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Duraisamy K, Kumar M, Nawabjan A, Lo EKK, Hui Lin M, Lefranc B, Bonnafé E, Treilhou M, El-Nezami H, Leprince J, Chow BKC. MRGPRB2/X2 and the analogous effects of its agonist and antagonist in DSS-induced colitis in mice. Biomed Pharmacother 2024; 174:116471. [PMID: 38547764 DOI: 10.1016/j.biopha.2024.116471] [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: 10/23/2023] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 05/01/2024] Open
Abstract
The mast cell receptor Mrgprb2, a mouse orthologue of human Mrgprx2, is known as an inflammatory receptor and its elevated expression is associated with various diseases such as ulcerative colitis. We aimed to elucidate the role of Mrgprb2/x2 and the effect of its ligands on a chemically induced murine colitis model. We showed that in Mrgprb2-/- mice, there is a differential regulation of cytokine releases in the blood plasma and severe colonic damages after DSS treatment. Unexpectedly, we demonstrated that known Mrgprb2/x2 agonists (peptide P17, P17 analogues and CST-14) and antagonist (GE1111) similarly increased the survival rate of WT mice subjected to 4% DSS-induced colitis, ameliorated the colonic damages of 2.5% DSS-induced colitis, restored major protein mRNA expression involved in colon integrity, reduced CD68+ and F4/80+ immune cell infiltration and restored cytokine levels. Collectively, our findings highlight the eminent role of Mrpgrb2/x2 in conferring a beneficial effect in the colitis model, and this significance is demonstrated by the heightened severity of colitis with altered cytokine releases and inflammatory immune cell infiltration observed in the Mrgprb2 knockout mice. Elevated expression of Mrgprb2 in WT colitis murine models may represent the organism's adaptive protective mechanism since Mrgprb2 knockout results in severe colitis. On the other hand, both agonist and antagonist of Mrgprb2 analogously mitigated the severity of colitis in DSS-induced colitis model by altering Mrgprb2 expression, immune cell infiltration and inflammatory cytokine releases.
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Affiliation(s)
- Karthi Duraisamy
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China; INSERM U1239 NorDiC, PRIMACEN, Université Rouen Normandie, Rouen, France
| | - Mukesh Kumar
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Abdullah Nawabjan
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Emily Kwun Kwan Lo
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Ming Hui Lin
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Benjamin Lefranc
- INSERM U1239 NorDiC, PRIMACEN, Université Rouen Normandie, Rouen, France
| | - Elsa Bonnafé
- EA7417 BTSB, Université Fédérale Toulouse Midi-Pyrénées, INU Champollion, Albi, France
| | - Michel Treilhou
- EA7417 BTSB, Université Fédérale Toulouse Midi-Pyrénées, INU Champollion, Albi, France
| | - Hani El-Nezami
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China; Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Jérôme Leprince
- INSERM U1239 NorDiC, PRIMACEN, Université Rouen Normandie, Rouen, France.
| | - Billy K C Chow
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
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2
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Zhang M, Chen T, Lu X, Lan X, Chen Z, Lu S. G protein-coupled receptors (GPCRs): advances in structures, mechanisms, and drug discovery. Signal Transduct Target Ther 2024; 9:88. [PMID: 38594257 PMCID: PMC11004190 DOI: 10.1038/s41392-024-01803-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/19/2024] [Accepted: 03/13/2024] [Indexed: 04/11/2024] Open
Abstract
G protein-coupled receptors (GPCRs), the largest family of human membrane proteins and an important class of drug targets, play a role in maintaining numerous physiological processes. Agonist or antagonist, orthosteric effects or allosteric effects, and biased signaling or balanced signaling, characterize the complexity of GPCR dynamic features. In this study, we first review the structural advancements, activation mechanisms, and functional diversity of GPCRs. We then focus on GPCR drug discovery by revealing the detailed drug-target interactions and the underlying mechanisms of orthosteric drugs approved by the US Food and Drug Administration in the past five years. Particularly, an up-to-date analysis is performed on available GPCR structures complexed with synthetic small-molecule allosteric modulators to elucidate key receptor-ligand interactions and allosteric mechanisms. Finally, we highlight how the widespread GPCR-druggable allosteric sites can guide structure- or mechanism-based drug design and propose prospects of designing bitopic ligands for the future therapeutic potential of targeting this receptor family.
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Affiliation(s)
- Mingyang Zhang
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ting Chen
- Department of Cardiology, Changzheng Hospital, Affiliated to Naval Medical University, Shanghai, 200003, China
| | - Xun Lu
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaobing Lan
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Ziqiang Chen
- Department of Orthopedics, Changhai Hospital, Affiliated to Naval Medical University, Shanghai, 200433, China.
| | - Shaoyong Lu
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China.
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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An D, Carrazoni GS, Souto das Neves BH, D’Hooge R, Peigneur S, Tytgat J. The Sobering Sting: Oleoyl Serotonin Is a Novel Stephanoconus Snail Venom-Derived Antagonist of Cannabinoid Receptors That Counteracts Learning and Memory Deficits. Biomedicines 2024; 12:454. [PMID: 38398056 PMCID: PMC10887214 DOI: 10.3390/biomedicines12020454] [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: 12/21/2023] [Revised: 01/26/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Cannabinoid receptors (CB1 and CB2) are promising targets for a better understanding of neurological diseases. Nevertheless, only a few ligands of CB have reached clinical application so far. Venoms are considered as interesting sources of novel biologically active compounds. Here, we describe an endocannabinoid-like molecule, oleoyl serotonin (OS), present in the venom of Stephanoconus snails. Using electrophysiological assays, it was shown that OS inhibits CB1 and CB2. Structure-activity relationship studies using a chimeric CB1/2 revealed that the domain encompassing the transmembrane helix V (TMHV)- intracellular loop 3 (ICL3)-TMHVI of the CB2 is critical for the binding and function of OS. We concluded that OS binds to sites of the CB2 that are different from the binding sites of the non-selective CB agonist WIN55,212-2. Behavioral assays in mice showed that OS counteracted learning and memory deficits caused by WIN55,212-2. Furthermore, a selectivity screening of OS showed high selectivity for CB over various ion channels and receptors. Overall, OS may represent a new approach to the prevention and treatment of learning and memory cognition impairment in neurological diseases.
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Affiliation(s)
- Dongchen An
- Toxicology and Pharmacology, KU Leuven, Campus Gasthuisberg, ON2, Herestraat 49, Box-922, 3000 Leuven, Belgium
| | - Guilherme Salgado Carrazoni
- Laboratory of Biological Psychology, KU Leuven, Tiensestraat 102, Box-3714, 3000 Leuven, Belgium; (G.S.C.); (B.-H.S.d.N.); (R.D.)
| | - Ben-Hur Souto das Neves
- Laboratory of Biological Psychology, KU Leuven, Tiensestraat 102, Box-3714, 3000 Leuven, Belgium; (G.S.C.); (B.-H.S.d.N.); (R.D.)
| | - Rudi D’Hooge
- Laboratory of Biological Psychology, KU Leuven, Tiensestraat 102, Box-3714, 3000 Leuven, Belgium; (G.S.C.); (B.-H.S.d.N.); (R.D.)
| | - Steve Peigneur
- Toxicology and Pharmacology, KU Leuven, Campus Gasthuisberg, ON2, Herestraat 49, Box-922, 3000 Leuven, Belgium
| | - Jan Tytgat
- Toxicology and Pharmacology, KU Leuven, Campus Gasthuisberg, ON2, Herestraat 49, Box-922, 3000 Leuven, Belgium
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4
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Velloso JPL, Kovacs AS, Pires DEV, Ascher DB. AI-driven GPCR analysis, engineering, and targeting. Curr Opin Pharmacol 2024; 74:102427. [PMID: 38219398 DOI: 10.1016/j.coph.2023.102427] [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: 10/26/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/16/2024]
Abstract
This article investigates the role of recent advances in Artificial Intelligence (AI) to revolutionise the study of G protein-coupled receptors (GPCRs). AI has been applied to many areas of GPCR research, including the application of machine learning (ML) in GPCR classification, prediction of GPCR activation levels, modelling GPCR 3D structures and interactions, understanding G-protein selectivity, aiding elucidation of GPCRs structures, and drug design. Despite progress, challenges in predicting GPCR structures and addressing the complex nature of GPCRs remain, providing avenues for future research and development.
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Affiliation(s)
- João P L Velloso
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia; Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Aaron S Kovacs
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Douglas E V Pires
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia; Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia.
| | - David B Ascher
- Structural Biology and Bioinformatics, Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Victoria, Australia; Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia; Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia.
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5
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Kee TR, Khan SA, Neidhart MB, Masters BM, Zhao VK, Kim YK, McGill Percy KC, Woo JAA. The multifaceted functions of β-arrestins and their therapeutic potential in neurodegenerative diseases. Exp Mol Med 2024; 56:129-141. [PMID: 38212557 PMCID: PMC10834518 DOI: 10.1038/s12276-023-01144-4] [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: 04/20/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 01/13/2024] Open
Abstract
Arrestins are multifunctional proteins that regulate G-protein-coupled receptor (GPCR) desensitization, signaling, and internalization. The arrestin family consists of four subtypes: visual arrestin1, β-arrestin1, β-arrestin2, and visual arrestin-4. Recent studies have revealed the multifunctional roles of β-arrestins beyond GPCR signaling, including scaffolding and adapter functions, and physically interacting with non-GPCR receptors. Increasing evidence suggests that β-arrestins are involved in the pathogenesis of a variety of neurodegenerative diseases, including Alzheimer's disease (AD), frontotemporal dementia (FTD), and Parkinson's disease (PD). β-arrestins physically interact with γ-secretase, leading to increased production and accumulation of amyloid-beta in AD. Furthermore, β-arrestin oligomers inhibit the autophagy cargo receptor p62/SQSTM1, resulting in tau accumulation and aggregation in FTD. In PD, β-arrestins are upregulated in postmortem brain tissue and an MPTP model, and the β2AR regulates SNCA gene expression. In this review, we aim to provide an overview of β-arrestin1 and β-arrestin2, and describe their physiological functions and roles in neurodegenerative diseases. The multifaceted roles of β-arrestins and their involvement in neurodegenerative diseases suggest that they may serve as promising therapeutic targets.
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Affiliation(s)
- Teresa R Kee
- Department of Pathology, CWRU School of Medicine, Cleveland, OH, 44106, USA
- Department of Molecular Medicine, USF Health College of Medicine, Tampa, FL, 33613, USA
| | - Sophia A Khan
- Department of Pathology, CWRU School of Medicine, Cleveland, OH, 44106, USA
| | - Maya B Neidhart
- Department of Pathology, CWRU School of Medicine, Cleveland, OH, 44106, USA
| | - Brianna M Masters
- Department of Pathology, CWRU School of Medicine, Cleveland, OH, 44106, USA
| | - Victoria K Zhao
- Department of Pathology, CWRU School of Medicine, Cleveland, OH, 44106, USA
| | - Yenna K Kim
- Department of Pathology, CWRU School of Medicine, Cleveland, OH, 44106, USA
| | | | - Jung-A A Woo
- Department of Pathology, CWRU School of Medicine, Cleveland, OH, 44106, USA.
