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Lin N, Miyamoto K, Ogawara T, Sakurai S, Kizaka-Kondoh S, Kadonosono T. Epitope binning for multiple antibodies simultaneously using mammalian cell display and DNA sequencing. Commun Biol 2024; 7:652. [PMID: 38806676 PMCID: PMC11133372 DOI: 10.1038/s42003-024-06363-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 05/21/2024] [Indexed: 05/30/2024] Open
Abstract
Epitope binning, an approach for grouping antibodies based on epitope similarities, is a critical step in antibody drug discovery. However, conventional methods are complex, involving individual antibody production. Here, we established Epitope Binning-seq, an epitope binning platform for simultaneously analyzing multiple antibodies. In this system, epitope similarity between the query antibodies (qAbs) displayed on antigen-expressing cells and a fluorescently labeled reference antibody (rAb) targeting a desired epitope is analyzed by flow cytometry. The qAbs with epitope similar to the rAb can be identified by next-generation sequencing analysis of fluorescence-negative cells. Sensitivity and reliability of this system are confirmed using rAbs, pertuzumab and trastuzumab, which target human epidermal growth factor receptor 2. Epitope Binning-seq enables simultaneous epitope evaluation of 14 qAbs at various abundances in libraries, grouping them into respective epitope bins. This versatile platform is applicable to diverse antibodies and antigens, potentially expediting the identification of clinically useful antibodies.
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Affiliation(s)
- Ning Lin
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Kotaro Miyamoto
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Takumi Ogawara
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Saki Sakurai
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Shinae Kizaka-Kondoh
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Tetsuya Kadonosono
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan.
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2
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Jhajj HS, Schardt JS, Khalasawi N, Yao EL, Lwo TS, Kwon NY, O'Meara RL, Desai AA, Tessier PM. Facile generation of biepitopic antibodies with intrinsic agonism for activating tumor necrosis factor receptors. Cell Chem Biol 2024; 31:944-954.e5. [PMID: 38653243 PMCID: PMC11142405 DOI: 10.1016/j.chembiol.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/28/2024] [Accepted: 03/29/2024] [Indexed: 04/25/2024]
Abstract
Agonist antibodies are being pursued for therapeutic applications ranging from neurodegenerative diseases to cancer. For the tumor necrosis factor (TNF) receptor superfamily, higher-order clustering of three or more receptors is key to their activation, which can be achieved using antibodies that recognize two unique epitopes. However, the generation of biepitopic (i.e., biparatopic) antibodies typically requires animal immunization and is laborious and unpredictable. Here, we report a simple method for identifying biepitopic antibodies that potently activate TNF receptors without the need for additional animal immunization. Our approach uses existing, receptor-specific IgGs, which lack intrinsic agonist activity, to block their corresponding epitopes, then selects single-chain antibodies that bind accessible epitopes. The selected antibodies are fused to the light chains of IgGs to generate human tetravalent antibodies. We highlight the broad utility of this approach by converting several clinical-stage antibodies against OX40 and CD137 (4-1BB) into biepitopic antibodies with potent agonist activity.
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MESH Headings
- Humans
- Epitopes/immunology
- Epitopes/chemistry
- Animals
- Receptors, Tumor Necrosis Factor/agonists
- Receptors, Tumor Necrosis Factor/immunology
- Receptors, Tumor Necrosis Factor/metabolism
- Tumor Necrosis Factor Receptor Superfamily, Member 9/agonists
- Tumor Necrosis Factor Receptor Superfamily, Member 9/immunology
- Tumor Necrosis Factor Receptor Superfamily, Member 9/metabolism
- Tumor Necrosis Factor Receptor Superfamily, Member 9/antagonists & inhibitors
- Receptors, OX40/agonists
- Receptors, OX40/immunology
- Receptors, OX40/metabolism
- Receptors, OX40/antagonists & inhibitors
- Antibodies/immunology
- Single-Chain Antibodies/immunology
- Single-Chain Antibodies/chemistry
- Single-Chain Antibodies/pharmacology
- Mice
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Affiliation(s)
- 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
| | - John S Schardt
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Namir Khalasawi
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Emily L Yao
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, 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
| | - Na-Young Kwon
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemical 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; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alec A Desai
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter M Tessier
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA.
