1
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Li M, Qing R, Tao F, Xu P, Zhang S. Inhibitory effect of truncated isoforms on GPCR dimerization predicted by combinatorial computational strategy. Comput Struct Biotechnol J 2024; 23:278-286. [PMID: 38173876 PMCID: PMC10762321 DOI: 10.1016/j.csbj.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/07/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
G protein-coupled receptors (GPCRs) play a pivotal role in fundamental biological processes and disease development. GPCR isoforms, derived from alternative splicing, can exhibit distinct signaling patterns. Some highly-truncated isoforms can impact functional performance of full-length receptors, suggesting their intriguing regulatory roles. However, how these truncated isoforms interact with full-length counterparts remains largely unexplored. Here, we computationally investigated the interaction patterns of three human GPCRs from three different classes, ADORA1 (Class A), mGlu2 (Class C) and SMO (Class F) with their respective truncated isoforms because their homodimer structures have been experimentally determined, and they have truncated isoforms deposited and identified at protein level in Uniprot database. Combining the neural network-based AlphaFold2 and two physics-based protein-protein docking tools, we generated multiple complex structures and assessed the binding affinity in the context of atomistic molecular dynamics simulations. Our computational results suggested all the four studied truncated isoforms showed potent binding to their counterparts and overlapping interfaces with homodimers, indicating their strong potential to block homodimerization of their counterparts. Our study offers insights into functional significance of GPCR truncated isoforms and supports the ubiquity of their regulatory roles.
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Affiliation(s)
- Mengke Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Rui Qing
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shuguang Zhang
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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2
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Matsoukas MT, Radomsky T, Panagiotopoulos V, Preez RD, Papadourakis M, Tsianakas K, Millar RP, Anderson RC, Spyroulias GA, Newton CL. Identification of Small-Molecule Antagonists Targeting the Growth Hormone Releasing Hormone Receptor (GHRHR). J Chem Inf Model 2024. [PMID: 39207455 DOI: 10.1021/acs.jcim.4c00577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The growth hormone-releasing hormone receptor (GHRHR) belongs to Class B1 of G protein-coupled receptors (GPCRs). Class B1 GPCR peptides such, as growth hormone-releasing hormone (GHRH), have been proposed to bind in a two-step model, where first the C-terminal region of the peptide interacts with the extracellular domain of the receptor and, subsequently, the N-terminus interacts with the seven transmembrane domain of the receptor, resulting in activation. The GHRHR has recently been highlighted as a promising drug target toward several types of cancer and has been shown to be overexpressed in prostate, breast, pancreatic, and ovarian cancer. Indeed, peptide GHRHR antagonists have displayed promising results in many cancer models. However, no nonpeptide GHRHR-targeting compounds have yet been identified. We have utilized several computational tools to target GHRHR and identify potential small-molecule compounds directed at this receptor. These compounds were validated in vitro using a cyclic adenosine monophosphate (cAMP) ELISA to measure activity at the GHRHR. In vitro results suggest that several of the novel small-molecule compounds could inhibit GHRH-induced cAMP accumulation. Preliminary analysis of the specificity/selectivity of one of the most effective hit compounds indicated that the effect seen was via inhibition of the GHRHR. We therefore report the first nonpeptide antagonists of GHRHR and propose a structural basis for inhibition induced by the compounds, which may assist in the future design of lead GHRHR compounds for treating disorders attributed to dysregulated/aberrant GHRHR signaling.
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Affiliation(s)
| | - Tarryn Radomsky
- Centre for Neuroendocrinology, Department of Immunology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
| | | | - Robin du Preez
- Centre for Neuroendocrinology, Department of Immunology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
| | | | | | - Robert P Millar
- Centre for Neuroendocrinology, Department of Immunology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9JZ, U.K
- Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- School of Medicine, University of St Andrews, St Andrews KY16 9TF, U.K
| | - Ross C Anderson
- Centre for Neuroendocrinology, Department of Immunology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
| | - Georgios A Spyroulias
- University of Patras, School of Health Sciences, Department of Pharmacy, University Campus, Rion, Patras 26500, Greece
| | - Claire L Newton
- Centre for Neuroendocrinology, Department of Immunology, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria 0031, South Africa
- Deanery of Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9JZ, U.K
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3
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Liang Y, Cao M, Zhang S. NeuroPred-ResSE: Predicting neuropeptides by integrating residual block and squeeze-excitation attention mechanism. Anal Biochem 2024; 695:115648. [PMID: 39154878 DOI: 10.1016/j.ab.2024.115648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/31/2024] [Accepted: 08/15/2024] [Indexed: 08/20/2024]
Abstract
Neuropeptides play crucial roles in regulating neurological function acting as signaling molecules, which provide new opportunity for developing drugs for the treatment of neurological diseases. Therefore, it is very necessary to develop a rapid and accurate prediction model for neuropeptides. Although a few prediction tools have been developed, there is room for improvement in prediction accuracy by using deep learning approach. In this paper, we establish the NeuroPred-ResSE model based on residual block and squeeze-excitation attention mechanism. Firstly, we extract multi-features by using one-hot coding based on the NT5CT5 sequence, dipeptide deviation from expected mean and natural vector. Then, we integrate residual block and squeeze-excitation attention mechanism, which can capture and identify the most relevant attribute features. Finally, the accuracies of the training set and test set are 97.16 % and 96.60 % based on the 5-fold cross-validation and independent test, respectively, and other evaluation metrics have also obtained satisfactory results. The experimental results show that the performance of the NeuroPred-ResSE model outperforms those of existing state-of-the-art models, and our model is an effective, intelligent and robust prediction tool. The datasets and source codes are available at https://github.com/yunyunliang88/NeuroPred-ResSE.
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Affiliation(s)
- Yunyun Liang
- School of Science, Xi'an Polytechnic University, Xi'an, 710048, PR China.
| | - Mengyi Cao
- School of Science, Xi'an Polytechnic University, Xi'an, 710048, PR China
| | - Shengli Zhang
- School of Mathematics and Statistics, Xidian University, Xi'an, 710071, PR China
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4
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Shihoya W, Iwama A, Sano FK, Nureki O. Cryo-EM advances in GPCR structure determination. J Biochem 2024; 176:1-10. [PMID: 38498911 DOI: 10.1093/jb/mvae029] [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: 08/01/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/20/2024] Open
Abstract
G-protein-coupled receptors (GPCRs) constitute a prominent superfamily in humans and are categorized into six classes (A-F) that play indispensable roles in cellular communication and therapeutics. Nonetheless, their structural comprehension has been limited by challenges in high-resolution data acquisition. This review highlights the transformative impact of cryogenic electron microscopy (cryo-EM) on the structural determinations of GPCR-G-protein complexes. Specific technologies, such as nanobodies and mini-G-proteins, stabilize complexes and facilitate structural determination. We discuss the structural alterations upon receptor activation in different GPCR classes, revealing their diverse mechanisms. This review highlights the robust foundation for comprehending GPCR function and pave the way for future breakthroughs in drug discovery and therapeutic targeting.
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Affiliation(s)
- Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Aika Iwama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Fumiya K Sano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
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5
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Birgül Iyison N, Abboud C, Abboud D, Abdulrahman AO, Bondar AN, Dam J, Georgoussi Z, Giraldo J, Horvat A, Karoussiotis C, Paz-Castro A, Scarpa M, Schihada H, Scholz N, Güvenc Tuna B, Vardjan N. ERNEST COST action overview on the (patho)physiology of GPCRs and orphan GPCRs in the nervous system. Br J Pharmacol 2024. [PMID: 38825750 DOI: 10.1111/bph.16389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/09/2024] [Accepted: 02/24/2024] [Indexed: 06/04/2024] Open
Abstract
G protein-coupled receptors (GPCRs) are a large family of cell surface receptors that play a critical role in nervous system function by transmitting signals between cells and their environment. They are involved in many, if not all, nervous system processes, and their dysfunction has been linked to various neurological disorders representing important drug targets. This overview emphasises the GPCRs of the nervous system, which are the research focus of the members of ERNEST COST action (CA18133) working group 'Biological roles of signal transduction'. First, the (patho)physiological role of the nervous system GPCRs in the modulation of synapse function is discussed. We then debate the (patho)physiology and pharmacology of opioid, acetylcholine, chemokine, melatonin and adhesion GPCRs in the nervous system. Finally, we address the orphan GPCRs, their implication in the nervous system function and disease, and the challenges that need to be addressed to deorphanize them.