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Maggio R, Fasciani I, Petragnano F, Coppolino MF, Scarselli M, Rossi M. Unraveling the Functional Significance of Unstructured Regions in G Protein-Coupled Receptors. Biomolecules 2023; 13:1431. [PMID: 37892113 PMCID: PMC10604838 DOI: 10.3390/biom13101431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Unstructured regions in functional proteins have gained attention in recent years due to advancements in informatics tools and biophysical methods. G protein-coupled receptors (GPCRs), a large family of cell surface receptors, contain unstructured regions in the form of the i3 loop and C-terminus. This review provides an overview of the functional significance of these regions in GPCRs. GPCRs transmit signals from the extracellular environment to the cell interior, regulating various physiological processes. The i3 loop, located between the fifth and sixth transmembrane helices, and the C-terminus, connected to the seventh transmembrane helix, are determinant of interactions with G proteins and with other intracellular partners such as arrestins. Recent studies demonstrate that the i3 loop and C-terminus play critical roles in allosterically regulating GPCR activation. They can act as autoregulators, adopting conformations that, by restricting G protein access, modulate receptor coupling specificity. The length and unstructured nature of the i3 loop and C-terminus provide unique advantages in GPCR interactions with intracellular protein partners. They act as "fishing lines", expanding the radius of interaction and enabling GPCRs to tether scaffolding proteins, thus facilitating receptor stability during cell membrane movements. Additionally, the i3 loop may be involved in domain swapping between GPCRs, generating novel receptor dimers with distinct binding and coupling characteristics. Overall, the i3 loop and C-terminus are now widely recognized as crucial elements in GPCR function and regulation. Understanding their functional roles enhances our comprehension of GPCR structure and signaling complexity and holds promise for advancements in receptor pharmacology and drug development.
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Affiliation(s)
- Roberto Maggio
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (I.F.); (F.P.); (M.R.)
| | - Irene Fasciani
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (I.F.); (F.P.); (M.R.)
| | - Francesco Petragnano
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (I.F.); (F.P.); (M.R.)
| | - Maria Francesca Coppolino
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Marco Scarselli
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, 56126 Pisa, Italy;
| | - Mario Rossi
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (I.F.); (F.P.); (M.R.)
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Wei J, Zhang H, Ma X, Li Y, Zhou W, Guo J, Jin T, Hu M. Effect of OR51E1 Single Nucleotide Polymorphisms on Glioma Susceptibility in the Chinese Han Population. Gene 2023; 875:147489. [PMID: 37207826 DOI: 10.1016/j.gene.2023.147489] [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: 03/23/2023] [Revised: 04/27/2023] [Accepted: 05/12/2023] [Indexed: 05/21/2023]
Abstract
BACKGROUND Glioma is one of the common primary intracranial tumors, which is heterogeneous among individuals with a low cure rate. Our study aimed to investigate the association between single nucleotide polymorphisms (SNPs) of the OR51E1 gene and glioma susceptibility in the Chinese Han population. METHODS A total of six SNPs on OR51E1 in 1,026 subjects (526 cases and 500 controls) were genotyped by MassARRAY iPLEX GOLD assay. The association between these SNPs and glioma susceptibility was analyzed using logistic regression, and odds ratios (ORs) and 95% confidence intervals (CIs) were also calculated. The multifactor dimensionality reduction (MDR) method was applied to detect "SNP-SNP" interactions. RESULTS In the overall sample, polymorphisms rs10768148, rs7102992, and rs10500608 were identified to be associated with glioma risk. In the stratified analysis based on gender, only polymorphism rs10768148 was observed to be associated with the risk of glioma. In the age-stratified analysis, rs7102992, rs74052483, and rs10500609 contributed to the risk of glioma in subjects aged > 40 years. And polymorphisms rs10768148 and rs7102992 were associated with the risk of glioma in subjects aged ≤ 40 years and subjects with astrocytoma. In addition, a strong synergistic relationship between rs74052483 and rs10768148, and a strong redundant relationship between rs7102992 and rs10768148 were identified in the study. CONCLUSIONS This study demonstrated the association of OR51E1 polymorphisms with glioma susceptibility, providing a basis for assessing glioma risk-associated variants in the Chinese Han population.
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Affiliation(s)
- Jie Wei
- The College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Huan Zhang
- The College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xiaoya Ma
- The College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yujie Li
- The College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Wenqian Zhou
- The College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Jinping Guo
- The College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Tianbo Jin
- School of Medicine, Northwest University, Xi'an 710069, China
| | - Mingjun Hu
- School of Medicine, Northwest University, Xi'an 710069, China; Department of Neurosurgery, Xi'an Changan District Hospital, Xi'an 710199, China.
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Alfonso-Prieto M, Capelli R. Machine Learning-Based Modeling of Olfactory Receptors in Their Inactive State: Human OR51E2 as a Case Study. J Chem Inf Model 2023; 63:2911-2917. [PMID: 37145455 DOI: 10.1021/acs.jcim.3c00380] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Atomistic-level investigation of olfactory receptors (ORs) is a challenging task due to the experimental/computational difficulties in the structural determination/prediction for members of this family of G-protein coupled receptors. Here, we have developed a protocol that performs a series of molecular dynamics simulations from a set of structures predicted de novo by recent machine learning algorithms and apply it to a well-studied receptor, the human OR51E2. Our study demonstrates the need for simulations to refine and validate such models. Furthermore, we demonstrate the need for the sodium ion at a binding site near D2.50 and E3.39 to stabilize the inactive state of the receptor. Considering the conservation of these two acidic residues across human ORs, we surmise this requirement also applies to the other ∼400 members of this family. Given the almost concurrent publication of a CryoEM structure of the same receptor in the active state, we propose this protocol as an in silico complement to the growing field of ORs structure determination.
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Affiliation(s)
- Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulation IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Wilhelm-Johnen-Straße, D-52428 Jülich, Germany
| | - Riccardo Capelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, I-20133 Milan, Italy
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Szwabowski GL, Baker DL, Parrill AL. Application of computational methods for class A GPCR Ligand discovery. J Mol Graph Model 2023; 121:108434. [PMID: 36841204 DOI: 10.1016/j.jmgm.2023.108434] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023]
Abstract
G protein-coupled receptors (GPCR) are integral membrane proteins of considerable interest as targets for drug development due to their role in transmitting cellular signals in a multitude of biological processes. Of the six classes categorizing GPCR (A, B, C, D, E, and F), class A contains the largest number of therapeutically relevant GPCR. Despite their importance as drug targets, many challenges exist for the discovery of novel class A GPCR ligands serving as drug precursors. Though knowledge of the structural and functional characteristics of GPCR has grown significantly over the past 20 years, a large portion of GPCR lack reported, experimentally determined structures. Furthermore, many GPCR have no known endogenous and/or synthetic ligands, limiting further exploration of their biochemical, cellular, and physiological roles. While many successes in GPCR ligand discovery have resulted from experimental high-throughput screening, computational methods have played an increasingly important role in GPCR ligand identification in the past decade. Here we discuss computational techniques applied to GPCR ligand discovery. This review summarizes class A GPCR structure/function and provides an overview of many obstacles currently faced in GPCR ligand discovery. Furthermore, we discuss applications and recent successes of computational techniques used to predict GPCR structure as well as present a summary of ligand- and structure-based methods used to identify potential GPCR ligands. Finally, we discuss computational hit list generation and refinement and provide comprehensive workflows for GPCR ligand identification.
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Affiliation(s)
| | - Daniel L Baker
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA
| | - Abby L Parrill
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA.
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10
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Hall G, Kelly S, Schaap P, Schilde C. Phylogeny-wide analysis of G-protein coupled receptors in social amoebas and implications for the evolution of multicellularity. OPEN RESEARCH EUROPE 2023; 2:134. [PMID: 37645274 PMCID: PMC10445921 DOI: 10.12688/openreseurope.15250.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/07/2023] [Indexed: 08/31/2023]
Abstract
G-protein coupled receptors (GPCRs) are seven-transmembrane proteins and constitute the largest group of receptors within eukaryotes. The presence of a large set of GPCRs in the unicellular Amoebozoa was surprising and is indicative of the largely undiscovered environmental sensing capabilities in this group. Evolutionary transitions from unicellular to multicellular lifestyles, like we see in social amoebas, have occurred several times independently in the Amoebozoa, and GPCRs may have been co-opted for new functions in cell-cell communication. Methods We have analysed a set of GPCRs from fully sequenced Amoebozoan genomes by Bayesian inference, compared their phylogenetic distribution and domain composition, and analysed their temporal and spatial expression patterns in five species of dictyostelids. Results We found evidence that most GPCRs are conserved deeply in the Amoebozoa and are probably performing roles in general cell functions and complex environmental sensing. All families of GPCRs (apart from the family 4 fungal pheromone receptors) are present in dictyostelids with family 5 being the largest and family 2 the one with the fewest members. For the first time, we identify the presence of family 1 rhodopsin-like GPCRs in dictyostelids. Some GPCRs have been amplified in the dictyostelids and in specific lineages thereof and through changes in expression patterns may have been repurposed for signalling in multicellular development. Discussion Our phylogenetic analysis suggests that GPCR families 1, 2 and 6 already diverged early in the Amoebozoa, whereas families 3 and 5 expanded later within the dictyostelids. The family 6 cAMP receptors that have experimentally supported roles in multicellular development in dictyostelids ( carA-carD; tasA/B) originated at the root of all dictyostelids and only have weakly associated homologs in Physarum polycephalum. Our analysis identified candidate GPCRs which have evolved in the dictyostelids and could have been co-opted for multicellular development.
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Affiliation(s)
- Grant Hall
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Sarah Kelly
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, EH16 4TJ, UK
| | - Pauline Schaap
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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Szwabowski GL, Cole JA, Baker DL, Parrill AL. Structure-based pharmacophore modeling 1. Automated random pharmacophore model generation. J Mol Graph Model 2023; 121:108429. [PMID: 36804368 DOI: 10.1016/j.jmgm.2023.108429] [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: 11/06/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 02/13/2023]
Abstract
Pharmacophores are three-dimensional arrangements of molecular features required for biological activity that are often used in virtual screening efforts to prioritize ligands for experimental testing. G protein-coupled receptors (GPCR) are integral membrane proteins of considerable interest as targets for ligand discovery and drug development. Ligand-based pharmacophore models can be constructed to identify structural commonalities between known bioactive ligands for targets including GPCR. However, structure-based pharmacophores (which only require an experimentally determined or modeled structure for a protein target) have gained more attention to aid in virtual screening efforts as the number of publicly available experimentally determined GPCR structures have increased (140 unique GPCR represented as of October 24, 2022). Thus, the goal of this study was to develop a method of structure-based pharmacophore model generation applicable to ligand discovery for GPCR that have few known ligands. Pharmacophore models were generated within the active sites of 8 class A GPCR crystal structures via automated annotation of 5 randomly selected functional group fragments to sample diverse combinations of pharmacophore features. Each of the 5000 generated pharmacophores was then used to search a database containing active and decoy/inactive compounds for 30 class A GPCR and scored using enrichment factor and goodness-of-hit metrics to assess performance. Application of this method to the set of 8 class A GPCR produced pharmacophore models possessing the theoretical maximum enrichment factor value in both resolved structures (8 of 8 cases) and homology models (7 of 8 cases), indicating that generated pharmacophore models can prove useful in the context of virtual screening.