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3
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Jhajj HS, Schardt JS, Khalasawi N, Yao EL, Lwo TS, Kwon NY, O’Meara RL, Desai AA, Tessier PM. Facile generation of biepitopic antibodies with intrinsic agonism for activating receptors in the tumor necrosis factor superfamily. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.11.571146. [PMID: 38168220 PMCID: PMC10760063 DOI: 10.1101/2023.12.11.571146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Agonist antibodies that activate cellular receptors are being pursued for therapeutic applications ranging from neurodegenerative diseases to cancer. For the tumor necrosis factor (TNF) receptor superfamily, higher-order clustering of three or more receptors is key to their potent activation. This can be achieved using antibodies that recognize two unique epitopes on the same receptor and mediate receptor superclustering. However, identifying compatible pairs of antibodies to generate biepitopic antibodies (also known as biparatopic antibodies) for activating TNF receptors typically requires animal immunization and is a laborious and unpredictable process. Here, we report a simple method for systematically identifying biepitopic antibodies that potently activate TNF receptors without the need for additional animal immunization. Our approach uses off-the-shelf, receptor-specific IgG antibodies, which lack intrinsic (Fc-gamma receptor-independent) agonist activity, to first block their corresponding epitopes. Next, we perform selections for single-chain antibodies from human nonimmune libraries that bind accessible epitopes on the same ectodomains using yeast surface display and fluorescence-activated cell sorting. The selected single-chain antibodies are finally fused to the light chains of IgGs to generate human tetravalent antibodies that engage two different receptor epitopes and mediate potent receptor activation. We highlight the broad utility of this approach by converting several existing clinical-stage antibodies against TNF receptors, including ivuxolimab and pogalizumab against OX40 and utomilumab against CD137, into biepitopic antibodies with highly potent agonist activity. We expect that this widely accessible methodology can be used to systematically generate biepitopic antibodies for activating other receptors in the TNF receptor superfamily and many other receptors whose activation is dependent on strong receptor clustering.
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Affiliation(s)
- 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
| | - John S. Schardt
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Namir Khalasawi
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Emily L. Yao
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Biointerfaces Institute, 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
| | - Na-Young Kwon
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemical 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
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alec A. Desai
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter M. Tessier
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
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4
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Rampuria P, Mosyak L, Root AR, Svenson K, Agostino MJ, LaVallie ER. Molecular insights into recognition of GUCY2C by T-cell engaging bispecific antibody anti-GUCY2CxCD3. Sci Rep 2023; 13:13408. [PMID: 37591971 PMCID: PMC10435522 DOI: 10.1038/s41598-023-40467-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 08/10/2023] [Indexed: 08/19/2023] Open
Abstract
The intestinal epithelial receptor Guanylyl Cyclase C (GUCY2C) is a tumor-associated cell surface antigen expressed across gastrointestinal malignancies that can serve as an efficacious target for colorectal cancer immunotherapy. Here, we describe a yeast surface-display approach combined with an orthogonal peptide-based mapping strategy to identify the GUCY2C binding epitope of a novel anti-GUCY2CxCD3 bispecific antibody (BsAb) that recently advanced into the clinic for the treatment of cancer. The target epitope was localized to the N-terminal helix H2 of human GUCY2C, which enabled the determination of the crystal structure of the minimal GUCY2C epitope in complex with the anti-GUCY2C antibody domain. To understand if this minimal epitope covers the entire antibody binding region and to investigate the impact of epitope position on the antibody's activity, we further determined the structure of this interaction in the context of the full-length extracellular domain (ECD) of GUCY2C. We found that this epitope is positioned on the protruding membrane-distal helical region of GUCY2C and that its specific location on the surface of GUCY2C dictates the close spatial proximity of the two antigen arms in a diabody arrangement essential to the tumor killing activity of GUCY2CxCD3 BsAb.