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Affiliation(s)
- Necla Birgül Iyison
- Department of Molecular Biology and Genetics, University of Bogazici, Istanbul, Turkey
| | - Clauda Abboud
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liege, Liege, Belgium
| | - Dayana Abboud
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liege, Liege, Belgium
| | | | - Ana-Nicoleta Bondar
- Faculty of Physics, University of Bucharest, Magurele, Romania
- Forschungszentrum Jülich, Institute for Computational Biomedicine (IAS-5/INM-9), Jülich, Germany
| | - Julie Dam
- Institut Cochin, CNRS, INSERM, Université Paris Cité, Paris, France
| | - Zafiroula Georgoussi
- Laboratory of Cellular Signalling and Molecular Pharmacology, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", Athens, Greece
| | - Jesús Giraldo
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística and Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, Madrid, Spain
- Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anemari Horvat
- Laboratory of Neuroendocrinology - Molecular Cell Physiology, Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Laboratory of Cell Engineering, Celica Biomedical, Ljubljana, Slovenia
| | - Christos Karoussiotis
- Laboratory of Cellular Signalling and Molecular Pharmacology, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", Athens, Greece
| | - Alba Paz-Castro
- Molecular Pharmacology of GPCRs research group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain
| | - Miriam Scarpa
- Division of Clinical Geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Hannes Schihada
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Nicole Scholz
- Rudolf Schönheimer Institute of Biochemistry, Division of General Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Bilge Güvenc Tuna
- Department of Biophysics, School of Medicine, Yeditepe University, Istanbul, Turkey
| | - Nina Vardjan
- Laboratory of Neuroendocrinology - Molecular Cell Physiology, Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Laboratory of Cell Engineering, Celica Biomedical, Ljubljana, Slovenia
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6
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Duan J, He XH, Li SJ, Xu HE. Cryo-electron microscopy for GPCR research and drug discovery in endocrinology and metabolism. Nat Rev Endocrinol 2024; 20:349-365. [PMID: 38424377 DOI: 10.1038/s41574-024-00957-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/29/2024] [Indexed: 03/02/2024]
Abstract
G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors, with many GPCRs having crucial roles in endocrinology and metabolism. Cryogenic electron microscopy (cryo-EM) has revolutionized the field of structural biology, particularly regarding GPCRs, over the past decade. Since the first pair of GPCR structures resolved by cryo-EM were published in 2017, the number of GPCR structures resolved by cryo-EM has surpassed the number resolved by X-ray crystallography by 30%, reaching >650, and the number has doubled every ~0.63 years for the past 6 years. At this pace, it is predicted that the structure of 90% of all human GPCRs will be completed within the next 5-7 years. This Review highlights the general structural features and principles that guide GPCR ligand recognition, receptor activation, G protein coupling, arrestin recruitment and regulation by GPCR kinases. The Review also highlights the diversity of GPCR allosteric binding sites and how allosteric ligands could dictate biased signalling that is selective for a G protein pathway or an arrestin pathway. Finally, the authors use the examples of glycoprotein hormone receptors and glucagon-like peptide 1 receptor to illustrate the effect of cryo-EM on understanding GPCR biology in endocrinology and metabolism, as well as on GPCR-related endocrine diseases and drug discovery.
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Affiliation(s)
- Jia Duan
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Xin-Heng He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shu-Jie Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Traditional Chinese Medicine, Fujian Medical University Union Hospital, Fuzhou, Fujian, China
| | - H Eric Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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7
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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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8
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Matsoukas MT, Panagiotopoulos V, Karageorgos V, Chrousos GP, Venihaki M, Liapakis G. Structural and Functional Insights into CRF Peptides and Their Receptors. BIOLOGY 2024; 13:120. [PMID: 38392338 PMCID: PMC10886364 DOI: 10.3390/biology13020120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/02/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024]
Abstract
Corticotropin-releasing factor or hormone (CRF or CRH) and the urocortins regulate a plethora of physiological functions and are involved in many pathophysiological processes. CRF and urocortins belong to the family of CRF peptides (CRF family), which includes sauvagine, urotensin, and many synthetic peptide and non-peptide CRF analogs. Several of the CRF analogs have shown considerable therapeutic potential in the treatment of various diseases. The CRF peptide family act by interacting with two types of plasma membrane proteins, type 1 (CRF1R) and type 2 (CRF2R), which belong to subfamily B1 of the family B G-protein-coupled receptors (GPCRs). This work describes the structure of CRF peptides and their receptors and the activation mechanism of the latter, which is compared with that of other GPCRs. It also discusses recent structural information that rationalizes the selective binding of various ligands to the two CRF receptor types and the activation of receptors by different agonists.
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Affiliation(s)
- Minos-Timotheos Matsoukas
- Department of Biomedical Engineering, School of Engineering, University of West Attica, 12243 Athens, Greece
| | - Vasilis Panagiotopoulos
- Department of Biomedical Engineering, School of Engineering, University of West Attica, 12243 Athens, Greece
| | - Vlasios Karageorgos
- Department of Pharmacology, Faculty of Medicine, University of Crete, 71003 Heraklion, Greece
| | - George P Chrousos
- University Research Institute of Maternal and Child Health and Precision Medicine and UNESCO, National and Kapodistrian University of Athens, Livadias 8, 11527 Athens, Greece
| | - Maria Venihaki
- Department of Clinical Chemistry, Faculty of Medicine, University of Crete, 71003 Heraklion, Greece
| | - George Liapakis
- Department of Pharmacology, Faculty of Medicine, University of Crete, 71003 Heraklion, Greece
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9
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Cong Z, Zhao F, Li Y, Luo G, Mai Y, Chen X, Chen Y, Lin S, Cai X, Zhou Q, Yang D, Wang MW. Molecular features of the ligand-free GLP-1R, GCGR and GIPR in complex with G s proteins. Cell Discov 2024; 10:18. [PMID: 38346960 PMCID: PMC10861504 DOI: 10.1038/s41421-024-00649-0] [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: 10/09/2023] [Accepted: 01/15/2024] [Indexed: 02/15/2024] Open
Abstract
Class B1 G protein-coupled receptors (GPCRs) are important regulators of many physiological functions such as glucose homeostasis, which is mainly mediated by three peptide hormones, i.e., glucagon-like peptide-1 (GLP-1), glucagon (GCG), and glucose-dependent insulinotropic polypeptide (GIP). They trigger a cascade of signaling events leading to the formation of an active agonist-receptor-G protein complex. However, intracellular signal transducers can also activate the receptor independent of extracellular stimuli, suggesting an intrinsic role of G proteins in this process. Here, we report cryo-electron microscopy structures of the human GLP-1 receptor (GLP-1R), GCG receptor (GCGR), and GIP receptor (GIPR) in complex with Gs proteins without the presence of cognate ligands. These ligand-free complexes share a similar intracellular architecture to those bound by endogenous peptides, in which, the Gs protein alone directly opens the intracellular binding cavity and rewires the extracellular orthosteric pocket to stabilize the receptor in a state unseen before. While the peptide-binding site is partially occupied by the inward folded transmembrane helix 6 (TM6)-extracellular loop 3 (ECL3) juncture of GIPR or a segment of GCGR ECL2, the extracellular portion of GLP-1R adopts a conformation close to the active state. Our findings offer valuable insights into the distinct activation mechanisms of these three important receptors. It is possible that in the absence of a ligand, the intracellular half of transmembrane domain is mobilized with the help of Gs protein, which in turn rearranges the extracellular half to form a transitional conformation, facilitating the entry of the peptide N-terminus.
