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Structural basis for chemokine recognition and receptor activation of chemokine receptor CCR5. Nat Commun 2021; 12:4151. [PMID: 34230484 PMCID: PMC8260604 DOI: 10.1038/s41467-021-24438-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/18/2021] [Indexed: 02/06/2023] Open
Abstract
The chemokine receptor CCR5 plays a vital role in immune surveillance and inflammation. However, molecular details that govern its endogenous chemokine recognition and receptor activation remain elusive. Here we report three cryo-electron microscopy structures of Gi1 protein-coupled CCR5 in a ligand-free state and in complex with the chemokine MIP-1α or RANTES, as well as the crystal structure of MIP-1α-bound CCR5. These structures reveal distinct binding modes of the two chemokines and a specific accommodate pattern of the chemokine for the distal N terminus of CCR5. Together with functional data, the structures demonstrate that chemokine-induced rearrangement of toggle switch and plasticity of the receptor extracellular region are critical for receptor activation, while a conserved tryptophan residue in helix II acts as a trigger of receptor constitutive activation.
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Isaikina P, Tsai CJ, Dietz N, Pamula F, Grahl A, Goldie KN, Guixà-González R, Branco C, Paolini-Bertrand M, Calo N, Cerini F, Schertler GFX, Hartley O, Stahlberg H, Maier T, Deupi X, Grzesiek S. Structural basis of the activation of the CC chemokine receptor 5 by a chemokine agonist. SCIENCE ADVANCES 2021; 7:7/25/eabg8685. [PMID: 34134983 PMCID: PMC8208711 DOI: 10.1126/sciadv.abg8685] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/29/2021] [Indexed: 05/10/2023]
Abstract
The human CC chemokine receptor 5 (CCR5) is a G protein-coupled receptor (GPCR) that plays a major role in inflammation and is involved in cancer, HIV, and COVID-19. Despite its importance as a drug target, the molecular activation mechanism of CCR5, i.e., how chemokine agonists transduce the activation signal through the receptor, is yet unknown. Here, we report the cryo-EM structure of wild-type CCR5 in an active conformation bound to the chemokine super-agonist [6P4]CCL5 and the heterotrimeric Gi protein. The structure provides the rationale for the sequence-activity relation of agonist and antagonist chemokines. The N terminus of agonist chemokines pushes onto specific structural motifs at the bottom of the orthosteric pocket that activate the canonical GPCR microswitch network. This activation mechanism differs substantially from other CC chemokine receptors that bind chemokines with shorter N termini in a shallow binding mode involving unique sequence signatures and a specialized activation mechanism.
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Affiliation(s)
- Polina Isaikina
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Ching-Ju Tsai
- Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
| | - Nikolaus Dietz
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Filip Pamula
- Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland
- Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Anne Grahl
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Kenneth N Goldie
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, CH-4058 Basel, Switzerland
| | | | - Camila Branco
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Marianne Paolini-Bertrand
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Nicolas Calo
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Fabrice Cerini
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Gebhard F X Schertler
- Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland.
- Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Oliver Hartley
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
- Orion Biotechnology, Ottawa, Canada
| | - Henning Stahlberg
- Center for Cellular Imaging and NanoAnalytics, Biozentrum, University of Basel, CH-4058 Basel, Switzerland
| | - Timm Maier
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Xavier Deupi
- Paul Scherrer Institute, CH-5232 Villigen PSI, Switzerland.
| | - Stephan Grzesiek
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, CH-4056 Basel, Switzerland.
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Mirza MU, Saadabadi A, Vanmeert M, Salo-Ahen OMH, Abdullah I, Claes S, De Jonghe S, Schols D, Ahmad S, Froeyen M. Discovery of HIV entry inhibitors via a hybrid CXCR4 and CCR5 receptor pharmacophore-based virtual screening approach. Eur J Pharm Sci 2020; 155:105537. [PMID: 32890663 PMCID: PMC7467125 DOI: 10.1016/j.ejps.2020.105537] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/10/2020] [Accepted: 08/30/2020] [Indexed: 12/30/2022]
Abstract
Chemokine receptors are key regulators of cell migration in terms of immunity and inflammation. Among these, CCR5 and CXCR4 play pivotal roles in cancer metastasis and HIV-1 transmission and infection. They act as essential co-receptors for HIV and furnish a route to the cell entry. In particular, inhibition of either CCR5 or CXCR4 leads very often the virus to shift to a more virulent dual-tropic strain. Therefore, dual receptor inhibition might improve the therapeutic strategies against HIV. In this study, we aimed to discover selective CCR5, CXCR4, and dual CCR5/CXCR4 antagonists using both receptor- and ligand-based computational methods. We employed this approach to fully incorporate the interaction attributes of the binding pocket together with molecular dynamics (MD) simulations and binding free energy calculations. The best hits were evaluated for their anti-HIV-1 activity against CXCR4- and CCR5-specific NL4.3 and BaL strains. Moreover, the Ca2+ mobilization assay was used to evaluate their antagonistic activity. From the 27 tested compounds, three were identified as inhibitors: compounds 27 (CCR5), 6 (CXCR4) and 3 (dual) with IC50 values ranging from 10.64 to 64.56 μM. The binding mode analysis suggests that the active compounds form a salt bridge with the glutamates and π-stacking interactions with the aromatic side chains binding site residues of the respective co-receptor. The presented hierarchical virtual screening approach provides essential aspects in identifying potential antagonists in terms of selectivity against a specific co-receptor. The compounds having multiple heterocyclic nitrogen atoms proved to be relatively more specific towards CXCR4 inhibition as compared to CCR5. The identified compounds serve as a starting point for further development of HIV entry inhibitors through synthesis and quantitative structure-activity relationship studies.
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Affiliation(s)
- Muhammad Usman Mirza
- Medicinal Chemistry, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Atefeh Saadabadi
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
| | - Michiel Vanmeert
- Medicinal Chemistry, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Outi M H Salo-Ahen
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
| | - Iskandar Abdullah
- Department of Chemistry, Faculty of Sciences, University Malaya, Kuala Lumpur 59100, Malaysia
| | - Sandra Claes
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Steven De Jonghe
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Sarfraz Ahmad
- Department of Chemistry, Faculty of Sciences, University Malaya, Kuala Lumpur 59100, Malaysia
| | - Matheus Froeyen
- Medicinal Chemistry, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium.
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Zhang Z, Zhang Q, Dexheimer TS, Ren J, Neubig RR, Li W. Two highly related odorant receptors specifically detect α-bile acid pheromones in sea lamprey ( Petromyzon marinus). J Biol Chem 2020; 295:12153-12166. [PMID: 32636305 PMCID: PMC7443511 DOI: 10.1074/jbc.ra119.011532] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 07/01/2020] [Indexed: 10/23/2022] Open
Abstract
Pheromones play critical roles in habitat identification and reproductive behavior synchronization in the sea lamprey (Petromyzon marinus). The bile acid 3-keto petromyzonol sulfate (3kPZS) is a major component of the sex pheromone mixture from male sea lamprey that induces specific olfactory and behavioral responses in conspecific individuals. Olfactory receptors interact directly with pheromones, which is the first step in their detection, but identifying the cognate receptors of specific pheromones is often challenging. Here, we deorphanized two highly related odorant receptors (ORs), OR320a and OR320b, of P. marinus that respond to 3kPZS. In a heterologous expression system coupled to a cAMP-responsive CRE-luciferase, OR320a and OR320b specifically responded to C24 5α-bile acids, and both receptors were activated by the same set of 3kPZS analogs. OR320a displayed larger responses to all 3kPZS analogs than did OR320b. This difference appeared to be largely determined by a single amino acid residue, Cys-792.56, the C-terminal sixth residue relative to the most conserved residue in the second transmembrane domain (2.56) of OR320a. This region of TM2 residues 2.56-2.60 apparently is critical for the detection of steroid compounds by odorant receptors in lamprey, zebrafish, and humans. Finally, we identified OR320 orthologs in Japanese lamprey (Lethenteron camtschaticum), suggesting that the OR320 family may be widely present in lamprey species and that OR320 may be under purifying selection. Our results provide a system to examine the origin of olfactory steroid detection in vertebrates and to define a highly conserved molecular mechanism for steroid-ligand detection by G protein-coupled receptors.
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Affiliation(s)
- Zhe Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Qinghua Zhang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Thomas S Dexheimer
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA
| | - Jianfeng Ren
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China; International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China; Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Richard R Neubig
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA.
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, USA.
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Ellwanger JH, Kulmann-Leal B, Kaminski VDL, Rodrigues AG, Bragatte MADS, Chies JAB. Beyond HIV infection: Neglected and varied impacts of CCR5 and CCR5Δ32 on viral diseases. Virus Res 2020; 286:198040. [PMID: 32479976 PMCID: PMC7260533 DOI: 10.1016/j.virusres.2020.198040] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/27/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022]
Abstract
CCR5 regulates multiple cell types (e.g., T regulatory and Natural Killer cells) and immune responses. The effects of CCR5, CCR5Δ32 (variant associated with reduced CCR5 expression) and CCR5 antagonists vary between infections. CCR5 affects the pathogenesis of flaviviruses, especially in the brain. The genetic variant CCR5Δ32 increases the risk of symptomatic West Nile virus infection. The triad “CCR5, extracellular vesicles and infections” is an emerging topic.
The interactions between chemokine receptors and their ligands may affect susceptibility to infectious diseases as well as their clinical manifestations. These interactions mediate both the traffic of inflammatory cells and virus-associated immune responses. In the context of viral infections, the human C-C chemokine receptor type 5 (CCR5) receives great attention from the scientific community due to its role as an HIV-1 co-receptor. The genetic variant CCR5Δ32 (32 base-pair deletion in CCR5 gene) impairs CCR5 expression on the cell surface and is associated with protection against HIV infection in homozygous individuals. Also, the genetic variant CCR5Δ32 modifies the CCR5-mediated inflammatory responses in various conditions, such as inflammatory and infectious diseases. CCR5 antagonists mimic, at least in part, the natural effects of the CCR5Δ32 in humans, which explains the growing interest in the potential benefits of using CCR5 modulators for the treatment of different diseases. Nevertheless, beyond HIV infection, understanding the effects of the CCR5Δ32 variant in multiple viral infections is essential to shed light on the potential effects of the CCR5 modulators from a broader perspective. In this context, this review discusses the involvement of CCR5 and the effects of the CCR5Δ32 in human infections caused by the following pathogens: West Nile virus, Influenza virus, Human papillomavirus, Hepatitis B virus, Hepatitis C virus, Poliovirus, Dengue virus, Human cytomegalovirus, Crimean-Congo hemorrhagic fever virus, Enterovirus, Japanese encephalitis virus, and Hantavirus. Subsequently, this review addresses the impacts of CCR5 gene editing and CCR5 modulation on health and viral diseases. Also, this article connects recent findings regarding extracellular vesicles (e.g., exosomes), viruses, and CCR5. Neglected and emerging topics in “CCR5 research” are briefly described, with focus on Rocio virus, Zika virus, Epstein-Barr virus, and Rhinovirus. Finally, the potential influence of CCR5 on the immune responses to coronaviruses is discussed.
