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Inan T, Flinko R, Lewis GK, MacKerell AD, Kurkcuoglu O. Identifying and Assessing Putative Allosteric Sites and Modulators for CXCR4 Predicted through Network Modeling and Site Identification by Ligand Competitive Saturation. J Phys Chem B 2024; 128:5157-5174. [PMID: 38647430 PMCID: PMC11139592 DOI: 10.1021/acs.jpcb.4c00925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
The chemokine receptor CXCR4 is a critical target for the treatment of several cancer types and HIV-1 infections. While orthosteric and allosteric modulators have been developed targeting its extracellular or transmembrane regions, the intramembrane region of CXCR4 may also include allosteric binding sites suitable for the development of allosteric drugs. To investigate this, we apply the Gaussian Network Model (GNM) to the monomeric and dimeric forms of CXCR4 to identify residues essential for its local and global motions located in the hinge regions of the protein. Residue interaction network (RIN) analysis suggests hub residues that participate in allosteric communication throughout the receptor. Mutual residues from the network models reside in regions with a high capacity to alter receptor dynamics upon ligand binding. We then investigate the druggability of these potential allosteric regions using the site identification by ligand competitive saturation (SILCS) approach, revealing two putative allosteric sites on the monomer and three on the homodimer. Two screening campaigns with Glide and SILCS-Monte Carlo docking using FDA-approved drugs suggest 20 putative hit compounds including antifungal drugs, anticancer agents, HIV protease inhibitors, and antimalarial drugs. In vitro assays considering mAB 12G5 and CXCL12 demonstrate both positive and negative allosteric activities of these compounds, supporting our computational approach. However, in vivo functional assays based on the recruitment of β-arrestin to CXCR4 do not show significant agonism and antagonism at a single compound concentration. The present computational pipeline brings a new perspective to computer-aided drug design by combining conformational dynamics based on network analysis and cosolvent analysis based on the SILCS technology to identify putative allosteric binding sites using CXCR4 as a showcase.
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Affiliation(s)
- Tugce Inan
- Department
of Chemical Engineering, Istanbul Technical
University, Istanbul 34469, Turkey
| | - Robin Flinko
- Institute
of Human Virology, University of Maryland
School of Medicine, Baltimore, Maryland 21201, United States
| | - George K. Lewis
- Institute
of Human Virology, University of Maryland
School of Medicine, Baltimore, Maryland 21201, United States
| | - Alexander D. MacKerell
- University
of Maryland Computer-Aided Drug Design Center, Department of Pharmaceutical
Sciences, School of Pharmacy, University
of Maryland, Baltimore, Maryland 21201, United States
| | - Ozge Kurkcuoglu
- Department
of Chemical Engineering, Istanbul Technical
University, Istanbul 34469, Turkey
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2
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Pervin B, Gizer M, Şeker ME, Erol ÖD, Gür SN, Polat EG, Değirmenci B, Korkusuz P, Aerts‐Kaya F. Bone marrow mesenchymal stromal cells support regeneration of intestinal damage in a colitis mouse model, independent of their CXCR4 expression. Clin Transl Sci 2024; 17:e13821. [PMID: 38742709 PMCID: PMC11092303 DOI: 10.1111/cts.13821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 04/04/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024] Open
Abstract
Inflammatory bowel disease (IBD) is characterized by a chronically dysregulated immune response in the gastrointestinal tract. Bone marrow multipotent mesenchymal stromal cells have an important immunomodulatory function and support regeneration of inflamed tissue by secretion of soluble factors as well as through direct local differentiation. CXCR4 is the receptor for CXCL12 (SDF-1, stromal-derived factor-1) and has been shown to be the main chemokine receptor, required for homing of MSCs. Increased expression of CXCL12 by inflamed intestinal tissue causes constitutive inflammation by attracting lymphocytes but can also be used to direct MSCs to sites of injury/inflammation. Trypsin is typically used to dissociate MSCs into single-cell suspensions but has also been shown to digest surface CXCR4. Here, we assessed the regenerative effects of CXCR4high and CXCR4low MSCs in an immune-deficient mouse model of DSS-induced colitis. We found that transplantation of MSCs resulted in clinical improvement and histological recovery of intestinal epithelium. In contrary to our expectations, the levels of CXCR4 on transplanted MSCs did not affect their regenerative supporting potential, indicating that paracrine effects of MSCs may be largely responsible for their regenerative/protective effects.
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Affiliation(s)
- Burcu Pervin
- Department of Stem Cell SciencesHacettepe University Graduate School of Health SciencesAnkaraTurkey
- Hacettepe University Center for Stem Cell Research and Development (PediSTEM)AnkaraTurkey
| | - Merve Gizer
- Department of Stem Cell SciencesHacettepe University Graduate School of Health SciencesAnkaraTurkey
- Micro‐Electro‐Mechanic Systems (MEMS) CenterMiddle East Technical UniversityAnkaraTurkey
| | - Mehmet Emin Şeker
- Department of Stem Cell SciencesHacettepe University Graduate School of Health SciencesAnkaraTurkey
- Hacettepe University Center for Stem Cell Research and Development (PediSTEM)AnkaraTurkey
| | - Özgür Doğuş Erol
- Department of Stem Cell SciencesHacettepe University Graduate School of Health SciencesAnkaraTurkey
- Hacettepe University Center for Stem Cell Research and Development (PediSTEM)AnkaraTurkey
| | - Sema Nur Gür
- Department of Stem Cell SciencesHacettepe University Graduate School of Health SciencesAnkaraTurkey
- Hacettepe University Center for Stem Cell Research and Development (PediSTEM)AnkaraTurkey
| | - Ece Gizem Polat
- Department of Stem Cell SciencesHacettepe University Graduate School of Health SciencesAnkaraTurkey
- Hacettepe University Center for Stem Cell Research and Development (PediSTEM)AnkaraTurkey
| | - Bahar Değirmenci
- Department of Molecular Biology and GeneticsBilkent UniversityAnkaraTurkey
| | - Petek Korkusuz
- Micro‐Electro‐Mechanic Systems (MEMS) CenterMiddle East Technical UniversityAnkaraTurkey
- Department of Histology and EmbryologyHacettepe University Faculty of MedicineAnkaraTurkey
| | - Fatima Aerts‐Kaya
- Department of Stem Cell SciencesHacettepe University Graduate School of Health SciencesAnkaraTurkey
- Hacettepe University Center for Stem Cell Research and Development (PediSTEM)AnkaraTurkey
- Hacettepe University Experimental Animals Application and Research Center (HÜDHAM)AnkaraTurkey
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3
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Prokopovich AK, Litvinova IS, Zubkova AE, Yudkin DV. CXCR4 Is a Potential Target for Anti-HIV Gene Therapy. Int J Mol Sci 2024; 25:1187. [PMID: 38256260 PMCID: PMC10816112 DOI: 10.3390/ijms25021187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
The human immunodeficiency virus (HIV) epidemic is a global issue. The estimated number of people with HIV is 39,000,000 to date. Antiviral therapy is the primary approach to treat the infection. However, it does not allow for a complete elimination of the pathogen. The advances in modern gene therapy methods open up new possibilities of effective therapy. One of these areas of possibility is the development of technologies to prevent virus penetration into the cell. Currently, a number of technologies aimed at either the prevention of virus binding to the CCR5 coreceptor or its knockout are undergoing various stages of clinical trials. Since HIV can also utilize the CXCR4 coreceptor, technologies to modify this receptor are also required. Standard knockout of CXCR4 is impossible due to its physiological significance. This review presents an analysis of interactions between individual amino acids in CXCR4 and physiological ligands and HIV gp120. It also discusses potential targets for gene therapy approaches aimed at modifying the coreceptor.
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Affiliation(s)
- Appolinaria K. Prokopovich
- State Research Center of Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Well-Being (FBRI SRC VB “Vector”, Rospotrebnadzor), 630559 Koltsovo, Russia; (A.K.P.); (I.S.L.); (A.E.Z.)
| | - Irina S. Litvinova
- State Research Center of Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Well-Being (FBRI SRC VB “Vector”, Rospotrebnadzor), 630559 Koltsovo, Russia; (A.K.P.); (I.S.L.); (A.E.Z.)
| | - Alexandra E. Zubkova
- State Research Center of Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Well-Being (FBRI SRC VB “Vector”, Rospotrebnadzor), 630559 Koltsovo, Russia; (A.K.P.); (I.S.L.); (A.E.Z.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova 2, 630090 Novosibirsk, Russia
| | - Dmitry V. Yudkin
- State Research Center of Virology and Biotechnology “Vector”, Federal Service for Surveillance on Consumer Rights Protection and Human Well-Being (FBRI SRC VB “Vector”, Rospotrebnadzor), 630559 Koltsovo, Russia; (A.K.P.); (I.S.L.); (A.E.Z.)
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4
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Meng Q, Zhu R, Mao Y, Zhu S, Wu Y, Huang L, Ciechanover A, An J, Xu Y, Huang Z. Biological and mutational analyses of CXCR4-antagonist interactions and design of new antagonistic analogs. Biosci Rep 2023; 43:BSR20230981. [PMID: 38131305 PMCID: PMC10987480 DOI: 10.1042/bsr20230981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/05/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
The chemokine receptor CXCR4 has become an attractive therapeutic target for HIV-1 infection, hematopoietic stem cell mobilization, and cancer metastasis. A wide variety of synthetic antagonists of CXCR4 have been developed and studied for a growing list of clinical applications. To compare the biological effects of different antagonists on CXCR4 functions and their common and/or distinctive molecular interactions with the receptor, we conducted head-to-head comparative cell-based biological and mutational analyses of the interactions with CXCR4 of eleven reported antagonists, including HC4319, DV3, DV1, DV1 dimer, V1, vMIP-II, CVX15, LY2510924, IT1t, AMD3100, and AMD11070 that were representative of different structural classes of D-peptides, L-peptide, natural chemokine, cyclic peptides, and small molecules. The results were rationalized by molecular modeling of CXCR4-antagonist interactions from which the common as well as different receptor binding sites of these antagonists were derived, revealing a number of important residues such as W94, D97, H113, D171, D262, and E288, mostly of negative charge. To further examine this finding, we designed and synthesized new antagonistic analogs by adding positively charged residues Arg to a D-peptide template to enhance the postulated charge-charge interactions. The newly designed analogs displayed significantly increased binding to CXCR4, which supports the notion that negatively charged residues of CXCR4 can engage in interactions with moieties of positive charge of the antagonistic ligands. The results from these mutational, modeling and new analog design studies shed new insight into the molecular mechanisms of different types of antagonists in recognizing CXCR4 and guide the development of new therapeutic agents.
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Affiliation(s)
- Qian Meng
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ruohan Zhu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yujia Mao
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Siyu Zhu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yi Wu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lina S.M. Huang
- Division of Infectious Diseases and Global Public Heath, Department of Medicine, School of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, U.S.A
| | - Aaron Ciechanover
- The Rapport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3109601, Israel
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, Chinese University of Hong Kong, Shenzhen 518172, China
| | - Jing An
- Division of Infectious Diseases and Global Public Heath, Department of Medicine, School of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, U.S.A
| | - Yan Xu
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, Chinese University of Hong Kong, Shenzhen 518172, China
| | - Ziwei Huang
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- Division of Infectious Diseases and Global Public Heath, Department of Medicine, School of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, U.S.A
- Ciechanover Institute of Precision and Regenerative Medicine, School of Medicine, Chinese University of Hong Kong, Shenzhen 518172, China
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5
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Hamshaw I, Cominetti MMD, Lai WY, Searcey M, Mueller A. The development of potent, competitive CXCR4 antagonists for the prevention of cancer metastasis. Biochem Pharmacol 2023; 218:115921. [PMID: 37956893 DOI: 10.1016/j.bcp.2023.115921] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Cancer metastasis is the cause of up to 90 % of cancer related mortality. The CXCR4 receptor and its cognate ligand, CXCL12, have major roles in enabling cancer metastasis and consequently, the CXCR4 receptor has become an attractive therapeutic target for the prevention of metastasis. Despite this, CXCR4 antagonists have had limited success in clinical trials due to cellular toxicity and poor stability and efficacy. In this study, we developed a novel, competitive CXCR4 antagonist (IS4) that through copper-catalysed-azide-alkyne-cycloaddition can be clicked to other chemical moieties such as fluorescent dyes (IS4-FAM) for CXCR4-based imaging. We determined that these CXCR4 antagonists were non-toxic and could be used to specifically label the CXCR4 receptor. Furthermore, IS4 and IS4-FAM inhibited CXCL12-stimulated cancer cell migration and Ca2+ release in both adherent and suspension cell lines with similar or improved potency as compared to two literature CXCR4 antagonists. Our results highlight the potential of IS4 and IS4-FAM as research tools and as potent CXCR4 antagonists for the prevention of metastasis.
