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Sun D, Sun Y, Janezic E, Zhou T, Johnson M, Azumaya C, Noreng S, Chiu C, Seki A, Arenzana TL, Nicoludis JM, Shi Y, Wang B, Ho H, Joshi P, Tam C, Payandeh J, Comps-Agrar L, Wang J, Rutz S, Koerber JT, Masureel M. Structural basis of antibody inhibition and chemokine activation of the human CC chemokine receptor 8. Nat Commun 2023; 14:7940. [PMID: 38040762 PMCID: PMC10692165 DOI: 10.1038/s41467-023-43601-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 11/14/2023] [Indexed: 12/03/2023] Open
Abstract
The C-C motif chemokine receptor 8 (CCR8) is a class A G-protein coupled receptor that has emerged as a promising therapeutic target in cancer. Targeting CCR8 with an antibody has appeared to be an attractive therapeutic approach, but the molecular basis for chemokine-mediated activation and antibody-mediated inhibition of CCR8 are not fully elucidated. Here, we obtain an antagonist antibody against human CCR8 and determine structures of CCR8 in complex with either the antibody or the endogenous agonist ligand CCL1. Our studies reveal characteristic antibody features allowing recognition of the CCR8 extracellular loops and CCL1-CCR8 interaction modes that are distinct from other chemokine receptor - ligand pairs. Informed by these structural insights, we demonstrate that CCL1 follows a two-step, two-site binding sequence to CCR8 and that antibody-mediated inhibition of CCL1 signaling can occur by preventing the second binding event. Together, our results provide a detailed structural and mechanistic framework of CCR8 activation and inhibition that expands our molecular understanding of chemokine - receptor interactions and offers insight into the development of therapeutic antibodies targeting chemokine GPCRs.
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Affiliation(s)
- Dawei Sun
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Yonglian Sun
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Eric Janezic
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Tricia Zhou
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Matthew Johnson
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Caleigh Azumaya
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Sigrid Noreng
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA
- Septerna Inc., South San Francisco, CA, 94080, USA
| | - Cecilia Chiu
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Akiko Seki
- Department of Cancer Immunology, Genentech Inc., South San Francisco, CA, 94080, USA
- Tune Therapeutics, Durham, NC, 27701, USA
| | - Teresita L Arenzana
- Department of Cancer Immunology, Genentech Inc., South San Francisco, CA, 94080, USA
- HIBio, South San Francisco, CA, 94080, USA
| | - John M Nicoludis
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Yongchang Shi
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Baomei Wang
- Department of Cancer Immunology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Hoangdung Ho
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Prajakta Joshi
- Department of Biomolecular Resources, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Christine Tam
- Department of Biomolecular Resources, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Jian Payandeh
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA
- Exelixis Inc., Alameda, CA, 94502, USA
| | - Laëtitia Comps-Agrar
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Jianyong Wang
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., South San Francisco, CA, 94080, USA
| | - Sascha Rutz
- Department of Cancer Immunology, Genentech Inc., South San Francisco, CA, 94080, USA.
| | - James T Koerber
- Department of Antibody Engineering, Genentech Inc., South San Francisco, CA, 94080, USA.
| | - Matthieu Masureel
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, 94080, USA.
