1
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Yahiro I, Barnuevo KDE, Sato O, Mohapatra S, Toyoda A, Itoh T, Ohno K, Matsuyama M, Chakraborty T, Ohta K. Modeling the SDF-1/CXCR4 protein using advanced artificial intelligence and antagonist screening for Japanese anchovy. Front Physiol 2024; 15:1349119. [PMID: 38370015 PMCID: PMC10869568 DOI: 10.3389/fphys.2024.1349119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/16/2024] [Indexed: 02/20/2024] Open
Abstract
SDF-1/CXCR4 chemokine signaling are indispensable for cell migration, especially the Primordial Germ Cell (PGC) migration towards the gonadal ridge during early development. We earlier found that this signaling is largely conserved in the Japanese anchovy (Engraulis japonicus, EJ), and a mere treatment of CXCR4 antagonist, AMD3100, leads to germ cell depletion and thereafter gonad sterilization. However, the effect of AMD3100 was limited. So, in this research, we scouted for CXCR4 antagonist with higher potency by employing advanced artificial intelligence deep learning-based computer simulations. Three potential candidates, AMD3465, WZ811, and LY2510924, were selected and in vivo validation was conducted using Japanese anchovy embryos. We found that seven transmembrane motif of EJ CXCR4a and EJ CXCR4b were extremely similar with human homolog while the CXCR4 chemokine receptor N terminal (PF12109, essential for SDF-1 binding) was missing in EJ CXCR4b. 3D protein analysis and cavity search predicted the cavity in EJ CXCR4a to be five times larger (6,307 ų) than that in EJ CXCR4b (1,241 ų). Docking analysis demonstrated lower binding energy of AMD3100 and AMD3465 to EJ CXCR4a (Vina score -9.6) and EJ CXCR4b (Vina score -8.8), respectively. Furthermore, we observed significant PGC mismigration in microinjected AMD3465 treated groups at 10, 100 and 1 × 105 nM concentration in 48 h post fertilized embryos. The other three antagonists showed various degrees of PGC dispersion, but no significant effect compared to their solvent control at tested concentrations was observed. Cumulatively, our results suggests that AMD3645 might be a better candidate for abnormal PGC migration in Japanese anchovy and warrants further investigation.
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Affiliation(s)
- Issei Yahiro
- Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | | | - Oga Sato
- Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Sipra Mohapatra
- Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Aqua-Bioresource Innovation Center, Kyushu University, Saga, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Shizuoka, Japan
| | - Takehiko Itoh
- School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Kanagawa, Japan
| | - Kaoru Ohno
- National Institute for Basic Biology (NIBB), Aichi, Japan
| | | | - Tapas Chakraborty
- Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Aqua-Bioresource Innovation Center, Kyushu University, Saga, Japan
| | - Kohei Ohta
- Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Aqua-Bioresource Innovation Center, Kyushu University, Saga, Japan
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2
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Zhou J, Li W, Guan S, Chen X, Liu X, Shao W. Discovery of Chemokine CXCL12 Inhibitors by Tandem Application of Virtual Screening and NMR Spectrometry. J Chem Inf Model 2022; 62:5729-5737. [PMID: 36288081 DOI: 10.1021/acs.jcim.2c01018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The CXC chemokine ligand CXCL12 and its receptor CXCR4 play critical roles in stem-cell homing, infectious diseases, and cancer, which led the CXCL12/CXCR4 signaling axis to attract much attention in drug discovery. CXCR4 is regarded as the primary target while CXCL12 is considered too small to be a druggable target. In this paper, we employed virtual screening approaches and ligand-based NMR screening methods from a SPECS library and in-house natural products to discover new CXCR12 inhibitors. Four natural triterpene saponins were confirmed, and the triterpene sapogenin was identified as the main binding epitope by saturation transfer difference-nuclear magnetic resonance and molecular docking studies. The pentacyclic triterpene scaffold and its elucidated structure-activity relationships provide a new and valuable research direction for the development of novel CXCL12 inhibitors.
