1
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Negro S, Zanetti G, Mattarei A, Valentini A, Megighian A, Tombesi G, Zugno A, Dianin V, Pirazzini M, Fillo S, Lista F, Rigoni M, Montecucco C. An Agonist of the CXCR4 Receptor Strongly Promotes Regeneration of Degenerated Motor Axon Terminals. Cells 2019; 8:E1183. [PMID: 31575088 PMCID: PMC6829515 DOI: 10.3390/cells8101183] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 12/19/2022] Open
Abstract
The activation of the G-protein coupled receptor CXCR4 by its ligand CXCL12α is involved in a large variety of physiological and pathological processes, including the growth of B cells precursors and of motor axons, autoimmune diseases, stem cell migration, inflammation, and several neurodegenerative conditions. Recently, we demonstrated that CXCL12α potently stimulates the functional recovery of damaged neuromuscular junctions via interaction with CXCR4. This result prompted us to test the neuroregeneration activity of small molecules acting as CXCR4 agonists, endowed with better pharmacokinetics with respect to the natural ligand. We focused on NUCC-390, recently shown to activate CXCR4 in a cellular system. We designed a novel and convenient chemical synthesis of NUCC-390, which is reported here. NUCC-390 was tested for its capability to induce the regeneration of motor axon terminals completely degenerated by the presynaptic neurotoxin α-Latrotoxin. NUCC-390 was found to strongly promote the functional recovery of the neuromuscular junction, as assayed by electrophysiology and imaging. This action is CXCR4 dependent, as it is completely prevented by AMD3100, a well-characterized CXCR4 antagonist. These data make NUCC-390 a strong candidate to be tested in human therapy to promote nerve recovery of function after different forms of neurodegeneration.
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Affiliation(s)
- Samuele Negro
- Department of Biomedical Sciences, University of Padua, Padua 35131, Italy.
| | - Giulia Zanetti
- Department of Biomedical Sciences, University of Padua, Padua 35131, Italy.
| | - Andrea Mattarei
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua 35131, Italy.
| | - Alice Valentini
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua 35131, Italy.
| | - Aram Megighian
- Department of Biomedical Sciences, University of Padua, Padua 35131, Italy.
- Padua Neuroscience Institute, Padua 35131, Italy.
| | - Giulia Tombesi
- Department of Biology, University of Padua, Padua 35131, Italy.
| | - Alessandro Zugno
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua 35131, Italy.
| | - Valentina Dianin
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua 35131, Italy.
| | - Marco Pirazzini
- Department of Biomedical Sciences, University of Padua, Padua 35131, Italy.
| | - Silvia Fillo
- Center of Medical and Veterinary Research of the Ministry of Defence, Rome 00184, Italy.
| | - Florigio Lista
- Center of Medical and Veterinary Research of the Ministry of Defence, Rome 00184, Italy.
| | - Michela Rigoni
- Department of Biomedical Sciences, University of Padua, Padua 35131, Italy.
| | - Cesare Montecucco
- Department of Biomedical Sciences, University of Padua, Padua 35131, Italy.
- CNR Institute of Neuroscience, Padua 35131, Italy.
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2
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Arimont M, Hoffmann C, de Graaf C, Leurs R. Chemokine Receptor Crystal Structures: What Can Be Learned from Them? Mol Pharmacol 2019; 96:765-777. [PMID: 31266800 DOI: 10.1124/mol.119.117168] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 06/21/2019] [Indexed: 12/18/2022] Open
Abstract
Chemokine receptors belong to the class A of G protein-coupled receptors (GPCRs) and are implicated in a wide variety of physiologic functions, mostly related to the homeostasis of the immune system. Chemokine receptors are also involved in multiple pathologic processes, including immune and autoimmune diseases, as well as cancer. Hence, several members of this GPCR subfamily are considered to be very relevant therapeutic targets. Since drug discovery efforts can be significantly reinforced by the availability of crystal structures, substantial efforts in the area of chemokine receptor structural biology could dramatically increase the outcome of drug discovery campaigns. This short review summarizes the available data on chemokine receptor crystal structures, discusses the numerous applications from chemokine receptor structures that can enhance the daily work of molecular pharmacologists, and describes the challenges and pitfalls to consider when relying on crystal structures for further research applications. SIGNIFICANCE STATEMENT: This short review summarizes the available data on chemokine receptor crystal structures, discusses the numerous applications from chemokine receptor structures that can enhance the daily work of molecular pharmacologists, and describes the challenges and pitfalls to consider when relying on crystal structures for further research applications.