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Affiliation(s)
- Pragya Rampuria
- Biomedicine Design, Pfizer Inc., 610 Main St., Cambridge, MA, 02139, USA.
| | - Lidia Mosyak
- Biomedicine Design, Pfizer Inc., 610 Main St., Cambridge, MA, 02139, USA.
| | - Adam R Root
- Generate Biomedicines Inc, Cambridge, MA, USA
| | - Kristine Svenson
- Biomedicine Design, Pfizer Inc., 610 Main St., Cambridge, MA, 02139, USA
| | | | - Edward R LaVallie
- Biomedicine Design, Pfizer Inc., 610 Main St., Cambridge, MA, 02139, USA
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5
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Ghanbarpour A, Jiang M, Foster D, Chai Q. Structure-free antibody paratope similarity prediction for in silico epitope binning via protein language models. iScience 2023; 26:106036. [PMID: 36824280 PMCID: PMC9941125 DOI: 10.1016/j.isci.2023.106036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/28/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Antibodies are an important group of biological molecules that are used as therapeutics and diagnostic tools. Although millions of antibody sequences are available, identifying their structural and functional similarity and their antigen binding sites remains a challenge at large scale. Here, we present a fast, sequence-based computational method for antibody paratope prediction based on protein language models. The paratope information is then used to measure similarity among antibodies via protein language models. Our computational method enables binning of antibody discovery hits into groups as the function of epitope engagement. We further demonstrate the utility of the method by identifying antibodies targeting highly similar epitopes of the same antigens from a large pool of antibody sequences, using two case studies: SARS CoV2 Receptor Binding Domain (RBD) and Epidermal Growth Factor Receptor (EGFR). Our approach highlights the potential in accelerating antibody discovery by enhancing hit prioritization and diversity selection.
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Affiliation(s)
- Ahmadreza Ghanbarpour
- Biotechnology Discovery Research, Lilly Biotechnology Center, 10300 Campus Point Drive, San Diego, CA 92121, USA
| | - Min Jiang
- Advanced Analytics and Data Sciences, Lilly Corporate Center, Indianapolis, IN 46225, USA
| | - Denisa Foster
- Biotechnology Discovery Research, Lilly Biotechnology Center, 10300 Campus Point Drive, San Diego, CA 92121, USA
| | - Qing Chai
- Biotechnology Discovery Research, Lilly Biotechnology Center, 10300 Campus Point Drive, San Diego, CA 92121, USA,Corresponding author
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6
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Dong T, Han C, Jiang M, Zhang T, Kang Q, Wang P, Zhou F. A Four-Channel Surface Plasmon Resonance Sensor Functionalized Online for Simultaneous Detections of Anti-SARS-CoV-2 Antibody, Free Viral Particles, and Neutralized Viral Particles. ACS Sens 2022; 7:3560-3570. [PMID: 36382569 DOI: 10.1021/acssensors.2c02067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Current tests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detect either the constituent nucleic acids/proteins of the viral particles or antibodies specific to the virus, but cannot provide information about viral neutralization by an antibody and the efficacy of an antibody. Such information is important about individuals' vulnerability to severe symptoms or their likelihood of showing no symptoms. We immobilized online SARS-CoV-2 spike (S1) protein and angiotensin-converting enzyme 2 (ACE2) into separate surface plasmon resonance (SPR) channels of a tris-nitrilotriacetic acid (tris-NTA) chip to simultaneously detect the anti-S1 antibody and viral particles in serum samples. In addition, with a high-molecular-weight-cutoff filter, we separated the neutralized viral particles from the free antibody molecules and used a sensing channel immobilized with Protein G to determine antibody-neutralized viral particles. The optimal density of probe molecules in each fluidic channel can be precisely controlled through the closure and opening of the specific ports. By utilizing the high surface density of ACE2, multiple assays can be carried out without regenerations. These three species can be determined with a short analysis time (<12 min per assay) and excellent sensor-to-sensor/cycle-to-cycle reproducibility (RSD < 5%). When coupled with an autosampler, continuous assays can be performed in an unattended manner at a single chip for up to 6 days. Such a sensor capable of assaying serum samples containing the three species at different levels provides additional insights into the disease status and immunity of persons being tested, which should be helpful for containing the SARS-CoV-2 spread during the era of incessant viral mutations.