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Affiliation(s)
- Zhaotong Cong
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Fenghui Zhao
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yang Li
- Shanghai Institute of Infectious Disease and Biosecurity, Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Gan Luo
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yiting Mai
- Research Center for Deepsea Bioresources, Sanya, Hainan, China
| | - Xianyue Chen
- Research Center for Deepsea Bioresources, Sanya, Hainan, China
| | - Yanyan Chen
- Research Center for Deepsea Bioresources, Sanya, Hainan, China
| | - Shi Lin
- Research Center for Deepsea Bioresources, Sanya, Hainan, China
| | - Xiaoqing Cai
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Qingtong Zhou
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai, China.
- Research Center for Deepsea Bioresources, Sanya, Hainan, China.
| | - Dehua Yang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- Research Center for Deepsea Bioresources, Sanya, Hainan, China.
| | - Ming-Wei Wang
- Research Center for Deepsea Bioresources, Sanya, Hainan, China.
- Department of Chemistry, School of Science, The University of Tokyo, Tokyo, Japan.
- School of Pharmacy, Hainan Medical University, Haikou, Hainan, China.
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10
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Mao C, Zhao RJ, Dong YJ, Gao M, Chen LN, Zhang C, Xiao P, Guo J, Qin J, Shen DD, Ji SY, Zang SK, Zhang H, Wang WW, Shen Q, Sun JP, Zhang Y. Conformational transitions and activation of the adhesion receptor CD97. Mol Cell 2024; 84:570-583.e7. [PMID: 38215752 DOI: 10.1016/j.molcel.2023.12.020] [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: 05/17/2023] [Revised: 09/23/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Adhesion G protein-coupled receptors (aGPCRs) are evolutionarily ancient receptors involved in a variety of physiological and pathophysiological processes. Modulators of aGPCR, particularly antagonists, hold therapeutic promise for diseases like cancer and immune and neurological disorders. Hindered by the inactive state structural information, our understanding of antagonist development and aGPCR activation faces challenges. Here, we report the cryo-electron microscopy structures of human CD97, a prototypical aGPCR that plays crucial roles in immune system, in its inactive apo and G13-bound fully active states. Compared with other family GPCRs, CD97 adopts a compact inactive conformation with a constrained ligand pocket. Activation induces significant conformational changes for both extracellular and intracellular sides, creating larger cavities for Stachel sequence binding and G13 engagement. Integrated with functional and metadynamics analyses, our study provides significant mechanistic insights into the activation and signaling of aGPCRs, paving the way for future drug discovery efforts.
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Affiliation(s)
- Chunyou Mao
- Center for Structural Pharmacology and Therapeutics Development, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China.
| | - Ru-Jia Zhao
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Ying-Jun Dong
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Mingxin Gao
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Li-Nan Chen
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Chao Zhang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Peng Xiao
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Jia Guo
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Jiao Qin
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Dan-Dan Shen
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Su-Yu Ji
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Shao-Kun Zang
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Huibing Zhang
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Wei-Wei Wang
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Qingya Shen
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Beijing Key Laboratory of Cardiovascular Receptors Research, Beijing 100191, China.
| | - Yan Zhang
- Center for Structural Pharmacology and Therapeutics Development, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China; Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China; MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou 310058, China.
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11
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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: 6] [Impact Index Per Article: 6.0] [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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12
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Li M, Qing R, Tao F, Xu P, Zhang S. Dynamic Dimerization of Chemokine Receptors and Potential Inhibitory Role of Their Truncated Isoforms Revealed through Combinatorial Prediction. Int J Mol Sci 2023; 24:16266. [PMID: 38003455 PMCID: PMC10671024 DOI: 10.3390/ijms242216266] [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: 10/07/2023] [Revised: 11/03/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Chemokine receptors play crucial roles in fundamental biological processes. Their malfunction may result in many diseases, including cancer, autoimmune diseases, and HIV. The oligomerization of chemokine receptors holds significant functional implications that directly affect their signaling patterns and pharmacological responses. However, the oligomerization patterns of many chemokine receptors remain poorly understood. Furthermore, several chemokine receptors have highly truncated isoforms whose functional role is not yet clear. Here, we computationally show homo- and heterodimerization patterns of four human chemokine receptors, namely CXCR2, CXCR7, CCR2, and CCR7, along with their interaction patterns with their respective truncated isoforms. By combining the neural network-based AlphaFold2 and physics-based protein-protein docking tool ClusPro, we predicted 15 groups of complex structures and assessed the binding affinities in the context of atomistic molecular dynamics simulations. Our results are in agreement with previous experimental observations and support the dynamic and diverse nature of chemokine receptor dimerization, suggesting possible patterns of higher-order oligomerization. Additionally, we uncover the strong potential of truncated isoforms to block homo- and heterodimerization of chemokine receptors, also in a dynamic manner. Our study provides insights into the dimerization patterns of chemokine receptors and the functional significance of their truncated isoforms.
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Affiliation(s)
- Mengke Li
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (R.Q.); (F.T.); (P.X.)
| | - Rui Qing
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (R.Q.); (F.T.); (P.X.)
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (R.Q.); (F.T.); (P.X.)
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (R.Q.); (F.T.); (P.X.)
| | - Shuguang Zhang
- Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
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13
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Li B, Maruszko K, Kim SK, Yang MY, Vo ADP, Goddard WA. Structure and Molecular Mechanism of Signaling for the Glucagon-like Peptide-1 Receptor Bound to Gs Protein and Exendin-P5 Biased Agonist. J Am Chem Soc 2023; 145:20422-20431. [PMID: 37672637 PMCID: PMC10777869 DOI: 10.1021/jacs.3c05996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
The glucagon-like peptide-1 receptor (GLP-1R) is a key regulator of blood glucose and a prime target for the treatment of type II diabetes and obesity with multiple public drugs. Here we present a comprehensive computational analysis of the interactions of the activated GLP-1R-Gs signaling complex with a G protein biased agonist, Exendin P5 (ExP5), which possesses a unique N-terminal sequence responsible for the signal bias. Using a refined all-atom model of the ExP5-GLP-1R-Gs complex in molecular dynamics (MD) simulations, we propose a novel mechanism of conformation transduction in which the unique interaction network of ExP5 N-terminus propagates the binding signal across an array of conserved residues at the transmembrane domain to enhance Gs protein coupling at the cytoplasmic end of the receptor. Our simulations reveal previously unobserved interactions important for activation by ExP5 toward GDP-GTP signaling, providing new insights into the mechanism of class B G protein-coupled receptor (GPCR) signaling. These findings offer a framework for the structure-based design of more effective therapeutics.