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Dong T, Han C, Liu X, Wang Z, Wang Y, Kang Q, Wang P, Zhou F. Live Cells versus Fixated Cells: Kinetic Measurements of Biomolecular Interactions with the LigandTracer Method and Surface Plasmon Resonance Microscopy. Mol Pharm 2023; 20:2094-2104. [PMID: 36939457 DOI: 10.1021/acs.molpharmaceut.2c01047] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
Cell-based kinetic studies of ligand or candidate drug binding to membrane proteins have produced affinity and kinetic values that are different from measurements using purified proteins. However, ligand binding to fixated cells whose membrane constituents (e.g., proteins and their glycosylated forms) are partially connected by a cross-linking reagent has not been compared to that to live cells. Under the same experimental conditions for the LigandTracer method, we measured the interactions of fluorophore-labeled lectins and antibody molecules with glycans at HFF cells and the human epithelial growth receptor 2 at SKBR3 cells, respectively. In conjunction with surface plasmon resonance microscopy, the effects of labels and cell/sub-cell heterogeneity on binding kinetics were investigated. Our results revealed that, for cell constituents whose structures and functions are not closely dependent on cell viability, the ligand binding kinetics at fixated cells is only slightly different from that at live cells. The altered kinetics is explained on the basis of a less mobile receptor confined in a local environment created by partially interconnected protein molecules. We show that cell/sub-cell heterogeneity and labels on the ligands can alter the binding reaction more significantly. Thus, fixating cells not only simplifies experimental procedures for drug screening and renders assays more robust but also provides reliable kinetic information about drug binding to cell constituents whose structures are not changed by chemical fixation.
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Affiliation(s)
- Tianbao Dong
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong 250022, P. R. China
| | - Chaowei Han
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong 250022, P. R. China
| | - Xin Liu
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong 250022, P. R. China
| | - Zhichao Wang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong 250022, P. R. China
| | - Yanhui Wang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong 250022, P. R. China
| | - Qing Kang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong 250022, P. R. China
| | - Pengcheng Wang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong 250022, P. R. China
| | - Feimeng Zhou
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong 250022, P. R. China
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Spiegelberg D, Stenberg J, Richalet P, Vanhove M. K D determination from time-resolved experiments on live cells with LigandTracer and reconciliation with end-point flow cytometry measurements. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:979-991. [PMID: 34302187 PMCID: PMC8448686 DOI: 10.1007/s00249-021-01560-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 06/16/2021] [Accepted: 07/01/2021] [Indexed: 11/30/2022]
Abstract
Design of next-generation therapeutics comes with new challenges and emulates technology and methods to meet them. Characterizing the binding of either natural ligands or therapeutic proteins to cell-surface receptors, for which relevant recombinant versions may not exist, represents one of these challenges. Here we report the characterization of the interaction of five different antibody therapeutics (Trastuzumab, Rituximab, Panitumumab, Pertuzumab, and Cetuximab) with their cognate target receptors using LigandTracer. The method offers the advantage of being performed on live cells, alleviating the need for a recombinant source of the receptor. Furthermore, time-resolved measurements, in addition to allowing the determination of the affinity of the studied drug to its target, give access to the binding kinetics thereby providing a full characterization of the system. In this study, we also compared time-resolved LigandTracer data with end-point KD determination from flow cytometry experiments and hypothesize that discrepancies between these two approaches, when they exist, generally come from flow cytometry titration curves being acquired prior to full equilibration of the system. Our data, however, show that knowledge of the kinetics of the interaction allows to reconcile the data obtained by flow cytometry and LigandTracer and demonstrate the complementarity of these two methods.
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Affiliation(s)
- Diana Spiegelberg
- Department of Surgical Sciences, Uppsala University, 751 85, Uppsala, Sweden
| | - Jonas Stenberg
- Ridgeview Instruments AB, Skillsta 4, 740 20, Vänge, Sweden.,A3P Biomedical AB, Vallongatan 1, 752 28, Uppsala, Sweden
| | | | - Marc Vanhove
- Marc Vanhove Consultancy, 4100, Boncelles, Belgium. .,Oxurion N.V., Gaston Geenslaan 1, 3001, Leuven, Belgium.
