1
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Lecchi G, Mocchetti C, Tunesi D, Berto A, Balasubramanian HB, Biswas S, Bagchi A, Pollastro F, Fresu LG, Talmon M. Single-Nucleotide Polymorphisms of TAS2R46 Affect the Receptor Downstream Calcium Regulation in Histamine-Challenged Cells. Cells 2024; 13:1204. [PMID: 39056786 PMCID: PMC11275237 DOI: 10.3390/cells13141204] [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: 05/08/2024] [Revised: 07/02/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Bitter taste receptors (TAS2Rs) expressed in extraoral tissues represent a whole-body sensory system, whose role and mechanisms could be of interest for the identification of new therapeutic targets. It is known that TAS2R46s in pre-contracted airway smooth muscle cells increase mitochondrial calcium uptake, leading to bronchodilation, and that several SNPs have been identified in its gene sequence. There are very few reports on the structure-function analysis of TAS2Rs. Thus, we delved into the subject by using mutagenesis and in silico studies. We generated a cellular model that expresses native TAS2R46 to evaluate the influence of the four most common SNPs on calcium fluxes following the activation of the receptor by its specific ligand absinthin. Then, docking studies were conducted to correlate the calcium flux results to the structural mutation. The analysed SNPs differently modulate the TAS2R46 signal cascade according to the altered protein domain. In particular, the SNP in the sixth transmembrane domain of the receptors did not modulate calcium homeostasis, while the SNPs in the sequence coding for the fourth transmembrane domain completely abolished the mitochondrial calcium uptake. In conclusion, these results indicate the fourth transmembrane domain of TAS2R46 is critical for the intrinsic receptor activity.
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Affiliation(s)
- Giulia Lecchi
- Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Via Solaroli, 17, 28100 Novara, Italy
| | - Chiara Mocchetti
- Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Via Solaroli, 17, 28100 Novara, Italy
| | - Davide Tunesi
- Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Via Solaroli, 17, 28100 Novara, Italy
| | - Arianna Berto
- Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Via Solaroli, 17, 28100 Novara, Italy
| | - Hari Baskar Balasubramanian
- Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Via Solaroli, 17, 28100 Novara, Italy
| | - Sima Biswas
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India
| | - Angshuman Bagchi
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741235, West Bengal, India
| | - Federica Pollastro
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
| | - Luigia Grazia Fresu
- Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Via Solaroli, 17, 28100 Novara, Italy
| | - Maria Talmon
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy
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2
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Kong D, Zhang Y, Li X, Dong Y, Dou Z, Yang Z, Zhang M, Wang H. The material basis of bitter constituents in Carbonized Typhae Pollen, based on the integration strategy of constituent analysis, taste sensing system and molecular docking. J Pharm Biomed Anal 2024; 242:116028. [PMID: 38395002 DOI: 10.1016/j.jpba.2024.116028] [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: 12/07/2023] [Revised: 02/08/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024]
Abstract
The discovery of bitter constituents is of great significance to the exploration of medicinal substances for they have potential physiological effects. Carbonized Typhae Pollen (CTP), which is a typical example of carbonized Traditional Chinese Medicine (TCM), has a bitter taste and hemostatic effect after carbonized processing. The objective of this study is to elucidate the material basis of bitter constituents in CTP. Firstly, the constituents of CTP extracts with 7 different solvents were characterized by UPLC-Q-TOF-MS. Then, multivariate statistical analysis was used to visualize the CTP extracts from 7 solvents. A total of 37 constituents were tentatively identified and 17 constituents were considered as the key constituents in differentiating 7 different solvent extracts. Subsequently, the bitter evaluation of extracts from different polar parts was investigated by using an electronic tongue. As a result, the order of bitterness of the extracts was as follows: ethanol > methanol > water > n-butyl alcohol > petroleum ether > butyl acetate > isopropanol. There were statistically significant differences in the bitter degree of extracts. By correlation analysis of bitter information and chemical constituents with partial least squares regression (PLSR), 8 potential bitterness constituents were discovered, including phenylalanine, valine, chlorogenic acid, isoquercitrin, palmitic acid, citric acid, quercetin-3-O-(2-α-L-rhamnosyl)-rutinoside, and typhaneoside. Additionally, molecular docking analysis was conducted to reveal the interaction of these constituents with the bitter taste receptor. The docking result showed that these constituents could be embedded well into the active pocket of T2R46 and had significant affinity interactions with critical amino acid residues by forming hydrogen bonds. This study provided a reliable theoretical basis for future research on biological activity of bitterness substances.
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Affiliation(s)
- Derong Kong
- Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China; Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China; School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Ying Zhang
- Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China; Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China; School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xinyue Li
- Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China; Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China; School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yanyu Dong
- Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China; Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China; School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zhiying Dou
- Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China; Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China; School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Zhen Yang
- Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China; School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Mixia Zhang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Hui Wang
- Tianjin Key Laboratory of Therapeutic Substance of Traditional Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China; Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China; School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China.
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3
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Xu W, Wu L, Liu S, Liu X, Cao X, Zhou C, Zhang J, Fu Y, Guo Y, Wu Y, Tan Q, Wang L, Liu J, Jiang L, Fan Z, Pei Y, Yu J, Cheng J, Zhao S, Hao X, Liu ZJ, Hua T. Structural basis for strychnine activation of human bitter taste receptor TAS2R46. Science 2022; 377:1298-1304. [DOI: 10.1126/science.abo1633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Taste sensing is a sophisticated chemosensory process, and bitter taste perception is mediated by type 2 taste receptors (TAS2Rs), or class T G protein–coupled receptors. Understanding the detailed molecular mechanisms behind taste sensation is hindered by a lack of experimental receptor structures. Here, we report the cryo–electron microscopy structures of human TAS2R46 complexed with chimeric mini–G protein gustducin, in both strychnine-bound and apo forms. Several features of TAS2R46 are disclosed, including distinct receptor structures that compare with known GPCRs, a new “toggle switch,” activation-related motifs, and precoupling with mini–G protein gustducin. Furthermore, the dynamic extracellular and more-static intracellular parts of TAS2R46 suggest possible diverse ligand-recognition and activation processes. This study provides a basis for further exploration of other bitter taste receptors and their therapeutic applications.
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Affiliation(s)
- Weixiu Xu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Lijie Wu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Shenhui Liu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiao Liu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiaoling Cao
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Cui Zhou
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jinyi Zhang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - You Fu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yu Guo
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Qiwen Tan
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Ling Wang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Junlin Liu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Longquan Jiang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhongbo Fan
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yuan Pei
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Jingyi Yu
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiaojiang Hao
- State Key Laboratory of Phytochemistry and Plant Resource in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650210, China
| | - Zhi-Jie Liu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Tian Hua
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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4
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Extracellular loop 2 of G protein-coupled olfactory receptors is critical for odorant recognition. J Biol Chem 2022; 298:102331. [PMID: 35926708 PMCID: PMC9442423 DOI: 10.1016/j.jbc.2022.102331] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 11/27/2022] Open
Abstract
G protein–coupled olfactory receptors (ORs) enable us to detect innumerous odorants. They are also ectopically expressed in nonolfactory tissues and emerging as attractive drug targets. ORs can be promiscuous or highly specific, which is part of a larger mechanism for odor discrimination. Here, we demonstrate that the OR extracellular loop 2 (ECL2) plays critical roles in OR promiscuity and specificity. Using site-directed mutagenesis and molecular modeling, we constructed 3D OR models in which ECL2 forms a lid over the orthosteric pocket. We demonstrate using molecular dynamics simulations that ECL2 controls the shape and volume of the odorant-binding pocket, maintains the pocket hydrophobicity, and acts as a gatekeeper of odorant binding. Therefore, we propose the interplay between the specific orthosteric pocket and the variable, less specific ECL2 controls OR specificity and promiscuity. Furthermore, the 3D models created here enabled virtual screening of new OR agonists and antagonists, which exhibited a 70% hit rate in cell assays. Our approach can potentially be generalized to structure-based ligand screening for other G protein–coupled receptors that lack high-resolution 3D structures.
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5
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Xu Z, Guo L, Qian X, Yu C, Li S, Zhu C, Ma X, Li H, Zhu G, Zhou H, Dai W, Li Q, Gao X. Two entry tunnels in mouse TAAR9 suggest the possibility of multi-entry tunnels in olfactory receptors. Sci Rep 2022; 12:2691. [PMID: 35177711 PMCID: PMC8854740 DOI: 10.1038/s41598-022-06591-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 01/24/2022] [Indexed: 12/16/2022] Open
Abstract
Orthosteric binding sites of olfactory receptors have been well understood for ligand-receptor interactions. However, a lack of explanation for subtle differences in ligand profile of olfactory receptors even with similar orthosteric binding sites promotes more exploration into the entry tunnels of the receptors. An important question regarding entry tunnels is the number of entry tunnels, which was previously believed to be one. Here, we used TAAR9 that recognizes important biogenic amines such as cadaverine, spermine, and spermidine as a model for entry tunnel study. We identified two entry tunnels in TAAR9 and described the residues that form the tunnels. In addition, we found two vestibular binding pockets, each located in one tunnel. We further confirmed the function of two tunnels through site-directed mutagenesis. Our study challenged the existing views regarding the number of entry tunnels in the subfamily of olfactory receptors and demonstrated the possible mechanism how the entry tunnels function in odorant recognition.
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Affiliation(s)
- ZhengRong Xu
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Center for Brain Science, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.,Department of Anatomy and Physiology, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - LingNa Guo
- Center for Brain Science, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.,Department of Anatomy and Physiology, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Key Laboratory for Developmental Genes and Human Disease, Ministry of Education, Jiangsu Province High-Tech Key Laboratory for Bio-Medical Research, Institute of Life Sciences, Southeast University, Nanjing, 210096, China
| | - XiaoYun Qian
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - ChenJie Yu
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - ShengJu Li
- Center for Brain Science, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China.,Department of Anatomy and Physiology, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - ChengWen Zhu
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - XiaoFeng Ma
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Hui Li
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - GuangJie Zhu
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - Han Zhou
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China
| | - WenXuan Dai
- Center for Brain Science, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China. .,Department of Anatomy and Physiology, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Qian Li
- Center for Brain Science, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China. .,Department of Anatomy and Physiology, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai, 201210, China.
| | - Xia Gao
- Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China. .,Research Institute of Otolaryngology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, 210008, China.