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Affiliation(s)
| | - Judith A Cole
- Department of Biological Sciences, The University of Memphis, Memphis, TN, 38152, USA
| | - Daniel L Baker
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA
| | - Abby L Parrill
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA.
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12
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Structural Basis for Agonistic Activity and Selectivity toward Melatonin Receptors hMT1 and hMT2. Int J Mol Sci 2023; 24:ijms24032863. [PMID: 36769183 PMCID: PMC9918025 DOI: 10.3390/ijms24032863] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Glaucoma, a major ocular neuropathy originating from a progressive degeneration of retinal ganglion cells, is often associated with increased intraocular pressure (IOP). Daily IOP fluctuations are physiologically influenced by the antioxidant and signaling activities of melatonin. This endogenous modulator has limited employment in treating altered IOP disorders due to its low stability and bioavailability. The search for low-toxic compounds as potential melatonin agonists with higher stability and bioavailability than melatonin itself could start only from knowing the molecular basis of melatonergic activity. Thus, using a computational approach, we studied the melatonin binding toward its natural macromolecular targets, namely melatonin receptors 1 (MT1) and 2 (MT2), both involved in IOP signaling regulation. Besides, agomelatine, a melatonin-derivative agonist and, at the same time, an atypical antidepressant, was also included in the study due to its powerful IOP-lowering effects. For both ligands, we evaluated both stability and ligand positioning inside the orthosteric site of MTs, mapping the main molecular interactions responsible for receptor activation. Affinity values in terms of free binding energy (ΔGbind) were calculated for the selected poses of the chosen compounds after stabilization through a dynamic molecular docking protocol. The results were compared with experimental in vivo effects, showing a higher potency and more durable effect for agomelatine with respect to melatonin, which could be ascribed both to its higher affinity for hMT2 and to its additional activity as an antagonist for the serotonin receptor 5-HT2c, in agreement with the in silico results.
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13
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Zhu P, Liu W, Zhang X, Li M, Liu G, Yu Y, Li Z, Li X, Du J, Wang X, Grueter CC, Li M, Zhou X. Correlated evolution of social organization and lifespan in mammals. Nat Commun 2023; 14:372. [PMID: 36720880 PMCID: PMC9889386 DOI: 10.1038/s41467-023-35869-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 01/05/2023] [Indexed: 02/02/2023] Open
Abstract
Discerning the relationship between sociality and longevity would permit a deeper understanding of how animal life history evolved. Here, we perform a phylogenetic comparative analysis of ~1000 mammalian species on three states of social organization (solitary, pair-living, and group-living) and longevity. We show that group-living species generally live longer than solitary species, and that the transition rate from a short-lived state to a long-lived state is higher in group-living than non-group-living species, altogether supporting the correlated evolution of social organization and longevity. The comparative brain transcriptomes of 94 mammalian species identify 31 genes, hormones and immunity-related pathways broadly involved in the association between social organization and longevity. Further selection features reveal twenty overlapping pathways under selection for both social organization and longevity. These results underscore a molecular basis for the influence of the social organization on longevity.
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Affiliation(s)
- Pingfen Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Weiqiang Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoxiao Zhang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meng Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Gaoming Liu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Yang Yu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Zihao Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuanjing Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Du
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China
| | - Cyril C Grueter
- School of Human Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Centre for Evolutionary Biology, School of Biological Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,International Center of Biodiversity and Primate Conservation, Dali University, Dali, Yunnan, 671003, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, 100101, China.
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14
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Willeford K. The Luminescence Hypothesis of Olfaction. SENSORS (BASEL, SWITZERLAND) 2023; 23:1333. [PMID: 36772376 PMCID: PMC9919928 DOI: 10.3390/s23031333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/12/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
A new hypothesis for the mechanism of olfaction is presented. It begins with an odorant molecule binding to an olfactory receptor. This is followed by the quantum biology event of inelastic electron tunneling as has been suggested with both the vibration and swipe card theories. It is novel in that it is not concerned with the possible effects of the tunneled electrons as has been discussed with the previous theories. Instead, the high energy state of the odorant molecule in the receptor following inelastic electron tunneling is considered. The hypothesis is that, as the high energy state decays, there is fluorescence luminescence with radiative emission of multiple photons. These photons pass through the supporting sustentacular cells and activate a set of olfactory neurons in near-simultaneous timing, which provides the temporal basis for the brain to interpret the required complex combinatorial coding as an odor. The Luminescence Hypothesis of Olfaction is the first to present the necessity of or mechanism for a 1:3 correspondence of odorant molecule to olfactory nerve activations. The mechanism provides for a consistent and reproducible time-based activation of sets of olfactory nerves correlated to an odor. The hypothesis has a biological precedent: an energy feasibility assessment is included, explaining the anosmia seen with COVID-19, and can be confirmed with existing laboratory techniques.
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Affiliation(s)
- Kenneth Willeford
- Coastal Carolinas Integrated Medicine, 10 Doctors Circle, STE 2, Supply, NC 28462, USA
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15
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Cwiklinski K, Dalton JP. Omics tools enabling vaccine discovery against fasciolosis. Trends Parasitol 2022; 38:1068-1079. [PMID: 36270885 DOI: 10.1016/j.pt.2022.09.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/05/2022]
Abstract
In the past decade significant advances in our understanding of liver fluke biology have been made through in-depth interrogation and analysis of evolving Fasciola hepatica and Fasciola gigantica omics datasets. This information is crucial for developing novel control strategies, particularly vaccines necessitated by the global spread of anthelmintic resistance. Distilling them down to a manageable number of testable vaccines requires combined rational, empirical, and collaborative approaches. Despite a lack of clear outstanding vaccine candidate(s), we must continue to identify salient parasite-host interacting molecules, likely in the secretory products, tegument, or extracellular vesicles, and perform robust trials especially in livestock, using present and emerging vaccinology technologies to discover that elusive liver fluke vaccine. Omics tools are bringing this prospect ever closer.
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Affiliation(s)
- Krystyna Cwiklinski
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
| | - John P Dalton
- Molecular Parasitology Laboratory, Centre for One Health (MPL), Ryan Institute, School of Natural Science, National University of Ireland Galway, Galway, Ireland
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16
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MSClustering: A Cytoscape Tool for Multi-Level Clustering of Biological Networks. Int J Mol Sci 2022; 23:ijms232214240. [PMID: 36430723 PMCID: PMC9699063 DOI: 10.3390/ijms232214240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
MSClustering is an efficient software package for visualizing and analyzing complex networks in Cytoscape. Based on the distance matrix of a network that it takes as input, MSClustering automatically displays the minimum span clustering (MSC) of the network at various characteristic levels. To produce a view of the overall network structure, the app then organizes the multi-level results into an MSC tree. Here, we demonstrate the package's phylogenetic applications in studying the evolutionary relationships of complex systems, including 63 beta coronaviruses and 197 GPCRs. The validity of MSClustering for large systems has been verified by its clustering of 3481 enzymes. Through an experimental comparison, we show that MSClustering outperforms five different state-of-the-art methods in the efficiency and reliability of their clustering.
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17
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Caniceiro AB, Bueschbell B, Schiedel AC, Moreira IS. Class A and C GPCR Dimers in Neurodegenerative Diseases. Curr Neuropharmacol 2022; 20:2081-2141. [PMID: 35339177 PMCID: PMC9886835 DOI: 10.2174/1570159x20666220327221830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/21/2022] [Accepted: 03/23/2022] [Indexed: 11/22/2022] Open
Abstract
Neurodegenerative diseases affect over 30 million people worldwide with an ascending trend. Most individuals suffering from these irreversible brain damages belong to the elderly population, with onset between 50 and 60 years. Although the pathophysiology of such diseases is partially known, it remains unclear upon which point a disease turns degenerative. Moreover, current therapeutics can treat some of the symptoms but often have severe side effects and become less effective in long-term treatment. For many neurodegenerative diseases, the involvement of G proteincoupled receptors (GPCRs), which are key players of neuronal transmission and plasticity, has become clearer and holds great promise in elucidating their biological mechanism. With this review, we introduce and summarize class A and class C GPCRs, known to form heterodimers or oligomers to increase their signalling repertoire. Additionally, the examples discussed here were shown to display relevant alterations in brain signalling and had already been associated with the pathophysiology of certain neurodegenerative diseases. Lastly, we classified the heterodimers into two categories of crosstalk, positive or negative, for which there is known evidence.
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Affiliation(s)
- Ana B. Caniceiro
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; ,These authors contributed equally to this work.
| | - Beatriz Bueschbell
- PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Casa Costa Alemão, 3030-789 Coimbra, Portugal; ,These authors contributed equally to this work.
| | - Anke C. Schiedel
- Department of Pharmaceutical & Medicinal Chemistry, Pharmaceutical Institute, University of Bonn, D-53121 Bonn, Germany;
| | - Irina S. Moreira
- University of Coimbra, Department of Life Sciences, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; ,Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, 3004-504 Coimbra, Portugal,Address correspondence to this author at the Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, 3004-504 Coimbra, Portugal; E-mail:
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18
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Han M, Lee S, Ha Y, Lee JY. Recognition of the Ligand-Induced Spatiotemporal Residue Pair Pattern of β2-Adrenergic Receptors Using 3-D Residual Networks Trained by the Time Series of Protein Distance Maps. Comput Struct Biotechnol J 2022; 20:6360-6374. [DOI: 10.1016/j.csbj.2022.10.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 10/06/2022] [Accepted: 10/23/2022] [Indexed: 12/01/2022] Open
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19
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ADGRL1 haploinsufficiency causes a variable spectrum of neurodevelopmental disorders in humans and alters synaptic activity and behavior in a mouse model. Am J Hum Genet 2022; 109:1436-1457. [PMID: 35907405 PMCID: PMC9388395 DOI: 10.1016/j.ajhg.2022.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/22/2022] [Indexed: 02/06/2023] Open
Abstract
ADGRL1 (latrophilin 1), a well-characterized adhesion G protein-coupled receptor, has been implicated in synaptic development, maturation, and activity. However, the role of ADGRL1 in human disease has been elusive. Here, we describe ten individuals with variable neurodevelopmental features including developmental delay, intellectual disability, attention deficit hyperactivity and autism spectrum disorders, and epilepsy, all heterozygous for variants in ADGRL1. In vitro, human ADGRL1 variants expressed in neuroblastoma cells showed faulty ligand-induced regulation of intracellular Ca2+ influx, consistent with haploinsufficiency. In vivo, Adgrl1 was knocked out in mice and studied on two genetic backgrounds. On a non-permissive background, mice carrying a heterozygous Adgrl1 null allele exhibited neurological and developmental abnormalities, while homozygous mice were non-viable. On a permissive background, knockout animals were also born at sub-Mendelian ratios, but many Adgrl1 null mice survived gestation and reached adulthood. Adgrl1-/- mice demonstrated stereotypic behaviors, sexual dysfunction, bimodal extremes of locomotion, augmented startle reflex, and attenuated pre-pulse inhibition, which responded to risperidone. Ex vivo synaptic preparations displayed increased spontaneous exocytosis of dopamine, acetylcholine, and glutamate, but Adgrl1-/- neurons formed synapses in vitro poorly. Overall, our findings demonstrate that ADGRL1 haploinsufficiency leads to consistent developmental, neurological, and behavioral abnormalities in mice and humans.
