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Allosteric modulation of the chemokine receptor-chemokine CXCR4-CXCL12 complex by tyrosine sulfation. Int J Biol Macromol 2022; 206:812-822. [PMID: 35306016 DOI: 10.1016/j.ijbiomac.2022.03.078] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/03/2022] [Accepted: 03/13/2022] [Indexed: 11/21/2022]
Abstract
The chemokine receptor CXCR4 and its cognate ligand CXCL12 mediate pathways that lead to cell migration and chemotaxis. Although the structural details of related receptor-ligand complexes have been resolved, the roles of the N-terminal domain of the receptor and post-translational sulfation that are determinants of ligand selectivity and affinity remain unclear. Here, we analyze the structural dynamics induced by receptor sulfation by combining molecular dynamics, docking and network analysis. The sulfotyrosine residues, 7YsN-term, 12YsN-term and 21YsN-term allow the N-terminal domain of the apo-sulfated receptor to adopt an "open" conformation that appears to facilitate ligand binding. The overall topology of the CXCR4-CXCL12 complex is independent of the sulfation state, but an extensive network of protein-protein interactions characterizes the sulfated receptor, in line with its increased ligand affinity. The altered interactions of sulfotyrosine residues, such as 21YsN-term-47RCXCL12 replacing the 21YN-term-13FCXCL12 interaction, propagate via allosteric pathways towards the receptor lumen. In particular, our results suggest that the experimentally-reported receptor-ligand interactions 262D6.58-8RCXCL12 and 277E7.28-12RCXCL12 could be dependent on the sulfation state of the receptor and need to be carefully analyzed. Our work is an important step in understanding chemokine-receptor interactions and how post-translational modifications could modulate receptor-ligand complexes.
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2
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Peng L, Zhu N, Mao J, Huang L, Yang Y, Zhou Z, Wang L, Wu B. Expression levels of CXCR4 and CXCL12 in patients with rheumatoid arthritis and its correlation with disease activity. Exp Ther Med 2020; 20:1925-1934. [PMID: 32782501 PMCID: PMC7401245 DOI: 10.3892/etm.2020.8950] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 02/26/2020] [Indexed: 12/15/2022] Open
Abstract
The present study aimed to investigate the expression levels of C-X-C motif chemokine receptor 4 (CXCR4) and CXC ligand 12 (CXCL12) in patients with rheumatoid arthritis (RA) and the correlation with disease activity. In total, 60 patients with RA were selected as the study group, comprising of 28 patients in active-stage and 32 patients in remission-stage. In addition, 60 patients with osteoarthritis were selected as the control group. Western blotting and ELISA were used to detect the expression of CXCR4 and CXCL12, respectively. The Spearman's correlation test was used to analyze correlations between CXCR4 and CXCL12, and erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), disease activity score 28 (DAS28) scores and rheumatoid factor (RF). The present results suggested that CXCR4 and CXCL12 expression levels in the serum and joint synovial fluid of the study group were significantly higher compared with the control group (P<0.05). Moreover, CXCR4 and CXCL12 expression levels in the RA-active group were higher compared with the remission (P<0.05) and control groups (P<0.01). The Pearson test results suggested that the expression levels of CXCR4 and CXCL12 in the serum and joint synovial fluid of patients with RA had a positive correlation with the ESR, CRP, RF and DAS28 scores (P<0.05). CXCL12 and CXCR4 were highly expressed in the serum and joint synovial fluid of patients with RA, and these expression levels were positively correlated with ESR, CRP, RF and DAS28 scores. Therefore, these clinical parameters may be used as indicators to evaluate the disease activity of patients with RA.