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Affiliation(s)
- Marta Arimont
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (M.A., R.L.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University, Jena, Germany (C.H.); and Sosei Heptares, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Carsten Hoffmann
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (M.A., R.L.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University, Jena, Germany (C.H.); and Sosei Heptares, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Chris de Graaf
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (M.A., R.L.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University, Jena, Germany (C.H.); and Sosei Heptares, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Rob Leurs
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (M.A., R.L.); Institute for Molecular Cell Biology, Centre for Molecular Biomedicine, University Hospital Jena, Friedrich Schiller University, Jena, Germany (C.H.); and Sosei Heptares, Great Abington, Cambridge, United Kingdom (C.d.G.)
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3
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Insight into structural requirements for selective and/or dual CXCR3 and CXCR4 allosteric modulators. Eur J Med Chem 2018; 154:68-90. [PMID: 29777988 DOI: 10.1016/j.ejmech.2018.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 04/18/2018] [Accepted: 05/09/2018] [Indexed: 11/21/2022]
Abstract
Based on the previously published pyrazolopyridine-based hit compound for which negative allosteric modulation of both CXCR3 and CXCR4 receptors was disclosed, we designed, synthesized and biologically evaluated a set of novel, not only negative, but also positive allosteric modulators with preserved pyrazolopyridine core. Compound 9e is a dual negative modulator, inhibiting G protein activity of both receptors. For CXCR4 receptor para-substituted aromatic group of compounds distinguishes between negative and positive modulation. Para-methoxy substitution leads to functional antagonism, while para-chloro triggers agonism. Additionally, we discovered that chemotaxis is not completely correlated with G protein pathways. This is the first work in which we have on a series of compounds successfully demonstrated that it is possible to produce selective as well as dual-acting modulators of chemokine receptors, which is very promising for future research in the field of discovery of selective or dual modulators of chemokine receptors.
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4
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Marshall GR, Ballante F. Limiting Assumptions in the Design of Peptidomimetics. Drug Dev Res 2017; 78:245-267. [DOI: 10.1002/ddr.21406] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
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5
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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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6
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Arnatt CK, Zhang Y. Bivalent ligands targeting chemokine receptor dimerization: molecular design and functional studies. Curr Top Med Chem 2016; 14:1606-18. [PMID: 25159160 DOI: 10.2174/1568026614666140827144752] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 05/14/2014] [Accepted: 05/14/2014] [Indexed: 12/27/2022]
Abstract
Increasing evidence has shown that chemokine receptors may form functional dimers with unique pharmacological profiles. A common practice to characterize such G protein-coupled receptor dimerization processes is to apply bivalent ligands as chemical probes which can interact with both receptors simultaneously. Currently, two chemokine receptor dimers have been studied by applying bivalent compounds: the CXCR4-CXCR4 homodimer and the CCR5-MOR heterodimer. These bivalent compounds have revealed how dimerization influences receptor function and may lead to novel therapeutics. Future design of bivalent ligands for chemokine receptor dimers may be aided with the recently available CXCR4 homodimer, and CCR5 monomer crystal structures by more accurately simulating chemokine receptors and their dimers.
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Affiliation(s)
| | - Yan Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, 800 East Leigh Street, Richmond, VA 23298, USA.