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Affiliation(s)
- Isabel Hamshaw
- School of Pharmacy, University of East Anglia, Norwich, UK
| | | | - Wing-Yee Lai
- School of Pharmacy, University of East Anglia, Norwich, UK
| | - Mark Searcey
- School of Pharmacy, University of East Anglia, Norwich, UK
| | - Anja Mueller
- School of Pharmacy, University of East Anglia, Norwich, UK.
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6
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Kumar N, Acharya V. Machine intelligence-driven framework for optimized hit selection in virtual screening. J Cheminform 2022; 14:48. [PMID: 35869511 PMCID: PMC9306080 DOI: 10.1186/s13321-022-00630-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 07/05/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractVirtual screening (VS) aids in prioritizing unknown bio-interactions between compounds and protein targets for empirical drug discovery. In standard VS exercise, roughly 10% of top-ranked molecules exhibit activity when examined in biochemical assays, which accounts for many false positive hits, making it an arduous task. Attempts for conquering false-hit rates were developed through either ligand-based or structure-based VS separately; however, nonetheless performed remarkably well. Here, we present an advanced VS framework—automated hit identification and optimization tool (A-HIOT)—comprises chemical space-driven stacked ensemble for identification and protein space-driven deep learning architectures for optimization of an array of specific hits for fixed protein receptors. A-HIOT implements numerous open-source algorithms intending to integrate chemical and protein space leading to a high-quality prediction. The optimized hits are the selective molecules which we retrieve after extreme refinement implying chemical space and protein space modules of A-HIOT. Using CXC chemokine receptor 4, we demonstrated the superior performance of A-HIOT for hit molecule identification and optimization with tenfold cross-validation accuracies of 94.8% and 81.9%, respectively. In comparison with other machine learning algorithms, A-HIOT achieved higher accuracies of 96.2% for hit identification and 89.9% for hit optimization on independent benchmark datasets for CXCR4 and 86.8% for hit identification and 90.2% for hit optimization on independent test dataset for androgen receptor (AR), thus, shows its generalizability and robustness. In conclusion, advantageous features impeded in A-HIOT is making a reliable approach for bridging the long-standing gap between ligand-based and structure-based VS in finding the optimized hits for the desired receptor. The complete resource (framework) code is available at https://gitlab.com/neeraj-24/A-HIOT.
Graphical Abstract
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7
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Yan C, Xu H, Rong C, Cao M, Miao Z, Zhou H. IL-31 expression in HIV-infected patients with different routes of disease transmission. Medicine (Baltimore) 2022; 101:e29509. [PMID: 35758393 PMCID: PMC9276414 DOI: 10.1097/md.0000000000029509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 05/06/2022] [Indexed: 11/26/2022] Open
Abstract
Acquired immunodeficiency syndrome (AIDS) is caused by the human immunodeficiency virus (HIV). AIDS is characterized by an impaired immune system and low cellular immunity. The main manifestation of AIDS is a reduction in the number of CD4+ T cells and alteration in cytokine concentration. The present work aimed to explore the expression of IL-31 in HIV infection and disease progression.Serum samples were collected from HIV-infected patients with different routes of disease transmission. The subjects included 24 patients who were infected with HIV upon blood transmission and 36 patients who had acquired the disease through sexual transmission (21 cases of homosexual transmission and 15 cases of heterosexual transmission). In addition, 20 normal healthy individuals were included to serve as the control group. The levels of IL-31 in the collected serum samples were estimated using the human IL-31 Platinum ELISA kit.The serum analysis results revealed that the concentration of IL-31 in the serum samples for the blood transmission, sexually transmission, and normal group patients was 4.07 ± 1.63 pg/L, 7.43 ± 1.15 pg/L, and 2.87 ± 1.04 pg/L, respectively. The statistical analysis revealed that the concentration of IL-31 in HIV-1 infection was higher than that in the normal control. In addition, the expression of IL-31 was significantly higher in the sexual transmission group compared to the blood transmission group (P < .05).IL-31 could have an important role in HIV infection, although the role of IL-31 in disease progression in HIV-infected individuals requires further research.
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Affiliation(s)
- Changxin Yan
- Department of Laboratory Diagnosis, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China
| | - Huafeng Xu
- Department of Radio-immunity, Heilongjiang Provincial Hospital, Harbin, Heilongjiang 150081, China
| | - Chunli Rong
- Department of Laboratory Diagnosis, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China
| | - Meilin Cao
- Department of Laboratory Diagnosis, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China
| | - Zhuo Miao
- Department of Laboratory Diagnosis, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China
| | - Haizhou Zhou
- Department of Laboratory Diagnosis, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China
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8
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CXCR4 as a novel target in immunology: moving away from typical antagonists. FUTURE DRUG DISCOVERY 2022; 4:FDD77. [PMID: 35875591 PMCID: PMC9298491 DOI: 10.4155/fdd-2022-0007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Abstract
CXCR4 has been a target of interest in drug discovery for numerous years. However, so far, most if not all studies focused on finding antagonists of CXCR4 function. Recent studies demonstrate that targeting a minor allosteric pocket of CXCR4 induces an immunomodulating effect in immune cells expressing CXCR4, connected to the TLR pathway. Compounds binding in this minor pocket seem to be functionally selective with inverse agonistic properties in selected GPCR signaling pathways (Gi activation), but additional signaling pathways are likely to be involved in the immunomodulating effects. In depth research into these CXCR4-targeted immunomodulators could lead to novel treatment options for (auto)-immune diseases.
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9
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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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A fragment integrational approach to GPCR inhibition: Identification of a high affinity small molecule CXCR4 antagonist. Eur J Med Chem 2022; 231:114150. [DOI: 10.1016/j.ejmech.2022.114150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/11/2022] [Accepted: 01/19/2022] [Indexed: 11/23/2022]
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Abstract
The introduction of antiretroviral therapy (ART) and highly active antiretroviral therapy (HAART) has transformed human immunodeficiency virus (HIV)-1 into a chronic, well-managed disease. However, these therapies do not eliminate all infected cells from the body despite suppressing viral load. Viral rebound is largely due to the presence of cellular reservoirs which support long-term persistence of HIV-1. A thorough understanding of the HIV-1 reservoir will facilitate the development of new strategies leading to its detection, reduction, and elimination, ultimately leading to curative therapies for HIV-1. Although immune cells derived from lymphoid and myeloid progenitors have been thoroughly studied as HIV-1 reservoirs, few studies have examined whether mesenchymal stromal/stem cells (MSCs) can assume this function. In this review, we evaluate published studies which have assessed whether MSCs contribute to the HIV-1 reservoir. MSCs have been found to express the receptors and co-receptors required for HIV-1 entry, albeit at levels of expression and receptor localisation that vary considerably between studies. Exposure to HIV-1 and HIV-1 proteins alters MSC properties in vitro, including their proliferation capacity and differentiation potential. However, in vitro and in vivo experiments investigating whether MSCs can become infected with and harbour latent integrated proviral DNA are lacking. In conclusion, MSCs appear to have the potential to contribute to the HIV-1 reservoir. However, further studies are needed using techniques such as those used to prove that cluster of differentiation (CD)4+ T cells constitute an HIV-1 reservoir before a reservoir function can definitively be ascribed to MSCs.
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12
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Serna N, Carratalá JV, Conchillo-Solé O, Martínez-Torró C, Unzueta U, Mangues R, Ferrer-Miralles N, Daura X, Vázquez E, Villaverde A. Antibacterial Activity of T22, a Specific Peptidic Ligand of the Tumoral Marker CXCR4. Pharmaceutics 2021; 13:1922. [PMID: 34834337 PMCID: PMC8621837 DOI: 10.3390/pharmaceutics13111922] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/21/2021] [Accepted: 11/05/2021] [Indexed: 12/13/2022] Open
Abstract
CXCR4 is a cytokine receptor used by HIV during cell attachment and infection. Overexpressed in the cancer stem cells of more than 20 human neoplasias, CXCR4 is a convenient antitumoral drug target. T22 is a polyphemusin-derived peptide and an effective CXCR4 ligand. Its highly selective CXCR4 binding can be exploited as an agent for the cell-targeted delivery and internalization of associated antitumor drugs. Sharing chemical and structural traits with antimicrobial peptides (AMPs), the capability of T22 as an antibacterial agent remains unexplored. Here, we have detected T22-associated antimicrobial activity and biofilm formation inhibition over Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa, in a spectrum broader than the reference AMP GWH1. In contrast to GWH1, T22 shows neither cytotoxicity over mammalian cells nor hemolytic activity and is active when displayed on protein-only nanoparticles through genetic fusion. Under the pushing need for novel antimicrobial agents, the discovery of T22 as an AMP is particularly appealing, not only as its mere addition to the expanding catalogue of antibacterial drugs. The recognized clinical uses of T22 might allow its combined and multivalent application in complex clinical conditions, such as colorectal cancer, that might benefit from the synchronous destruction of cancer stem cells and local bacterial biofilms.
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Affiliation(s)
- Naroa Serna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (N.S.); (J.V.C.); (O.C.-S.); (C.M.-T.); (N.F.-M.); (E.V.)
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain;
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain;
| | - José Vicente Carratalá
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (N.S.); (J.V.C.); (O.C.-S.); (C.M.-T.); (N.F.-M.); (E.V.)
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain;
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain;
| | - Oscar Conchillo-Solé
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (N.S.); (J.V.C.); (O.C.-S.); (C.M.-T.); (N.F.-M.); (E.V.)
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain;
| | - Carlos Martínez-Torró
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (N.S.); (J.V.C.); (O.C.-S.); (C.M.-T.); (N.F.-M.); (E.V.)
| | - Ugutz Unzueta
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain;
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain;
- Biomedical Research Institute Sant Pau (IIB-Sant Pau), Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
- Josep Carreras Research Institute, 08916 Barcelona, Spain
| | - Ramón Mangues
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain;
- Biomedical Research Institute Sant Pau (IIB-Sant Pau), Hospital de la Santa Creu i Sant Pau, 08025 Barcelona, Spain
- Josep Carreras Research Institute, 08916 Barcelona, Spain
| | - Neus Ferrer-Miralles
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (N.S.); (J.V.C.); (O.C.-S.); (C.M.-T.); (N.F.-M.); (E.V.)
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain;
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain;
| | - Xavier Daura
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (N.S.); (J.V.C.); (O.C.-S.); (C.M.-T.); (N.F.-M.); (E.V.)
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain;
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (N.S.); (J.V.C.); (O.C.-S.); (C.M.-T.); (N.F.-M.); (E.V.)
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain;
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain;
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (N.S.); (J.V.C.); (O.C.-S.); (C.M.-T.); (N.F.-M.); (E.V.)