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Mitchell RA, Luwor RB, Burgess AW. Epidermal growth factor receptor: Structure-function informing the design of anticancer therapeutics. Exp Cell Res 2018; 371:1-19. [PMID: 30098332 DOI: 10.1016/j.yexcr.2018.08.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/30/2018] [Accepted: 08/01/2018] [Indexed: 12/19/2022]
Abstract
Research on the epidermal growth factor (EGF) family and the family of receptors (EGFR) has progressed rapidly in recent times. New crystal structures of the ectodomains with different ligands, the activation of the kinase domain through oligomerisation and the use of fluorescence techniques have revealed profound conformational changes on ligand binding. The control of cell signaling from the EGFR-family is complex, with heterodimerisation, ligand affinity and signaling cross-talk influencing cellular outcomes. Analysis of tissue homeostasis indicates that the control of pro-ligand processing is likely to be as important as receptor activation events. Several members of the EGFR-family are overexpressed and/or mutated in cancer cells. The perturbation of EGFR-family signaling drives the malignant phenotype of many cancers and both inhibitors and antagonists of signaling from these receptors have already produced therapeutic benefits for patients. The design of affibodies, antibodies, small molecule inhibitors and even immunotherapeutic drugs targeting the EGFR-family has yielded promising new approaches to improving outcomes for cancer patients. In this review, we describe recent discoveries which have increased our understanding of the structure and dynamics of signaling from the EGFR-family, the roles of ligand processing and receptor cross-talk. We discuss the relevance of these studies to the development of strategies for designing more effective targeted treatments for cancer patients.
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Affiliation(s)
- Ruth A Mitchell
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Victoria 3052, Australia; Department of Surgery, The University of Melbourne, The Royal Melbourne Hospital, Parkville, Victoria 3050, Australia
| | - Rodney B Luwor
- Department of Surgery, The University of Melbourne, The Royal Melbourne Hospital, Parkville, Victoria 3050, Australia
| | - Antony W Burgess
- Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Victoria 3052, Australia; Department of Surgery, The University of Melbourne, The Royal Melbourne Hospital, Parkville, Victoria 3050, Australia.
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5
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Bondza S, Björkelund H, Nestor M, Andersson K, Buijs J. Novel Real-Time Proximity Assay for Characterizing Multiple Receptor Interactions on Living Cells. Anal Chem 2017; 89:13212-13218. [PMID: 29160688 DOI: 10.1021/acs.analchem.7b02983] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cellular receptor activity is often controlled through complex mechanisms involving interactions with multiple molecules, which can be soluble ligands and/or other cell surface molecules. In this study, we combine a fluorescence-based technology for real-time interaction analysis with fluorescence quenching to create a novel time-resolved proximity assay to study protein-receptor interactions on living cells. This assay extracts the binding kinetics and affinity for two proteins if they bind in proximity on the cell surface. One application of real-time proximity interaction analysis is to study relative levels of receptor dimerization. The method was primarily evaluated using the HER2 binding antibodies Trastuzumab and Pertuzumab and two EGFR binding antibodies including Cetuximab. Using Cetuximab and Trastuzumab, proximity of EGFR and HER2 was investigated before and after treatment of cells with the tyrosine-kinase inhibitor Gefitinib. Treated cells displayed 50% increased proximity signal, whereas the binding characteristics of the two antibodies were not significantly affected, implying an increase in the EGFR-HER2 dimer level. These results demonstrate that real-time proximity interaction analysis enables determination of the interaction rate constants and affinity of two ligands while simultaneously quantifying their relative colocalization on living cells.