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Affiliation(s)
- Joel Henrique Ellwanger
- Laboratório de Imunobiologia e Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Bruna Kulmann-Leal
- Laboratório de Imunobiologia e Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Valéria de Lima Kaminski
- Laboratório de Imunobiologia e Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil; Programa de Pós-Graduação em Biotecnologia, Laboratório de Imunologia Aplicada, Instituto de Ciência e Tecnologia - ICT, Universidade Federal de São Paulo - UNIFESP, São José dos Campos, São Paulo, Brazil
| | - Andressa Gonçalves Rodrigues
- Laboratório de Imunobiologia e Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - Marcelo Alves de Souza Bragatte
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil; Núcleo de Bioinformática do Laboratório de Imunobiologia e Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil
| | - José Artur Bogo Chies
- Laboratório de Imunobiologia e Imunogenética, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, Brazil.
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Arendt V, Amand M, Iserentant G, Lemaire M, Masquelier C, Ndayisaba GF, Verhofstede C, Karita E, Allen S, Chevigné A, Schmit J, Bercoff DP, Seguin‐Devaux C. Predominance of the heterozygous CCR5 delta-24 deletion in African individuals resistant to HIV infection might be related to a defect in CCR5 addressing at the cell surface. J Int AIDS Soc 2019; 22:e25384. [PMID: 31486251 PMCID: PMC6727025 DOI: 10.1002/jia2.25384] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 07/31/2019] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION The chemokine receptor CCR5 is the main co-receptor for R5-tropic HIV-1 variants. We have previously described a novel 24-base pair deletion in the coding region of CCR5 among individuals from Rwanda. Here, we investigated the prevalence of hCCR5Δ24 in different cohorts and its impact on CCR5 expression and HIV-1 infection in vitro. METHODS We screened hCCR5Δ24 in a total of 3232 individuals which were either HIV-1 uninfected, high-risk HIV-1 seronegative and seropositive partners from serodiscordant couples, Long-Term Survivors, or HIV-1 infected volunteers from Africa (Rwanda, Kenya, Guinea-Conakry) and Luxembourg, using a real-time PCR assay. The role of the 24-base pair deletion on CCR5 expression and HIV infection was assessed in cell lines and PBMC using mRNA quantification, confocal analysis, flow and imaging cytometry. RESULTS AND DISCUSSION Among the 1661 patients from Rwanda, 12 individuals were heterozygous for hCCR5Δ24 but none were homozygous. Although heterozygosity for this allele may not confer complete resistance to HIV-1 infection, the prevalence of the mutation was 2.41% (95%CI: 0.43; 8.37) in 83 Long-Term Survivors (LTS) and 0.99% (95%CI: 0.45; 2.14) in 613 HIV-1 exposed seronegative members as compared with 0.35% (95% Cl: 0.06; 1.25) in 579 HIV-1 seropositive members. The prevalence of hCCR5Δ24 was 0.55% (95%CI: 0.15; 1.69) in 547 infants from Kenya but the mutation was not detected in 224 infants from Guinea-Conakry nor in 800 Caucasian individuals from Luxembourg. Expression of hCCR5Δ24 in cell lines and PBMC showed that the hCCR5Δ24 protein is stably expressed but is not transported to the plasma membrane due to a conformational change. Instead, the mutant receptor was retained intracellularly, colocalized with an endoplasmic reticulum marker and did not mediate HIV-1 infection. Co-transfection of hCCR5Δ24 and wtCCR5 did not indicate a transdominant negative effect of CCR5Δ24 on wtCCR5. CONCLUSIONS Our findings indicate that hCCR5Δ24 is not expressed at the cell surface. This could explain the higher prevalence of the heterozygous hCCR5Δ24 in LTS and HIV-1 exposed seronegative members from serodiscordant couples. Our data suggest an East-African localization of this deletion, which needs to be confirmed in larger cohorts from African and non-African countries.
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Affiliation(s)
- Vic Arendt
- Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
- Centre Hospitalier de LuxembourgNational Service of Infectious DiseasesLuxembourgLuxembourg
| | - Mathieu Amand
- Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | - Gilles Iserentant
- Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | - Morgane Lemaire
- Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | - Cécile Masquelier
- Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | | | - Chris Verhofstede
- Department of Clinical Chemistry, Microbiology and ImmunologyAIDS Reference LaboratoryGhent UniversityGhentBelgium
| | - Etienne Karita
- Department of Pathology and Laboratory MedicineEmory University School of MedicineAtlantaGAUSA
| | - Susan Allen
- Department of Pathology and Laboratory MedicineEmory University School of MedicineAtlantaGAUSA
| | - Andy Chevigné
- Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | - Jean‐Claude Schmit
- Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | - Danielle Perez Bercoff
- Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
| | - Carole Seguin‐Devaux
- Department of Infection and ImmunityLuxembourg Institute of HealthEsch‐sur‐AlzetteLuxembourg
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Zhang F, Yuan Y, Li H, Shen L, Guo Y, Wen Z, Pu X. Using accelerated molecular dynamics simulation to shed light on the mechanism of activation/deactivation upon mutations for CCR5. RSC Adv 2018; 8:37855-37865. [PMID: 35558583 PMCID: PMC9089863 DOI: 10.1039/c8ra07686c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 11/06/2018] [Indexed: 12/27/2022] Open
Abstract
In this work, accelerated molecular dynamics (aMD) simulations were used to study different effects of G286F and R126 mutations on the activity of CCR5. Potential of Mean Force (PMF) results indicate that there are stable inactive-like states and active-like ones existing in the conformation space of the wild type (WT), confirming that CCR5 could possess to some extent constitutive activity. But the R126N mutation could constrain CCR5 in the inactive state through influencing the TXP motif and limiting the movements of TM5 and TM6. In contrast, the G286F mutation promotes the activity of the receptor by increasing the distance of TM2–TM6 and the flexibility of the intracellular part of TM5 and changing the H-bonding in the TXP motif. The observations from the cross correlation analysis further show that the R126N mutation dramatically reduces the motion correlations between TMs, which should partly contribute to the deactivation of CCR5. Compared with the WT system, TM6 and TM7 in the G286F mutant are loosely correlated with other regions, which should be conducive to drive the movement of TM6 and TM7 toward the active conformation. In addition, the result from the protein structure network (PSN) analysis reveals that the shortest pathways connecting the extracellular and the intracellular domains are highly conserved in the three systems despite the different mutations, in which the hydrogen bond plays a pivotal role. However, the G286F mutation shortens the lifetime of the pathway with respect to the R126N mutation, which may be associated with the different activities of the two mutants. The pathway connecting the ligand-binding site and the G-protein region reveals that the allosteric communication between TM6 and TM7 is enhanced by the R126N mutation while the G286F mutation induces the activation of the G-protein pocket by arousing more residues in the NPxxY region to participate in the pathway. In this work, accelerated molecular dynamics (aMD) simulations were used to study different effects of G286F and R126 mutations on the activity of CCR5.![]()
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Affiliation(s)
- Fuhui Zhang
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Yuan Yuan
- College of Management
- Southwest University for Nationalities
- Chengdu 610041
- P. R. China
| | - Haiyan Li
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Liting Shen
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Yanzhi Guo
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Zhining Wen
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
| | - Xuemei Pu
- Faculty of Chemistry
- Sichuan University
- Chengdu
- People's Republic of China
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8
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Ziarek JJ, Kleist AB, London N, Raveh B, Montpas N, Bonneterre J, St-Onge G, DiCosmo-Ponticello CJ, Koplinski CA, Roy I, Stephens B, Thelen S, Veldkamp CT, Coffman FD, Cohen MC, Dwinell MB, Thelen M, Peterson FC, Heveker N, Volkman BF. Structural basis for chemokine recognition by a G protein-coupled receptor and implications for receptor activation. Sci Signal 2017; 10:10/471/eaah5756. [PMID: 28325822 DOI: 10.1126/scisignal.aah5756] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chemokines orchestrate cell migration for development, immune surveillance, and disease by binding to cell surface heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs). The array of interactions between the nearly 50 chemokines and their 20 GPCR targets generates an extensive signaling network to which promiscuity and biased agonism add further complexity. The receptor CXCR4 recognizes both monomeric and dimeric forms of the chemokine CXCL12, which is a distinct example of ligand bias in the chemokine family. We demonstrated that a constitutively monomeric CXCL12 variant reproduced the G protein-dependent and β-arrestin-dependent responses that are associated with normal CXCR4 signaling and lead to cell migration. In addition, monomeric CXCL12 made specific contacts with CXCR4 that are not present in the structure of the receptor in complex with a dimeric form of CXCL12, a biased agonist that stimulates only G protein-dependent signaling. We produced an experimentally validated model of an agonist-bound chemokine receptor that merged a nuclear magnetic resonance-based structure of monomeric CXCL12 bound to the amino terminus of CXCR4 with a crystal structure of the transmembrane domains of CXCR4. The large CXCL12:CXCR4 protein-protein interface revealed by this structure identified previously uncharacterized functional interactions that fall outside of the classical "two-site model" for chemokine-receptor recognition. Our model suggests a mechanistic hypothesis for how interactions on the extracellular face of the receptor may stimulate the conformational changes required for chemokine receptor-mediated signal transduction.
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Affiliation(s)
- Joshua J Ziarek
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Andrew B Kleist
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Nir London
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Barak Raveh
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nicolas Montpas
- Centre de Recherche, Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Julien Bonneterre
- Centre de Recherche, Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Geneviève St-Onge
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | | | - Chad A Koplinski
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ishan Roy
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Bryan Stephens
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 93093, USA
| | - Sylvia Thelen
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vela 6, Bellinzona CH-6500, Switzerland
| | | | - Frederick D Coffman
- Department of Pathology and Laboratory Medicine and Center for Biophysical Pathology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Marion C Cohen
- Rutgers Graduate School of Biomedical Sciences, Newark, NJ 07101, USA
| | - Michael B Dwinell
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Marcus Thelen
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vela 6, Bellinzona CH-6500, Switzerland
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Nikolaus Heveker
- Centre de Recherche, Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec H3T 1J4, Canada
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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9
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Arimont M, Sun SL, Leurs R, Smit M, de Esch IJP, de Graaf C. Structural Analysis of Chemokine Receptor-Ligand Interactions. J Med Chem 2017; 60:4735-4779. [PMID: 28165741 PMCID: PMC5483895 DOI: 10.1021/acs.jmedchem.6b01309] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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This
review focuses on the construction and application of structural chemokine
receptor models for the elucidation of molecular determinants of chemokine
receptor modulation and the structure-based discovery and design of
chemokine receptor ligands. A comparative analysis of ligand binding
pockets in chemokine receptors is presented, including a detailed
description of the CXCR4, CCR2, CCR5, CCR9, and US28 X-ray structures,
and their implication for modeling molecular interactions of chemokine
receptors with small-molecule ligands, peptide ligands, and large
antibodies and chemokines. These studies demonstrate how the integration
of new structural information on chemokine receptors with extensive
structure–activity relationship and site-directed mutagenesis
data facilitates the prediction of the structure of chemokine receptor–ligand
complexes that have not been crystallized. Finally, a review of structure-based
ligand discovery and design studies based on chemokine receptor crystal
structures and homology models illustrates the possibilities and challenges
to find novel ligands for chemokine receptors.