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Affiliation(s)
- Jiao Zhou
- Instrumental Analysis & Research Center, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wei Li
- Instrumental Analysis & Research Center, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Shanyue Guan
- Instrumental Analysis & Research Center, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xiaohong Chen
- Instrumental Analysis & Research Center, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xiang Liu
- School of Chemistry and Chemical Engineering, Guangdong Pharmaceutical University, Zhongshan 528458, China
| | - Weiyan Shao
- School of Pharmaceutical Science, Sun Yat-Sen University, Guangzhou 510006, China
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3
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Lewandowski EM, Kroeck KG, Jacobs LM, Fenske TG, Witt RN, Hintz AM, Ramsden ER, Zhang X, Peterson F, Volkman BF, Veldkamp CT, Chen Y. Structural Insights into Molecular Recognition by Human Chemokine CCL19. Biochemistry 2022; 61:311-318. [PMID: 35156805 PMCID: PMC9254573 DOI: 10.1021/acs.biochem.1c00759] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The human chemokines CCL19 and CCL21 bind to the G protein-coupled receptor (GPCR) CCR7 and play an important role in the trafficking of immune cells as well as cancer metastasis. Conserved binding sites for sulfotyrosine residues on the receptor contribute significantly to the chemokine/GPCR interaction and have been shown to provide promising targets for new drug-discovery efforts to disrupt the chemokine/GPCR interaction and, consequently, tumor metastasis. Here, we report the first X-ray crystal structure of a truncated CCL19 (residues 7-70) at 2.50 Å resolution, revealing molecular details crucial for protein-protein interactions. Although the overall structure is similar to the previously determined NMR model, there are important variations, particularly near the N terminus and the so-called 30's and 40's loops. Computational analysis using the FTMap server indicates the potential importance of these areas in ligand binding and the differences in binding hotspots compared to CCL21. NMR titration experiments using a CCR7-derived peptide (residues 5-11, TDDYIGD) further demonstrate potential receptor recognition sites, such as those near the C terminus and 40's loop, which consist of both positively charged and hydrophobic residues that may be important for receptor binding. Taken together, the X-ray, NMR, and computational analysis herein provide insights into the overall structure and molecular features of CCL19 and enables investigation into this chemokine's function and inhibitor development.
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Affiliation(s)
- Eric M. Lewandowski
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd., Tampa, Florida 33612, United States
| | - Kyle G. Kroeck
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd., Tampa, Florida 33612, United States
| | - Lian M.C. Jacobs
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd., Tampa, Florida 33612, United States
| | - Tyler G. Fenske
- Department of Biochemistry and Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Robin N. Witt
- Department of Chemistry, University of Wisconsin Whitewater, Whitewater, Wisconsin 53190, United States
| | - Alyssa M. Hintz
- Department of Chemistry, University of Wisconsin Whitewater, Whitewater, Wisconsin 53190, United States
| | - Elizabeth R. Ramsden
- Department of Chemistry, University of Wisconsin Whitewater, Whitewater, Wisconsin 53190, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd., Tampa, Florida 33612, United States
| | - Francis Peterson
- Department of Biochemistry and Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Brian F. Volkman
- Department of Biochemistry and Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States,Corresponding authors: Brian F. Volkman, , Christopher T. Veldkamp, , Yu Chen,
| | - Christopher T. Veldkamp
- Department of Chemistry, University of Wisconsin Whitewater, Whitewater, Wisconsin 53190, United States,Corresponding authors: Brian F. Volkman, , Christopher T. Veldkamp, , Yu Chen,
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd., Tampa, Florida 33612, United States,Corresponding authors: Brian F. Volkman, , Christopher T. Veldkamp, , Yu Chen,
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4
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Sprague DJ, Getschman AE, Fenske TG, Volkman BF, Smith BC. Trisubstituted 1,3,5-Triazines: The First Ligands of the sY12-Binding Pocket on Chemokine CXCL12. ACS Med Chem Lett 2021; 12:1773-1782. [PMID: 34795867 PMCID: PMC8592115 DOI: 10.1021/acsmedchemlett.1c00388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/21/2021] [Indexed: 12/17/2022] Open
Abstract
![]()
CXCL12, a CXC-type
chemokine, binds its receptor CXCR4, and the
resulting signaling cascade is essential during development and subsequently
in immune function. Pathologically, the CXCL12–CXCR4 signaling
axis is involved in many cancers and inflammatory diseases and thus
has sparked continued interest in the development of therapeutics.