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Affiliation(s)
- Tianbao Dong
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong, P. R. China, 250022
| | - Chaowei Han
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong, P. R. China, 250022
| | - Meng Jiang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong, P. R. China, 250022
| | - Tiantian Zhang
- University Hospital, University of Jinan, Jinan, Shandong, P. R. China, 250022
| | - Qing Kang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong, P. R. China, 250022
| | - Pengcheng Wang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong, P. R. China, 250022
| | - Feimeng Zhou
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan, Shandong, P. R. China, 250022
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7
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Agnihotri P, Mishra AK, Agarwal P, Vignali KM, Workman CJ, Vignali DAA, Mariuzza RA. Epitope Mapping of Therapeutic Antibodies Targeting Human LAG3. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:1586-1594. [PMID: 36104110 PMCID: PMC9696730 DOI: 10.4049/jimmunol.2200309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/11/2022] [Indexed: 12/12/2022]
Abstract
Lymphocyte activation gene 3 protein (LAG3; CD223) is an inhibitory receptor that is highly upregulated on exhausted T cells in tumors and chronic viral infection. Consequently, LAG3 is now a major immunotherapeutic target for the treatment of cancer, and many mAbs against human (h) LAG3 (hLAG3) have been generated to block its inhibitory activity. However, little or no information is available on the epitopes they recognize. We selected a panel of seven therapeutic mAbs from the patent literature for detailed characterization. These mAbs were expressed as Fab or single-chain variable fragments and shown to bind hLAG3 with nanomolar affinities, as measured by biolayer interferometry. Using competitive binding assays, we found that the seven mAbs recognize four distinct epitopes on hLAG3. To localize the epitopes, we carried out epitope mapping using chimeras between hLAG3 and mouse LAG3. All seven mAbs are directed against the first Ig-like domain (D1) of hLAG3, despite their different origins. Three mAbs almost exclusively target a unique 30-residue loop of D1 that forms at least part of the putative binding site for MHC class II, whereas four mainly recognize D1 determinants outside this loop. However, because all the mAbs block binding of hLAG3 to MHC class II, each of the epitopes they recognize must at least partially overlap the MHC class II binding site.
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Affiliation(s)
- Pragati Agnihotri
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD
| | - Arjun K Mishra
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD
| | - Priyanka Agarwal
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA; and
| | - Kate M Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA; and
| | - Creg J Workman
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA; and
| | - Dario A A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA; and
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA
| | - Roy A Mariuzza
- W.M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD;
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD
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8
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Wilder BK, Vigdorovich V, Carbonetti S, Minkah N, Hertoghs N, Raappana A, Cardamone H, Oliver BG, Trakhimets O, Kumar S, Dambrauskas N, Arredondo SA, Camargo N, Seilie AM, Murphy SC, Kappe SHI, Sather DN. Anti-TRAP/SSP2 monoclonal antibodies can inhibit sporozoite infection and may enhance protection of anti-CSP monoclonal antibodies. NPJ Vaccines 2022; 7:58. [PMID: 35618791 PMCID: PMC9135708 DOI: 10.1038/s41541-022-00480-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 04/22/2022] [Indexed: 11/10/2022] Open
Abstract
Vaccine-induced sterilizing protection from infection by Plasmodium parasites, the pathogens that cause malaria, will be essential in the fight against malaria as it would prevent both malaria-related disease and transmission. Stopping the relatively small number of parasites injected by the mosquito before they can migrate from the skin to the liver is an attractive means to this goal. Antibody-eliciting vaccines have been used to pursue this objective by targeting the major parasite surface protein present during this stage, the circumsporozoite protein (CSP). While CSP-based vaccines have recently had encouraging success in disease reduction, this was only achieved with extremely high antibody titers and appeared less effective for a complete block of infection (i.e., sterile protection). While such disease reduction is important, these and other results indicate that strategies focusing on CSP alone may not achieve the high levels of sterile protection needed for malaria eradication. Here, we show that monoclonal antibodies (mAbs) recognizing another sporozoite protein, TRAP/SSP2, exhibit a range of inhibitory activity and that these mAbs may augment CSP-based protection despite conferring no sterile protection on their own. Therefore, pursuing a multivalent subunit vaccine immunization is a promising strategy for improving infection-blocking malaria vaccines.