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Affiliation(s)
- Marta Arimont
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Shan-Liang Sun
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Rob Leurs
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Martine Smit
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Chris de Graaf
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute of Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam , De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
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10
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Corbisier J, Huszagh A, Galés C, Parmentier M, Springael JY. Partial Agonist and Biased Signaling Properties of the Synthetic Enantiomers J113863/UCB35625 at Chemokine Receptors CCR2 and CCR5. J Biol Chem 2016; 292:575-584. [PMID: 27895119 DOI: 10.1074/jbc.m116.757559] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/21/2016] [Indexed: 12/22/2022] Open
Abstract
Biased agonism at G protein-coupled receptors constitutes a promising area of research for the identification of new therapeutic molecules. In this study we identified two novel biased ligands for the chemokine receptors CCR2 and CCR5 and characterized their functional properties. We showed that J113863 and its enantiomer UCB35625, initially identified as high affinity antagonists for CCR1 and CCR3, also bind with low affinity to the closely related receptors CCR2 and CCR5. Binding of J113863 and UCB35625 to CCR2 or CCR5 resulted in the full or partial activation of the three Gi proteins and the two Go isoforms. Unlike chemokines, the compounds did not activate G12 Binding of J113863 to CCR2 or CCR5 also induced the recruitment of β-arrestin 2, whereas UCB35625 did not. UCB35625 induced the chemotaxis of L1.2 cells expressing CCR2 or CCR5. In contrast, J113863 induced the migration of L1.2-CCR2 cells but antagonized the chemokine-induced migration of L1.2-CCR5 cells. We also showed that replacing the phenylalanine 3.33 in CCR5 TM3 by the corresponding histidine of CCR2 converts J113863 from an antagonist for cell migration and a partial agonist in other assays to a full agonist in all assays. Further analyses indicated that F3.33H substitution strongly increased the activation of G proteins and β-arrestin 2 by J113863. These results highlight the biased nature of the J113863 and UCB35625 that act either as antagonist, partial agonist, or full agonist according to the receptor, the enantiomer, and the signaling pathway investigated.
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Affiliation(s)
- Jenny Corbisier
- From the Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM) Université Libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, B-1070 Brussels, Belgium and
| | - Alexandre Huszagh
- From the Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM) Université Libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, B-1070 Brussels, Belgium and
| | - Céline Galés
- Institut des Maladies Métaboliques et Cardiovasculaires, INSERM, Université Toulouse III Paul Sabatier, 31432 Toulouse, France
| | - Marc Parmentier
- From the Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM) Université Libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, B-1070 Brussels, Belgium and
| | - Jean-Yves Springael
- From the Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM) Université Libre de Bruxelles (ULB), Campus Erasme, 808 Route de Lennik, B-1070 Brussels, Belgium and
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11
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Karlshøj S, Amarandi RM, Larsen O, Daugvilaite V, Steen A, Brvar M, Pui A, Frimurer TM, Ulven T, Rosenkilde MM. Molecular Mechanism of Action for Allosteric Modulators and Agonists in CC-chemokine Receptor 5 (CCR5). J Biol Chem 2016; 291:26860-26874. [PMID: 27834679 DOI: 10.1074/jbc.m116.740183] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 11/09/2016] [Indexed: 12/22/2022] Open
Abstract
The small molecule metal ion chelators bipyridine and terpyridine complexed with Zn2+ (ZnBip and ZnTerp) act as CCR5 agonists and strong positive allosteric modulators of CCL3 binding to CCR5, weak modulators of CCL4 binding, and competitors for CCL5 binding. Here we describe their binding site using computational modeling, binding, and functional studies on WT and mutated CCR5. The metal ion Zn2+ is anchored to the chemokine receptor-conserved Glu-283VII:06/7.39 Both chelators interact with aromatic residues in the transmembrane receptor domain. The additional pyridine ring of ZnTerp binds deeply in the major binding pocket and, in contrast to ZnBip, interacts directly with the Trp-248VI:13/6.48 microswitch, contributing to its 8-fold higher potency. The impact of Trp-248 was further confirmed by ZnClTerp, a chloro-substituted version of ZnTerp that showed no inherent agonism but maintained positive allosteric modulation of CCL3 binding. Despite a similar overall binding mode of all three metal ion chelator complexes, the pyridine ring of ZnClTerp blocks the conformational switch of Trp-248 required for receptor activation, thereby explaining its lack of activity. Importantly, ZnClTerp becomes agonist to the same extent as ZnTerp upon Ala mutation of Ile-116III:16/3.40, a residue that constrains the Trp-248 microswitch in its inactive conformation. Binding studies with 125I-CCL3 revealed an allosteric interface between the chemokine and the small molecule binding site, including residues Tyr-37I:07/1.39, Trp-86II:20/2.60, and Phe-109III:09/3.33 The small molecules and CCL3 approach this interface from opposite directions, with some residues being mutually exploited. This study provides new insight into the molecular mechanism of CCR5 activation and paves the way for future allosteric drugs for chemokine receptors.
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Affiliation(s)
- Stefanie Karlshøj
- From the Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Roxana Maria Amarandi
- From the Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark.,the Faculty of Chemistry, Alexandru Ioan Cuza University of Iaşi, Bd. Carol I No. 11, RO-700506 Iaşi, Romania
| | - Olav Larsen
- From the Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Viktorija Daugvilaite
- From the Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Anne Steen
- From the Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Matjaž Brvar
- the Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Aurel Pui
- the Faculty of Chemistry, Alexandru Ioan Cuza University of Iaşi, Bd. Carol I No. 11, RO-700506 Iaşi, Romania
| | - Thomas Michael Frimurer
- the Novo Nordisk Foundation Center for Basic Metabolic Research, Section for Metabolic Receptology and Enteroendocrinology, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark, and
| | - Trond Ulven
- the Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Mette Marie Rosenkilde
- From the Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark,
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12
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Barington L, Rummel PC, Lückmann M, Pihl H, Larsen O, Daugvilaite V, Johnsen AH, Frimurer TM, Karlshøj S, Rosenkilde MM. Role of Conserved Disulfide Bridges and Aromatic Residues in Extracellular Loop 2 of Chemokine Receptor CCR8 for Chemokine and Small Molecule Binding. J Biol Chem 2016; 291:16208-20. [PMID: 27226537 DOI: 10.1074/jbc.m115.706747] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Indexed: 11/06/2022] Open
Abstract
Chemokine receptors play important roles in the immune system and are linked to several human diseases. The initial contact of chemokines with their receptors depends on highly specified extracellular receptor features. Here we investigate the importance of conserved extracellular disulfide bridges and aromatic residues in extracellular loop 2 (ECL-2) for ligand binding and activation in the chemokine receptor CCR8. We used inositol 1,4,5-trisphosphate accumulation and radioligand binding experiments to determine the impact of receptor mutagenesis on both chemokine and small molecule agonist and antagonist binding and action in CCR8. We find that the seven-transmembrane (TM) receptor conserved disulfide bridge (7TM bridge) linking transmembrane helix III (TMIII) and ECL-2 is crucial for chemokine and small molecule action, whereas the chemokine receptor conserved disulfide bridge between the N terminus and TMVII is needed only for chemokines. Furthermore, we find that two distinct aromatic residues in ECL-2, Tyr(184) (Cys + 1) and Tyr(187) (Cys + 4), are crucial for binding of the CC chemokines CCL1 (agonist) and MC148 (antagonist), respectively, but not for small molecule binding. Finally, using in silico modeling, we predict an aromatic cluster of interaction partners for Tyr(187) in TMIV (Phe(171)) and TMV (Trp(194)). We show in vitro that these residues are crucial for the binding and action of MC148, thus supporting their participation in an aromatic cluster with Tyr(187) This aromatic cluster appears to be present in a large number of CC chemokine receptors and thereby could play a more general role to be exploited in future drug development targeting these receptors.
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Affiliation(s)
| | - Pia C Rummel
- From the Department of Neuroscience and Pharmacology
| | - Michael Lückmann
- From the Department of Neuroscience and Pharmacology, the Novo Nordisk Foundation Center for Basic Metabolic Research, and
| | - Heidi Pihl
- From the Department of Neuroscience and Pharmacology
| | - Olav Larsen
- From the Department of Neuroscience and Pharmacology
| | | | - Anders H Johnsen
- the Department of Clinical Biochemistry, Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Thomas M Frimurer
- the Novo Nordisk Foundation Center for Basic Metabolic Research, and the Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark and
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13
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Kleist AB, Getschman AE, Ziarek JJ, Nevins AM, Gauthier PA, Chevigné A, Szpakowska M, Volkman BF. New paradigms in chemokine receptor signal transduction: Moving beyond the two-site model. Biochem Pharmacol 2016; 114:53-68. [PMID: 27106080 DOI: 10.1016/j.bcp.2016.04.007] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/13/2016] [Indexed: 10/21/2022]
Abstract
Chemokine receptor (CKR) signaling forms the basis of essential immune cellular functions, and dysregulated CKR signaling underpins numerous disease processes of the immune system and beyond. CKRs, which belong to the seven transmembrane domain receptor (7TMR) superfamily, initiate signaling upon binding of endogenous, secreted chemokine ligands. Chemokine-CKR interactions are traditionally described by a two-step/two-site mechanism, in which the CKR N-terminus recognizes the chemokine globular core (i.e. site 1 interaction), followed by activation when the unstructured chemokine N-terminus is inserted into the receptor TM bundle (i.e. site 2 interaction). Several recent studies challenge the structural independence of sites 1 and 2 by demonstrating physical and allosteric links between these supposedly separate sites. Others contest the functional independence of these sites, identifying nuanced roles for site 1 and other interactions in CKR activation. These developments emerge within a rapidly changing landscape in which CKR signaling is influenced by receptor PTMs, chemokine and CKR dimerization, and endogenous non-chemokine ligands. Simultaneous advances in the structural and functional characterization of 7TMR biased signaling have altered how we understand promiscuous chemokine-CKR interactions. In this review, we explore new paradigms in CKR signal transduction by considering studies that depict a more intricate architecture governing the consequences of chemokine-CKR interactions.
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Affiliation(s)
- Andrew B Kleist
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Anthony E Getschman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Joshua J Ziarek
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA.
| | - Amanda M Nevins
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Pierre-Arnaud Gauthier
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg.
| | - Andy Chevigné
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg.
| | - Martyna Szpakowska
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg.
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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14
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Salmas RE, Yurtsever M, Durdagi S. Investigation of Inhibition Mechanism of Chemokine Receptor CCR5 by Micro-second Molecular Dynamics Simulations. Sci Rep 2015; 5:13180. [PMID: 26299310 PMCID: PMC4547396 DOI: 10.1038/srep13180] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 07/15/2015] [Indexed: 12/20/2022] Open
Abstract
Chemokine receptor 5 (CCR5) belongs to G protein coupled receptors (GPCRs) and plays an important role in treatment of human immunodeficiency virus (HIV) infection since HIV uses CCR5 protein as a co-receptor. Recently, the crystal structure of CCR5-bound complex with an approved anti-retroviral drug (maroviroc) was resolved. During the crystallization procedure, amino acid residues (i.e., Cys224, Arg225, Asn226 and Glu227) at the third intra-cellular loop were replaced by the rubredoxin for stability reasons. In the current study, we aimed to understand the impact of the incorporated rubredoxin on the conformations of TM domains of the target protein. For this reason, rubredoxin was deleted from the crystal structure and the missing amino acids were engineered. The resultant structure was subjected to long (μs) molecular dynamics (MD) simulations to shed light into the inhibitory mechanism. The derived model structure displayed a significant deviation in the cytoplasmic domain of TM5 and IC3 in the absence of rubredoxin. The principal component analyses (PCA) and MD trajectory analyses revealed important structural and dynamical differences at apo and holo forms of the CCR5.