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6
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Topin J, Bouysset C, Pacalon J, Kim Y, Rhyu MR, Fiorucci S, Golebiowski J. Functional molecular switches of mammalian G protein-coupled bitter-taste receptors. Cell Mol Life Sci 2021; 78:7605-7615. [PMID: 34687318 PMCID: PMC11073308 DOI: 10.1007/s00018-021-03968-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/20/2021] [Accepted: 09/26/2021] [Indexed: 10/20/2022]
Abstract
Bitter taste receptors (TAS2Rs) are a poorly understood subgroup of G protein-coupled receptors (GPCRs). The experimental structure of these receptors has yet to be determined, and key-residues controlling their function remain mostly unknown. We designed an integrative approach to improve comparative modeling of TAS2Rs. Using current knowledge on class A GPCRs and existing experimental data in the literature as constraints, we pinpointed conserved motifs to entirely re-align the amino-acid sequences of TAS2Rs. We constructed accurate homology models of human TAS2Rs. As a test case, we examined the accuracy of the TAS2R16 model with site-directed mutagenesis and in vitro functional assays. This combination of in silico and in vitro results clarifies sequence-function relationships and proposes functional molecular switches that encode agonist sensing and downstream signaling mechanisms within mammalian TAS2Rs sequences.
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Affiliation(s)
- Jérémie Topin
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France.
| | - Cédric Bouysset
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France
| | - Jody Pacalon
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France
| | - Yiseul Kim
- Korea Food Research Institute, 245 Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Mee-Ra Rhyu
- Korea Food Research Institute, 245 Iseo-myeon, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Sébastien Fiorucci
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France.
| | - Jérôme Golebiowski
- Institut de Chimie de Nice UMR7272, Université Côte d'Azur, CNRS, Nice, France
- Department of Brain and Cognitive Sciences, DGIST, 333, Techno JungAng, Daero, HyeongPoong Myeon, Daegu, 711-873, Republic of Korea
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7
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On the human taste perception: Molecular-level understanding empowered by computational methods. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.07.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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8
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Yang MY, Kim SK, Kim D, Liggett SB, Goddard WA. Structures and Agonist Binding Sites of Bitter Taste Receptor TAS2R5 Complexed with Gi Protein and Validated against Experiment. J Phys Chem Lett 2021; 12:9293-9300. [PMID: 34542294 PMCID: PMC8650975 DOI: 10.1021/acs.jpclett.1c02162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bitter taste receptors (TAS2Rs) function in taste perception, but are also expressed in many extraoral tissues, presenting attractive therapeutic targets. TAS2R5s expressed on human airway smooth muscle cells can induce bronchodilation for treating asthma and other obstructive diseases. But TAS2R5s display low agonist affinity and the lack of a 3D structure has hindered efforts to design more active ligands. We report the structure of the activated TAS2R5 coupled to the Gi protein and bound to each of 19 agonists, using computational approaches. These agonists bind to two polar residues in TM3 that are unique for TAS2R5 among 25 TAS2R subtypes. Our predicted results correlate well with experimental results of agonist-receptor signaling coefficients, providing validation of the predicted structure. These results provide highly specific data on how agonists activate TAS2R5, how modifications of ligand structure alter receptor activation, and a guide to structure-based drug design.
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Affiliation(s)
- Moon Young Yang
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA, 91125
| | - Soo-Kyung Kim
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA, 91125
| | - Donghwa Kim
- Department of Internal Medicine, University of South Florida Morsani College of Medicine, Tampa, Florida, 33602
| | - Stephen B. Liggett
- Department of Internal Medicine, University of South Florida Morsani College of Medicine, Tampa, Florida, 33602
- Departments of Medicine and Molecular Pharmacology and Physiology, Medical Engineering, and Internal Medicine, University of South Florida Morsani College of Medicine, Tampa, Florida, 33602
| | - William A. Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA, 91125
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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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Kojima H, Kurihara T, Yoshida M, Haraguchi T, Nishikawa H, Ikegami S, Okuno T, Yamashita T, Nishikawa J, Tsujino H, Arisawa M, Habara M, Ikezaki H, Uchida T. A New Bitterness Evaluation Index Obtained Using the Taste Sensor for 48 Active Pharmaceutical Ingredients of Pediatric Medicines. Chem Pharm Bull (Tokyo) 2021; 69:537-547. [PMID: 34078800 DOI: 10.1248/cpb.c20-01014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The aim of this study was to evaluate bitterness by using "CCDP; Change in concentration-dependent potential" considering dose-dependency of active pharmaceutical ingredients (APIs) as new and useful bitterness evaluation index compared with bitter sensor output value which is conventional bitterness evaluation index for 48 pediatric medicines from the recent edition of the WHO model list of essential medicines for children (7th edn, 2019). Solutions (0.01, 0.03, 0.1 mM) of the compounds were evaluated by an artificial taste sensor using membranes sensitive to bitterness. The dose-response slope of the sensor outputs was defined as CCDP. On the basis of principal component analysis of CCDPs, chlorpromazine hydrochloride, amitriptyline hydrochloride, propranolol hydrochloride, primaquine phosphate and haloperidol were predicted to express the strongest levels of basic bitterness, surpassing that of quinine hydrochloride. Correlation analysis (Fisher's exact tests and multiple regression analysis) was performed to determine the relation between CCDPs and various physicochemical properties participated in hydrophilicity and hydrophobicity. It is revealed that contribution physicochemical factors are different by individual basic bitterness sensor (AC0, AN0 or BT0), and this result becomes the criterion of the sensor choice to evaluate basic bitterness intensity using basic bitterness sensors. Hydrophobic and hydrophilic interactions could be simulated by ligand docking modeling for haloperidol, miconazole and quinine hydrochloride. The pharmaceutical products need a bitterness evaluation in consideration of concentration-dependency to vary in a dose depending on a patient individual. Thus, it was concluded that CCDP correlated to hydrophilicity and hydrophobicity is useful as a bitterness evaluation index of APIs in pediatric medicines.
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Affiliation(s)
- Honami Kojima
- Faculty of Pharmaceutical Science, Mukogawa Women's University
| | - Toshio Kurihara
- Faculty of Pharmaceutical Science, Mukogawa Women's University
| | - Miyako Yoshida
- Faculty of Pharmaceutical Science, Mukogawa Women's University
| | | | | | - Saeri Ikegami
- Faculty of Pharmaceutical Science, Mukogawa Women's University
| | - Takayoshi Okuno
- Faculty of Pharmaceutical Science, Mukogawa Women's University
| | - Taku Yamashita
- Faculty of Pharmaceutical Science, Mukogawa Women's University
| | | | | | | | | | | | - Takahiro Uchida
- Faculty of Pharmaceutical Science, Mukogawa Women's University
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11
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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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12
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Behrens M, Di Pizio A, Redel U, Meyerhof W, Korsching SI. At the Root of T2R Gene Evolution: Recognition Profiles of Coelacanth and Zebrafish Bitter Receptors. Genome Biol Evol 2020; 13:6045956. [PMID: 33355666 PMCID: PMC7851594 DOI: 10.1093/gbe/evaa264] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2020] [Indexed: 12/22/2022] Open
Abstract
The careful evaluation of food is important for survival throughout the animal kingdom, and specialized chemoreceptors have evolved to recognize nutrients, minerals, acids, and many toxins. Vertebrate bitter taste, mediated by the taste receptor type 2 (T2R) family, warns against potentially toxic compounds. During evolution T2R receptors appear first in bony fish, but the functional properties of bony fish T2R receptors are mostly unknown. We performed a phylogenetic analysis showing the “living fossil” coelacanth (Latimeria chalumnae) and zebrafish (Danio rerio) to possess T2R repertoires typical for early-diverged species in the lobe-finned and the ray-finned clade, respectively. Receptors from these two species were selected for heterologous expression assays using a diverse panel of bitter substances. Remarkably, the ligand profile of the most basal coelacanth receptor, T2R01, is identical to that of its ortholog in zebrafish, consistent with functional conservation across >400 Myr of separate evolution. The second coelacanth receptor deorphaned, T2R02, is activated by steroid hormones and bile acids, evolutionary old molecules that are potentially endogenously synthesized agonists for extraoral T2Rs. For zebrafish, we report the presence of both specialized and promiscuous T2R receptors. Moreover, we identified an antagonist for one of the zebrafish receptors suggesting that bitter antagonism contributed to shape this receptor family throughout evolution.