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7
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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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8
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Thiele S, Mungalpara J, Steen A, Rosenkilde MM, Våbenø J. Determination of the binding mode for the cyclopentapeptide CXCR4 antagonist FC131 using a dual approach of ligand modifications and receptor mutagenesis. Br J Pharmacol 2015; 171:5313-29. [PMID: 25039237 DOI: 10.1111/bph.12842] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 06/25/2014] [Accepted: 07/08/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND AND PURPOSE The cyclopentapeptide FC131 (cyclo(-L-Arg(1) -L-Arg(2) -L-2-Nal(3) -Gly(4) -D-Tyr(5) -)) is an antagonist at the CXC chemokine receptor CXCR4, which plays a role in human immunodeficiency virus infection, cancer and stem cell recruitment. Binding modes for FC131 in CXCR4 have previously been suggested based on molecular docking guided by structure-activity relationship (SAR) data; however, none of these have been verified by in vitro experiments. EXPERIMENTAL APPROACH Heterologous (125) I-12G5-competition binding and functional assays (inhibition of CXCL12-mediated activation) of FC131 and three analogues were performed on wild-type CXCR4 and 25 receptor mutants. Computational modelling was used to rationalize the experimental data. KEY RESULTS The Arg(2) and 2-Nal(3) side chains of FC131 interact with residues in TM-3 (His(113) , Asp(171) ) and TM-5 (hydrophobic pocket) respectively. Arg(1) forms charge-charge interactions with Asp(187) in ECL-2, while D-Tyr(5) points to the extracellular side of CXCR4. Furthermore, the backbone of FC131 interacts with the chemokine receptor-conserved Glu(288) via two water molecules. Intriguingly, Tyr(116) and Glu(288) form a H-bond in CXCR4 crystal structures and mutation of either residue to Ala abolishes CXCR4 activity. CONCLUSIONS AND IMPLICATIONS Ligand modification, receptor mutagenesis and computational modelling approaches were used to identify the binding mode of FC131 in CXCR4, which was in agreement with binding modes suggested from previous SAR studies. Furthermore, insights into the mechanism for CXCR4 activation by CXCL12 were gained. The combined findings will facilitate future design of novel CXCR4 antagonists.
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Affiliation(s)
- S Thiele
- Laboratory for Molecular Pharmacology, Department of Neuroscience and Pharmacology, Faculty of Health and Medical Sciences, The Panum Institute, University of Copenhagen, Copenhagen, Denmark
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9
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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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10
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Oishi S, Kuroyanagi T, Kubo T, Montpas N, Yoshikawa Y, Misu R, Kobayashi Y, Ohno H, Heveker N, Furuya T, Fujii N. Development of Novel CXC Chemokine Receptor 7 (CXCR7) Ligands: Selectivity Switch from CXCR4 Antagonists with a Cyclic Pentapeptide Scaffold. J Med Chem 2015; 58:5218-25. [DOI: 10.1021/acs.jmedchem.5b00216] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Shinya Oishi
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Tomoko Kuroyanagi
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Tatsuhiko Kubo
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Nicolas Montpas
- Département
de Biochimie, Université de Montréal, Montréal, H3T 1J4, Canada
- Research Centre,
Sainte-Justine Hospital, University of Montreal, Montréal, H3T 1C5, Canada
| | - Yasushi Yoshikawa
- Drug Discovery Department, Research & Development Division, PharmaDesign Inc., 2-19-8 Hatchobori, Chuo-ku, Tokyo, 104-0032, Japan
| | - Ryosuke Misu
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yuka Kobayashi
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hiroaki Ohno
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Nikolaus Heveker
- Département
de Biochimie, Université de Montréal, Montréal, H3T 1J4, Canada
- Research Centre,
Sainte-Justine Hospital, University of Montreal, Montréal, H3T 1C5, Canada
| | - Toshio Furuya
- Drug Discovery Department, Research & Development Division, PharmaDesign Inc., 2-19-8 Hatchobori, Chuo-ku, Tokyo, 104-0032, Japan
| | - Nobutaka Fujii
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto, 606-8501, Japan
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11
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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: 283] [Impact Index Per Article: 31.4] [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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12
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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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13
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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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14
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Yeudall WA, Miyazaki H. Chemokines and squamous cancer of the head and neck: targets for therapeutic intervention? Expert Rev Anticancer Ther 2014; 7:351-60. [PMID: 17338654 DOI: 10.1586/14737140.7.3.351] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The biological properties of squamous carcinoma cells are intimately regulated by a multitude of cytokines and growth factors; the most well studied of these include epidermal growth factor receptor agonists and members of the transforming growth factor-beta family. The recent explosion of research in the field of chemokine function as a mediator of tumor progression has led to the possibility that these small, immunomodulatory proteins also play key roles in squamous carcinogenesis and may, therefore, be potential targets for novel therapeutic approaches.
