1
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Yang N, Yun WJ, Cui ZG, Zheng HC. The oncogenic roles of GPR176 in ovarian cancer: a molecular target for aggressiveness and gene therapy. J OBSTET GYNAECOL 2024; 44:2347430. [PMID: 38835234 DOI: 10.1080/01443615.2024.2347430] [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: 03/14/2023] [Accepted: 08/01/2023] [Indexed: 06/06/2024]
Abstract
BACKGROUND At present, the discovery of new biomarkers is of great significance for the early diagnosis, treatment and prognosis assessment of ovarian cancer. Previous findings indicated that aberrant G-protein-coupled receptor 176 (GPR176) expression might contribute to tumorigenesis and subsequent progression. However, the expression of GPR176 and the molecular mechanisms in ovarian cancer had not been investigated. METHODS GPR176 expression was compared with clinicopathological features of ovarian cancer using immunohistochemical and bioinformatics analyses. GPR176-related genes and pathways were analysed using bioinformatics analysis. Additionally, the effects of GPR176 on ovarian cancer cell phenotypes were investigated. RESULTS GPR176 expression positively correlated with elder age, clinicopathological staging, tumour residual status, and unfavourable survival of ovarian cancer, but negatively with purity loss, infiltration of B cells, and CD8+ T cells. Gene Set Enrichment Analysis showed that differential expression of GPR176 was involved in focal adhesion, ECM-receptor interaction, cell adhesion molecules and so on. STRING and Cytoscape were used to determine the top 10 nodes. Kyoto Encyclopaedia of Genes and Genomes analysis indicated that GPR176-related genes were involved in the ECM structural constituent and organisation and so on. GPR176 overexpression promoted the proliferation, anti-apoptosis, anti-pyroptosis, migration and invasion of ovarian cancer cells with overexpression of N-cadherin, Zeb1, Snail, Twist1, and under-expression of gasdermin D, caspase 1, and E-cadherin. CONCLUSION GPR176 might be involved in the progression of ovarian cancer. It might be used as a biomarker to indicate the aggressive behaviour and poor prognosis of ovarian cancer and a target of genetic therapy.
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Affiliation(s)
- Ning Yang
- Department of Oncology and Central Laboratory, The Affiliated Hospital of Chengde Medical University, Chengde, China
| | - Wen-Jing Yun
- Department of Oncology and Central Laboratory, The Affiliated Hospital of Chengde Medical University, Chengde, China
| | - Zheng-Guo Cui
- Department of Environmental Health, University of Fukui School of Medical Science, Fukui, Japan
| | - Hua-Chuan Zheng
- Department of Oncology and Central Laboratory, The Affiliated Hospital of Chengde Medical University, Chengde, China
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2
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Barrett J, Leysen S, Galmiche C, Al-Mossawi H, Bowness P, Edwards TE, Lawson AD. Chimeric antigens displaying GPR65 extracellular loops on a soluble scaffold enabled the discovery of antibodies, which recognized native receptor. Bioengineered 2024; 15:2299522. [PMID: 38184821 PMCID: PMC10773626 DOI: 10.1080/21655979.2023.2299522] [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: 09/26/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024] Open
Abstract
GPR65 is a proton-sensing G-protein coupled receptor associated with multiple immune-mediated inflammatory diseases, whose function is relatively poorly understood. With few reagents commercially available to probe the biology of receptor, generation of an anti-GPR65 monoclonal antibody was desired. Using soluble chimeric scaffolds, such as ApoE3, displaying the extracellular loops of GPR65, together with established phage display technology, native GPR65 loop-specific antibodies were identified. Phage-derived loop-binding antibodies recognized the wild-type native receptor to which they had not previously been exposed, generating confidence in the use of chimeric soluble proteins to act as efficient surrogates for membrane protein extracellular loop antigens. This technique provides promise for the rational design of chimeric antigens in facilitating the discovery of specific antibodies to GPCRs.
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Affiliation(s)
- Janine Barrett
- UK Research Department, UCB Pharma, Slough, UK
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | | | | | - Hussein Al-Mossawi
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Paul Bowness
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
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3
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Shi W, Xu C, Lei P, Sun X, Song M, Guo Y, Song W, Li Y, Yu L, Zhang H, Wang H, Zhang DL. A correlation study of adhesion G protein-coupled receptors as potential therapeutic targets for breast cancer. Breast Cancer Res Treat 2024; 207:417-434. [PMID: 38834774 DOI: 10.1007/s10549-024-07373-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/14/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Adhesion G protein-coupled receptors (aGPCRs), a distinctive subset of the G protein-coupled receptor (GPCR) superfamily, play crucial roles in various physiological and pathological processes, with implications in tumor development. Despite the global prevalence of breast cancer (BRCA), specific aGPCRs as potential drug targets or biomarkers remain underexplored. METHODS UALCAN, GEPIA, Kaplan-Meier Plotter, MethSurv, cBiopportal, String, GeneMANIA, DAVID, Timer, Metascape, and qPCR were applied in this work. RESULTS Our analysis revealed significantly increased transcriptional levels of ADGRB2, ADGRC1, ADGRC2, ADGRC3, ADGRE1, ADGRF2, ADGRF4, and ADGRL1 in BRCA primary tumors. Further analysis indicated a significant correlation between the expressions of certain aGPCRs and the pathological stage of BRCA. High expression of ADGRA1, ADGRF2, ADGRF4, ADGRG1, ADGRG2, ADGRG4, ADGRG6, and ADGRG7 was significantly correlated with poor overall survival (OS) in BRCA patients. Additionally, high expression of ADGRF2 and ADGRF4 indicated inferior recurrence-free survival (RFS) in BRCA patients. The RT-qPCR experiments also confirmed that the mRNA levels of ADGRF2 and ADGRF4 were higher in BRCA cells and tissues. Functional analysis highlighted the diverse roles of aGPCRs, encompassing GPCR signaling and metabolic energy reserves. Moreover, aGPCRs may exert influence or actively participate in the development of BRCA through their impact on immune status. CONCLUSION aGPCRs, particularly ADGRF2 and ADGRF4, hold promise as immunotherapeutic targets and prognostic biomarkers in BRCA.
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Affiliation(s)
- Wenning Shi
- Department of Protein and Antibody Engineering, School of Pharmacy, Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Cong Xu
- Department of Cell Biology, School of Pharmacy, Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Ping Lei
- Department of Obstetrics and Gynecology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Xiaoli Sun
- Department of Obstetrics and Gynecology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Mengju Song
- Department of Protein and Antibody Engineering, School of Pharmacy, Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Yacong Guo
- Department of Protein and Antibody Engineering, School of Pharmacy, Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Wenxuan Song
- Department of Protein and Antibody Engineering, School of Pharmacy, Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Yizheng Li
- The Second School of Clinical Medicine, Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Liting Yu
- Department of Protein and Antibody Engineering, School of Pharmacy, Binzhou Medical University, Yantai, 264003, Shandong, China
| | - Hui Zhang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Shandong First Medical University, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian, 271000, China.
| | - Hongmei Wang
- Shaanxi University of Chinese Medicine, No.1, Middle Century Avenue, Chenyangzhai, Xianyang, 712046, Shaanxi, China.
| | - Dao-Lai Zhang
- Department of Protein and Antibody Engineering, School of Pharmacy, Binzhou Medical University, Yantai, 264003, Shandong, China.
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4
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Hao W, Luo D, Jiang Y, Wan S, Li X. An overview of sphingosine-1-phosphate receptor 2: Structure, biological function, and small-molecule modulators. Med Res Rev 2024; 44:2331-2362. [PMID: 38665010 DOI: 10.1002/med.22044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/02/2024] [Accepted: 04/14/2024] [Indexed: 08/09/2024]
Abstract
Over the past decade, there has been a notable increase in research on sphingosine-1-phosphate receptor 2 (S1PR2), which is a type of G-protein-coupled receptor. Upon activation by S1P or other ligands, S1PR2 initiates downstream signaling pathways such as phosphoinositide 3-kinase (PI3K), Mitogen-activated protein kinase (MAPK), Rho/Rho-associated coiled-coil containing kinases (ROCK), and others, contributing to the diverse biological functions of S1PR2 and playing a pivotal role in various physiological processes and disease progressions, such as multiple sclerosis, fibrosis, inflammation, and tumors. Due to the extensive biological functions of S1PR2, many S1PR2 modulators, including agonists and antagonists, have been developed and discovered by pharmaceutical companies (e.g., Novartis and Galapagos NV) and academic medicinal chemists for disease diagnosis and treatment. However, few reviews have been published that comprehensively overview the functions and regulators of S1PR2. Herein, we provide an in-depth review of the advances in the function of S1PR2 and its modulators. We first summarize the structure and biological function of S1PR2 and its pathological role in human diseases. We then focus on the discovery approach, design strategy, development process, and biomedical application of S1PR2 modulators. Additionally, we outline the major challenges and future directions in this field. Our comprehensive review will aid in the discovery and development of more effective and clinically applicable S1PR2 modulators.
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Affiliation(s)
- Wanting Hao
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Dongdong Luo
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Yuqi Jiang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Shengbiao Wan
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Xiaoyang Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Marine Biomedical Research, Institute of Qingdao, Qingdao, China
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5
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Cola RB, Niethammer SN, Rajamannar P, Gresch A, Bhat MA, Assoumou K, Williams ET, Hauck P, Hartrampf N, Benke D, Stoeber M, Levkowitz G, Melzer S, Patriarchi T. Probing PAC1 receptor activation across species with an engineered sensor. eLife 2024; 13:RP96496. [PMID: 39145773 DOI: 10.7554/elife.96496] [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] [Indexed: 08/16/2024] Open
Abstract
Class-B1 G-protein-coupled receptors (GPCRs) are an important family of clinically relevant drug targets that remain difficult to investigate via high-throughput screening and in animal models. Here, we engineered PAClight1P78A, a novel genetically encoded sensor based on a class-B1 GPCR (the human PAC1 receptor, hmPAC1R) endowed with high dynamic range (ΔF/F0 = 1100%), excellent ligand selectivity, and rapid activation kinetics (τON = 1.15 s). To showcase the utility of this tool for in vitro applications, we thoroughly characterized and compared its expression, brightness and performance between PAClight1P78A-transfected and stably expressing cells. Demonstrating its use in animal models, we show robust expression and fluorescence responses upon exogenous ligand application ex vivo and in vivo in mice, as well as in living zebrafish larvae. Thus, the new GPCR-based sensor can be used for a wide range of applications across the life sciences empowering both basic research and drug development efforts.
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Affiliation(s)
- Reto B Cola
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - Salome N Niethammer
- Medical University of Vienna, Center for Brain Research, Department for Neuronal Cell Biology, Vienna, Austria
| | - Preethi Rajamannar
- Department of Molecular Neuroscience & Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Andrea Gresch
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - Musadiq A Bhat
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
| | - Kevin Assoumou
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Elyse T Williams
- Department of Chemistry, University of Zürich, Zürich, Switzerland
| | - Patrick Hauck
- Department of Chemistry, University of Zürich, Zürich, Switzerland
| | - Nina Hartrampf
- Department of Chemistry, University of Zürich, Zürich, Switzerland
| | - Dietmar Benke
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
- Neuroscience Center Zurich, University and ETH Zürich, Zürich, Switzerland
| | - Miriam Stoeber
- Department of Cell Physiology and Metabolism, University of Geneva, Geneva, Switzerland
| | - Gil Levkowitz
- Department of Molecular Neuroscience & Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sarah Melzer
- Medical University of Vienna, Center for Brain Research, Department for Neuronal Cell Biology, Vienna, Austria
| | - Tommaso Patriarchi
- Institute of Pharmacology and Toxicology, University of Zürich, Zurich, Switzerland
- Neuroscience Center Zurich, University and ETH Zürich, Zürich, Switzerland
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6
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Gareri C, Pfeiffer CT, Jiang X, Paulo JA, Gygi SP, Pham U, Chundi A, Wingler LM, Staus DP, Stepniewski TM, Selent J, Lucero EY, Grogan A, Rajagopal S, Rockman HA. Phosphorylation patterns in the AT1R C-terminal tail specify distinct downstream signaling pathways. Sci Signal 2024; 17:eadk5736. [PMID: 39137246 DOI: 10.1126/scisignal.adk5736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/01/2023] [Accepted: 07/23/2024] [Indexed: 08/15/2024]
Abstract
Different ligands stabilize specific conformations of the angiotensin II type 1 receptor (AT1R) that direct distinct signaling cascades mediated by heterotrimeric G proteins or β-arrestin. These different active conformations are thought to engage distinct intracellular transducers because of differential phosphorylation patterns in the receptor C-terminal tail (the "barcode" hypothesis). Here, we identified the AT1R barcodes for the endogenous agonist AngII, which stimulates both G protein activation and β-arrestin recruitment, and for a synthetic biased agonist that only stimulates β-arrestin recruitment. The endogenous and β-arrestin-biased agonists induced two different ensembles of phosphorylation sites along the C-terminal tail. The phosphorylation of eight serine and threonine residues in the proximal and middle portions of the tail was required for full β-arrestin functionality, whereas phosphorylation of the serine and threonine residues in the distal portion of the tail had little influence on β-arrestin function. Similarly, molecular dynamics simulations showed that the proximal and middle clusters of phosphorylated residues were critical for stable β-arrestin-receptor interactions. These findings demonstrate that ligands that stabilize different receptor conformations induce different phosphorylation clusters in the C-terminal tail as barcodes to evoke distinct receptor-transducer engagement, receptor trafficking, and signaling.