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Affiliation(s)
- Maik Behrens
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany.,Department of Molecular Genetics, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Antonella Di Pizio
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Ulrike Redel
- Department of Molecular Genetics, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Wolfgang Meyerhof
- Department of Molecular Genetics, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany.,Center for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany
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13
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Ahmad R, Dalziel JE. G Protein-Coupled Receptors in Taste Physiology and Pharmacology. Front Pharmacol 2020; 11:587664. [PMID: 33390961 PMCID: PMC7774309 DOI: 10.3389/fphar.2020.587664] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/09/2020] [Indexed: 12/14/2022] Open
Abstract
Heterotrimeric G protein-coupled receptors (GPCRs) comprise the largest receptor family in mammals and are responsible for the regulation of most physiological functions. Besides mediating the sensory modalities of olfaction and vision, GPCRs also transduce signals for three basic taste qualities of sweet, umami (savory taste), and bitter, as well as the flavor sensation kokumi. Taste GPCRs reside in specialised taste receptor cells (TRCs) within taste buds. Type I taste GPCRs (TAS1R) form heterodimeric complexes that function as sweet (TAS1R2/TAS1R3) or umami (TAS1R1/TAS1R3) taste receptors, whereas Type II are monomeric bitter taste receptors or kokumi/calcium-sensing receptors. Sweet, umami and kokumi receptors share structural similarities in containing multiple agonist binding sites with pronounced selectivity while most bitter receptors contain a single binding site that is broadly tuned to a diverse array of bitter ligands in a non-selective manner. Tastant binding to the receptor activates downstream secondary messenger pathways leading to depolarization and increased intracellular calcium in TRCs, that in turn innervate the gustatory cortex in the brain. Despite recent advances in our understanding of the relationship between agonist binding and the conformational changes required for receptor activation, several major challenges and questions remain in taste GPCR biology that are discussed in the present review. In recent years, intensive integrative approaches combining heterologous expression, mutagenesis and homology modeling have together provided insight regarding agonist binding site locations and molecular mechanisms of orthosteric and allosteric modulation. In addition, studies based on transgenic mice, utilizing either global or conditional knock out strategies have provided insights to taste receptor signal transduction mechanisms and their roles in physiology. However, the need for more functional studies in a physiological context is apparent and would be enhanced by a crystallized structure of taste receptors for a more complete picture of their pharmacological mechanisms.
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Affiliation(s)
- Raise Ahmad
- Food Nutrition and Health Team, Food and Bio-based Products Group, AgResearch, Palmerston North, New Zealand
| | - Julie E Dalziel
- Food Nutrition and Health Team, Food and Bio-based Products Group, AgResearch, Palmerston North, New Zealand
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14
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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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15
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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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16
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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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17
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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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18
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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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19
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Baldessari F, Capelli R, Carloni P, Giorgetti A. Coevolutionary data-based interaction networks approach highlighting key residues across protein families: The case of the G-protein coupled receptors. Comput Struct Biotechnol J 2020; 18:1153-1159. [PMID: 32489528 PMCID: PMC7260681 DOI: 10.1016/j.csbj.2020.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 12/26/2022] Open
Abstract
We present an approach that, by integrating structural data with Direct Coupling Analysis, is able to pinpoint most of the interaction hotspots (i.e. key residues for the biological activity) across very sparse protein families in a single run. An application to the Class A G-protein coupled receptors (GPCRs), both in their active and inactive states, demonstrates the predictive power of our approach. The latter can be easily extended to any other kind of protein family, where it is expected to highlight most key sites involved in their functional activity.
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Affiliation(s)
- Filippo Baldessari
- Department of Biotechnology, Università di Verona, Ca Vignal 1, strada Le Grazie 15, I-37134 Verona, Italy
| | - Riccardo Capelli
- Computational Biomedicine Section, IAS-5/INM-9, Forschungzentrum Jülich, Wilhelm-Johnen-straße, D-52425 Jülich, Germany
| | - Paolo Carloni
- Computational Biomedicine Section, IAS-5/INM-9, Forschungzentrum Jülich, Wilhelm-Johnen-straße, D-52425 Jülich, Germany
| | - Alejandro Giorgetti
- Department of Biotechnology, Università di Verona, Ca Vignal 1, strada Le Grazie 15, I-37134 Verona, Italy
- Computational Biomedicine Section, IAS-5/INM-9, Forschungzentrum Jülich, Wilhelm-Johnen-straße, D-52425 Jülich, Germany
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20
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Okuno T, Morimoto S, Nishikawa H, Haraguchi T, Kojima H, Tsujino H, Arisawa M, Yamashita T, Nishikawa J, Yoshida M, Habara M, Ikezaki H, Uchida T. Bitterness-Suppressing Effect of Umami Dipeptides and Their Constituent Amino Acids on Diphenhydramine: Evaluation by Gustatory Sensation and Taste Sensor Testing. Chem Pharm Bull (Tokyo) 2020; 68:234-243. [DOI: 10.1248/cpb.c19-00736] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Takayoshi Okuno
- School of Pharmaceutical Sciences, Mukogawa Women’s University
| | - Shiori Morimoto
- School of Pharmaceutical Sciences, Mukogawa Women’s University
| | | | | | - Honami Kojima
- School of Pharmaceutical Sciences, Mukogawa Women’s University
| | | | | | - Taku Yamashita
- School of Pharmaceutical Sciences, Mukogawa Women’s University
| | | | - Miyako Yoshida
- School of Pharmaceutical Sciences, Mukogawa Women’s University
| | | | | | - Takahiro Uchida
- School of Pharmaceutical Sciences, Mukogawa Women’s University
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21
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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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22
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Di Pizio A, Waterloo LAW, Brox R, Löber S, Weikert D, Behrens M, Gmeiner P, Niv MY. Rational design of agonists for bitter taste receptor TAS2R14: from modeling to bench and back. Cell Mol Life Sci 2020; 77:531-542. [PMID: 31236627 PMCID: PMC11104859 DOI: 10.1007/s00018-019-03194-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 06/11/2019] [Accepted: 06/14/2019] [Indexed: 12/15/2022]
Abstract
Human bitter taste receptors (TAS2Rs) are a subfamily of 25 G protein-coupled receptors that mediate bitter taste perception. TAS2R14 is the most broadly tuned bitter taste receptor, recognizing a range of chemically diverse agonists with micromolar-range potency. The receptor is expressed in several extra-oral tissues and is suggested to have physiological roles related to innate immune responses, male fertility, and cancer. Higher potency ligands are needed to investigate TAS2R14 function and to modulate it for future clinical applications. Here, a structure-based modeling approach is described for the design of TAS2R14 agonists beginning from flufenamic acid, an approved non-steroidal anti-inflammatory analgesic that activates TAS2R14 at sub-micromolar concentrations. Structure-based molecular modeling was integrated with experimental data to design new TAS2R14 agonists. Subsequent chemical synthesis and in vitro profiling resulted in new TAS2R14 agonists with improved potency compared to the lead. The integrated approach provides a validated and refined structural model of ligand-TAS2R14 interactions and a general framework for structure-based discovery in the absence of closely related experimental structures.
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Affiliation(s)
- Antonella Di Pizio
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science and Nutrition, The Hebrew University, Rehovot, Israel
- Section In Silico Biology & Machine Learning, Leibniz-Institute for Food Systems Biology at the Technical University of Munich, 85354, Freising, Germany
| | - Lukas A W Waterloo
- Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Regine Brox
- Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
- Department of Transfusion Medicine and Haemostaseology, University Hospital, Erlangen, Germany
| | - Stefan Löber
- Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Dorothee Weikert
- Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany
| | - Maik Behrens
- Section Chemoreception and Biosignals, Leibniz-Institute for Food Systems Biology at the Technical University of Munich, 85354, Freising, Germany.
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Erlangen, Germany.
| | - Masha Y Niv
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science and Nutrition, The Hebrew University, Rehovot, Israel.
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23
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Barroso da Silva FL, Carloni P, Cheung D, Cottone G, Donnini S, Foegeding EA, Gulzar M, Jacquier JC, Lobaskin V, MacKernan D, Mohammad Hosseini Naveh Z, Radhakrishnan R, Santiso EE. Understanding and Controlling Food Protein Structure and Function in Foods: Perspectives from Experiments and Computer Simulations. Annu Rev Food Sci Technol 2020; 11:365-387. [PMID: 31951485 DOI: 10.1146/annurev-food-032519-051640] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The structure and interactions of proteins play a critical role in determining the quality attributes of many foods, beverages, and pharmaceutical products. Incorporating a multiscale understanding of the structure-function relationships of proteins can provide greater insight into, and control of, the relevant processes at play. Combining data from experimental measurements, human sensory panels, and computer simulations through machine learning allows the construction of statistical models relating nanoscale properties of proteins to the physicochemical properties, physiological outcomes, and tastes of foods. This review highlights several examples of advanced computer simulations at molecular, mesoscale, and multiscale levels that shed light on the mechanisms at play in foods, thereby facilitating their control. It includes a practical simulation toolbox for those new to in silico modeling.
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Affiliation(s)
- Fernando Luís Barroso da Silva
- School of Pharmaceutical Sciences at Ribeirão Preto, University of São Paulo, BR-14040-903, Ribeirão Preto, São Paulo, Brazil
| | - Paolo Carloni
- Institute for Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, 52425 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52062 Aachen, Germany
| | - David Cheung
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
| | - Grazia Cottone
- Department of Physics and Chemistry, University of Palermo, 90128 Palermo, Italy
| | - Serena Donnini
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä 40014, Finland
| | - E Allen Foegeding
- Department of Food, Bioprocessing, & Nutrition Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Muhammad Gulzar
- UCD School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland
| | | | | | - Donal MacKernan
- UCD School of Physics, University College Dublin, Dublin 4, Ireland
| | | | - Ravi Radhakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, USA
| | - Erik E Santiso
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695, USA
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24
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Shaik FA, Jaggupilli A, Chelikani P. Highly conserved intracellular H208 residue influences agonist selectivity in bitter taste receptor T2R14. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:183057. [PMID: 31493373 DOI: 10.1016/j.bbamem.2019.183057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/23/2019] [Accepted: 08/26/2019] [Indexed: 11/19/2022]
Abstract
Bitter taste receptors (T2Rs) are a specialized class of cell membrane receptors of the G protein-coupled receptor family and perform a crucial role in chemosensation. The 25 T2Rs in humans are activated by structurally diverse ligands of plant, animal and microbial origin. The mechanisms of activation of these receptors are poorly understood. Therefore, identification of structural determinants of T2Rs that regulate its efficacy could be beneficial in understanding the molecular mechanisms of T2R activation. In this work, we characterized a highly conserved histidine (H208), present at TM5-ICL3 region of T2R14 and its role in agonist-induced T2R14 signaling. Surprisingly, mutation of the conserved H208 (H208A) did not result in increased basal activity of T2R14, in contrast to similar H206A mutation in T2R4 that showed constitutive or basal activity. However, H208A mutation in T2R14 resulted in an increase in agonist-induced efficacy for Flufenamic acid (FFA). Interestingly, H208A did not affect the potency of another T2R14 agonist Diphenhydramine (DPH). The H208R compensatory mutation showed FFA response similar to wild-type T2R14. Molecular modeling suggests a FFA-induced shift in TM3 and TM5 helices of H208A, which changes the network of interactions connecting TM5-ICL3-TM6. This report identifies a crucial residue on the intracellular surface of T2Rs that is involved in bitter ligand selectivity. It also highlights the varied roles carried out by some conserved residues in different T2Rs.
