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Shenol A, Tenente R, Lückmann M, Frimurer TM, Schwartz TW. Multiple recent HCAR2 structures demonstrate a highly dynamic ligand binding and G protein activation mode. Nat Commun 2024; 15:5364. [PMID: 38918366 PMCID: PMC11199501 DOI: 10.1038/s41467-024-49536-y] [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: 03/25/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024] Open
Abstract
A surprisingly clear picture of the allosteric mechanism connecting G protein-coupled receptor agonists with G protein binding-and back - is revealed by a puzzle of thirty novel 3D structures of the hydroxycarboxylic acid receptor 2 (HCAR2) in complex with eight different orthosteric and a single allosteric agonist. HCAR2 is a sensor of β-hydroxybutyrate, niacin and certain anti-inflammatory drugs. Surprisingly, agonists with and without on-target side effects bound very similarly and in a completely occluded orthosteric binding site. Thus, despite the many structures we are still left with a pertinent need to understand the molecular dynamics of this and similar systems.
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Affiliation(s)
- Aslihan Shenol
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ricardo Tenente
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Lückmann
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas M Frimurer
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thue W Schwartz
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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2
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Shen S, Wu C, Lin G, Yang X, Zhou Y, Zhao C, Miao Z, Tian X, Wang K, Yang Z, Liu Z, Guo N, Li Y, Xia A, Zhou P, Liu J, Yan W, Ke B, Yang S, Shao Z. Structure-based identification of a G protein-biased allosteric modulator of cannabinoid receptor CB1. Proc Natl Acad Sci U S A 2024; 121:e2321532121. [PMID: 38830102 PMCID: PMC11181136 DOI: 10.1073/pnas.2321532121] [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] [Accepted: 04/01/2024] [Indexed: 06/05/2024] Open
Abstract
Cannabis sativa is known for its therapeutic benefit in various diseases including pain relief by targeting cannabinoid receptors. The primary component of cannabis, Δ9-tetrahydrocannabinol (THC), and other agonists engage the orthosteric site of CB1, activating both Gi and β-arrestin signaling pathways. The activation of diverse pathways could result in on-target side effects and cannabis addiction, which may hinder therapeutic potential. A significant challenge in pharmacology is the design of a ligand that can modulate specific signaling of CB1. By leveraging insights from the structure-function selectivity relationship (SFSR), we have identified Gi signaling-biased agonist-allosteric modulators (ago-BAMs). Further, two cryoelectron microscopy (cryo-EM) structures reveal the binding mode of ago-BAM at the extrahelical allosteric site of CB1. Combining mutagenesis and pharmacological studies, we elucidated the detailed mechanism of ago-BAM-mediated biased signaling. Notably, ago-BAM CB-05 demonstrated analgesic efficacy with fewer side effects, minimal drug toxicity and no cannabis addiction in mouse pain models. In summary, our finding not only suggests that ago-BAMs of CB1 provide a potential nonopioid strategy for pain management but also sheds light on BAM identification for GPCRs.