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain;
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), 28029 Madrid, Spain;
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13
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Hayn M, Blötz A, Rodríguez A, Vidal S, Preising N, Ständker L, Wiese S, Stürzel CM, Harms M, Gross R, Jung C, Kiene M, Jacob T, Pöhlmann S, Forssmann WG, Münch J, Sparrer KMJ, Seuwen K, Hahn BH, Kirchhoff F. Natural cystatin C fragments inhibit GPR15-mediated HIV and SIV infection without interfering with GPR15L signaling. Proc Natl Acad Sci U S A 2021; 118:e2023776118. [PMID: 33431697 PMCID: PMC7826402 DOI: 10.1073/pnas.2023776118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
GPR15 is a G protein-coupled receptor (GPCR) proposed to play a role in mucosal immunity that also serves as a major entry cofactor for HIV-2 and simian immunodeficiency virus (SIV). To discover novel endogenous GPR15 ligands, we screened a hemofiltrate (HF)-derived peptide library for inhibitors of GPR15-mediated SIV infection. Our approach identified a C-terminal fragment of cystatin C (CysC95-146) that specifically inhibits GPR15-dependent HIV-1, HIV-2, and SIV infection. In contrast, GPR15L, the chemokine ligand of GPR15, failed to inhibit virus infection. We found that cystatin C fragments preventing GPR15-mediated viral entry do not interfere with GPR15L signaling and are generated by proteases activated at sites of inflammation. The antiretroviral activity of CysC95-146 was confirmed in primary CD4+ T cells and is conserved in simian hosts of SIV infection. Thus, we identified a potent endogenous inhibitor of GPR15-mediated HIV and SIV infection that does not interfere with the physiological function of this GPCR.
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Affiliation(s)
- Manuel Hayn
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Andrea Blötz
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Armando Rodríguez
- Core Facility Functional Peptidomics, Ulm University Medical Center, 89081 Ulm, Germany
- Core Unit Mass Spectrometry and Proteomics, Ulm University Medical Center, 89081 Ulm, Germany
- PHARIS Biotec GmbH, 30625 Hannover, Germany
| | - Solange Vidal
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Nico Preising
- Core Facility Functional Peptidomics, Ulm University Medical Center, 89081 Ulm, Germany
| | - Ludger Ständker
- Core Facility Functional Peptidomics, Ulm University Medical Center, 89081 Ulm, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University Medical Center, 89081 Ulm, Germany
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Rüdiger Gross
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | - Christoph Jung
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany
| | - Miriam Kiene
- Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, 37077 Göttingen, Germany
| | - Timo Jacob
- Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center-Leibniz Institute for Primate Research, 37077 Göttingen, Germany
- Faculty of Biology and Psychology, University Göttingen, 37073 Göttingen, Germany
| | | | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany
| | | | - Klaus Seuwen
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6076;
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6076
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany;
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14
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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: 22] [Impact Index Per Article: 5.5] [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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15
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Fang X, Meng Q, Zhang H, Liang B, Zhu S, Wang J, Zhang C, Huang LS, Zhang X, Schooley RT, An J, Xu Y, Huang Z. Design, synthesis, and biological characterization of a new class of symmetrical polyamine-based small molecule CXCR4 antagonists. Eur J Med Chem 2020; 200:112410. [PMID: 32492596 DOI: 10.1016/j.ejmech.2020.112410] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/14/2020] [Accepted: 04/27/2020] [Indexed: 12/27/2022]
Abstract
CXCR4, a well-studied coreceptor of human immunodeficiency virus type 1 (HIV-1) entry, recognizes its cognate ligand SDF-1α (also named CXCL12) which plays many important roles, including regulating immune cells, controlling hematopoietic stem cells, and directing cancer cells migration. These pleiotropic roles make CXCR4 an attractive target to mitigate human disorders. Here a new class of symmetrical polyamines was designed and synthesized as potential small molecule CXCR4 antagonists. Among them, a representative compound 21 (namely HF50731) showed strong CXCR4 binding affinity (mean IC50 = 19.8 nM) in the CXCR4 competitive binding assay. Furthermore, compound 21 significantly inhibited SDF-1α-induced calcium mobilization and cell migration, and blocked HIV-1 infection via antagonizing CXCR4 coreceptor function. The structure-activity relationship analysis, site-directed mutagenesis, and molecular docking were conducted to further elucidate the binding mode of compound 21, suggesting that compound 21 could primarily occupy the minor subpocket of CXCR4 and partially bind in the major subpocket by interacting with residues W94, D97, D171, and E288. Our studies provide not only new insights for the fragment-based design of small molecule CXCR4 antagonists for clinical applications, but also a new and effective molecular probe for CXCR4-targeting biological studies.
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Affiliation(s)
- Xiong Fang
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qian Meng
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Huijun Zhang
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Boqiang Liang
- Nobel Institute of Biomedicine, Zhuhai, 519080, China
| | - Siyu Zhu
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Juan Wang
- Nobel Institute of Biomedicine, Zhuhai, 519080, China
| | - Chaozai Zhang
- Department of Medicine, University of California at San Diego, La Jolla, CA, 92037, USA
| | - Lina S Huang
- Department of Medicine, University of California at San Diego, La Jolla, CA, 92037, USA
| | - Xingquan Zhang
- Department of Medicine, University of California at San Diego, La Jolla, CA, 92037, USA
| | - Robert T Schooley
- Department of Medicine, University of California at San Diego, La Jolla, CA, 92037, USA
| | - Jing An
- Department of Medicine, University of California at San Diego, La Jolla, CA, 92037, USA
| | - Yan Xu
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China; School of Life and Health Sciences, Chinese University of Hong Kong, Shenzhen, China.
| | - Ziwei Huang
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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16
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Ngo T, Stephens BS, Gustavsson M, Holden LG, Abagyan R, Handel TM, Kufareva I. Crosslinking-guided geometry of a complete CXC receptor-chemokine complex and the basis of chemokine subfamily selectivity. PLoS Biol 2020; 18:e3000656. [PMID: 32271748 PMCID: PMC7173943 DOI: 10.1371/journal.pbio.3000656] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 04/21/2020] [Accepted: 03/02/2020] [Indexed: 12/15/2022] Open
Abstract
Chemokines and their receptors are orchestrators of cell migration in humans. Because dysregulation of the receptor-chemokine system leads to inflammation and cancer, both chemokines and receptors are highly sought therapeutic targets. Yet one of the barriers for their therapeutic targeting is the limited understanding of the structural principles behind receptor-chemokine recognition and selectivity. The existing structures do not include CXC subfamily complexes and lack information about the receptor distal N-termini, despite the importance of the latter in signaling, regulation, and bias. Here, we report the discovery of the geometry of the complex between full-length CXCR4, a prototypical CXC receptor and driver of cancer metastasis, and its endogenous ligand CXCL12. By comprehensive disulfide cross-linking, we establish the existence and the structure of a novel interface between the CXCR4 distal N-terminus and CXCL12 β1-strand, while also recapitulating earlier findings from nuclear magnetic resonance, modeling and crystallography of homologous receptors. A cross-linking-informed high-resolution model of the CXCR4-CXCL12 complex pinpoints the interaction determinants and reveals the occupancy of the receptor major subpocket by the CXCL12 proximal N terminus. This newly found positioning of the chemokine proximal N-terminus provides a structural explanation of CXC receptor-chemokine selectivity against other subfamilies. Our findings challenge the traditional two-site understanding of receptor-chemokine recognition, suggest the possibility of new affinity and signaling determinants, and fill a critical void on the structural map of an important class of therapeutic targets. These results will aid the rational design of selective chemokine-receptor targeting small molecules and biologics with novel pharmacology.
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Affiliation(s)
- Tony Ngo
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Bryan S. Stephens
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Lauren G. Holden
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ruben Abagyan
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Tracy M. Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, United States of America
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17
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Renard I, Archibald SJ. CXCR4-targeted metal complexes for molecular imaging. Med Chem 2020. [DOI: 10.1016/bs.adioch.2019.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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18
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Suttisintong K, Kaewchangwat N, Thanayupong E, Nerungsi C, Srikun O, Pungpo P. Recent Progress in the Development of HIV-1 Entry Inhibitors: From Small Molecules to Potent Anti-HIV Agents. Curr Top Med Chem 2019; 19:1599-1620. [DOI: 10.2174/1568026619666190712204050] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 06/07/2019] [Accepted: 06/21/2019] [Indexed: 01/21/2023]
Abstract
Viral entry, the first process in the reproduction of viruses, primarily involves attachment of the viral envelope proteins to membranes of the host cell. The crucial components that play an important role in viral entry include viral surface glycoprotein gp120, viral transmembrane glycoprotein gp41, host cell glycoprotein (CD4), and host cell chemokine receptors (CCR5 and CXCR4). Inhibition of the multiple molecular interactions of these components can restrain viruses, such as HIV-1, from fusion with the host cell, blocking them from reproducing. This review article specifically focuses on the recent progress in the development of small-molecule HIV-1 entry inhibitors and incorporates important aspects of their structural modification that lead to the discovery of new molecular scaffolds with more potency.
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Affiliation(s)
- Khomson Suttisintong
- National Nanotechnology Center (NANOTEC), National Science and Technology, Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Narongpol Kaewchangwat
- National Nanotechnology Center (NANOTEC), National Science and Technology, Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Eknarin Thanayupong
- National Nanotechnology Center (NANOTEC), National Science and Technology, Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Chakkrapan Nerungsi
- The Government Pharmaceutical Organization, 75/1 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand
| | - Onsiri Srikun
- The Government Pharmaceutical Organization, 75/1 Rama VI Road, Ratchathewi, Bangkok 10400, Thailand
| | - Pornpan Pungpo
- Department of Chemistry, Faculty of Science, Ubon Ratchathani University, 85 Sathonlamark Road, Warinchamrap, Ubon Ratchathani 34190, Thailand
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19
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Heuninck J, Perpiñá Viciano C, Işbilir A, Caspar B, Capoferri D, Briddon SJ, Durroux T, Hill SJ, Lohse MJ, Milligan G, Pin JP, Hoffmann C. Context-Dependent Signaling of CXC Chemokine Receptor 4 and Atypical Chemokine Receptor 3. Mol Pharmacol 2019; 96:778-793. [PMID: 31092552 DOI: 10.1124/mol.118.115477] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/21/2019] [Indexed: 02/06/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are regulated by complex molecular mechanisms, both in physiologic and pathologic conditions, and their signaling can be intricate. Many factors influence their signaling behavior, including the type of ligand that activates the GPCR, the presence of interacting partners, the kinetics involved, or their location. The two CXC-type chemokine receptors, CXC chemokine receptor 4 (CXCR4) and atypical chemokine receptor 3 (ACKR3), both members of the GPCR superfamily, are important and established therapeutic targets in relation to cancer, human immunodeficiency virus infection, and inflammatory diseases. Therefore, it is crucial to understand how the signaling of these receptors works to be able to specifically target them. In this review, we discuss how the signaling pathways activated by CXCR4 and ACKR3 can vary in different situations. G protein signaling of CXCR4 depends on the cellular context, and discrepancies exist depending on the cell lines used. ACKR3, as an atypical chemokine receptor, is generally reported to not activate G proteins but can broaden its signaling spectrum upon heteromerization with other receptors, such as CXCR4, endothelial growth factor receptor, or the α 1-adrenergic receptor (α 1-AR). Also, CXCR4 forms heteromers with CC chemokine receptor (CCR) 2, CCR5, the Na+/H+ exchanger regulatory factor 1, CXCR3, α 1-AR, and the opioid receptors, which results in differential signaling from that of the monomeric subunits. In addition, CXCR4 is present on membrane rafts but can go into the nucleus during cancer progression, probably acquiring different signaling properties. In this review, we also provide an overview of the currently known critical amino acids involved in CXCR4 and ACKR3 signaling.