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Affiliation(s)
- Feroz Ahmed Shaik
- Manitoba Chemosensory Biology Research Group, Department of Oral Biology, University of Manitoba, Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Appalaraju Jaggupilli
- Manitoba Chemosensory Biology Research Group, Department of Oral Biology, University of Manitoba, Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada
| | - Prashen Chelikani
- Manitoba Chemosensory Biology Research Group, Department of Oral Biology, University of Manitoba, Children's Hospital Research Institute of Manitoba, Winnipeg, MB, Canada.
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25
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Luo M, Ni K, Jin Y, Yu Z, Deng L. Toward the Identification of Extra-Oral TAS2R Agonists as Drug Agents for Muscle Relaxation Therapies via Bioinformatics-Aided Screening of Bitter Compounds in Traditional Chinese Medicine. Front Physiol 2019; 10:861. [PMID: 31379593 PMCID: PMC6647893 DOI: 10.3389/fphys.2019.00861] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/20/2019] [Indexed: 12/29/2022] Open
Abstract
Significant advances have been made in the past decade in mapping the distributions and the physiological functions of extra-oral bitter taste receptors (TAS2Rs) in non-gustatory tissues. In particular, it has been found that TAS2Rs are expressed in various muscle tissues and activation of TAS2Rs can lead to muscle cell relaxation, which suggests that TAS2Rs may be important new targets in muscle relaxation therapy for various muscle-related diseases. So far, however, there is a lack of potent extra-oral TAS2R agonists that can be used as novel drug agents in muscle relaxation therapies. Interestingly, traditional Chinese medicine (TCM) often characterizes a drug’s property in terms of five distinct flavors (bitter, sweet, sour, salty, and pungent) according to its taste and function, and commonly regards “bitterness” as an intrinsic property of “good medicine.” In addition, many bitter flavored TCM are known in practice to cause muscle relaxation after long term use, and in lab experiments the compounds identified from some bitter flavored TCM do activate TAS2Rs and thus relax muscle cells. Therefore, it is highly possible to discover very useful extra-oral TAS2R agonists for muscle relaxation therapies among the abundant bitter compounds used in bitter flavored TCM. With this perspective, we reviewed in literature the distribution of TAS2Rs in different muscle systems with a focus on the map of bitter flavored TCM which can regulate muscle contractility and related functional chemical components. We also reviewed the recently established databases of TCM chemical components and the bioinformatics software which can be used for high-throughput screening and data mining of the chemical components associated with bitter flavored TCM. All together, we aim to present a knowledge-based approach and technological platform for identification or discovery of extra-oral TAS2R agonists that can be used as novel drug agents for muscle relaxation therapies through screening and evaluation of chemical compounds used in bitter flavored TCM.
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Affiliation(s)
- Mingzhi Luo
- Changzhou Key Laboratory of Respiratory Medical Engineering, Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, China
| | - Kai Ni
- Changzhou Key Laboratory of Respiratory Medical Engineering, Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, China
| | - Yang Jin
- Bioengineering College, Chongqing University, Chongqing, China
| | - Zifan Yu
- Changzhou Key Laboratory of Respiratory Medical Engineering, Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, China
| | - Linhong Deng
- Changzhou Key Laboratory of Respiratory Medical Engineering, Institute of Biomedical Engineering and Health Sciences, Changzhou University, Changzhou, China
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26
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Ntie-Kang F. Mechanistic role of plant-based bitter principles and bitterness prediction for natural product studies I: Database and methods. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2018-0117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
This chapter discusses the rationale behind the bitter sensation elicited by chemical compounds, focusing on natural products. Emphasis has been placed on a brief presentation of BitterDB (the database of bitter compounds), along with available methods for the prediction of bitterness in compounds. The fundamental basis for explaining bitterness has been provided, based on the structural features of human bitter taste receptors and have been used to shed light on the mechanistic role of a few out of the 25 known human taste receptors to provide the foundation for understanding how bitter compounds interact with their receptors. Some case studies of ligand-based prediction models based on 2D fingerprints and 3D pharmacophores, along with machine learning methods have been provided. The chapter closes with an attempt to establish the relationship between bitterness and toxicity.
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27
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Fierro F, Giorgetti A, Carloni P, Meyerhof W, Alfonso-Prieto M. Dual binding mode of "bitter sugars" to their human bitter taste receptor target. Sci Rep 2019; 9:8437. [PMID: 31186454 PMCID: PMC6560132 DOI: 10.1038/s41598-019-44805-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/22/2019] [Indexed: 12/21/2022] Open
Abstract
The 25 human bitter taste receptors (hTAS2Rs) are responsible for detecting bitter molecules present in food, and they also play several physiological and pathological roles in extraoral compartments. Therefore, understanding their ligand specificity is important both for food research and for pharmacological applications. Here we provide a molecular insight into the exquisite molecular recognition of bitter β-glycopyranosides by one of the members of this receptor subclass, hTAS2R16. Most of its agonists have in common the presence of a β-glycopyranose unit along with an extremely structurally diverse aglycon moiety. This poses the question of how hTAS2R16 can recognize such a large number of "bitter sugars". By means of hybrid molecular mechanics/coarse grained molecular dynamics simulations, here we show that the three hTAS2R16 agonists salicin, arbutin and phenyl-β-D-glucopyranoside interact with the receptor through a previously unrecognized dual binding mode. Such mechanism may offer a seamless way to fit different aglycons inside the binding cavity, while maintaining the sugar bound, similar to the strategy used by several carbohydrate-binding lectins. Our prediction is validated a posteriori by comparison with mutagenesis data and also rationalizes a wealth of structure-activity relationship data. Therefore, our findings not only provide a deeper molecular characterization of the binding determinants for the three ligands studied here, but also give insights applicable to other hTAS2R16 agonists. Together with our results for other hTAS2Rs, this study paves the way to improve our overall understanding of the structural determinants of ligand specificity in bitter taste receptors.
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Affiliation(s)
- Fabrizio Fierro
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany
- Department of Biology, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - 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
- JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany
- JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany
- Department of Physics, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
- VNU Key Laboratory "Multiscale Simulation of Complex Systems", VNU University of Science, Vietnam National University, Hanoi, Vietnam
| | - Wolfgang Meyerhof
- Center for Integrative Physiology and Molecular Medicine (CIPMM), Saarland University, Homburg, Germany
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Jülich, Germany.
- JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, Jülich, 52425, Germany.
- Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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28
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Utilization of Biased G Protein-Coupled ReceptorSignaling towards Development of Safer andPersonalized Therapeutics. Molecules 2019; 24:molecules24112052. [PMID: 31146474 PMCID: PMC6600667 DOI: 10.3390/molecules24112052] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/19/2019] [Accepted: 05/24/2019] [Indexed: 12/12/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are involved in a wide variety of physiological processes. Therefore, approximately 40% of currently prescribed drugs have targeted this receptor family. Discovery of β-arrestin mediated signaling and also separability of G protein and β-arrestin signaling pathways have switched the research focus in the GPCR field towards development of biased ligands, which provide engagement of the receptor with a certain effector, thus enriching a specific signaling pathway. In this review, we summarize possible factors that impact signaling profiles of GPCRs such as oligomerization, drug treatment, disease conditions, genetic background, etc. along with relevant molecules that can be used to modulate signaling properties of GPCRs such as allosteric or bitopic ligands, ions, aptamers and pepducins. Moreover, we also discuss the importance of inclusion of pharmacogenomics and molecular dynamics simulations to achieve a holistic understanding of the relation between genetic background and structure and function of GPCRs and GPCR-related proteins. Consequently, specific downstream signaling pathways can be enriched while those that bring unwanted side effects can be prevented on a patient-specific basis. This will improve studies that centered on development of safer and personalized therapeutics, thus alleviating the burden on economy and public health.
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29
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Alfonso-Prieto M, Navarini L, Carloni P. Understanding Ligand Binding to G-Protein Coupled Receptors Using Multiscale Simulations. Front Mol Biosci 2019; 6:29. [PMID: 31131282 PMCID: PMC6510167 DOI: 10.3389/fmolb.2019.00029] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 04/11/2019] [Indexed: 12/18/2022] Open
Abstract
Human G-protein coupled receptors (GPCRs) convey a wide variety of extracellular signals inside the cell and they are one of the main targets for pharmaceutical intervention. Rational drug design requires structural information on these receptors; however, the number of experimental structures is scarce. This gap can be filled by computational models, based on homology modeling and docking techniques. Nonetheless, the low sequence identity across GPCRs and the chemical diversity of their ligands may limit the quality of these models and hence refinement using molecular dynamics simulations is recommended. This is the case for olfactory and bitter taste receptors, which constitute the first and third largest GPCR groups and show sequence identities with the available GPCR templates below 20%. We have developed a molecular dynamics approach, based on the combination of molecular mechanics and coarse grained (MM/CG), tailored to study ligand binding in GPCRs. This approach has been applied so far to bitter taste receptor complexes, showing significant predictive power. The protein/ligand interactions observed in the simulations were consistent with extensive mutagenesis and functional data. Moreover, the simulations predicted several binding residues not previously tested, which were subsequently verified by carrying out additional experiments. Comparison of the simulations of two bitter taste receptors with different ligand selectivity also provided some insights into the binding determinants of bitter taste receptors. Although the MM/CG approach has been applied so far to a limited number of GPCR/ligand complexes, the excellent agreement of the computational models with the mutagenesis and functional data supports the applicability of this method to other GPCRs for which experimental structures are missing. This is particularly important for the challenging case of GPCRs with low sequence identity with available templates, for which molecular docking shows limited predictive power.