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Affiliation(s)
| | - Mine Yurtsever
- Department of Chemistry, Istanbul Technical University, Istanbul, Turkey
| | - Serdar Durdagi
- Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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15
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Roumen L, Scholten DJ, de Kruijf P, de Esch IJP, Leurs R, de Graaf C. C(X)CR in silico: Computer-aided prediction of chemokine receptor-ligand interactions. DRUG DISCOVERY TODAY. TECHNOLOGIES 2014; 9:e281-91. [PMID: 24990665 DOI: 10.1016/j.ddtec.2012.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
This review will focus on the construction, refinement, and validation of chemokine receptor models for the purpose of structure-based virtual screening and ligand design. The review will present a comparative analysis of ligand binding pockets in chemokine receptors, including a review of the recently released CXCR4 X-ray structures, and their implication on chemokine receptor (homology) modeling. The recommended protein-ligand modeling procedure as well as the use of experimental anchors to steer the modeling procedure is discussed and an overview of several successful structure-based ligand discovery and design studies is provided. This review shows that receptor models, despite structural inaccuracies, can be efficiently used to find novel ligands for chemokine receptors.:
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Affiliation(s)
- L Roumen
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry, Department of Pharmacochemistry, Faculty of Exact Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - D J Scholten
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry, Department of Pharmacochemistry, Faculty of Exact Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - P de Kruijf
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry, Department of Pharmacochemistry, Faculty of Exact Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - I J P de Esch
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry, Department of Pharmacochemistry, Faculty of Exact Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - R Leurs
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry, Department of Pharmacochemistry, Faculty of Exact Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - C de Graaf
- Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry, Department of Pharmacochemistry, Faculty of Exact Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.
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16
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Elucidating a key anti-HIV-1 and cancer-associated axis: the structure of CCL5 (Rantes) in complex with CCR5. Sci Rep 2014; 4:5447. [PMID: 24965094 PMCID: PMC4894430 DOI: 10.1038/srep05447] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 06/05/2014] [Indexed: 01/01/2023] Open
Abstract
CCL5 (RANTES) is an inflammatory chemokine which binds to chemokine receptor CCR5 and induces signaling. The CCL5:CCR5 associated chemotactic signaling is of critical biological importance and is a potential HIV-1 therapeutic axis. Several studies provided growing evidence for the expression of CCL5 and CCR5 in non-hematological malignancies. Therefore, the delineation of the CCL5:CCR5 complex structure can pave the way for novel CCR5-targeted drugs. We employed a computational protocol which is primarily based on free energy calculations and molecular dynamics simulations, and report, what is to our knowledge, the first computationally derived CCL5:CCR5 complex structure which is in excellent agreement with experimental findings and clarifies the functional role of CCL5 and CCR5 residues which are associated with binding and signaling. A wealth of polar and non-polar interactions contributes to the tight CCL5:CCR5 binding. The structure of an HIV-1 gp120 V3 loop in complex with CCR5 has recently been derived through a similar computational protocol. A comparison between the CCL5 : CCR5 and the HIV-1 gp120 V3 loop : CCR5 complex structures depicts that both the chemokine and the virus primarily interact with the same CCR5 residues. The present work provides insights into the blocking mechanism of HIV-1 by CCL5.
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17
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Gadhe CG, Kothandan G, Cho SJ. Computational modeling of human coreceptor CCR5 antagonist as a HIV-1 entry inhibitor: using an integrated homology modeling, docking, and membrane molecular dynamics simulation analysis approach. J Biomol Struct Dyn 2013; 31:1251-76. [DOI: 10.1080/07391102.2012.732342] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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18
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Ahn KH, Scott CE, Abrol R, Goddard WA, Kendall DA. Computationally-predicted CB1 cannabinoid receptor mutants show distinct patterns of salt-bridges that correlate with their level of constitutive activity reflected in G protein coupling levels, thermal stability, and ligand binding. Proteins 2013; 81:1304-17. [PMID: 23408552 DOI: 10.1002/prot.24264] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 12/21/2013] [Accepted: 01/21/2013] [Indexed: 11/09/2022]
Abstract
The cannabinoid receptor 1 (CB1), a member of the class A G-protein-coupled receptor (GPCR) family, possesses an observable level of constitutive activity. Its activation mechanism, however, has yet to be elucidated. Previously we discovered dramatic changes in CB1 activity due to single mutations; T3.46A, which made the receptor inactive, and T3.46I and L3.43A, which made it essentially fully constitutively active. Our subsequent prediction of the structures of these mutant receptors indicated that these changes in activity are explained in terms of the pattern of salt-bridges in the receptor region involving transmembrane domains 2, 3, 5, and 6. Here we identified key salt-bridges, R2.37 + D6.30 and D2.63 + K3.28, critical for CB1 inactive and active states, respectively, and generated new mutant receptors that we predicted would change CB1 activity by either precluding or promoting these interactions. We find that breaking the R2.37 + D6.30 salt-bridge resulted in substantial increase in G-protein coupling activity and reduced thermal stability relative to the wild-type reflecting the changes in constitutive activity from inactive to active. In contrast, breaking the D2.63 + K3.28 salt-bridge produced the opposite profile suggesting this interaction is critical for the receptor activation. Thus, we demonstrate an excellent correlation with the predicted pattern of key salt-bridges and experimental levels of activity and conformational flexibility. These results are also consistent with the extended ternary complex model with respect to shifts in agonist and inverse agonist affinity and provide a powerful framework for understanding the molecular basis for the multiple stages of CB1 activation and that of other GPCRs in general.
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Affiliation(s)
- Kwang H Ahn
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269-3092, USA
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19
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Abuelsaad ASA, Al-Ghamdi AS, Al-Ghamdi AN, Alakkas EA, Alsulaimani AA, Al-Harthi AA, Abdel-Moneim AS. Detection of new mutant sites of HIV-1 coreceptor CCR5 among Saudi populations. J Interferon Cytokine Res 2013; 33:783-9. [PMID: 23742258 DOI: 10.1089/jir.2013.0024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The genetic association of CCR5 with human immunodeficiency virus-1 (HIV-1) pathogenesis is well known. The HIV-1 entry into target cells is initiated by the binding of the viral envelope glycoproteins (gp120-gp41) with the cell surface receptor (CD4) and the coreceptor (CCR5), followed by fusion of the viral and cell membranes. Genetic variants of the gene-encoding HIV-1 coreceptor are implicated in the susceptibility to HIV-1 infection. The prevalence of these mutations may vary according to population ethnicity. In the current study, characterization and frequency distribution of the HIV-related gene variants in 135 samples of the Saudi populations were conducted. Polymerase chain reaction (PCR) of 276 bp amplicons was used to rapidly detect Δ32 deletion in the initial sample of DNA. The direct sequence of 2 overlapping PCR amplicons flanking 1,059 bp was used to detect single-nucleotide polymorphisms. A single hetrozygous Δ32 deletion allele and 6 single-nucleotide polymorphisms were detected. Only one of the identified haplotypes, Taif-1, which was found in the majority of the tested sample, is identical to CCR5 wild-type alleles. Furthermore, the results of this study raised a concern about the prospective role of the mutations detected among Saudi nationals in the HIV pathogenesis and the clinical use of CCR5 antagonists, which are currently being developed as therapeutics for HIV-1 and inflammatory diseases.
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20
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Use of G-protein-coupled and -uncoupled CCR5 receptors by CCR5 inhibitor-resistant and -sensitive human immunodeficiency virus type 1 variants. J Virol 2013; 87:6569-81. [PMID: 23468486 DOI: 10.1128/jvi.00099-13] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Small-molecule CCR5 inhibitors such as vicriviroc (VVC) and maraviroc (MVC) are allosteric modulators that impair HIV-1 entry by stabilizing a CCR5 conformation that the virus recognizes inefficiently. Viruses resistant to these compounds are able to bind the inhibitor-CCR5 complex while also interacting with the free coreceptor. CCR5 also interacts intracellularly with G proteins, as part of its signal transduction functions, and this process alters its conformation. Here we investigated whether the action of VVC against inhibitor-sensitive and -resistant viruses is affected by whether or not CCR5 is coupled to G proteins such as Gαi. Treating CD4(+) T cells with pertussis toxin to uncouple the Gαi subunit from CCR5 increased the potency of VVC against the sensitive viruses and revealed that VVC-resistant viruses use the inhibitor-bound form of Gαi-coupled CCR5 more efficiently than they use uncoupled CCR5. Supportive evidence was obtained by expressing a signaling-deficient CCR5 mutant with an impaired ability to bind to G proteins, as well as two constitutively active mutants that activate G proteins in the absence of external stimuli. The implication of these various studies is that the association of intracellular domains of CCR5 with the signaling machinery affects the conformation of the external and transmembrane domains and how they interact with small-molecule inhibitors of HIV-1 entry.
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21
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de Voux A, Chan MC, Folefoc AT, Madziva MT, Flanagan CA. Constitutively active CCR5 chemokine receptors differ in mediating HIV envelope-dependent fusion. PLoS One 2013; 8:e54532. [PMID: 23355876 PMCID: PMC3552960 DOI: 10.1371/journal.pone.0054532] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 12/12/2012] [Indexed: 11/18/2022] Open
Abstract
The CCR5 chemokine receptor is a rhodopsin-like G protein-coupled receptor that mediates the effects of pro-inflammatory β-chemokines. CCR5 is also the major co-receptor for entry of human immunodeficiency virus (HIV) into human cells. G protein-coupled receptors exist in ensembles of active and inactive conformations. Active receptor conformations can be stabilized by mutations. Although binding of the HIV envelope protein to CCR5 stimulates cellular signaling, the CCR5 conformation that induces fusion of the viral membrane with cellular membranes is not known. We mutated conserved amino acids to generate constitutively active CCR5 receptors, which are stabilized in active conformations, and tested the ability of constitutively active CCR5 receptors to mediate HIV envelope-directed membrane fusion. Mutation of the Asp3.49(125) and Arg6.32(225) residues of CCR5 did not cause constitutive activity, but Lys or Pro substitutions for Thr2.56(82), in the TxP motif, caused high basal inositol phosphate signaling. Signaling did not increase in response to MIP-1β, suggesting that the Thr2.56(82) mutants were fully stabilized in active conformations. The Thr2.56(82)Lys mutation severely decreased cell surface CCR5 expression. Combining the Thr2.56(82)Lys mutation with an Arg6.32(225)Gln mutation partially reversed the decrease in expression. Mutants with Thr2.56(82)Lys substitutions were poor mediators of HIV envelope-directed membrane fusion, but mutants with the Thr2.65(82)Pro substitution exhibited full co-receptor function. Our results suggest that the Thr2.65(82)Lys and Thr2.65(82)Pro mutations stabilize distinct constitutively active CCR5 conformations. Lys in position 2.65(82) stabilizes activated receptor conformations that appear to be constitutively internalized and do not induce envelope-dependent membrane fusion, whereas Pro stabilizes activated conformations that are not constitutively internalized and fully mediate envelope-directed membrane fusion.