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Affiliation(s)
- Clarice Gareri
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Conrad T Pfeiffer
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Xue Jiang
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Uyen Pham
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Anand Chundi
- Department of Biomedical Engineering, Duke University, Durham, NC 27710, USA
| | - Laura M Wingler
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC 27710, USA
| | - Dean P Staus
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Tomasz Maciej Stepniewski
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)-Pompeu Fabra University (UPF), 08003 Barcelona, Spain
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Warsaw, Poland
- InterAx Biotech AG, PARK InnovAARE, 5234 Villigen, Switzerland
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)-Pompeu Fabra University (UPF), 08003 Barcelona, Spain
| | - Emilio Y Lucero
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Alyssa Grogan
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Sudarshan Rajagopal
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Howard A Rockman
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA
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7
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Ciancetta A, Malfacini D, Gozzi M, Marzola E, Camilotto R, Calò G, Guerrini R. A Multi-Angle Approach to Predict Peptide-GPCR Complexes: The N/OFQ-NOP System as a Successful AlphaFold Application Case Study. J Chem Inf Model 2024. [PMID: 39137328 DOI: 10.1021/acs.jcim.4c00499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
With nearly 700 structures solved and a growing number of customized structure prediction algorithms being developed at a fast pace, G protein-coupled receptors (GPCRs) are an optimal test case for validating new approaches for the prediction of receptor active state and ligand bioactive conformation complexes. In this study, we leveraged the availability of hundreds of peptide GPCRs in the active state and both classical homology and artificial intelligence (AI) based protein modeling combined with docking and AI-based peptide structure prediction approaches to predict the nociceptin/orphanin FQ-NOP receptor active state complex (N/OFQ-NOPa). The In Silico generated hypotheses were validated via the design, synthesis, and pharmacological characterization of novel linear N/OFQ(1-13)-NH2 analogues, leading to the discovery of a novel antagonist (3B; pKB = 6.63) bearing a single ring-constrained residue in place of the Gly2-Gly3 motif of the N/OFQ message sequence (FGGF). While the experimental validation was ongoing, the availability of the Cryo-EM structure of the predicted complex enabled us to unambiguously validate the generated hypotheses. To the best of our knowledge, this is the first example of a peptide-GPCR complex predicted with atomistic accuracy (full complex Cα RMSD < 1.0 Å) and of the N/OFQ message moiety being successfully modified with a rigid scaffold.
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Affiliation(s)
- Antonella Ciancetta
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Davide Malfacini
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
| | - Matteo Gozzi
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Erika Marzola
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy
| | - Riccardo Camilotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
| | - Girolamo Calò
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova 35131, Italy
| | - Remo Guerrini
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121 Ferrara, Italy
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8
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Thompson MD, Reiner-Link D, Berghella A, Rana BK, Rovati GE, Capra V, Gorvin CM, Hauser AS. G protein-coupled receptor (GPCR) pharmacogenomics. Crit Rev Clin Lab Sci 2024:1-44. [PMID: 39119983 DOI: 10.1080/10408363.2024.2358304] [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: 06/15/2023] [Revised: 09/03/2023] [Accepted: 05/18/2024] [Indexed: 08/10/2024]
Abstract
The field of pharmacogenetics, the investigation of the influence of one or more sequence variants on drug response phenotypes, is a special case of pharmacogenomics, a discipline that takes a genome-wide approach. Massively parallel, next generation sequencing (NGS), has allowed pharmacogenetics to be subsumed by pharmacogenomics with respect to the identification of variants associated with responders and non-responders, optimal drug response, and adverse drug reactions. A plethora of rare and common naturally-occurring GPCR variants must be considered in the context of signals from across the genome. Many fundamentals of pharmacogenetics were established for G protein-coupled receptor (GPCR) genes because they are primary targets for a large number of therapeutic drugs. Functional studies, demonstrating likely-pathogenic and pathogenic GPCR variants, have been integral to establishing models used for in silico analysis. Variants in GPCR genes include both coding and non-coding single nucleotide variants and insertion or deletions (indels) that affect cell surface expression (trafficking, dimerization, and desensitization/downregulation), ligand binding and G protein coupling, and variants that result in alternate splicing encoding isoforms/variable expression. As the breadth of data on the GPCR genome increases, we may expect an increase in the use of drug labels that note variants that significantly impact the clinical use of GPCR-targeting agents. We discuss the implications of GPCR pharmacogenomic data derived from the genomes available from individuals who have been well-phenotyped for receptor structure and function and receptor-ligand interactions, and the potential benefits to patients of optimized drug selection. Examples discussed include the renin-angiotensin system in SARS-CoV-2 (COVID-19) infection, the probable role of chemokine receptors in the cytokine storm, and potential protease activating receptor (PAR) interventions. Resources dedicated to GPCRs, including publicly available computational tools, are also discussed.
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Affiliation(s)
- Miles D Thompson
- Krembil Brain Institute, Toronto Western Hospital, Toronto, Ontario, Canada
| | - David Reiner-Link
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alessandro Berghella
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Brinda K Rana
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - G Enrico Rovati
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Valerie Capra
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Caroline M Gorvin
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom
| | - Alexander S Hauser
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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9
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Díaz-Holguín A, Saarinen M, Vo DD, Sturchio A, Branzell N, Cabeza de Vaca I, Hu H, Mitjavila-Domènech N, Lindqvist A, Baranczewski P, Millan MJ, Yang Y, Carlsson J, Svenningsson P. AlphaFold accelerated discovery of psychotropic agonists targeting the trace amine-associated receptor 1. SCIENCE ADVANCES 2024; 10:eadn1524. [PMID: 39110804 PMCID: PMC11305387 DOI: 10.1126/sciadv.adn1524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 06/28/2024] [Indexed: 08/10/2024]
Abstract
Artificial intelligence is revolutionizing protein structure prediction, providing unprecedented opportunities for drug design. To assess the potential impact on ligand discovery, we compared virtual screens using protein structures generated by the AlphaFold machine learning method and traditional homology modeling. More than 16 million compounds were docked to models of the trace amine-associated receptor 1 (TAAR1), a G protein-coupled receptor of unknown structure and target for treating neuropsychiatric disorders. Sets of 30 and 32 highly ranked compounds from the AlphaFold and homology model screens, respectively, were experimentally evaluated. Of these, 25 were TAAR1 agonists with potencies ranging from 12 to 0.03 μM. The AlphaFold screen yielded a more than twofold higher hit rate (60%) than the homology model and discovered the most potent agonists. A TAAR1 agonist with a promising selectivity profile and drug-like properties showed physiological and antipsychotic-like effects in wild-type but not in TAAR1 knockout mice. These results demonstrate that AlphaFold structures can accelerate drug discovery.
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Affiliation(s)
- Alejandro Díaz-Holguín
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Marcus Saarinen
- Neuro Svenningsson, Department of Clinical Neuroscience, Karolinska Institute, SE-171 76 Stockholm, Sweden
| | - Duc Duy Vo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Andrea Sturchio
- Neuro Svenningsson, Department of Clinical Neuroscience, Karolinska Institute, SE-171 76 Stockholm, Sweden
- Department of Neurology, James J. and Joan A. Gardner Family Center for Parkinson's Disease and Movement Disorders, University of Cincinnati, Cincinnati, OH, USA
| | - Niclas Branzell
- Neuro Svenningsson, Department of Clinical Neuroscience, Karolinska Institute, SE-171 76 Stockholm, Sweden
| | - Israel Cabeza de Vaca
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Huabin Hu
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Núria Mitjavila-Domènech
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Annika Lindqvist
- Department of Pharmacy, SciLifeLab Drug Discovery and Development Platform, Uppsala University, Box 580, SE-751 23 Uppsala, Sweden
| | - Pawel Baranczewski
- Department of Pharmacy, SciLifeLab Drug Discovery and Development Platform, Uppsala University, Box 580, SE-751 23 Uppsala, Sweden
| | - Mark J. Millan
- Neuroinflammation Therapeutic Area, Institut de Recherches Servier, Centre de Recherches de Croissy, Paris, France and Institute of Neuroscience and Psychology, College of Medicine, Vet and Life Sciences, Glasgow University, Scotland, Glasgow, UK
| | - Yunting Yang
- Neuro Svenningsson, Department of Clinical Neuroscience, Karolinska Institute, SE-171 76 Stockholm, Sweden
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Per Svenningsson
- Neuro Svenningsson, Department of Clinical Neuroscience, Karolinska Institute, SE-171 76 Stockholm, Sweden
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10
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Eberle SA, Gustavsson M. Bilayer lipids modulate ligand binding to atypical chemokine receptor 3. Structure 2024; 32:1174-1183.e5. [PMID: 38776922 DOI: 10.1016/j.str.2024.04.018] [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: 10/18/2023] [Revised: 02/28/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
Chemokine receptors belong to the large class of G protein-coupled receptors (GPCRs) and are involved in a number of (patho)physiological processes. Previous studies highlighted the importance of membrane lipids for modulating GPCR structure and function. However, the underlying mechanisms of how lipids regulate GPCRs are often poorly understood. Here, we report that anionic lipid bilayers increase the binding affinity of the chemokine CXCL12 for the atypical chemokine receptor 3 (ACKR3) by modulating the CXCL12 binding kinetics. Notably, the anionic bilayer favors CXCL12 over the more positively charged chemokine CXCL11, which we explained by bilayer interactions orienting CXCL12 but not CXCL11 for productive ACKR3 binding. Furthermore, our data suggest a stabilization of active ACKR3 conformations in anionic bilayers. Taken together, the described regulation of chemokine selectivity of ACKR3 by the lipid bilayer proposes an extended version of the classical model of chemokine binding including the lipid environment of the receptor.
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Affiliation(s)
- Stefanie Alexandra Eberle
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Martin Gustavsson
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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11
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Peng Q, Jiang H, Cheng X, Wang N, Zhou S, Zhang Y, Yang T, Chen Y, Zhang W, Lv S, Nan W, Wang J, Fan GH, Li J, Zhang J. Cryo-EM Structure and Biochemical Analysis of the Human Chemokine Receptor CCR8. Biochemistry 2024; 63:1892-1900. [PMID: 38985857 DOI: 10.1021/acs.biochem.4c00121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
The C-C motif chemokine receptor 8 (CCR8) is a class A G-protein-coupled receptor that has emerged as a promising therapeutic target in cancer and autoimmune diseases. In the present study, we solved the cryo-electron microscopy (cryo-EM) structure of the human CCR8-Gi complex in the absence of a ligand at 2.58 Å. Structural analysis and comparison revealed that our apo CCR8 structure undergoes some conformational changes and is similar to that in the CCL1-CCR8 complex structure, indicating an active state. In addition, the key residues of CCR8 involved in the recognition of LMD-009, a potent nonpeptide agonist, were investigated by mutating CCR8 and testing the calcium flux induced by LMD-009-CCR8 interaction. Three mutants of CCR8, Y1133.32A, Y1724.64A, and E2867.39A, showed a dramatically decreased ability in mediating calcium mobilization, indicating their key interaction with LMD-009 and key roles in activation. These structural and biochemical analyses enrich molecular insights into the agonism and activation of CCR8 and will facilitate CCR8-targeted therapy.
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Affiliation(s)
- Qi Peng
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
- The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Haihai Jiang
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
- The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Xinyu Cheng
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
- The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Na Wang
- Cobio Biotechnology Co., Ltd., No. 9 Building, Building 16 of SHUWU, No. 73 Tanmi Road, Jiangbei New District, Nanjing 211500, China
| | - Sili Zhou
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
| | - Yuting Zhang
- Shenzhen Crystalo Biopharmaceutical Co., Ltd, Shenzhen, Guangdong 518118, China
| | - Tingting Yang
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
- The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Yixiang Chen
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
- The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Wei Zhang
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
- The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Sijia Lv
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
- The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - Weiwei Nan
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
- The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
| | - JianFei Wang
- Executive Office, Immunophage Biotech Co., Ltd., No 10. Lv Zhou Huan Road, Shanghai 201112, China
| | - Guo-Huang Fan
- Executive Office, Immunophage Biotech Co., Ltd., No 10. Lv Zhou Huan Road, Shanghai 201112, China
| | - Jian Li
- College of Pharmacy, Gannan Medical University, Ganzhou 341000, China
| | - Jin Zhang
- The MOE Basic Research and Innovation Center for the Targeted Therapeutics of Solid Tumors, School of Basic Medical Sciences, Jiangxi Medical College, Nanchang University, Nanchang 330031, China
- The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang 330006, China
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12
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Wu Z, Sun X, Su J, Zhang X, Hu J, Li C. Revealing the graded activation mechanism of neurotensin receptor 1. Int J Biol Macromol 2024; 278:134488. [PMID: 39111461 DOI: 10.1016/j.ijbiomac.2024.134488] [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: 04/17/2024] [Revised: 08/02/2024] [Accepted: 08/02/2024] [Indexed: 08/16/2024]
Abstract
Graded activation contributes to the precise regulation of GPCR activity, presenting new opportunities for drug design. In this work, a total of 10 μs enhanced-sampling simulations are performed to provide molecular insights into the binding dynamics differences of the neurotensin receptor 1 (NTSR1) to the full agonist SRI-9829, partial agonist RTI-3a and inverse agonist SR48692. The possible graded activation mechanism of NTSR1 is revealed by an integrated analysis utilizing the reweighted potential of mean force (PMF), deep learning (DL) and transfer entropy (TE). Specifically, the orthosteric pocket is observed to undergo expansion and contraction, with the G-protein-binding site experiencing interconversions among the inactive, intermediate and active-like states. Detailed structural comparisons capture subtle conformational differences arising from ligand binding in allosteric signaling, which can well explain the graded activation. Critical microswitches that contribute to graded activation are efficiently identified with the DL model. TE calculations enable the visualization of allosteric communication networks within the receptor, elucidating the driver-responder relationships associated with signal transduction. Fortunately, the dissociation of the full agonist from the orthosteric pocket is observed. The current findings systematically reveal the mechanism of NTSR1 graded activation, and also provide implications for structure-based drug design.