Small molecules targeting CXCR4 have had mixed results in clinical
trials. Alternatively, small molecules targeting the chemokine instead
of the receptor provide a largely unexplored space for therapeutic
development. Here we report that trisubstituted 1,3,5-triazines are
competent ligands for the sY12-binding pocket of CXCL12. The initial
hit was optimized to be more synthetically tractable. Fifty unique
triazines were synthesized, and the structure–activity relationship
was probed. Using computational modeling, we suggest key structural
interactions that are responsible for ligand–chemokine binding.
The lipophilic ligand efficiency was improved, resulting in more soluble,
drug-like molecules with chemical handles for future development and
structural studies.
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Affiliation(s)
- Daniel J. Sprague
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Anthony E. Getschman
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Tyler G. Fenske
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Brian F. Volkman
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Brian C. Smith
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
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5
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Rosenberg EM, Herrington J, Rajasekaran D, Murphy JW, Pantouris G, Lolis EJ. The N-terminal length and side-chain composition of CXCL13 affect crystallization, structure and functional activity. Acta Crystallogr D Struct Biol 2020; 76:1033-1049. [PMID: 33021505 PMCID: PMC7543660 DOI: 10.1107/s2059798320011687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/25/2020] [Indexed: 01/18/2023] Open
Abstract
CXCL13 is the cognate chemokine agonist of CXCR5, a class A G-protein-coupled receptor (GPCR) that is essential for proper humoral immune responses. Using a `methionine scanning' mutagenesis method on the N-terminus of CXCL13, which is the chemokine signaling region, it was shown that minor length alterations and side-chain substitutions still result in CXCR5 activation. This observation indicates that the orthosteric pocket of CXCR5 can tolerate these changes without severely affecting the activity. The introduction of bulk on the ligand was well tolerated by the receptor, whereas a loss of contacts was less tolerated. Furthermore, two crystal structures of CXCL13 mutants were solved, both of which represent the first uncomplexed structures of the human protein. These structures were stabilized by unique interactions formed by the N-termini of the ligands, indicating that CXCL13 exhibits substantial N-terminal flexibility while the chemokine core domain remains largely unchanged. Additionally, it was observed that CXCL13 harbors a large degree of flexibility in the C-terminal extension of the ligand. Comparisons with other published structures of human and murine CXCL13 validate the relative rigidity of the core domain as well as the N- and C-terminal mobilities. Collectively, these mutants and their structures provide the field with additional insights into how CXCL13 interacts with CXCR5.
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Affiliation(s)
- Eric M. Rosenberg
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - James Herrington
- Yale Center for Molecular Discovery, Yale West Campus, West Haven, CT 06516, USA
| | - Deepa Rajasekaran
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - James W. Murphy
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Georgios Pantouris
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Elias J. Lolis
- Department of Pharmacology, Yale School of Medicine, New Haven, CT 06520, USA
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6
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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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7
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Chemokines in COPD: From Implication to Therapeutic Use. Int J Mol Sci 2019; 20:ijms20112785. [PMID: 31174392 PMCID: PMC6600384 DOI: 10.3390/ijms20112785] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/03/2019] [Accepted: 06/03/2019] [Indexed: 02/07/2023] Open
Abstract
: Chronic Obstructive Pulmonary Disease (COPD) represents the 3rd leading cause of death in the world. The underlying pathophysiological mechanisms have been the focus of extensive research in the past. The lung has a complex architecture, where structural cells interact continuously with immune cells that infiltrate into the pulmonary tissue. Both types of cells express chemokines and chemokine receptors, making them sensitive to modifications of concentration gradients. Cigarette smoke exposure and recurrent exacerbations, directly and indirectly, impact the expression of chemokines and chemokine receptors. Here, we provide an overview of the evidence regarding chemokines involvement in COPD, and we hypothesize that a dysregulation of this tightly regulated system is critical in COPD evolution, both at a stable state and during exacerbations. Targeting chemokines and chemokine receptors could be highly attractive as a mean to control both chronic inflammation and bronchial remodeling. We present a special focus on the CXCL8-CXCR1/2, CXCL9/10/11-CXCR3, CCL2-CCR2, and CXCL12-CXCR4 axes that seem particularly involved in the disease pathophysiology.