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Affiliation(s)
- Bo Li
- Division of Chemistry and Chemical Engineering and Materials Process and Simulation Center, California Institute of Technology, Pasadena, California 91125, United States
| | - Krystyna Maruszko
- Division of Chemistry and Chemical Engineering and Materials Process and Simulation Center, California Institute of Technology, Pasadena, California 91125, United States
| | - Soo-Kyung Kim
- Division of Chemistry and Chemical Engineering and Materials Process and Simulation Center, California Institute of Technology, Pasadena, California 91125, United States
| | - Moon Young Yang
- Division of Chemistry and Chemical Engineering and Materials Process and Simulation Center, California Institute of Technology, Pasadena, California 91125, United States
| | - Amy-Doan P Vo
- Division of Chemistry and Chemical Engineering and Materials Process and Simulation Center, California Institute of Technology, Pasadena, California 91125, United States
| | - William A Goddard
- Division of Chemistry and Chemical Engineering and Materials Process and Simulation Center, California Institute of Technology, Pasadena, California 91125, United States
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14
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Gibadullin R, Kim TW, Tran LML, Gellman SH. Hormone Analogues with Unique Signaling Profiles from Replacement of α-Residue Triads with β/γ Diads. J Am Chem Soc 2023; 145:20539-20550. [PMID: 37697685 PMCID: PMC10588032 DOI: 10.1021/jacs.3c06703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
We have applied an underexplored backbone modification strategy to generate new analogues of peptides that activate two clinically important class B1 G protein-coupled receptors (GPCRs). Most peptide modification strategies involve changing side chains or, less commonly, changing the configuration at side chain-bearing carbons (i.e., l residues replaced by d residues). In contrast, backbone modifications alter the number of backbone atoms and the identities of backbone atoms relative to a poly-α-amino acid backbone. Starting from the peptide agonists PTH(1-34) (the first 34 residues of the parathyroid hormone, used clinically as the drug teriparatide) and glucagon-like peptide-1 (7-36) (GLP-1(7-36)), we replaced native α-residue triads with a diad composed of a β-amino acid residue and a γ-amino acid residue. The β/γ diad retains the number of backbone atoms in the ααα triad. Because the β and γ residue each bear a single side chain, we implemented ααα→βγ replacements at sites that contained a Gly residue (i.e., at α-residue triads that presented only two side chains). All seven of the α/β/γ-peptides derived from PTH(1-34) or GLP-1(7-36) bind to the cognate receptor (the PTHR1 or the GLP-1R), but they vary considerably in their activity profiles. Outcomes include functional mimicry of the all-α agonist, receptor-selective agonist activity, biased agonism, or strong binding with weak activation, which could lead to antagonist development. Collectively, these findings demonstrate that ααα→βγ replacements, which are easily implemented via solid-phase synthesis, can generate peptide hormone analogues that display unique and potentially useful signaling behavior.
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Affiliation(s)
- Ruslan Gibadullin
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Present address: Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Tae Wook Kim
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lauren My-Linh Tran
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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15
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Zhao LH, He Q, Yuan Q, Gu Y, He X, Shan H, Li J, Wang K, Li Y, Hu W, Wu K, Shen J, Xu HE. Conserved class B GPCR activation by a biased intracellular agonist. Nature 2023; 621:635-641. [PMID: 37524305 DOI: 10.1038/s41586-023-06467-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/20/2023] [Indexed: 08/02/2023]
Abstract
Class B G-protein-coupled receptors (GPCRs), including glucagon-like peptide 1 receptor (GLP1R) and parathyroid hormone 1 receptor (PTH1R), are important drug targets1-5. Injectable peptide drugs targeting these receptors have been developed, but orally available small-molecule drugs remain under development6,7. Here we report the high-resolution structure of human PTH1R in complex with the stimulatory G protein (Gs) and a small-molecule agonist, PCO371, which reveals an unexpected binding mode of PCO371 at the cytoplasmic interface of PTH1R with Gs. The PCO371-binding site is totally different from all binding sites previously reported for small molecules or peptide ligands in GPCRs. The residues that make up the PCO371-binding pocket are conserved in class B GPCRs, and a single alteration in PTH2R and two residue alterations in GLP1R convert these receptors to respond to PCO371. Functional assays reveal that PCO371 is a G-protein-biased agonist that is defective in promoting PTH1R-mediated arrestin signalling. Together, these results uncover a distinct binding site for designing small-molecule agonists for PTH1R and possibly other members of the class B GPCRs and define a receptor conformation that is specific only for G-protein activation but not arrestin signalling. These insights should facilitate the design of distinct types of class B GPCR small-molecule agonist for various therapeutic indications.
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MESH Headings
- Humans
- Arrestin/metabolism
- Binding Sites
- GTP-Binding Protein alpha Subunits, Gs/metabolism
- Imidazolidines/pharmacology
- Ligands
- Peptides/pharmacology
- Protein Conformation
- Receptor, Parathyroid Hormone, Type 1/agonists
- Receptor, Parathyroid Hormone, Type 1/classification
- Receptor, Parathyroid Hormone, Type 1/metabolism
- Receptors, G-Protein-Coupled/agonists
- Receptors, G-Protein-Coupled/classification
- Receptors, G-Protein-Coupled/metabolism
- Signal Transduction/drug effects
- Spiro Compounds/pharmacology
- Drug Design
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Affiliation(s)
- Li-Hua Zhao
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Qian He
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qingning Yuan
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yimin Gu
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinheng He
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong Shan
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Junrui Li
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Kai Wang
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yang Li
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wen Hu
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Kai Wu
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Jianhua Shen
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - H Eric Xu
- State Key Laboratory of Drug Research, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
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16
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Vishnoi S, Bhattacharya S, Walsh EM, Okoh GI, Thompson D. Computational Peptide Design Cotargeting Glucagon and Glucagon-like Peptide-1 Receptors. J Chem Inf Model 2023; 63:4934-4947. [PMID: 37523325 PMCID: PMC10428222 DOI: 10.1021/acs.jcim.3c00752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Indexed: 08/02/2023]
Abstract
Peptides are sustainable alternatives to conventional therapeutics for G protein-coupled receptor (GPCR) linked disorders, promising biocompatible and tailorable next-generation therapeutics for metabolic disorders including type-2 diabetes, as agonists of the glucagon receptor (GCGR) and the glucagon-like peptide-1 receptor (GLP-1R). However, single agonist peptides activating GLP-1R to stimulate insulin secretion also suppress obesity-linked glucagon release. Hence, bioactive peptides cotargeting GCGR and GLP-1R may remediate the blood glucose and fatty acid metabolism imbalance, tackling both diabetes and obesity to supersede current monoagonist therapy. Here, we design and model optimized peptide sequences starting from peptide sequences derived from earlier phage-displayed library screening, identifying those with predicted molecular binding profiles for dual agonism of GCGR and GLP-1R. We derive design rules from extensive molecular dynamics simulations based on peptide-receptor binding. Our newly designed coagonist peptide exhibits improved predicted coupled binding affinity for GCGR and GLP-1R relative to endogenous ligands and could in the future be tested experimentally, which may provide superior glycemic and weight loss control.
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Affiliation(s)
- Shubham Vishnoi
- Department
of Physics, Bernal Institute, University
of Limerick, Limerick V94T9PX, Ireland
| | - Shayon Bhattacharya
- Department
of Physics, Bernal Institute, University
of Limerick, Limerick V94T9PX, Ireland
| | | | | | - Damien Thompson
- Department
of Physics, Bernal Institute, University
of Limerick, Limerick V94T9PX, Ireland
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17
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Xiao H, Sun Q, Sun Q. A promising small molecule binding pocket in class B GPCRs: expanding potential for drug development. Signal Transduct Target Ther 2023; 8:313. [PMID: 37567868 PMCID: PMC10421945 DOI: 10.1038/s41392-023-01598-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 08/09/2023] [Indexed: 08/13/2023] Open
Affiliation(s)
- Huan Xiao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu, 610041, China
| | - Qian Sun
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu, 610041, China
- West China Medical Publishers, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Qiu Sun
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University/West China School of Nursing, Sichuan University, Chengdu, 610041, China.
- West China Medical Publishers, West China Hospital, Sichuan University, Chengdu, 610041, China.
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18
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Qian T, Wang H, Xia X, Li Y. Current and emerging methods for probing neuropeptide transmission. Curr Opin Neurobiol 2023; 81:102751. [PMID: 37487399 DOI: 10.1016/j.conb.2023.102751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/23/2023] [Accepted: 06/27/2023] [Indexed: 07/26/2023]
Abstract
Neuropeptides comprise the most diverse category of neurochemicals in the brain, playing critical roles in a wide range of physiological and pathophysiological processes. Monitoring neuropeptides with high spatial and temporal resolution is essential for understanding how peptidergic transmission is regulated throughout the central nervous system. In this review, we provide an overview of current non-optical and optical approaches used to detect neuropeptides, including their design principles, intrinsic properties, and potential limitations. We also highlight the advantages of using G protein‒coupled receptor (GPCR) activation‒based (GRAB) sensors to monitor neuropeptides in vivo with high sensitivity, good specificity, and high spatiotemporal resolution. Finally, we present a promising outlook regarding the development and optimization of new GRAB neuropeptide sensors, as well as their potential applications.
