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Li N, Li C, Zheng A, Liu W, Shi Y, Jiang M, Xiao Y, Qiu Z, Qiu Y, Jia A. Ultra-high-performance liquid chromatography-mass spectrometry combined with molecular docking and molecular dynamics simulation reveals the source of bitterness in the traditional Chinese medicine formula Runchang-Tongbian. Biomed Chromatogr 2024:e5929. [PMID: 38881323 DOI: 10.1002/bmc.5929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 03/20/2024] [Indexed: 06/18/2024]
Abstract
The Runchang-Tongbian (RCTB) formula is a traditional Chinese medicine (TCM) formula consisting of four herbs, namely Cannabis Fructus (Huomaren), Rehmanniae Radix (Dihuang), Atractylodis Macrocephalae Rhizoma (Baizhu), and Aurantii Fructus (Zhiqiao). It is widely used clinically because of its beneficial effect on constipation. However, its strong bitter taste leads to poor patient compliance. The bitter components of TCM compounds are complex and numerous, and inhibiting the bitter taste of TCM has become a major clinical challenge. Here, we use ultra-high-performance liquid chromatography coupled with mass spectrometry (UPLC-MS) and high-resolution mass spectrometry to identify 59 chemical components in the TCM compound RCTB formula. Next, four bitter taste receptors, TAS2R39, TAS2R14, TAS2R7, and TAS2R5, which are tightly bound to the compounds in RCTB, were screened as molecular docking receptors using the BitterX database. The top-three-scoring receptor-small-molecule complexes for each of the four receptors were selected for molecular dynamics simulation. Finally, seven bitter components were identified, namely six flavonoids (rhoifolin, naringin, poncirin, diosmin, didymin, and narirutin) and one phenylpropanoid (purpureaside C). Thus, we proposed a new method for identifying the bitter components in TCM compounds, which provides a theoretical reference for bitter taste inhibition in TCM compounds.
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Affiliation(s)
- Na Li
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Chunyu Li
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Aizhu Zheng
- The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, China
| | - Weipeng Liu
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Yuwen Shi
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Mengcheng Jiang
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Yusheng Xiao
- Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, China
| | - Zhidong Qiu
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Ye Qiu
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
| | - Ailing Jia
- College of Pharmacy, Changchun University of Chinese Medicine, Changchun, China
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Chandrasekaran S, Gonzalez de Mejia E. Germinated chickpea protein ficin hydrolysate and its peptides inhibited glucose uptake and affected the bitter receptor signaling pathway in vitro. Food Funct 2023; 14:8467-8486. [PMID: 37646191 DOI: 10.1039/d3fo01408h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The objective of this study was to evaluate germinated chickpea protein hydrolysate (GCPH) in vitro for its effect on markers of type 2 diabetes (T2D) and bitter taste receptor expression in intestinal epithelial cells. Protein hydrolysate was obtained using ficin, and the resulting peptides were sequenced using LC-ESI-MS/MS. Caco-2 cells were used to determine glucose uptake and extra-oral bitter receptor activation. Three peptides, VVFW, GEAGR, and FDLPAL, were identified in legumin. FDLPAL was the most potent peptide in molecular docking studies with a DPP-IV energy of affinity of -9.8 kcal mol-1. GCPH significantly inhibited DPP-IV production by Caco-2 cells (IC50 = 2.1 mM). Glucose uptake was inhibited in a dose-dependent manner (IC25 = 2.0 mM). A negative correlation was found between glucose uptake and PLCβ2 expression in Caco-2 cells (R value, -0.62). Thus, GCPH has the potential to be commercialized as a functional ingredient.
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Affiliation(s)
- Subhiksha Chandrasekaran
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Elvira Gonzalez de Mejia
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Tokmakova A, Kim D, Guthrie B, Kim SK, Goddard WA, Liggett SB. Predicted structure and cell signaling of TAS2R14 reveal receptor hyper-flexibility for detecting diverse bitter tastes. iScience 2023; 26:106422. [PMID: 37096045 PMCID: PMC10121769 DOI: 10.1016/j.isci.2023.106422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/24/2023] [Accepted: 03/11/2023] [Indexed: 03/18/2023] Open
Abstract
The 25 human bitter taste receptors (TAS2Rs) are expressed on taste and extra-oral cells representing an integrated chemosensory system. The archetypal TAS2R14 is activated by > 150 topographically diverse agonists, raising the question of how this uncharacteristic accommodation is achieved for these GPCRs. We report the computationally derived structure of TAS2R14 with binding sites and energies for five highly diverse agonists. Remarkably, the binding pocket is the same for all five agonists. The energies derived from molecular dynamics are consistent with experiments determining signal transduction coefficients in live cells. TAS2R14 accommodates agonists through the breaking of a TMD3 H-bond instead of the prototypic strong salt bridge, a TMD1,2,7 interaction different from Class A GPCRs, and agonist-promoted TMD3 salt bridges for high affinity (which we confirmed by receptor mutagenesis). Thus, the broadly tuned TAS2Rs accommodate diverse agonists via a single (vs multiple) binding pocket through unique TM interactions for sensing disparate micro-environments.