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Affiliation(s)
- Siyuan Shen
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu610212, Sichuan, China
| | - Chao Wu
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
| | - Guifeng Lin
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
| | - Xin Yang
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
| | - Yangli Zhou
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
| | - Chang Zhao
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
| | - Zhuang Miao
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
| | - Xiaowen Tian
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
| | - Kexin Wang
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
| | - Zhiqian Yang
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
| | - Zhiyu Liu
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
| | - Nihong Guo
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
| | - Yueshan Li
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
| | - Anjie Xia
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
| | - Pei Zhou
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
| | - Jingming Liu
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
| | - Wei Yan
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
| | - Bowen Ke
- Department of Anesthesiology, Laboratory of Anesthesia and Critical Care Medicine, National-Local Joint Engineering Research Centre of Translational Medicine of Anesthesiology, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
| | - Shengyong Yang
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu610212, Sichuan, China
| | - Zhenhua Shao
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, Sichuan, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu610212, Sichuan, China
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3
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Wang T, Tang W, Zhu X, Lv Z, Chen J, Li Y, Sun X, Lv H, Gu Q, Li F, Wang J. Molecular activation and G protein coupling selectivity of human succinate receptor SUCR1. Cell Res 2024:10.1038/s41422-024-00968-7. [PMID: 38744983 DOI: 10.1038/s41422-024-00968-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/18/2024] [Indexed: 05/16/2024] Open
Affiliation(s)
- Tianxin Wang
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wenqin Tang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Biomacromolecules, Chinese Academy of Sciences, Beijing, China
| | - Xiaolei Zhu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Biomacromolecules, Chinese Academy of Sciences, Beijing, China
| | - Zhenyu Lv
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Biomacromolecules, Chinese Academy of Sciences, Beijing, China
| | - Jiayan Chen
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yongze Li
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Biomacromolecules, Chinese Academy of Sciences, Beijing, China
| | - Xiaoyu Sun
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Biomacromolecules, Chinese Academy of Sciences, Beijing, China
| | - Haoyu Lv
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Quanchang Gu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Biomacromolecules, Chinese Academy of Sciences, Beijing, China
| | - Fahui Li
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Biomacromolecules, Chinese Academy of Sciences, Beijing, China.
| | - Jiangyun Wang
- iHuman Institute, ShanghaiTech University, Shanghai, China.
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- School of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Biomacromolecules, Chinese Academy of Sciences, Beijing, China.
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4
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Zhang M, Chen T, Lu X, Lan X, Chen Z, Lu S. G protein-coupled receptors (GPCRs): advances in structures, mechanisms, and drug discovery. Signal Transduct Target Ther 2024; 9:88. [PMID: 38594257 PMCID: PMC11004190 DOI: 10.1038/s41392-024-01803-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/19/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024] Open
Abstract
G protein-coupled receptors (GPCRs), the largest family of human membrane proteins and an important class of drug targets, play a role in maintaining numerous physiological processes. Agonist or antagonist, orthosteric effects or allosteric effects, and biased signaling or balanced signaling, characterize the complexity of GPCR dynamic features. In this study, we first review the structural advancements, activation mechanisms, and functional diversity of GPCRs. We then focus on GPCR drug discovery by revealing the detailed drug-target interactions and the underlying mechanisms of orthosteric drugs approved by the US Food and Drug Administration in the past five years. Particularly, an up-to-date analysis is performed on available GPCR structures complexed with synthetic small-molecule allosteric modulators to elucidate key receptor-ligand interactions and allosteric mechanisms. Finally, we highlight how the widespread GPCR-druggable allosteric sites can guide structure- or mechanism-based drug design and propose prospects of designing bitopic ligands for the future therapeutic potential of targeting this receptor family.
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Affiliation(s)
- Mingyang Zhang
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ting Chen
- Department of Cardiology, Changzheng Hospital, Affiliated to Naval Medical University, Shanghai, 200003, China
| | - Xun Lu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaobing Lan
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Ziqiang Chen
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, 200433, China.
| | - Shaoyong Lu
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China.