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Affiliation(s)
- Tongrui Qian
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, 100871, China; PKU-IDG/McGovern Institute for Brain Research, Beijing, 100871, China
| | - Huan Wang
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, 100871, China; PKU-IDG/McGovern Institute for Brain Research, Beijing, 100871, China
| | - Xiju Xia
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, 100871, China; PKU-IDG/McGovern Institute for Brain Research, Beijing, 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Yulong Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, 100871, China; PKU-IDG/McGovern Institute for Brain Research, Beijing, 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China; Chinese Institute for Brain Research, Beijing, 102206, China; National Biomedical Imaging Center, Peking University, Beijing, 100871, China.
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19
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Seufert F, Chung YK, Hildebrand PW, Langenhan T. 7TM domain structures of adhesion GPCRs: what's new and what's missing? Trends Biochem Sci 2023; 48:726-739. [PMID: 37349240 DOI: 10.1016/j.tibs.2023.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/05/2023] [Accepted: 05/19/2023] [Indexed: 06/24/2023]
Abstract
Adhesion-type G protein-coupled receptors (aGPCRs) have long resisted approaches to resolve the structural details of their heptahelical transmembrane (7TM) domains. Single-particle cryogenic electron microscopy (cryo-EM) has recently produced aGPCR 7TM domain structures for ADGRD1, ADGRG1, ADGRG2, ADGRG3, ADGRG4, ADGRG5, ADGRF1, and ADGRL3. We review the unique properties, including the position and conformation of their activating tethered agonist (TA) and signaling motifs within the 7TM bundle, that the novel structures have helped to identify. We also discuss questions that the kaleidoscope of novel aGPCR 7TM domain structures have left unanswered. These concern the relative positions, orientations, and interactions of the 7TM and GPCR autoproteolysis-inducing (GAIN) domains with one another. Clarifying their interplay remains an important goal of future structural studies on aGPCRs.
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Affiliation(s)
- Florian Seufert
- Institute of Medical Physics and Biophysics, Medical Faculty, Leipzig University, Härtelstrasse 16-18, 04107 Leipzig, Germany
| | - Yin Kwan Chung
- Rudolf Schönheimer Institute of Biochemistry, Division of General Biochemistry, Medical Faculty, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany
| | - Peter W Hildebrand
- Institute of Medical Physics and Biophysics, Medical Faculty, Leipzig University, Härtelstrasse 16-18, 04107 Leipzig, Germany; Institute of Medical Physics and Biophysics, Charité - Universitätsmedizin Berlin, Berlin, Germany.
| | - Tobias Langenhan
- Rudolf Schönheimer Institute of Biochemistry, Division of General Biochemistry, Medical Faculty, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany.
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20
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Horváth D, Dürvanger Z, K Menyhárd D, Sulyok-Eiler M, Bencs F, Gyulai G, Horváth P, Taricska N, Perczel A. Polymorphic amyloid nanostructures of hormone peptides involved in glucose homeostasis display reversible amyloid formation. Nat Commun 2023; 14:4621. [PMID: 37528104 PMCID: PMC10394066 DOI: 10.1038/s41467-023-40294-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/21/2023] [Indexed: 08/03/2023] Open
Abstract
A large group of hormones are stored as amyloid fibrils in acidic secretion vesicles before they are released into the bloodstream and readopt their functional state. Here, we identify an evolutionarily conserved hexapeptide sequence as the major aggregation-prone region (APR) of gastrointestinal peptides of the glucagon family: xFxxWL. We determine nine polymorphic crystal structures of the APR segments of glucagon-like peptides 1 and 2, and exendin and its derivatives. We follow amyloid formation by CD, FTIR, ThT assays, and AFM. We propose that the pH-dependent changes of the protonation states of glutamate/aspartate residues of APRs initiate switching between the amyloid and the folded, monomeric forms of the hormones. We find that pH sensitivity diminishes in the absence of acidic gatekeepers and amyloid formation progresses over a broad pH range. Our results highlight the dual role of short aggregation core motifs in reversible amyloid formation and receptor binding.
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Affiliation(s)
- Dániel Horváth
- ELKH-ELTE Protein Modeling Research Group ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Zsolt Dürvanger
- ELKH-ELTE Protein Modeling Research Group ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
- Laboratory of Structural Chemistry and Biology ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Dóra K Menyhárd
- ELKH-ELTE Protein Modeling Research Group ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
- Laboratory of Structural Chemistry and Biology ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Máté Sulyok-Eiler
- Laboratory of Structural Chemistry and Biology ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Fruzsina Bencs
- Laboratory of Structural Chemistry and Biology ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Gergő Gyulai
- Laboratory of Interfaces and Nanostructures, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Péter Horváth
- Department of Pharmaceutical Chemistry, Semmelweis University, Hőgyes Endre utca 9, Budapest, 1092, Hungary
| | - Nóra Taricska
- ELKH-ELTE Protein Modeling Research Group ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - András Perczel
- ELKH-ELTE Protein Modeling Research Group ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary.
- Laboratory of Structural Chemistry and Biology ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary.
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21
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Kobayashi K, Kawakami K, Kusakizako T, Tomita A, Nishimura M, Sawada K, Okamoto HH, Hiratsuka S, Nakamura G, Kuwabara R, Noda H, Muramatsu H, Shimizu M, Taguchi T, Inoue A, Murata T, Nureki O. Class B1 GPCR activation by an intracellular agonist. Nature 2023; 618:1085-1093. [PMID: 37286611 PMCID: PMC10307627 DOI: 10.1038/s41586-023-06169-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 05/04/2023] [Indexed: 06/09/2023]
Abstract
G protein-coupled receptors (GPCRs) generally accommodate specific ligands in the orthosteric-binding pockets. Ligand binding triggers a receptor allosteric conformational change that leads to the activation of intracellular transducers, G proteins and β-arrestins. Because these signals often induce adverse effects, the selective activation mechanism for each transducer must be elucidated. Thus, many orthosteric-biased agonists have been developed, and intracellular-biased agonists have recently attracted broad interest. These agonists bind within the receptor intracellular cavity and preferentially tune the specific signalling pathway over other signalling pathways, without allosteric rearrangement of the receptor from the extracellular side1-3. However, only antagonist-bound structures are currently available1,4-6, and there is no evidence to support that biased agonist binding occurs within the intracellular cavity. This limits the comprehension of intracellular-biased agonism and potential drug development. Here we report the cryogenic electron microscopy structure of a complex of Gs and the human parathyroid hormone type 1 receptor (PTH1R) bound to a PTH1R agonist, PCO371. PCO371 binds within an intracellular pocket of PTH1R and directly interacts with Gs. The PCO371-binding mode rearranges the intracellular region towards the active conformation without extracellularly induced allosteric signal propagation. PCO371 stabilizes the significantly outward-bent conformation of transmembrane helix 6, which facilitates binding to G proteins rather than β-arrestins. Furthermore, PCO371 binds within the highly conserved intracellular pocket, activating 7 out of the 15 class B1 GPCRs. Our study identifies a new and conserved intracellular agonist-binding pocket and provides evidence of a biased signalling mechanism that targets the receptor-transducer interface.
