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Low S, Wu H, Jerath K, Tibolla A, Fogal B, Conrad R, MacDougall M, Kerr S, Berger V, Dave R, Villalona J, Pantages L, Ahlberg J, Li H, Van Hoorick D, Ververken C, Broadwater J, Waterman A, Singh S, Kroe-Barrett R. VHH antibody targeting the chemokine receptor CX3CR1 inhibits progression of atherosclerosis. MAbs 2021; 12:1709322. [PMID: 31924119 PMCID: PMC6973309 DOI: 10.1080/19420862.2019.1709322] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
CX3CR1 has been identified as a highly attractive target for several therapeutic interventions. Despite this potential, no potent antagonists, either small molecule or monoclonal antibody, have been identified. Here we describe the lead finding and engineering approach that lead to the identification of BI 655088, a potent biotherapeutic antagonist to CX3CR1. BI 655088 is a potent CX3CR1 antagonist that, upon therapeutic dosing, significantly inhibits plaque progression in the standard mouse model of atherosclerosis. BI 655088 represents a novel and highly selective biotherapeutic that could reduce inflammation in the atherosclerotic plaque when added to standard of care treatment including statins, which could result in a significant decrease in atherothrombotic events in patients with existing cardiovascular disease.
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Affiliation(s)
- Sarah Low
- Biotherapeutics Molecule Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Haixia Wu
- Biotherapeutics Molecule Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Kavita Jerath
- Biotherapeutics Molecule Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Annette Tibolla
- Cardiometabolic Disease Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Birgit Fogal
- Cardiometabolic Disease Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Rebecca Conrad
- Cardiometabolic Disease Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Margit MacDougall
- Cardiometabolic Disease Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Steven Kerr
- Cardiometabolic Disease Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Valentina Berger
- Cardiometabolic Disease Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Rajvee Dave
- Cardiometabolic Disease Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Jorge Villalona
- Cardiometabolic Disease Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Lynn Pantages
- Cardiometabolic Disease Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Jennifer Ahlberg
- Biotherapeutics Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Hua Li
- Biotherapeutics Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | | | - Cedric Ververken
- Project Management, Ablynx a Sanofi Company, Zwijnaarde, Belgium
| | - John Broadwater
- Cardiometabolic Disease Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Alisa Waterman
- Cardiometabolic Disease Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Sanjaya Singh
- Biotherapeutics Molecule Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
| | - Rachel Kroe-Barrett
- Biotherapeutics Molecule Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, USA
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Cheloha RW, Harmand TJ, Wijne C, Schwartz TU, Ploegh HL. Exploring cellular biochemistry with nanobodies. J Biol Chem 2020; 295:15307-15327. [PMID: 32868455 PMCID: PMC7650250 DOI: 10.1074/jbc.rev120.012960] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/27/2020] [Indexed: 12/21/2022] Open
Abstract
Reagents that bind tightly and specifically to biomolecules of interest remain essential in the exploration of biology and in their ultimate application to medicine. Besides ligands for receptors of known specificity, agents commonly used for this purpose are monoclonal antibodies derived from mice, rabbits, and other animals. However, such antibodies can be expensive to produce, challenging to engineer, and are not necessarily stable in the context of the cellular cytoplasm, a reducing environment. Heavy chain-only antibodies, discovered in camelids, have been truncated to yield single-domain antibody fragments (VHHs or nanobodies) that overcome many of these shortcomings. Whereas they are known as crystallization chaperones for membrane proteins or as simple alternatives to conventional antibodies, nanobodies have been applied in settings where the use of standard antibodies or their derivatives would be impractical or impossible. We review recent examples in which the unique properties of nanobodies have been combined with complementary methods, such as chemical functionalization, to provide tools with unique and useful properties.
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Affiliation(s)
- Ross W Cheloha
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Thibault J Harmand
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Charlotte Wijne
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | - Thomas U Schwartz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA.
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Structure-based engineering of anti-GFP nanobody tandems as ultra-high-affinity reagents for purification. Sci Rep 2020; 10:6239. [PMID: 32277083 PMCID: PMC7148334 DOI: 10.1038/s41598-020-62606-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/16/2020] [Indexed: 11/17/2022] Open
Abstract
Green fluorescent proteins (GFPs) are widely used in biological research. Although GFP can be visualized easily, its precise manipulation through binding partners is still burdensome because of the limited availability of high-affinity binding partners and related structural information. Here, we report the crystal structure of GFPuv in complex with the anti-GFP nanobody LaG16 at 1.67 Å resolution, revealing the details of the binding between GFPuv and LaG16. The LaG16 binding site was on the opposite side of the GFP β-barrel from the binding site of the GFP-enhancer, another anti-GFP nanobody, indicating that the GFP-enhancer and LaG16 can bind to GFP together. Thus, we further designed 3 linkers of different lengths to fuse LaG16 and GFP-enhancer together, and the GFP binding of the three constructs was further tested by ITC. The construct with the (GGGGS)4 linker had the highest affinity with a KD of 0.5 nM. The GFP-enhancer-(GGGGS)4-LaG16 chimeric nanobody was further covalently linked to NHS-activated agarose and then used in the purification of a GFP-tagged membrane protein, GFP-tagged zebrafish P2X4, resulting in higher yield than purification with the GFP-enhancer nanobody alone. This work provides a proof of concept for the design of ultra-high-affinity binders of target proteins through dimerized nanobody chimaeras, and this strategy may also be applied to link interesting target protein nanobodies without overlapping binding surfaces.