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8
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Regenass P, Abboud D, Daubeuf F, Lehalle C, Gizzi P, Riché S, Hachet-Haas M, Rohmer F, Gasparik V, Boeglin D, Haiech J, Knehans T, Rognan D, Heissler D, Marsol C, Villa P, Galzi JL, Hibert M, Frossard N, Bonnet D. Discovery of a Locally and Orally Active CXCL12 Neutraligand (LIT-927) with Anti-inflammatory Effect in a Murine Model of Allergic Airway Hypereosinophilia. J Med Chem 2018; 61:7671-7686. [PMID: 30106292 DOI: 10.1021/acs.jmedchem.8b00657] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We previously reported Chalcone-4 (1) that binds the chemokine CXCL12, not its cognate receptors CXCR4 or CXCR7, and neutralizes its biological activity. However, this neutraligand suffers from limitations such as poor chemical stability, solubility, and oral activity. Herein, we report on the discovery of pyrimidinone 57 (LIT-927), a novel neutraligand of CXCL12 which displays a higher solubility than 1 and is no longer a Michael acceptor. While both 1 and 57 reduce eosinophil recruitment in a murine model of allergic airway hypereosinophilia, 57 is the only one to display inhibitory activity following oral administration. Thereby, we here describe 57 as the first orally active CXCL12 neutraligand with anti-inflammatory properties. Combined with a high binding selectivity for CXCL12 over other chemokines, 57 represents a powerful pharmacological tool to investigate CXCL12 physiology in vivo and to explore the activity of chemokine neutralization in inflammatory and related diseases.
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Affiliation(s)
- Pierre Regenass
- Laboratoire d'Innovation Thérapeutique , Faculté de Pharmacie, UMR7200 CNRS/Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - Dayana Abboud
- Biotechnologie et Signalisation Cellulaire , Ecole Supérieure de Biotechnologie de Strasbourg, UMR 7242 CNRS/Université de Strasbourg , Bld Sébastien Brant , 67412 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - François Daubeuf
- Laboratoire d'Innovation Thérapeutique , Faculté de Pharmacie, UMR7200 CNRS/Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France.,Plate-forme de chimie biologique intégrative de Strasbourg , UMS 3286 CNRS/Université de Strasbourg , 67412 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - Christine Lehalle
- Laboratoire d'Innovation Thérapeutique , Faculté de Pharmacie, UMR7200 CNRS/Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France.,Plate-forme de chimie biologique intégrative de Strasbourg , UMS 3286 CNRS/Université de Strasbourg , 67412 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - Patrick Gizzi
- Plate-forme de chimie biologique intégrative de Strasbourg , UMS 3286 CNRS/Université de Strasbourg , 67412 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - Stéphanie Riché
- Laboratoire d'Innovation Thérapeutique , Faculté de Pharmacie, UMR7200 CNRS/Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - Muriel Hachet-Haas
- Biotechnologie et Signalisation Cellulaire , Ecole Supérieure de Biotechnologie de Strasbourg, UMR 7242 CNRS/Université de Strasbourg , Bld Sébastien Brant , 67412 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - François Rohmer
- Laboratoire d'Innovation Thérapeutique , Faculté de Pharmacie, UMR7200 CNRS/Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - Vincent Gasparik
- Laboratoire d'Innovation Thérapeutique , Faculté de Pharmacie, UMR7200 CNRS/Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - Damien Boeglin
- Laboratoire d'Innovation Thérapeutique , Faculté de Pharmacie, UMR7200 CNRS/Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - Jacques Haiech
- Laboratoire d'Innovation Thérapeutique , Faculté de Pharmacie, UMR7200 CNRS/Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - Tim Knehans
- Laboratoire d'Innovation Thérapeutique , Faculté de Pharmacie, UMR7200 CNRS/Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - Didier Rognan
- Laboratoire d'Innovation Thérapeutique , Faculté de Pharmacie, UMR7200 CNRS/Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - Denis Heissler
- Laboratoire d'Innovation Thérapeutique , Faculté de Pharmacie, UMR7200 CNRS/Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - Claire Marsol
- Laboratoire d'Innovation Thérapeutique , Faculté de Pharmacie, UMR7200 CNRS/Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France.,Plate-forme de chimie biologique intégrative de Strasbourg , UMS 3286 CNRS/Université de Strasbourg , 67412 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - Pascal Villa