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Affiliation(s)
- Brandon K Wilder
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
- Vaccine and Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR, 97006, USA
| | - Vladimir Vigdorovich
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Sara Carbonetti
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Nana Minkah
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Nina Hertoghs
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Andrew Raappana
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Hayley Cardamone
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Brian G Oliver
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Olesya Trakhimets
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Nicholas Dambrauskas
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Silvia A Arredondo
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Nelly Camargo
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Annette M Seilie
- Department of Laboratory Medicine and Pathology and Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, WA, USA
| | - Sean C Murphy
- Department of Laboratory Medicine and Pathology and Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, WA, USA
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Stefan H I Kappe
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA.
- Department of Pediatrics, University of Washington, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA.
| | - D Noah Sather
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA.
- Department of Pediatrics, University of Washington, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA.
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9
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Houy C, Ming M, Ettorre L, Jin R, Thangavadivel N, Chen T, Su J, Gajewska B. Epitope Profiling of Diphtheria Toxoid Provides Enhanced Monitoring for Consistency Testing during Manufacturing Process Changes. Vaccines (Basel) 2022; 10:vaccines10050775. [PMID: 35632531 PMCID: PMC9147534 DOI: 10.3390/vaccines10050775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/30/2022] [Accepted: 05/10/2022] [Indexed: 11/16/2022] Open
Abstract
In the vaccine industry, multiple physicochemical, immunological, in vitro and in vivo analytical methods are applied throughout the manufacturing process to characterize and monitor the quality of vaccines. Presented here is the Single Epitope Antigenicity Test (SEAT), an innovative, quantitative epitope profiling method which provides an extended immunochemical analysis for diphtheria toxoid (DTxd) to be used for consistency testing during manufacturing process changes. The method uses BioLayer Interferometry (BLI) and a panel of monoclonal antibodies (mAbs) to independently assess nine individual antigenic sites of DTxd. The panel includes mAbs which are functional, bind distinct sites on DTxd and are able to distinguish intact DTxd from that which has been exposed to heat treatment. The SEAT method was qualified for precision, accuracy, and linearity, and was used to define a preliminary comparability range for DTxd made using the current manufacturing process. DTxd lots manufactured using alternate processes were assessed in the context of this range to determine the impact on DTxd antigenicity. Epitope profiling by SEAT provides quantitative information on the integrity of multiple important antigenic regions of DTxd, and therefore represents a valuable tool in a comprehensive analytical test package which can be used to support manufacturing process changes for vaccines.
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Affiliation(s)
- Camille Houy
- Correspondence: ; Tel.: +1-476-667-2700 (ext. 7629)
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10
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Brooks BD, Beland A, Aguero G, Taylor N, Towne FD. Moving beyond Titers. Vaccines (Basel) 2022; 10:vaccines10050683. [PMID: 35632439 PMCID: PMC9144832 DOI: 10.3390/vaccines10050683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 01/27/2023] Open
Abstract
Vaccination to prevent and even eliminate disease is amongst the greatest achievements of modern medicine. Opportunities remain in vaccine development to improve protection across the whole population. A next step in vaccine development is the detailed molecular characterization of individual humoral immune responses against a pathogen, especially the rapidly evolving pathogens. New technologies such as sequencing the immune repertoire in response to disease, immunogenomics/vaccinomics, particularly the individual HLA variants, and high-throughput epitope characterization offer new insights into disease protection. Here, we highlight the emerging technologies that could be used to identify variation within the human population, facilitate vaccine discovery, improve vaccine safety and efficacy, and identify mechanisms of generating immunological memory. In today’s vaccine-hesitant climate, these techniques used individually or especially together have the potential to improve vaccine effectiveness and safety and thus vaccine uptake rates. We highlight the importance of using these techniques in combination to understand the humoral immune response as a whole after vaccination to move beyond neutralizing titers as the standard for immunogenicity and vaccine efficacy, especially in clinical trials.