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Affiliation(s)
- Joyce Heuninck
- IGF, CNRS, Inserm, Université de Montpellier, Montpellier, France (J.H., T.D., J.-P.P.); Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany (C.P.V., A.I., M.J.L., C.H.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Max Delbrück Center for Molecular Medicine, Berlin, Germany (A.I., M.J.L.); Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (D.C., G.M.); Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (B.C., S.J.B., S.J.H.); and Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, United Kingdom (B.C., S.J.B., S.J.H.)
| | - Cristina Perpiñá Viciano
- IGF, CNRS, Inserm, Université de Montpellier, Montpellier, France (J.H., T.D., J.-P.P.); Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany (C.P.V., A.I., M.J.L., C.H.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Max Delbrück Center for Molecular Medicine, Berlin, Germany (A.I., M.J.L.); Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (D.C., G.M.); Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (B.C., S.J.B., S.J.H.); and Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, United Kingdom (B.C., S.J.B., S.J.H.)
| | - Ali Işbilir
- IGF, CNRS, Inserm, Université de Montpellier, Montpellier, France (J.H., T.D., J.-P.P.); Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany (C.P.V., A.I., M.J.L., C.H.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Max Delbrück Center for Molecular Medicine, Berlin, Germany (A.I., M.J.L.); Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (D.C., G.M.); Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (B.C., S.J.B., S.J.H.); and Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, United Kingdom (B.C., S.J.B., S.J.H.)
| | - Birgit Caspar
- IGF, CNRS, Inserm, Université de Montpellier, Montpellier, France (J.H., T.D., J.-P.P.); Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany (C.P.V., A.I., M.J.L., C.H.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Max Delbrück Center for Molecular Medicine, Berlin, Germany (A.I., M.J.L.); Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (D.C., G.M.); Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (B.C., S.J.B., S.J.H.); and Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, United Kingdom (B.C., S.J.B., S.J.H.)
| | - Davide Capoferri
- IGF, CNRS, Inserm, Université de Montpellier, Montpellier, France (J.H., T.D., J.-P.P.); Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany (C.P.V., A.I., M.J.L., C.H.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Max Delbrück Center for Molecular Medicine, Berlin, Germany (A.I., M.J.L.); Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (D.C., G.M.); Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (B.C., S.J.B., S.J.H.); and Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, United Kingdom (B.C., S.J.B., S.J.H.)
| | - Stephen J Briddon
- IGF, CNRS, Inserm, Université de Montpellier, Montpellier, France (J.H., T.D., J.-P.P.); Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany (C.P.V., A.I., M.J.L., C.H.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Max Delbrück Center for Molecular Medicine, Berlin, Germany (A.I., M.J.L.); Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (D.C., G.M.); Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (B.C., S.J.B., S.J.H.); and Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, United Kingdom (B.C., S.J.B., S.J.H.)
| | - Thierry Durroux
- IGF, CNRS, Inserm, Université de Montpellier, Montpellier, France (J.H., T.D., J.-P.P.); Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany (C.P.V., A.I., M.J.L., C.H.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Max Delbrück Center for Molecular Medicine, Berlin, Germany (A.I., M.J.L.); Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (D.C., G.M.); Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (B.C., S.J.B., S.J.H.); and Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, United Kingdom (B.C., S.J.B., S.J.H.)
| | - Stephen J Hill
- IGF, CNRS, Inserm, Université de Montpellier, Montpellier, France (J.H., T.D., J.-P.P.); Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany (C.P.V., A.I., M.J.L., C.H.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Max Delbrück Center for Molecular Medicine, Berlin, Germany (A.I., M.J.L.); Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (D.C., G.M.); Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (B.C., S.J.B., S.J.H.); and Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, United Kingdom (B.C., S.J.B., S.J.H.)
| | - Martin J Lohse
- IGF, CNRS, Inserm, Université de Montpellier, Montpellier, France (J.H., T.D., J.-P.P.); Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany (C.P.V., A.I., M.J.L., C.H.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Max Delbrück Center for Molecular Medicine, Berlin, Germany (A.I., M.J.L.); Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (D.C., G.M.); Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (B.C., S.J.B., S.J.H.); and Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, United Kingdom (B.C., S.J.B., S.J.H.)
| | - Graeme Milligan
- IGF, CNRS, Inserm, Université de Montpellier, Montpellier, France (J.H., T.D., J.-P.P.); Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany (C.P.V., A.I., M.J.L., C.H.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Max Delbrück Center for Molecular Medicine, Berlin, Germany (A.I., M.J.L.); Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (D.C., G.M.); Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (B.C., S.J.B., S.J.H.); and Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, United Kingdom (B.C., S.J.B., S.J.H.)
| | - Jean-Philippe Pin
- IGF, CNRS, Inserm, Université de Montpellier, Montpellier, France (J.H., T.D., J.-P.P.); Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany (C.P.V., A.I., M.J.L., C.H.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Max Delbrück Center for Molecular Medicine, Berlin, Germany (A.I., M.J.L.); Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (D.C., G.M.); Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (B.C., S.J.B., S.J.H.); and Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, United Kingdom (B.C., S.J.B., S.J.H.)
| | - Carsten Hoffmann
- IGF, CNRS, Inserm, Université de Montpellier, Montpellier, France (J.H., T.D., J.-P.P.); Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany (C.P.V., A.I., M.J.L., C.H.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University Jena, Jena, Germany (C.P.V., C.H.); Max Delbrück Center for Molecular Medicine, Berlin, Germany (A.I., M.J.L.); Centre for Translational Pharmacology, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom (D.C., G.M.); Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom (B.C., S.J.B., S.J.H.); and Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, United Kingdom (B.C., S.J.B., S.J.H.)
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20
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Koksal AC, Pennini ME, Marelli M, Xiao X, Dall'Acqua WF. Functional mimetic of the G-protein coupled receptor CXCR4 on a soluble antibody scaffold. MAbs 2019; 11:725-734. [PMID: 30900513 DOI: 10.1080/19420862.2019.1596703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
G-protein coupled receptors (GPCRs) constitute major drug targets due to their involvement in critical biological functions and pathophysiological disorders. The leading challenge in their structural and functional characterization has been the need for a lipid environment to accommodate their hydrophobic cores. Here, we report an antibody scaffold mimetic (ASM) platform where we have recapitulated the extracellular functional domains of the GPCR, C-X-C chemokine receptor 4 (CXCR4) on a soluble antibody framework. The engineered ASM molecule can accommodate the N-terminal loop and all three extracellular loops of CXCR4. These extracellular features are important players in ligand recruitment and interaction for allostery and signal transduction. Our study shows that ASMCXCR4 can be recognized by the anti-CXCR4 antibodies, MEDI3185, 2B11, and 12G5, and that ASMCXCR4 can bind the HIV-1 glycoprotein ligand gp120, and the natural chemokine ligand SDF-1α. Further, we show that ASMCXCR4 can competitively inhibit the SDF-1α signaling pathway, and be used as an immunogen to generate CXCR4-specific antibodies. This platform will be useful in the study of GPCR biology in a soluble receptor context for evaluating its extracellular ligand interactions.
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Affiliation(s)
- Adem C Koksal
- a Department of Antibody Discovery and Protein Engineering , AstraZeneca , Gaithersburg , MD , USA
| | - Meghan E Pennini
- b Microbial Sciences , MedImmune, AstraZeneca , Gaithersburg , MD , USA
| | - Marcello Marelli
- a Department of Antibody Discovery and Protein Engineering , AstraZeneca , Gaithersburg , MD , USA
| | - Xiaodong Xiao
- a Department of Antibody Discovery and Protein Engineering , AstraZeneca , Gaithersburg , MD , USA
| | - William F Dall'Acqua
- a Department of Antibody Discovery and Protein Engineering , AstraZeneca , Gaithersburg , MD , USA
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21
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CXCR4-targeting nanobodies differentially inhibit CXCR4 function and HIV entry. Biochem Pharmacol 2018; 158:402-412. [PMID: 30342024 DOI: 10.1016/j.bcp.2018.10.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 10/15/2018] [Indexed: 01/10/2023]
Abstract
The chemokine receptor CXCR4 and its ligand CXCL12 contribute to a variety of human diseases, such as cancer. CXCR4 is also a major co-receptor facilitating HIV entry. Accordingly, CXCR4 is considered as an attractive therapeutic target. Drug side effects and poor pharmacokinetic properties have been major hurdles that have prevented the implementation of CXCR4-directed inhibitors in treatment regimes. We evaluated the activity of a new and promising class of biologics, namely CXCR4-targeting nanobodies, with the purpose of identifying nanobodies that would preferentially inhibit HIV infection, while minimally disturbing other CXCR4-related functions. All CXCR4-interacting nanobodies inhibited CXCL12 binding and receptor-mediated calcium mobilization with comparable relative potencies. Importantly, the anti-HIV-1 activity of the nanobodies did not always correlate with their ability to modulate CXCR4 signaling and function, indicating that the anti-HIV and anti-CXCR4 activity are not entirely overlapping and may be functionally separated. Three nanobodies with divergent activity profiles (VUN400, VUN401 and VUN402) were selected for in depth biological evaluation. While all three nanobodies demonstrated inhibitory activity against a wide range of HIV (X4) strains, VUN402 poorly blocked CXCL12-induced CXCR4 internalization, chemotaxis and changes in cell morphology. Each of these nanobodies recognized distinct, although partially overlapping epitopes on CXCR4, which might underlie their distinct activity profiles. Our results demonstrate the potential of CXCR4-targeting nanobody VUN402 as a novel lead and starting point for the development of a more potent and selective anti-HIV agent.
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22
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Peng D, Cao B, Zhou YJ, Long YQ. The chemical diversity and structure-based evolution of non-peptide CXCR4 antagonists with diverse therapeutic potential. Eur J Med Chem 2018; 149:148-169. [PMID: 29500940 DOI: 10.1016/j.ejmech.2018.02.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 02/11/2018] [Accepted: 02/13/2018] [Indexed: 12/11/2022]
Abstract
The CXC chemokine receptor 4 (CXCR4) is a highly reserved G-protein coupled 7-transmembrane (TM) chemokine receptor which consists of 352 amino acids. CXCR4 has only one endogenous chemokine ligand of CXCL12, besides several other natural nonchemokine ligands such as extracellular ubiquitin and noncognate ligand of MIF. CXCR4 strongly binds to CXCL12 and the resulting CXCLl2/CXCR4 axis is the molecular basis of their various biological functions, which include: (1) mediating immune and inflammatory response; (2) regulation of hematopoietic stem cell migration and homing; (3) an essential co-receptor for HIV entry into host cells; (4) participation in the process of embryonic development; (5) malignant tumor invasion and metastasis; (6) myocardial infarction, ischemic stroke and acute kidney injury. Correspondingly, CXCR4 antagonists find potential therapeutic applications in HIV infection, as well as hematopoietic stem cell migration, inflammation, immune-related diseases, tumor and ischemic diseases. Recently, great achievements have been made and a number of non-peptide CXCR4 antagonists with diversity scaffolds have been discovered. In this review, the discovery of small molecule CXCR4 antagonists focused on the structures, activities, evolution and development of representative CXCR4 antagonists is comprehensively described. The central role of CXCR4 in diverse cellular signaling pathways and its involvement in several diseases progressions are discussed as well.
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Affiliation(s)
- Dian Peng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Bin Cao
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ying-Jun Zhou
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Ya-Qiu Long
- College of Pharmaceutical Sciences, Soochow University Medical College, Suzhou 215123, China.