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Affiliation(s)
- Mercedes Alfonso-Prieto
- Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany.,Medical Faculty, Cécile and Oskar Vogt Institute for Brain Research, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Paolo Carloni
- Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany.,Institute for Neuroscience and Medicine INM-11, Forschungszentrum Jülich, Jülich, Germany.,Department of Physics, Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen University, Aachen, Germany.,VNU Key Laboratory "Multiscale Simulation of Complex Systems", VNU University of Science, Vietnam National University, Hanoi, Vietnam
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30
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Alfonso-Prieto M, Giorgetti A, Carloni P. Multiscale simulations on human Frizzled and Taste2 GPCRs. Curr Opin Struct Biol 2019; 55:8-16. [PMID: 30933747 DOI: 10.1016/j.sbi.2019.02.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 02/19/2019] [Indexed: 01/24/2023]
Abstract
Recently, molecular dynamics simulations, from all atom and coarse grained to hybrid methods bridging the two scales, have provided exciting functional insights into class F (Frizzled and Taste2) GPCRs (about 40 members in humans). Findings include: (i) The activation of one member of the Frizzled receptors (FZD4) involves a bending of transmembrane helix TM7 far larger than that in class A GPCRs. (ii) The affinity of an anticancer drug targeting another member (Smoothened receptor) decreases in a specific drug-resistant variant, because the mutation ultimately disrupts the binding cavity and affects TM6. (iii) A novel two-state recognition mechanism explains the very large agonist diversity for at least one member of the Taste2 GPCRs, hTAS2R46.
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Affiliation(s)
- Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Biotechnology, University of Verona, Verona, Italy
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Physics, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany; JARA Institute Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich GmbH, Jülich, Germany; VNU Key Laboratory "Multiscale Simulation of Complex Systems", VNU University of Science, Vietnam National University, Hanoi, Viet Nam.
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31
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Di Pizio A, Behrens M, Krautwurst D. Beyond the Flavour: The Potential Druggability of Chemosensory G Protein-Coupled Receptors. Int J Mol Sci 2019; 20:E1402. [PMID: 30897734 PMCID: PMC6471708 DOI: 10.3390/ijms20061402] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 12/21/2022] Open
Abstract
G protein-coupled receptors (GPCRs) belong to the largest class of drug targets. Approximately half of the members of the human GPCR superfamily are chemosensory receptors, including odorant receptors (ORs), trace amine-associated receptors (TAARs), bitter taste receptors (TAS2Rs), sweet and umami taste receptors (TAS1Rs). Interestingly, these chemosensory GPCRs (csGPCRs) are expressed in several tissues of the body where they are supposed to play a role in biological functions other than chemosensation. Despite their abundance and physiological/pathological relevance, the druggability of csGPCRs has been suggested but not fully characterized. Here, we aim to explore the potential of targeting csGPCRs to treat diseases by reviewing the current knowledge of csGPCRs expressed throughout the body and by analysing the chemical space and the drug-likeness of flavour molecules.
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Affiliation(s)
- Antonella Di Pizio
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, 85354, Germany.
| | - Maik Behrens
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, 85354, Germany.
| | - Dietmar Krautwurst
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, 85354, Germany.
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32
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Tarenzi T, Calandrini V, Potestio R, Carloni P. Open-Boundary Molecular Mechanics/Coarse-Grained Framework for Simulations of Low-Resolution G-Protein-Coupled Receptor-Ligand Complexes. J Chem Theory Comput 2019; 15:2101-2109. [PMID: 30763087 PMCID: PMC6433333 DOI: 10.1021/acs.jctc.9b00040] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Indexed: 12/18/2022]
Abstract
G-protein-coupled receptors (GPCRs) constitute as much as 30% of the overall proteins targeted by FDA-approved drugs. However, paucity of structural experimental information and low sequence identity between members of the family impair the reliability of traditional docking approaches and atomistic molecular dynamics simulations for in silico pharmacological applications. We present here a dual-resolution approach tailored for such low-resolution models. It couples a hybrid molecular mechanics/coarse-grained (MM/CG) scheme, previously developed by us for GPCR-ligand complexes, with a Hamiltonian-based adaptive resolution scheme (H-AdResS) for the solvent. This dual-resolution approach removes potentially inaccurate atomistic details from the model while building a rigorous statistical ensemble-the grand canonical one-in the high-resolution region. We validate the method on a well-studied GPCR-ligand complex, for which the 3D structure is known, against atomistic simulations. This implementation paves the way for future accurate in silico studies of low-resolution ligand/GPCRs models.
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Affiliation(s)
- Thomas Tarenzi
- Computation-based Science and Technology Research Center CaSToRC , The Cyprus Institute , 20 Konstaninou Kavafi Street , 2121 Aglantzia, Nicosia , Cyprus
- Departments of Physics , Faculty of Mathematics, Computer Science and Natural Sciences, Aachen University , Otto-Blumenthal Straße , 52062 Aachen , Germany
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9 , Forschungszentrum Jülich , 52428 Jülich , Germany
| | - Vania Calandrini
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9 , Forschungszentrum Jülich , 52428 Jülich , Germany
| | - Raffaello Potestio
- Department of Physics , University of Trento , via Sommarive 14 Povo , Trento 38123 , Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications , I-38123 Trento , Italy
| | - Paolo Carloni
- Departments of Physics , Faculty of Mathematics, Computer Science and Natural Sciences, Aachen University , Otto-Blumenthal Straße , 52062 Aachen , Germany
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9 , Forschungszentrum Jülich , 52428 Jülich , Germany
- JARA-HPC, Jülich Supercomputing Center , Forschungszentrum Jülich , 52428 Jülich , Germany
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33
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Bushdid C, de March CA, Topin J, Do M, Matsunami H, Golebiowski J. Mammalian class I odorant receptors exhibit a conserved vestibular-binding pocket. Cell Mol Life Sci 2019; 76:995-1004. [PMID: 30599066 PMCID: PMC7313674 DOI: 10.1007/s00018-018-2996-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 12/22/2022]
Abstract
Odorant receptors represent the largest family of mammalian G protein-coupled receptors. Phylogenetically, they are split into two classes (I and II). By analyzing the entire subclass I odorant receptors sequences, we identified two class I-specific and highly conserved motifs. These are predicted to face each other at the extra-cellular portion of the transmembrane domain, forming a vestibular site at the entrance to the orthosteric-binding cavity. Molecular dynamics simulation combined with site-directed mutagenesis and in vitro functional assays confirm the functional role of this vestibular site in ligand-driven activation. Mutations at this part of the receptor differentially affect the receptor response to four agonists. Since this vestibular site is involved in ligand recognition, it could serve ligand design that targets specifically this sub-genome of mammalian odorant receptors.
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Affiliation(s)
- Caroline Bushdid
- Institute of Chemistry - Nice, UMR CNRS 7272, Université Côte d'Azur, Nice, France
| | - Claire A de March
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Jérémie Topin
- Institute of Chemistry - Nice, UMR CNRS 7272, Université Côte d'Azur, Nice, France
| | - Matthew Do
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA.
- Department of Neurobiology, Duke Institute for Brain Sciences, Duke University, Durham, NC, 27710, USA.
| | - Jérôme Golebiowski
- Institute of Chemistry - Nice, UMR CNRS 7272, Université Côte d'Azur, Nice, France.
- Department of Brain and Cognitive Sciences, DGIST, Daegu, Republic of Korea.
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34
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Behrens M, Briand L, de March CA, Matsunami H, Yamashita A, Meyerhof W, Weyand S. Structure-Function Relationships of Olfactory and Taste Receptors. Chem Senses 2019; 43:81-87. [PMID: 29342245 DOI: 10.1093/chemse/bjx083] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The field of chemical senses has made major progress in understanding the cellular mechanisms of olfaction and taste in the past 2 decades. However, the molecular understanding of odor and taste recognition is still lagging far behind and will require solving multiple structures of the relevant full-length receptors in complex with native ligands to achieve this goal. However, the development of multiple complimentary strategies for the structure determination of G protein-coupled receptors (GPCRs) makes this goal realistic. The common conundrum of how multi-specific receptors that recognize a large number of different ligands results in a sensory perception in the brain will only be fully understood by a combination of high-resolution receptor structures and functional studies. This review discusses the first steps on this pathway, including biochemical and physiological assays, forward genetics approaches, molecular modeling, and the first steps towards the structural biology of olfactory and taste receptors.
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Affiliation(s)
- Maik Behrens
- Department of Molecular Genetics, German Institute of Human Nutrition Potsdam-Rehbruecke, Germany
| | - Loïc Briand
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Univ. de Bourgogne- Franche-Comté, France
| | - Claire A de March
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, USA
| | - Hiroaki Matsunami
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, USA
| | - Atsuko Yamashita
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Japan
| | - Wolfgang Meyerhof
- Department of Molecular Genetics, German Institute of Human Nutrition Potsdam-Rehbruecke, Germany
| | - Simone Weyand
- Department of Biochemistry, University of Cambridge, UK
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35
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Abstract
This chapter summarizes the available data about taste receptor functions and their role in perception of food with emphasis on the human system. In addition we illuminate the widespread presence of these receptors throughout the body and discuss some of their extraoral functions. Finally, we describe clinical aspects where taste receptor signaling could be relevant.
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Affiliation(s)
- Jonas C Töle
- Department of Molecular Genetics, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Maik Behrens
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Wolfgang Meyerhof
- Center for Integrative Physiology and Molecular Medicine, Saarland University, Homburg, Germany.