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MESH Headings
- Amino Acid Motifs
- Amino Acid Sequence
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Carcinoma, Squamous Cell/blood supply
- Carcinoma, Squamous Cell/drug therapy
- Carcinoma, Squamous Cell/physiopathology
- Cell Survival
- Cell Transformation, Neoplastic
- Chemokines/antagonists & inhibitors
- Chemokines/physiology
- Chemokines, CXC/antagonists & inhibitors
- Chemokines, CXC/physiology
- Disease Progression
- Drug Design
- ErbB Receptors/antagonists & inhibitors
- ErbB Receptors/physiology
- Head and Neck Neoplasms/blood supply
- Head and Neck Neoplasms/drug therapy
- Head and Neck Neoplasms/physiopathology
- Humans
- Molecular Sequence Data
- Neoplasm Invasiveness
- Neoplasm Proteins/antagonists & inhibitors
- Neoplasm Proteins/physiology
- Neovascularization, Pathologic/drug therapy
- Neovascularization, Pathologic/physiopathology
- Receptors, Chemokine/drug effects
- Receptors, Chemokine/physiology
- Sequence Alignment
- Sequence Homology, Amino Acid
- Signal Transduction
- Transforming Growth Factor beta/antagonists & inhibitors
- Transforming Growth Factor beta/physiology
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Affiliation(s)
- W Andrew Yeudall
- Virginia Commonwealth University School of Dentistry, Philips Institute for Oral & Craniofacial Molecular Biology, Department of Biochemistry and Massey Cancer Center, Richmond, VA 23298, USA.
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15
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Karaboga AS, Planesas JM, Petronin F, Teixidó J, Souchet M, Pérez-Nueno VI. Highly SpecIfic and Sensitive Pharmacophore Model for Identifying CXCR4 Antagonists. Comparison with Docking and Shape-Matching Virtual Screening Performance. J Chem Inf Model 2013; 53:1043-56. [DOI: 10.1021/ci400037y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Arnaud S. Karaboga
- Harmonic Pharma, Espace Transfert, 615 rue du Jardin Botanique, 54600
Villers lès Nancy, France
| | - Jesús M. Planesas
- Grup d’Enginyeria Molecular,
Institut Químic de Sarrià (IQS), Universitat Ramon Llull, Barcelona, Spain
| | - Florent Petronin
- Harmonic Pharma, Espace Transfert, 615 rue du Jardin Botanique, 54600
Villers lès Nancy, France
| | - Jordi Teixidó
- Grup d’Enginyeria Molecular,
Institut Químic de Sarrià (IQS), Universitat Ramon Llull, Barcelona, Spain
| | - Michel Souchet
- Harmonic Pharma, Espace Transfert, 615 rue du Jardin Botanique, 54600
Villers lès Nancy, France
| | - Violeta I. Pérez-Nueno
- Harmonic Pharma, Espace Transfert, 615 rue du Jardin Botanique, 54600
Villers lès Nancy, France
- Grup d’Enginyeria Molecular,
Institut Químic de Sarrià (IQS), Universitat Ramon Llull, Barcelona, Spain
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16
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Mungalpara J, Thiele S, Eriksen Ø, Eksteen J, Rosenkilde MM, Våbenø J. Rational Design of Conformationally Constrained Cyclopentapeptide Antagonists for C-X-C Chemokine Receptor 4 (CXCR4). J Med Chem 2012; 55:10287-91. [DOI: 10.1021/jm300926y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
| | - Stefanie Thiele
- 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
| | | | - Johann Eksteen
- Lytix Biopharma, Tromsø Science Park AS, P.O. Box 6447, NO-9294 Tromsø,
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
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17
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Planesas JM, Pérez-Nueno VI, Borrell JI, Teixidó J. Impact of the CXCR4 structure on docking-based virtual screening of HIV entry inhibitors. J Mol Graph Model 2012; 38:123-36. [DOI: 10.1016/j.jmgm.2012.06.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Revised: 06/24/2012] [Accepted: 06/25/2012] [Indexed: 11/26/2022]
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18
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Kuil J, Buckle T, van Leeuwen FWB. Imaging agents for the chemokine receptor 4 (CXCR4). Chem Soc Rev 2012; 41:5239-61. [PMID: 22743644 DOI: 10.1039/c2cs35085h] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The interaction between the chemokine receptor 4 (CXCR4) and stromal cell-derived factor-1 (SDF-1, also known as CXCL12) is a natural regulatory process in the human body. However, CXCR4 over-expression is also found in diseases such as cancer, where it plays a role in, among others, the metastatic spread. For this reason it is an interesting biomarker for the field of diagnostic oncology, and therefore, it is gaining increasing interest for applications in molecular imaging. Especially "small-molecule" imaging agents based on T140, FC131 and AMD3100 have been extensively studied. SDF-1, antibodies, pepducins and bioluminescence have also been used to visualize CXCR4. In this critical review reported CXCR4 targeting imaging agents are described based on their affinity, specificity and biodistribution. The level wherein CXCR4 is up-regulated in cancer patients and its relation to the different cell lines and animal models used to evaluate the efficacy of the imaging agents is also discussed (221 references).