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Affiliation(s)
- Liping Peng
- Department of Rheumatology and Immunology, First People's Hospital of Jingzhou, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434000, P.R. China
| | - Ning Zhu
- Department of Rheumatology and Immunology, First People's Hospital of Jingzhou, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434000, P.R. China
| | - Jing Mao
- Department of Rheumatology and Immunology, First People's Hospital of Jingzhou, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434000, P.R. China
| | - Li Huang
- Department of Rheumatology and Immunology, First People's Hospital of Jingzhou, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434000, P.R. China
| | - Yameng Yang
- Department of Rheumatology and Immunology, First People's Hospital of Jingzhou, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434000, P.R. China
| | - Zhengju Zhou
- Department of Rheumatology and Immunology, First People's Hospital of Jingzhou, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434000, P.R. China
| | - Li Wang
- Department of Rheumatology and Immunology, First People's Hospital of Jingzhou, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434000, P.R. China
| | - Bin Wu
- Department of Rheumatology and Immunology, First People's Hospital of Jingzhou, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei 434000, P.R. China
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3
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Stephens BS, Ngo T, Kufareva I, Handel TM. Functional anatomy of the full-length CXCR4-CXCL12 complex systematically dissected by quantitative model-guided mutagenesis. Sci Signal 2020; 13:eaay5024. [PMID: 32665413 PMCID: PMC7437921 DOI: 10.1126/scisignal.aay5024] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Because of their prominent roles in development, cancer, and HIV, the chemokine receptor CXCR4 and its ligand CXCL12 have been the subject of numerous structural and functional studies, but the determinants of ligand binding, selectivity, and signaling are still poorly understood. Here, building on our latest structural model, we used a systematic mutagenesis strategy to dissect the functional anatomy of the CXCR4-CXCL12 complex. Key charge swap mutagenesis experiments provided evidence for pairwise interactions between oppositely charged residues in the receptor and chemokine, confirming the accuracy of the predicted orientation of the chemokine relative to the receptor and providing insight into ligand selectivity. Progressive deletion of N-terminal residues revealed an unexpected contribution of the receptor N terminus to chemokine signaling. This finding challenges a longstanding "two-site" hypothesis about the essential features of the receptor-chemokine interaction in which the N terminus contributes only to binding affinity. Our results suggest that although the interaction of the chemokine N terminus with the receptor-binding pocket is the key driver of signaling, the signaling amplitude depends on the extent to which the receptor N terminus binds the chemokine. Together with systematic characterization of other epitopes, these data enable us to propose an experimentally consistent structural model for how CXCL12 binds CXCR4 and initiates signal transmission through the receptor transmembrane domain.
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Affiliation(s)
- Bryan S Stephens
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Tony Ngo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA.
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA.
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4
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von Hundelshausen P, Agten SM, Eckardt V, Blanchet X, Schmitt MM, Ippel H, Neideck C, Bidzhekov K, Leberzammer J, Wichapong K, Faussner A, Drechsler M, Grommes J, van Geffen JP, Li H, Ortega-Gomez A, Megens RTA, Naumann R, Dijkgraaf I, Nicolaes GAF, Döring Y, Soehnlein O, Lutgens E, Heemskerk JWM, Koenen RR, Mayo KH, Hackeng TM, Weber C. Chemokine interactome mapping enables tailored intervention in acute and chronic inflammation. Sci Transl Med 2017; 9:9/384/eaah6650. [PMID: 28381538 DOI: 10.1126/scitranslmed.aah6650] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 01/18/2017] [Accepted: 03/01/2017] [Indexed: 12/21/2022]
Abstract
Chemokines orchestrate leukocyte trafficking and function in health and disease. Heterophilic interactions between chemokines in a given microenvironment may amplify, inhibit, or modulate their activity; however, a systematic evaluation of the chemokine interactome has not been performed. We used immunoligand blotting and surface plasmon resonance to obtain a comprehensive map of chemokine-chemokine interactions and to confirm their specificity. Structure-function analyses revealed that chemokine activity can be enhanced by CC-type heterodimers but inhibited by CXC-type heterodimers. Functional synergism was achieved through receptor heteromerization induced by CCL5-CCL17 or receptor retention at the cell surface via auxiliary proteoglycan binding of CCL5-CXCL4. In contrast, inhibitory activity relied on conformational changes (in CXCL12), affecting receptor signaling. Obligate CC-type heterodimers showed high efficacy and potency and drove acute lung injury and atherosclerosis, processes abrogated by specific CCL5-derived peptide inhibitors or knock-in of an interaction-deficient CXCL4 variant. Atheroprotective effects of CCL17 deficiency were phenocopied by a CCL5-derived peptide disrupting CCL5-CCL17 heterodimers, whereas a CCL5 α-helix peptide mimicked inhibitory effects on CXCL12-driven platelet aggregation. Thus, formation of specific chemokine heterodimers differentially dictates functional activity and can be exploited for therapeutic targeting.