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Affiliation(s)
- Zhixiang Wu
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Xiaohan Sun
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Jingjie Su
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Xinyu Zhang
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China.
| | - Chunhua Li
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China.
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13
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Chalopin Y. GPCR Signaling: A Study of the Interplay Between Structure, Energy, and Function. Proteins 2024. [PMID: 39095933 DOI: 10.1002/prot.26724] [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: 02/10/2024] [Revised: 04/26/2024] [Accepted: 06/12/2024] [Indexed: 08/04/2024]
Abstract
G protein-coupled receptors (GPCRs) exemplify sophisticated allosteric communication, transducing extracellular signals through ligand-induced structural rearrangements that resonate through the molecular scaffold. Despite extensive study, the biophysical underpinnings of how conformational changes spread remain unclear. This work employs a novel physics-based framework to characterize the role of energy dissipation in directing intramolecular signaling pathways. By modeling each residue as a network of coupled oscillators, we generate a localization landscape depicting the vibrational energy distribution throughout the protein scaffold. Quantifying directional energy flux between residues reveals distinct pathways for energy and information transfer, illuminating sequences of allosteric communication. Our analysis of CB1 and CCR5 crystal structures unveils an anisotropic pattern of energy dissipation aligning with key functional dynamics, such as activation-related conformational changes. These anisotropic patterns of vibrational energy flow constitute pre-configured channels for allosteric signaling. Elucidating the relationship between structural topology and energy dissipation patterns provides key insights into the thermodynamic drivers of conformational signaling. This methodology significantly advances our mechanistic understanding of allostery in GPCRs and presents a broadly applicable approach for rationally dissecting allosteric communication pathways, with potential implications for structure-based drug design targeting these critical receptors.
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Affiliation(s)
- Yann Chalopin
- Structures, Properties and Modeling of Solids Laboratory Physics Department, CentraleSupélec/National Center for the Scientific Research, University of Paris-Saclay, Gif-sur-Yvette, France
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14
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Xu L, Yang Q, Zhou J. Mechanisms of Abnormal Lipid Metabolism in the Pathogenesis of Disease. Int J Mol Sci 2024; 25:8465. [PMID: 39126035 PMCID: PMC11312913 DOI: 10.3390/ijms25158465] [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: 06/25/2024] [Revised: 07/26/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
Lipid metabolism is a critical component in preserving homeostasis and health, and lipids are significant chemicals involved in energy metabolism in living things. With the growing interest in lipid metabolism in recent years, an increasing number of studies have demonstrated the close relationship between abnormalities in lipid metabolism and the development of numerous human diseases, including cancer, cardiovascular, neurological, and endocrine system diseases. Thus, understanding how aberrant lipid metabolism contributes to the development of related diseases and how it works offers a theoretical foundation for treating and preventing related human diseases as well as new avenues for the targeted treatment of related diseases. Therefore, we discuss the processes of aberrant lipid metabolism in various human diseases in this review, including diseases of the cardiovascular system, neurodegenerative diseases, endocrine system diseases (such as obesity and type 2 diabetes mellitus), and other diseases including cancer.
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Affiliation(s)
| | | | - Jinghua Zhou
- School of Basic Medicine Sciences, Hangzhou Normal University, Hangzhou 311121, China
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15
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Neri P, Leblay N, Lee H, Gulla A, Bahlis NJ, Anderson KC. Just scratching the surface: novel treatment approaches for multiple myeloma targeting cell membrane proteins. Nat Rev Clin Oncol 2024; 21:590-609. [PMID: 38961233 DOI: 10.1038/s41571-024-00913-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2024] [Indexed: 07/05/2024]
Abstract
A better understanding of the roles of the adaptive and innate immune systems in the oncogenesis of cancers including multiple myeloma (MM) has led to the development of novel immune-based therapies. B cell maturation antigen (BCMA), G protein-coupled receptor family C group 5 member D (GPRC5D) and Fc receptor-like protein 5 (FcRL5, also known as FcRH5) are cell-surface transmembrane proteins expressed by plasma cells, and have been identified as prominent immunotherapeutic targets in MM, with promising activity demonstrated in patients with heavily pretreated relapsed and/or refractory disease. Indeed, since 2020, antibody-drug conjugates, bispecific T cell engagers and autologous chimeric antigen receptor T cells targeting BCMA or GPRC5D have been approved for the treatment of relapsed and/or refractory MM. However, responses to these therapies are not universal, and acquired resistance invariably occurs. In this Review, we discuss the various immunotherapeutic approaches targeting BCMA, GPRC5D and FcRL5 that are currently either available or in clinical development for patients with MM. We also review the mechanisms underlying resistance to such therapies, and discuss potential strategies to overcome these mechanisms and improve patient outcomes.
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Affiliation(s)
- Paola Neri
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Noémie Leblay
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Holly Lee
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Annamaria Gulla
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Nizar J Bahlis
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta, Canada
| | - Kenneth C Anderson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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16
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Gedam M, Zheng H. Complement C3aR signaling: Immune and metabolic modulation and its impact on Alzheimer's disease. Eur J Immunol 2024; 54:e2350815. [PMID: 38778507 PMCID: PMC11305912 DOI: 10.1002/eji.202350815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder and the most common cause of dementia among the elderly population. Despite its widespread prevalence, our comprehension of the intricate mechanisms governing the pathogenesis of the disease remains incomplete, posing a challenge for the development of efficient therapies. Pathologically characterized by the presence of amyloid β plaques and neurofibrillary tau tangles, AD is also accompanied by the hyperactivation of glial cells and the immune system. The complement cascade, the evolutionarily conserved innate immune pathway, has emerged as a significant contributor to AD. This review focuses on one of the complement components, the C3a receptor (C3aR), covering its structure, ligand-receptor interaction, intracellular signaling and its functional consequences. Drawing insights from cellular and AD mouse model studies, we present the multifaceted role of complement C3aR signaling in AD and attempt to convey to the readers that C3aR acts as a crucial immune and metabolic modulator to influence AD pathogenesis. Building on this framework, the objective of this review is to inform future research endeavors and facilitate the development of therapeutic strategies for this challenging condition.
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Affiliation(s)
- Manasee Gedam
- Department of Molecular and Human Genetics, Huffington Center on Aging, Baylor College of Medicine, Houston, Texas, USA
| | - Hui Zheng
- Department of Molecular and Human Genetics, Huffington Center on Aging, Baylor College of Medicine, Houston, Texas, USA
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17
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Kapolka NJ, Taghon GJ, Isom DG. Advances in yeast synthetic biology for human G protein-coupled receptor biology and pharmacology. Curr Opin Biotechnol 2024; 88:103176. [PMID: 39079313 DOI: 10.1016/j.copbio.2024.103176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/04/2024] [Accepted: 07/12/2024] [Indexed: 08/11/2024]
Abstract
G protein-coupled receptors (GPCRs) are the largest family of transmembrane receptors in humans. Over 800 GPCRs regulate the (patho)biology of every organ, tissue, and cell type. Consequently, GPCRs are the most prominent therapeutic targets in medicine. Although over 30% of current U.S. Food and Drug Administration-approved drugs target GPCR signaling, most receptors remain understudied and therapeutically underutilized. Challenges include an incomplete understanding of GPCR signaling, pharmacology, structural biology, and the multiplicity of endogenous GPCR ligands, in addition to a scarcity of biological and pharmacological tools for elucidating GPCR-mediated cellular processes beyond initial signaling events. Various mammalian, insect, and yeast cell models currently address some of these needs. Here, we review recent advances in yeast synthetic biology that are helping to catalyze new and unexpected conceptual and technical breakthroughs in GPCR-based medicine and biotechnology.
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Affiliation(s)
- Nicholas J Kapolka
- Department of Pharmacology, University of North Carolina, Chapel Hill, USA
| | - Geoffrey J Taghon
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Daniel G Isom
- Department of Molecular and Cellular Pharmacology, University of Miami School of Medicine, USA; Sylvester Comprehensive Cancer Center, Tumor Biology Program, USA; Frost Institute for Data Science and Computing, USA
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18
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Thompson MD, Percy ME, Cole DEC, Bichet DG, Hauser AS, Gorvin CM. G protein-coupled receptor (GPCR) gene variants and human genetic disease. Crit Rev Clin Lab Sci 2024; 61:317-346. [PMID: 38497103 DOI: 10.1080/10408363.2023.2286606] [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: 05/24/2023] [Revised: 08/28/2023] [Accepted: 11/19/2023] [Indexed: 03/19/2024]
Abstract
Genetic variations in the genes encoding G protein-coupled receptors (GPCRs) can disrupt receptor structure and function, which can result in human genetic diseases. Disease-causing mutations have been reported in at least 55 GPCRs for more than 66 monogenic diseases in humans. The spectrum of pathogenic and likely pathogenic variants includes loss of function variants that decrease receptor signaling on one extreme and gain of function that may result in biased signaling or constitutive activity, originally modeled on prototypical rhodopsin GPCR variants identified in retinitis pigmentosa, on the other. GPCR variants disrupt ligand binding, G protein coupling, accessory protein function, receptor desensitization and receptor recycling. Next generation sequencing has made it possible to identify variants of uncertain significance (VUS). We discuss variants in receptors known to result in disease and in silico strategies for disambiguation of VUS such as sorting intolerant from tolerant and polymorphism phenotyping. Modeling of variants has contributed to drug development and precision medicine, including drugs that target the melanocortin receptor in obesity and interventions that reverse loss of gonadotropin-releasing hormone receptor from the cell surface in idiopathic hypogonadotropic hypogonadism. Activating and inactivating variants of the calcium sensing receptor (CaSR) gene that are pathogenic in familial hypocalciuric hypercalcemia and autosomal dominant hypocalcemia have enabled the development of calcimimetics and calcilytics. Next generation sequencing has continued to identify variants in GPCR genes, including orphan receptors, that contribute to human phenotypes and may have therapeutic potential. Variants of the CaSR gene, some encoding an arginine-rich region that promotes receptor phosphorylation and intracellular retention, have been linked to an idiopathic epilepsy syndrome. Agnostic strategies have identified variants of the pyroglutamylated RF amide peptide receptor gene in intellectual disability and G protein-coupled receptor 39 identified in psoriatic arthropathy. Coding variants of the G protein-coupled receptor L1 (GPR37L1) orphan receptor gene have been identified in a rare familial progressive myoclonus epilepsy. The study of the role of GPCR variants in monogenic, Mendelian phenotypes has provided the basis of modeling the significance of more common variants of pharmacogenetic significance.
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Affiliation(s)
- Miles D Thompson
- Krembil Brain Institute, Toronto Western Hospital, Toronto, ON, Canada
| | - Maire E Percy
- Departments of Physiology and Obstetrics & Gynaecology, University of Toronto, Toronto, ON, Canada
| | - David E C Cole
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Daniel G Bichet
- Department of Physiology and Medicine, Hôpital du Sacré-Coeur, Université de Montréal, QC, Canada
| | - Alexander S Hauser
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Caroline M Gorvin
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, West Midlands, UK
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19
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Hu S, Wang D, Liu W, Wang Y, Chen J, Cai X. Apelin receptor dimer: Classification, future prospects, and pathophysiological perspectives. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167257. [PMID: 38795836 DOI: 10.1016/j.bbadis.2024.167257] [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: 02/08/2024] [Revised: 04/25/2024] [Accepted: 05/17/2024] [Indexed: 05/28/2024]
Abstract
Apelin receptor (APJ), a member of the class A family of G protein-coupled receptor (GPCR), plays a crucial role in regulating cardiovascular and central nervous systems function. APJ influences the onset and progression of various diseases such as hypertension, atherosclerosis, and cerebral stroke, making it an important target for drug development. Our preliminary findings indicate that APJ can form homodimers, heterodimers, or even higher-order oligomers, which participate in different signaling pathways and have distinct functions compared with monomers. APJ homodimers can serve as neuroprotectors against, and provide new pharmaceutical targets for vascular dementia (VD). This review article aims to summarize the structural characteristics of APJ dimers and their roles in physiology and pathology, as well as explore their potential pharmacological applications.