- Plate-forme de chimie biologique intégrative de Strasbourg , UMS 3286 CNRS/Université de Strasbourg , 67412 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - Jean-Luc Galzi
- Biotechnologie et Signalisation Cellulaire , Ecole Supérieure de Biotechnologie de Strasbourg, UMR 7242 CNRS/Université de Strasbourg , Bld Sébastien Brant , 67412 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - Marcel Hibert
- Laboratoire d'Innovation Thérapeutique , Faculté de Pharmacie, UMR7200 CNRS/Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - Nelly Frossard
- Laboratoire d'Innovation Thérapeutique , Faculté de Pharmacie, UMR7200 CNRS/Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
| | - Dominique Bonnet
- Laboratoire d'Innovation Thérapeutique , Faculté de Pharmacie, UMR7200 CNRS/Université de Strasbourg , 74 route du Rhin , 67401 Illkirch , France.,Labex MEDALIS , Université de Strasbourg , 67000 Strasbourg , France
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9
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Martinez-Rosell G, Harvey MJ, De Fabritiis G. Molecular-Simulation-Driven Fragment Screening for the Discovery of New CXCL12 Inhibitors. J Chem Inf Model 2018; 58:683-691. [PMID: 29481075 DOI: 10.1021/acs.jcim.7b00625] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fragment-based drug discovery (FBDD) has become a mainstream approach in drug design because it allows the reduction of the chemical space and screening libraries while identifying fragments with high protein-ligand efficiency interactions that can later be grown into drug-like leads. In this work, we leverage high-throughput molecular dynamics (MD) simulations to screen a library of 129 fragments for a total of 5.85 ms against the CXCL12 monomer, a chemokine involved in inflammation and diseases such as cancer. Our in silico binding assay was able to recover binding poses, affinities, and kinetics for the selected library and was able to predict 8 mM-affinity fragments with ligand efficiencies higher than 0.3. All of the fragment hits present a similar chemical structure, with a hydrophobic core and a positively charged group, and bind to either sY7 or H1S68 pockets, where they share pharmacophoric properties with experimentally resolved natural binders. This work presents a large-scale screening assay using an exclusive combination of thousands of short MD adaptive simulations analyzed with a Markov state model (MSM) framework.
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Affiliation(s)
- Gerard Martinez-Rosell
- Computational Biophysics Laboratory (GRIB-IMIM) , Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB) , C/Doctor Aiguader 88 , 08003 Barcelona , Spain
| | - Matt J Harvey
- Acellera, Barcelona Biomedical Research Park (PRBB) , C/Doctor Aiguader 88 , 08003 , Barcelona , Spain
| | - Gianni De Fabritiis
- Computational Biophysics Laboratory (GRIB-IMIM) , Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB) , C/Doctor Aiguader 88 , 08003 Barcelona , Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA) , Passeig Lluis Companys 23 , Barcelona 08010 , Spain
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10
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Miller MC, Mayo KH. Chemokines from a Structural Perspective. Int J Mol Sci 2017; 18:ijms18102088. [PMID: 28974038 PMCID: PMC5666770 DOI: 10.3390/ijms18102088] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 08/30/2017] [Accepted: 09/26/2017] [Indexed: 01/04/2023] Open
Abstract
Chemokines are a family of small, highly conserved cytokines that mediate various biological processes, including chemotaxis, hematopoiesis, and angiogenesis, and that function by interacting with cell surface G-Protein Coupled Receptors (GPCRs). Because of their significant involvement in various biological functions and pathologies, chemokines and their receptors have been the focus of therapeutic discovery for clinical intervention. There are several sub-families of chemokines (e.g., CXC, CC, C, and CX3C) defined by the positions of sequentially conserved cysteine residues. Even though all chemokines also have a highly conserved, three-stranded β-sheet/α-helix tertiary structural fold, their quarternary structures vary significantly with their sub-family. Moreover, their conserved tertiary structures allow for subunit swapping within and between sub-family members, thus promoting the concept of a “chemokine interactome”. This review is focused on structural aspects of CXC and CC chemokines, their functional synergy and ability to form heterodimers within the chemokine interactome, and some recent developments in structure-based chemokine-targeted drug discovery.
