaging, Institute for Neuroscience and Medicine INM-11/JARA-BRAIN Institute JBI-2, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
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21
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Lang T, Lang R, Di Pizio A, Mittermeier VK, Schlagbauer V, Hofmann T, Behrens M. Numerous Compounds Orchestrate Coffee's Bitterness. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:6692-6700. [PMID: 32437139 DOI: 10.1021/acs.jafc.0c01373] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Coffee is one of the most consumed hot beverages worldwide and is highly regarded because of its stimulating effect despite having a pronounced bitterness. Even though numerous bitter ingredients have been identified, the detailed molecular basis for coffee's bitterness is not well understood except for caffeine, which activates five human bitter taste receptors. We elucidated the contribution of other bitter coffee constituents in addition to caffeine with functional calcium imaging experiments using mammalian cells expressing the cDNAs of human bitter taste receptors, sensory experiments, and in silico modeling approaches. We identified two human bitter taste receptors, TAS2R43 and TAS2R46, that responded to the bitter substance mozambioside with much higher sensitivity than to caffeine. Further, the structurally related bitter substances bengalensol, cafestol, and kahweol also activated the same pair of bitter taste receptors much more potently than the prototypical coffee bitter substance caffeine. However, for kahweol, a potent but weak activator of TAS2R43 and TAS2R46, we observed an inhibitory effect when simultaneously applied together with mozambioside to TAS2R43 expressing cells. Molecular modeling experiments showed overlapping binding sites in the receptor's ligand binding cavity that suggest that the partial agonist kahweol might be useful to reduce the overall bitterness of coffee-containing beverages. Taken together, we found that the bitterness of coffee is determined by a complex interaction of multiple bitter compounds with several human bitter taste receptors.
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Affiliation(s)
- Tatjana Lang
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany
| | - Roman Lang
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany
| | - Antonella Di Pizio
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany
| | - Verena Karolin Mittermeier
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany
| | - Verena Schlagbauer
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany
| | - Thomas Hofmann
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany
| | - Maik Behrens
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Str. 34, 85354 Freising, Germany
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22
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Fotsing JR, Darmohusodo V, Patron AP, Ching BW, Brady T, Arellano M, Chen Q, Davis TJ, Liu H, Servant G, Zhang L, Williams M, Saganich M, Ditschun T, Tachdjian C, Karanewsky DS. Discovery and Development of S6821 and S7958 as Potent TAS2R8 Antagonists. J Med Chem 2020; 63:4957-4977. [PMID: 32330040 DOI: 10.1021/acs.jmedchem.0c00388] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In humans, bitter taste is mediated by 25 TAS2Rs. Many compounds, including certain active pharmaceutical ingredients, excipients, and nutraceuticals, impart their bitter taste (or in part) through TAS2R8 activation. However, effective TAS2R8 blockers that can either suppress or reduce the bitterness of these compounds have not been described. We are hereby reporting a series of novel 3-(pyrazol-4-yl) imidazolidine-2,4-diones as potent and selective TAS2R8 antagonists. In human sensory tests, S6821 and S7958, two of the most potent analogues from the series, demonstrated efficacy in blocking TAS2R8-mediated bitterness and were selected for development. Following data evaluation by expert panels of a number of national and multinational regulatory bodies, including the US, the EU, and Japan, S6821 and S7958 were approved as safe under conditions of intended use as bitter taste blockers.
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Affiliation(s)
- Joseph R Fotsing
- Firmenich SA, R&D North America, San Diego site, 4767 Nexus Centre Drive, San Diego, California 92121, United States
| | - Vincent Darmohusodo
- Firmenich SA, R&D North America, San Diego site, 4767 Nexus Centre Drive, San Diego, California 92121, United States
| | - Andrew P Patron
- Firmenich SA, R&D North America, San Diego site, 4767 Nexus Centre Drive, San Diego, California 92121, United States
| | - Brett W Ching
- Firmenich SA, R&D North America, San Diego site, 4767 Nexus Centre Drive, San Diego, California 92121, United States
| | - Thomas Brady
- Firmenich SA, R&D North America, San Diego site, 4767 Nexus Centre Drive, San Diego, California 92121, United States
| | - Melissa Arellano
- Firmenich SA, R&D North America, San Diego site, 4767 Nexus Centre Drive, San Diego, California 92121, United States
| | - Qing Chen
- Firmenich SA, R&D North America, San Diego site, 4767 Nexus Centre Drive, San Diego, California 92121, United States
| | - Timothy J Davis
- Firmenich SA, R&D North America, San Diego site, 4767 Nexus Centre Drive, San Diego, California 92121, United States
| | - Hanghui Liu
- Firmenich SA, R&D North America, San Diego site, 4767 Nexus Centre Drive, San Diego, California 92121, United States
| | - Guy Servant
- Firmenich SA, R&D North America, San Diego site, 4767 Nexus Centre Drive, San Diego, California 92121, United States
| | - Lan Zhang
- Firmenich SA, R&D North America, San Diego site, 4767 Nexus Centre Drive, San Diego, California 92121, United States
| | - Mark Williams
- Firmenich SA, R&D North America, San Diego site, 4767 Nexus Centre Drive, San Diego, California 92121, United States
| | - Michael Saganich
- Firmenich SA, R&D North America, San Diego site, 4767 Nexus Centre Drive, San Diego, California 92121, United States
| | - Tanya Ditschun
- Firmenich SA, R&D North America, San Diego site, 4767 Nexus Centre Drive, San Diego, California 92121, United States
| | - Catherine Tachdjian
- Firmenich SA, R&D North America, San Diego site, 4767 Nexus Centre Drive, San Diego, California 92121, United States
| | - Donald S Karanewsky
- Firmenich SA, R&D North America, San Diego site, 4767 Nexus Centre Drive, San Diego, California 92121, United States
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Spaggiari G, Di Pizio A, Cozzini P. Sweet, umami and bitter taste receptors: State of the art of in silico molecular modeling approaches. Trends Food Sci Technol 2020. [DOI: 10.1016/j.tifs.2019.12.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Cazzola M, Rogliani P, Matera MG. The future of bronchodilation: looking for new classes of bronchodilators. Eur Respir Rev 2019; 28:28/154/190095. [PMID: 31871127 DOI: 10.1183/16000617.0095-2019] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/03/2019] [Indexed: 12/13/2022] Open
Abstract
Available bronchodilators can satisfy many of the needs of patients suffering from airway disorders, but they often do not relieve symptoms and their long-term use raises safety concerns. Therefore, there is interest in developing new classes that could help to overcome the limits that characterise the existing classes.At least nine potential new classes of bronchodilators have been identified: 1) selective phosphodiesterase inhibitors; 2) bitter-taste receptor agonists; 3) E-prostanoid receptor 4 agonists; 4) Rho kinase inhibitors; 5) calcilytics; 6) agonists of peroxisome proliferator-activated receptor-γ; 7) agonists of relaxin receptor 1; 8) soluble guanylyl cyclase activators; and 9) pepducins. They are under consideration, but they are mostly in a preclinical phase and, consequently, we still do not know which classes will actually be developed for clinical use and whether it will be proven that a possible clinical benefit outweighs the impact of any adverse effect.It is likely that if developed, these new classes may be a useful addition to, rather than a substitution of, the bronchodilator therapy currently used, in order to achieve further optimisation of bronchodilation.
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Affiliation(s)
- Mario Cazzola
- Dept of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Paola Rogliani
- Dept of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy
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