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Affiliation(s)
- Benjamin D. Brooks
- Department of Biomedical Sciences, Rocky Vista University, Ivins, UT 84738, USA
- Inovan Inc., Fargo, ND 58103, USA
- Correspondence: ; Tel.: +1-(435)-222-1304
| | - Alexander Beland
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80112, USA; (A.B.); (G.A.); (N.T.); (F.D.T.)
| | - Gabriel Aguero
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80112, USA; (A.B.); (G.A.); (N.T.); (F.D.T.)
| | - Nicholas Taylor
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80112, USA; (A.B.); (G.A.); (N.T.); (F.D.T.)
| | - Francina D. Towne
- College of Osteopathic Medicine, Rocky Vista University, Parker, CO 80112, USA; (A.B.); (G.A.); (N.T.); (F.D.T.)
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11
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Jiang M, Dong T, Han C, Liu L, Zhang T, Kang Q, Wang P, Zhou F. Regenerable and high-throughput surface plasmon resonance assay for rapid screening of anti-SARS-CoV-2 antibody in serum samples. Anal Chim Acta 2022; 1208:339830. [PMID: 35525598 PMCID: PMC9006689 DOI: 10.1016/j.aca.2022.339830] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/30/2022] [Accepted: 04/11/2022] [Indexed: 12/12/2022]
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12
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Mahita J, Kim DG, Son S, Choi Y, Kim HS, Bailey-Kellogg C. Computational epitope binning reveals functional equivalence of sequence-divergent paratopes. Comput Struct Biotechnol J 2022; 20:2169-2180. [PMID: 35615020 PMCID: PMC9118127 DOI: 10.1016/j.csbj.2022.04.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 11/26/2022] Open
Abstract
Epitope binning groups target-specific protein binders recognizing the same binding region. The “Epibin” method utilizes docking models to computationally predict competition and identify bins. Epibin recapitulated binding competition of repebody variants as determined by immunoassays. In addition, Epibin enabled identification of ‘paratope-equivalent’ residues in sequence-dissimilar variants. Computational epitope binning can scale to allow characterization of entire antigen-specific antibody repertoires.
The therapeutic efficacy of a protein binder largely depends on two factors: its binding site and its binding affinity. Advances in in vitro library display screening and next-generation sequencing have enabled accelerated development of strong binders, yet identifying their binding sites still remains a major challenge. The differentiation, or “binning”, of binders into different groups that recognize distinct binding sites on their target is a promising approach that facilitates high-throughput screening of binders that may show different biological activity. Here we study the extent to which the information contained in the amino acid sequences comprising a set of target-specific binders can be leveraged to bin them, inferring functional equivalence of their binding regions, or paratopes, based directly on comparison of the sequences, their modeled structures, or their modeled interactions. Using a leucine-rich repeat binding scaffold known as a “repebody” as the source of diversity in recognition against interleukin-6 (IL-6), we show that the “Epibin” approach introduced here effectively utilized structural modelling and docking to extract specificity information encoded in the repebody amino acid sequences and thereby successfully recapitulate IL-6 binding competition observed in immunoassays. Furthermore, our computational binning provided a basis for designing in vitro mutagenesis experiments to pinpoint specificity-determining residues. Finally, we demonstrate that the Epibin approach can extend to antibodies, retrospectively comparing its predictions to results from antigen-specific antibody competition studies. The study thus demonstrates the utility of modeling structure and binding from the amino acid sequences of different binders against the same target, and paves the way for larger-scale binning and analysis of entire repertoires.