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Affiliation(s)
- Alex de Voux
- Medical Research Council Receptor Biology Research Unit, Division of Medical Biochemistry, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mei-Chi Chan
- Medical Research Council Receptor Biology Research Unit, Division of Medical Biochemistry, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Asongna T. Folefoc
- Medical Research Council Receptor Biology Research Unit, Division of Medical Biochemistry, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Michael T. Madziva
- Medical Research Council Receptor Biology Research Unit, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
| | - Colleen A. Flanagan
- Medical Research Council Receptor Biology Research Unit, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
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22
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CCR5 mutations distinguish N-terminal modifications of RANTES (CCL5) with agonist versus antagonist activity. J Virol 2012; 86:10218-20. [PMID: 22787219 DOI: 10.1128/jvi.00353-12] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CCR5 is the major HIV-1 entry coreceptor. RANTES/CCL5 analogs are more potent inhibitors of infection than native chemokines; one class activates and internalizes CCR5, one neither activates nor internalizes, and a third partially internalizes without activation. Here we show that mutations in CCR5 transmembrane domains differentially impact the activity of these three inhibitor classes, suggesting that the transmembrane region of CCR5, a key interaction site for inhibitors, is a sensitive molecular switch, modulating receptor activity.
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Scholten DJ, Canals M, Maussang D, Roumen L, Smit MJ, Wijtmans M, de Graaf C, Vischer HF, Leurs R. Pharmacological modulation of chemokine receptor function. Br J Pharmacol 2012; 165:1617-1643. [PMID: 21699506 DOI: 10.1111/j.1476-5381.2011.01551.x] [Citation(s) in RCA: 181] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
G protein-coupled chemokine receptors and their peptidergic ligands are interesting therapeutic targets due to their involvement in various immune-related diseases, including rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease, chronic obstructive pulmonary disease, HIV-1 infection and cancer. To tackle these diseases, a lot of effort has been focused on discovery and development of small-molecule chemokine receptor antagonists. This has been rewarded by the market approval of two novel chemokine receptor inhibitors, AMD3100 (CXCR4) and Maraviroc (CCR5) for stem cell mobilization and treatment of HIV-1 infection respectively. The recent GPCR crystal structures together with mutagenesis and pharmacological studies have aided in understanding how small-molecule ligands interact with chemokine receptors. Many of these ligands display behaviour deviating from simple competition and do not interact with the chemokine binding site, providing evidence for an allosteric mode of action. This review aims to give an overview of the evidence supporting modulation of this intriguing receptor family by a range of ligands, including small molecules, peptides and antibodies. Moreover, the computer-assisted modelling of chemokine receptor-ligand interactions is discussed in view of GPCR crystal structures. Finally, the implications of concepts such as functional selectivity and chemokine receptor dimerization are considered.
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Affiliation(s)
- D J Scholten
- Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, Faculty of Science, VU University Amsterdam, Amsterdam, the Netherlands
| | - M Canals
- Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, Faculty of Science, VU University Amsterdam, Amsterdam, the Netherlands
| | - D Maussang
- Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, Faculty of Science, VU University Amsterdam, Amsterdam, the Netherlands
| | - L Roumen
- Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, Faculty of Science, VU University Amsterdam, Amsterdam, the Netherlands
| | - M J Smit
- Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, Faculty of Science, VU University Amsterdam, Amsterdam, the Netherlands
| | - M Wijtmans
- Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, Faculty of Science, VU University Amsterdam, Amsterdam, the Netherlands
| | - C de Graaf
- Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, Faculty of Science, VU University Amsterdam, Amsterdam, the Netherlands
| | - H F Vischer
- Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, Faculty of Science, VU University Amsterdam, Amsterdam, the Netherlands
| | - R Leurs
- Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, Faculty of Science, VU University Amsterdam, Amsterdam, the Netherlands
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24
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Kothandan G, Gadhe CG, Cho SJ. Structural insights from binding poses of CCR2 and CCR5 with clinically important antagonists: a combined in silico study. PLoS One 2012; 7:e32864. [PMID: 22479344 PMCID: PMC3314010 DOI: 10.1371/journal.pone.0032864] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 01/31/2012] [Indexed: 11/19/2022] Open
Abstract
Chemokine receptors are G protein-coupled receptors that contain seven transmembrane domains. In particular, CCR2 and CCR5 and their ligands have been implicated in the pathophysiology of a number of diseases, including rheumatoid arthritis and multiple sclerosis. Based on their roles in disease, they have been attractive targets for the pharmaceutical industry, and furthermore, targeting both CCR2 and CCR5 can be a useful strategy. Owing to the importance of these receptors, information regarding the binding site is of prime importance. Structural studies have been hampered due to the lack of X-ray crystal structures, and templates with close homologs for comparative modeling. Most of the previous models were based on the bovine rhodopsin and β2-adrenergic receptor. In this study, based on a closer homolog with higher resolution (CXCR4, PDB code: 3ODU 2.5 Å), we constructed three-dimensional models. The main aim of this study was to provide relevant information on binding sites of these receptors. Molecular dynamics simulation was done to refine the homology models and PROCHECK results indicated that the models were reasonable. Here, binding poses were checked with some established inhibitors of high pharmaceutical importance against the modeled receptors. Analysis of interaction modes gave an integrated interpretation with detailed structural information. The binding poses confirmed that the acidic residues Glu291 (CCR2) and Glu283 (CCR5) are important, and we also found some additional residues. Comparisons of binding sites of CCR2/CCR5 were done sequentially and also by docking a potent dual antagonist. Our results can be a starting point for further structure-based drug design.
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Affiliation(s)
- Gugan Kothandan
- Department of Bio-New Drug Development, College of Medicine, Chosun University, Gwangju, Korea
| | - Changdev G. Gadhe
- Department of Bio-New Drug Development, College of Medicine, Chosun University, Gwangju, Korea
| | - Seung Joo Cho
- Department of Bio-New Drug Development, College of Medicine, Chosun University, Gwangju, Korea
- Department of Cellular Molecular Medicine, Research Center for Resistant Cells, College of Medicine, Chosun University, Gwangju, Korea
- * E-mail:
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25
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Metz M, Bourque E, Labrecque J, Danthi SJ, Langille J, Harwig C, Yang W, Darkes MC, Lau G, Santucci Z, Bridger GJ, Schols D, Fricker SP, Skerlj RT. Prospective CCR5 small molecule antagonist compound design using a combined mutagenesis/modeling approach. J Am Chem Soc 2011; 133:16477-85. [PMID: 21942640 DOI: 10.1021/ja2043722] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The viral resistance of marketed antiviral drugs including the emergence of new viral resistance of the only marketed CCR5 entry inhibitor, maraviroc, makes it necessary to develop new CCR5 allosteric inhibitors. A mutagenesis/modeling approach was used (a) to remove the potential hERG liability in an otherwise very promising series of compounds and (b) to design a new class of compounds with an unique mutant fingerprint profile depending on residues in the N-terminus and the extracellular loop 2. On the basis of residues, which were identified by mutagenesis as key interaction sites, binding modes of compounds were derived and utilized for compound design in a prospective manner. The compounds were then synthesized, and in vitro evaluation not only showed that they had good antiviral potency but also fulfilled the requirement of low hERG inhibition, a criterion necessary because a potential approved drug would be administered chronically. This work utilized an interdisciplinary approach including medicinal chemistry, molecular biology, and computational chemistry merging the structural requirements for potency with the requirements of an acceptable in vitro profile for allosteric CCR5 inhibitors. The obtained mutant fingerprint profiles of CCR5 inhibitors were used to translate the CCR5 allosteric binding site into a general pharmacophore, which can be used for discovering new inhibitors.
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Affiliation(s)
- Markus Metz
- Department of Medicinal Chemistry, Genzyme Corporation, 153 Second Avenue, Waltham, Massachusetts 02451, USA
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26
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De Wachter R, de Graaf C, Keresztes A, Vandormael B, Ballet S, Tóth G, Rognan D, Tourwé D. Synthesis, Biological Evaluation, and Automated Docking of Constrained Analogues of the Opioid Peptide H-Dmt-d-Ala-Phe-Gly-NH2 Using the 4- or 5-Methyl Substituted 4-Amino-1,2,4,5-tetrahydro-2-benzazepin-3-one Scaffold. J Med Chem 2011; 54:6538-47. [DOI: 10.1021/jm2003574] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rien De Wachter
- Department of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Chris de Graaf
- Structural Chemogenomics, UMR 7200 CNRS-UdS, Université de Strasbourg, Illkirch F-67401, France
- Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, Faculty of Science, VU University Amsterdam, Amsterdam, The Netherlands
| | - Atilla Keresztes
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Bart Vandormael
- Department of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Steven Ballet
- Department of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Géza Tóth
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Didier Rognan
- Structural Chemogenomics, UMR 7200 CNRS-UdS, Université de Strasbourg, Illkirch F-67401, France
| | - Dirk Tourwé
- Department of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
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27
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Garcia-Perez J, Rueda P, Alcami J, Rognan D, Arenzana-Seisdedos F, Lagane B, Kellenberger E. Allosteric model of maraviroc binding to CC chemokine receptor 5 (CCR5). J Biol Chem 2011; 286:33409-21. [PMID: 21775441 DOI: 10.1074/jbc.m111.279596] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Maraviroc is a nonpeptidic small molecule human immunodeficiency virus type 1 (HIV-1) entry inhibitor that has just entered the therapeutic arsenal for the treatment of patients. We recently demonstrated that maraviroc binding to the HIV-1 coreceptor, CC chemokine receptor 5 (CCR5), prevents it from binding the chemokine CCL3 and the viral envelope glycoprotein gp120 by an allosteric mechanism. However, incomplete knowledge of ligand-binding sites and the lack of CCR5 crystal structures have hampered an in-depth molecular understanding of how the inhibitor works. Here, we addressed these issues by combining site-directed mutagenesis (SDM) with homology modeling and docking. Six crystal structures of G-protein-coupled receptors were compared for their suitability for CCR5 modeling. All CCR5 models had equally good geometry, but that built from the recently reported dimeric structure of the other HIV-1 coreceptor CXCR4 bound to the peptide CVX15 (Protein Data Bank code 3OE0) best agreed with the SDM data and discriminated CCR5 from non-CCR5 binders in a virtual screening approach. SDM and automated docking predicted that maraviroc inserts deeply in CCR5 transmembrane cavity where it can occupy three different binding sites, whereas CCL3 and gp120 lie on distinct yet overlapped regions of the CCR5 extracellular loop 2. Data suggesting that the transmembrane cavity remains accessible for maraviroc in CCL3-bound and gp120-bound CCR5 help explain our previous observation that the inhibitor enhances dissociation of preformed ligand-CCR5 complexes. Finally, we identified residues in the predicted CCR5 dimer interface that are mandatory for gp120 binding, suggesting that receptor dimerization might represent a target for new CCR5 entry inhibitors.