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23
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Ramachandran R, Piramanyagam S. Pharmacophore modeling, atom based 3D-QSAR and Molecular docking approaches to screen C-X-C chemokine receptor type 4 antagonists as microbicides for human immunodeficiency virus-1. Virusdisease 2018; 28:272-280. [PMID: 29291213 DOI: 10.1007/s13337-017-0397-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 08/28/2017] [Indexed: 01/10/2023] Open
Abstract
The C-X-C chemokine receptor type 4 receptor CXCR4 which acts as a co-receptor for human immunodeficiency virus-1, expressed in the later stages of infection is considered as an attractive and new target for drug design. Microbicides acting as co-receptor blockers are highly significant as these drugs block HIV lifecycle at early stage itself. The urgent need for a safe and effective microbicide urges to explore new CXCR4 antagonists which could be developed as microbicides. The pharmacophore based 3D-QSAR models and docking models were developed using PHASE and GLIDE modules of Schrodinger software. Three-dimensional quantitative structure-activity relationships (3D-QSAR) studies and pharmacophore modelling was carried out on a dataset of 114 CXCR4 antagonists with the intention of exploring entry inhibitors with better therapeutic potential. A training set of 43 compounds was used to create 3D-QSAR models and they were validated using a test set of 28 compounds. CXCR4 antagonists with good inhibitory activity could be designed and structurally modified based upon the QSAR model developed with necessary pharmacophore features. The results revealed that the common pharmacophore hypothesis ADHPR.1 was used for 3D-QSAR model development and the most active compound, CXCR4 antagonist no.44 which is a imidazopyridine-tetrahydro-8-quinolinamine derivative interacted with the CXCR4 receptor residue ASP 97 by the formation of a hydrogen bond. Also, the docking studies were carried out for the dataset for analyzing the binding conformation of CXCR4 and 114 antagonists. The results obtained from the 3D-QSAR studies and docking simulation can be used for designing new and potent CXCR4 antagonists. The compound identified from this study can be taken up further for validation by in vitro/in vivo studies.
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Affiliation(s)
- Radhika Ramachandran
- Department of Bioinformatics, Bharathiar University, Coimbatore, Tamilnadu 641 046 India
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24
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Sand LGL, Buckle T, van Leeuwen FWB, Corver WE, Kruisselbrink AB, Jochemsen AG, Hogendoorn PCW, Szuhai K. Fluorescent CXCR4 targeting peptide as alternative for antibody staining in Ewing sarcoma. BMC Cancer 2017; 17:383. [PMID: 28549419 PMCID: PMC5446759 DOI: 10.1186/s12885-017-3352-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 05/12/2017] [Indexed: 01/07/2023] Open
Abstract
Background Ewing sarcoma is an aggressive, highly metastatic primary bone and soft tissue tumor most frequently occurring in the bone of young adolescents. Patients, especially those diagnosed with a metastatic disease, have a poor overall survival. Chemokine receptor CXCR4 has a key pro-tumorigenic role in the tumor microenvironment of Ewing sarcoma and has been suggested to be involved in the increased metastatic propensity. Earlier studies on CXCR4 protein expression in Ewing sarcoma yielded contradictory results when compared to CXCR4 RNA expression studies. Previously, we demonstrated that CXCR4 expression could be detected in vivo using the fluorescently tagged CXCR4-specific peptide MSAP-Ac-TZ14011. Therefore, we studied the membranous CXCR4 expression in Ewing sarcoma cell lines using MSAP-Ac-TZ14011. Methods The CXCR4 membrane expression levels were studied in EWS cell lines by flow cytometry using the hybrid peptide MSAP-Ac-TZ14011 and were correlated to CXCR4 RNA expression levels. The measurements were compared to levels detected using the CXCR4 antibody ab2074 under various cell preparation conditions. In addition, the staining patterns were analyzed by confocal fluorescence microscopy over time. Results The hybrid peptide MSAP-Ac-TZ14011 levels showed a strong and better correlation of CXCR4 membrane expression with the CXCR4 RNA expression levels than observed with the anti-CXCR4 antibody ab2074. With the hybrid peptide MSAP-Ac-TZ14011 using live cell confocal microscopy CXCR4 membrane staining and internalization was detected and the signal intensity correlated well with CXCR4 mRNA expression levels. Conclusions The fluorescently labeled CXCR4 targeting peptide-based method provides a reliable alternative to antibody staining to study the CXCR4 membrane expression in live cells using either flow cytometry or live cell fluorescence microscopy. The fluorescently tagged CXCR4 targeting peptide could enable in vivo detection of CXCR4 expression in Ewing sarcoma which may help to stratify cases for anti-CXCR4 therapy. Electronic supplementary material The online version of this article (doi:10.1186/s12885-017-3352-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laurens G L Sand
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tessa Buckle
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden, The Netherlands.,Division of Molecular Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Fijs W B van Leeuwen
- Interventional Molecular Imaging Laboratory, Department of Radiology, Leiden, The Netherlands
| | - Willem E Corver
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Aart G Jochemsen
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, Postbus 9600, 2300 RC, The Netherlands
| | | | - Károly Szuhai
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, Postbus 9600, 2300 RC, The Netherlands.
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25
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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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26
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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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27
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Signal transmission through the CXC chemokine receptor 4 (CXCR4) transmembrane helices. Proc Natl Acad Sci U S A 2016; 113:9928-33. [PMID: 27543332 DOI: 10.1073/pnas.1601278113] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The atomic-level mechanisms by which G protein-coupled receptors (GPCRs) transmit extracellular ligand binding events through their transmembrane helices to activate intracellular G proteins remain unclear. Using a comprehensive library of mutations covering all 352 residues of the GPCR CXC chemokine receptor 4 (CXCR4), we identified 41 amino acids that are required for signaling induced by the chemokine ligand CXCL12 (stromal cell-derived factor 1). CXCR4 variants with each of these mutations do not signal properly but remain folded, based on receptor surface trafficking, reactivity to conformationally sensitive monoclonal antibodies, and ligand binding. When visualized on the structure of CXCR4, the majority of these residues form a continuous intramolecular signaling chain through the transmembrane helices; this chain connects chemokine binding residues on the extracellular side of CXCR4 to G protein-coupling residues on its intracellular side. Integrated into a cohesive model of signal transmission, these CXCR4 residues cluster into five functional groups that mediate (i) chemokine engagement, (ii) signal initiation, (iii) signal propagation, (iv) microswitch activation, and (v) G protein coupling. Propagation of the signal passes through a "hydrophobic bridge" on helix VI that coordinates with nearly every known GPCR signaling motif. Our results agree with known conserved mechanisms of GPCR activation and significantly expand on understanding the structural principles of CXCR4 signaling.
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28
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Mishra RK, Shum AK, Platanias LC, Miller RJ, Schiltz GE. Discovery and characterization of novel small-molecule CXCR4 receptor agonists and antagonists. Sci Rep 2016; 6:30155. [PMID: 27456816 PMCID: PMC4960487 DOI: 10.1038/srep30155] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 06/29/2016] [Indexed: 01/01/2023] Open
Abstract
The chemokine CXCL12 (SDF-1) and its cognate receptor CXCR4 are involved in a large number of physiological processes including HIV-1 infectivity, inflammation, tumorigenesis, stem cell migration, and autoimmune diseases. While previous efforts have identified a number of CXCR4 antagonists, there have been no small molecule agonists reported. Herein, we describe the identification of a novel series of CXCR4 modulators, including the first small molecules to display agonist behavior against this receptor, using a combination of structure- and ligand-based virtual screening. These agonists produce robust calcium mobilization in human melanoma cell lines which can be blocked by the CXCR4-selective antagonist AMD3100. We also demonstrate the ability of these new agonists to induce receptor internalization, ERK activation, and chemotaxis, all hallmarks of CXCR4 activation. Our results describe a new series of biologically relevant small molecules that will enable further study of the CXCR4 receptor and may contribute to the development of new therapeutics.
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Affiliation(s)
- Rama K Mishra
- The Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston IL, USA
| | - Andrew K Shum
- Department of Pharmacology, Northwestern University, Chicago IL, USA
| | - Leonidas C Platanias
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago IL, USA.,Department of Medicine, Jesse Brown Veterans Affairs Medical Center, Chicago IL, USA
| | - Richard J Miller
- Department of Pharmacology, Northwestern University, Chicago IL, USA
| | - Gary E Schiltz
- The Center for Molecular Innovation and Drug Discovery, Northwestern University, Evanston IL, USA.,Department of Pharmacology, Northwestern University, Chicago IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago IL, USA
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29
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Cutolo P, Basdevant N, Bernadat G, Bachelerie F, Ha-Duong T. Interaction of chemokine receptor CXCR4 in monomeric and dimeric state with its endogenous ligand CXCL12: coarse-grained simulations identify differences. J Biomol Struct Dyn 2016; 35:399-412. [PMID: 26813575 DOI: 10.1080/07391102.2016.1145142] [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] [Indexed: 01/19/2023]
Abstract
Despite the recent resolutions of the crystal structure of the chemokine receptor CXCR4 in complex with small antagonists or viral chemokine, a description at the molecular level of the interactions between the full-length CXCR4 and its endogenous ligand, the chemokine CXCL12, in relationship with the receptor recognition and activation, is not yet completely elucidated. Moreover, since CXCR4 is able to form dimers, the question of whether the CXCR4-CXCL12 complex has a 1:1 or 2:1 preferential stoichiometry is still an open question. We present here results of coarse-grained protein-protein docking and molecular dynamics simulations of CXCL12 in association with CXCR4 in monomeric and dimeric states. Our proposed models for the 1:1 and 2:1 CXCR4-CXCL12 quaternary structures are consistent with recognition and activation motifs of both partners provided by the available site-directed mutagenesis data. Notably, we observed that in the 2:1 complex, the chemokine N-terminus makes more steady contacts with the receptor residues critical for binding and activation than in the 1:1 structure, suggesting that the 2:1 stoichiometry would favor the receptor signaling activity with respect to the 1:1 association.
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Affiliation(s)
- Pasquale Cutolo
- a UMR996 - Inflammation, Chemokines and Immunopathology , Inserm, Université Paris-Sud, Université Paris-Saclay , Clamart , France
| | - Nathalie Basdevant
- b LAMBE - UMR 8587, Université d'Evry-Val-d'Essonne, CNRS , Evry , France
| | - Guillaume Bernadat
- c BioCIS - UMR 8076, Université Paris-Sud, CNRS, Université Paris-Saclay , Châtenay-Malabry , France
| | - Françoise Bachelerie
- a UMR996 - Inflammation, Chemokines and Immunopathology , Inserm, Université Paris-Sud, Université Paris-Saclay , Clamart , France
| | - Tâp Ha-Duong
- c BioCIS - UMR 8076, Université Paris-Sud, CNRS, Université Paris-Saclay , Châtenay-Malabry , France
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30
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Zachariassen ZG, Karlshøj S, Haug BE, Rosenkilde MM, Våbenø J. Probing the Molecular Interactions between CXC Chemokine Receptor 4 (CXCR4) and an Arginine-Based Tripeptidomimetic Antagonist (KRH-1636). J Med Chem 2015; 58:8141-53. [PMID: 26397724 DOI: 10.1021/acs.jmedchem.5b00987] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We here report an experimentally verified binding mode for the known tripeptidomimetic CXCR4 antagonist KRH-1636 (1). A limited SAR study based on the three functionalities of 1 was first conducted, followed by site-directed mutagenesis studies. The receptor mapping showed that both the potency and affinity of 1 were dependent on the transmembrane residues His(113), Asp(171), Asp(262), and His(281) and also suggested the involvement of Tyr(45) and Gln(200) (potency) and Tyr(116) and Glu(288) (affinity). Molecular docking of 1 to an X-ray structure of CXCR4 showed that the l-Arg guanidino group of 1 forms polar interactions with His(113) and Asp(171) and the (pyridin-2-ylmethyl)amino moiety is anchored by Asp(262) and His(281), whereas the naphthalene ring is tightly packed in a hydrophobic subpocket formed by the aromatic side chains of Trp(94), Tyr(45), and Tyr(116). The detailed picture of ligand-receptor interactions provided here will assist in structure-based design and further development of small-molecule peptidomimetic CXCR4 antagonists.