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20
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Einspahr J, Tilley DG. Pathophysiological Impact of the Adhesion G-Protein Coupled Receptor Family. Am J Physiol Cell Physiol 2022; 323:C640-C647. [PMID: 35848619 PMCID: PMC9359651 DOI: 10.1152/ajpcell.00445.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
G-Protein Coupled Receptors (GPCRs) represent one of the most targeted drug classes in the human genome, accounting for greater than 40% of all FDA-approved drugs. However, the second-largest family of GPCRs, known as Adhesion GPCRs (aGPCR), have yet to serve as a clinical target despite increasing evidence of their physiological and pathological functions, which suggest an opportunity toward the development of novel therapeutics. To date, the pathophysiological function of aGPCRs is associated with a plethora of diseases including cancer, CNS disorders, immunity and inflammation, and others. To highlight their potential as pharmacologic targets, we will review three distinct aGPCR members (ADGRG1, ADGRE5 and ADGRF5), highlighting their molecular mechanisms of action and contributions to the development of pathophysiology.
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Affiliation(s)
- Jeanette Einspahr
- Center for Translational Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania, United States
| | - Douglas G Tilley
- Center for Translational Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania, United States
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21
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Guo S, Zhao T, Yun Y, Xie X. Recent Progress in Assays for GPCR Drug Discovery. Am J Physiol Cell Physiol 2022; 323:C583-C594. [PMID: 35816640 DOI: 10.1152/ajpcell.00464.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
G-protein coupled receptors (GPCRs), also known as 7 transmembrane receptors, are the largest family of cell surface receptors in eukaryotes. There are ~800 GPCRs in human, regulating diverse physiological processes. GPCRs are the most intensively studied drug targets. Drugs that target GPCRs account for about a quarter of the global market share of therapeutic drugs. Therefore, to develop physiologically relevant and robust assays to search new GPCR ligands or modulators remain the major focus of drug discovery research worldwide. Early functional GPCR assays are mainly depend on the measurement of G protein-mediated second messenger generation. Recent development in GPCR biology indicate the signaling of these receptors is much more complex than the oversimplified classical view. GPCRs have been found to activate multiple G proteins simultaneously and induce b-arrestin-mediated signaling. GPCRs have also been found to interacte with other cytosolic scaffolding proteins and form dimer or heteromer with GPCRs or other transmembrane proteins. Here we mainly discuss technologies focused on detecting protein-protein interactions, such as FRET/BRET, NanoBiT, Tango, etc, and their applications in measuring GPCRs interacting with various signaling partners. In the final part, we also discuss the species differences in GPCRs when using animal models to study the in vivofunctions of GPCR ligands, and possible ways to solve this problem with modern genetic tools.
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Affiliation(s)
- Shimeng Guo
- grid.419093.6Shanghai Institute of Materia Medica, Shanghai, China
| | - Tingting Zhao
- grid.419093.6Shanghai Institute of Materia Medica, Shanghai, China
| | - Ying Yun
- grid.419093.6Shanghai Institute of Materia Medica, Shanghai, China
| | - Xin Xie
- grid.419093.6Shanghai Institute of Materia Medica, Shanghai, China
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22
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Lei P, Wang H, Yu L, Xu C, Sun H, Lyu Y, Li L, Zhang DL. A correlation study of adhesion G protein-coupled receptors as potential therapeutic targets in Uterine Corpus Endometrial cancer. Int Immunopharmacol 2022; 108:108743. [DOI: 10.1016/j.intimp.2022.108743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/23/2022] [Accepted: 03/29/2022] [Indexed: 12/11/2022]
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23
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Homology Modeling and Molecular Docking Approaches for the Proposal of Novel Insecticides against the African Malaria Mosquito ( Anopheles gambiae). MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123846. [PMID: 35744972 PMCID: PMC9227062 DOI: 10.3390/molecules27123846] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/03/2022] [Accepted: 06/10/2022] [Indexed: 11/29/2022]
Abstract
Vector-borne infectious diseases are responsible for the deaths of over 700,000 people annually, than 400,000 of them resulting from malaria. The mosquito Anopheles gambiae is one of the dominant vector species of human malaria transmission. A significant issue of the conventional insecticides which target the arthropod borne infectious diseases is their induced resistance. To overcome this inconvenience, insecticides with new modes of action are required. One of the most promising targets for the development of new potential insecticides as evidenced by current studies is the D1-like dopamine receptor (DAR). To get a deeper understanding of the structural information of this receptor, the 3D homology model was built. The possible sites within the protein were identified and the most probable binding site was highlighted. The homology model along with a series of DAR antagonists with known activity against Anopheles gambiae larvae were used in docking experiments to gain insight into their intermolecular interactions. Furthermore, virtual screening of the natural compounds from the SPECS database led to the prediction of toxicity and environmental hazards for one potential new insecticide against the Anopheles gambiae mosquito.
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24
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Fernández-Dueñas V, Bonaventura J, Aso E, Luján R, Ferré S, Ciruela F. Overcoming the Challenges of Detecting GPCR Oligomerization in the Brain. Curr Neuropharmacol 2022; 20:1035-1045. [PMID: 34736381 PMCID: PMC9886828 DOI: 10.2174/1570159x19666211104145727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/14/2021] [Accepted: 10/14/2021] [Indexed: 11/22/2022] Open
Abstract
G protein-coupled receptors (GPCRs) constitute the largest group of membrane receptor proteins controlling brain activity. Accordingly, GPCRs are the main target of commercial drugs for most neurological and neuropsychiatric disorders. One of the mechanisms by which GPCRs regulate neuronal function is by homo- and heteromerization, with the establishment of direct protein-protein interactions between the same and different GPCRs. The occurrence of GPCR homo- and heteromers in artificial systems is generally well accepted, but more specific methods are necessary to address GPCR oligomerization in the brain. Here, we revise some of the techniques that have mostly contributed to reveal GPCR oligomers in native tissue, which include immunogold electron microscopy, proximity ligation assay (PLA), resonance energy transfer (RET) between fluorescent ligands and the Amplified Luminescent Proximity Homogeneous Assay (ALPHA). Of note, we use the archetypical GPCR oligomer, the adenosine A2A receptor (A2AR)-dopamine D2 receptor (D2R) heteromer as an example to illustrate the implementation of these techniques, which can allow visualizing GPCR oligomers in the human brain under normal and pathological conditions. Indeed, GPCR oligomerization may be involved in the pathophysiology of neurological and neuropsychiatric disorders.
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Affiliation(s)
- Víctor Fernández-Dueñas
- Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907 L’Hospitalet de Llobregat, Spain;,Neuropharmacology & Pain Group, Neuroscience Program, Bellvitge Institute for Biomedical Research, 08907 L’Hospitalet de Llobregat, Spain;,Address correspondence to these authors at the Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907 L’Hospitalet de Llobregat, Spain; E-mails: ,
| | - Jordi Bonaventura
- Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907 L’Hospitalet de Llobregat, Spain;,Neuropharmacology & Pain Group, Neuroscience Program, Bellvitge Institute for Biomedical Research, 08907 L’Hospitalet de Llobregat, Spain
| | - Ester Aso
- Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907 L’Hospitalet de Llobregat, Spain;,Neuropharmacology & Pain Group, Neuroscience Program, Bellvitge Institute for Biomedical Research, 08907 L’Hospitalet de Llobregat, Spain
| | - Rafael Luján
- Synaptic Structure Laboratory, Instituto de Investigación en Discapacidades Neurológicas (IDINE), Departamento de Ciencias Médicas, Facultad de Medicina, Universidad Castilla-La Mancha, Albacete, Spain
| | - Sergi Ferré
- Integrative Neurobiology Section, National Institute on Drug Abuse, Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | - Francisco Ciruela
- Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907 L’Hospitalet de Llobregat, Spain;,Neuropharmacology & Pain Group, Neuroscience Program, Bellvitge Institute for Biomedical Research, 08907 L’Hospitalet de Llobregat, Spain;,Address correspondence to these authors at the Pharmacology Unit, Department of Pathology and Experimental Therapeutics, School of Medicine and Health Sciences, Institute of Neurosciences, University of Barcelona, 08907 L’Hospitalet de Llobregat, Spain; E-mails: ,
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25
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GPR37 Receptors and Megalencephalic Leukoencephalopathy with Subcortical Cysts. Int J Mol Sci 2022; 23:ijms23105528. [PMID: 35628339 PMCID: PMC9144339 DOI: 10.3390/ijms23105528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/30/2022] Open
Abstract
Megalencephalic leukoencephalopathy with subcortical cysts (MLC) is a rare type of vacuolating leukodystrophy (white matter disorder), which is mainly caused by defects in MLC1 or glial cell adhesion molecule (GlialCAM) proteins. In addition, autoantibodies to GlialCAM are involved in the pathology of multiple sclerosis. MLC1 and GLIALCAM genes encode for membrane proteins of unknown function, which has been linked to the regulation of different ion channels and transporters, such as the chloride channel VRAC (volume regulated anion channel), ClC-2 (chloride channel 2), and connexin 43 or the Na+/K+-ATPase pump. However, the mechanisms by which MLC proteins regulate these ion channels and transporters, as well as the exact function of MLC proteins remain obscure. It has been suggested that MLC proteins might regulate signalling pathways, but the mechanisms involved are, at present, unknown. With the aim of answering these questions, we have recently described the brain GlialCAM interactome. Within the identified proteins, we could validate the interaction with several G protein-coupled receptors (GPCRs), including the orphan GPRC5B and the proposed prosaposin receptors GPR37L1 and GPR37. In this review, we summarize new aspects of the pathophysiology of MLC disease and key aspects of the interaction between GPR37 receptors and MLC proteins.