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28
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29
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Deflorian F, Jacobson KA. Comparison of three GPCR structural templates for modeling of the P2Y12 nucleotide receptor. J Comput Aided Mol Des 2011; 25:329-38. [PMID: 21461952 PMCID: PMC3157290 DOI: 10.1007/s10822-011-9423-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 03/20/2011] [Indexed: 11/26/2022]
Abstract
The P2Y(12) receptor (P2Y(12)R) is an ADP-activated G protein-coupled receptor (GPCR) that is an important target for antithrombotic drugs. Three homology models of P2Y(12)R were compared, based on different GPCR structural templates: bovine rhodopsin (bRHO), human A(2A) adenosine receptor (A(2A)AR), and human C-X-C chemokine receptor type 4 (CXCR4). By criteria of sequence analysis (25.6% identity in transmembrane region), deviation from helicity in the second transmembrane helix (TM2), docked poses of ligands highlighting the role of key residues, accessibility of a conserved disulfide bridge that is reactive toward irreversibly-binding antagonists, and the presence of a shared disulfide bridge between the third extracellular loop (EL3) and the N-terminus, the CXCR4-based model appeared to be the most consistent with known characteristics of P2Y(12)R. The docked poses of agonist 2MeSADP and charged anthraquinone antagonist PSB-0739 in the binding pocket of P2Y(12)R-CXC agree with previously published site-directed mutagenesis studies of Arg256 and Lys280. A sulfonate at position 2 of the anthraquinone core created a strong interaction with the Lys174(EL2) side chain. The docking poses of the irreversibly-binding, active metabolite (existing as two diastereoisomers in vivo) of the clinically utilized antagonist Clopidogrel were compared. The free thiol group of the 4S diastereoisomer, but not the 4R isomer, was found in close proximity (~4.7 Å) to the sulfur atom of a disulfide bridge involving Cys175, suggesting greater activity in covalent binding. Therefore, ligand docking to the CXCR4-based model of the P2Y(12)R predicted poses of both reversibly and irreversibly-binding small molecules, consistent with observed pharmacology and mutagenesis studies.
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MESH Headings
- Amino Acid Sequence
- Animals
- Binding Sites
- Cattle
- Humans
- Ligands
- Models, Molecular
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Nucleotides/chemistry
- Protein Structure, Secondary
- Receptor, Adenosine A2A/chemistry
- Receptors, CXCR4/chemistry
- Receptors, Purinergic P2Y12/chemistry
- Receptors, Purinergic P2Y12/genetics
- Receptors, Purinergic P2Y12/metabolism
- Rhodopsin/chemistry
- Sequence Homology, Nucleic Acid
- Structural Homology, Protein
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Affiliation(s)
- Francesca Deflorian
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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30
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Abstract
The directed migration of cells in response to chemical cues is known as chemoattraction, and plays a key role in the temporal and spatial positioning of cells in lower- and higher-order life forms. Key molecules in this process are the chemotactic cytokines, or chemokines, which, in humans, constitute a family of approx. 40 molecules. Chemokines exert their effects by binding to specific GPCRs (G-protein-coupled receptors) which are present on a wide variety of mature cells and their progenitors, notably leucocytes. The inappropriate or excessive generation of chemokines is a key component of the inflammatory response observed in several clinically important diseases, notably allergic diseases such as asthma. Consequently, much time and effort has been directed towards understanding which chemokine receptors and ligands are important in the allergic response with a view to therapeutic intervention. Such strategies can take several forms, although, as the superfamily of GPCRs has historically proved amenable to blockade by small molecules, the development of specific antagonists has been has been a major focus of several groups. In the present review, I detail the roles of chemokines and their receptors in allergic disease and also highlight current progress in the development of relevant chemokine receptor antagonists.
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31
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Labrecque J, Metz M, Lau G, Darkes MC, Wong RSY, Bogucki D, Carpenter B, Chen G, Li T, Nan S, Schols D, Bridger GJ, Fricker SP, Skerlj RT. HIV-1 entry inhibition by small-molecule CCR5 antagonists: a combined molecular modeling and mutant study using a high-throughput assay. Virology 2011; 413:231-43. [PMID: 21388649 DOI: 10.1016/j.virol.2011.02.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 02/13/2011] [Accepted: 02/18/2011] [Indexed: 02/01/2023]
Abstract
Based on the attrition rate of CCR5 small molecule antagonists in the clinic the discovery and development of next generation antagonists with an improved pharmacology and safety profile is necessary. Herein, we describe a combined molecular modeling, CCR5-mediated cell fusion, and receptor site-directed mutagenesis approach to study the molecular interactions of six structurally diverse compounds (aplaviroc, maraviroc, vicriviroc, TAK-779, SCH-C and a benzyloxycarbonyl-aminopiperidin-1-yl-butane derivative) with CCR5, a coreceptor for CCR5-tropic HIV-1 strains. This is the first study using an antifusogenic assay, a model of the interaction of the gp120 envelope protein with CCR5. This assay avoids the use of radioactivity and HIV infection assays, and can be used in a high throughput mode. The assay was validated by comparison with other established CCR5 assays. Given the hydrophobic nature of the binding pocket several binding models are suggested which could prove useful in the rational drug design of new lead compounds.
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Affiliation(s)
- Jean Labrecque
- Department of Biology, AnorMED Inc. now Genzyme Corporation, 500 Kendall Street, Cambridge, MA 02142, USA
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32
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Shahlaei M, Madadkar-Sobhani A, Mahnam K, Fassihi A, Saghaie L, Mansourian M. Homology modeling of human CCR5 and analysis of its binding properties through molecular docking and molecular dynamics simulation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2010; 1808:802-17. [PMID: 21167131 DOI: 10.1016/j.bbamem.2010.12.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Revised: 11/23/2010] [Accepted: 12/06/2010] [Indexed: 11/18/2022]
Abstract
In this study, homology modeling, molecular docking and molecular dynamics simulation were performed to explore structural features and binding mechanism of some inhibitors of chemokine receptor type 5 (CCR5), and to construct a model for designing new CCR5 inhibitors for preventing HIV attachment to the host cell. A homology modeling procedure was employed to construct a 3D model of CCR5. For this procedure, the X-ray crystal structure of bovine rhodopsin (1F88A) at 2.80Å resolution was used as template. After inserting the constructed model into a hydrated lipid bilayer, a 20ns molecular dynamics (MD) simulation was performed on the whole system. After reaching the equilibrium, twenty-four CCR5 inhibitors were docked in the active site of the obtained model. The binding models of the investigated antagonists indicate the mechanism of binding of the studied compounds to the CCR5 obviously. Moreover, 3D pictures of inhibitor-protein complex provided precious data regarding the binding orientation of each antagonist into the active site of this protein. One additional 20 ns MD simulation was performed on the initial structure of the CCR5-ligand 21 complex, resulted from the previous docking calculations, embedded in a hydrated POPE bilayer to explore the effects of the presence of lipid bilayer in the vicinity of CCR5-ligand complex. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes.
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Affiliation(s)
- Mohsen Shahlaei
- Department of Medicinal Chemistry, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
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33
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Garcia-Perez J, Rueda P, Staropoli I, Kellenberger E, Alcami J, Arenzana-Seisdedos F, Lagane B. New insights into the mechanisms whereby low molecular weight CCR5 ligands inhibit HIV-1 infection. J Biol Chem 2010; 286:4978-90. [PMID: 21118814 DOI: 10.1074/jbc.m110.168955] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
CC chemokine receptor 5 (CCR5) is a G-protein-coupled receptor for the chemokines CCL3, -4, and -5 and a coreceptor for entry of R5-tropic strains of human immunodeficiency virus type 1 (HIV-1) into CD4(+) T-cells. We investigated the mechanisms whereby nonpeptidic, low molecular weight CCR5 ligands block HIV-1 entry and infection. Displacement binding assays and dissociation kinetics demonstrated that two of these molecules, i.e. TAK779 and maraviroc (MVC), inhibit CCL3 and the HIV-1 envelope glycoprotein gp120 binding to CCR5 by a noncompetitive and allosteric mechanism, supporting the view that they bind to regions of CCR5 distinct from the gp120- and CCL3-binding sites. We observed that TAK779 and MVC are full and weak inverse agonists for CCR5, respectively, indicating that they stabilize distinct CCR5 conformations with impaired abilities to activate G-proteins. Dissociation of [(125)I]CCL3 from CCR5 was accelerated by TAK779, to a lesser extent by MVC, and by GTP analogs, suggesting that inverse agonism contributes to allosteric inhibition of the chemokine binding to CCR5. TAK779 and MVC also promote dissociation of [(35)S]gp120 from CCR5 with an efficiency that correlates with their ability to act as inverse agonists. Displacement experiments revealed that affinities of MVC and TAK779 for the [(35)S]gp120-binding receptors are in the same range (IC(50) ∼6.4 versus 22 nm), although we found that MVC is 100-fold more potent than TAK779 for inhibiting HIV infection. This suggests that allosteric CCR5 inhibitors not only act by blocking gp120 binding but also alter distinct steps of CCR5 usage in the course of HIV infection.
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Affiliation(s)
- Javier Garcia-Perez
- INSERM U819/Unité de Pathogénie Virale, Institut Pasteur, 75724 Paris Cedex 15, France
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34
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Iturrioz X, Gerbier R, Leroux V, Alvear-Perez R, Maigret B, Llorens-Cortes C. By interacting with the C-terminal Phe of apelin, Phe255 and Trp259 in helix VI of the apelin receptor are critical for internalization. J Biol Chem 2010; 285:32627-37. [PMID: 20675385 DOI: 10.1074/jbc.m110.127167] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Apelin is the endogenous ligand of the orphan seven-transmembrane domain (TM) G protein-coupled receptor APJ. Apelin is involved in the regulation of body fluid homeostasis and cardiovascular functions. We previously showed the importance of the C-terminal Phe of apelin 17 (K17F) in the hypotensive activity of this peptide. Here, we show either by deleting the Phe residue (K16P) or by substituting it by an Ala (K17A), that it plays a crucial role in apelin receptor internalization but not in apelin binding or in Gα(i)-protein coupling. Then we built a homology three-dimensional model of the human apelin receptor using the cholecystokinin receptor-1 model as a template, and we subsequently docked K17F into the binding site. We visualized a hydrophobic cavity at the bottom of the binding pocket in which the C-terminal Phe of K17F was embedded by Trp(152) in TMIV and Trp(259) and Phe(255) in TMVI. Using molecular modeling and site-directed mutagenesis studies, we further showed that Phe(255) and Trp(259) are key residues in triggering receptor internalization without playing a role in apelin binding or in Gα(i)-protein coupling. These findings bring new insights into apelin receptor activation and show that Phe(255) and Trp(259), by interacting with the C-terminal Phe of the pyroglutamyl form of apelin 13 (pE13F) or K17F, are crucial for apelin receptor internalization.
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Affiliation(s)
- Xavier Iturrioz
- INSERM, U691, Collège de France, Université Pierre et Marie-Curie Paris 6, Paris FR-75005, France
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35
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Abstract
PURPOSE OF REVIEW Class A G protein-coupled receptors (GPCRs), including the chemokine receptors, CCR5 and CXCR4, share a seven transmembrane-spanning alpha-helix architecture that accommodates signal propagation from across biological membranes. CXCR4 and CCR5 are utilized as co-receptors during HIV viral entry and, therefore, crystal structures of GPCRs aid in the understanding of their function in viral entry. RECENT FINDINGS Recent progress in structure determination of class A GPCRs, which include vertebrate and invertebrate rhodopsin as well as adrenergic and adenosine receptors, provides molecular templates for how this diverse group of transmembrane receptors functions. Each of these GPCRs differs in how specific ligands bind to the transmembrane core, underscoring that additional structures of GPCRs from other subfamilies are needed to facilitate rational drug design. More recent studies also indicate a need to consider the more complex character of GPCRs, such as their oligomerization and dynamics. SUMMARY Recently, the atomic structures of invertebrate rhodopsin, beta1-adrenergic and beta2-adrenergic receptors and the A(2A)-adenosine receptor have been solved via X-ray crystallography. The impact that these structures have on the biochemistry of viral entry and signal transduction is discussed. Because the chemokine receptors have proven refractory to structural studies thus far, further structural study of the chemokine receptors will be essential to understanding ligand binding, activation and function as co-receptors during viral entry.