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Affiliation(s)
- Zack G Zachariassen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway , Breivika, NO-9037 Tromsø, Norway
| | - Stefanie Karlshøj
- Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute, University of Copenhagen , Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Bengt Erik Haug
- Department of Chemistry and Centre for Pharmacy, University of Bergen , Allégaten 41, NO-5007 Bergen, Norway
| | - Mette M Rosenkilde
- Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute, University of Copenhagen , Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Jon Våbenø
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway , Breivika, NO-9037 Tromsø, Norway
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31
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Sand LGL, Jochemsen AG, Beletkaia E, Schmidt T, Hogendoorn PCW, Szuhai K. Novel splice variants of CXCR4 identified by transcriptome sequencing. Biochem Biophys Res Commun 2015; 466:89-94. [PMID: 26321665 DOI: 10.1016/j.bbrc.2015.08.113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 08/25/2015] [Indexed: 10/23/2022]
Abstract
Chemokine receptor CXCR4 is involved in tumor growth, angiogenesis and metastasis. Its function is regulated in many ways and one of them is alternative splicing. We identified two novel coding splice variants (CXCR4-3 and CXCR4-4) of CXCR4 in Ewing sarcoma (EWS) cell lines by whole transcriptome sequencing and validated these with reverse transcriptase- PCR and Sanger sequencing. The novel splice variants were expressed at RNA level in Ewing sarcoma samples and in other tumor cell lines and placenta, but not in lung. Due to inclusion of an additional exon the new isoforms have a 70 and 33 amino acid elongation of the N-terminal end of CXCR4. For validation at protein and functional level, the identified isoforms and normal CXCR4 were cloned into an EYFP tagged vector and ectopically expressed in HEK293T cell line and EWS cell line A673. Of the novel isoforms CXCR4-3 showed cell membrane localization and a functional response after addition of CXCR4 ligand CXCL12a. CXCR4-4 showed strong cytoplasmic accumulation and no response to ligand treatment. The role of the newly discovered isoforms in CXCR4 signaling is likely to be limited. Our data stresses the importance of functional validation of newly identified isoforms.
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Affiliation(s)
- L G L Sand
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - A G Jochemsen
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - E Beletkaia
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - T Schmidt
- Huygens-Kamerlingh Onnes Laboratory, Leiden Institute of Physics, Leiden University, Leiden, The Netherlands
| | - P C W Hogendoorn
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - K Szuhai
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands.
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32
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Hanes MS, Salanga CL, Chowdry AB, Comerford I, McColl SR, Kufareva I, Handel TM. Dual targeting of the chemokine receptors CXCR4 and ACKR3 with novel engineered chemokines. J Biol Chem 2015. [PMID: 26216880 DOI: 10.1074/jbc.m115.675108] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The chemokine CXCL12 and its G protein-coupled receptors CXCR4 and ACKR3 are implicated in cancer and inflammatory and autoimmune disorders and are targets of numerous antagonist discovery efforts. Here, we describe a series of novel, high affinity CXCL12-based modulators of CXCR4 and ACKR3 generated by selection of N-terminal CXCL12 phage libraries on live cells expressing the receptors. Twelve of 13 characterized CXCL12 variants are full CXCR4 antagonists, and four have Kd values <5 nm. The new variants also showed high affinity for ACKR3. The variant with the highest affinity for CXCR4, LGGG-CXCL12, showed efficacy in a murine model for multiple sclerosis, demonstrating translational potential. Molecular modeling was used to elucidate the structural basis of binding and antagonism of selected variants and to guide future designs. Together, this work represents an important step toward the development of therapeutics targeting CXCR4 and ACKR3.
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Affiliation(s)
- Melinda S Hanes
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093 and
| | - Catherina L Salanga
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093 and
| | - Arnab B Chowdry
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093 and
| | - Iain Comerford
- Chemokine Biology Group, The School of Molecular and Biomedical Science, The University of Adelaide, North Terrace Campus, Adelaide, South Australia 5005, Australia
| | - Shaun R McColl
- Chemokine Biology Group, The School of Molecular and Biomedical Science, The University of Adelaide, North Terrace Campus, Adelaide, South Australia 5005, Australia
| | - Irina Kufareva
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093 and
| | - Tracy M Handel
- From the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093 and
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33
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Sand LGL, Szuhai K, Hogendoorn PCW. Sequencing Overview of Ewing Sarcoma: A Journey across Genomic, Epigenomic and Transcriptomic Landscapes. Int J Mol Sci 2015; 16:16176-215. [PMID: 26193259 PMCID: PMC4519945 DOI: 10.3390/ijms160716176] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 07/03/2015] [Accepted: 07/07/2015] [Indexed: 12/17/2022] Open
Abstract
Ewing sarcoma is an aggressive neoplasm occurring predominantly in adolescent Caucasians. At the genome level, a pathognomonic EWSR1-ETS translocation is present. The resulting fusion protein acts as a molecular driver in the tumor development and interferes, amongst others, with endogenous transcription and splicing. The Ewing sarcoma cell shows a poorly differentiated, stem-cell like phenotype. Consequently, the cellular origin of Ewing sarcoma is still a hot discussed topic. To further characterize Ewing sarcoma and to further elucidate the role of EWSR1-ETS fusion protein multiple genome, epigenome and transcriptome level studies were performed. In this review, the data from these studies were combined into a comprehensive overview. Presently, classical morphological predictive markers are used in the clinic and the therapy is dominantly based on systemic chemotherapy in combination with surgical interventions. Using sequencing, novel predictive markers and candidates for immuno- and targeted therapy were identified which were summarized in this review.
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Affiliation(s)
- Laurens G L Sand
- Department of Pathology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands.
| | - Karoly Szuhai
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands.
| | - Pancras C W Hogendoorn
- Department of Pathology, Leiden University Medical Center, Leiden 2333 ZA, The Netherlands.
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34
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Planesas JM, Pérez-Nueno VI, Borrell JI, Teixidó J. Studying the binding interactions of allosteric agonists and antagonists of the CXCR4 receptor. J Mol Graph Model 2015; 60:1-14. [PMID: 26080355 DOI: 10.1016/j.jmgm.2015.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 05/06/2015] [Accepted: 05/07/2015] [Indexed: 12/01/2022]
Abstract
Several examples of allosteric modulators of GPCRs have been reported recently in the literature, but understanding their molecular mechanism presents a new challenge for medicinal chemistry. For the specific case of the cellular receptor CXCR4, it is known that pepducins (lipidated fragments of intracellular GPCR loops) such as ATI-2341 modulate CXCR4 activity agonistically via an allosteric mechanism. Moreover, there are also examples of small organic molecules such as AMD11070 and GSK812397 which may also act as allosteric antagonists. However, incomplete knowledge of the ligand-binding sites has hampered a detailed molecular understanding of how these inhibitors work. Here, we attempt to answer this question by analysing the binding interactions between the CXCR4 receptor and the above-mentioned allosteric modulators. We propose two different allosteric binding sites, one located in the intracellular loops 1, 2 and 3 (ICL1, ICL2 and ICL3) which binds the pepducin agonist ATI-2341, and the other at a subsite of the main extracellular orthosteric binding pocket between extracellular loops 1 and 2 and the N-terminus, which binds the antagonists AMD11070 and GSK812397. Allosteric interactions between the CXCR4 and ATI-2341 were predicted by combining different modeling approaches. First, a rotational blind docking search was applied and the best poses were subsequently refined using flexible docking methods and molecular dynamic simulations. For the AMD11070 and GSK812397 antagonists, the entire CXCR4 protein surface was explored by blind docking in order to define the binding region. A second docking analysis by subsites was then performed to refine the allosteric interactions. Finally, we identified the binding residues that appear to be essential for CXCR4 allosteric modulators.
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Affiliation(s)
- Jesús M Planesas
- Grup d'Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain
| | - Violeta I Pérez-Nueno
- Grup d'Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain; Harmonic Pharma, Espace Transfert, 615 rue du Jardin Botanique, 54600 Villers lès Nancy, France.
| | - José I Borrell
- Grup d'Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain
| | - Jordi Teixidó
- Grup d'Enginyeria Molecular, Institut Químic de Sarriá (IQS), Universitat Ramon Llull, Barcelona, Spain.
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35
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Groß A, Brox R, Damm D, Tschammer N, Schmidt B, Eichler J. Ligand selectivity of a synthetic CXCR4 mimetic peptide. Bioorg Med Chem 2015; 23:4050-5. [PMID: 25801155 DOI: 10.1016/j.bmc.2015.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/20/2015] [Accepted: 03/02/2015] [Indexed: 11/17/2022]
Abstract
The chemokine receptor CXCR4 belongs to the family of seven-transmembrane G-protein coupled receptors (GPCRs). It is activated by its natural ligand SDF-1α. In addition, CXCR4, along with CCR5, serve as coreceptors during HIV-1 entry into its target cell. Recently, we introduced a CXCR4 mimetic peptide, termed CX4-M1, which presents the three extracellular loops (ECLs) of the receptor. CX4-M1 was shown to selectively bind to gp120 of X4-tropic, that is, CXCR4 using, HIV-1, as well as to peptides that present the V3-loops of these gp120 proteins. Furthermore, CX4-M1 selectively inhibits infection of cells with X4-tropic HIV-1. We have now adapted the sequence of the ECLs presented by CX4-M1 to the recently published crystal structure of CXCR4. The binding behavior, as well as the effect on HIV-1 infection, of the resulting peptide (CX4-Mc) was very similar to CX4-M1, validating retrospectively the original design of CX4-M1. A peptide presenting the ECLs of CCR5 (CR5-M), on the other hand, did neither bind to gp120 from X4-tropic HIV-1, nor did it inhibit infection of cells with X4-tropic HIV-1. Furthermore, we could show that CX4-M1, as well as CX4-Mc, but not CR5-M, are selectively recognized by anti-CXCR4 antibodies, bind to SDF-1α, and also inhibit SDF-1α signaling, extending the scope of selective functional CXCR4 mimicry through CX4-M1.
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Affiliation(s)
- Andrea Groß
- Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, Schuhstrasse 19, 91052 Erlangen, Germany
| | - Regine Brox
- Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, Schuhstrasse 19, 91052 Erlangen, Germany
| | - Dominik Damm
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Nuška Tschammer
- Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, Schuhstrasse 19, 91052 Erlangen, Germany
| | - Barbara Schmidt
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, University of Erlangen-Nurnberg, Schuhstrasse 19, 91052 Erlangen, Germany.
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36
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Wu CH, Wang CJ, Chang CP, Cheng YC, Song JS, Jan JJ, Chou MC, Ke YY, Ma J, Wong YC, Hsieh TC, Tien YC, Gullen EA, Lo CF, Cheng CY, Liu YW, Sadani AA, Tsai CH, Hsieh HP, Tsou LK, Shia KS. Function-oriented development of CXCR4 antagonists as selective human immunodeficiency virus (HIV)-1 entry inhibitors. J Med Chem 2015; 58:1452-65. [PMID: 25584630 DOI: 10.1021/jm501772w] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Motivated by the pivotal role of CXCR4 as an HIV entry co-receptor, we herein report a de novo hit-to-lead effort on the identification of subnanomolar purine-based CXCR4 antagonists against HIV-1 infection. Compound 24, with an EC50 of 0.5 nM against HIV-1 entry into host cells and an IC50 of 16.4 nM for inhibition of radioligand stromal-derived factor-1α (SDF-1α) binding to CXCR4, was also found to be highly selective against closely related chemokine receptors. We rationalized that compound 24 complementarily interacted with the critical CXCR4 residues that are essential for binding to HIV-1 gp120 V3 loop and subsequent viral entry. Compound 24 showed a 130-fold increase in anti-HIV activity compared to that of the marketed CXCR4 antagonist, AMD3100 (Plerixafor), whereas both compounds exhibited similar potency in mobilization of CXCR4(+)/CD34(+) stem cells at a high dose. Our study offers insight into the design of anti-HIV therapeutics devoid of major interference with SDF-1α function.