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26
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Engineered Allosteric Regulation of Protein Function. J Mol Biol 2022; 434:167620. [PMID: 35513109 DOI: 10.1016/j.jmb.2022.167620] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/27/2022] [Accepted: 04/26/2022] [Indexed: 11/20/2022]
Abstract
Allosteric regulation of proteins has been utilized to study various aspects of cell signaling, from unicellular events to organism-wide phenotypes. However, traditional methods of allosteric regulation, such as constitutively active mutants and inhibitors, lack tight spatiotemporal control. This often leads to unintended signaling consequences that interfere with data interpretation. To overcome these obstacles, researchers employed protein engineering approaches that enable tight control of protein function through allosteric mechanisms. These methods provide high specificity as well as spatial and temporal precision in regulation of protein activity in vitro and in vivo. In this review, we focus on the recent advancements in engineered allosteric regulation and discuss the various bioengineered allosteric techniques available now, from chimeric GPCRs to chemogenetic and optogenetic switches. We highlight the benefits and pitfalls of each of these techniques as well as areas in which future improvements can be made. Additionally, we provide a brief discussion on implementation of engineered allosteric regulation approaches, demonstrating that these tools can shed light on elusive biological events and have the potential to be utilized in precision medicine.
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27
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Wang PP, Jiang X, Zhu L, Zhou D, Hong M, He L, Chen L, Yao S, Zhao Y, Chen G, Wang C, Cui L, Cao Y, Zhu X. A G-Protein-Coupled Receptor Modulates Gametogenesis via PKG-Mediated Signaling Cascade in Plasmodium berghei. Microbiol Spectr 2022; 10:e0015022. [PMID: 35404079 PMCID: PMC9045217 DOI: 10.1128/spectrum.00150-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/20/2022] [Indexed: 12/13/2022] Open
Abstract
Gametogenesis is essential for malaria parasite transmission, but the molecular mechanism of this process remains to be refined. Here, we identified a G-protein-coupled receptor 180 (GPR180) that plays a critical role in signal transduction during gametogenesis in Plasmodium. The P. berghei GPR180 was predominantly expressed in gametocytes and ookinetes and associated with the plasma membrane in female gametes and ookinetes. Knockout of pbgpr180 (Δpbgpr180) had no noticeable effect on blood-stage development but impaired gamete formation and reduced transmission of the parasites to mosquitoes. Transcriptome analysis revealed that a large proportion of the dysregulated genes in the Δpbgpr180 gametocytes had assigned functions in cyclic nucleotide signal transduction. In the Δpbgpr180 gametocytes, the intracellular cGMP level was significantly reduced, and the cytosolic Ca2+ mobilization showed a delay and a reduction in the magnitude during gametocyte activation. These results suggest that PbGPR180 functions upstream of the cGMP-protein kinase G-Ca2+ signaling pathway. In line with this functional prediction, the PbGPR180 protein was found to interact with several transmembrane transporter proteins and the small GTPase Rab6 in activated gametocytes. Allele replacement of pbgpr180 with the P. vivax ortholog pvgpr180 showed equal competence of the transgenic parasite in sexual development, suggesting functional conservation of this gene in Plasmodium spp. Furthermore, an anti-PbGPR180 monoclonal antibody and the anti-PvGPR180 serum possessed robust transmission-blocking activities. These results indicate that GPR180 is involved in signal transduction during gametogenesis in malaria parasites and is a promising target for blocking parasite transmission. IMPORTANCE Environmental changes from humans to mosquitoes activate gametogenesis of the malaria parasite, an obligative process for parasite transmission, but how the signals are relayed remains poorly understood. Here, we show the identification of a Plasmodium G-protein-coupled receptor, GPR180, and the characterization of its function in gametogenesis. In P. berghei, GPR180 is dispensable for asexual development and gametocytogenesis, but its deletion impairs gametogenesis and reduces transmission to mosquitoes. GPR180 appears to function upstream of the cGMP-protein kinase G-Ca2+ signaling pathway and is required for the maximum activity of this pathway. Genetic complementation shows that the GPR180 ortholog from the human malaria parasite P. vivax was fully functional in P. berghei, indicating functional conservation of GPR180 in Plasmodium spp. With predominant expression and membrane association of GPR180 in sexual stages, GPR180 is a promising target for blocking transmission, and antibodies against GPR180 possess robust transmission-blocking activities.
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Affiliation(s)
- Peng-peng Wang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xuefeng Jiang
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Liying Zhu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Dan Zhou
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Mingyang Hong
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Lu He
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Lumeng Chen
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Shijie Yao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Yan Zhao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Guang Chen
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
- Department of Basic Medical Sciences, Taizhou University Hospital, Taizhou University, Taizhou, China
| | - Chengqi Wang
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
| | - Xiaotong Zhu
- Department of Immunology, College of Basic Medical Sciences, China Medical University, Shenyang, China
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Neville GM, Edler KJ, Price GJ. Fluorescent styrene maleic acid copolymers to facilitate membrane protein studies in lipid nanodiscs. NANOSCALE 2022; 14:5689-5693. [PMID: 35315461 DOI: 10.1039/d1nr07230g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Fluorescently-labelled variants of poly(styrene-co-maleic acid), SMA, have been synthesised by RAFT copolymerisation. We show that low ratios of vinyl fluorophores, analogous to styrene, can be successfully incorporated during polymerisation without detriment to nanodisc formation upon interaction with lipids. These novel copolymers are capable of encapuslating lipids and the model membrane protein, gramicidin, and hence have the potential to be applied in fluorescence-based biological studies. To demonstrate this, energy transfer is used to probe polymer-protein interactions in nanodiscs. The copolymers may also be used to monitor nanodisc self assembly by exploiting aggregation-caused-quenching (ACQ).
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Affiliation(s)
| | - Karen J Edler
- Department of Chemistry, University of Bath, Bath, BA2 7AY, UK
| | - Gareth J Price
- Department of Chemistry, University of Bath, Bath, BA2 7AY, UK
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Bueschbell B, Manga P, Schiedel AC. The Many Faces of G Protein-Coupled Receptor 143, an Atypical Intracellular Receptor. Front Mol Biosci 2022; 9:873777. [PMID: 35495622 PMCID: PMC9039016 DOI: 10.3389/fmolb.2022.873777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/10/2022] [Indexed: 12/24/2022] Open
Abstract
GPCRs transform extracellular stimuli into a physiological response by activating an intracellular signaling cascade initiated via binding to G proteins. Orphan G protein-coupled receptors (GPCRs) hold the potential to pave the way for development of new, innovative therapeutic strategies. In this review we will introduce G protein-coupled receptor 143 (GPR143), an enigmatic receptor in terms of classification within the GPCR superfamily and localization. GPR143 has not been assigned to any of the GPCR families due to the lack of common structural motifs. Hence we will describe the most important motifs of classes A and B and compare them to the protein sequence of GPR143. While a precise function for the receptor has yet to be determined, the protein is expressed abundantly in pigment producing cells. Many GPR143 mutations cause X-linked Ocular Albinism Type 1 (OA1, Nettleship-Falls OA), which results in hypopigmentation of the eyes and loss of visual acuity due to disrupted visual system development and function. In pigment cells of the skin, loss of functional GPR143 results in abnormally large melanosomes (organelles in which pigment is produced). Studies have shown that the receptor is localized internally, including at the melanosomal membrane, where it may function to regulate melanosome size and/or facilitate protein trafficking to the melanosome through the endolysosomal system. Numerous additional roles have been proposed for GPR143 in determining cancer predisposition, regulation of blood pressure, development of macular degeneration and signaling in the brain, which we will briefly describe as well as potential ligands that have been identified. Furthermore, GPR143 is a promiscuous receptor that has been shown to interact with multiple other melanosomal proteins and GPCRs, which strongly suggests that this orphan receptor is likely involved in many different physiological actions.
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Affiliation(s)
- Beatriz Bueschbell
- Department of Pharmaceutical and Medicinal Chemistry, Pharmaceutical Institute, University of Bonn, Bonn, Germany
| | - Prashiela Manga
- Ronald O. Perelman Department of Dermatology, Grossman School of Medicine, New York University, New York City, NY, United States
| | - Anke C. Schiedel
- Department of Pharmaceutical and Medicinal Chemistry, Pharmaceutical Institute, University of Bonn, Bonn, Germany
- *Correspondence: Anke C. Schiedel,
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30
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Wang H, Du D, Huang J, Wang S, He X, Yuan S, Xiao J. GPR27 Regulates Hepatocellular Carcinoma Progression via MAPK/ERK Pathway. Cancer Manag Res 2022; 14:1165-1177. [PMID: 35330739 PMCID: PMC8938170 DOI: 10.2147/cmar.s335749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/08/2022] [Indexed: 12/24/2022] Open
Abstract
Purpose Orphan GPCRs (GPRs) play important roles in the malignant progression of cancer and have the potential to develop into anti-tumor drug targets. However, the biological processes and molecular mechanisms of GPR27 have not been properly assessed in cancer. Our objective was to reveal the effect of GPR27 on the progression of hepatocellular carcinoma (HCC). Methods GPR27 levels were detected in HCC cell lines using quantitative reverse transcriptase-polymerase chain reaction and Western blot analysis. Next, the changes of phenotypes after GPR27 knockdown or overexpression were evaluated using in vitro methods. Finally, the mechanism of GPR27 in HCC was tested using RNA-seq and in vivo mouse xenograft model. Results In the present study, we reported that suppression of GPR27 expression inhibited proliferation, colony formation, cell viability, and induced cell S phase arrest of HCC cells, whereas GPR27 overexpression led to the opposite outcomes. Moreover, suppression of GPR27 expression resulted in blocking MAPK/ERK signal pathway which indicated the inhibition of HCC cells proliferation. Further study in vivo confirmed that GPR27 can affect the proliferation of HCC cells through the MAPK/ERK pathway. Conclusion Taken together, the findings of the present study uncover biological functions of GPR27 in HCC cells, and delineate preliminary molecular mechanisms of GPR27 in modulating HCC development and progression.