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Affiliation(s)
- Shujuan Hu
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang, Shandong 261042, PR China
| | - Dexiu Wang
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang, Shandong 261042, PR China
| | - Wenkai Liu
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang, Shandong 261042, PR China
| | - Yixiang Wang
- School of Clinical Medicine, Shandong Second Medical University, Weifang, Shandong 261042, PR China
| | - Jing Chen
- Neurobiology Institute, Jining Medical University, Jining, Shandong 272067, PR China; Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK.
| | - Xin Cai
- School of Basic Medical Sciences, Shandong Second Medical University, Weifang, Shandong 261042, PR China.
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20
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Anversa RG, Barron ML, Walker LC, Lawrence AJ. Emerging GPCR targets for AUD: Insights from preclinical studies. Curr Opin Neurobiol 2024; 87:102896. [PMID: 38971113 DOI: 10.1016/j.conb.2024.102896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/13/2024] [Accepted: 06/13/2024] [Indexed: 07/08/2024]
Abstract
G protein-coupled receptors (GPCRs) are the largest group of membrane receptors in the central nervous system and one of the key proteins for signal transduction between cells. Currently, many drugs available on the market act via GPCRs and these receptors remain attractive targets for the treatment of brain disorders, including alcohol use disorder (AUD). Here, we describe the most recent literature, with a primary focus on the past 5 years, on GPCR targets with the potential for reducing behaviours associated with excessive alcohol intake. Specifically, we focus on preclinical evidence of compounds with attractive pharmacological profiles and potential for future clinical investigation for the treatment of AUD.
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Affiliation(s)
- Roberta Goncalves Anversa
- Florey Institute of Neuroscience and Mental Health, Melbourne 3052, Australia; Florey Department of Neuroscience and Mental Health, University of Melbourne, Melbourne 3052, Australia
| | - Maiya L Barron
- Florey Institute of Neuroscience and Mental Health, Melbourne 3052, Australia; School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Leigh C Walker
- Florey Institute of Neuroscience and Mental Health, Melbourne 3052, Australia; Florey Department of Neuroscience and Mental Health, University of Melbourne, Melbourne 3052, Australia
| | - Andrew J Lawrence
- Florey Institute of Neuroscience and Mental Health, Melbourne 3052, Australia; Florey Department of Neuroscience and Mental Health, University of Melbourne, Melbourne 3052, Australia.
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21
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Yoon YE, Jung YJ, Lee SJ. A Food Odorant, α-Ionone, Inhibits Skin Cancer Tumorigenesis by Activation of OR10A6. Mol Nutr Food Res 2024; 68:e2400085. [PMID: 39021302 DOI: 10.1002/mnfr.202400085] [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: 02/02/2024] [Revised: 06/02/2024] [Indexed: 07/20/2024]
Abstract
SCOPE This study aims to investigate the anticancer properties of α-ionone in squamous cell carcinoma (SCC). METHODS AND RESULTS The expression of OR10A6 together with olfactory receptor signaling components is demonstrated in A431 human SCC cells via RT-PCR and qRT-PCR analysis. OR10A6 activation in A431 cells using the ligand α-ionone inhibits proliferation and migration but induces apoptosis which is confirmed by proliferation assay, colony formation, and western blotting. The mechanism involves the core proteins of the Hippo pathway, where the phosphorylation of large tumor suppressor kinase (LATS), yes-associated protein (YAP), and transcriptional coactivator with PDZ-binding motif (TAZ) is confirmed by western blotting. However, the anticancer effects of α-ionone are abrogated in A431 cells with OR10A6 gene knockdown. In A431 xenograft mouse model, the injection of α-ionone suppresses tumor growth, induces apoptosis, and increases phosphorylation of the LATS-YAP-TAZ signaling axis in the Hippo pathway. None of these effects are observed in xenografted tumors with OR10A6 gene knockdown. CONCLUSION These findings collectively demonstrate that activation of ectopic OR OR10A6 by α-ionone in SCC cells stimulates the Hippo pathway and suppresses tumorigenesis both in vitro and in vivo, suggesting a novel therapeutic candidate for the treatment of SCC.
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Affiliation(s)
- Ye Eun Yoon
- Department of Biotechnology, Graduate school of Life Sciences & Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02846, Republic of Korea
| | - Young Jae Jung
- Department of Biotechnology, Graduate school of Life Sciences & Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02846, Republic of Korea
| | - Sung-Joon Lee
- Department of Food Bioscience and Technology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02855, Republic of Korea
- Interdisciplinary Program in Precision Public Hesalth, Korea University, Seoul, 02846, Republic of Korea
- BK21 Four Institute of Precision Public Health, Korea University, Seoul, 02846, Republic of Korea
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22
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Sanz-Martinez P, Tascher G, Cano-Franco S, Cabrerizo-Poveda P, Münch C, Homan EJ, Stolz A. GPCR Function in Autophagy Control: A Systematic Approach of Chemical Intervention. J Mol Biol 2024; 436:168643. [PMID: 38848865 DOI: 10.1016/j.jmb.2024.168643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 05/10/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Autophagy facilitates the degradation of cellular content via the lysosome and is involved in cellular homeostasis and stress response pathways. As such, malfunction of autophagy is linked to a variety of diseases ranging from organ-specific illnesses like cardiomyopathy to systemic illnesses such as cancer or metabolic syndromes. Given the variety of autophagic functions within a cell and tissue, regulation of autophagy is complex and contains numerous positive and negative feedback loops. While our knowledge of mechanisms for cargo selectivity has significantly improved over the last decade, our understanding of signaling routes activating individual autophagy pathways remains rather sparse. In this resource study, we report on a well-characterized chemical library containing 77 GPCR-targeting ligands that was used to systematically analyze LC3B-based autophagy as well as ER-phagy flux upon compound treatment. Upon others, compounds TC-G 1004, BAY 60-6583, PSNCBAM-1, TC-G 1008, LPA2 Antagonist 1, ML-154, JTC-801 and ML-290 targeting adenosine receptor A2a (ADORA2A), adenosine receptor A2b (ADORA2B), cannabinoid receptor 1 (CNR1), G-protein coupled receptor 39 (GPR39), lysophosphatidic acid receptor 2 (LPAR2), neuropeptide S receptor 1 (NPSR1), opioid related nociceptin receptor 1 (OPRL1), and relaxin receptor 1 (RXFP1), respectively, were hit compounds for general autophagy flux. From these compounds, only JTC-801 markly increased ER-phagy flux. In addition, the global impact of these selected hit compounds were analyzed by TMT-based mass spectrometry and demonstrated the differential impact of targeting GPCRs on autophagy-associated proteins. This chemical screening exercise indicates to a significant cross-talk between GPCR signaling and regulation of autophagy pathways.
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Affiliation(s)
- Pablo Sanz-Martinez
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Georg Tascher
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Sara Cano-Franco
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Paloma Cabrerizo-Poveda
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Evert J Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Solna, Sweden.
| | - Alexandra Stolz
- Institute of Biochemistry II (IBC2), Faculty of Medicine, Goethe University, Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany.
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23
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Raskovalov A, Kim D, Cherezov V. ONE-GO: Direct detection of context-dependent GPCR activity. Cell Res 2024; 34:543-544. [PMID: 38688989 PMCID: PMC11291849 DOI: 10.1038/s41422-024-00966-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024] Open
Affiliation(s)
- Aleksey Raskovalov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
- Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
| | - Donggyun Kim
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
- Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
| | - Vadim Cherezov
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
- Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.
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24
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Zell L, Hofer TS, Schubert M, Popoff A, Höll A, Marschhofer M, Huber-Cantonati P, Temml V, Schuster D. Impact of 2-hydroxypropyl-β-cyclodextrin inclusion complex formation on dopamine receptor-ligand interaction - A case study. Biochem Pharmacol 2024; 226:116340. [PMID: 38848779 DOI: 10.1016/j.bcp.2024.116340] [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: 02/08/2024] [Revised: 05/10/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
The octanol-water distribution coefficient (logP), used as a measure of lipophilicity, plays a major role in the drug design and discovery processes. While average logP values remain unchanged in approved oral drugs since 1983, current medicinal chemistry trends towards increasingly lipophilic compounds that require adapted analytical workflows and drug delivery systems. Solubility enhancers like cyclodextrins (CDs), especially 2-hydroxypropyl-β-CD (2-HP-β-CD), have been studied in vitro and in vivo investigating their ADMET (adsorption, distribution, metabolism, excretion and toxicity)-related properties. However, data is scarce regarding the applicability of CD inclusion complexes (ICs) in vitro compared to pure compounds. In this study, dopamine receptor (DR) ligands were used as a case study, utilizing a combined in silico/in vitro workflow. Media-dependent solubility and IC stoichiometry were investigated using HPLC. NMR was used to observe IC formation-caused chemical shift deviations while in silico approaches utilizing basin hopping global minimization were used to propose putative IC binding modes. A cell-based in vitro homogeneous time-resolved fluorescence (HTRF) assay was used to quantify ligand binding affinity at the DR subtype 2 (D2R). While all ligands showed increased solubility using 2-HP-β-CD, they differed regarding IC stoichiometry and receptor binding affinity. This case study shows that IC-formation was ligand-dependent and sometimes altering in vitro binding. Therefore, IC complex formation can't be recommended as a general means of improving compound solubility for in vitro studies as they may alter ligand binding.
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Affiliation(s)
- Lukas Zell
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria
| | - Thomas S Hofer
- Institute of General, Inorganic and Theoretical Chemistry, Center for Biochemistry and Biomedicine, University of Innsbruck, 6020 Innsbruck, Austria
| | - Mario Schubert
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria; Department of Chemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Alexander Popoff
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria
| | - Anna Höll
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria
| | - Moritz Marschhofer
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria
| | - Petra Huber-Cantonati
- Department of Pharmaceutical Biology, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria
| | - Veronika Temml
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria
| | - Daniela Schuster
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University, 5020 Salzburg, Austria; Research and Innovation Center for Novel Therapies and Regenerative Medicine, Austria.
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25
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Otvos L. The latest trends in peptide drug discovery and future challenges. Expert Opin Drug Discov 2024; 19:869-872. [PMID: 38860697 DOI: 10.1080/17460441.2024.2365969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/05/2024] [Indexed: 06/12/2024]
Affiliation(s)
- Laszlo Otvos
- OLPE Pharmaceutical Consultants, Audubon, USA
- The Institute for Microbiology, Semmelweis University, Budapest, Hungary
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26
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Picard LP, Orazietti A, Tran DP, Tucs A, Hagimoto S, Qi Z, Huang SK, Tsuda K, Kitao A, Sljoka A, Prosser RS. Balancing G protein selectivity and efficacy in the adenosine A 2A receptor. Nat Chem Biol 2024:10.1038/s41589-024-01682-6. [PMID: 39085516 DOI: 10.1038/s41589-024-01682-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 06/23/2024] [Indexed: 08/02/2024]
Abstract
The adenosine A2A receptor (A2AR) engages several G proteins, notably Go and its cognate Gs protein. This coupling promiscuity is facilitated by a dynamic ensemble, revealed by 19F nuclear magnetic resonance imaging of A2AR and G protein. Two transmembrane helix 6 (TM6) activation states, formerly associated with partial and full agonism, accommodate the differing volumes of Gs and Go. While nucleotide depletion biases TM7 toward a fully active state in A2AR-Gs, A2AR-Go is characterized by a dynamic inactive/intermediate fraction. Molecular dynamics simulations reveal that the NPxxY motif, a highly conserved switch, establishes a unique configuration in the A2AR-Go complex, failing to stabilize the helix-8 interface with Gs, and adoption of the active state. The resulting TM7 dynamics hamper G protein coupling, suggesting kinetic gating may be responsible for reduced efficacy in the noncognate G protein complex. Thus, dual TM6 activation states enable greater diversity of coupling partners while TM7 dynamics dictate coupling efficacy.
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Affiliation(s)
- Louis-Philippe Picard
- Department of Chemical and Physical Sciences, University of Toronto Mississauga (UTM), Mississauga, Ontario, Canada
| | | | - Duy Phuoc Tran
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Andrejs Tucs
- Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
- Center for Advanced Intelligence Project, RIKEN, Tokyo, Japan
| | - Sari Hagimoto
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Zhenzhou Qi
- Department of Chemical and Physical Sciences, University of Toronto Mississauga (UTM), Mississauga, Ontario, Canada
| | - Shuya Kate Huang
- Department of Chemical and Physical Sciences, University of Toronto Mississauga (UTM), Mississauga, Ontario, Canada
| | - Koji Tsuda
- Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
- Center for Advanced Intelligence Project, RIKEN, Tokyo, Japan
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Adnan Sljoka
- Center for Advanced Intelligence Project, RIKEN, Tokyo, Japan
- Department of Chemistry, York University, Toronto, Ontario, Canada
| | - R Scott Prosser
- Department of Chemical and Physical Sciences, University of Toronto Mississauga (UTM), Mississauga, Ontario, Canada.
