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Schardt JS, Jhajj HS, O’Meara RL, Lwo TS, Smith MD, Tessier PM. Agonist antibody discovery: Experimental, computational, and rational engineering approaches. Drug Discov Today 2022; 27:31-48. [PMID: 34571277 PMCID: PMC8714685 DOI: 10.1016/j.drudis.2021.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/19/2021] [Accepted: 09/20/2021] [Indexed: 01/03/2023]
Abstract
Agonist antibodies that activate cellular signaling have emerged as promising therapeutics for treating myriad pathologies. Unfortunately, the discovery of rare antibodies with the desired agonist functions is a major bottleneck during drug development. Nevertheless, there has been important recent progress in discovering and optimizing agonist antibodies against a variety of therapeutic targets that are activated by diverse signaling mechanisms. Herein, we review emerging high-throughput experimental and computational methods for agonist antibody discovery as well as rational molecular engineering methods for optimizing their agonist activity.
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Affiliation(s)
- John S. Schardt
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Harkamal S. Jhajj
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ryen L. O’Meara
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Timon S. Lwo
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew D. Smith
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter M. Tessier
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
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2
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Ganaie SS, Schwarz MM, McMillen CM, Price DA, Feng AX, Albe JR, Wang W, Miersch S, Orvedahl A, Cole AR, Sentmanat MF, Mishra N, Boyles DA, Koenig ZT, Kujawa MR, Demers MA, Hoehl RM, Moyle AB, Wagner ND, Stubbs SH, Cardarelli L, Teyra J, McElroy A, Gross ML, Whelan SPJ, Doench J, Cui X, Brett TJ, Sidhu SS, Virgin HW, Egawa T, Leung DW, Amarasinghe GK, Hartman AL. Lrp1 is a host entry factor for Rift Valley fever virus. Cell 2021; 184:5163-5178.e24. [PMID: 34559985 DOI: 10.1016/j.cell.2021.09.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 04/29/2021] [Accepted: 09/01/2021] [Indexed: 12/26/2022]
Abstract
Rift Valley fever virus (RVFV) is a zoonotic pathogen with pandemic potential. RVFV entry is mediated by the viral glycoprotein (Gn), but host entry factors remain poorly defined. Our genome-wide CRISPR screen identified low-density lipoprotein receptor-related protein 1 (mouse Lrp1/human LRP1), heat shock protein (Grp94), and receptor-associated protein (RAP) as critical host factors for RVFV infection. RVFV Gn directly binds to specific Lrp1 clusters and is glycosylation independent. Exogenous addition of murine RAP domain 3 (mRAPD3) and anti-Lrp1 antibodies neutralizes RVFV infection in taxonomically diverse cell lines. Mice treated with mRAPD3 and infected with pathogenic RVFV are protected from disease and death. A mutant mRAPD3 that binds Lrp1 weakly failed to protect from RVFV infection. Together, these data support Lrp1 as a host entry factor for RVFV infection and define a new target to limit RVFV infections.
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Affiliation(s)
- Safder S Ganaie
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Madeline M Schwarz
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Cynthia M McMillen
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - David A Price
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Annie X Feng
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Joseph R Albe
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wenjie Wang
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Shane Miersch
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Anthony Orvedahl
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Aidan R Cole
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Monica F Sentmanat
- Genome Engineering and iPSC Center (GEiC), Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Nawneet Mishra
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Devin A Boyles
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zachary T Koenig
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael R Kujawa
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew A Demers
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ryan M Hoehl
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Austin B Moyle
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Nicole D Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Sarah H Stubbs
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Lia Cardarelli
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Joan Teyra
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Anita McElroy
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Pediatrics, Division of Pediatric Infectious Disease, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University in St. Louis, St. Louis, MO, USA
| | - John Doench
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xiaoxia Cui
- Genome Engineering and iPSC Center (GEiC), Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Tom J Brett
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Herbert W Virgin
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA; Current address: Vir Biotechnology, San Francisco, CA, USA
| | - Takeshi Egawa
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Daisy W Leung
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA; Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
| | - Amy L Hartman
- Center for Vaccine Research, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA; Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA.