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Affiliation(s)
- David T Lodowski
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106-4965, USA.
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36
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An indel in transmembrane helix 2 helps to trace the molecular evolution of class A G-protein-coupled receptors. J Mol Evol 2009; 68:475-89. [PMID: 19357801 DOI: 10.1007/s00239-009-9214-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Revised: 02/05/2009] [Accepted: 02/16/2009] [Indexed: 10/25/2022]
Abstract
Class A G-protein-coupled receptors (GPCRs) constitute a large family of transmembrane receptors. Helical distortions play a major role in the overall fold of these receptors. Most are related to conserved proline residues. However, in transmembrane helix 2, the proline pattern is not conserved, and when present, proline may be located at position 2.58, 2.59, or 2.60. Sequence analysis, three-dimensional data mining, and molecular modeling were undertaken to investigate the origin of this unusual pattern. Taken together, the data strongly support the assumption that an indel led to two structural motifs for helix 2: a bulged structure in P2.59 and P2.60 receptors and a "typical" proline kink in P2.58 receptors. The proline pattern of helix 2 can be used as an evolutionary marker and helps to trace the molecular evolution of class A GPCRs. Two indel events yielding functional receptors occurred independently. One indel arose very early in GPCR evolution, in a bilaterian ancestor, before the protostome-deuterostome divergence. This indel led to the split between the P2.58 somatostatin/opioid receptors and other peptide receptors with the P2.59 pattern. A second indel also occurred in insect opsins and corresponds to a deletion. Subfamilies with proline at position 2.59 or no proline expanded earlier, whereas P2.60 receptors remained marginal throughout evolution. P2.58 receptors underwent rapid expansion in vertebrates with the development of the chemokine and purinergic receptor subfamilies from somatostatin/opioid-related ancestors.
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Hall SE, Mao A, Nicolaidou V, Finelli M, Wise EL, Nedjai B, Kanjanapangka J, Harirchian P, Chen D, Selchau V, Ribeiro S, Schyler S, Pease JE, Horuk R, Vaidehi N. Elucidation of binding sites of dual antagonists in the human chemokine receptors CCR2 and CCR5. Mol Pharmacol 2009; 75:1325-36. [PMID: 19297521 DOI: 10.1124/mol.108.053470] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Design of dual antagonists for the chemokine receptors CCR2 and CCR5 will be greatly facilitated by knowledge of the structural differences of their binding sites. Thus, we computationally predicted the binding site of the dual CCR2/CCR5 antagonist N-dimethyl-N-[4-[[[2-(4-methylphenyl)-6,7-dihydro-5H-benzohepten-8-yl] carbonyl]amino]benzyl]tetrahydro-2H-pyran-4-aminium (TAK-779), and a CCR2-specific antagonist N-(carbamoylmethyl)-3-trifluoromethyl benzamido-parachlorobenzyl 3-aminopyrrolidine (Teijin compound 1) in an ensemble of predicted structures of human CCR2 and CCR5. Based on our predictions of the protein-ligand interactions, we examined the activity of the antagonists for cells expressing thirteen mutants of CCR2 and five mutants of CCR5. The results show that residues Trp98(2.60) and Thr292(7.40) contribute significantly to the efficacy of both TAK-779 and Teijin compound 1, whereas His121(3.33) and Ile263(6.55) contribute significantly only to the antagonistic effect of Teijin compound 1 at CCR2. Mutation of residues Trp86(2.60) and Tyr108(3.32) adversely affected the efficacy of TAK-779 in antagonizing CCR5-mediated chemotaxis. Y49A(1.39) and E291A(7.39) mutants of CCR2 showed a complete loss of CCL2 binding and chemotaxis, despite robust cell surface expression, suggesting that these residues are critical in maintaining the correct receptor architecture. Modeling studies support the hypothesis that the residues Tyr49(1.39), Trp98(2.60), Tyr120(3.32), and Glu291(7.39) of CCR2 form a tight network of aromatic cluster and polar contacts between transmembrane helices 1, 2, 3, and 7.
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Affiliation(s)
- Spencer E Hall
- Department of Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
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Graham GJ. D6 and the atypical chemokine receptor family: novel regulators of immune and inflammatory processes. Eur J Immunol 2009; 39:342-51. [PMID: 19130487 DOI: 10.1002/eji.200838858] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Chemokines are key regulators of leukocyte migration and play important roles in a number of physiological and pathological immune and inflammatory contexts. In addition to the classical signalling chemokine receptors there has emerged, recently, a new subclass of atypical chemokine receptors. This subfamily is characterised by an apparent lack of signalling and, in some cases, by an ability to internalise and degrade chemokine ligands. This review describes the family of atypical chemokine receptors with particular emphasis on the D6 receptor. The in vitro and in vivo biology of D6 is described, which indicates that D6 is active as a scavenger of inflammatory CC-chemokines and appears to play essential roles in the regulation of inflammatory responses.
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Affiliation(s)
- Gerard J Graham
- Division of Immunology, Infection and Inflammation, Glasgow Biomedical Research Centre, University of Glasgow, Glasgow, UK.
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39
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Lebon G, Langmead CJ, Tehan BG, Hulme EC. Mutagenic mapping suggests a novel binding mode for selective agonists of M1 muscarinic acetylcholine receptors. Mol Pharmacol 2008; 75:331-41. [PMID: 19001633 DOI: 10.1124/mol.108.050963] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Point mutations and molecular modeling have been used to study the activation of the M(1) muscarinic acetylcholine receptor (mAChR) by the functionally selective agonists 4-n-butyl-1-[4-(2-methylphenyl)-4-oxo-1-butyl]-piperidine (AC-42), and 1-[3-(4-butyl-1-piperidinyl)propyl]-3,4-dihydro-2(1H)-quinolinone (77-LH-28-1), comparing them with N-desmethylclozapine (NDMC) and acetylcholine (ACh). Unlike NDMC and ACh, the activities of AC-42 and 77-LH-28-1 were undiminished by mutations of Tyr404 and Cys407 (transmembrane helix 7), although they were reduced by mutations of Tyr408. Signaling by AC-42, 77-LH-28-1, and NDMC was reduced by L102A and abolished by D105E, suggesting that all three may interact with transmembrane helix 3 at or near the binding site Asp105 to activate the M(1) mAChR. In striking contrast to NDMC and ACh, the affinities of AC-42 and 77-LH-28-1 were increased 100-fold by W101A, and their signaling activities were abolished by Y82A. Tyr82 and Leu102 contact the indole ring of Trp101 in a structural model of the M(1) mAChR. We suggest the hypothesis that the side chain of Trp101 undergoes conformational isomerization, opening a novel binding site for the aromatic side chain of the AC-42 analogs. This may allow the positively charged piperidine nitrogen of the ligands to access the neighboring Asp105 carboxylate to activate signaling following a vector within the binding site that is distinct from that of acetylcholine. NDMC does not seem to use this mechanism. Subtype-specific differences in the free energy of rotation of the side chain and indole ring of Trp101 might underlie the M(1) selectivity of the AC-42 analogs. Tryptophan conformational isomerization may open up new avenues in selective muscarinic receptor drug design.
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Affiliation(s)
- Guillaume Lebon
- Division of Physical Biochemistry, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
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40
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Wong RSY, Bodart V, Metz M, Labrecque J, Bridger G, Fricker SP. Comparison of the potential multiple binding modes of bicyclam, monocylam, and noncyclam small-molecule CXC chemokine receptor 4 inhibitors. Mol Pharmacol 2008; 74:1485-95. [PMID: 18768385 DOI: 10.1124/mol.108.049775] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
CXC chemokine receptor (CXCR)4 is an HIV coreceptor and a chemokine receptor that plays an important role in several physiological and pathological processes, including hematopoiesis, leukocyte homing and trafficking, metastasis, and angiogenesis. This receptor belongs to the class A family of G protein-coupled receptors and is a validated target for the development of a new class of antiretroviral therapeutics. This study compares the interactions of three structurally diverse small-molecule CXCR4 inhibitors with the receptor and is the first report of the molecular interactions of the nonmacrocyclic CXCR4 inhibitor (S)-N'-(1H-benzimidazol-2-ylmethyl)-N'-(5,6,7,8-tetrahydroquinolin-8-yl)butene-1,4-diamine (AMD11070). Fourteen CXCR4 single-site mutants representing amino acid residues that span the entire putative ligand binding pocket were used in this study. These mutants were used in binding studies to examine how each single-site mutation affected the ability of the inhibitors to compete with (125)I-stromal-derived factor-1alpha binding. Our data suggest that these CXCR4 inhibitors bind to overlapping but not identical amino acid residues in the transmembrane regions of the receptor. In addition, our results identified amino acid residues that are involved in unique interactions with two of the CXCR4 inhibitors studied. These data suggest an extended binding pocket in the transmembrane regions close to the second extracellular loop of the receptor. Based on site-directed mutagenesis and molecular modeling, several potential binding modes were proposed for each inhibitor. These mechanistic studies might prove to be useful for the development of future generations of CXCR4 inhibitors with improved clinical pharmacology and safety profiles.
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41
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Petit S, Chayen N, Pease J. Site-directed mutagenesis of the chemokine receptor CXCR6 suggests a novel paradigm for interactions with the ligand CXCL16. Eur J Immunol 2008; 38:2337-50. [DOI: 10.1002/eji.200838269] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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42
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Benned-Jensen T, Rosenkilde MM. Structural motifs of importance for the constitutive activity of the orphan 7TM receptor EBI2: analysis of receptor activation in the absence of an agonist. Mol Pharmacol 2008; 74:1008-21. [PMID: 18628402 DOI: 10.1124/mol.108.049676] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The Epstein-Barr induced receptor 2 (EBI2) is a lymphocyte-expressed orphan seven transmembrane-spanning (7TM) receptor that signals constitutively through Galphai, as shown, for instance by guanosine 5'-O-(3-thio)triphosphate incorporation. Two regions of importance for the constitutive activity were identified by a systematic mutational analysis of 29 residues in EBI2. The cAMP response element-binding protein transcription factor was used as a measure of receptor activity and was correlated to the receptor surface expression. PheVI:13 (Phe257), and the neighboring CysVI:12 (Cys256), in the conserved CW/FxP motif in TM 6, acted as negative regulators as Ala substitutions at these positions increased the constitutive activity 5.7- and 2.3-fold, respectively, compared with EBI2 wild type (wt). In contrast, ArgII:20 (Arg87) in TM-2 acted as a positive regulator, as substitution to Ala, but not to Lys, decreased the constitutive activity more than 7-fold compared with wt EBI2. IleIII:03 (Ile106) is located only 4 A from ArgII:20, and a favorable electrostatic interaction with ArgII:20 was created by introduction of Glu in III:03, given that the activity increased to 4.4-fold of that wt EBI2. It is noteworthy that swapping these charges by introduction of Glu in II:20 and Arg in III:03 resulted in a 2.7-fold increase compared with wt EBI2, thereby rescuing the two signaling-deficient single mutations, which exhibited a 3.8- to 4.5-fold decrease in constitutive activity. The uncovering of these molecular mechanisms for EBI2 activation is important from a drug development point of view, in that it may facilitate the rational design and development of small-molecule inverse agonists against EBI2 of putative importance as antiviral- or immune modulatory therapy.