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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5
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Yadav MK, Sarma P, Maharana J, Ganguly M, Mishra S, Zaidi N, Dalal A, Singh V, Saha S, Mahajan G, Sharma S, Chami M, Banerjee R, Shukla AK. Structure-guided engineering of biased-agonism in the human niacin receptor via single amino acid substitution. Nat Commun 2024; 15:1939. [PMID: 38431681 PMCID: PMC10908815 DOI: 10.1038/s41467-024-46239-2] [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: 07/31/2023] [Accepted: 02/18/2024] [Indexed: 03/05/2024] Open
Abstract
The Hydroxycarboxylic acid receptor 2 (HCA2), also known as the niacin receptor or GPR109A, is a prototypical GPCR that plays a central role in the inhibition of lipolytic and atherogenic activities. Its activation also results in vasodilation that is linked to the side-effect of flushing associated with dyslipidemia drugs such as niacin. GPR109A continues to be a target for developing potential therapeutics in dyslipidemia with minimized flushing response. Here, we present cryo-EM structures of the GPR109A in complex with dyslipidemia drugs, niacin or acipimox, non-flushing agonists, MK6892 or GSK256073, and recently approved psoriasis drug, monomethyl fumarate (MMF). These structures elucidate the binding mechanism of agonists, molecular basis of receptor activation, and insights into biased signaling elicited by some of the agonists. The structural framework also allows us to engineer receptor mutants that exhibit G-protein signaling bias, and therefore, our study may help in structure-guided drug discovery efforts targeting this receptor.
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Affiliation(s)
- Manish K Yadav
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Parishmita Sarma
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Jagannath Maharana
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Manisankar Ganguly
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Sudha Mishra
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Nashrah Zaidi
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Annu Dalal
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Vinay Singh
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Sayantan Saha
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Gargi Mahajan
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Saloni Sharma
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India
| | - Mohamed Chami
- BioEM Lab, Biozentrum, Universität Basel, Basel, Switzerland
| | - Ramanuj Banerjee
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India.
| | - Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, 08016, India.
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6
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Cheng L, Xia F, Li Z, Shen C, Yang Z, Hou H, Sun S, Feng Y, Yong X, Tian X, Qin H, Yan W, Shao Z. Structure, function and drug discovery of GPCR signaling. MOLECULAR BIOMEDICINE 2023; 4:46. [PMID: 38047990 PMCID: PMC10695916 DOI: 10.1186/s43556-023-00156-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/06/2023] [Indexed: 12/05/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are versatile and vital proteins involved in a wide array of physiological processes and responses, such as sensory perception (e.g., vision, taste, and smell), immune response, hormone regulation, and neurotransmission. Their diverse and essential roles in the body make them a significant focus for pharmaceutical research and drug development. Currently, approximately 35% of marketed drugs directly target GPCRs, underscoring their prominence as therapeutic targets. Recent advances in structural biology have substantially deepened our understanding of GPCR activation mechanisms and interactions with G-protein and arrestin signaling pathways. This review offers an in-depth exploration of both traditional and recent methods in GPCR structure analysis. It presents structure-based insights into ligand recognition and receptor activation mechanisms and delves deeper into the mechanisms of canonical and noncanonical signaling pathways downstream of GPCRs. Furthermore, it highlights recent advancements in GPCR-related drug discovery and development. Particular emphasis is placed on GPCR selective drugs, allosteric and biased signaling, polyphamarcology, and antibody drugs. Our goal is to provide researchers with a thorough and updated understanding of GPCR structure determination, signaling pathway investigation, and drug development. This foundation aims to propel forward-thinking therapeutic approaches that target GPCRs, drawing upon the latest insights into GPCR ligand selectivity, activation, and biased signaling mechanisms.
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Affiliation(s)
- Lin Cheng
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
- Department of Otolaryngology Head and Neck Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 610000, China
| | - Fan Xia
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ziyan Li
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Chenglong Shen
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Zhiqian Yang
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Hanlin Hou
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Suyue Sun
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Yuying Feng
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xihao Yong
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Xiaowen Tian
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Hongxi Qin
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Wei Yan
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Zhenhua Shao
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China.
- Tianfu Jincheng Laboratory, Frontiers Medical Center, Chengdu, 610212, China.