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Affiliation(s)
- Michelle C Miller
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Kevin H Mayo
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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11
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CCR7 Sulfotyrosine Enhances CCL21 Binding. Int J Mol Sci 2017; 18:ijms18091857. [PMID: 28841151 PMCID: PMC5618506 DOI: 10.3390/ijms18091857] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/18/2017] [Accepted: 08/22/2017] [Indexed: 01/05/2023] Open
Abstract
Chemokines are secreted proteins that direct the migration of immune cells and are involved in numerous disease states. For example, CCL21 (CC chemokine ligand 21) and CCL19 (CC chemokine ligand 19) recruit antigen-presenting dendritic cells and naïve T-cells to the lymph nodes and are thought to play a role in lymph node metastasis of CCR7 (CC chemokine receptor 7)-expressing cancer cells. For many chemokine receptors, N-terminal posttranslational modifications, particularly the sulfation of tyrosine residues, increases the affinity for chemokine ligands and may contribute to receptor ligand bias. Chemokine sulfotyrosine (sY) binding sites are also potential targets for drug development. In light of the structural similarity between sulfotyrosine and phosphotyrosine (pY), the interactions of CCL21 with peptide fragments of CCR7 containing tyrosine, pY, or sY were compared using protein NMR (nuclear magnetic resonance) spectroscopy in this study. Various N-terminal CCR7 peptides maintain binding site specificity with Y8-, pY8-, or sY8-containing peptides binding near the α-helix, while Y17-, pY17-, and sY17-containing peptides bind near the N-loop and β3-stand of CCL21. All modified CCR7 peptides showed enhanced binding affinity to CCL21, with sY having the largest effect.
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12
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Kufareva I, Gustavsson M, Zheng Y, Stephens BS, Handel TM. What Do Structures Tell Us About Chemokine Receptor Function and Antagonism? Annu Rev Biophys 2017; 46:175-198. [PMID: 28532213 PMCID: PMC5764094 DOI: 10.1146/annurev-biophys-051013-022942] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Chemokines and their cell surface G protein-coupled receptors are critical for cell migration, not only in many fundamental biological processes but also in inflammatory diseases and cancer. Recent X-ray structures of two chemokines complexed with full-length receptors provided unprecedented insight into the atomic details of chemokine recognition and receptor activation, and computational modeling informed by new experiments leverages these insights to gain understanding of many more receptor:chemokine pairs. In parallel, chemokine receptor structures with small molecules reveal the complicated and diverse structural foundations of small molecule antagonism and allostery, highlight the inherent physicochemical challenges of receptor:chemokine interfaces, and suggest novel epitopes that can be exploited to overcome these challenges. The structures and models promote unique understanding of chemokine receptor biology, including the interpretation of two decades of experimental studies, and will undoubtedly assist future drug discovery endeavors.
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Affiliation(s)
- Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
| | - Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
| | - Yi Zheng
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
| | - Bryan S Stephens
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
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13
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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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14
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Stone MJ, Hayward JA, Huang C, E Huma Z, Sanchez J. Mechanisms of Regulation of the Chemokine-Receptor Network. Int J Mol Sci 2017; 18:E342. [PMID: 28178200 PMCID: PMC5343877 DOI: 10.3390/ijms18020342] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/18/2017] [Accepted: 01/26/2017] [Indexed: 12/18/2022] Open
Abstract
The interactions of chemokines with their G protein-coupled receptors promote the migration of leukocytes during normal immune function and as a key aspect of the inflammatory response to tissue injury or infection. This review summarizes the major cellular and biochemical mechanisms by which the interactions of chemokines with chemokine receptors are regulated, including: selective and competitive binding interactions; genetic polymorphisms; mRNA splice variation; variation of expression, degradation and localization; down-regulation by atypical (decoy) receptors; interactions with cell-surface glycosaminoglycans; post-translational modifications; oligomerization; alternative signaling responses; and binding to natural or pharmacological inhibitors.
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Affiliation(s)
- Martin J Stone
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Jenni A Hayward
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Cheng Huang
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Zil E Huma
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
| | - Julie Sanchez
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia.