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36
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Role of Extracellular Loops and Membrane Lipids for Ligand Recognition in the Neuronal Adenosine Receptor Type 2A: An Enhanced Sampling Simulation Study. Molecules 2018; 23:molecules23102616. [PMID: 30322034 PMCID: PMC6222423 DOI: 10.3390/molecules23102616] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 01/12/2023] Open
Abstract
Human G-protein coupled receptors (GPCRs) are important targets for pharmaceutical intervention against neurological diseases. Here, we use molecular simulation to investigate the key step in ligand recognition governed by the extracellular domains in the neuronal adenosine receptor type 2A (hA2AR), a target for neuroprotective compounds. The ligand is the high-affinity antagonist (4-(2-(7-amino-2-(furan-2-yl)-[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-ylamino)ethyl)phenol), embedded in a neuronal membrane mimic environment. Free energy calculations, based on well-tempered metadynamics, reproduce the experimentally measured binding affinity. The results are consistent with the available mutagenesis studies. The calculations identify a vestibular binding site, where lipids molecules can actively participate to stabilize ligand binding. Bioinformatic analyses suggest that such vestibular binding site and, in particular, the second extracellular loop, might drive the ligand toward the orthosteric binding pocket, possibly by allosteric modulation. Taken together, these findings point to a fundamental role of the interaction between extracellular loops and membrane lipids for ligands’ molecular recognition and ligand design in hA2AR.
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Allosteric sodium binding cavity in GPR3: a novel player in modulation of Aβ production. Sci Rep 2018; 8:11102. [PMID: 30038319 PMCID: PMC6056553 DOI: 10.1038/s41598-018-29475-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 07/10/2018] [Indexed: 01/01/2023] Open
Abstract
The orphan G-protein coupled receptor 3 (GPR3) belongs to class A G-protein coupled receptors (GPCRs) and is highly expressed in central nervous system neurons. Among other functions, it is likely associated with neuron differentiation and maturation. Recently, GPR3 has also been linked to the production of Aβ peptides in neurons. Unfortunately, the lack of experimental structural information for this receptor hampers a deep characterization of its function. Here, using an in-silico and in-vitro combined approach, we describe, for the first time, structural characteristics of GPR3 receptor underlying its function: the agonist binding site and the allosteric sodium binding cavity. We identified and validated by alanine-scanning mutagenesis the role of three functionally relevant residues: Cys2676.55, Phe1203.36 and Asp2.50. The latter, when mutated into alanine, completely abolished the constitutive and agonist-stimulated adenylate cyclase activity of GPR3 receptor by disrupting its sodium binding cavity. Interestingly, this is correlated with a decrease in Aβ production in a model cell line. Taken together, these results suggest an important role of the allosteric sodium binding site for GPR3 activity and open a possible avenue for the modulation of Aβ production in the Alzheimer’s Disease.
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Nowak S, Di Pizio A, Levit A, Niv MY, Meyerhof W, Behrens M. Reengineering the ligand sensitivity of the broadly tuned human bitter taste receptor TAS2R14. Biochim Biophys Acta Gen Subj 2018; 1862:2162-2173. [PMID: 30009876 DOI: 10.1016/j.bbagen.2018.07.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/10/2018] [Accepted: 07/11/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND In humans, bitterness perception is mediated by ~25 bitter taste receptors present in the oral cavity. Among these receptors three, TAS2R10, TAS2R14 and TAS2R46, exhibit extraordinary wide agonist profiles and hence contribute disproportionally high to the perception of bitterness. Perhaps the most broadly tuned receptor is the TAS2R14, which may represent, because of its prominent expression in extraoral tissues, a receptor of particular importance for the physiological actions of bitter compounds beyond taste. METHODS To investigate how the architecture and composition of the TAS2R14 binding pocket enables specific interactions with a complex array of chemically diverse bitter agonists, we carried out homology modeling and ligand docking experiments, subjected the receptor to point-mutagenesis of binding site residues and performed functional calcium mobilization assays. RESULTS In total, 40 point-mutated receptor constructs were generated to investigate the contribution of 19 positions presumably located in the receptor's binding pocket to activation by 7 different TAS2R14 agonists. All investigated positions exhibited moderate to pronounced agonist selectivity. CONCLUSIONS Since numerous modifications of the TAS2R14 binding pocket resulted in improved responses to individual agonists, we conclude that this bitter taste receptor might represent a suitable template for the engineering of the agonist profile of a chemoreceptive receptor. GENERAL SIGNIFICANCE The detailed structure-function analysis of the highly promiscuous and widely expressed TAS2R14 suggests that this receptor must be considered as potentially frequent target for known and novel drugs including undesired off-effects.
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Affiliation(s)
- Stefanie Nowak
- German Institute of Human Nutrition Potsdam-Rehbruecke, Dept. Molecular Genetics, 14558 Nuthetal, Germany
| | - Antonella Di Pizio
- The Institute of Biochemistry, Food and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University, 76100 Rehovot, Israel; The Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 91904, Israel
| | - Anat Levit
- The Institute of Biochemistry, Food and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University, 76100 Rehovot, Israel; The Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 91904, Israel; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158-2280, USA
| | - Masha Y Niv
- The Institute of Biochemistry, Food and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University, 76100 Rehovot, Israel; The Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 91904, Israel
| | - Wolfgang Meyerhof
- German Institute of Human Nutrition Potsdam-Rehbruecke, Dept. Molecular Genetics, 14558 Nuthetal, Germany; Center for Integrative Physiology and Molecular Medicine, Saarland University, 66421 Homburg, Germany
| | - Maik Behrens
- German Institute of Human Nutrition Potsdam-Rehbruecke, Dept. Molecular Genetics, 14558 Nuthetal, Germany; Leibniz-Institute for Food Systems Biology, Technical University of Munich, 85354 Freising, Germany.
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Di Pizio A, Ben Shoshan-Galeczki Y, Hayes JE, Niv MY. Bitter and sweet tasting molecules: It's complicated. Neurosci Lett 2018; 700:56-63. [PMID: 29679682 DOI: 10.1016/j.neulet.2018.04.027] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 03/22/2018] [Accepted: 04/16/2018] [Indexed: 12/12/2022]
Abstract
"Bitter" and "sweet" are frequently framed in opposition, both functionally and metaphorically, in regard to affective responses, emotion, and nutrition. This oppositional relationship is complicated by the fact that some molecules are simultaneously bitter and sweet. In some cases, a small chemical modification, or a chirality switch, flips the taste from sweet to bitter. Molecules humans describe as bitter are recognized by a 25-member subfamily of class A G-protein coupled receptors (GPCRs) known as TAS2Rs. Molecules humans describe as sweet are recognized by a TAS1R2/TAS1R3 heterodimer of class C GPCRs. Here we characterize the chemical space of bitter and sweet molecules: the majority of bitter compounds show higher hydrophobicity compared to sweet compounds, while sweet molecules have a wider range of sizes. Importantly, recent evidence indicates that TAS1Rs and TAS2Rs are not limited to the oral cavity; moreover, some bitterants are pharmacologically promiscuous, with the hERG potassium channel, cytochrome P450 enzymes, and carbonic anhydrases as common off-targets. Further focus on polypharmacology may unravel new physiological roles for tastant molecules.
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Affiliation(s)
- Antonella Di Pizio
- The Institute of Biochemistry, Food and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University, 76100, Rehovot, Israel; The Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem, 91904, Israel
| | - Yaron Ben Shoshan-Galeczki
- The Institute of Biochemistry, Food and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University, 76100, Rehovot, Israel; The Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem, 91904, Israel
| | - John E Hayes
- Department of Food Science, College of Agricultural Sciences, The Pennsylvania State University, University Park PA, USA
| | - Masha Y Niv
- The Institute of Biochemistry, Food and Nutrition, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University, 76100, Rehovot, Israel; The Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem, 91904, Israel.
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40
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Zheng S, Jiang M, Zhao C, Zhu R, Hu Z, Xu Y, Lin F. e-Bitter: Bitterant Prediction by the Consensus Voting From the Machine-Learning Methods. Front Chem 2018; 6:82. [PMID: 29651416 PMCID: PMC5885771 DOI: 10.3389/fchem.2018.00082] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/12/2018] [Indexed: 11/25/2022] Open
Abstract
In-silico bitterant prediction received the considerable attention due to the expensive and laborious experimental-screening of the bitterant. In this work, we collect the fully experimental dataset containing 707 bitterants and 592 non-bitterants, which is distinct from the fully or partially hypothetical non-bitterant dataset used in the previous works. Based on this experimental dataset, we harness the consensus votes from the multiple machine-learning methods (e.g., deep learning etc.) combined with the molecular fingerprint to build the bitter/bitterless classification models with five-fold cross-validation, which are further inspected by the Y-randomization test and applicability domain analysis. One of the best consensus models affords the accuracy, precision, specificity, sensitivity, F1-score, and Matthews correlation coefficient (MCC) of 0.929, 0.918, 0.898, 0.954, 0.936, and 0.856 respectively on our test set. For the automatic prediction of bitterant, a graphic program “e-Bitter” is developed for the convenience of users via the simple mouse click. To our best knowledge, it is for the first time to adopt the consensus model for the bitterant prediction and develop the first free stand-alone software for the experimental food scientist.
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Affiliation(s)
- Suqing Zheng
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China.,Chemical Biology Research Center, Wenzhou Medical University, Wenzhou, China
| | - Mengying Jiang
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Chengwei Zhao
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Rui Zhu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhicheng Hu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yong Xu
- Center of Chemical Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Fu Lin
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
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41
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Behrens M, Meyerhof W. Vertebrate Bitter Taste Receptors: Keys for Survival in Changing Environments. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:2204-2213. [PMID: 28013542 DOI: 10.1021/acs.jafc.6b04835] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Research on bitter taste receptors has made enormous progress during recent years. Although in the early period after the discovery of this highly interesting receptor family special emphasis was placed on the deorphanization of mainly human bitter taste receptors, the research focus has shifted to sophisticated structure-function analyses, the discovery of small-molecule interactors, and the pharmacological profiling of nonhuman bitter taste receptors. These findings allowed novel perspectives on, for example, evolutionary and ecological questions that have arisen and that are discussed.