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7
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Pan X, Ye F, Ning P, Zhang Z, Li X, Zhang B, Wang Q, Chen G, Gao W, Qiu C, Wu Z, Li J, Zhu L, Xia J, Gong K, Du Y. Structural insights into ligand recognition and selectivity of the human hydroxycarboxylic acid receptor HCAR2. Cell Discov 2023; 9:118. [PMID: 38012147 PMCID: PMC10682194 DOI: 10.1038/s41421-023-00610-7] [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: 03/11/2023] [Accepted: 09/28/2023] [Indexed: 11/29/2023] Open
Abstract
Hydroxycarboxylic acid receptor 2 (HCAR2) belongs to the family of class A G protein-coupled receptors with key roles in regulating lipolysis and free fatty acid formation in humans. It is deeply involved in many pathophysiological processes and serves as an attractive target for the treatment of cardiovascular, neoplastic, autoimmune, neurodegenerative, inflammatory, and metabolic diseases. Here, we report four cryo-EM structures of human HCAR2-Gi1 complexes with or without agonists, including the drugs niacin (2.69 Å) and acipimox (3.23 Å), the highly subtype-specific agonist MK-6892 (3.25 Å), and apo form (3.28 Å). Combined with molecular dynamics simulation and functional analysis, we have revealed the recognition mechanism of HCAR2 for different agonists and summarized the general pharmacophore features of HCAR2 agonists, which are based on three key residues R1113.36, S17945.52, and Y2847.43. Notably, the MK-6892-HCAR2 structure shows an extended binding pocket relative to other agonist-bound HCAR2 complexes. In addition, the key residues that determine the ligand selectivity between the HCAR2 and HCAR3 are also illuminated. Our findings provide structural insights into the ligand recognition, selectivity, activation, and G protein coupling mechanism of HCAR2, which shed light on the design of new HCAR2-targeting drugs for greater efficacy, higher selectivity, and fewer or no side effects.
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Affiliation(s)
- Xin Pan
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
- Department of Cardiology, Central Laboratory, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, China
| | - Fang Ye
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Peiruo Ning
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Zhiyi Zhang
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Xinyu Li
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Binghao Zhang
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Qian Wang
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Geng Chen
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Wei Gao
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Chen Qiu
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Zhangsong Wu
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China
| | - Jiancheng Li
- Instrumental Analysis Center, Shenzhen University, Shenzhen, Guangdong, China
| | - Lizhe Zhu
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China.
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
| | - Kaizheng Gong
- Department of Cardiology, Central Laboratory, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, Jiangsu, China.
| | - Yang Du
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Futian Biomedical Innovation R&D Center, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong, China.
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刘 颖, 马 良, 付 平. [Ketone Body Metabolism and Renal Diseases]. SICHUAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF SICHUAN UNIVERSITY. MEDICAL SCIENCE EDITION 2023; 54:1091-1096. [PMID: 38162055 PMCID: PMC10752776 DOI: 10.12182/20231160202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Indexed: 01/03/2024]
Abstract
A ketogenic diet limits energy supply from glucose and stimulates lipolysis, lipid oxidation, and ketogenesis, resulting in elevated levels of ketone bodies in the bloodstream. Ketone bodies are synthesized in the mitochondrial matrix of liver cells and β-hydroxybutyric acid (BHB) is the most abundant type of ketone body. Herein, we reviewed published findings on the metabolism of ketone bodies and the role of BHB in renal diseases. Through blood circulation, ketone bodies reach metabolically active tissues and provides an alternative source of energy. BHB, being a signaling molecule, mediates various types of cellular signal transduction and participates in the development and progression of many diseases. BHB also has protective and therapeutic effects on a variety of renal diseases. BHB improves the prognosis of renal diseases, such as diabetic kidney disease, chronic kidney disease, acute kidney injury, and polycystic kidney disease, through its antioxidant, anti-inflammatory, and stress response mechanisms. Previous studies have focused on the role of ketone bodies in regulating inflammation and oxidative stress in immune cells. Investigations into the effect of elevated levels of ketone bodies on the metabolism of renal podocytes and tubular cells remain inconclusive. Further research is needed to investigate the effect of BHB on podocyte damage and podocyte senescence in renal diseases.