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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27
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Sajkowska JJ, Tsang CH, Kozielewicz P. Application of FRET- and BRET-based live-cell biosensors in deorphanization and ligand discovery studies on orphan G protein-coupled receptors. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100174. [PMID: 39084335 DOI: 10.1016/j.slasd.2024.100174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/16/2024] [Accepted: 07/26/2024] [Indexed: 08/02/2024]
Abstract
Bioluminescence- and fluorescence-based resonance energy transfer assays have gained considerable attention in pharmacological research as high-throughput scalable tools applicable to drug discovery. To this end, G protein-coupled receptors represent the biggest target class for marketed drugs, and among them, orphan G protein-coupled receptors have the biggest untapped therapeutic potential. In this review, the cases where biophysical methods, BRET and FRET, were employed for deorphanization and ligand discovery studies on orphan G protein-coupled receptors are listed and discussed.
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Affiliation(s)
- Joanna J Sajkowska
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden; Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Warsaw, Poland; Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Choi Har Tsang
- Department of Physiology and Pharmacology, Molecular Pharmacology of GPCRs, Karolinska Institute, Stockholm, Sweden
| | - Paweł Kozielewicz
- Department of Physiology and Pharmacology, Molecular Pharmacology of GPCRs, Karolinska Institute, Stockholm, Sweden.
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28
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Khetan R, Eldi P, Lokman NA, Ricciardelli C, Oehler MK, Blencowe A, Garg S, Pillman K, Albrecht H. Unveiling G-protein coupled receptors as potential targets for ovarian cancer nanomedicines: from RNA sequencing data analysis to in vitro validation. J Ovarian Res 2024; 17:156. [PMID: 39068454 PMCID: PMC11282829 DOI: 10.1186/s13048-024-01479-0] [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: 05/22/2024] [Accepted: 07/16/2024] [Indexed: 07/30/2024] Open
Abstract
Genetic heterogeneity in ovarian cancer indicates the need for personalised treatment approaches. Currently, very few G-protein coupled receptors (GPCRs) have been investigated for active targeting with nanomedicines such as antibody-conjugated drugs and drug-loaded nanoparticles, highlighting a neglected potential to develop personalised treatment. To address the genetic heterogeneity of ovarian cancer, a future personalised approach could include the identification of unique GPCRs expressed in cancer biopsies, matched with personalised GPCR-targeted nanomedicines, for the delivery of lethal drugs to tumour tissue before, during and after surgery. Here we report on the systematic analysis of public ribonucleic acid-sequencing (RNA-seq) gene expression data, which led to prioritisation of 13 GPCRs as candidates with frequent overexpression in ovarian cancer tissues. Subsequently, primary ovarian cancer cells derived from ascites and ovarian cancer cell lines were used to confirm frequent gene expression for the selected GPCRs. However, the expression levels showed high variability within our selection of samples, therefore, supporting and emphasising the need for the future development of case-to-case personalised targeting approaches.
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Affiliation(s)
- Riya Khetan
- Centre of Pharmaceutical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Preethi Eldi
- UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Noor A Lokman
- Discipline of Obstetrics and Gynaecology, Adelaide Medical School, Robinson Research Institute, University of Adelaide, Adelaide, South Australia, 5000, Australia
| | - Carmela Ricciardelli
- Discipline of Obstetrics and Gynaecology, Adelaide Medical School, Robinson Research Institute, University of Adelaide, Adelaide, South Australia, 5000, Australia
| | - Martin K Oehler
- Discipline of Obstetrics and Gynaecology, Adelaide Medical School, Robinson Research Institute, University of Adelaide, Adelaide, South Australia, 5000, Australia
- Department of Gynaecological Oncology, Royal Adelaide Hospital, Adelaide, South Australia, 5000, Australia
| | - Anton Blencowe
- Applied Chemistry and Translational Biomaterials Group, Centre of Pharmaceutical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Sanjay Garg
- Centre of Pharmaceutical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia
| | - Katherine Pillman
- Centre for Cancer Biology, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia.
| | - Hugo Albrecht
- Centre of Pharmaceutical Innovation, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, 5000, Australia.
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29
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Lin KY, Gujar MR, Lin J, Ding WY, Huang J, Gao Y, Tan YS, Teng X, Christine LSL, Kanchanawong P, Toyama Y, Wang H. Astrocytes control quiescent NSC reactivation via GPCR signaling-mediated F-actin remodeling. SCIENCE ADVANCES 2024; 10:eadl4694. [PMID: 39047090 PMCID: PMC11268418 DOI: 10.1126/sciadv.adl4694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 06/18/2024] [Indexed: 07/27/2024]
Abstract
The transitioning of neural stem cells (NSCs) between quiescent and proliferative states is fundamental for brain development and homeostasis. Defects in NSC reactivation are associated with neurodevelopmental disorders. Drosophila quiescent NSCs extend an actin-rich primary protrusion toward the neuropil. However, the function of the actin cytoskeleton during NSC reactivation is unknown. Here, we reveal the fine filamentous actin (F-actin) structures in the protrusions of quiescent NSCs by expansion and super-resolution microscopy. We show that F-actin polymerization promotes the nuclear translocation of myocardin-related transcription factor, a microcephaly-associated transcription factor, for NSC reactivation and brain development. F-actin polymerization is regulated by a signaling cascade composed of G protein-coupled receptor Smog, G protein αq subunit, Rho1 guanosine triphosphatase, and Diaphanous (Dia)/Formin during NSC reactivation. Further, astrocytes secrete a Smog ligand folded gastrulation to regulate Gαq-Rho1-Dia-mediated NSC reactivation. Together, we establish that the Smog-Gαq-Rho1 signaling axis derived from astrocytes, an NSC niche, regulates Dia-mediated F-actin dynamics in NSC reactivation.
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Affiliation(s)
- Kun-Yang Lin
- Neuroscience and Behavioral Disorders Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Mahekta R. Gujar
- Neuroscience and Behavioral Disorders Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jiaen Lin
- Neuroscience and Behavioral Disorders Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Wei Yung Ding
- Neuroscience and Behavioral Disorders Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Jiawen Huang
- Neuroscience and Behavioral Disorders Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Yang Gao
- Neuroscience and Behavioral Disorders Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Ye Sing Tan
- Neuroscience and Behavioral Disorders Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
| | - Xiang Teng
- Mechanobiology Institute, Level 5, T-lab Building, 5A Engineering Drive 1, Singapore, 117411, Singapore
| | - Low Siok Lan Christine
- Mechanobiology Institute, Level 5, T-lab Building, 5A Engineering Drive 1, Singapore, 117411, Singapore
| | - Pakorn Kanchanawong
- Mechanobiology Institute, Level 5, T-lab Building, 5A Engineering Drive 1, Singapore, 117411, Singapore
| | - Yusuke Toyama
- Mechanobiology Institute, Level 5, T-lab Building, 5A Engineering Drive 1, Singapore, 117411, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Hongyan Wang
- Neuroscience and Behavioral Disorders Programme, Duke-NUS Medical School, 8 College Road, Singapore 169857, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Integrative Sciences and Engineering Programme, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
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30
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Philibert CE, Garcia-Marcos M. Smooth operator(s): dialing up and down neurotransmitter responses by G-protein regulators. Trends Cell Biol 2024:S0962-8924(24)00140-5. [PMID: 39054106 DOI: 10.1016/j.tcb.2024.07.002] [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: 05/09/2024] [Revised: 06/19/2024] [Accepted: 07/01/2024] [Indexed: 07/27/2024]
Abstract
G-protein-coupled receptors (GPCRs) are essential mediators of neuromodulation and prominent pharmacological targets. While activation of heterotrimeric G-proteins (Gαβɣ) by GPCRs is essential in this process, much less is known about the postreceptor mechanisms that influence G-protein activity. Neurons express G-protein regulators that shape the amplitude and kinetics of GPCR-mediated synaptic responses. Although many of these operate by directly altering how G-proteins handle guanine-nucleotides enzymatically, recent discoveries have revealed alternative mechanisms by which GPCR-stimulated G-protein responses are modulated at the synapse. In this review, we cover the molecular basis for, and consequences of, the action of two G-protein regulators that do not affect the enzymatic activity of G-proteins directly: Gα inhibitory interacting protein (GINIP), which binds active Gα subunits, and potassium channel tetramerization domain-containing 12 (KCTD12), which binds active Gβγ subunits.
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Affiliation(s)
- Clementine E Philibert
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | - Mikel Garcia-Marcos
- Department of Biochemistry and Cell Biology, Chobanian and Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; Department of Biology, College of Arts and Sciences, Boston University, Boston, MA 02115, USA.
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31
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Yang X, Zhou P, Shen S, Hu Q, Tian C, Xia A, Wang Y, Yang Z, Nan J, Zhou Y, Chen S, Tian X, Wu C, Lin G, Zhang L, Wang K, Zheng T, Zou J, Yan W, Shao Z, Yang S. Entropy drives the ligand recognition in G-protein-coupled receptor subtypes. Proc Natl Acad Sci U S A 2024; 121:e2401091121. [PMID: 39024109 PMCID: PMC11287286 DOI: 10.1073/pnas.2401091121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/22/2024] [Indexed: 07/20/2024] Open
Abstract
Achieving ligand subtype selectivity within highly homologous subtypes of G-protein-coupled receptor (GPCR) is critical yet challenging for GPCR drug discovery, primarily due to the unclear mechanism underlying ligand subtype selectivity, which hampers the rational design of subtype-selective ligands. Herein, we disclose an unusual molecular mechanism of entropy-driven ligand recognition in cannabinoid (CB) receptor subtypes, revealed through atomic-level molecular dynamics simulations, cryoelectron microscopy structure, and mutagenesis experiments. This mechanism is attributed to the distinct conformational dynamics of the receptor's orthosteric pocket, leading to variations in ligand binding entropy and consequently, differential binding affinities, which culminate in specific ligand recognition. We experimentally validated this mechanism and leveraged it to design ligands with enhanced or ablated subtype selectivity. One such ligand demonstrated favorable pharmacokinetic properties and significant efficacy in rodent inflammatory analgesic models. More importantly, it is precisely due to the high subtype selectivity obtained based on this mechanism that this ligand does not show addictive properties in animal models. Our findings elucidate the unconventional role of entropy in CB receptor subtype selectivity and suggest a strategy for rational design of ligands to achieve entropy-driven subtype selectivity for many pharmaceutically important GPCRs.
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Affiliation(s)
- Xin Yang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Pei Zhou
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Siyuan Shen
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Qian Hu
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Chenyu Tian
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Anjie Xia
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- Department of Ophthalmology and Research Laboratory of Macular Disease, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Yifei Wang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Zhiqian Yang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Jinshan Nan
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Yangli Zhou
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Shasha Chen
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Xiaowen Tian
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Chao Wu
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Guifeng Lin
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Liting Zhang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Kexin Wang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Tao Zheng
- Engineering Research Center of Medical Information Technology, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Jun Zou
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Wei Yan
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Zhenhua Shao
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- Division of Nephrology and Kidney Research Institute, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- Frontier Medical Center, Tianfu Jincheng Laboratory, Chengdu, Sichuan610212, China
| | - Shengyong Yang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- Frontier Medical Center, Tianfu Jincheng Laboratory, Chengdu, Sichuan610212, China
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32
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Wang J, Miao Y. Ligand Gaussian Accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides. J Chem Theory Comput 2024; 20:5829-5841. [PMID: 39002136 DOI: 10.1021/acs.jctc.4c00502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2024]
Abstract
Binding thermodynamics and kinetics play critical roles in drug design. However, it has proven challenging to efficiently predict ligand binding thermodynamics and kinetics of small molecules and flexible peptides using conventional molecular dynamics (cMD), due to limited simulation time scales. Based on our previously developed ligand Gaussian accelerated molecular dynamics (LiGaMD) method, we present a new approach, termed "LiGaMD3″, in which we introduce triple boosts into three individual energy terms that play important roles in small-molecule/peptide dissociation, rebinding, and system conformational changes to improve the sampling efficiency of small-molecule/peptide interactions with target proteins. To validate the performance of LiGaMD3, MDM2 bound by a small molecule (Nutlin 3) and two highly flexible peptides (PMI and P53) were chosen as the model systems. LiGaMD3 could efficiently capture repetitive small-molecule/peptide dissociation and binding events within 2 μs simulations. The predicted binding kinetic constant rates and free energies from LiGaMD3 were in agreement with the available experimental values and previous simulation results. Therefore, LiGaMD3 provides a more general and efficient approach to capture dissociation and binding of both small-molecule ligands and flexible peptides, allowing for accurate prediction of their binding thermodynamics and kinetics.