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Affiliation(s)
- Tau Benned-Jensen
- Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, The Panum Institute, Copenhagen University, Blegdamsvej 2, 2200 Copenhagen, Denmark
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43
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Wang T, Duan Y. Binding modes of CCR5-targetting HIV entry inhibitors: partial and full antagonists. J Mol Graph Model 2007; 26:1287-95. [PMID: 18249144 DOI: 10.1016/j.jmgm.2007.12.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2007] [Revised: 12/06/2007] [Accepted: 12/10/2007] [Indexed: 11/25/2022]
Abstract
Since the CC-chemokine receptor 5 (CCR5) was identified as a major co-receptor for human immunodeficiency virus type 1 (HIV-1) entry into a host cell, CCR5-targetting HIV entry inhibitors have been developed and some of them are currently in clinical trials. Most of these inhibitors also inhibit the physiological chemokine reaction function of CCR5, which is so far considered to be safe to patients based on the observation that individuals that naturally lack CCR5 do not show apparent health problems. Nevertheless, to minimize the toxicity and side effects, it would be ideal to preserve the chemokine receptor activity. In this work, we simulated the flexible docking of two small molecule inhibitors to CCR5 in a solvated phospholipid bilayer environment. One of the inhibitors, aplaviroc has a unique feature of preserving two of the natural chemokine ligands binding to CCR5 and subsequent activation whereas the other one, SCH-C fully blocks chemokine-CCR5 interactions. Our results revealed significantly different binding modes of these two inhibitors although both established extensive interaction networks with CCR5. Comparison of the different binding modes suggests that avoiding the deep insertion of inhibitors into the transmembrane helix bundle may be able to preserve chemokine-CCR5 interactions. These results could help design HIV co-receptor activity-specific inhibitors.
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Affiliation(s)
- Ting Wang
- Genome Center and Bioinformatics Program and Department of Applied Science, 431 East Health Science Drive, University of California, Davis, CA 95616-8816, USA.
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44
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Sharp EL, Farrell HE, Borchers K, Holmes EC, Davis-Poynter NJ. Sequence analysis of the equid herpesvirus 2 chemokine receptor homologues E1, ORF74 and E6 demonstrates high sequence divergence between field isolates. J Gen Virol 2007; 88:2450-2462. [PMID: 17698654 DOI: 10.1099/vir.0.82942-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Equid herpesvirus 2 (EHV-2), in common with other members of the subfamily Gammaherpesvirinae, encodes homologues of cellular seven-transmembrane receptors (7TMR), namely open reading frames (ORFs) E1, 74 and E6, which each show some similarity to cellular chemokine receptors. Whereas ORF74 and E6 are members of gammaherpesvirus-conserved 7TMR gene families, E1 is currently unique to EHV-2. To investigate their genetic variability, EHV-2 7TMRs from a panel of equine gammaherpesvirus isolates were sequenced. A region of gB was sequenced to provide comparative sequence data. Phylogenetic analysis revealed six 'genogroups' for E1 and four for ORF74, which exhibited approximately 10-38 and 11-27 % amino acid difference between groups, respectively. In contrast, E6 was highly conserved, with two genogroups identified. The greatest variation was observed within the N-terminal domains and other extracellular regions. Nevertheless, analysis of the number of non-synonymous (d(N)) and synonymous (d(S)) substitutions per site generally supported the hypothesis that the 7TMRs are under negative selective pressure to retain functionally important residues, although some site-specific positive selection (d(N)>d(S)) was also observed. Collectively, these data are consistent with transmembrane and cytoplasmic domains being less tolerant of mutations with adverse effects upon function. Finally, there was no evidence for genetic linkage between the different gB, E1, ORF74 and E6 genotypes, suggesting frequent intergenic recombination between different EHV-2 strains.
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Affiliation(s)
- Emma L Sharp
- Department of Infectious Diseases, Animal Health Trust, Kentford, Newmarket CB8 7UU, UK
| | - Helen E Farrell
- Sir Albert Sakzewski Virus Research Centre, University of Queensland, Herston, QLD 4029, Australia
- Department of Infectious Diseases, Animal Health Trust, Kentford, Newmarket CB8 7UU, UK
| | - Kerstin Borchers
- Institute for Virology, FU Berlin, Königin-Luise-Str. 49, 14195 Berlin, Germany
| | - Edward C Holmes
- Department of Biology, The Pennsylvania State University, PA 16802, USA
| | - Nicholas J Davis-Poynter
- Sir Albert Sakzewski Virus Research Centre, University of Queensland, Herston, QLD 4029, Australia
- Department of Infectious Diseases, Animal Health Trust, Kentford, Newmarket CB8 7UU, UK
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45
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Wise E, Pease JE. Unravelling the mechanisms underpinning chemokine receptor activation and blockade by small molecules: a fine line between agonism and antagonism? Biochem Soc Trans 2007; 35:755-9. [PMID: 17635141 DOI: 10.1042/bst0350755] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Chemokines are a family of small basic proteins which induce the directed migration of cells, notably leucocytes, by binding to specific GPCRs (G-protein-coupled receptors). Both chemokines and their receptors have been implicated in a host of clinically important diseases, leading to the notion that antagonism of the chemokine–chemokine receptor network may be therapeutically advantageous. Consequently, considerable effort has been put into the development of small-molecule antagonists of chemokine receptors and several such compounds have been described in the literature. One curious by-product of this activity has been the description of several small-molecule agonists of the receptors, which are typically discovered following the optimization of lead antagonists. In this review we discuss these findings and conclude that these small-molecule agonists might be exploited to further our understanding of the molecular mechanisms by which chemokine receptors are activated.
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Affiliation(s)
- E Wise
- Leukocyte Biology Section, NHLI Division, Faculty of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
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46
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Wise EL, Duchesnes C, da Fonseca PCA, Allen RA, Williams TJ, Pease JE. Small molecule receptor agonists and antagonists of CCR3 provide insight into mechanisms of chemokine receptor activation. J Biol Chem 2007; 282:27935-43. [PMID: 17635911 PMCID: PMC2151197 DOI: 10.1074/jbc.m703255200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chemokine receptor CCR3 is highly expressed by eosinophils and signals in response to binding of the eotaxin family of chemokines, which are up-regulated in allergic disorders. Consequently, CCR3 blockade is of interest as a possible therapeutic approach for the treatment of allergic disease. We have described previously a bispecific antagonist of CCR1 and CCR3 named UCB35625 that was proposed to interact with the transmembrane residues Tyr-41, Tyr-113, and Glu-287 of CCR1, all of which are conserved in CCR3. Here, we show that cells expressing the CCR3 constructs Y113A and E287Q are insensitive to antagonism by UCB35625 and also exhibit impaired chemotaxis in response to CCL11/eotaxin, suggesting that these residues are important for antagonist binding and also receptor activation. Furthermore, mutation of the residue Tyr-113 to alanine was found to turn the antagonist UCB35625 into a CCR3 agonist. Screens of small molecule libraries identified a novel specific agonist of CCR3 named CH0076989. This was able to activate eosinophils and transfectants expressing both wild-type CCR3 and a CCR1-CCR3 chimeric receptor lacking the CCR3 amino terminus, indicating that this region of CCR3 is not required for CH0076989 binding. A direct interaction with the transmembrane helices of CCR3 was supported by mutation of the residues Tyr-41, Tyr-113, and Glu-287 that resulted in complete loss of CH0076989 activity, suggesting that the compound mimics activation by CCL11. We conclude that both agonists and antagonists of CCR3 appear to occupy overlapping sites within the transmembrane helical bundle, suggesting a fine line between agonism and antagonism of chemokine receptors.
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Affiliation(s)
- Emma L Wise
- Leukocyte Biology Section, National Heart and Lung Institute Division, Faculty of Medicine, Sir Alexander Fleming Building, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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47
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Dölker N, Deupi X, Pardo L, Campillo M. Charge-charge and cation-π interactions in ligand binding to G protein-coupled receptors. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0341-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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48
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Kellenberger E, Springael JY, Parmentier M, Hachet-Haas M, Galzi JL, Rognan D. Identification of Nonpeptide CCR5 Receptor Agonists by Structure-based Virtual Screening. J Med Chem 2007; 50:1294-303. [PMID: 17311371 DOI: 10.1021/jm061389p] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A three-dimensional model of the chemokine receptor CCR5 has been built to fulfill structural peculiarities of its alpha-helix bundle and to distinguish known CCR5 antagonists from randomly chosen drug-like decoys. In silico screening of a library of 1.6 million commercially available compounds against the CCR5 model by sequential filters (drug-likeness, 2-D pharmacophore, 3-D docking, scaffold clustering) yielded a hit list of 59 compounds, out of which 10 exhibited a detectable binding affinity to the CCR5 receptor. Unexpectedly, most binders tested in a functional assay were shown to be agonists of the CCR5 receptor. A follow-up database query based on similarity to the most potent binders identified three new CCR5 agonists. Despite a moderate affinity of all nonpeptide ligands for the CCR5 receptor, one of the agonists was shown to promote efficient receptor internalization, which is a process therapeutically favorable for protection against HIV-1 infection.
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49
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Masquelier C, Servais JY, Rusanganwa E, Roman F, Havuga E, Servais J, Tuyizere S, Omes C, Karasi JC, Coruteille O, Karita E, Allen S, Schmit JC, Arendt V. A novel 24-base pair deletion in the coding region of CCR5 in an African population. AIDS 2007; 21:111-3. [PMID: 17148978 DOI: 10.1097/01.aids.0000254687.86122.fa] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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50
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Fox JM, Najarro P, Smith GL, Struyf S, Proost P, Pease JE. Structure/Function Relationships of CCR8 Agonists and Antagonists. J Biol Chem 2006; 281:36652-61. [PMID: 17023422 DOI: 10.1074/jbc.m605584200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We describe here the interactions of CCR8 with its ligands using both CCR8 transfectants and a T-cell line expressing the receptor endogenously. Of the CCR8 agonists reported previously, only CCL1 and vMIP-I exhibited potency in assays of intracellular calcium flux, chemotaxis, and receptor internalization, this latter mechanism being dependent upon the expression of beta-arrestins 1 and 2 but independent of Galpha(i) signaling. NH(2)-terminal extension of the mature CCL1 sequence by a serine residue (Ser-CCL1) resulted in a partial agonist with a reduced affinity for CCR8, suggesting that the NH(2) terminus of the ligand plays a role in ligand binding to an intrahelical site. Attempts to identify key residues within this site revealed that the conserved glutamic acid residue in transmembrane helix 7, Glu-286, is crucial for trafficking of the receptor to the cell surface, while Asp-97 of transmembrane helix 2 is dispensable. CCL7 was found to inhibit both Ser-CCL1 and vMIP-I responses but not those of CCL1 itself. Similarly, vMIP-I responses were more than 2 orders of magnitude more sensitive to the specific CCR8 antagonist MC148 than those induced by CCL1, which is difficult to reconcile with the reported affinities for the receptor. Collectively, these data suggest that the CCR8 ligands are allotropic, binding to distinct sites within CCR8 and that the human immune system may have evolved to use CCL7 as a selective antagonist of viral chemokine activity at CCR8 but not those of the host ligand.
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Affiliation(s)
- James M Fox
- National Heart and Lung Institute Division, Faculty of Medicine, Sir Alexander Fleming Building, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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