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13
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Conformation-locking antibodies for the discovery and characterization of KRAS inhibitors. Nat Biotechnol 2022; 40:769-778. [PMID: 34992247 DOI: 10.1038/s41587-021-01126-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 10/07/2021] [Indexed: 11/08/2022]
Abstract
Small molecules that stabilize inactive protein conformations are an underutilized strategy for drugging dynamic or otherwise intractable proteins. To facilitate the discovery and characterization of such inhibitors, we created a screening platform to identify conformation-locking antibodies for molecular probes (CLAMPs) that distinguish and induce rare protein conformational states. Applying the approach to KRAS, we discovered CLAMPs that recognize the open conformation of KRASG12C stabilized by covalent inhibitors. One CLAMP enables the visualization of KRASG12C covalent modification in vivo and can be used to investigate response heterogeneity to KRASG12C inhibitors in patient tumors. A second CLAMP enhances the affinity of weak ligands binding to the KRASG12C switch II region (SWII) by stabilizing a specific conformation of KRASG12C, thereby enabling the discovery of such ligands that could serve as leads for the development of drugs in a high-throughput screen. We show that combining the complementary properties of antibodies and small molecules facilitates the study and drugging of dynamic proteins.
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14
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Rhea K. Determining the Binding Kinetics of Peptide Macrocycles Using Bio-Layer Interferometry (BLI). METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2371:355-372. [PMID: 34596858 DOI: 10.1007/978-1-0716-1689-5_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Bio-Layer Interferometry (BLI) enables the detection and characterization of molecular interactions in real-time without the hassle and interference of labeling. The affinity constant (KD) obtained in the BLI analysis is an excellent indicator of quality of biomolecules such as antibodies, aptamers, peptides, etc. This method was used to analyze a peptide macrocycle against the Abrax protein, but can be used for any peptide macrocycle/analyte system.
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Affiliation(s)
- Katherine Rhea
- EXCET, Inc., Springfield, VA, USA. .,US Army Combat Capabilities Development Command, Chemical Biological Center (DEVCOM-CBC), Edgewood, MD, USA.
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15
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Corless E, Hao Y, Jia H, Kongsuphol P, Tay DMY, Ng SY, Sikes HD. Generation of Thermally Stable Affinity Pairs for Sensitive, Specific Immunoassays. Methods Mol Biol 2022; 2491:417-469. [PMID: 35482202 DOI: 10.1007/978-1-0716-2285-8_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Many point-of-care diagnostic tests rely on a pair of monoclonal antibodies that bind to two distinct epitopes of a molecule of interest. This protocol describes the identification and generation of such affinity pairs based on an easily produced small protein scaffold rcSso7d which can substitute monoclonal antibodies. These strong binding variants are identified from a large yeast display library. The approach described can be significantly faster than antibody generation and epitope binning, yielding affinity pairs synthesized in common bacterial protein synthesis strains, enabling the rapid generation of novel diagnostic tools.
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Affiliation(s)
- Elliot Corless
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yining Hao
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Huan Jia
- Antimicrobial Resistance Interdisciplinary Research Group (AMR-IRG), Singapore-MIT Alliance in Research and Technology (SMART), Singapore, Singapore
| | - Patthara Kongsuphol
- Antimicrobial Resistance Interdisciplinary Research Group (AMR-IRG), Singapore-MIT Alliance in Research and Technology (SMART), Singapore, Singapore
| | - Dousabel M Y Tay
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Say Yong Ng
- Antimicrobial Resistance Interdisciplinary Research Group (AMR-IRG), Singapore-MIT Alliance in Research and Technology (SMART), Singapore, Singapore
| | - Hadley D Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Antimicrobial Resistance Interdisciplinary Research Group (AMR-IRG), Singapore-MIT Alliance in Research and Technology (SMART), Singapore, Singapore.