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Affiliation(s)
- Jinan Wang
- Computational Medicine Program and Department of Pharmacology, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Yinglong Miao
- Computational Medicine Program and Department of Pharmacology, University of North Carolina-Chapel Hill, Chapel Hill, North Carolina 27599, United States
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33
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Xu X, Lu Y, Cao L, Miao Y, Li Y, Cui Y, Han T. Tumor-intrinsic P2RY6 drives immunosuppression by enhancing PGE 2 production. Cell Rep 2024; 43:114469. [PMID: 38996067 DOI: 10.1016/j.celrep.2024.114469] [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: 11/19/2023] [Revised: 05/21/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024] Open
Abstract
Despite the success of anti-programmed cell death-1 (anti-PD-1) immunotherapy, many cancer patients remain unresponsive, and reliable predictive biomarkers are lacking. Here, we show that aberrant expression of the pyrimidinergic receptor P2RY6 is frequent in human cancers and causes immune evasion. In mouse syngeneic and human xenograft tumor models, ectopic expression of P2RY6 shapes an immunosuppressive tumor microenvironment (TME) to enhance tumor growth and resistance to immunotherapy, whereas deletion of P2RY6 from tumors with high P2RY6 expression inflames the TME to inhibit tumor growth. As a G protein-coupled receptor, P2RY6 activates Gq/phospholipase C-β signaling and stimulates the synthesis of prostaglandin E2, which is a key mediator of immunosuppression in the TME. In contrast to the essential role of P2RY6 in tumors, global deletion of P2ry6 from mice does not compromise viability. Our study thus nominates P2RY6 as a precision immunotherapy target for patients with high tumor-intrinsic P2RY6 expression.
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Affiliation(s)
- Xilong Xu
- College of Life Sciences, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Yi Lu
- National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China
| | - Longzhi Cao
- National Institute of Biological Sciences, Beijing 102206, China; Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yang Miao
- National Institute of Biological Sciences, Beijing 102206, China; PTN Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yamei Li
- National Institute of Biological Sciences, Beijing 102206, China; Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yue Cui
- College of Life Sciences, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Ting Han
- College of Life Sciences, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China.
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34
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Aguilar-Pineda J, González-Melchor M. Influence of the Water Model on the Structure and Interactions of the GPR40 Protein with the Lipid Membrane and the Solvent: Rigid versus Flexible Water Models. J Chem Theory Comput 2024; 20:6369-6387. [PMID: 38991114 PMCID: PMC11270832 DOI: 10.1021/acs.jctc.4c00571] [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: 04/28/2024] [Revised: 06/07/2024] [Accepted: 06/21/2024] [Indexed: 07/13/2024]
Abstract
G protein-coupled receptors (GPCR) are responsible for modulating various physiological functions and are thus related to the pathophysiology of different diseases. Being potential therapeutic targets, multiple computational methodologies have been developed to analyze their behavior and interactions with other species. The solvent, on the other hand, has received much less attention. In this work, we analyzed the effect of four explicit water models on the structure and interactions of the GPR40 receptor in its apo form. We employed the rigid SPC/E and TIP4P models, and their flexible versions, the FBA/ϵ and TIP4P/ϵflex. We explored the structural changes and their correlation with some bulk dynamic properties of water. Our results showed an adverse effect on the conservation of the secondary structure of the receptor with all the models due to the breaking of the intramolecular hydrogen bond network, being more evident for the TIP4P models. Notably, all four models brought the receptor to states similar to the active one, modifying the intracellular part of the TM5 and TM6 domains in a "hinge" type movement, allowing the opening of the structure. Regarding the dynamic properties, the rigid models showed results comparable to those obtained in other studies on membrane systems. However, flexible models exhibit disparities in the molecular representation of systems. Surprisingly, the FBA/ϵ model improves the molecular picture of several properties, even though their agreement with bulk diffusion is poorer. These findings reinforce our idea that exploring other water models or improving the current ones, to better represent the membrane interface, can lead to a positive impact on the description of the signal transduction mechanisms and the search of new drugs by targeting these receptors.
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Affiliation(s)
- Jorge
Alberto Aguilar-Pineda
- Instituto de Física
“Luis Rivera Terrazas”, Benemérita Universidad
Autónoma de Puebla, Av San Claudio, Cd Universitaria, Apdo. Postal
J-48, Puebla 72570, México
| | - Minerva González-Melchor
- Instituto de Física
“Luis Rivera Terrazas”, Benemérita Universidad
Autónoma de Puebla, Av San Claudio, Cd Universitaria, Apdo. Postal
J-48, Puebla 72570, México
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35
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Tóth AD, Turu G, Hunyady L. Functional consequences of spatial, temporal and ligand bias of G protein-coupled receptors. Nat Rev Nephrol 2024:10.1038/s41581-024-00869-3. [PMID: 39039165 DOI: 10.1038/s41581-024-00869-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2024] [Indexed: 07/24/2024]
Abstract
G protein-coupled receptors (GPCRs) regulate every aspect of kidney function by mediating the effects of various endogenous and exogenous substances. A key concept in GPCR function is biased signalling, whereby certain ligands may selectively activate specific pathways within the receptor's signalling repertoire. For example, different agonists may induce biased signalling by stabilizing distinct active receptor conformations - a concept that is supported by advances in structural biology. However, the processes underlying functional selectivity in receptor signalling are extremely complex, involving differences in subcellular compartmentalization and signalling dynamics. Importantly, the molecular mechanisms of spatiotemporal bias, particularly its connection to ligand binding kinetics, have been detailed for GPCRs critical to kidney function, such as the AT1 angiotensin receptor (AT1R), V2 vasopressin receptor (V2R) and the parathyroid hormone 1 receptor (PTH1R). This expanding insight into the multifaceted nature of biased signalling paves the way for innovative strategies for targeting GPCR functions; the development of novel biased agonists may represent advanced pharmacotherapeutic approaches to the treatment of kidney diseases and related systemic conditions, such as hypertension, diabetes and heart failure.
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Affiliation(s)
- András D Tóth
- Institute of Molecular Life Sciences, Centre of Excellence of the Hungarian Academy of Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Department of Internal Medicine and Haematology, Semmelweis University, Budapest, Hungary
| | - Gábor Turu
- Institute of Molecular Life Sciences, Centre of Excellence of the Hungarian Academy of Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary
| | - László Hunyady
- Institute of Molecular Life Sciences, Centre of Excellence of the Hungarian Academy of Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary.
- Department of Physiology, Faculty of Medicine, Semmelweis University, Budapest, Hungary.
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36
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Okamoto Y, Kitakaze K, Takenouchi Y, Matsui R, Koga D, Miyashima R, Ishimaru H, Tsuboi K. GPR176 promotes fibroblast-to-myofibroblast transition in organ fibrosis progression. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119798. [PMID: 39047914 DOI: 10.1016/j.bbamcr.2024.119798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/20/2024] [Accepted: 07/14/2024] [Indexed: 07/27/2024]
Abstract
Fibrosis is characterized by excessive deposition of extracellular matrix proteins, particularly collagen, caused by myofibroblasts in response to chronic inflammation. Although G protein-coupled receptors (GPCRs) are among the targets of current antifibrotic drugs, no drug has yet been approved to stop fibrosis progression. Herein, we aimed to identify GPCRs with profibrotic effects. In gene expression analysis of mouse lungs with induced fibrosis, eight GPCRs were identified, showing a >2-fold increase in mRNA expression after fibrosis induction. Among them, we focused on Gpr176 owing to its significant correlation with a myofibroblast marker α-smooth muscle actin (αSMA), the profibrotic factor transforming growth factor β1 (TGFβ1), and collagen in a human lung gene expression database. Similar to the lung fibrosis model, increased Gpr176 expression was also observed in other organs affected by fibrosis, including the kidney, liver, and heart, suggesting its role in fibrosis across various organs. Furthermore, fibroblasts abundantly expressed Gpr176 compared to alveolar epithelial cells, endothelial cells, and macrophages in the fibrotic lung. GPR176 expression was unaffected by TGFβ1 stimulation in rat renal fibroblast NRK-49 cells, whereas knockdown of Gpr176 by siRNA reduced TGFβ1-induced expression of αSMA, fibronectin, and collagen as well as Smad2 phosphorylation. This suggested that Gpr176 regulates fibroblast activation. Consequently, Gpr176 acts in a profibrotic manner, and inhibiting its activity could potentially prevent myofibroblast differentiation and improve fibrosis. Developing a GPR176 inverse agonist or allosteric modulator is a promising therapeutic approach for fibrosis.
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Affiliation(s)
- Yasuo Okamoto
- Department of Pharmacology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan.
| | - Keisuke Kitakaze
- Department of Pharmacology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan
| | - Yasuhiro Takenouchi
- Department of Pharmacology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan
| | - Rena Matsui
- Department of Medical Technology, Kawasaki University of Medical Welfare, Kurashiki, Okayama 701-0192, Japan
| | - Daisuke Koga
- Department of Pharmacology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan
| | - Ryo Miyashima
- Department of Pharmacology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan
| | - Hironobu Ishimaru
- Department of Pharmacology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan
| | - Kazuhito Tsuboi
- Department of Pharmacology, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama 701-0192, Japan
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37
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Wen X, Chen M, Li Z, Liu W, Xu K, Wang J, Zhao X. Site-specific immobilization of Cysteinyl leukotriene receptor 1 through enzymatic DNA-protein conjugation strategy for lead screening. J Chromatogr A 2024; 1727:464948. [PMID: 38759460 DOI: 10.1016/j.chroma.2024.464948] [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: 03/09/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/19/2024]
Abstract
Immobilization of functional protein, especially G protein-coupled receptors (GPCRs), is particularly significant in various fields such as the development of assays for diagnosis, lead compound screening, as well as drug-protein interaction analysis. However, there are still some challenges with the immobilized proteins such as undefined loads, orientations, and the loss of activity. Herein, we introduced a DNA conjugation strategy into the immobilization of Cysteinyl leukotriene receptor 1(CysLTR1) which enables exquisite molecular control and higher activity of the receptor. We used the bacterial relaxases VirD2 as an immobilized tag fused at the C terminus of CysLTR1. Tyrosine residue(Y29) at the core binding site of the VirD2 tag can react with the single-strand piece of DNA(T-DNA) in the form of a covalent bond. Inspired by this strategy, we developed a new immobilization method by mixing the T-DNA-modified silica gel with the cell lysate containing the expressed VirD2-tagged CysLTR1 for 1 hour. We found that the successful formation of DNA-protein conjugate enables the immobilization of CysLTR1 fast, site-specific, and with minimal loss of activity. The feasibility of the immobilized CysLTR1 was evaluated in drug-protein binding interaction by frontal analysis and adsorption energy distribution analysis. The binding of pranlukast, zafirlukast, and MK571 to the immobilized CysLTR1 was realized, and the association constants presented good agreement between the two methods. Rosmarinic acid was retained in the immobilized CysLTR1 column, and the in-vitro test revealed that the compound binds to the receptor in one type of binding site mode. Despite these results, we concluded that the DNA-protein conjugate strategy will probably open up the possibilities for capturing other functional proteins in covalent and site-specific modes from the complex matrices and the immobilized receptor preserves the potential in fishing out lead compounds from natural products.
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Affiliation(s)
- Xin Wen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Minyu Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Zimeng Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Weiyao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ke Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Jing Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China.
| | - Xinfeng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
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38
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Lin B, Zhou Y, Huang Z, Ma M, Qi M, Jiang Z, Li G, Xu Y, Yan J, Wang D, Wang X, Jiang W, Zhou R. GPR34 senses demyelination to promote neuroinflammation and pathologies. Cell Mol Immunol 2024:10.1038/s41423-024-01204-3. [PMID: 39030423 DOI: 10.1038/s41423-024-01204-3] [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: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 07/21/2024] Open
Abstract
Sterile neuroinflammation is a major driver of multiple neurological diseases. Myelin debris can act as an inflammatory stimulus to promote inflammation and pathologies, but the mechanism is poorly understood. Here, we showed that lysophosphatidylserine (LysoPS)-GPR34 axis played a critical role in microglia-mediated myelin debris sensing and the subsequent neuroinflammation. Myelin debris-induced microglia activation and proinflammatory cytokine expression relied on its lipid component LysoPS. Both myelin debris and LysoPS promoted microglia activation and the production of proinflammatory cytokines via GPR34 and its downstream PI3K-AKT and ERK signaling. In vivo, reducing the content of LysoPS in myelin or inhibition of GPR34 with genetic or pharmacological approaches reduced neuroinflammation and pathologies in the mouse models of multiple sclerosis and stroke. Thus, our results identify GPR34 as a key receptor to sense demyelination and CNS damage and promote neuroinflammation, and suggest it as a potential therapeutic target for demyelination-associated diseases.
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Affiliation(s)
- Bolong Lin
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yubo Zhou
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Zonghui Huang
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, China
| | - Ming Ma
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Minghui Qi
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhongjun Jiang
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Guoyang Li
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yueli Xu
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Jiaxian Yan
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Di Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaqiong Wang
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Wei Jiang
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
| | - Rongbin Zhou
- Key Laboratory of immune response and immunotherapy, Center for Advanced Interdisciplinary Science and Biomedicine of IHM, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, China.