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Ding L, Wang Z, Zhong P, Jiang H, Zhao Z, Zhang Y, Ren Z, Ding Y. Structural insights into the mechanism of single domain VHH antibody binding to cortisol. FEBS Lett 2019; 593:1248-1256. [PMID: 31049949 DOI: 10.1002/1873-3468.13398] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/26/2019] [Accepted: 04/29/2019] [Indexed: 12/13/2022]
Abstract
To date, few structural models of VHH antibody binding to low molecular weight haptens have been reported. Here, we report the crystal structure of cortisol binding to its VHH antibody NbCor at pH 3.5 and 10.5. Cortisol binds to NbCor mainly by burying itself under the tunnel formed by the complementarity determining region 1 (CDR1) of NbCor. The affinity of NbCor binding to cortisol and similar compounds was also verified by a microscale thermophoresis assay. Combining our findings with several previously reported structures of hapten-VHH antibody complexes, we propose that VHH antibodies exhibit a special mechanism of binding small haptens by encapsulating them in a tunnel formed by CDR1. Our findings provide useful structural information for the further development and optimization of hapten-specific VHH antibodies.
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Affiliation(s)
- Lulu Ding
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Ziying Wang
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Peiyu Zhong
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - He Jiang
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhixuan Zhao
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Yiran Zhang
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhen Ren
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Yu Ding
- Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
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Colley CS, England E, Linley JE, Wilkinson TCI. Screening Strategies for the Discovery of Ion Channel Monoclonal Antibodies. ACTA ACUST UNITED AC 2018; 82:e44. [DOI: 10.1002/cpph.44] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Caroline S. Colley
- Antibody Discovery and Protein Engineering, MedImmune; Cambridge United Kingdom
| | - Elizabeth England
- Antibody Discovery and Protein Engineering, MedImmune; Cambridge United Kingdom
| | - John E. Linley
- Neuroscience, IMED Biotech Unit, AstraZeneca; Cambridge United Kingdom
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Banihashemi SR, Hosseini AZ, Rahbarizadeh F, Ahmadvand D. Development of specific nanobodies (VHH) for CD19 immuno-targeting of human B-lymphocytes. IRANIAN JOURNAL OF BASIC MEDICAL SCIENCES 2018; 21:455-464. [PMID: 29922424 PMCID: PMC6000210 DOI: 10.22038/ijbms.2018.26778.6557] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 09/28/2017] [Indexed: 12/13/2022]
Abstract
OBJECTIVES CD19 is a transmembrane glycoprotein of immunoglobulin superfamily. In order to treat lymphoma, monoclonal antibodies (mAb) can target different antigens, including CD19, CD20 and CD22 on the surface of B-cells. Along with biotechnology progress, a new generation of antibodies is introduced, with the purpose of eliminating the defects of the previous generation. Among the most developed one are nanobodies (Nb). Nbs are a unique kind of camelid single domain antibody fragments with a broad range of medical applications. Unique physicochemical properties of Nbs have made them ideal candidates for therapeutic and diagnostic applications. MATERIALS AND METHODS An immune gene library was created, and several CD19 specific Nbs were selected through antigen panning process, and their molecular properties as well as specificity, sensitivity, affinity and immunoreactivity against CD19 positive and negative cells were evaluated. RESULTS The Nb library was prepared with 7.2 x107 members. We managed to isolate a panel of CD19-specific Nbs after the last round of selection with the affinity of isolated Nbs being estimated at the standard range of 15-35 nM. Sequence analysis of positive clones was indicative of the fact that 12 variable sequences were confirmed. Of all these 12 clones, 2 clones with the greatest level signal in ELISA underwent subsequent analysis. Our sequencing results indicated high sequence homology (approximately 90%) between the Nb and Homa variable immunoglobulin domains. CONCLUSION Specific Nbs possess the potential to be used as novel therapeutic approaches in order to treat autoimmune diseases and B-cell lymphoma.