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Affiliation(s)
- 颖 刘
- 四川大学华西医院 肾脏内科 (成都 610041)Department of Nephrology, West China Hospital, Sichuan University, Chengdu 610041, China
- 四川大学华西医院 肾脏病研究所 (成都 610041)Kidney Research Institute, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 良 马
- 四川大学华西医院 肾脏内科 (成都 610041)Department of Nephrology, West China Hospital, Sichuan University, Chengdu 610041, China
- 四川大学华西医院 肾脏病研究所 (成都 610041)Kidney Research Institute, West China Hospital, Sichuan University, Chengdu 610041, China
| | - 平 付
- 四川大学华西医院 肾脏内科 (成都 610041)Department of Nephrology, West China Hospital, Sichuan University, Chengdu 610041, China
- 四川大学华西医院 肾脏病研究所 (成都 610041)Kidney Research Institute, West China Hospital, Sichuan University, Chengdu 610041, China
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Park JH, Kawakami K, Ishimoto N, Ikuta T, Ohki M, Ekimoto T, Ikeguchi M, Lee DS, Lee YH, Tame JRH, Inoue A, Park SY. Structural basis for ligand recognition and signaling of hydroxy-carboxylic acid receptor 2. Nat Commun 2023; 14:7150. [PMID: 37932263 PMCID: PMC10628104 DOI: 10.1038/s41467-023-42764-8] [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: 03/17/2023] [Accepted: 10/19/2023] [Indexed: 11/08/2023] Open
Abstract
Hydroxycarboxylic acid receptors (HCAR1, HCAR2, and HCAR3) transduce Gi/o signaling upon biding to molecules such as lactic acid, butyric acid and 3-hydroxyoctanoic acid, which are associated with lipolytic and atherogenic activity, and neuroinflammation. Although many reports have elucidated the function of HCAR2 and its potential as a therapeutic target for treating not only dyslipidemia but also neuroimmune disorders such as multiple sclerosis and Parkinson's disease, the structural basis of ligand recognition and ligand-induced Gi-coupling remains unclear. Here we report three cryo-EM structures of the human HCAR2-Gi signaling complex, each bound with different ligands: niacin, acipimox or GSK256073. All three agonists are held in a deep pocket lined by residues that are not conserved in HCAR1 and HCAR3. A distinct hairpin loop at the HCAR2 N-terminus and extra-cellular loop 2 (ECL2) completely enclose the ligand. These structures also reveal the agonist-induced conformational changes propagated to the G-protein-coupling interface during activation. Collectively, the structures presented here are expected to help in the design of ligands specific for HCAR2, leading to new drugs for the treatment of various diseases such as dyslipidemia and inflammation.
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Affiliation(s)
- Jae-Hyun Park
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, 230-0045, Japan
| | - Kouki Kawakami
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Naito Ishimoto
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, 230-0045, Japan
| | - Tatsuya Ikuta
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Mio Ohki
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, 230-0045, Japan
| | - Toru Ekimoto
- Computational Life Science Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama City University, Tsurumi, Yokohama, 230-0045, Japan
| | - Mitsunori Ikeguchi
- Computational Life Science Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama City University, Tsurumi, Yokohama, 230-0045, Japan
- HPC- and AI-driven Drug Development Platform Division, Center for Computational Science, RIKEN, Yokohama, 230-0045, Japan
| | - Dong-Sun Lee
- Bio-Health Materials Core-Facility Center and Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju, 63243, Republic of Korea
| | - Young-Ho Lee
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Ochang, Chungbuk, 28119, Republic of Korea
- Bio-Analytical Science, University of Science and Technology, Daejeon, 34113, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Republic of Korea
- Department of Systems Biotechnology, Chung-Ang University, Gyeonggi, 17546, Republic of Korea
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Miyagi, 980-8578, Japan
| | - Jeremy R H Tame
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, 230-0045, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan.
| | - Sam-Yong Park
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, 230-0045, Japan.
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