- Department of Geriatrics, Gerontology Institute of Anhui Province, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
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39
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Beerkens BL, Andrianopoulou V, Wang X, Liu R, van Westen GJP, Jespers W, IJzerman AP, Heitman LH, van der Es D. N-Acyl- N-Alkyl Sulfonamide Probes for Ligand-Directed Covalent Labeling of GPCRs: The Adenosine A 2B Receptor as Case Study. ACS Chem Biol 2024; 19:1554-1562. [PMID: 38920052 PMCID: PMC11267576 DOI: 10.1021/acschembio.4c00210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/05/2024] [Accepted: 06/17/2024] [Indexed: 06/27/2024]
Abstract
Small molecular tool compounds play an essential role in the study of G protein-coupled receptors (GPCRs). However, tool compounds most often occupy the orthosteric binding site, hampering the study of GPCRs upon ligand binding. To overcome this problem, ligand-directed labeling techniques have been developed that leave a reporter group covalently bound to the GPCR, while allowing subsequent orthosteric ligands to bind. In this work, we applied such a labeling strategy to the adenosine A2B receptor (A2BAR). We have synthetically implemented the recently reported N-acyl-N-alkyl sulfonamide (NASA) warhead into a previously developed ligand and show that the binding of the A2BAR is not restricted by NASA incorporation. Furthermore, we have investigated ligand-directed labeling of the A2BAR using SDS-PAGE, flow cytometric, and mass spectrometry techniques. We have found one of the synthesized probes to specifically label the A2BAR, although detection was hindered by nonspecific protein labeling most likely due to the intrinsic reactivity of the NASA warhead. Altogether, this work aids the future development of ligand-directed probes for the detection of GPCRs.
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Affiliation(s)
- Bert L.
H. Beerkens
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333
CC Leiden, The Netherlands
- Oncode
Institute, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| | - Vasiliki Andrianopoulou
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Xuesong Wang
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Rongfang Liu
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Gerard J. P. van Westen
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Willem Jespers
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Adriaan P. IJzerman
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333
CC Leiden, The Netherlands
| | - Laura H. Heitman
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333
CC Leiden, The Netherlands
- Oncode
Institute, Einsteinweg
55, 2333 CC Leiden, The Netherlands
| | - Daan van der Es
- Division
of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333
CC Leiden, The Netherlands
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40
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Wang C, Gu Y, Chen C, Li Y, Li L, Chai Y, Jiang Z, Chen X, Yuan Y. One-Step Synthesis and Oriented Immobilization of Strep-Tag II Fused PDGFRβ for Screening Intracellular Domain-Targeted Ligands. Anal Chem 2024; 96:11479-11487. [PMID: 38943570 DOI: 10.1021/acs.analchem.4c02067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2024]
Abstract
Accurate orientations and stable conformations of membrane receptor immobilization are particularly imperative for accurate drug screening and ligand-protein affinity analysis. However, there remain challenges associated with (1) traditional recombination, purification, and immobilization of membrane receptors, which are time-consuming and labor-intensive; (2) the orientations on the stationary phase are not easily controlled. Herein, a novel one-step synthesis and oriented-immobilization membrane-receptor affinity chromatography (oSOMAC) method was developed to realize high-throughput and accurate drug screening targeting specific domains of membrane receptors. We employed Strep-tag II as a noncovalent immobilization tag fused into platelet-derived growth factor receptor β (PDGFRβ) through CFPS, and meanwhile, the Strep-Tactin-modified monolithic columns are prepared in batches. The advantages of oSOMAC are as follows: (1) targeted membrane receptors can be expressed independent of living cell within 1-2 h; (2) orientation of membrane receptors can be flexibly controlled and active sites can expose accurately; and (3) targeted membrane receptors can be synthesized, purified, and orientation-immobilized on monolithic columns in one step. Accordingly, three potential PDGFRβ intracellular domain targeted ligands: tanshinone IIA (Tan IIA), hydroxytanshinone IIA, and dehydrotanshinone IIA were successfully screened out from Salvia miltiorrhiza extract through oSOMAC. Pharmacological experiments and molecular docking further demonstrated that Tan IIA could attenuate hepatic stellate cells activation by targeting the protein kinase domain of PDGFRβ with a KD value of 9.7 μM. Ultimately, the novel oSOMAC method provides an original insight for accurate drug screening and interaction analysis which can be applied in other membrane receptors.
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Affiliation(s)
- Chengliang Wang
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201999, China
| | - Yanqiu Gu
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201999, China
| | - Chun Chen
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201999, China
| | - Yanting Li
- Department of Pharmaceutical Analysis, School of Pharmacy, Ningxia Medical University, 1160 Shenli Street, Yinchuan 750004, China
| | - Ling Li
- School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai 200433, China
| | - Yifeng Chai
- School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai 200433, China
| | - Zhengjin Jiang
- Institute of Pharmaceutical Analysis, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Xiaofei Chen
- School of Pharmacy, Naval Medical University (Second Military Medical University), Shanghai 200433, China
| | - Yongfang Yuan
- Department of Pharmacy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201999, China
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41
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Leinonen H, Zhang J, Occelli LM, Seemab U, Choi EH, L P Marinho LF, Querubin J, Kolesnikov AV, Galinska A, Kordecka K, Hoang T, Lewandowski D, Lee TT, Einstein EE, Einstein DE, Dong Z, Kiser PD, Blackshaw S, Kefalov VJ, Tabaka M, Foik A, Petersen-Jones SM, Palczewski K. A combination treatment based on drug repurposing demonstrates mutation-agnostic efficacy in pre-clinical retinopathy models. Nat Commun 2024; 15:5943. [PMID: 39009597 PMCID: PMC11251169 DOI: 10.1038/s41467-024-50033-5] [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: 08/11/2023] [Accepted: 06/21/2024] [Indexed: 07/17/2024] Open
Abstract
Inherited retinopathies are devastating diseases that in most cases lack treatment options. Disease-modifying therapies that mitigate pathophysiology regardless of the underlying genetic lesion are desirable due to the diversity of mutations found in such diseases. We tested a systems pharmacology-based strategy that suppresses intracellular cAMP and Ca2+ activity via G protein-coupled receptor (GPCR) modulation using tamsulosin, metoprolol, and bromocriptine coadministration. The treatment improves cone photoreceptor function and slows degeneration in Pde6βrd10 and RhoP23H/WT retinitis pigmentosa mice. Cone degeneration is modestly mitigated after a 7-month-long drug infusion in PDE6A-/- dogs. The treatment also improves rod pathway function in an Rpe65-/- mouse model of Leber congenital amaurosis but does not protect from cone degeneration. RNA-sequencing analyses indicate improved metabolic function in drug-treated Rpe65-/- and rd10 mice. Our data show that catecholaminergic GPCR drug combinations that modify second messenger levels via multiple receptor actions provide a potential disease-modifying therapy against retinal degeneration.
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Affiliation(s)
- Henri Leinonen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonranta 1C, 70211, Kuopio, Finland.
| | - Jianye Zhang
- Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, 92697, USA
| | - Laurence M Occelli
- Small Animal Clinical Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Umair Seemab
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonranta 1C, 70211, Kuopio, Finland
| | - Elliot H Choi
- Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, 92697, USA
| | | | - Janice Querubin
- Small Animal Clinical Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Alexander V Kolesnikov
- Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, 92697, USA
| | - Anna Galinska
- International Centre for Translational Eye Research, Warsaw, Poland
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Kordecka
- International Centre for Translational Eye Research, Warsaw, Poland
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Thanh Hoang
- Department of Ophthalmology, Department of Cell & Developmental Biology, Ann Arbor, MI, 48105, USA
| | - Dominik Lewandowski
- Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, 92697, USA
| | - Timothy T Lee
- Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, 92697, USA
| | - Elliott E Einstein
- Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, 92697, USA
| | - David E Einstein
- Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, 92697, USA
| | - Zhiqian Dong
- Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, 92697, USA
| | - Philip D Kiser
- Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, 92697, USA
- Department of Physiology and Biophysics, School of Medicine, University of California - Irvine, Irvine, CA, 92697, USA
- Department of Clinical Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University of California - Irvine, Irvine, CA, 92697, USA
- Research Service, VA Long Beach Healthcare System, Long Beach, California, 90822, USA
| | - Seth Blackshaw
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Vladimir J Kefalov
- Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, 92697, USA
- Department of Physiology and Biophysics, School of Medicine, University of California - Irvine, Irvine, CA, 92697, USA
| | - Marcin Tabaka
- International Centre for Translational Eye Research, Warsaw, Poland
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Andrzej Foik
- International Centre for Translational Eye Research, Warsaw, Poland
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | | | - Krzysztof Palczewski
- Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, 92697, USA.
- Department of Physiology and Biophysics, School of Medicine, University of California - Irvine, Irvine, CA, 92697, USA.
- Department of Chemistry, University of California-Irvine, Irvine, CA, 92697, USA.
- Department of Molecular Biology and Biochemistry, University of California-Irvine, Irvine, CA, 92697, USA.
- Gavin Herbert Eye Institute-Center for Translational Vision Research, Department of Ophthalmology, University of California, Irvine, CA, 92697, USA.
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Cui Y, Auclair H, He R, Zhang Q. GPCR-mediated regulation of beige adipocyte formation: Implications for obesity and metabolic health. Gene 2024; 915:148421. [PMID: 38561165 DOI: 10.1016/j.gene.2024.148421] [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: 01/11/2024] [Revised: 03/10/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Obesity and its associated complications pose a significant burden on health. The non-shivering thermogenesis (NST) and metabolic capacity properties of brown adipose tissue (BAT), which are distinct from those of white adipose tissue (WAT), in combating obesity and its related metabolic diseases has been well documented. However, beige adipose tissue, the third and relatively novel type of adipose tissue, which emerges in extensive presence of WAT and shares similar favorable metabolic properties with BAT, has garnered considerable attention in recent years. In this review, we focused on the role of G protein-coupled receptors (GPCRs), the largest receptor family and the most successful class of drug targets in humans, in the induction of beige adipocytes. More importantly, we highlight researchers' clinical treatment attempts to ameliorate obesity and other related metabolic diseases through the formation and activation of beige adipose tissue. In summary, this review provides valuable insights into the formation of beige adipose tissue and the involvement of GPCRs, based on the latest advancements in scientific research.
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Affiliation(s)
- Yuanxu Cui
- Animal Zoology Department, Kunming Medical University, Kunming, China; Science and Technology Achievement Incubation Center, Kunming Medical University, Kunming, China
| | - Hugo Auclair
- Faculty of Medicine, François-Rabelais University, Tours, France
| | - Rong He
- Animal Zoology Department, Kunming Medical University, Kunming, China
| | - Qiang Zhang
- Animal Zoology Department, Kunming Medical University, Kunming, China.
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43
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Karimova D, Rostami E, Chubarev VN, Tarasov VV, Schiöth HB, Rask-Andersen M. Advances in development of biomarkers for brain damage and ischemia. Mol Biol Rep 2024; 51:803. [PMID: 39001884 PMCID: PMC11246271 DOI: 10.1007/s11033-024-09708-x] [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: 02/23/2024] [Accepted: 06/06/2024] [Indexed: 07/15/2024]
Abstract
Acquired brain injury is an urgent situation that requires rapid diagnosis and treatment. Magnetic resonance imaging (MRI) and computed tomography (CT) are required for accurate diagnosis. However, these methods are costly and require substantial infrastructure and specialized staff. Circulatory biomarkers of acute brain injury may help in the management of patients with acute cerebrovascular events and prevent poor outcome and mortality. The purpose of this review is to provide an overview of the development of potential biomarkers of brain damage to increase diagnostic possibilities. For this purpose, we searched the PubMed database of studies on the diagnostic potential of brain injury biomarkers. We also accessed information from Clinicaltrials.gov to identify any clinical trials of biomarker measurements for the diagnosis of brain damage. In total, we present 41 proteins, enzymes and hormones that have been considered as biomarkers for brain injury, of which 20 have been studied in clinical trials. Several microRNAs have also emerged as potential clinical biomarkers for early diagnosis. Combining multiple biomarkers in a panel, along with other parameters, is yielding promising outcomes.
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Affiliation(s)
- Diana Karimova
- Functional Pharmacology and Neuroscience, Department of Surgical Sciences, Uppsala, University, Uppsala, Sweden
| | - Elham Rostami
- Department of Medical Sciences, Section of Neurosurgery, Uppsala University, Uppsala, Sweden
| | - Vladimir N Chubarev
- Advanced Molecular Technology, Limited Liable Company (LLC), Moscow, 354340, Russia
| | - Vadim V Tarasov
- Advanced Molecular Technology, Limited Liable Company (LLC), Moscow, 354340, Russia
| | - Helgi B Schiöth
- Functional Pharmacology and Neuroscience, Department of Surgical Sciences, Uppsala, University, Uppsala, Sweden
| | - Mathias Rask-Andersen
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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44
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Gaiser BI, Danielsen M, Xu X, Røpke Jørgensen K, Fronik P, Märcher-Rørsted E, Wróbel TM, Liu X, Mosolff Mathiesen J, Sejer Pedersen D. Bitopic Ligands Support the Presence of a Metastable Binding Site at the β 2 Adrenergic Receptor. J Med Chem 2024; 67:11053-11068. [PMID: 38952152 DOI: 10.1021/acs.jmedchem.4c00578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Metastable binding sites (MBS) have been observed in a multitude of molecular dynamics simulations and can be considered low affinity allosteric binding sites (ABS) that function as stepping stones as the ligand moves toward the orthosteric binding site (OBS). Herein, we show that MBS can be utilized as ABS in ligand design, resulting in ligands with improved binding kinetics. Four homobivalent bitopic ligands (1-4) were designed by molecular docking of (S)-alprenolol ((S)-ALP) in the cocrystal structure of the β2 adrenergic receptor (β2AR) bound to the antagonist ALP. Ligand 4 displayed a potency and affinity similar to (S)-ALP, but with a >4-fold increase in residence time. The proposed binding mode was confirmed by X-ray crystallography of ligand 4 in complex with the β2AR. This ligand design principle can find applications beyond the β2AR and G protein-coupled receptors (GPCRs) as a general approach for improving the pharmacological profile of orthosteric ligands by targeting the OBS and an MBS simultaneously.