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15
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Kufareva I. Chemokines and their receptors: insights from molecular modeling and crystallography. Curr Opin Pharmacol 2016; 30:27-37. [PMID: 27459124 PMCID: PMC5071139 DOI: 10.1016/j.coph.2016.07.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/07/2016] [Accepted: 07/07/2016] [Indexed: 10/21/2022]
Abstract
Chemokines are small secreted proteins that direct cell migration in development, immunity, inflammation, and cancer. They do so by binding and activating specific G protein coupled receptors on the surface of migrating cells. Despite the importance of receptor:chemokine interactions, their structural basis remained unclear for a long time. In 2015, the first atomic resolution insights were obtained with the publication of X-ray structures for two distantly related receptors bound to chemokines. In conjunction with experiment-guided molecular modeling, the structures suggest a conserved receptor:chemokine complex architecture, while highlighting the diverse details and functional roles of individual interaction epitopes. Novel findings promote the development and detailed structural interpretation of the canonical two-site hypothesis of receptor:chemokine recognition, and suggest new avenues for pharmacological modulation of chemokine receptors.
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Affiliation(s)
- Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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16
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Smith EW, Lewandowski EM, Moussouras NA, Kroeck KG, Volkman BF, Veldkamp CT, Chen Y. Crystallographic Structure of Truncated CCL21 and the Putative Sulfotyrosine-Binding Site. Biochemistry 2016; 55:5746-5753. [PMID: 27617343 DOI: 10.1021/acs.biochem.6b00304] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
CCL21 chemokine binds the G protein-coupled receptor CCR7, aiding not only in immune response but also in cancer metastasis. Compared with other chemokines, CCL21 has a unique extended unstructured C-terminus that is truncated in some naturally occurring variants. We have determined the X-ray crystallographic structure of a truncated CCL21 (residues 1-79) lacking the extended C-terminus and identified, via two-dimensional nuclear magnetic resonance (NMR), a putative sulfotyrosine-binding site that may recognize such post-translationally modified tyrosine residues on the receptor. Compared to the previously determined NMR structure of full-length CCL21, the crystal structure presents new druggable binding hot spots resulting from an alternative N-loop conformation. In addition, whereas the previous NMR structure did not provide any structural information after residue 70, the C-terminus of the truncated CCL21, ordered up to Ala77 in our crystal structure, is placed near the N-loop and sulfotyrosine-binding site, indicating that the extended C-terminus of full-length CCL21 can interact with this important region for receptor binding. These observations suggest a potential origin for the autoinhibition of CCL21 activity that was recently described. The new crystal structure and binding hot spot analysis have important implications for the function of the CCL21 C-terminus and drug discovery.
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Affiliation(s)
- Emmanuel W Smith
- Department of Molecular Medicine, University of South Florida , Tampa, Florida 33612, United States
| | - Eric M Lewandowski
- Department of Molecular Medicine, University of South Florida , Tampa, Florida 33612, United States
| | - Natasha A Moussouras
- Department of Biochemistry, Medical College of Wisconsin , Milwaukee, Wisconsin 53226, United States
| | - Kyle G Kroeck
- Department of Molecular Medicine, University of South Florida , Tampa, Florida 33612, United States
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin , Milwaukee, Wisconsin 53226, United States
| | - Christopher T Veldkamp
- Department of Chemistry, University of Wisconsin-Whitewater , Whitewater, Wisconsin 53190, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida , Tampa, Florida 33612, United States
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17
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Smith EW, Nevins AM, Qiao Z, Liu Y, Getschman AE, Vankayala SL, Kemp MT, Peterson FC, Li R, Volkman BF, Chen Y. Structure-Based Identification of Novel Ligands Targeting Multiple Sites within a Chemokine-G-Protein-Coupled-Receptor Interface. J Med Chem 2016; 59:4342-51. [PMID: 27058821 DOI: 10.1021/acs.jmedchem.5b02042] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
CXCL12 is a human chemokine that recognizes the CXCR4 receptor and is involved in immune responses and metastatic cancer. Interactions between CXCL12 and CXCR4 are an important drug target but, like other elongated protein-protein interfaces, present challenges for small molecule ligand discovery due to the relatively shallow and featureless binding surfaces. Calculations using an NMR complex structure revealed a binding hot spot on CXCL12 that normally interacts with the I4/I6 residues from CXCR4. Virtual screening was performed against the NMR model, and subsequent testing has verified the specific binding of multiple docking hits to this site. Together with our previous results targeting two other binding pockets that recognize sulfotyrosine residues (sY12 and sY21) of CXCR4, including a new analog against the sY12 binding site reported herein, we demonstrate that protein-protein interfaces can often possess multiple sites for engineering specific small molecule ligands that provide lead compounds for subsequent optimization by fragment based approaches.