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Affiliation(s)
- Maik Behrens
- Department of Molecular Genetics , German Institute of Human Nutrition Potsdam-Rehbruecke , Arthur-Scheunert-Allee 114-116 , 14558 Nuthetal , Germany
| | - Wolfgang Meyerhof
- Department of Molecular Genetics , German Institute of Human Nutrition Potsdam-Rehbruecke , Arthur-Scheunert-Allee 114-116 , 14558 Nuthetal , Germany
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42
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Xue AY, Di Pizio A, Levit A, Yarnitzky T, Penn O, Pupko T, Niv MY. Independent Evolution of Strychnine Recognition by Bitter Taste Receptor Subtypes. Front Mol Biosci 2018; 5:9. [PMID: 29552563 PMCID: PMC5840161 DOI: 10.3389/fmolb.2018.00009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 01/19/2018] [Indexed: 01/02/2023] Open
Abstract
The 25 human bitter taste receptors (hT2Rs) recognize thousands of structurally and chemically diverse bitter substances. The binding modes of human bitter taste receptors hT2R10 and hT2R46, which are responsible for strychnine recognition, were previously established using site-directed mutagenesis, functional assays, and molecular modeling. Here we construct a phylogenetic tree and reconstruct ancestral sequences of the T2R10 and T2R46 clades. We next analyze the binding sites in view of experimental data to predict their ability to recognize strychnine. This analysis suggests that the common ancestor of hT2R10 and hT2R46 is unlikely to bind strychnine in the same mode as either of its two descendants. Estimation of relative divergence times shows that hT2R10 evolved earlier than hT2R46. Strychnine recognition was likely acquired first by the earliest common ancestor of the T2R10 clade before the separation of primates from other mammals, and was highly conserved within the clade. It was probably independently acquired by the common ancestor of T2R43-47 before the homo-ape speciation, lost in most T2Rs within this clade, but enhanced in the hT2R46 after humans diverged from the rest of primates. Our findings suggest hypothetical strychnine T2R receptors in several species, and serve as an experimental guide for further study. Improved understanding of how bitter taste receptors acquire the ability to be activated by particular ligands is valuable for the development of sensors for bitterness and for potential toxicity.
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Affiliation(s)
- Ava Yuan Xue
- Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot, Israel
- The Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Antonella Di Pizio
- Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot, Israel
- The Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anat Levit
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States
| | - Tali Yarnitzky
- Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot, Israel
- Tali Yarnitzky Scientific Consulting, Maccabim-Reut, Israel
| | - Osnat Penn
- Modeling, Analysis and Theory Group, Allen Institute for Brain Science, Seattle, WA, United States
| | - Tal Pupko
- The Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Masha Y. Niv
- Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot, Israel
- The Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, Jerusalem, Israel
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43
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Liu K, Jaggupilli A, Premnath D, Chelikani P. Plasticity of the ligand binding pocket in the bitter taste receptor T2R7. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:991-999. [PMID: 29355483 DOI: 10.1016/j.bbamem.2018.01.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/03/2018] [Accepted: 01/11/2018] [Indexed: 01/12/2023]
Abstract
Bitter taste receptors (T2Rs) are a group of 25 G protein-coupled receptors (GPCRs) in humans. The cognate agonists and the mechanism of ligand binding to the majority of the T2Rs remain unknown. Here we report the first structure-function analysis of T2R7 and study the ability of this receptor to bind to different agonists by site-directed mutagenesis. Screening of ligands for T2R7 in calcium based assays lead to the identification of novel compounds that activate this receptor. Quinine, diphenidol, dextromethorphan and diphenhydramine showed substantial activation of T2R7. Interestingly, these bitter compounds showed different pharmacological characteristics. To investigate the structural features in T2R7 that might contribute to the observed differences in agonist specificities, molecular model guided ligand docking and site-directed mutagenesis was pursued. Amino acids D65, D86, W89, N167, T169, W170, S181, T255 and E271 in the ligand-binding pocket were replaced and the mutants characterized pharmacologically. Our results suggest D86, S181 and W170 present on the extracellular side of transmembrane 3 (TM3), TM5 and in extracellular loop 2 (ECL2) are essential for agonist binding in T2R7. Mutations of these amino acids lead to loss-of-function. We also identified gain-of-function residues that are agonist specific. These results suggest that agonists bind at an extracellular site rather than deep within the TM core involving residues present in both ECL2 and TM helices in T2R7. Similar to majority of the Class A GPCRs, ECL2 in T2R7 plays a significant role in agonist binding and activation.
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Affiliation(s)
- Kun Liu
- From the Manitoba Chemosensory Biology Research Group and Department of Oral Biology, University of Manitoba, Children's Hospital Research Institute of Manitoba (CHRIM), Winnipeg, MB R3E 0W4. Canada
| | - Appalaraju Jaggupilli
- From the Manitoba Chemosensory Biology Research Group and Department of Oral Biology, University of Manitoba, Children's Hospital Research Institute of Manitoba (CHRIM), Winnipeg, MB R3E 0W4. Canada
| | - Dhanaraj Premnath
- From the Manitoba Chemosensory Biology Research Group and Department of Oral Biology, University of Manitoba, Children's Hospital Research Institute of Manitoba (CHRIM), Winnipeg, MB R3E 0W4. Canada
| | - Prashen Chelikani
- From the Manitoba Chemosensory Biology Research Group and Department of Oral Biology, University of Manitoba, Children's Hospital Research Institute of Manitoba (CHRIM), Winnipeg, MB R3E 0W4. Canada.
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44
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Schneider J, Korshunova K, Musiani F, Alfonso-Prieto M, Giorgetti A, Carloni P. Predicting ligand binding poses for low-resolution membrane protein models: Perspectives from multiscale simulations. Biochem Biophys Res Commun 2018; 498:366-374. [PMID: 29409902 DOI: 10.1016/j.bbrc.2018.01.160] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 12/21/2022]
Abstract
Membrane receptors constitute major targets for pharmaceutical intervention. Drug design efforts rely on the identification of ligand binding poses. However, the limited experimental structural information available may make this extremely challenging, especially when only low-resolution homology models are accessible. In these cases, the predictions may be improved by molecular dynamics simulation approaches. Here we review recent developments of multiscale, hybrid molecular mechanics/coarse-grained (MM/CG) methods applied to membrane proteins. In particular, we focus on our in-house MM/CG approach. It is especially tailored for G-protein coupled receptors, the largest membrane receptor family in humans. We show that our MM/CG approach is able to capture the atomistic details of the receptor/ligand binding interactions, while keeping the computational cost low by representing the protein frame and the membrane environment in a highly simplified manner. We close this review by discussing ongoing improvements and challenges of the current implementation of our MM/CG code.
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Affiliation(s)
- Jakob Schneider
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Physics, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany; JARA Institute Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ksenia Korshunova
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Physics, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Biotechnology, University of Verona, Verona, Italy
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich, Germany; Department of Physics, Rheinisch-Westfälische Technische Hochschule Aachen, Aachen, Germany; JARA Institute Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich GmbH, Jülich, Germany; VNU Key Laboratory "Multiscale Simulation of Complex Systems", VNU University of Science, Vietnam National University, Hanoi, Viet Nam.
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45
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Tarenzi T, Calandrini V, Potestio R, Giorgetti A, Carloni P. Open Boundary Simulations of Proteins and Their Hydration Shells by Hamiltonian Adaptive Resolution Scheme. J Chem Theory Comput 2017; 13:5647-5657. [PMID: 28992702 DOI: 10.1021/acs.jctc.7b00508] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The recently proposed Hamiltonian adaptive resolution scheme (H-AdResS) allows the performance of molecular simulations in an open boundary framework. It allows changing, on the fly, the resolution of specific subsets of molecules (usually the solvent), which are free to diffuse between the atomistic region and the coarse-grained reservoir. So far, the method has been successfully applied to pure liquids. Coupling the H-AdResS methodology to hybrid models of proteins, such as the molecular mechanics/coarse-grained (MM/CG) scheme, is a promising approach for rigorous calculations of ligand binding free energies in low-resolution protein models. Toward this goal, here we apply for the first time H-AdResS to two atomistic proteins in dual-resolution solvent, proving its ability to reproduce structural and dynamic properties of both the proteins and the solvent, as obtained from atomistic simulations.