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Affiliation(s)
- Seyed Reza Banihashemi
- Department of Medical Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ahmad Zavaran Hosseini
- Department of Medical Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Rahbarizadeh
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Davoud Ahmadvand
- Department of Medical Biochemistry, Faculty of Applied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
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Miya Shaik M, Tamargo IA, Abubakar MB, Kamal MA, Greig NH, Gan SH. The Role of microRNAs in Alzheimer's Disease and Their Therapeutic Potentials. Genes (Basel) 2018; 9:genes9040174. [PMID: 29561798 PMCID: PMC5924516 DOI: 10.3390/genes9040174] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/05/2018] [Accepted: 03/05/2018] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are short, endogenous, non-coding RNAs that post-transcriptionally regulate gene expression by base pairing with mRNA targets. Altered miRNA expression profiles have been observed in several diseases, including neurodegeneration. Multiple studies have reported altered expressions of miRNAs in the brains of individuals with Alzheimer’s disease (AD) as compared to those of healthy elderly adults. Some of the miRNAs found to be dysregulated in AD have been reported to correlate with neuropathological changes, including plaque and tangle accumulation, as well as altered expressions of species that are known to be involved in AD pathology. To examine the potentially pathogenic functions of several dysregulated miRNAs in AD, we review the current literature with a focus on the activities of ten miRNAs in biological pathways involved in AD pathogenesis. Comprehensive understandings of the expression profiles and activities of these miRNAs will illuminate their roles as potential therapeutic targets in AD brain and may lead to the discovery of breakthrough treatment strategies for AD.
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Affiliation(s)
- Munvar Miya Shaik
- School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Malaysia.
| | - Ian A Tamargo
- Drug Design and Development Section, Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Murtala B Abubakar
- Department of Physiology, Faculty of Basic Medical Sciences, College of Health Sciences, Usmanu Danfodiyo University, PMB 2254 Sokoto, Nigeria.
| | - Mohammad A Kamal
- Metabolomics and Enzymology Unit, Fundamental and Applied Biology Group, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia.
| | - Nigel H Greig
- Drug Design and Development Section, Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
| | - Siew Hua Gan
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Selangor, Malaysia.
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Harmansa S, Affolter M. Protein binders and their applications in developmental biology. Development 2018; 145:145/2/dev148874. [PMID: 29374062 DOI: 10.1242/dev.148874] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Developmental biology research would benefit greatly from tools that enable protein function to be regulated, both systematically and in a precise spatial and temporal manner, in vivo In recent years, functionalized protein binders have emerged as versatile tools that can be used to target and manipulate proteins. Such protein binders can be based on various scaffolds, such as nanobodies, designed ankyrin repeat proteins (DARPins) and monobodies, and can be used to block or perturb protein function in living cells. In this Primer, we provide an overview of the protein binders that are currently available and highlight recent progress made in applying protein binder-based tools in developmental and synthetic biology.
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Affiliation(s)
- Stefan Harmansa
- Growth and Development, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Markus Affolter
- Growth and Development, Biozentrum, University of Basel, 4056 Basel, Switzerland
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Eden T, Menzel S, Wesolowski J, Bergmann P, Nissen M, Dubberke G, Seyfried F, Albrecht B, Haag F, Koch-Nolte F. A cDNA Immunization Strategy to Generate Nanobodies against Membrane Proteins in Native Conformation. Front Immunol 2018; 8:1989. [PMID: 29410663 PMCID: PMC5787055 DOI: 10.3389/fimmu.2017.01989] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/21/2017] [Indexed: 12/20/2022] Open
Abstract
Nanobodies (Nbs) are soluble, versatile, single-domain binding modules derived from the VHH variable domain of heavy-chain antibodies naturally occurring in camelids. Nbs hold huge promise as novel therapeutic biologics. Membrane proteins are among the most interesting targets for therapeutic Nbs because they are accessible to systemically injected biologics. In order to be effective, therapeutic Nbs must recognize their target membrane protein in native conformation. However, raising Nbs against membrane proteins in native conformation can pose a formidable challenge since membrane proteins typically contain one or more hydrophobic transmembrane regions and, therefore, are difficult to purify in native conformation. Here, we describe a highly efficient genetic immunization strategy that circumvents these difficulties by driving expression of the target membrane protein in native conformation by cells of the immunized camelid. The strategy encompasses ballistic transfection of skin cells with cDNA expression plasmids encoding one or more orthologs of the membrane protein of interest and, optionally, other costimulatory proteins. The plasmid is coated onto 1 µm gold particles that are then injected into the shaved and depilated skin of the camelid. A gene gun delivers a helium pulse that accelerates the DNA-coated particles to a velocity sufficient to penetrate through multiple layers of cells in the skin. This results in the exposure of the extracellular domains of the membrane protein on the cell surface of transfected cells. Repeated immunization drives somatic hypermutation and affinity maturation of target-specific heavy-chain antibodies. The VHH/Nb coding region is PCR-amplified from B cells obtained from peripheral blood or a lymph node biopsy. Specific Nbs are selected by phage display or by screening of Nb-based heavy-chain antibodies expressed as secretory proteins in transfected HEK cells. Using this strategy, we have successfully generated agonistic and antagonistic Nbs against several cell surface ecto-enzymes and ligand-gated ion channels.
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Affiliation(s)
- Thomas Eden
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephan Menzel
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Janusz Wesolowski
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Philine Bergmann
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marion Nissen
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gudrun Dubberke
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fabienne Seyfried
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Birte Albrecht
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Haag
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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