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Affiliation(s)
- Emmanuel W Smith
- Department of Molecular Medicine, University of South Florida , 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Amanda M Nevins
- Department of Biochemistry, Medical College of Wisconsin , 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Zhen Qiao
- Department of Pharmaceutical Sciences, Center for Drug Discovery, College of Pharmacy, and Cancer Genes and Molecular Regulation Program, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center , 986805 Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Yan Liu
- Department of Pharmaceutical Sciences, Center for Drug Discovery, College of Pharmacy, and Cancer Genes and Molecular Regulation Program, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center , 986805 Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Anthony E Getschman
- Department of Biochemistry, Medical College of Wisconsin , 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Sai L Vankayala
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - M Trent Kemp
- Department of Chemistry, University of South Florida , 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Francis C Peterson
- Department of Biochemistry, Medical College of Wisconsin , 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Rongshi Li
- Department of Pharmaceutical Sciences, Center for Drug Discovery, College of Pharmacy, and Cancer Genes and Molecular Regulation Program, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center , 986805 Nebraska Medical Center, Omaha, Nebraska 68198, United States
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin , 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida , 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
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18
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Seibert C, Sanfiz A, Sakmar TP, Veldkamp CT. Preparation and Analysis of N-Terminal Chemokine Receptor Sulfopeptides Using Tyrosylprotein Sulfotransferase Enzymes. Methods Enzymol 2015; 570:357-88. [PMID: 26921955 DOI: 10.1016/bs.mie.2015.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In most chemokine receptors, one or multiple tyrosine residues have been identified within the receptor N-terminal domain that are, at least partially, modified by posttranslational tyrosine sulfation. For example, tyrosine sulfation has been demonstrated for Tyr-3, -10, -14, and -15 of CCR5, for Tyr-3, -14, and -15 of CCR8, and for Tyr-7, -12, and -21 of CXCR4. While there is evidence for several chemokine receptors that tyrosine sulfation is required for optimal interaction with the chemokine ligands, the precise role of tyrosine sulfation for chemokine receptor function remains unclear. Furthermore, the function of the chemokine receptor N-terminal domain in chemokine binding and receptor activation is also not well understood. Sulfotyrosine peptides corresponding to the chemokine receptor N-termini are valuable tools to address these important questions both in structural and functional studies. However, due to the lability of the sulfotyrosine modification, these peptides are difficult to obtain using standard peptide chemistry methods. In this chapter, we provide methods to prepare sulfotyrosine peptides by enzymatic in vitro sulfation of peptides using purified recombinant tyrosylprotein sulfotransferase (TPST) enzymes. In addition, we also discuss alternative approaches for the generation of sulfotyrosine peptides and methods for sulfopeptide analysis.
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Affiliation(s)
- Christoph Seibert
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, USA
| | - Anthony Sanfiz
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, USA
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, USA
| | - Christopher T Veldkamp
- Department of Chemistry, University of Wisconsin-Whitewater, Whitewater, Wisconsin, USA.
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19
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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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20
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Kufareva I, Salanga CL, Handel TM. Chemokine and chemokine receptor structure and interactions: implications for therapeutic strategies. Immunol Cell Biol 2015; 93:372-83. [PMID: 25708536 DOI: 10.1038/icb.2015.15] [Citation(s) in RCA: 143] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Revised: 01/09/2015] [Accepted: 01/09/2015] [Indexed: 12/15/2022]
Abstract
The control of cell migration by chemokines involves interactions with two types of receptors: seven transmembrane chemokine-type G protein-coupled receptors and cell surface or extracellular matrix-associated glycosaminoglycans. Coordinated interaction of chemokines with both types of receptors is required for directional migration of cells in numerous physiological and pathological processes. Accumulated structural information, culminating most recently in the structure of a chemokine receptor in complex with a chemokine, has led to a view where chemokine oligomers bind to glycosaminoglycans through epitopes formed when chemokine subunits come together, while chemokine monomers bind to receptors in a pseudo two-step mechanism of receptor activation. Exploitation of this structural knowledge has and will continue to provide important information for therapeutic strategies, as described in this review.
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Affiliation(s)
- Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Catherina L Salanga
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
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21
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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: 291] [Impact Index Per Article: 32.3] [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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