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Affiliation(s)
- Joeri Kuil
- Department of Radiology, Interventional Molecular Imaging, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
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19
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Kobayashi K, Oishi S, Hayashi R, Tomita K, Kubo T, Tanahara N, Ohno H, Yoshikawa Y, Furuya T, Hoshino M, Fujii N. Structure–Activity Relationship Study of a CXC Chemokine Receptor Type 4 Antagonist, FC131, Using a Series of Alkene Dipeptide Isosteres. J Med Chem 2012; 55:2746-57. [DOI: 10.1021/jm2016914] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kazuya Kobayashi
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto
606-8501, Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto
606-8501, Japan
| | - Ryoko Hayashi
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto
606-8501, Japan
| | - Kenji Tomita
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto
606-8501, Japan
| | - Tatsuhiko Kubo
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto
606-8501, Japan
| | - Noriko Tanahara
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto
606-8501, Japan
| | - Hiroaki Ohno
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto
606-8501, Japan
| | | | | | - Masaru Hoshino
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto
606-8501, Japan
| | - Nobutaka Fujii
- Graduate School of Pharmaceutical
Sciences, Kyoto University, Sakyo-ku, Kyoto
606-8501, Japan
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20
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Yoshikawa Y, Kobayashi K, Oishi S, Fujii N, Furuya T. Molecular modeling study of cyclic pentapeptide CXCR4 antagonists: New insight into CXCR4–FC131 interactions. Bioorg Med Chem Lett 2012; 22:2146-50. [DOI: 10.1016/j.bmcl.2012.01.134] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 01/27/2012] [Accepted: 01/31/2012] [Indexed: 11/15/2022]
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21
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Oishi S, Fujii N. Peptide and peptidomimetic ligands for CXC chemokine receptor 4 (CXCR4). Org Biomol Chem 2012; 10:5720-31. [DOI: 10.1039/c2ob25107h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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22
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Fanelli F, De Benedetti PG. Update 1 of: computational modeling approaches to structure-function analysis of G protein-coupled receptors. Chem Rev 2011; 111:PR438-535. [PMID: 22165845 DOI: 10.1021/cr100437t] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Francesca Fanelli
- Dulbecco Telethon Institute, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
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23
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Kawatkar SP, Yan M, Gevariya H, Lim MY, Eisold S, Zhu X, Huang Z, An J. Computational analysis of the structural mechanism of inhibition of chemokine receptor CXCR4 by small molecule antagonists. Exp Biol Med (Maywood) 2011; 236:844-50. [PMID: 21697335 DOI: 10.1258/ebm.2011.010345] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding the structural mechanism of receptor-ligand interactions for the chemokine receptor CXCR4 is essential for determining its physiological and pathological functions and for developing new therapies targeted to CXCR4. We have recently reported a structural mechanism for CXCR4 antagonism by a novel synthetic CXCR4 antagonist RCP168 and compared its effectiveness against the natural agonist SDF-1α. In the present study, using molecular docking, we further investigate the binding modes of another seven small molecules known to act as CXCR4 antagonists. The predicted binding modes were compared with previously published mutagenesis data for two of these (AMD3100 and AMD11070). Four antagonists, including AMD3100, AMD11070, FC131 and KRH-1636, bound in a similar fashion to CXCR4. Two important acidic amino acid residues (Asp262 and Glu288) on CXCR4, previously found essential for AMD3100 binding, were also involved in binding of the other ligands. These four antagonists use a binding site in common with that used by RCP168, which is a novel synthetic derivative of vMIP-II in which the first 10 residues are replaced by D-amino acids. Comparison of binding modes suggested that this binding site is different from the binding region occupied by the N-terminus of SDF-1α, the only known natural ligand of CXCR4. These observations suggest the presence of a ligand-binding site (site A) that co-exists with the agonist (SDF-1α) binding site (site B). The other three antagonists, including MSX123, MSX202 and WZ811, are smaller in size and had very similar binding poses, but binding was quite different from that of AMD3100. These three antagonists bound at both sites A and B, thereby blocking both binding and signaling by SDF-1α.