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Affiliation(s)
- Hongxv Wang
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, Guangdong, 519000, People’s Republic of China
| | - Danyu Du
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing, Jiangsu, People’s Republic of China
| | - Jianwen Huang
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, Guangdong, People’s Republic of China
| | - Shuai Wang
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing, Jiangsu, People’s Republic of China
| | - Xv He
- Zhuhai Interventional Medical Center, Zhuhai Precision Medical Center, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, Guangdong, People’s Republic of China
| | - Shengtao Yuan
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing, Jiangsu, People’s Republic of China
| | - Jing Xiao
- Zhuhai Precision Medical Center, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Jinan University, Zhuhai, Guangdong, 519000, People’s Republic of China
- Correspondence: Jing Xiao; Shengtao Yuan, Tel +86 15118802570; +86 13914798635, Email ;
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The Role of Neuropeptide-Stimulated cAMP-EPACs Signalling in Cancer Cells. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27010311. [PMID: 35011543 PMCID: PMC8746471 DOI: 10.3390/molecules27010311] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 02/06/2023]
Abstract
Neuropeptides are autocrine and paracrine signalling factors and mainly bind to G protein-coupled receptors (GPCRs) to trigger intracellular secondary messenger release including adenosine 3′, 5′-cyclic monophosphate (cAMP), thus modulating cancer progress in different kind of tumours. As one of the downstream effectors of cAMP, exchange proteins directly activated by cAMP (EPACs) play dual roles in cancer proliferation and metastasis. More evidence about the relationship between neuropeptides and EPAC pathways have been proposed for their potential role in cancer development; hence, this review focuses on the role of neuropeptide/GPCR system modulation of cAMP/EPACs pathways in cancers. The correlated downstream pathways between neuropeptides and EPACs in cancer cell proliferation, migration, and metastasis is discussed to glimmer the direction of future research.
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Song J, Zheng H, Xue J, Liu J, Sun Q, Yang W, Liu F, Xiang X, He K, Chen Y, Cheng J, Li W, Jin J, Brosius J, Deng C. GPR15-C10ORF99 functional pairing initiates colonic Treg homing in amniotes. EMBO Rep 2021; 23:e53246. [PMID: 34939731 PMCID: PMC8892231 DOI: 10.15252/embr.202153246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 10/29/2021] [Accepted: 12/06/2021] [Indexed: 02/05/2023] Open
Abstract
Regulatory T lymphocyte (Treg) homing reactions mediated by G protein‐coupled receptor (GPCR)–ligand interactions play a central role in maintaining intestinal immune homeostasis by restraining inappropriate immune responses in the gastrointestinal tract. However, the origin of Treg homing to the colon remains mysterious. Here, we report that the C10ORF99 peptide (also known as CPR15L and AP57), a cognate ligand of GPR15 that controls Treg homing to the colon, originates from a duplication of the flanking CDHR1 gene and is functionally paired with GPR15 in amniotes. Evolutionary analysis and experimental data indicate that the GPR15–C10ORF99 pair is functionally conserved to mediate colonic Treg homing in amniotes and their expression patterns are positively correlated with herbivore diet in the colon. With the first herbivorous diet in early amniotes, a new biological process (herbivorous diet short‐chain fatty acid‐C10ORF99/GPR15‐induced Treg homing colon immune homeostasis) emerged, and we propose an evolutionary model whereby GPR15–C10ORF99 functional pairing has initiated the first colonic Treg homing reaction in amniotes. Our findings also highlight that GPCR–ligand pairing leads to physiological adaptation during vertebrate evolution.
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Affiliation(s)
- Jingjing Song
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Huaping Zheng
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Jingwen Xue
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jian Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qian Sun
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Fang Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiangyin Xiang
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Kai He
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University, Guangzhou, China
| | - Younan Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Jingqiu Cheng
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Li
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Jin Jin
- MOE Laboratory of Biosystem Homeostasis and Protection, and Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Juergen Brosius
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Cheng Deng
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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Root-Bernstein R, Churchill B. Co-Evolution of Opioid and Adrenergic Ligands and Receptors: Shared, Complementary Modules Explain Evolution of Functional Interactions and Suggest Novel Engineering Possibilities. Life (Basel) 2021; 11:life11111217. [PMID: 34833093 PMCID: PMC8623292 DOI: 10.3390/life11111217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/29/2021] [Accepted: 11/03/2021] [Indexed: 12/14/2022] Open
Abstract
Cross-talk between opioid and adrenergic receptors is well-characterized and involves second messenger systems, the formation of receptor heterodimers, and the presence of extracellular allosteric binding regions for the complementary ligand; however, the evolutionary origins of these interactions have not been investigated. We propose that opioid and adrenergic ligands and receptors co-evolved from a common set of modular precursors so that they share binding functions. We demonstrate the plausibility of this hypothesis through a review of experimental evidence for molecularly complementary modules and report unexpected homologies between the two receptor types. Briefly, opioids form homodimers also bind adrenergic compounds; opioids bind to conserved extracellular regions of adrenergic receptors while adrenergic compounds bind to conserved extracellular regions of opioid receptors; opioid-like modules appear in both sets of receptors within key ligand-binding regions. Transmembrane regions associated with homodimerization of each class of receptors are also highly conserved across receptor types and implicated in heterodimerization. This conservation of multiple functional modules suggests opioid–adrenergic ligand and receptor co-evolution and provides mechanisms for explaining the evolution of their crosstalk. These modules also suggest the structure of a primordial receptor, providing clues for engineering receptor functions.
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Le HTT, Murugesan A, Ramesh T, Yli-Harja O, Konda Mani S, Kandhavelu M. Molecular interaction of HIC, an agonist of P2Y1 receptor, and its role in prostate cancer apoptosis. Int J Biol Macromol 2021; 189:142-150. [PMID: 34425116 DOI: 10.1016/j.ijbiomac.2021.08.103] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022]
Abstract
Prostate cancer is a heterogeneous, slow growing asymptomatic cancer that predominantly affects man. A purinergic G-protein coupled receptor, P2Y1R, is targeted for its therapeutic value since it plays a crucial role in many key molecular events of cancer progression and invasion. Our previous study demonstrated that indoline derivative, 1 ((1-(2-Hydroxy-5-nitrophenyl) (4-hydroxyphenyl) methyl)indoline-4‑carbonitrile; HIC), stimulates prostate cancer cell (PCa) growth inhibition via P2Y1R. However, the mode of interaction of P2Y1R with HIC involved in this process remains unclear. Here, we have reported the molecular interactions of HIC with P2Y1R. Molecular dynamics simulation was performed that revealed the stable specific binding of the protein-ligand complex. In vitro analysis has shown increased apoptosis of PCa-cells, PC3, and DU145, upon specific interaction of P2Y1R-HIC. This was further validated using siRNA analysis that showed a higher percentage of apoptotic cells in PCa-cells transfected with P2Y-siRNA-MRS2365 than P2Y-siRNA-HIC treatment. Decreased mitochondrial membrane potential (MMP) activity and reduced glutathione (GSH) level show their role in P2Y1R-HIC mediated apoptosis. These in silico and in vitro results confirmed that HIC could induce mitochondrial apoptotic signaling through the P2Y1R activation. Thus, HIC being a potential ligand upon interaction with P2Y1R might have therapeutic value for the treatment of prostate cancer.
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Affiliation(s)
- Hien Thi Thu Le
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland
| | - Akshaya Murugesan
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland; Department of Biotechnology, Lady Doak College, Thallakulam, Madurai 625002, India
| | - Thiyagarajan Ramesh
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Olli Yli-Harja
- Computational Systems Biology Group, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland; Institute for Systems Biology, 1441N 34th Street, Seattle, WA 98103-8904, USA
| | - Saravanan Konda Mani
- Scigen Research and Innovation Pvt Ltd, Periyar Technology Business Incubator, Thanjavur 613403, Tamil Nadu, India
| | - Meenakshisundaram Kandhavelu
- Molecular Signaling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland.
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Wittlake A, Prömel S, Schöneberg T. The Evolutionary History of Vertebrate Adhesion GPCRs and Its Implication on Their Classification. Int J Mol Sci 2021; 22:ijms222111803. [PMID: 34769233 PMCID: PMC8584163 DOI: 10.3390/ijms222111803] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/21/2021] [Accepted: 10/26/2021] [Indexed: 11/16/2022] Open
Abstract
Adhesion G protein-coupled receptors (aGPCRs) form a structurally separate class of GPCRs with an unresolved evolutionary history and classification. Based on phylogenetic relations of human aGPCRs, nine families (A-G, L, V) were distinguished. Taking advantage of available genome data, we determined the aGPCR repertoires in all vertebrate classes. Although most aGPCR families show a high numerical stability in vertebrate genomes, the full repertoire of family E, F, and G members appeared only after the fish-tetrapod split. We did not find any evidence for new aGPCR families in vertebrates which are not present in the human genome. Based on ortholog sequence alignments, selection analysis clearly indicated two types of tetrapod aGPCRs: (i) aGPCR under strong purifying selection in tetrapod evolution (families A, B, D, L, V); and (ii) aGPCR with signatures of positive selection in some tetrapod linages (families C, E, G, F). The alignments of aGPCRs also allowed for a revised definition of reference positions within the seven-transmembrane-helix domain (relative position numbering scheme). Based on our phylogenetic cluster analysis, we suggest a revised nomenclature of aGPCRs including their transcript variants. Herein, the former families E and L are combined to one family (L) and GPR128/ADGRG7 forms a separate family (E). Furthermore, our analyses provide valuable information about the (patho)physiological relevance of individual aGPCR members.
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Affiliation(s)
- Aline Wittlake
- Division of Molecular Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103 Leipzig, Germany;
| | - Simone Prömel
- Division of Molecular Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103 Leipzig, Germany;
- Department of Biology, Institute of Cell Biology, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
- Correspondence: (S.P.); (T.S.); Tel.: +49-341-972-2150 (T.S.)
| | - Torsten Schöneberg
- Division of Molecular Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103 Leipzig, Germany;
- Correspondence: (S.P.); (T.S.); Tel.: +49-341-972-2150 (T.S.)
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G-protein-coupled receptors as therapeutic targets for glioblastoma. Drug Discov Today 2021; 26:2858-2870. [PMID: 34271165 DOI: 10.1016/j.drudis.2021.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/03/2021] [Accepted: 07/05/2021] [Indexed: 12/29/2022]
Abstract
Glioblastoma multiforme (GBM) is the most common and aggressive primary brain tumour in adults. Treatments include surgical resection, radiotherapy, and chemotherapy. Despite this, the prognosis remains poor, with an impacted quality of life during treatment coupled with brain tumour recurrence; thus, new treatments are desperately needed. In this review, we focus on recent advances in G-protein-coupled receptor (GPCR) targets. To date, the most promising targets are the chemokine, cannabinoid, and dopamine receptors, but future work should further examine the melanocortin receptor-4 (MC4R), adhesion, lysophosphatidic acid (LPA) and smoothened (Smo) receptors to initiate new drug-screening strategies and targeted delivery of safe and effective GBM therapies.
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Obesity-induced changes in human islet G protein-coupled receptor expression: Implications for metabolic regulation. Pharmacol Ther 2021; 228:107928. [PMID: 34174278 DOI: 10.1016/j.pharmthera.2021.107928] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/10/2021] [Accepted: 05/18/2021] [Indexed: 12/22/2022]
Abstract
G protein-coupled receptors (GPCRs) are a large family of cell surface receptors that are the targets for many different classes of pharmacotherapy. The islets of Langerhans are central to appropriate glucose homeostasis through their secretion of insulin, and islet function can be modified by ligands acting at the large number of GPCRs that islets express. The human islet GPCRome is not a static entity, but one that is altered under pathophysiological conditions and, in this review, we have compared expression of GPCR mRNAs in human islets obtained from normal weight range donors, and those with a weight range classified as obese. We have also considered the likely outcomes on islet function that the altered GPCR expression status confers and the possible impact that adipokines, secreted from expanded fat depots, could have at those GPCRs showing altered expression in obesity.