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Affiliation(s)
- Kazuhiro Kobayashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kouki Kawakami
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Atsuhiro Tomita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Preferred Networks, Tokyo, Japan
| | - Michihiro Nishimura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Sawada
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki H Okamoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Suzune Hiratsuka
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Gaku Nakamura
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Riku Kuwabara
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Hiroshi Noda
- Research Division, Chugai Pharmaceutical, Shizuoka, Japan
| | | | - Masaru Shimizu
- Research Division, Chugai Pharmaceutical, Shizuoka, Japan
| | - Tomohiko Taguchi
- Laboratory of Organelle Pathophysiology, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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22
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Yuan S, Xia L, Wang C, Wu F, Zhang B, Pan C, Fan Z, Lei X, Stevens RC, Sali A, Sun L, Shui W. Conformational Dynamics of the Activated GLP-1 Receptor-G s Complex Revealed by Cross-Linking Mass Spectrometry and Integrative Structure Modeling. ACS CENTRAL SCIENCE 2023; 9:992-1007. [PMID: 37252352 PMCID: PMC10214531 DOI: 10.1021/acscentsci.3c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Indexed: 05/31/2023]
Abstract
Despite advances in characterizing the structures and functions of G protein-coupled receptors (GPCRs), our understanding of GPCR activation and signaling is still limited by the lack of information on conformational dynamics. It is particularly challenging to study the dynamics of GPCR complexes with their signaling partners because of their transient nature and low stability. Here, by combining cross-linking mass spectrometry (CLMS) with integrative structure modeling, we map the conformational ensemble of an activated GPCR-G protein complex at near-atomic resolution. The integrative structures describe heterogeneous conformations for a high number of potential alternative active states of the GLP-1 receptor-Gs complex. These structures show marked differences from the previously determined cryo-EM structure, especially at the receptor-Gs interface and in the interior of the Gs heterotrimer. Alanine-scanning mutagenesis coupled with pharmacological assays validates the functional significance of 24 interface residue contacts only observed in the integrative structures, yet absent in the cryo-EM structure. Through the integration of spatial connectivity data from CLMS with structure modeling, our study provides a new approach that is generalizable to characterizing the conformational dynamics of GPCR signaling complexes.
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Affiliation(s)
- Shijia Yuan
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Lisha Xia
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenxi Wang
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Fan Wu
- Structure
Therapeutics, South San Francisco, California 94080, United States
| | - Bingjie Zhang
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Chen Pan
- National
Facility for Protein Science in Shanghai, Shanghai Advanced Research
Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Zhiran Fan
- Biocreater
(WuHan) Biotechnology Co., Ltd, Wuhan 430075, China
| | - Xiaoguang Lei
- Beijing
National Laboratory for Molecular Sciences, State Key Laboratory of
Natural and Biomimetic Drugs, Key Laboratory of Bioorganic Chemistry
and Molecular Engineering of Ministry of Education, Department of
Chemical Biology, College of Chemistry and Molecular Engineering,
Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Raymond C. Stevens
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- Structure
Therapeutics, South San Francisco, California 94080, United States
| | - Andrej Sali
- Quantitative
Biosciences Institute, University of California,
San Francisco, San Francisco, California 94143, United States
- Department
of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94143, United States
- Department
of Pharmaceutical Chemistry, University
of California, San Francisco, San
Francisco, California 94143, United States
| | - Liping Sun
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Wenqing Shui
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
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23
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Cary BP, Gerrard EJ, Belousoff MJ, Fletcher MM, Jiang Y, Russell IC, Piper SJ, Wootten D, Sexton PM. Molecular insights into peptide agonist engagement with the PTH receptor. Structure 2023:S0969-2126(23)00125-9. [PMID: 37148874 DOI: 10.1016/j.str.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/30/2022] [Accepted: 04/03/2023] [Indexed: 05/08/2023]
Abstract
The parathyroid hormone (PTH) 1 receptor (PTH1R) is a G protein-coupled receptor (GPCR) that regulates skeletal development and calcium homeostasis. Here, we describe cryo-EM structures of the PTH1R in complex with fragments of the two hormones, PTH and PTH-related protein, the drug abaloparatide, as well as the engineered tool compounds, long-acting PTH (LA-PTH) and the truncated peptide, M-PTH(1-14). We found that the critical N terminus of each agonist engages the transmembrane bundle in a topologically similar fashion, reflecting similarities in measures of Gαs activation. The full-length peptides induce subtly different extracellular domain (ECD) orientations relative to the transmembrane domain. In the structure bound to M-PTH, the ECD is unresolved, demonstrating that the ECD is highly dynamic when unconstrained by a peptide. High resolutions enabled identification of water molecules near peptide and G protein binding sites. Our results illuminate the action of orthosteric agonists of the PTH1R.
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Affiliation(s)
- Brian P Cary
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia.
| | - Elliot J Gerrard
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Matthew J Belousoff
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Madeleine M Fletcher
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Yan Jiang
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Isabella C Russell
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Sarah J Piper
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia
| | - Denise Wootten
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia.
| | - Patrick M Sexton
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia; ARC Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, VIC, Australia.
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24
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Zhang L, Mobbs JI, May LT, Glukhova A, Thal DM. The impact of cryo-EM on determining allosteric modulator-bound structures of G protein-coupled receptors. Curr Opin Struct Biol 2023; 79:102560. [PMID: 36848776 DOI: 10.1016/j.sbi.2023.102560] [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: 10/27/2022] [Revised: 01/23/2023] [Accepted: 01/31/2023] [Indexed: 02/27/2023]
Abstract
G-protein coupled receptors (GPCRs) are important therapeutic targets for the treatment of human disease. Although GPCRs are highly successful drug targets, there are many challenges associated with the discovery and translation of small molecule ligands that target the endogenous ligand-binding site for GPCRs. Allosteric modulators are a class of ligands that target alternative binding sites known as allosteric sites and offer fresh opportunities for the development of new therapeutics. However, only a few allosteric modulators have been approved as drugs. Advances in GPCR structural biology enabled by the cryogenic electron microscopy (cryo-EM) revolution have provided new insights into the molecular mechanism and binding location of small molecule allosteric modulators. This review highlights the latest findings from allosteric modulator-bound structures of Class A, B, and C GPCRs with a focus on small molecule ligands. Emerging methods that will facilitate cryo-EM structures of more difficult ligand-bound GPCR complexes are also discussed. The results of these studies are anticipated to aid future structure-based drug discovery efforts across many different GPCRs.
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Affiliation(s)
- Liudi Zhang
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria Australia; ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria Australia
| | - Jesse I Mobbs
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria Australia; ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria Australia. https://twitter.com/@JesseMobbs
| | - Lauren T May
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria Australia. https://twitter.com/@laurentmay
| | - Alisa Glukhova
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria Australia; ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, Victoria 3010, Australia. https://twitter.com/@gl_alisa
| | - David M Thal
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria Australia; ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Victoria Australia.
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25
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Chen Y, Zhou Q, Wang J, Xu Y, Wang Y, Yan J, Wang Y, Zhu Q, Zhao F, Li C, Chen CW, Cai X, Bathgate RAD, Shen C, Eric Xu H, Yang D, Liu H, Wang MW. Ligand recognition mechanism of the human relaxin family peptide receptor 4 (RXFP4). Nat Commun 2023; 14:492. [PMID: 36717591 PMCID: PMC9886975 DOI: 10.1038/s41467-023-36182-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 01/19/2023] [Indexed: 02/01/2023] Open
Abstract
Members of the insulin superfamily regulate pleiotropic biological processes through two types of target-specific but structurally conserved peptides, insulin/insulin-like growth factors and relaxin/insulin-like peptides. The latter bind to the human relaxin family peptide receptors (RXFPs). Here, we report three cryo-electron microscopy structures of RXFP4-Gi protein complexes in the presence of the endogenous ligand insulin-like peptide 5 (INSL5) or one of the two small molecule agonists, compound 4 and DC591053. The B chain of INSL5 adopts a single α-helix that penetrates into the orthosteric pocket, while the A chain sits above the orthosteric pocket, revealing a peptide-binding mode previously unknown. Together with mutagenesis and functional analyses, the key determinants responsible for the peptidomimetic agonism and subtype selectivity were identified. Our findings not only provide insights into ligand recognition and subtype selectivity among class A G protein-coupled receptors, but also expand the knowledge of signaling mechanisms in the insulin superfamily.