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3
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Perez-Witzke D, Parmar R, Blancq I, Turpin MA, Ponchel F. Development of a long-term, IL7 dependent cell death rescue assay in CD4+ T-cells. J Immunol Methods 2021; 493:113020. [PMID: 33705736 DOI: 10.1016/j.jim.2021.113020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 02/12/2021] [Accepted: 03/04/2021] [Indexed: 10/22/2022]
Abstract
Interfering with signalling pathways by targeting cell surface proteins has become an important strategy in the development of novel therapeutic agents. Notably, interfering with cytokine signalling revolutionised the treatment of chronic diseases. Cytokines can induce a range of effects that are not always accounted for in assays detecting cytokine binding to cell surface receptors and/or proximal signalling interference. Hence, robust assays are needed to characterise the activity of potential drug candidates targeting such effects. We chose interleukin-7 (IL7) as a cytokine model due to its long-term effect on T-cells. In this report we describe the development and refinement of an in vitro assay for measuring the long-term effect of IL7, more specifically on CD4+ T-cells, while the assay could be adapted to look at CD8+ T-cells. PBMCs and/or purified CD4+ T-cells stained with VPD450 (cell cycle dye) were expanded for 5 days using the mitogen Phytohemagglutinin and/or CD3/CD28 agonists. This resulted in cell proliferation (VPD450 dilution) and activation-induced cell death (7-AAD uptake) which was rescued by the addition of IL7, resulting in cell survival over a further 5 days. JAK-inhibitor (Tofactinib) or a blocking anti-IL7Rα antibody (clone R34.34) abolished cell survival suggesting antagonism, while another antibody (clone A019D5) displayed an agonist effect. These results were confirmed at the proximal signalling level using an IL7/STAT5-luciferase reporter assay. This novel assay for a biological long term effect may be useful for the characterisation of potential therapeutic drugs targeting the IL7/IL7R in CD4+ T-cells.
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Affiliation(s)
- Daniel Perez-Witzke
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, UK
| | - Rekha Parmar
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, UK
| | - Ileana Blancq
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, UK
| | - Marie-Alix Turpin
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, UK
| | - Frederique Ponchel
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, UK.
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Liu S, Miersch S, Li P, Bai B, Liu C, Qin W, Su J, Huang H, Pan J, Sidhu SS, Wu D. A Synthetic Human Antibody Antagonizes IL-18Rβ Signaling Through an Allosteric Mechanism. J Mol Biol 2020; 432:1169-1182. [PMID: 31954129 DOI: 10.1016/j.jmb.2020.01.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/07/2020] [Accepted: 01/08/2020] [Indexed: 01/01/2023]
Abstract
The interleukin-18 subfamily belongs to the interleukin-1 family and plays an important role in modulating innate and adaptive immune responses. Dysregulation of IL-18 has been implicated in or correlated with numerous diseases, including inflammatory diseases, autoimmune disorders, and cancer. Thus, blockade of IL-18 signaling may offer therapeutic benefits in many pathological settings. Here, we report the development of synthetic human antibodies that target human IL-18Rβ and block IL-18-mediated IFN-γ secretion by inhibiting NF-κB and MAPK dependent pathways. The crystal structure of a potent antagonist antibody in complex with IL-18Rβ revealed inhibition through an unexpected allosteric mechanism. Our findings offer a novel means for therapeutic intervention in the IL-18 pathway and may provide a new strategy for targeting cytokine receptors.
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Affiliation(s)
- Shusu Liu
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Shane Miersch
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Ping Li
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China; Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, China
| | - Bingxin Bai
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Chunchun Liu
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Wenming Qin
- National Facility for Protein Science (Shanghai), Shanghai Advanced Research Institute (Zhangjiang Lab), Chinese Academy of Sciences, Shanghai, China
| | - Jie Su
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Haiming Huang
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Shanghai Asian United Antibody Medical Co., Shanghai, China
| | - James Pan
- Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Sachdev S Sidhu
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China; Banting and Best Department of Medical Research, Terrence Donnelly Center for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
| | - Donghui Wu
- Laboratory of Antibody Engineering, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.