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Affiliation(s)
- Sameer P Kawatkar
- Raylight Corporation, Chemokine Pharmaceutical Inc, San Diego, CA 92126, USA.
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24
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Inokuchi E, Oishi S, Kubo T, Ohno H, Shimura K, Matsuoka M, Fujii N. Potent CXCR4 antagonists containing amidine type Peptide bond isosteres. ACS Med Chem Lett 2011; 2:477-80. [PMID: 24900333 DOI: 10.1021/ml200047e] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 03/27/2011] [Indexed: 02/02/2023] Open
Abstract
A series of FC131 [cyclo(-d-Tyr-Arg-Arg-Nal-Gly-)] analogues containing amidine type peptide bond isosteres were synthesized as selective CXC chemokine receptor type 4 (CXCR4) antagonists. An isosteric amidine substructure was constructed by a macrocyclization process using nitrile oxide-mediated C-N bond formation. All of the amidine-containing FC131 analogues exhibited potent SDF-1 binding inhibition to CXCR4. The Nal-Gly-substituted analogue was characterized as one of the most potent cyclic pentapeptide-based CXCR4 antagonists reported to date. The improved activity against human immunodeficiency virus (HIV) type-1 X4 strains suggested that addition of another basic amidine group to the peptide backbone effectively increases the selective binding of the peptides to CXCR4 receptor.
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Affiliation(s)
- Eriko Inokuchi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tatsuhiko Kubo
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroaki Ohno
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kazuya Shimura
- Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Masao Matsuoka
- Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Nobutaka Fujii
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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25
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Franzen S. A comparison of peptide and folate receptor targeting of cancer cells: from single agent to nanoparticle. Expert Opin Drug Deliv 2011; 8:281-98. [DOI: 10.1517/17425247.2011.554816] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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26
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Tanaka T, Nomura W, Narumi T, Masuda A, Tamamura H. Bivalent ligands of CXCR4 with rigid linkers for elucidation of the dimerization state in cells. J Am Chem Soc 2010; 132:15899-901. [PMID: 20973474 DOI: 10.1021/ja107447w] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
To date, challenges in the design of bivalent ligands for G protein-coupled receptors (GPCRs) have revealed difficulties stemming from lack of knowledge of the state of oligomerization of the GPCR. The synthetic bivalent ligands with rigid linkers that are presented here can predict the dimer form of CXCR4 and be applied to molecular probes in cancerous cells. This "molecular ruler" approach would be useful in elucidating the details of CXCR4 oligomer formation.
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Affiliation(s)
- Tomohiro Tanaka
- Department of Medicinal Chemistry, Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan
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27
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Nikiforovich GV, Marshall GR, Baranski TJ. Modeling molecular mechanisms of binding of the anaphylatoxin C5a to the C5a receptor. Biochemistry 2008; 47:3117-30. [PMID: 18275159 DOI: 10.1021/bi702321a] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study presents the 3D model of the complex between the anaphylatoxin C5a and its specific receptor, C5aR. This is the first 3D model of a G-protein-coupled receptor (GPCR) complex with a peptide ligand deduced by a molecular modeling procedure analyzing various conformational possibilities of the extracellular loops and the N-terminal segment of the GPCR. The modeling results indicated two very different ways of interacting between C5a and C5aR at the two interaction sites suggested earlier based on the data of site-directed mutagenesis. Specifically, C5a and C5aR can be involved in "mutual-induced fit", where the interface between the molecules is determined by both the receptor and the ligand. The rigid core of the C5a ligand selects the proper conformations of the highly flexible N-terminal segment of C5aR (the first interaction site). At the same time, the binding conformation of the flexible C-terminal fragment of C5a is selected by well-defined interactions with the TM region of the C5aR receptor (the second interaction site). The proposed 3D model of C5a/C5aR complex was built without direct use of structural constraints derived from site-directed mutagenesis reserving those data for validation of the model. The available data of site-directed mutagenesis of C5a and C5aR were successfully rationalized with the help of the model. Also, the modeling results predicted that the full-length C5a and C5a-des74 metabolite would have different binding modes with C5aR. Modeling approaches employed in this study are readily applicable for studies of molecular mechanisms of binding of other polypeptide ligands to their specific GPCRs.
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Affiliation(s)
- Gregory V Nikiforovich
- Center for Computational Biology, Department of Biochemistry and Molecular Biophysics, Washington University Medical School, St. Louis, Missouri 63110, USA.
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