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Affiliation(s)
- Yan Chen
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Qingtong Zhou
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jiang Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,Lingang Laboratory, Shanghai, 200031, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China
| | - Youwei Xu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yun Wang
- Genova Biotech (Changzhou) Co., Ltd, Changzhou, 213125, China
| | - Jiahui Yan
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yibing Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Qi Zhu
- Genova Biotech (Changzhou) Co., Ltd, Changzhou, 213125, China
| | - Fenghui Zhao
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Chenghao Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China
| | - Chuan-Wei Chen
- Research Center for Deepsea Bioresources, Sanya, Hainan, 572025, China
| | - Xiaoqing Cai
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Ross A D Bathgate
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, Victoria, 3052, Australia.,Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Chun Shen
- Genova Biotech (Changzhou) Co., Ltd, Changzhou, 213125, China
| | - H Eric Xu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Dehua Yang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Research Center for Deepsea Bioresources, Sanya, Hainan, 572025, China.
| | - Hong Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou, 310024, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Ming-Wei Wang
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China. .,The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China. .,Research Center for Deepsea Bioresources, Sanya, Hainan, 572025, China. .,Department of Chemistry, School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
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26
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Kotliar IB, Lorenzen E, Schwenk JM, Hay DL, Sakmar TP. Elucidating the Interactome of G Protein-Coupled Receptors and Receptor Activity-Modifying Proteins. Pharmacol Rev 2023; 75:1-34. [PMID: 36757898 PMCID: PMC9832379 DOI: 10.1124/pharmrev.120.000180] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 09/27/2022] [Indexed: 12/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are known to interact with several other classes of integral membrane proteins that modulate their biology and pharmacology. However, the extent of these interactions and the mechanisms of their effects are not well understood. For example, one class of GPCR-interacting proteins, receptor activity-modifying proteins (RAMPs), comprise three related and ubiquitously expressed single-transmembrane span proteins. The RAMP family was discovered more than two decades ago, and since then GPCR-RAMP interactions and their functional consequences on receptor trafficking and ligand selectivity have been documented for several secretin (class B) GPCRs, most notably the calcitonin receptor-like receptor. Recent bioinformatics and multiplexed experimental studies suggest that GPCR-RAMP interactions might be much more widespread than previously anticipated. Recently, cryo-electron microscopy has provided high-resolution structures of GPCR-RAMP-ligand complexes, and drugs have been developed that target GPCR-RAMP complexes. In this review, we provide a summary of recent advances in techniques that allow the discovery of GPCR-RAMP interactions and their functional consequences and highlight prospects for future advances. We also provide an up-to-date list of reported GPCR-RAMP interactions based on a review of the current literature. SIGNIFICANCE STATEMENT: Receptor activity-modifying proteins (RAMPs) have emerged as modulators of many aspects of G protein-coupled receptor (GPCR)biology and pharmacology. The application of new methodologies to study membrane protein-protein interactions suggests that RAMPs interact with many more GPCRs than had been previously known. These findings, especially when combined with structural studies of membrane protein complexes, have significant implications for advancing GPCR-targeted drug discovery and the understanding of GPCR pharmacology, biology, and regulation.
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Affiliation(s)
- Ilana B Kotliar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York (I.B.K., E.L., T.P.S.); Tri-Institutional PhD Program in Chemical Biology, New York, New York (I.B.K.); Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Solna, Sweden (J.M.S.); Department of Pharmacology and Toxicology, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin, New Zealand (D.L.H.); and Department of Neurobiology, Care Sciences and Society (NVS), Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden (T.P.S.)
| | - Emily Lorenzen
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York (I.B.K., E.L., T.P.S.); Tri-Institutional PhD Program in Chemical Biology, New York, New York (I.B.K.); Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Solna, Sweden (J.M.S.); Department of Pharmacology and Toxicology, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin, New Zealand (D.L.H.); and Department of Neurobiology, Care Sciences and Society (NVS), Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden (T.P.S.)
| | - Jochen M Schwenk
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York (I.B.K., E.L., T.P.S.); Tri-Institutional PhD Program in Chemical Biology, New York, New York (I.B.K.); Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Solna, Sweden (J.M.S.); Department of Pharmacology and Toxicology, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin, New Zealand (D.L.H.); and Department of Neurobiology, Care Sciences and Society (NVS), Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden (T.P.S.)
| | - Debbie L Hay
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York (I.B.K., E.L., T.P.S.); Tri-Institutional PhD Program in Chemical Biology, New York, New York (I.B.K.); Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Solna, Sweden (J.M.S.); Department of Pharmacology and Toxicology, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin, New Zealand (D.L.H.); and Department of Neurobiology, Care Sciences and Society (NVS), Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden (T.P.S.)
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York (I.B.K., E.L., T.P.S.); Tri-Institutional PhD Program in Chemical Biology, New York, New York (I.B.K.); Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Solna, Sweden (J.M.S.); Department of Pharmacology and Toxicology, School of Biomedical Sciences, Division of Health Sciences, University of Otago, Dunedin, New Zealand (D.L.H.); and Department of Neurobiology, Care Sciences and Society (NVS), Division for Neurogeriatrics, Center for Alzheimer Research, Karolinska Institutet, Solna, Sweden (T.P.S.)
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27
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Chen Y, Zhang J, Weng Y, Xu Y, Lu W, Liu W, Liu M, Hua T, Song G. Cryo-EM structure of the human adenosine A 2B receptor-G s signaling complex. SCIENCE ADVANCES 2022; 8:eadd3709. [PMID: 36563137 PMCID: PMC9788782 DOI: 10.1126/sciadv.add3709] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 11/22/2022] [Indexed: 06/03/2023]
Abstract
The human adenosine A2B receptor (A2BR) is a class A G protein-coupled receptor that is involved in several major physiological and pathological processes throughout the body. A2BR recognizes its ligands adenosine and NECA with relatively low affinity, but the detailed mechanism for its ligand recognition and signaling is still elusive. Here, we present two structures determined by cryo-electron microscopy of A2BR bound to its agonists NECA and BAY60-6583, each coupled to an engineered Gs protein. The structures reveal conserved orthosteric binding pockets with subtle differences, whereas the selectivity or specificity can mainly be attributed to regions extended from the orthosteric pocket. We also found that BAY60-6583 occupies a secondary pocket, where residues V2506.51 and N2737.36 were two key determinants for its selectivity against A2BR. This study offers a better understanding of ligand selectivity for the adenosine receptor family and provides a structural template for further development of A2BR ligands for related diseases.
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Affiliation(s)
- Ying Chen
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jinyi Zhang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yuan Weng
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yueming Xu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Weiqiang Lu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Wei Liu
- Cancer Center and Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Mingyao Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Tian Hua
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Gaojie Song
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
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28
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Li M, Bao Y, Xu R, Li M, Xi L, Guo J. Understanding the Allosteric Modulation of PTH1R by a Negative Allosteric Modulator. Cells 2022; 12:cells12010041. [PMID: 36611834 PMCID: PMC9818451 DOI: 10.3390/cells12010041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/02/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
The parathyroid hormone type 1 receptor (PTH1R) acts as a canonical class B G protein-coupled receptor, regulating crucial functions including calcium homeostasis and bone formation. The identification and development of PTH1R non-peptide allosteric modulators have obtained widespread attention. It has been found that a negative allosteric modulator (NAM) could inhibit the activation of PTH1R, but the implied mechanism remains unclear. Herein, extensive molecular dynamics simulations together with multiple analytical approaches are utilized to unravel the mechanism of PTH1R allosteric inhibition. The results suggest that the binding of NAM destabilizes the structure of the PTH1R-PTH-spep/qpep (the C terminus of Gs/Gq proteins) complexes. Moreover, the presence of NAM weakens the binding of PTH/peps (spep and qpep) and PTH1R. The intra- and inter-molecular couplings are also weakened in PTH1R upon NAM binding. Interestingly, compared with our previous study of the positive allosteric effects induced by extracellular Ca2+, the enhanced correlation between the PTH and G-protein binding sites is significantly reduced by the replacement of this negative allosteric regulator. Our findings might contribute to the development of new therapeutic agents for diseases caused by the abnormal activation of PTH1R.