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O'Regan A, O'Brien CJ, Eivers SB. The lysophosphatidic acid axis in fibrosis: Implications for glaucoma. Wound Repair Regen 2021; 29:613-626. [PMID: 34009724 DOI: 10.1111/wrr.12929] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/13/2021] [Accepted: 04/28/2021] [Indexed: 12/27/2022]
Abstract
Glaucoma is a common progressive optic neuropathy that results in visual field defects and can lead to irreversible blindness. The pathophysiology of glaucoma involves dysregulated extracellular matrix remodelling in both the trabecular meshwork in the anterior chamber and in the lamina cribrosa of the optic nerve head. Fibrosis in these regions leads to raised intraocular pressure and retinal ganglion cell degeneration, respectively. Lysophosphatidic acid (LPA) is a bioactive lipid mediator which acts via six G-protein coupled receptors on the cell surface to activate intracellular pathways that promote cell proliferation, transcription and survival. LPA signalling has been implicated in both normal wound healing and pathological fibrosis. LPA enhances fibroblast proliferation, migration and contraction, and induces expression of pro-fibrotic mediators such as connective tissue growth factor. The LPA axis plays a major role in diseases such as idiopathic pulmonary fibrosis, where it has been identified as an important pharmacological target. In glaucoma, LPA is present in high levels in the aqueous humour, and its signalling has been found to increase resistance to aqueous humour outflow through altered trabecular meshwork cellular contraction and extracellular matrix deposition. LPA signalling may, therefore, also represent an attractive target for treatment of glaucoma. In this review we wish to describe the role of LPA and its related proteins in tissue fibrosis and glaucoma.
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Affiliation(s)
- Amy O'Regan
- UCD Clinical Research Centre, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Colm J O'Brien
- UCD Clinical Research Centre, Mater Misericordiae University Hospital, Dublin, Ireland.,Department of Ophthalmology, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Sarah B Eivers
- UCD Clinical Research Centre, Mater Misericordiae University Hospital, Dublin, Ireland
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39
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Liu N, Li T, Wang Y, Liu S. G-Protein Coupled Receptors (GPCRs) in Insects-A Potential Target for New Insecticide Development. Molecules 2021; 26:2993. [PMID: 34069969 PMCID: PMC8157829 DOI: 10.3390/molecules26102993] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/10/2021] [Accepted: 05/12/2021] [Indexed: 02/07/2023] Open
Abstract
G-protein coupled receptors (GPCRs) play important roles in cell biology and insects' physiological processes, toxicological response and the development of insecticide resistance. New information on genome sequences, proteomic and transcriptome analysis and expression patterns of GPCRs in organs such as the central nervous system in different organisms has shown the importance of these signaling regulatory GPCRs and their impact on vital cell functions. Our growing understanding of the role played by GPCRs at the cellular, genome, transcriptome and tissue levels is now being utilized to develop new targets that will sidestep many of the problems currently hindering human disease control and insect pest management. This article reviews recent work on the expression and function of GPCRs in insects, focusing on the molecular complexes governing the insect physiology and development of insecticide resistance and examining the genome information for GPCRs in two medically important insects, mosquitoes and house flies, and their orthologs in the model insect species Drosophila melanogaster. The tissue specific distribution and expression of the insect GPCRs is discussed, along with fresh insights into practical aspects of insect physiology and toxicology that could be fundamental for efforts to develop new, more effective, strategies for pest control and resistance management.
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Affiliation(s)
- Nannan Liu
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA; (T.L.); (Y.W.)
| | - Ting Li
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA; (T.L.); (Y.W.)
| | - Yifan Wang
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA; (T.L.); (Y.W.)
| | - Shikai Liu
- College of Fisheries, Ocean University of China, Qingdao 266100, China;
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40
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Lee T, Lee S, Kang M, Kim S. Deep hierarchical embedding for simultaneous modeling of GPCR proteins in a unified metric space. Sci Rep 2021; 11:9543. [PMID: 33953216 PMCID: PMC8100104 DOI: 10.1038/s41598-021-88623-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 04/13/2021] [Indexed: 11/23/2022] Open
Abstract
GPCR proteins belong to diverse families of proteins that are defined at multiple hierarchical levels. Inspecting relationships between GPCR proteins on the hierarchical structure is important, since characteristics of the protein can be inferred from proteins in similar hierarchical information. However, modeling of GPCR families has been performed separately for each of the family, subfamily, and sub-subfamily level. Relationships between GPCR proteins are ignored in these approaches as they process the information in the proteins with several disconnected models. In this study, we propose DeepHier, a deep learning model to simultaneously learn representations of GPCR family hierarchy from the protein sequences with a unified single model. Novel loss term based on metric learning is introduced to incorporate hierarchical relations between proteins. We tested our approach using a public GPCR sequence dataset. Metric distances in the deep feature space corresponded to the hierarchical family relation between GPCR proteins. Furthermore, we demonstrated that further downstream tasks, like phylogenetic reconstruction and motif discovery, are feasible in the constructed embedding space. These results show that hierarchical relations between sequences were successfully captured in both of technical and biological aspects.
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Affiliation(s)
- Taeheon Lee
- Looxid Labs, Seoul, 06628, Republic of Korea
| | - Sangseon Lee
- BK21 FOUR Intelligence Computing, Seoul National University, Seoul, 08826, Republic of Korea
| | - Minji Kang
- Department of Computer Science, Stanford University, Stanford, CA, 94305, USA
| | - Sun Kim
- Bioinformatics Institute, Seoul National University, Seoul, 08826, Republic of Korea. .,Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea. .,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea. .,Institute of Engineering Research, Seoul National University, Seoul, 08826, Republic of Korea.
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41
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Lengger B, Jensen MK. Engineering G protein-coupled receptor signalling in yeast for biotechnological and medical purposes. FEMS Yeast Res 2021; 20:5673487. [PMID: 31825496 PMCID: PMC6977407 DOI: 10.1093/femsyr/foz087] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) comprise the largest class of membrane proteins in the human genome, with a common denominator of seven-transmembrane domains largely conserved among eukaryotes. Yeast is naturally armoured with three different GPCRs for pheromone and sugar sensing, with the pheromone pathway being extensively hijacked for characterising heterologous GPCR signalling in a model eukaryote. This review focusses on functional GPCR studies performed in yeast and on the elucidated hotspots for engineering, and discusses both endogenous and heterologous GPCR signalling. Key emphasis will be devoted to studies describing important engineering parameters to consider for successful coupling of GPCRs to the yeast mating pathway. We also review the various means of applying yeast for studying GPCRs, including the use of yeast armed with heterologous GPCRs as a platform for (i) deorphanisation of orphan receptors, (ii) metabolic engineering of yeast for production of bioactive products and (iii) medical applications related to pathogen detection and drug discovery. Finally, this review summarises the current challenges related to expression of functional membrane-bound GPCRs in yeast and discusses the opportunities to continue capitalising on yeast as a model chassis for functional GPCR signalling studies.
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Affiliation(s)
- Bettina Lengger
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, Kgs. Lyngby, 2800, Denmark
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, Kgs. Lyngby, 2800, Denmark
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42
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Jabeen A, Vijayram R, Ranganathan S. BIO-GATS: A Tool for Automated GPCR Template Selection Through a Biophysical Approach for Homology Modeling. Front Mol Biosci 2021; 8:617176. [PMID: 33898512 PMCID: PMC8059640 DOI: 10.3389/fmolb.2021.617176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/24/2021] [Indexed: 11/13/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest family of membrane proteins with more than 800 members. GPCRs are involved in numerous physiological functions within the human body and are the target of more than 30% of the United States Food and Drug Administration (FDA) approved drugs. At present, over 400 experimental GPCR structures are available in the Protein Data Bank (PDB) representing 76 unique receptors. The absence of an experimental structure for the majority of GPCRs demand homology models for structure-based drug discovery workflows. The generation of good homology models requires appropriate templates. The commonly used methods for template selection are based on sequence identity. However, there exists low sequence identity among the GPCRs. Sequences with similar patterns of hydrophobic residues are often structural homologs, even with low sequence identity. Extending this, we propose a biophysical approach for template selection based principally on hydrophobicity correspondence between the target and the template. Our approach takes into consideration other relevant parameters, including resolution, similarity within the orthosteric binding pocket of GPCRs, and structure completeness, for template selection. The proposed method was implemented in the form of a free tool called Bio-GATS, to provide the user with easy selection of the appropriate template for a query GPCR sequence. Bio-GATS was successfully validated with recent published benchmarking datasets. An application to an olfactory receptor to select an appropriate template has also been provided as a case study.
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Affiliation(s)
- Amara Jabeen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ramya Vijayram
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Shoba Ranganathan
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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Yang D, Zhou Q, Labroska V, Qin S, Darbalaei S, Wu Y, Yuliantie E, Xie L, Tao H, Cheng J, Liu Q, Zhao S, Shui W, Jiang Y, Wang MW. G protein-coupled receptors: structure- and function-based drug discovery. Signal Transduct Target Ther 2021; 6:7. [PMID: 33414387 PMCID: PMC7790836 DOI: 10.1038/s41392-020-00435-w] [Citation(s) in RCA: 208] [Impact Index Per Article: 69.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/30/2020] [Accepted: 12/05/2020] [Indexed: 02/08/2023] Open
Abstract
As one of the most successful therapeutic target families, G protein-coupled receptors (GPCRs) have experienced a transformation from random ligand screening to knowledge-driven drug design. We are eye-witnessing tremendous progresses made recently in the understanding of their structure-function relationships that facilitated drug development at an unprecedented pace. This article intends to provide a comprehensive overview of this important field to a broader readership that shares some common interests in drug discovery.
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Affiliation(s)
- Dehua Yang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Qingtong Zhou
- School of Basic Medical Sciences, Fudan University, 200032, Shanghai, China
| | - Viktorija Labroska
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Shanshan Qin
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Sanaz Darbalaei
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Elita Yuliantie
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Linshan Xie
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Houchao Tao
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Qing Liu
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China. .,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
| | - Yi Jiang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.
| | - Ming-Wei Wang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China. .,The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China. .,School of Basic Medical Sciences, Fudan University, 200032, Shanghai, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China. .,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China. .,School of Pharmacy, Fudan University, 201203, Shanghai, China.