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Affiliation(s)
- Thomas Tarenzi
- Computation-Based Science and Technology Research Center CaSToRC, The Cyprus Institute , 20 Konstantinou Kavafi Street, 2121, Aglantzia, Nicosia, Cyprus
- Department of Physics, Faculty of Mathematics, Computer Science and Natural Sciences, Aachen University , Otto-Blumenthal-Straße, 52074 Aachen, Germany
| | - Vania Calandrini
- Computational Biomedicine, Institute for Advanced Simulation IAS-5, and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
| | - Raffaello Potestio
- Max Planck Institute for Polymer Research , Ackermannweg 10, 55128 Mainz, Germany
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5, and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
- Department of Biotechnology, University of Verona , Ca' Vignal 1, Strada Le Grazie 15, 37134 Verona, Italy
| | - Paolo Carloni
- Department of Physics, Faculty of Mathematics, Computer Science and Natural Sciences, Aachen University , Otto-Blumenthal-Straße, 52074 Aachen, Germany
- Computational Biomedicine, Institute for Advanced Simulation IAS-5, and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich , 52425 Jülich, Germany
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46
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Fierro F, Suku E, Alfonso-Prieto M, Giorgetti A, Cichon S, Carloni P. Agonist Binding to Chemosensory Receptors: A Systematic Bioinformatics Analysis. Front Mol Biosci 2017; 4:63. [PMID: 28932739 PMCID: PMC5592726 DOI: 10.3389/fmolb.2017.00063] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/22/2017] [Indexed: 12/17/2022] Open
Abstract
Human G-protein coupled receptors (hGPCRs) constitute a large and highly pharmaceutically relevant membrane receptor superfamily. About half of the hGPCRs' family members are chemosensory receptors, involved in bitter taste and olfaction, along with a variety of other physiological processes. Hence these receptors constitute promising targets for pharmaceutical intervention. Molecular modeling has been so far the most important tool to get insights on agonist binding and receptor activation. Here we investigate both aspects by bioinformatics-based predictions across all bitter taste and odorant receptors for which site-directed mutagenesis data are available. First, we observe that state-of-the-art homology modeling combined with previously used docking procedures turned out to reproduce only a limited fraction of ligand/receptor interactions inferred by experiments. This is most probably caused by the low sequence identity with available structural templates, which limits the accuracy of the protein model and in particular of the side-chains' orientations. Methods which transcend the limited sampling of the conformational space of docking may improve the predictions. As an example corroborating this, we review here multi-scale simulations from our lab and show that, for the three complexes studied so far, they significantly enhance the predictive power of the computational approach. Second, our bioinformatics analysis provides support to previous claims that several residues, including those at positions 1.50, 2.50, and 7.52, are involved in receptor activation.
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Affiliation(s)
- Fabrizio Fierro
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany
| | - Eda Suku
- Department of Biotechnology, University of VeronaVerona, Italy
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany.,Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University DüsseldorfDüsseldorf, Germany
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany.,Department of Biotechnology, University of VeronaVerona, Italy
| | - Sven Cichon
- Institute of Neuroscience and Medicine INM-1, Forschungszentrum JülichJülich, Germany.,Institute for Human Genetics, Department of Genomics, Life&Brain Center, University of BonnBonn, Germany.,Division of Medical Genetics, Department of Biomedicine, University of BaselBasel, Switzerland
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum JülichJülich, Germany.,Department of Physics, Rheinisch-Westfälische Technische Hochschule AachenAachen, Germany.,VNU Key Laboratory "Multiscale Simulation of Complex Systems", VNU University of Science, Vietnam National UniversityHanoi, Vietnam
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47
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Shelley MY, Selvan ME, Zhao J, Babin V, Liao C, Li J, Shelley JC. A New Mixed All-Atom/Coarse-Grained Model: Application to Melittin Aggregation in Aqueous Solution. J Chem Theory Comput 2017; 13:3881-3897. [PMID: 28636825 PMCID: PMC5551643 DOI: 10.1021/acs.jctc.7b00071] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Indexed: 11/28/2022]
Abstract
We introduce a new mixed resolution, all-atom/coarse-grained approach (AACG), for modeling peptides in aqueous solution and apply it to characterizing the aggregation of melittin. All of the atoms in peptidic components are represented, while a single site is used for each water molecule. With the full flexibility of the peptide retained, our AACG method achieves speedups by a factor of 3-4 for CPU time reduction and another factor of roughly 7 for diffusion. An Ewald treatment permits the inclusion of long-range electrostatic interactions. These characteristics fit well with the requirements for studying peptide association and aggregation, where the system sizes and time scales require considerable computational resources with all-atom models. In particular, AACG is well suited for biologics since changes in peptide shape and long-range electrostatics may play an important role. The application of AACG to melittin, a 26-residue peptide with a well-known propensity to aggregate in solution, serves as an initial demonstration of this technology for studying peptide aggregation. We observed the formation of melittin aggregates during our simulations and characterized the time-evolution of aggregate size distribution, buried surface areas, and residue contacts. Key interactions including π-cation and π-stacking involving TRP19 were also examined. Our AACG simulations demonstrated a clear salt effect and a moderate temperature effect on aggregation and support the molten globule model of melittin aggregates. As a showcase, this work illustrates the useful role for AACG in investigations of peptide aggregation and its potential to guide formulation and design of biologics.
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Affiliation(s)
- Mee Y. Shelley
- Schrödinger,
Inc., 101 SW Main Street,
Suite 1300, Portland, Oregon 97204, United States
| | - Myvizhi Esai Selvan
- Schrödinger,
Inc., 120 W. 45th Street,
17th Floor, New York, New
York 10036, United
States
| | - Jun Zhao
- Cancer
and Inflammation Program, National Cancer
Institute, Frederick, Maryland 21702, United
States
| | - Volodymyr Babin
- Schrödinger,
Inc., 101 SW Main Street,
Suite 1300, Portland, Oregon 97204, United States
| | - Chenyi Liao
- Department
of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
| | - Jianing Li
- Department
of Chemistry, University of Vermont, Burlington, Vermont 05405, United States
| | - John C. Shelley
- Schrödinger,
Inc., 101 SW Main Street,
Suite 1300, Portland, Oregon 97204, United States
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48
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Radu BM, Osculati AMM, Suku E, Banciu A, Tsenov G, Merigo F, Di Chio M, Banciu DD, Tognoli C, Kacer P, Giorgetti A, Radu M, Bertini G, Fabene PF. All muscarinic acetylcholine receptors (M 1-M 5) are expressed in murine brain microvascular endothelium. Sci Rep 2017; 7:5083. [PMID: 28698560 PMCID: PMC5506046 DOI: 10.1038/s41598-017-05384-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/30/2017] [Indexed: 12/25/2022] Open
Abstract
Clinical and experimental studies indicate that muscarinic acetylcholine receptors are potential pharmacological targets for the treatment of neurological diseases. Although these receptors have been described in human, bovine and rat cerebral microvascular tissue, a subtype functional characterization in mouse brain endothelium is lacking. Here, we show that all muscarinic acetylcholine receptors (M1-M5) are expressed in mouse brain microvascular endothelial cells. The mRNA expression of M2, M3, and M5 correlates with their respective protein abundance, but a mismatch exists for M1 and M4 mRNA versus protein levels. Acetylcholine activates calcium transients in brain endothelium via muscarinic, but not nicotinic, receptors. Moreover, although M1 and M3 are the most abundant receptors, only a small fraction of M1 is present in the plasma membrane and functions in ACh-induced Ca2+ signaling. Bioinformatic analyses performed on eukaryotic muscarinic receptors demonstrate a high degree of conservation of the orthosteric binding site and a great variability of the allosteric site. In line with previous studies, this result indicates muscarinic acetylcholine receptors as potential pharmacological targets in future translational studies. We argue that research on drug development should especially focus on the allosteric binding sites of the M1 and M3 receptors.
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Affiliation(s)
- Beatrice Mihaela Radu
- Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, 37134, Italy.,Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, 050095, Romania
| | | | - Eda Suku
- Department of Biotechnology, University of Verona, Verona, 37134, Italy
| | - Adela Banciu
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, 050095, Romania.,Engineering Faculty, Constantin Brancusi' University, Calea Eroilor 30, Targu Jiu, 210135, Romania
| | - Grygoriy Tsenov
- Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, 37134, Italy
| | - Flavia Merigo
- Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, 37134, Italy
| | - Marzia Di Chio
- Department of Public Health and Community Medicine, University of Verona, Verona, 37134, Italy
| | - Daniel Dumitru Banciu
- Department of Anatomy, Animal Physiology and Biophysics, Faculty of Biology, University of Bucharest, Bucharest, 050095, Romania
| | - Cristina Tognoli
- Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, 37134, Italy
| | - Petr Kacer
- National Institute of Mental Health, Klecany, 25067, Czech Republic
| | | | - Mihai Radu
- Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, 37134, Italy. .,Department of Life and Environmental Physics, Horia Hulubei National Institute for Physics and Nuclear Engineering, PO Box MG-6, Reactorului 30, Magurele, 077125, Romania.
| | - Giuseppe Bertini
- Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, 37134, Italy
| | - Paolo Francesco Fabene
- Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, 37134, Italy
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49
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Bahia MS, Nissim I, Niv MY. Bitterness prediction in-silico: A step towards better drugs. Int J Pharm 2017; 536:526-529. [PMID: 28363856 DOI: 10.1016/j.ijpharm.2017.03.076] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 11/30/2022]
Abstract
Bitter taste is innately aversive and thought to protect against consuming poisons. Bitter taste receptors (Tas2Rs) are G-protein coupled receptors, expressed both orally and extra-orally and proposed as novel targets for several indications, including asthma. Many clinical drugs elicit bitter taste, suggesting the possibility of drugs re-purposing. On the other hand, the bitter taste of medicine presents a major compliance problem for pediatric drugs. Thus, efficient tools for predicting, measuring and masking bitterness of active pharmaceutical ingredients (APIs) are required by the pharmaceutical industry. Here we highlight the BitterDB database of bitter compounds and survey the main computational approaches to prediction of bitter taste based on compound's chemical structure. Current in silico bitterness prediction methods provide encouraging results, can be constantly improved using growing experimental data, and present a reliable and efficient addition to the APIs development toolbox.
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Affiliation(s)
- Malkeet Singh Bahia
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel; The Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, 91904, Israel
| | - Ido Nissim
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel; The Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, 91904, Israel
| | - Masha Y Niv
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, 76100, Israel; The Fritz Haber Center for Molecular Dynamics, The Hebrew University of Jerusalem, 91904, Israel.
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50
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Fronik P, Gaiser BI, Sejer Pedersen D. Bitopic Ligands and Metastable Binding Sites: Opportunities for G Protein-Coupled Receptor (GPCR) Medicinal Chemistry. J Med Chem 2017; 60:4126-4134. [DOI: 10.1021/acs.jmedchem.6b01601] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Philipp Fronik
- Department of Drug Design
and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Birgit I. Gaiser
- Department of Drug Design
and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Daniel Sejer Pedersen
- Department of Drug Design
and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
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