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Affiliation(s)
- Chien-Huang Wu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes , Miaoli County 35053, Taiwan, R.O.C
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37
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Qin L, Kufareva I, Holden LG, Wang C, Zheng Y, Zhao C, Fenalti G, Wu H, Han GW, Cherezov V, Abagyan R, Stevens RC, Handel TM. Structural biology. Crystal structure of the chemokine receptor CXCR4 in complex with a viral chemokine. Science 2015; 347:1117-22. [PMID: 25612609 DOI: 10.1126/science.1261064] [Citation(s) in RCA: 296] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chemokines and their receptors control cell migration during development, immune system responses, and in numerous diseases, including inflammation and cancer. The structural basis of receptor:chemokine recognition has been a long-standing unanswered question due to the challenges of structure determination for membrane protein complexes. Here, we report the crystal structure of the chemokine receptor CXCR4 in complex with the viral chemokine antagonist vMIP-II at 3.1 angstrom resolution. The structure revealed a 1:1 stoichiometry and a more extensive binding interface than anticipated from the paradigmatic two-site model. The structure helped rationalize a large body of mutagenesis data and together with modeling provided insights into CXCR4 interactions with its endogenous ligand CXCL12, its ability to recognize diverse ligands, and the specificity of CC and CXC receptors for their respective chemokines.
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Affiliation(s)
- Ling Qin
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA
| | - Irina Kufareva
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA.
| | - Lauren G Holden
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA
| | - Chong Wang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yi Zheng
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA
| | - Chunxia Zhao
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA
| | - Gustavo Fenalti
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Huixian Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Gye Won Han
- Department of Chemistry, Bridge Institute. Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | | | - Ruben Abagyan
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA
| | - Raymond C Stevens
- Department of Chemistry, Bridge Institute. Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.
| | - Tracy M Handel
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA.
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38
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Stoichiometry and geometry of the CXC chemokine receptor 4 complex with CXC ligand 12: molecular modeling and experimental validation. Proc Natl Acad Sci U S A 2014; 111:E5363-72. [PMID: 25468967 DOI: 10.1073/pnas.1417037111] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chemokines and their receptors regulate cell migration during development, immune system function, and in inflammatory diseases, making them important therapeutic targets. Nevertheless, the structural basis of receptor:chemokine interaction is poorly understood. Adding to the complexity of the problem is the persistently dimeric behavior of receptors observed in cell-based studies, which in combination with structural and mutagenesis data, suggest several possibilities for receptor:chemokine complex stoichiometry. In this study, a combination of computational, functional, and biophysical approaches was used to elucidate the stoichiometry and geometry of the interaction between the CXC-type chemokine receptor 4 (CXCR4) and its ligand CXCL12. First, relevance and feasibility of a 2:1 stoichiometry hypothesis was probed using functional complementation experiments with multiple pairs of complementary nonfunctional CXCR4 mutants. Next, the importance of dimers of WT CXCR4 was explored using the strategy of dimer dilution, where WT receptor dimerization is disrupted by increasing expression of nonfunctional CXCR4 mutants. The results of these experiments were supportive of a 1:1 stoichiometry, although the latter could not simultaneously reconcile existing structural and mutagenesis data. To resolve the contradiction, cysteine trapping experiments were used to derive residue proximity constraints that enabled construction of a validated 1:1 receptor:chemokine model, consistent with the paradigmatic two-site hypothesis of receptor activation. The observation of a 1:1 stoichiometry is in line with accumulating evidence supporting monomers as minimal functional units of G protein-coupled receptors, and suggests transmission of conformational changes across the dimer interface as the most probable mechanism of altered signaling by receptor heterodimers.
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39
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Nomiyama H, Yoshie O. Functional roles of evolutionary conserved motifs and residues in vertebrate chemokine receptors. J Leukoc Biol 2014; 97:39-47. [PMID: 25416815 DOI: 10.1189/jlb.2ru0614-290r] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Chemokine receptors regulate cell migration and homing. They belong to the rhodopsin-like family of GPCRs. Their ancestor genes emerged in the early stages of vertebrate evolution. Since then, the family has been greatly expanded through whole and segmental genome duplication events. During evolution, many amino acid changes have been introduced in individual chemokine receptors, but certain motifs and residues are highly conserved. Previously, we proposed a nomenclature system of the vertebrate chemokine receptors based on their evolutionary history and phylogenetic analyses. With the use of this classification system, we are now able to confidently assign the species orthologs of vertebrate chemokine receptors. Here, we systematically analyze conserved motifs and residues of each group of orthologous chemokine receptors that may play important roles in their signaling and biologic functions. Our present analysis may provide useful information on how individual chemokine receptors are activated upon ligand binding.
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Affiliation(s)
- Hisayuki Nomiyama
- *Department of Molecular Enzymology, Kumamoto University Graduate School of Medical Sciences, Honjo, Kumamoto, Japan; and Department of Microbiology, Kinki University Faculty of Medicine, Osaka-Sayama, Osaka, Japan
| | - Osamu Yoshie
- *Department of Molecular Enzymology, Kumamoto University Graduate School of Medical Sciences, Honjo, Kumamoto, Japan; and Department of Microbiology, Kinki University Faculty of Medicine, Osaka-Sayama, Osaka, Japan
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40
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Role of 3D Structures in Understanding, Predicting, and Designing Molecular Interactions in the Chemokine Receptor Family. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/7355_2014_77] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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41
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Kashima K, Watanabe M, Sato Y, Hata J, Ishii N, Aoki Y. Inhibition of metastasis of rhabdomyosarcoma by a novel neutralizing antibody to CXC chemokine receptor-4. Cancer Sci 2014; 105:1343-50. [PMID: 25154453 PMCID: PMC4462355 DOI: 10.1111/cas.12490] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 07/17/2014] [Accepted: 07/22/2014] [Indexed: 12/18/2022] Open
Abstract
Rhabdomyosarcoma is the most common soft tissue sarcoma affecting children, and the overall cure rate of children with metastatic disease remains below 30%. The CXC chemokine receptor-4 (CXCR4)/stromal cell-derived factor-1 (SDF1) axis has been implicated in the promotion of metastatic potential in several tumors. In this study, we developed a novel anti-CXCR4 mAb, CF172, and investigated its antimetastatic activity against rhabdomyosarcoma cells in vitro and in vivo, to evaluate its potential as a therapeutic antibody to treat rhabdomyosarcoma. The CF172 molecule showed a specific binding reactivity against human CXCR4, as well as a specific neutralizing activity against CXCR4/SDF1 signal transduction. Using CF172, we determined that SJCRH30 rhabdomyosarcoma cells expressed high levels of CXCR4. In addition, CF172 was found to inhibit the SDF1-induced migration activity of SJCRH30 cells in vitro. Using xenograft models of SJCRH30 cells, we carried out in vivo efficacy studies for peritoneal and lymph node metastasis, which were clinically observed in rhabdomyosarcoma. These studies indicated that CF172 significantly decreased both types of metastasis of SJCRH30. In conclusion, we found that a novel anti-CXCR4 mAb, CF172, with specific reactivity against human CXCR4, prevented peritoneal metastasis and lymph node metastasis of rhabdomyosarcoma in animal models. These results suggest that CF172 is a potential antimetastasis therapeutic antibody for rhabdomyosarcoma treatment.
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Affiliation(s)
- Kenji Kashima
- Research Division, Chugai Pharmaceutical Co. Ltd., Kanagawa, Japan
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42
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Zhang C, Du C, Feng Z, Zhu J, Li Y. Hologram Quantitative Structure Activity Relationship, Docking, and Molecular Dynamics Studies of Inhibitors for CXCR4. Chem Biol Drug Des 2014; 85:119-36. [DOI: 10.1111/cbdd.12377] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 05/31/2014] [Accepted: 06/02/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Chongqian Zhang
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology; Soochow University; Suzhou 215123 China
| | - Chunmiao Du
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology; Soochow University; Suzhou 215123 China
| | - Zhiwei Feng
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology; Soochow University; Suzhou 215123 China
| | - Jingyu Zhu
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology; Soochow University; Suzhou 215123 China
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM) and Collaborative Innovation Center of Suzhou Nano Science and Technology; Soochow University; Suzhou 215123 China
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43
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Chen G, Wang W, Meng S, Zhang L, Wang W, Jiang Z, Yu M, Cui Q, Li M. CXC chemokine CXCL12 and its receptor CXCR4 in tree shrews (Tupaia belangeri): structure, expression and function. PLoS One 2014; 9:e98231. [PMID: 24858548 PMCID: PMC4032326 DOI: 10.1371/journal.pone.0098231] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 04/30/2014] [Indexed: 12/11/2022] Open
Abstract
Chemokines are small secreted proteins functionally involved in the immune system's regulation of lymphocyte migration across numerous mammalian species. Given its growing popularity in immunological models, we investigated the structure and function of chemokine CXCL12 protein in tree shrews. We found that CXCL12 and its receptor CXCR4 in tree shrew had structural similarities to their homologous human proteins. Phylogenetic analysis supports the view that tree shrew is evolutionarily-close to the primates. Our results also showed that the human recombinant CXCL12 protein directly enhanced the migration of tree shrew's lymphocytes in vitro, while AMD3100 enhanced the mobilization of hematopoietic progenitor cells (HPCs) from bone marrow into peripheral blood in tree shrew in vivo. Collectively, these findings suggested that chemokines in tree shrews may play the same or similar roles as those in humans, and that the tree shrew is a viable animal model for studying human immunological diseases.
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Affiliation(s)
- Guiyuan Chen
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming, China
- Department of Biochemistry & Molecular Biology, School of Basic Medicine, Dali University, Dali, China
| | - Wei Wang
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming, China
- Department of Rheumatology & Immunology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Shengke Meng
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming, China
| | - Lichao Zhang
- Department of Hepatobiliary Surgery, Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Wenxue Wang
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming, China
| | - Zongmin Jiang
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming, China
| | - Min Yu
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming, China
| | - Qinghua Cui
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming, China
| | - Meizhang Li
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Yunnan University, Kunming, China
- * E-mail:
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Molecular recognition of CXCR4 by a dual tropic HIV-1 gp120 V3 loop. Biophys J 2014; 105:1502-14. [PMID: 24048002 DOI: 10.1016/j.bpj.2013.07.049] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 07/16/2013] [Accepted: 07/29/2013] [Indexed: 01/01/2023] Open
Abstract
HIV-1 cell entry is initiated by the interaction of the viral envelope glycoprotein gp120 with CD4, and chemokine coreceptors CXCR4 and CCR5. The molecular recognition of CXCR4 or CCR5 by the HIV-1 gp120 is mediated through the V3 loop, a fragment of gp120. The binding of the V3 loop to CXCR4 or CCR5 determines the cell tropism of HIV-1 and constitutes a key step before HIV-1 cell entry. Thus, elucidating the molecular recognition of CXCR4 by the V3 loop is important for understanding HIV-1 viral infectivity and tropism, and for the design of HIV-1 inhibitors. We employed a comprehensive set of computational tools, predominantly based on free energy calculations and molecular-dynamics simulations, to investigate the molecular recognition of CXCR4 by a dual tropic V3 loop. We report what is, to our knowledge, the first HIV-1 gp120 V3 loop:CXCR4 complex structure. The computationally derived structure reveals an abundance of polar and nonpolar intermolecular interactions contributing to the HIV-1 gp120:CXCR4 binding. Our results are in remarkable agreement with previous experimental findings. Therefore, this work sheds light on the functional role of HIV-1 gp120 V3 loop and CXCR4 residues associated with HIV-1 coreceptor activity.