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Affiliation(s)
- Sina Bondza
- Department of Immunology, Genetics and Pathology, Uppsala University , 751 05 Uppsala, Sweden.,Ridgeview Instruments AB , Dag Hammarskjölds väg 28, 75237 Uppsala, Sweden
| | - Hanna Björkelund
- Ridgeview Instruments AB , Dag Hammarskjölds väg 28, 75237 Uppsala, Sweden
| | - Marika Nestor
- Department of Immunology, Genetics and Pathology, Uppsala University , 751 05 Uppsala, Sweden
| | - Karl Andersson
- Department of Immunology, Genetics and Pathology, Uppsala University , 751 05 Uppsala, Sweden.,Ridgeview Instruments AB , Dag Hammarskjölds väg 28, 75237 Uppsala, Sweden
| | - Jos Buijs
- Department of Immunology, Genetics and Pathology, Uppsala University , 751 05 Uppsala, Sweden.,Ridgeview Instruments AB , Dag Hammarskjölds väg 28, 75237 Uppsala, Sweden
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6
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Bondza S, Foy E, Brooks J, Andersson K, Robinson J, Richalet P, Buijs J. Real-time Characterization of Antibody Binding to Receptors on Living Immune Cells. Front Immunol 2017; 8:455. [PMID: 28484455 PMCID: PMC5401896 DOI: 10.3389/fimmu.2017.00455] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 04/04/2017] [Indexed: 11/19/2022] Open
Abstract
Understanding molecular interactions on immune cells is crucial for drug development to treat cancer and autoimmune diseases. When characterizing molecular interactions, the use of a relevant living model system is important, as processes such as receptor oligomerization and clustering can influence binding patterns. We developed a protocol to enable time-resolved analysis of ligand binding to receptors on living suspension cells. Different suspension cell lines and weakly adhering cells were tethered to Petri dishes with the help of a biomolecular anchor molecule, and antibody binding was analyzed using LigandTracer. The protocol and assay described in this report were used to characterize interactions involving eight cell lines. Experiments were successfully conducted in three different laboratories, demonstrating the robustness of the protocol. For various antibodies, affinities and kinetic rate constants were obtained for binding to CD20 on both Daudi and Ramos B-cells, the T-cell co-receptor CD3 on Jurkat cells, and the Fcγ receptor CD32 on transfected HEK293 cells, respectively. Analyzing the binding of Rituximab to B-cells resulted in an affinity of 0.7–0.9 nM, which is similar to values reported previously for living B-cells. However, we observed a heterogeneous behavior for Rituximab interacting with B-cells, which to our knowledge has not been described previously. The understanding of complex interactions will be facilitated with the possibility to characterize binding processes in real-time on living immune cells. This provides the chance to broaden the understanding of how binding kinetics relate to biological function.
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Affiliation(s)
- Sina Bondza
- Ridgeview Instruments AB, Vänge, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Eleanor Foy
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | | | - Karl Andersson
- Ridgeview Instruments AB, Vänge, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - James Robinson
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK
| | | | - Jos Buijs
- Ridgeview Instruments AB, Vänge, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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7
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Barta P, Janousek J, Zilkova K, Trejtnar F. In vitroevaluation of concentration, labeling effectiveness and stability for131I-labeled radioimmunoassay ligand using real-time detection technology. J Labelled Comp Radiopharm 2016; 60:80-86. [DOI: 10.1002/jlcr.3478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 10/31/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Pavel Barta
- Department of Biophysics and Physical Chemistry, Faculty of Pharmacy; Charles University; Hradec Kralove Czech Republic
| | - Jiri Janousek
- Department of Pharmacology and Toxicology, Faculty of Pharmacy; Charles University; Hradec Kralove Czech Republic
| | - Katerina Zilkova
- Department of Nuclear Medicine; Faculty Hospital Hradec Kralove; Czech Republic
| | - Frantisek Trejtnar
- Department of Pharmacology and Toxicology, Faculty of Pharmacy; Charles University; Hradec Kralove Czech Republic
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8
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Bondza S, Stenberg J, Nestor M, Andersson K, Björkelund H. Conjugation Effects on Antibody–Drug Conjugates: Evaluation of Interaction Kinetics in Real Time on Living Cells. Mol Pharm 2014; 11:4154-63. [DOI: 10.1021/mp500379d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sina Bondza