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Affiliation(s)
- Birgit Isabel Gaiser
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Mia Danielsen
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Xinyu Xu
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084 ,China
| | - Kira Røpke Jørgensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Philipp Fronik
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Emil Märcher-Rørsted
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Tomasz M Wróbel
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Chodźki 4a, 20093 Lublin, Poland
| | - Xiangyu Liu
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084 ,China
| | - Jesper Mosolff Mathiesen
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Daniel Sejer Pedersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
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45
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Bao Y, Tang Z, Chen R, Yu X, Qi X. Pan-cancer analysis identifies olfactory receptor family 7 subfamily A member 5 as a potential biomarker for glioma. PeerJ 2024; 12:e17631. [PMID: 39006026 PMCID: PMC11246023 DOI: 10.7717/peerj.17631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 06/04/2024] [Indexed: 07/16/2024] Open
Abstract
Background Human olfactory receptors (ORs) account for approximately 60% of all human G protein-coupled receptors. The functions of ORs extend beyond olfactory perception and have garnered significant attention in tumor biology. However, a comprehensive pan-cancer analysis of ORs in human cancers is lacking. Methods Using data from public databases, such as HPA, TCGA, GEO, GTEx, TIMER2, TISDB, UALCAN, GEPIA2, and GSCA, this study investigated the role of olfactory receptor family 7 subfamily A member 5 (OR7A5) in various cancers. Functional analysis of OR7A5 in LGG and GBM was performed using the CGGA database. Molecular and cellular experiments were performed to validate the expression and biological function of OR7A5 in gliomas. Results The results revealed heightened OR7A5 expression in certain tumors, correlating with the expression levels of immune checkpoints and immune infiltration. In patients with gliomas, the expression levels of OR7A5 were closely associated with adverse prognosis, 1p/19p co-deletion status, and wild-type IDH status. Finally, in vitro experiments confirmed the inhibitory effect of OR7A5 knockdown on the proliferative capacity of glioma cells and on the expression levels of proteins related to lipid metabolism. Conclusion This study establishes OR7A5 as a novel biomarker, potentially offering a novel therapeutic target for gliomas.
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Affiliation(s)
- Yanqiu Bao
- Department of Medical Research Center, Shaoxing People’s Hospital, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing, Zhejiang, China
| | - Ziqi Tang
- Institute of Psychology, Chinese Academy of Sciences, Beijing, China
| | - Renli Chen
- Department of Neurosurgery, Shaoxing People’s Hospital, Shaoxing, Zhejiang, China
| | - Xuebin Yu
- Department of Neurosurgery, Shaoxing People’s Hospital, Shaoxing, Zhejiang, China
| | - Xuchen Qi
- Department of Neurosurgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of Neurosurgery, Shaoxing People’s Hospital, Shaoxing Hospital, Zhejiang University School of Medicine, Shaoxing, Zhejiang, China
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46
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Hazan S, Tauber M, Ben-Chaim Y. Voltage dependence of M2 muscarinic receptor antagonists and allosteric modulators. Biochem Pharmacol 2024; 227:116421. [PMID: 38996933 DOI: 10.1016/j.bcp.2024.116421] [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: 02/15/2024] [Revised: 06/12/2024] [Accepted: 07/09/2024] [Indexed: 07/14/2024]
Abstract
Muscarinic receptors are G protein-coupled receptors (GPCRs) that play a role in various physiological functions. Previous studies have shown that these receptors, along with other GPCRs, are voltage-sensitive; both their affinity toward agonists and their activation are regulated by membrane potential. To our knowledge, whether the effect of antagonists on these receptors is voltage-dependent has not yet been studied. In this study, we used Xenopus oocytes expressing the M2 muscarinic receptor (M2R) to investigate this question. Our results indicate that the potencies of two M2R antagonists, atropine and scopolamine, are voltage-dependent; they are more effective at resting potential than under depolarization. In contrast, the M2R antagonist AF-DX 386 did not exhibit voltage-dependent potency.Furthermore, we discovered that the voltage dependence of M2R activation by acetylcholine remains unchanged in the presence of two allosteric modulators, the negative modulator gallamine and the positive modulator LY2119620. These findings enhance our understanding of GPCRs' voltage dependence and may have pharmacological implications.
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Affiliation(s)
- Shimrit Hazan
- Department of Natural Sciences, The Open University of Israel, Ra'anana, Israel
| | - Merav Tauber
- Department of Natural Sciences, The Open University of Israel, Ra'anana, Israel
| | - Yair Ben-Chaim
- Department of Natural Sciences, The Open University of Israel, Ra'anana, Israel.
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47
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Stein C. Effects of pH on opioid receptor activation and implications for drug design. Biophys J 2024:S0006-3495(24)00446-6. [PMID: 38970252 DOI: 10.1016/j.bpj.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/29/2024] [Accepted: 07/02/2024] [Indexed: 07/08/2024] Open
Abstract
G-protein-coupled receptors are integral membrane proteins that transduce chemical signals from the extracellular matrix into the cell. Traditional drug design has considered ligand-receptor interactions only under normal conditions. However, studies on opioids indicate that such interactions are very different in diseased tissues. In such microenvironments, protons play an important role in structural and functional alterations of both ligands and receptors. The pertinent literature strongly suggests that future drug design should take these aspects into account in order to reduce adverse side effects while preserving desired effects of novel compounds.
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Affiliation(s)
- Christoph Stein
- Charité Universitätsmedizin Berlin, Campus Benjamin Franklin, Experimental Anaesthesiology, Berlin, Germany.
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48
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Xie A, Zhang X, Ju F, Zhou Y, Wu D, Han J. Sevoflurane impedes neuropathic pain by maintaining endoplasmic reticulum stress and oxidative stress homeostasis through inhibiting the activation of the PLCγ/CaMKII/IP3R signaling pathway. Aging (Albany NY) 2024; 16:11062-11071. [PMID: 38975935 PMCID: PMC11272110 DOI: 10.18632/aging.206001] [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: 06/13/2023] [Accepted: 05/29/2024] [Indexed: 07/09/2024]
Abstract
OBJECTIVE To investigate the effect of sevoflurane on neuropathic pain induced by chronic constriction injury (CCI) of sciatic nerve in mice, and to elucidate its mechanism by animal experiments. METHODS AND RESULTS Thirty-two C57BL/6 mice were randomly divided into four groups: Sham group, Model group, Control group and Sevoflurane group. First, a mouse model of neuropathic pain was established. Then, the mice in each group were killed on Day 14 after operation to harvest the enlarged lumbosacral spinal cord. In contrast with the Model group, the Sevoflurane group displayed a significantly increased paw withdrawal mechanical threshold (PWMT) and significantly prolonged paw withdrawal thermal latency (PWTL) from Day 5 after operation. The morphological changes of lumbosacral spinal cord were observed by hematoxylin-eosin (HE) staining and transmission electron microscopy. Pathological results showed that sevoflurane reduced nuclear pyknosis in lumbosacral spinal cord tissue, with a large number of mitochondrial crista disappearance and mitochondrial swelling. The results of Western blotting showed that sevoflurane significantly decreased the protein expressions of phosphorylated phospholipase Cγ (p-PLCγ), phosphorylated calcium/calmodulin-dependent protein kinase II (p-CaMKII) and phosphorylated inositol 1,4,5-triphosphate receptor (p-IP3R), and reduced the protein expressions of endoplasmic reticulum (ER) stress proteins glucose-regulated protein 78 (GRP78) and GRP94, oxidative stress-related proteins P22 and P47 and inflammatory factors nucleotide-binding oligomerization domain-like receptor protein 3 (NLRP3), interleukin-1 β (IL-1β), and tumor necrosis factor-α (TNF-α). CONCLUSIONS Sevoflurane inhibits neuropathic pain by maintaining ER stress and oxidative stress homeostasis through inhibiting the activation of the PLCγ/CaMKII/IP3R signaling pathway.
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Affiliation(s)
- An Xie
- Department of Anesthesiology, People’s Hospital of Deyang, Deyang, Sichuan, China
| | - Xianjie Zhang
- Department of Anesthesiology, People’s Hospital of Deyang, Deyang, Sichuan, China
| | - Feng Ju
- Department of Anesthesiology, People’s Hospital of Deyang, Deyang, Sichuan, China
| | - Yukai Zhou
- Department of Anesthesiology, People’s Hospital of Deyang, Deyang, Sichuan, China
| | - Dan Wu
- Department of Anesthesiology, People’s Hospital of Deyang, Deyang, Sichuan, China
| | - Jia Han
- Department of Anesthesiology, People’s Hospital of Deyang, Deyang, Sichuan, China
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49
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Zhang T, An W, You S, Chen S, Zhang S. G protein-coupled receptors and traditional Chinese medicine: new thinks for the development of traditional Chinese medicine. Chin Med 2024; 19:92. [PMID: 38956679 PMCID: PMC11218379 DOI: 10.1186/s13020-024-00964-4] [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: 04/26/2024] [Accepted: 06/19/2024] [Indexed: 07/04/2024] Open
Abstract
G protein-coupled receptors (GPCRs) widely exist in vivo and participate in many physiological processes, thus emerging as important targets for drug development. Approximately 30% of the Food and Drug Administration (FDA)-approved drugs target GPCRs. To date, the 'one disease, one target, one molecule' strategy no longer meets the demands of drug development. Meanwhile, small-molecule drugs account for 60% of FDA-approved drugs. Traditional Chinese medicine (TCM) has garnered widespread attention for its unique theoretical system and treatment methods. TCM involves multiple components, targets and pathways. Centered on GPCRs and TCM, this paper discusses the similarities and differences between TCM and GPCRs from the perspectives of syndrome of TCM, the consistency of TCM's multi-component and multi-target approaches and the potential of GPCRs and TCM in the development of novel drugs. A novel strategy, 'simultaneous screening of drugs and targets', was proposed and applied to the study of GPCRs. We combine GPCRs with TCM to facilitate the modernisation of TCM, provide valuable insights into the rational application of TCM and facilitate the research and development of novel drugs. This study offers theoretical support for the modernisation of TCM and introduces novel ideas for development of safe and effective drugs.
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Affiliation(s)
- Ting Zhang
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611100, China
| | - Wenqiao An
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611100, China
| | - Shengjie You
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Sanyin Zhang
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611100, China.
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50
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An Y, Lim J, Glavatskikh M, Wang X, Norris-Drouin J, Hardy PB, Leisner TM, Pearce KH, Kireev D. In silico fragment-based discovery of CIB1-directed anti-tumor agents by FRASE-bot. Nat Commun 2024; 15:5564. [PMID: 38956119 PMCID: PMC11219766 DOI: 10.1038/s41467-024-49892-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 06/19/2024] [Indexed: 07/04/2024] Open
Abstract
Chemical probes are an indispensable tool for translating biological discoveries into new therapies, though are increasingly difficult to identify since novel therapeutic targets are often hard-to-drug proteins. We introduce FRASE-based hit-finding robot (FRASE-bot), to expedite drug discovery for unconventional therapeutic targets. FRASE-bot mines available 3D structures of ligand-protein complexes to create a database of FRAgments in Structural Environments (FRASE). The FRASE database can be screened to identify structural environments similar to those in the target protein and seed the target structure with relevant ligand fragments. A neural network model is used to retain fragments with the highest likelihood of being native binders. The seeded fragments then inform ultra-large-scale virtual screening of commercially available compounds. We apply FRASE-bot to identify ligands for Calcium and Integrin Binding protein 1 (CIB1), a promising drug target implicated in triple negative breast cancer. FRASE-based virtual screening identifies a small-molecule CIB1 ligand (with binding confirmed in a TR-FRET assay) showing specific cell-killing activity in CIB1-dependent cancer cells, but not in CIB1-depletion-insensitive cells.
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Affiliation(s)
- Yi An
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
| | - Jiwoong Lim
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
| | - Marta Glavatskikh
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
| | - Xiaowen Wang
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
- Chemistry department, University of Missouri, Columbia, Columbia, MO, 65211, USA
| | - Jacqueline Norris-Drouin
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
| | - P Brian Hardy
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
| | - Tina M Leisner
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA
| | - Kenneth H Pearce
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA.
| | - Dmitri Kireev
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, 27513, USA.
- Chemistry department, University of Missouri, Columbia, Columbia, MO, 65211, USA.
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