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Affiliation(s)
- Mengrong Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiqiong Bao
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Ran Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Miaomiao Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Lili Xi
- Office of Institution of Drug Clinical Trial, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Science, Macao Polytechnic University, Macao 999078, China
- Engineering Research Centre of Applied Technology on Machine Translation and Artificial Intelligence, Macao Polytechnic University, Macao 999078, China
- Correspondence:
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29
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Yu Z, Cary BP, Kim TW, Nguyen KD, Gardella TJ, Gellman SH. Kinetic and Thermodynamic Insights into Agonist Interactions with the Parathyroid Hormone Receptor-1 from a New NanoBRET Assay. ACS Chem Biol 2022; 17:3148-3158. [PMID: 36282520 PMCID: PMC9747329 DOI: 10.1021/acschembio.2c00595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Polypeptides that activate the parathyroid hormone receptor-1 (PTHR1) are important in human physiology and medicine. Most previous studies of peptide binding to this receptor have involved the displacement of a radiolabeled ligand. We report a new assay format based on bioluminescence resonance energy transfer (BRET). Fusion of a NanoLuc luciferase (nLuc) unit to the N-terminus of the PTHR1 allows the direct detection of binding by an agonist peptide bearing a tetramethylrhodamine (TMR) unit. Affinity measurements from the BRET assay align well with results previously obtained via radioligand displacement. The BRET assay offers substantial operational benefits relative to affinity measurements involving radioactive compounds. The convenience of the new assay allowed us to explore several questions raised by earlier reports. For example, we show that although the first two residues of PTH(1-34) (the drug teriparatide) are critical for PTHR1 activation, these two residues contribute little or nothing to affinity. Comparisons among the well-studied agonists PTH(1-34), PTHrP(1-34), and "long-acting PTH" (LA-PTH) reveal that the high affinity of LA-PTH arises largely from a diminished rate constant for dissociation relative to the other two. A D-peptide recently reported to be comparable to PTH(1-34) as an agonist of the PTHR1 was found not to bind detectably to the receptor and to be a very weak agonist.
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Affiliation(s)
- Zhen Yu
- Department of Chemistry, University of Wisconsin - Madison, Madison, WI 53706 USA
| | - Brian P. Cary
- Department of Chemistry, University of Wisconsin - Madison, Madison, WI 53706 USA
| | - Tae Wook Kim
- Department of Chemistry, University of Wisconsin - Madison, Madison, WI 53706 USA
| | - Kevin D. Nguyen
- Department of Chemistry, University of Wisconsin - Madison, Madison, WI 53706 USA
| | - Thomas J. Gardella
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114 USA
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin - Madison, Madison, WI 53706 USA
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30
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Poudel H, Leitner DM. Energy Transport in Class B GPCRs: Role of Protein-Water Dynamics and Activation. J Phys Chem B 2022; 126:8362-8373. [PMID: 36256609 DOI: 10.1021/acs.jpcb.2c03960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We compute energy exchange networks (EENs) through glucagon-like peptide-1 receptor (GLP-1R), a class B G-protein-coupled receptor (GPCR), in inactive and two active states, one activated by a peptide ligand and the other by a small molecule agonist, from results of molecular dynamics simulations. The reorganized network upon activation contains contributions from structural as well as from dynamic changes and corresponding entropic contributions to the free energy of activation, which are estimated in terms of the change in rates of energy transfer across non-covalent contacts. The role of water in the EENs and in activation of GLP-1R is also investigated. The dynamics of water in contact with the central polar network of the transmembrane region is found to be significantly slower for both activated states compared to the inactive state. This result is consistent with the contribution of water molecules to activation of GLP-1R previously suggested and resembles water dynamics in parts of the transmembrane region found in earlier studies of rhodopsin-like GPCRs.
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Affiliation(s)
- Humanath Poudel
- Department of Chemistry, University of Nevada, Reno, Nevada89557, United States
| | - David M Leitner
- Department of Chemistry, University of Nevada, Reno, Nevada89557, United States
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31
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Zhai X, Mao C, Shen Q, Zang S, Shen DD, Zhang H, Chen Z, Wang G, Zhang C, Zhang Y, Liu Z. Molecular insights into the distinct signaling duration for the peptide-induced PTH1R activation. Nat Commun 2022; 13:6276. [PMID: 36271004 PMCID: PMC9586930 DOI: 10.1038/s41467-022-34009-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/06/2022] [Indexed: 02/08/2023] Open
Abstract
The parathyroid hormone type 1 receptor (PTH1R), a class B1 G protein-coupled receptor, plays critical roles in bone turnover and Ca2+ homeostasis. Teriparatide (PTH) and Abaloparatide (ABL) are terms as long-acting and short-acting peptide, respectively, regarding their marked duration distinctions of the downstream signaling. However, the mechanistic details remain obscure. Here, we report the cryo-electron microscopy structures of PTH- and ABL-bound PTH1R-Gs complexes, adapting similar overall conformations yet with notable differences in the receptor ECD regions and the peptide C-terminal portions. 3D variability analysis and site-directed mutagenesis studies uncovered that PTH-bound PTH1R-Gs complexes display less motions and are more tolerant of mutations in affecting the receptor signaling than ABL-bound complexes. Furthermore, we combined the structural analysis and signaling assays to delineate the molecular basis of the differential signaling durations induced by these peptides. Our study deepens the mechanistic understanding of ligand-mediated prolonged or transient signaling.
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Affiliation(s)
- Xiuwen Zhai
- grid.89957.3a0000 0000 9255 8984National Clinical Research Center of Kidney Diseases, Jinling Clinical Medical College of Nanjing Medical University, Nanjing, 211166 Jiangsu China
| | - Chunyou Mao
- grid.13402.340000 0004 1759 700XCenter for Structural Pharmacology and Therapeutics Development, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China ,grid.415999.90000 0004 1798 9361Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Qingya Shen
- grid.13402.340000 0004 1759 700XLiangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Shaokun Zang
- grid.13402.340000 0004 1759 700XDepartment of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dan-Dan Shen
- grid.13402.340000 0004 1759 700XDepartment of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huibing Zhang
- grid.13402.340000 0004 1759 700XDepartment of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhaohong Chen
- grid.89957.3a0000 0000 9255 8984National Clinical Research Center of Kidney Diseases, Jinling Clinical Medical College of Nanjing Medical University, Nanjing, 211166 Jiangsu China
| | - Gang Wang
- grid.89957.3a0000 0000 9255 8984National Clinical Research Center of Kidney Diseases, Jinling Clinical Medical College of Nanjing Medical University, Nanjing, 211166 Jiangsu China
| | - Changming Zhang
- grid.89957.3a0000 0000 9255 8984National Clinical Research Center of Kidney Diseases, Jinling Clinical Medical College of Nanjing Medical University, Nanjing, 211166 Jiangsu China
| | - Yan Zhang
- grid.13402.340000 0004 1759 700XCenter for Structural Pharmacology and Therapeutics Development, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China ,grid.13402.340000 0004 1759 700XLiangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China ,grid.13402.340000 0004 1759 700XDepartment of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China ,grid.13402.340000 0004 1759 700XMOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang China ,Zhejiang Provincial Key Laboratory of Immunity and Inflammatory diseases, Hangzhou, Zhejiang China
| | - Zhihong Liu
- grid.89957.3a0000 0000 9255 8984National Clinical Research Center of Kidney Diseases, Jinling Clinical Medical College of Nanjing Medical University, Nanjing, 211166 Jiangsu China ,grid.13402.340000 0004 1759 700XLiangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
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32
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Witkin JM. The romantic age of pharmacological science. Pharmacol Biochem Behav 2022; 214:173354. [DOI: 10.1016/j.pbb.2022.173354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 11/25/2022]
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