- Section
of Biomedical Radiation Sciences, Department of Radiology, Oncology
and Radiation Science, Rudbeck Laboratory, Uppsala University, SE-751
85 Uppsala, Sweden
| | - Jonas Stenberg
- Section
of Biomedical Radiation Sciences, Department of Radiology, Oncology
and Radiation Science, Rudbeck Laboratory, Uppsala University, SE-751
85 Uppsala, Sweden
- Ridgeview Instruments AB, Vänge, Sweden
| | - Marika Nestor
- Section
of Biomedical Radiation Sciences, Department of Radiology, Oncology
and Radiation Science, Rudbeck Laboratory, Uppsala University, SE-751
85 Uppsala, Sweden
- Section
of Otolaryngology and Head and Neck Surgery, Department of Surgical
Sciences, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Karl Andersson
- Section
of Biomedical Radiation Sciences, Department of Radiology, Oncology
and Radiation Science, Rudbeck Laboratory, Uppsala University, SE-751
85 Uppsala, Sweden
- Ridgeview Instruments AB, Vänge, Sweden
| | - Hanna Björkelund
- Section
of Biomedical Radiation Sciences, Department of Radiology, Oncology
and Radiation Science, Rudbeck Laboratory, Uppsala University, SE-751
85 Uppsala, Sweden
- Ridgeview Instruments AB, Vänge, Sweden
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Barta P, Volkova M, Dascalu A, Spiegelberg D, Trejtnar F, Andersson K. Determination of receptor protein binding site specificity and relative binding strength using a time-resolved competition assay. J Pharmacol Toxicol Methods 2014; 70:145-51. [PMID: 25084055 DOI: 10.1016/j.vascn.2014.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 07/17/2014] [Accepted: 07/17/2014] [Indexed: 10/25/2022]
Abstract
INTRODUCTION Competitive binding assays can be used to decipher not only the binding kinetics of studied ligands but also the binding site preference. Such assays are an essential step in the characterization of radioligands. However, the currently used competition assays require high concentrations of usually expensive ligands and still provide only binding site preference. By employing the time-resolved competition assay presented in this paper, binding characteristics including binding site preference can be obtained using less ligand. METHODS To demonstrate the appropriateness of the time-resolved competition assay, we developed an assay in which the ligand binding was interrupted with a competitor. Experiments were performed on human carcinoma cell lines expressing epidermal growth factor receptor (EGFR). The targeting of the receptor was performed with radio-iodinated epidermal growth factor (EGF). The employed competitors involved either natural ligand transforming growth factor alpha (TGF-α) or anti-EGFR antibodies cetuximab and panitumumab targeting the same EGFR domain. RESULTS Radio-iodinated EGF bound to EGFR was displaced with either low concentrations of cetuximab or high concentrations of panitumumab. In the case of TGF-α, we observed no competitive displacement of bound EGF at either high or low concentrations. When comparing the time-resolved competition assay with a manual competition assay, the resulting data of measured inhibition constants were in agreement. DISCUSSION The results summarised in this study confirm the appropriateness of the time-resolved competition assay for assessing ligand binding properties. The assay has the potential to complement or replace conventional competition assays for determining binding site preference in the future.
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Affiliation(s)
- Pavel Barta
- Faculty of Pharmacy in Hradec Kralove, Department of Pharmacology and Toxicology, Charles University in Prague, Hyerovskeho 1203, 50005 Hradec Kralove, Czech Republic.
| | - Marie Volkova
- Faculty of Pharmacy in Hradec Kralove, Department of Pharmacology and Toxicology, Charles University in Prague, Hyerovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - Adrian Dascalu
- Rudbeck Laboratory/BMS, Department of Radiology, Oncology and Radiation Sciences, Uppsala University, Dag Hammarskjölds väg 20, 75185, Uppsala, Sweden
| | - Diana Spiegelberg
- Rudbeck Laboratory/BMS, Department of Radiology, Oncology and Radiation Sciences, Uppsala University, Dag Hammarskjölds väg 20, 75185, Uppsala, Sweden
| | - Frantisek Trejtnar
- Faculty of Pharmacy in Hradec Kralove, Department of Pharmacology and Toxicology, Charles University in Prague, Hyerovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - Karl Andersson
- Rudbeck Laboratory/BMS, Department of Radiology, Oncology and Radiation Sciences, Uppsala University, Dag Hammarskjölds väg 20, 75185, Uppsala, Sweden; Ridgeview Instruments AB, Skillsta 4, 74020 Vänge, Sweden
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