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Spangler JB, Moraga I, Jude KM, Savvides CS, Garcia KC. A strategy for the selection of monovalent antibodies that span protein dimer interfaces. J Biol Chem 2019; 294:13876-13886. [PMID: 31387945 PMCID: PMC6755802 DOI: 10.1074/jbc.ra119.009213] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/15/2019] [Indexed: 11/06/2022] Open
Abstract
Ligand-induced dimerization is the predominant mechanism through which secreted proteins activate cell surface receptors to transmit essential biological signals. Cytokines are a large class of soluble proteins that dimerize transmembrane receptors into precise signaling topologies, but there is a need for alternative, engineerable ligand scaffolds that specifically recognize and stabilize these protein interactions. Recombinant antibodies can potentially serve as robust and versatile platforms for cytokine complex stabilization, and their specificity allows for tunable modulation of dimerization equilibrium. Here, we devised an evolutionary strategy to isolate monovalent antibody fragments that bridge together two different receptor subunits in a cytokine-receptor complex, precisely as the receptors are disposed in their natural signaling orientations. To do this, we screened a naive antibody library against a stabilized ligand-receptor ternary complex that acted as a "molecular cast" of the natural receptor dimer conformation. Our selections elicited "stapler" single-chain variable fragments (scFvs) of antibodies that specifically engage the interleukin-4 receptor heterodimer. The 3.1 Å resolution crystal structure of one such stapler revealed that, as intended, this scFv recognizes a composite epitope between the two receptors as they are positioned in the complex. Extending our approach, we evolved a stapler scFv that specifically binds to and stabilizes the interface between the interleukin-2 cytokine and one of its receptor subunits, leading to a 15-fold enhancement in interaction affinity. This demonstration that scFvs can be selected to recognize epitopes that span protein interfaces presents new opportunities to engineer structurally defined antibodies for a broad range of research and therapeutic applications.
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Affiliation(s)
- Jamie B Spangler
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305 .,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218
| | - Ignacio Moraga
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
| | - Kevin M Jude
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
| | - Christina S Savvides
- Department of Biology, Stanford University School of Medicine, Stanford, California 94305
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305 .,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
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6
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Ebersberger A. The analgesic potential of cytokine neutralization with biologicals. Eur J Pharmacol 2018; 835:19-30. [DOI: 10.1016/j.ejphar.2018.07.040] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/26/2018] [Accepted: 07/19/2018] [Indexed: 12/13/2022]
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7
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Imkeller K, Wardemann H. Assessing human B cell repertoire diversity and convergence. Immunol Rev 2018; 284:51-66. [DOI: 10.1111/imr.12670] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - Hedda Wardemann
- German Cancer Research Center; B Cell Immunology; Heidelberg Germany
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Miersch S, Kuruganti S, Walter MR, Sidhu SS. A panel of synthetic antibodies that selectively recognize and antagonize members of the interferon alpha family. Protein Eng Des Sel 2017; 30:697-704. [PMID: 28981904 PMCID: PMC5914384 DOI: 10.1093/protein/gzx048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/25/2017] [Accepted: 08/09/2017] [Indexed: 11/12/2022] Open
Abstract
The 12 distinct subtypes that comprise the interferon alpha (IFNα) family of cytokines possess anti-viral, anti-proliferative and immunomodulatory activities. They are implicated in the etiology and progression of many diseases, and also used as therapeutic agents for viral and oncologic disorders. However, a deeper understanding of their role in disease is limited by a lack of tools to evaluate single subtypes at the protein level. Antibodies that selectively inhibit single IFNα subtypes could enable interrogation of each protein in biological samples and could be used for characterization and treatment of disease. Using phage-displayed synthetic antibody libraries, we have conducted selections against 12 human IFNα subtypes to explore our ability to obtain fine-specificity antibodies that recognize and antagonize the biological signals induced by a single IFNα subtype. For the first time, we have isolated antibodies that specifically recognize individual IFNα subtypes (IFNα2a/b, IFNα6, IFNα8b and IFNα16) with high affinity that antagonize signaling. Our results show that highly specific antibodies capable of distinguishing between closely related cytokines can be isolated from synthetic libraries and can be used to characterize cytokine abundance and function.
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Affiliation(s)
- S Miersch
- The Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada M5G 1L6
| | - S Kuruganti
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - M R Walter
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - S S Sidhu
- The Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada M5G 1L6
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