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Affiliation(s)
- Alina Tokmakova
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA 91125, USA
| | - Donghwa Kim
- Department of Medicine, University of South Florida Morsani College of Medicine, Tampa, FL 33612, USA
- Center for Personalized Medicine and Genomics, University of South Florida Morsani College of Medicine, Tampa, FL 33612, USA
| | - Brian Guthrie
- Cargill Global Food Research Center, Wayzata, MN 55391, USA
| | - Soo-Kyung Kim
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA 91125, USA
| | - William A. Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA 91125, USA
| | - Stephen B. Liggett
- Department of Medicine, University of South Florida Morsani College of Medicine, Tampa, FL 33612, USA
- Center for Personalized Medicine and Genomics, University of South Florida Morsani College of Medicine, Tampa, FL 33612, USA
- Department of Molecular Pharmacology and Physiology, University of South Florida Morsani College of Medicine, Tampa, FL 33612, USA
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G protein coupling and activation of the metabotropic GABA B heterodimer. Nat Commun 2022; 13:4612. [PMID: 35941188 PMCID: PMC9360005 DOI: 10.1038/s41467-022-32213-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/21/2022] [Indexed: 11/22/2022] Open
Abstract
Metabotropic γ-aminobutyric acid receptor (GABABR), a class C G protein-coupled receptor (GPCR) heterodimer, plays a crucial role in the central nervous system. Cryo-electron microscopy studies revealed a drastic conformational change upon activation and a unique G protein (GP) binding mode. However, little is known about the mechanism for GP coupling and activation for class C GPCRs. Here, we use molecular metadynamics computations to predict the mechanism by which the inactive GP induces conformational changes in the GABABR transmembrane domain (TMD) to form an intermediate pre-activated state. We find that the inactive GP first interacts with TM3, which further leads to the TMD rearrangement and deeper insertion of the α5 helix that causes the Gα subunit to open, releasing GDP, and forming the experimentally observed activated structure. This mechanism provides fresh insights into the mechanistic details of class C GPCRs activation expected to be useful for designing selective agonists and antagonists. Despite its crucial role in the central nervous system, little is known about the activation mechanism of GABAB receptor. Here, the authors predict that the inactive G protein induces conformational changes of the receptor to form an intermediate state.
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Jang J, Kim SK, Guthrie B, Goddard WA. Synergic Effects in the Activation of the Sweet Receptor GPCR Heterodimer for Various Sweeteners Predicted Using Molecular Metadynamics Simulations. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:12250-12261. [PMID: 34613740 DOI: 10.1021/acs.jafc.1c03779] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The sweet taste is elicited by activation of the TAS1R2/1R3 heterodimer G protein-coupled receptor. This is a therapeutic target for treatment of obesity and metabolic dysfunctions. Sweetener blends provide attractive strategies to lower the sugar level while preserving the attractive taste of food. To understand the synergic effect of various sweetener blend combinations of artificial and natural sweeteners, we carried out our molecular dynamics studies using predicted structures of the TAS1R2/1R3 heterodimer and predicted structures for the sweeteners. We used as a measure of activation the intracellular ionic lock distance between transmembrane helices 3 and 6 of TAS1R3. We find that full synergic combinations [rebaudioside A (Reb-A)/acesulfame K and Reb-A/sucralose] and partial synergic combinations (sucralose/acesulfame K) show significantly more negative changes in the free energy compared to single-ligand cases, while a pair known to be suppressive (saccharin and acesulfame K) shows significantly less changes than for the single-ligand case. This study provides an atomistic understanding of the mechanism for synergy and identifies new combinations of sweeteners to reduce the caloric content for treating diseases.
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Affiliation(s)
- Jaewan Jang
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, California 91125, United States
| | - Soo-Kyung Kim
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, California 91125, United States
| | - Brian Guthrie
- Cargill Global Core Research, Wayzata, Minnesota 55391, United States
| | - William A Goddard
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, California 91125, United States
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Mafi A, Kim SK, Chou KC, Güthrie B, Goddard WA. Predicted Structure of Fully Activated Tas1R3/1R3' Homodimer Bound to G Protein and Natural Sugars: Structural Insights into G Protein Activation by a Class C Sweet Taste Homodimer with Natural Sugars. J Am Chem Soc 2021; 143:16824-16838. [PMID: 34585929 DOI: 10.1021/jacs.1c08839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The Tas1R3 G protein-coupled receptor constitutes the main component of sweet taste sensory response in humans via forming a heterodimer with Tas1R2 or a homodimer with Tas1R3. The Tas1R3/1R3' homodimer serves as a low-affinity sweet taste receptor, stimulating gustducin G protein (GGust) signaling in the presence of a high concentration of natural sugars. This provides an additional means to detect the taste of natural sugars, thereby differentiating the flavors between natural sugars and artificial sweeteners. We report here the predicted 3D structure of active state Tas1R3/1R3' homodimer complexed with heterotrimeric GGust and sucrose. We discovered that the GGust makes ionic anchors to intracellular loops 1 and 2 of Tas1R3 while the Gα-α5 helix engages the cytoplasmic region extensively through salt bridge and hydrophobic interactions. We show that in the activation of this complex the Venus flytrap domains of the homodimer undergo a remarkable twist up to ∼100° rotation around the vertical axis to adopt a closed-closed conformation while the intracellular region relaxes to an open-open conformation. We find that binding of sucrose to the homodimer stabilizes a preactivated conformation with a largely open intracellular region that recruits and activates the GGust. Upon activation, the Gα subunit spontaneously opens up the nucleotide-binding site, making nucleotide exchange facile for signaling. This activation of GGust promotes the interdomain twist of the Venus flytrap domains. These structures and transformations could potentially be a basis for the design of new sweeteners with higher activity and less unpleasant flavors.
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Affiliation(s)
- Amirhossein Mafi
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, California 91125, United States
| | - Soo-Kyung Kim
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, California 91125, United States
| | - Keng C Chou
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Brian Güthrie
- Cargill Global Food Research, Wayzata, Minnesota 55391, United States
| | - William A Goddard
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, California 91125, United States
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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: 4] [Impact Index Per Article: 1.3] [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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