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45
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Tamamis P, Floudas CA. Elucidating a key component of cancer metastasis: CXCL12 (SDF-1α) binding to CXCR4. J Chem Inf Model 2014; 54:1174-88. [PMID: 24660779 PMCID: PMC4004218 DOI: 10.1021/ci500069y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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The chemotactic signaling induced
by the binding of chemokine CXCL12
(SDF-1α) to chemokine receptor CXCR4 is of significant biological
importance and is a potential therapeutic axis against HIV-1. However,
as CXCR4 is overexpressed in certain cancer cells, the CXCL12:CXCR4
signaling is involved in tumor metastasis, progression, angiogenesis,
and survival. Motivated by the pivotal role of the CXCL12:CXCR4 axis
in cancer, we employed a comprehensive set of computational tools,
predominantly based on free energy calculations and molecular dynamics
simulations, to obtain insights into the molecular recognition of
CXCR4 by CXCL12. We report, what is to our knowledge, the first computationally
derived CXCL12:CXCR4 complex structure which is in remarkable agreement
with experimental findings and sheds light into the functional role
of CXCL12 and CXCR4 residues which are associated with binding and
signaling. Our results reveal that the CXCL12 N-terminal domain is
firmly bound within the CXCR4 transmembrane domain, and the central
24–50 residue domain of CXCL12 interacts with the upper N-terminal
domain of CXCR4. The stability of the CXCL12:CXCR4 complex structure
is attributed to an abundance of nonpolar and polar intermolecular
interactions, including salt bridges formed between positively charged
CXCL12 residues and negatively charged CXCR4 residues. The success
of the computational protocol can mainly be attributed to the nearly
exhaustive docking conformational search, as well as the heterogeneous
dielectric implicit water-membrane-water model used to simulate and
select the optimum conformations. We also recently utilized this protocol
to elucidate the binding of an HIV-1 gp120 V3 loop in complex with
CXCR4, and a comparison between the molecular recognition of CXCR4
by CXCL12 and the HIV-1 gp120 V3 loop shows that both CXCL12 and the
HIV-1 gp120 V3 loop share the same CXCR4 binding pocket, as they mostly
interact with the same CXCR4 residues.
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Affiliation(s)
- Phanourios Tamamis
- Department of Chemical and Biological Engineering, Princeton University , New Jersey 08544, United States
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46
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Ray-Saha S, Huber T, Sakmar TP. Antibody epitopes on g protein-coupled receptors mapped with genetically encoded photoactivatable cross-linkers. Biochemistry 2014; 53:1302-10. [PMID: 24490954 PMCID: PMC3985944 DOI: 10.1021/bi401289p] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
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We
developed a strategy for creating epitope maps of monoclonal
antibodies (mAbs) that bind to G protein-coupled receptors (GPCRs)
containing photo-cross-linkers. Using human CXC chemokine receptor
4 (CXCR4) as a model system, we genetically incorporated the photolabile
unnatural amino acid p-azido-l-phenylalanine
(azF) at various positions within extracellular loop 2 (EC2). We then
mapped the interactions of the azF-CXCR4 variants with mAb 12G5 using
targeted loss-of-function studies and photo-cross-linking in whole
cells in a microplate-based format. We used a novel variation of a
whole cell enzyme-linked immunosorbent assay to quantitate cross-linking
efficiency. 12G5 cross-linked primarily to residues 184, 178, and
189 in EC2 of CXCR4. Mapping of the data to the crystal structure
of CXCR4 showed a distinct mAb epitope footprint with the photo-cross-linked
residues clustered around the loss-of-function sites. We also used
the targeted photo-cross-linking approach to study the interaction
of human CC chemokine receptor 5 (CCR5) with PRO 140, a humanized
mAb that inhibits human immunodeficiency virus-1 cellular entry, and
2D7. The mAbs produced distinct cross-linking patterns on EC2 of CCR5.
PRO 140 cross-linked primarily to residues 174 and 175 at the amino-terminal
end of EC2, and 2D7 cross-linked mainly to residues 170, 176, and
184. These results were mapped to the recent crystal structure of
CCR5 in complex with maraviroc, showing cross-linked residues at the
tip of the maraviroc binding crevice formed by EC2. As a strategy
for mapping mAb epitopes on GPCRs, our targeted photo-cross-linking
method is complementary to loss-of-function mutagenesis results and
should be especially useful for studying mAbs with discontinuous epitopes.
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Affiliation(s)
- Sarmistha Ray-Saha
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , 1230 York Avenue, New York, New York 10065, United States
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Neutralising properties of peptides derived from CXCR4 extracellular loops towards CXCL12 binding and HIV-1 infection. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1031-41. [PMID: 24480462 DOI: 10.1016/j.bbamcr.2014.01.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Revised: 12/23/2013] [Accepted: 01/17/2014] [Indexed: 01/01/2023]
Abstract
The chemokine receptor CXCR4 interacts with a single endogenous chemokine, CXCL12, and regulates a wide variety of physiological and pathological processes including inflammation and metastasis development. CXCR4 also binds the HIV-1 envelope glycoprotein, gp120, resulting in viral entry into host cells. Therefore, CXCR4 and its ligands represent valuable drug targets. In this study, we investigated the inhibitory properties of synthetic peptides derived from CXCR4 extracellular loops (ECL1-X4, ECL2-X4 and ECL3-X4) towards HIV-1 infection and CXCL12-mediated receptor activation. Among these peptides, ECL1-X4 displayed anti-HIV-1 activity against X4, R5/X4 and R5 viruses (IC50=24 to 76μM) in cell viability assay without impairing physiological CXCR4-CXCL12 signalling. In contrast, ECL2-X4 only inhibited X4 and R5/X4 strains, interfering with HIV-entry into cells. At the same time, ECL2-X4 strongly and specifically interacted with CXCL12, blocking its binding to CXCR4 and its second receptor, CXCR7 (IC50=20 and 100μM). Further analysis using mutated and truncated peptides showed that ECL2 of CXCR4 forms multiple contacts with the gp120 protein and the N-terminus of CXCL12. Chemokine neutralisation was mainly driven by four aspartates and the C-terminal residues of ECL2-X4. These results demonstrate that ECL2 represents an important structural determinant in CXCR4 activation. We identified the putative site for the binding of CXCL12 N-terminus and provided new structural elements to explain the recognition of gp120 and dimeric CXCR4 ligands.
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48
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Aiamkitsumrit B, Dampier W, Antell G, Rivera N, Martin-Garcia J, Pirrone V, Nonnemacher MR, Wigdahl B. Bioinformatic analysis of HIV-1 entry and pathogenesis. Curr HIV Res 2014; 12:132-61. [PMID: 24862329 PMCID: PMC4382797 DOI: 10.2174/1570162x12666140526121746] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 03/18/2014] [Accepted: 05/06/2014] [Indexed: 02/07/2023]
Abstract
The evolution of human immunodeficiency virus type 1 (HIV-1) with respect to co-receptor utilization has been shown to be relevant to HIV-1 pathogenesis and disease. The CCR5-utilizing (R5) virus has been shown to be important in the very early stages of transmission and highly prevalent during asymptomatic infection and chronic disease. In addition, the R5 virus has been proposed to be involved in neuroinvasion and central nervous system (CNS) disease. In contrast, the CXCR4-utilizing (X4) virus is more prevalent during the course of disease progression and concurrent with the loss of CD4(+) T cells. The dual-tropic virus is able to utilize both co-receptors (CXCR4 and CCR5) and has been thought to represent an intermediate transitional virus that possesses properties of both X4 and R5 viruses that can be encountered at many stages of disease. The use of computational tools and bioinformatic approaches in the prediction of HIV-1 co-receptor usage has been growing in importance with respect to understanding HIV-1 pathogenesis and disease, developing diagnostic tools, and improving the efficacy of therapeutic strategies focused on blocking viral entry. Current strategies have enhanced the sensitivity, specificity, and reproducibility relative to the prediction of co-receptor use; however, these technologies need to be improved with respect to their efficient and accurate use across the HIV-1 subtypes. The most effective approach may center on the combined use of different algorithms involving sequences within and outside of the env-V3 loop. This review focuses on the HIV-1 entry process and on co-receptor utilization, including bioinformatic tools utilized in the prediction of co-receptor usage. It also provides novel preliminary analyses for enabling identification of linkages between amino acids in V3 with other components of the HIV-1 genome and demonstrates that these linkages are different between X4 and R5 viruses.
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Affiliation(s)
| | | | | | | | | | | | | | - Brian Wigdahl
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N. 15th Street, Philadelphia, PA 19102.
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49
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Xu L, Li Y, Sun H, Li D, Hou T. Structural basis of the interactions between CXCR4 and CXCL12/SDF-1 revealed by theoretical approaches. MOLECULAR BIOSYSTEMS 2013; 9:2107-17. [PMID: 23702796 DOI: 10.1039/c3mb70120d] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The G protein-coupled chemokine receptor CXCR4 is implicated in a variety of physiological responses that also share several downstream effectors involved in multiple pathological processes. The interaction between CXCR4 and its natural ligand CXCL12/stromal-derived factor-1 (SDF-1) plays important roles in cancer metastasis, HIV-1 infection, and inflammatory diseases. Therefore, investigating the CXCR4-CXCL12 interaction is critical for understanding the molecular mechanisms of the modulation of chemokine-receptor functions and designing new pharmaceutical agents to target the CXCR4-CXCL12 pathway. Based on known experimental data, the interaction between CXCR4 and CXCL12 was predicted by an integrated protocol, which combines protein-protein docking, molecular dynamics (MD) simulations, Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) binding free energy calculations, and MM/GBSA binding free energy decomposition analysis. The predicted CXCR4-CXCL12 binding pattern is in good agreement with the experimental data. Analysis of the binding structure reveals an obvious electrostatic complementarity between CXCR4 and CXCL12. Moreover, significant conformational rearrangements were observed during the 50 ns MD simulations. In particular, the basic Lys1 at the CXCL12 N-terminus, an essential residue in receptor activation, forms a strong polar interaction with the Glu32 in the CXCR4 extracellular region. It facilitates the significant movement of TM5 and TM6 in the conformational transition, which is coupled to the association with the intracellular signal transduction pathways via heterotrimer G-protein. Based on the dynamic and energetic analyses, a two-site binding model was proposed. We believe that our study provides useful information for understanding the mechanisms of CXCR4 ligand binding and structure-based drug design of CXCR4.
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Affiliation(s)
- Lei Xu
- Institute of Functional Nano & Soft Materials FUNSOM and Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, Jiangsu 215123, China
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50
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Choi WT, Kumar S, Madani N, Han X, Tian S, Dong CZ, Liu D, Duggineni S, Yuan J, Sodroski JG, Huang Z, An J. A novel synthetic bivalent ligand to probe chemokine receptor CXCR4 dimerization and inhibit HIV-1 entry. Biochemistry 2012; 51:7078-86. [PMID: 22897429 DOI: 10.1021/bi2016712] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemokine receptor CXCR4 is one of two principal coreceptors for the entry of HIV-1 into target cells. CXCR4 is known to form homodimers. We previously demonstrated that the amino terminus of viral macrophage protein II (vMIP-II) is the major determinant for CXCR4 recognition, and that V1 peptide derived from the N-terminus of vMIP-II (1-21 residues) showed significant CXCR4 binding. Interestingly, an all-d-amino acid analogue of V1 peptide, DV1 peptide, displayed an even higher binding affinity and strong antiviral activity in inhibiting the replication of CXCR4-dependent HIV-1 strains. In this study, we synthetically linked two DV1 peptides with the formation of a disulfide bond between the two cysteine residues present in the peptide sequence to generate a dimeric molecule potentially capable of interacting with two CXCR4 receptors. DV1 dimer exhibited enhanced binding affinity and antiviral activity compared with those of DV1 monomer. Ligand binding site mapping experiments showed that DV1 dimer overlaps with HIV-1 gp120 on CXCR4 binding sites, including several transmembrane (TM) residues located close to the extracellular side and the N-terminus of CXCR4. This finding was supported by the molecular modeling of CXCR4 dimer-DV1 dimer interaction based on the crystal structure of CXCR4, which showed that DV1 dimer is capable of interacting with the CXCR4 dimeric structure by allowing the N-terminus of each DV1 monomer to reach into the binding pocket of CXCR4 monomer. The development of this bivalent ligand provides a tool for further probing the functions of CXCR4 dimerization and studying CXCR4 heterodimerization with other receptors.
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Affiliation(s)
- Won-Tak Choi
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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