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Affiliation(s)
- Philipp von Hundelshausen
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Stijn M Agten
- Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
| | - Veit Eckardt
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Xavier Blanchet
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Martin M Schmitt
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Hans Ippel
- Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
| | - Carlos Neideck
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kiril Bidzhekov
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Julian Leberzammer
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kanin Wichapong
- Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
| | - Alexander Faussner
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maik Drechsler
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jochen Grommes
- Department of Vascular Surgery, RWTH Aachen University, Aachen, Germany
| | - Johanna P van Geffen
- Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
| | - He Li
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Almudena Ortega-Gomez
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Remco T A Megens
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ronald Naumann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ingrid Dijkgraaf
- Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
| | - Gerry A F Nicolaes
- Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
| | - Yvonne Döring
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Oliver Soehnlein
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany.,Department of Physiology and Pharmacology, Karolinksa Institutet, Stockholm, Sweden
| | - Esther Lutgens
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany.,Department of Medical Biochemistry, AMC, Amsterdam, Netherlands
| | - Johan W M Heemskerk
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Rory R Koenen
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany.,Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
| | - Kevin H Mayo
- Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands.,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Tilman M Hackeng
- Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität München, Munich, Germany. .,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany.,Cardiovascular Research Institute Maastricht, Maastricht University, Maastricht, Netherlands
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5
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Lupala CS, Rasaeifar B, Gomez-Gutierrez P, Perez JJ. Using molecular dynamics for the refinement of atomistic models of GPCRs by homology modeling. J Biomol Struct Dyn 2017; 36:2436-2448. [PMID: 28728517 DOI: 10.1080/07391102.2017.1357503] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Despite GPCRs sharing a common seven helix bundle, analysis of the diverse crystallographic structures available reveal specific features that might be relevant for ligand design. Despite the number of crystallographic structures of GPCRs steadily increasing, there are still challenges that hamper the availability of new structures. In the absence of a crystallographic structure, homology modeling remains one of the important techniques for constructing 3D models of proteins. In the present study we investigated the use of molecular dynamics simulations for the refinement of GPCRs models constructed by homology modeling. Specifically, we investigated the relevance of template selection, ligand inclusion as well as the length of the simulation on the quality of the GPCRs models constructed. For this purpose we chose the crystallographic structure of the rat muscarinic M3 receptor as reference and constructed diverse atomistic models by homology modeling, using different templates. Specifically, templates used in the present work include the human muscarinic M2; the more distant human histamine H1 and the even more distant bovine rhodopsin as shown in the GPCRs phylogenetic tree. We also investigated the use or not of a ligand in the refinement process. Hence, we conducted the refinement process of the M3 model using the M2 muscarinic as template with tiotropium or NMS docked in the orthosteric site and compared with the results obtained with a model refined without any ligand bound.
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Affiliation(s)
- Cecylia S Lupala
- a Department of Chemical Engineering (ETSEIB) , Universitat Politecnica de Catalunya , Av. Diagonal, 647. 08028 Barcelona , Spain
| | - Bahareh Rasaeifar
- a Department of Chemical Engineering (ETSEIB) , Universitat Politecnica de Catalunya , Av. Diagonal, 647. 08028 Barcelona , Spain
| | - Patricia Gomez-Gutierrez
- a Department of Chemical Engineering (ETSEIB) , Universitat Politecnica de Catalunya , Av. Diagonal, 647. 08028 Barcelona , Spain
| | - Juan J Perez
- a Department of Chemical Engineering (ETSEIB) , Universitat Politecnica de Catalunya , Av. Diagonal, 647. 08028 Barcelona , Spain
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6
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de Wit RH, Heukers R, Brink HJ, Arsova A, Maussang D, Cutolo P, Strubbe B, Vischer HF, Bachelerie F, Smit MJ. CXCR4-Specific Nanobodies as Potential Therapeutics for WHIM syndrome. J Pharmacol Exp Ther 2017; 363:35-44. [PMID: 28768817 DOI: 10.1124/jpet.117.242735] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 07/10/2017] [Indexed: 12/15/2022] Open
Abstract