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45
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Huang D, Zhang B, Han T, Liu G, Chen X, Zhao Z, Feng J, Yang J, Wang T. Genome-wide prediction and comparative transcriptomic analysis reveals the G protein-coupled receptors involved in gonadal development of Apostichopus japonicus. Genomics 2020; 113:967-978. [PMID: 33144216 DOI: 10.1016/j.ygeno.2020.10.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/26/2020] [Accepted: 10/28/2020] [Indexed: 01/14/2023]
Abstract
The sea cucumber Apostichopus japonicus is dioecious, with seasonal reproduction. G protein-coupled receptor (GPCR)-mediated signaling systems might play critical roles in the reproductive control of A. japonicus. Here, we classified GPCR from the genome in silico and used transcriptomic analyses to further mine those that function in gonadal-development control. Totally, 487 GPCRs were predicted from A. japonicus, and 183 of these were further annotated to molecular pathways. Transcriptome analysis revealed 327 GPCRs expressed in gonads, and these were classified into four families and 19 subfamilies. Three pathways were apparently associated with reproduction, including neuroactive ligand-receptor interaction, the mTOR and Wnt signaling pathways. Seven and eight ovary- and testis-specific GPCRs were filtered, and the gene expression profiles were determined in multiple tissues and gonads at different developmental stages by qPCR. These results provide new insights into the discovery of GPCR-mediated signaling control in sea cucumber reproduction, especially in gonadal development control.
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Affiliation(s)
- Dexiang Huang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Bing Zhang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Tao Han
- Department of Aquaculture, Zhejiang Ocean University, 316022, Zhoushan, Zhejiang, People's Republic of China
| | - Guangbin Liu
- Marine Biology Institute of Shandong Province, 266104 Qingdao, Shandong, People's Republic of China
| | - Xu Chen
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Zihao Zhao
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Jiaqian Feng
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China
| | - Jingwen Yang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China; National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China.
| | - Tianming Wang
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China; National Engineering Research Center of Marine Facilities Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, Zhoushan, Zhejiang 316022, People's Republic of China.
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46
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Odoemelam CS, Percival B, Wallis H, Chang MW, Ahmad Z, Scholey D, Burton E, Williams IH, Kamerlin CL, Wilson PB. G-Protein coupled receptors: structure and function in drug discovery. RSC Adv 2020; 10:36337-36348. [PMID: 35517958 PMCID: PMC9057076 DOI: 10.1039/d0ra08003a] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
The G-protein coupled receptors (GPCRs) superfamily comprise similar proteins arranged into families or classes thus making it one of the largest in the mammalian genome. GPCRs take part in many vital physiological functions making them targets for numerous novel drugs. GPCRs share some distinctive features, such as the seven transmembrane domains, they also differ in the number of conserved residues in their transmembrane domain. Here we provide an introductory and accessible review detailing the computational advances in GPCR pharmacology and drug discovery. An overview is provided on family A-C GPCRs; their structural differences, GPCR signalling, allosteric binding and cooperativity. The dielectric constant (relative permittivity) of proteins is also discussed in the context of site-specific environmental effects.
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Affiliation(s)
| | - Benita Percival
- Nottingham Trent University 50 Shakespeare St Nottingham NG1 4FQ UK
| | - Helen Wallis
- Nottingham Trent University 50 Shakespeare St Nottingham NG1 4FQ UK
| | - Ming-Wei Chang
- Nanotechnology and Integrated Bioengineering Centre, University of Ulster Jordanstown Campus Newtownabbey BT37 0QB Northern Ireland UK
| | - Zeeshan Ahmad
- De Montfort University The Gateway Leicester LE1 9BH UK
| | - Dawn Scholey
- Nottingham Trent University 50 Shakespeare St Nottingham NG1 4FQ UK
| | - Emily Burton
- Nottingham Trent University 50 Shakespeare St Nottingham NG1 4FQ UK
| | - Ian H Williams
- Department of Chemistry, University of Bath Claverton Down Bath BA1 7AY UK
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Benchmarking GPCR homology model template selection in combination with de novo loop generation. J Comput Aided Mol Des 2020; 34:1027-1044. [PMID: 32737667 DOI: 10.1007/s10822-020-00325-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/16/2020] [Indexed: 01/08/2023]
Abstract
G protein-coupled receptors (GPCR) comprise the largest family of membrane proteins and are of considerable interest as targets for drug development. However, many GPCR structures remain unsolved. To address the structural ambiguity of these receptors, computational tools such as homology modeling and loop modeling are often employed to generate predictive receptor structures. Here we combined both methods to benchmark a protocol incorporating homology modeling based on a locally selected template and extracellular loop modeling that additionally evaluates the presence of template ligands during these modeling steps. Ligands were also docked using three docking methods and two pose selection methods to elucidate an optimal ligand pose selection method. Results suggest that local template-based homology models followed by loop modeling produce more accurate and predictive receptor models than models produced without loop modeling, with decreases in average receptor and ligand RMSD of 0.54 Å and 2.91 Å, respectively. Ligand docking results showcased the ability of MOE induced fit docking to produce ligand poses with atom root-mean-square deviation (RMSD) values at least 0.20 Å lower (on average) than the other two methods benchmarked in this study. In addition, pose selection methods (software-based scoring, ligand complementation) selected lower RMSD poses with MOE induced fit docking than either of the other methods (averaging at least 1.57 Å lower), indicating that MOE induced fit docking is most suited for docking into GPCR homology models in our hands. In addition, target receptor models produced with a template ligand present throughout the modeling process most often produced target ligand poses with RMSD values ≤ 4.5 Å and Tanimoto coefficients > 0.6 after selection based on ligand complementation than target receptor models produced in the absence of template ligands. Overall, the findings produced by this study support the use of local template homology modeling in combination with de novo ECL2 modeling in the presence of a ligand from the template crystal structure to generate GPCR models intended to study ligand binding interactions.
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48
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Almeida MJ, Matos A. Designer Nucleases: Gene-Editing Therapies using CCR5 as an Emerging Target in HIV. Curr HIV Res 2020; 17:306-323. [PMID: 31652113 DOI: 10.2174/1570162x17666191025112918] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 02/08/2023]
Abstract
Acquired Immunodeficiency Syndrome (AIDS), caused by the Human Immunodeficiency Virus (HIV), is a life-threatening disorder that persists worldwide as a severe health problem. Since it was linked with the HIV attachment process, the Chemokine receptor, CCR5, has been at the development leading edge of several gene-based therapies. Given the shortcomings of the current antiretroviral treatment procedure and the non-availability of a licensed vaccine, the aptitude to modify complex genomes with Designer Nucleases has had a noteworthy impact on biotechnology. Over the last years, ZFN, TALEN and CRISPR/Cas9 gene-editing technology have appeared as a promising solution that mimics the naturally occurring CCR5/Δ32 mutation and permanently guarantees the absence of CCR5-expression on the surface of HIV target-cells, leading to a continuous resistance to the virus entry and, ultimately, proving that cellular immunization from infection could be, in fact, a conceivable therapeutic approach to finally achieve the long-awaited functional cure of HIV.
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Affiliation(s)
- Maria João Almeida
- Laboratory of Microbiology, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Ana Matos
- Laboratory of Microbiology, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.,Research Centre on Chemical Processes Engineering and Forest Products (CIEPQF), Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
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49
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Onogi Y, Khalil AEMM, Ussar S. Identification and characterization of adipose surface epitopes. Biochem J 2020; 477:2509-2541. [PMID: 32648930 PMCID: PMC7360119 DOI: 10.1042/bcj20190462] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/11/2020] [Accepted: 06/12/2020] [Indexed: 12/14/2022]
Abstract
Adipose tissue is a central regulator of metabolism and an important pharmacological target to treat the metabolic consequences of obesity, such as insulin resistance and dyslipidemia. Among the various cellular compartments, the adipocyte cell surface is especially appealing as a drug target as it contains various proteins that when activated or inhibited promote adipocyte health, change its endocrine function and eventually maintain or restore whole-body insulin sensitivity. In addition, cell surface proteins are readily accessible by various drug classes. However, targeting individual cell surface proteins in adipocytes has been difficult due to important functions of these proteins outside adipose tissue, raising various safety concerns. Thus, one of the biggest challenges is the lack of adipose selective surface proteins and/or targeting reagents. Here, we discuss several receptor families with an important function in adipogenesis and mature adipocytes to highlight the complexity at the cell surface and illustrate the problems with identifying adipose selective proteins. We then discuss that, while no unique adipocyte surface protein might exist, how splicing, posttranslational modifications as well as protein/protein interactions can create enormous diversity at the cell surface that vastly expands the space of potentially unique epitopes and how these selective epitopes can be identified and targeted.
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Affiliation(s)
- Yasuhiro Onogi
- RG Adipocytes and Metabolism, Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Ahmed Elagamy Mohamed Mahmoud Khalil
- RG Adipocytes and Metabolism, Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
| | - Siegfried Ussar
- RG Adipocytes and Metabolism, Institute for Diabetes and Obesity, Helmholtz Diabetes Center, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, 85764 Neuherberg, Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Department of Medicine, Technische Universität München, Munich, Germany
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50
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Dziedzic A, Miller E, Saluk-Bijak J, Bijak M. The GPR17 Receptor-A Promising Goal for Therapy and a Potential Marker of the Neurodegenerative Process in Multiple Sclerosis. Int J Mol Sci 2020; 21:ijms21051852. [PMID: 32182666 PMCID: PMC7084627 DOI: 10.3390/ijms21051852] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 02/29/2020] [Accepted: 03/06/2020] [Indexed: 12/28/2022] Open
Abstract
One of the most important goals in the treatment of demyelinating diseases such as multiple sclerosis (MS) is, in addition to immunomodulation, reconstruction of the lost myelin sheath. The modulator of the central nervous system myelination is the metabotropic receptor coupled to the G-protein: GPR17. GPR17 receptors are considered to be sensors of local damage to the myelin sheath, and play a role in the reconstruction and repair of demyelinating plaques caused by ongoing inflammatory processes. GPR17 receptors are present on nerve cells and precursor oligodendrocyte cells. Under physiological conditions, they are responsible for the differentiation and subsequent maturation of oligodendrocytes, while under pathological conditions (during damage to nerve cells), their expression increases to become mediators in the demyelinating processes. Moreover, they are essential not only in both the processes of inducing damage and the death of neurons, but also in the local repair of the damaged myelin sheath. Therefore, GPR17 receptors may be recognized as the potential goal in creating innovative therapies for the treatment of the neurodegenerative process in MS, based on the acceleration of the remyelination processes. This review examines the role of GRP17 in pathomechanisms of MS development.
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Affiliation(s)
- Angela Dziedzic
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (A.D.); (J.S.-B.)
| | - Elzbieta Miller
- Department of Neurological Rehabilitation, Medical University of Lodz, Milionowa 14, 93-113 Lodz, Poland;
| | - Joanna Saluk-Bijak
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland; (A.D.); (J.S.-B.)
| | - Michal Bijak
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
- Correspondence: ; Tel.: +48-42-635-4336
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