WHIM syndrome is a rare congenital immunodeficiency disease, named after its main clinical manifestations: warts, hypogammaglobulinemia, infections, and myelokathexis, which refers to abnormal accumulation of mature neutrophils in the bone marrow. The disease is primarily caused by C-terminal truncation mutations of the chemokine receptor CXCR4, giving these CXCR4-WHIM mutants a gain of function in response to their ligand CXCL12. Considering the broad functions of CXCR4 in maintaining leukocyte homeostasis, patients are panleukopenic and display altered immune responses, likely as a consequence of impairment in the differentiation and trafficking of leukocytes. Treatment of WHIM patients currently consists of symptom relief, leading to unsatisfactory clinical responses. As an alternative and potentially more effective approach, we tested the potency and efficacy of CXCR4-specific nanobodies on inhibiting CXCR4-WHIM mutants. Nanobodies are therapeutic proteins based on the smallest functional fragments of heavy chain antibodies. They combine the advantages of small-molecule drugs and antibody-based therapeutics due to their relative small size, high stability, and high affinity. We compared the potential of monovalent and bivalent CXCR4-specific nanobodies to inhibit CXCL12-induced CXCR4-WHIM-mediated signaling with the small-molecule clinical candidate AMD3100. The CXCR4-targeting nanobodies displace CXCL12 binding and bind CXCR4-wild type and CXCR4-WHIM (R334X/S338X) mutants and with (sub-) nanomolar affinities. The nanobodies' epitope was mapped to extracellular loop 2 of CXCR4, overlapping with the binding site of CXCL12. Monovalent, and in particular bivalent, nanobodies were more potent than AMD3100 in reducing CXCL12-mediated G protein activation. In addition, CXCR4-WHIM-dependent calcium flux and wound healing of human papillomavirus-immortalized cell lines in response to CXCL12 was effectively inhibited by the nanobodies. Based on these in vitro results, we conclude that CXCR4 nanobodies hold significant potential as alternative therapeutics for CXCR4-associated diseases such as WHIM syndrome.
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Affiliation(s)
- Raymond H de Wit
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
| | - Raimond Heukers
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
| | - Hendrik J Brink
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
| | - Angela Arsova
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
| | - David Maussang
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
| | - Pasquale Cutolo
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
| | - Beatrijs Strubbe
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
| | - Henry F Vischer
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
| | - Françoise Bachelerie
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
| | - Martine J Smit
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
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7
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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
![]()
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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8
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Periole X. Interplay of G Protein-Coupled Receptors with the Membrane: Insights from Supra-Atomic Coarse Grain Molecular Dynamics Simulations. Chem Rev 2016; 117:156-185. [PMID: 28073248 DOI: 10.1021/acs.chemrev.6b00344] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
G protein-coupled receptors (GPCRs) are central to many fundamental cellular signaling pathways. They transduce signals from the outside to the inside of cells in physiological processes ranging from vision to immune response. It is extremely challenging to look at them individually using conventional experimental techniques. Recently, a pseudo atomistic molecular model has emerged as a valuable tool to access information on GPCRs, more specifically on their interactions with their environment in their native cell membrane and the consequences on their supramolecular organization. This approach uses the Martini coarse grain (CG) model to describe the receptors, lipids, and solvent in molecular dynamics (MD) simulations and in enough detail to allow conserving the chemical specificity of the different molecules. The elimination of unnecessary degrees of freedom has opened up large-scale simulations of the lipid-mediated supramolecular organization of GPCRs. Here, after introducing the Martini CGMD method, we review these studies carried out on various members of the GPCR family, including rhodopsin (visual receptor), opioid receptors, adrenergic receptors, adenosine receptors, dopamine receptor, and sphingosine 1-phosphate receptor. These studies have brought to light an interesting set of novel biophysical principles. The insights range from revealing localized and heterogeneous deformations of the membrane bilayer at the surface of the protein, specific interactions of lipid molecules with individual GPCRs, to the effect of the membrane matrix on global GPCR self-assembly. The review ends with an overview of the lessons learned from the use of the CGMD method, the biophysical-chemical findings on lipid-protein interplay.
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Affiliation(s)
- Xavier Periole
- Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747AG Groningen, The Netherlands
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9
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Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor. J Mol Model 2016; 22:227. [DOI: 10.1007/s00894-016-3092-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/08/2016] [Indexed: 01/10/2023]
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Omer A, Singh P. An integrated approach of network-based systems biology, molecular docking, and molecular dynamics approach to unravel the role of existing antiviral molecules against AIDS-associated cancer. J Biomol Struct Dyn 2016; 35:1547-1558. [DOI: 10.1080/07391102.2016.1188417] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Ankur Omer
- Division of Toxicology, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi 110 001, India
| | - Poonam Singh
- Division of Toxicology, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, P.O. Box 173, Lucknow 226031, India
- Academy of Scientific and Innovative Research (AcSIR), New Delhi 110 001, India
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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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