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16
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Matharu Z, Bee C, Schwarz F, Chen H, Tomlinson M, Wu G, Rakestraw G, Hornsby M, Drake A, Strop P, Rajpal A, Dollinger G. High-Throughput Surface Plasmon Resonance Biosensors for Identifying Diverse Therapeutic Monoclonal Antibodies. Anal Chem 2021; 93:16474-16480. [PMID: 34854675 DOI: 10.1021/acs.analchem.1c03548] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Identification of antibodies targeting diverse functional epitopes on an antigen is highly crucial for discovering effective therapeutic candidates. Employing a traditional stepwise antibody "screening funnel" as well as prioritizing affinity-based selections over epitope-based selections, result in lead antibody panels lacking epitope diversity. In the present study, we employed an array-based surface plasmon resonance (SPR) platform to perform high-throughput epitope binning analysis on a large number of monoclonal antibodies (mAbs) generated in the early drug discovery process. The mAb panel contained clones from different antibody generation techniques and diverse transgenic mouse strains. The epitope binning results were analyzed in unique ways using various visualizations in the form of dendrograms and network plots, which assisted in determining diversity and redundancy in the mAb sample set. The binning data were further integrated with affinity information to evaluate the performance of seven different transgenic mouse strains. The combination of epitope binning results with binding kinetics and sequence analysis provided an effective and efficient way of selecting high affinity antibodies representing a diverse set of sequence families and epitopes.
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Affiliation(s)
- Zimple Matharu
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Christine Bee
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States.,Frontier Medicines, South San Francisco, California 94080, United States
| | - Flavio Schwarz
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Haibin Chen
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Matthew Tomlinson
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Gabriel Wu
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Ginger Rakestraw
- Bristol Myers Squibb, Cambridge, Massachusetts 02142, United States
| | - Michael Hornsby
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Andrew Drake
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
| | - Pavel Strop
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States.,Biologics Discovery, Tallac Therapeutics, Burlingame, California 94010, United States
| | - Arvind Rajpal
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States.,Large Molecule Drug Discovery, Genentech, Inc., South San Francisco, California 94080, United States
| | - Gavin Dollinger
- Discovery Biotherapeutics, Bristol Myers Squibb, Redwood City, California 94063, United States
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17
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Su X, Ramírez-Escudero M, Sun F, van den Dikkenberg JB, van Steenbergen MJ, Pieters RJ, Janssen BJC, van Hasselt PM, Hennink WE, van Nostrum CF. Internalization and Transport of PEGylated Lipid-Based Mixed Micelles across Caco-2 Cells Mediated by Scavenger Receptor B1. Pharmaceutics 2021; 13:2022. [PMID: 34959304 PMCID: PMC8703698 DOI: 10.3390/pharmaceutics13122022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/12/2021] [Accepted: 11/17/2021] [Indexed: 11/16/2022] Open
Abstract
The aim of this study was to get insight into the internalization and transport of PEGylat-ed mixed micelles loaded by vitamin K, as mediated by Scavenger Receptor B1 (SR-B1) that is abundantly expressed by intestinal epithelium cells as well as by differentiated Caco-2 cells. Inhibition of SR-B1 reduced endocytosis and transport of vitamin-K-loaded 0%, 30% and 50% PEGylated mixed micelles and decreased colocalization of the micelles with SR-B1. Confocal fluorescence microscopy, fluorescence-activated cell sorting (FACS) analysis, and surface plasmon resonance (SPR) were used to study the interaction between the mixed micelles of different compositions (varying vitamin K loading and PEG content) and SR-B1. Interaction of PEGylated micelles was independent of the vitamin K content, indicating that the PEG shell prevented vitamin K exposure at the surface of the micelles and binding with the receptor and that the PEG took over the micelles' ability to bind to the receptor. Molecular docking calculations corroborated the dual binding of both vita-min K and PEG with the binding domain of SR-B1. In conclusion, the improved colloidal stability of PEGylated mixed micelles did not compromise their cellular uptake and transport due to the affinity of PEG for SR-B1. SR-B1 is able to interact with PEGylated nanoparticles and mediates their subsequent internalization and transport.
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Affiliation(s)
- Xiangjie Su
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands; (X.S.); (F.S.); (J.B.v.d.D.); (M.J.v.S.); (W.E.H.)
| | - Mercedes Ramírez-Escudero
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.R.-E.); (B.J.C.J.)
| | - Feilong Sun
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands; (X.S.); (F.S.); (J.B.v.d.D.); (M.J.v.S.); (W.E.H.)
| | - Joep B. van den Dikkenberg
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands; (X.S.); (F.S.); (J.B.v.d.D.); (M.J.v.S.); (W.E.H.)
| | - Mies J. van Steenbergen
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands; (X.S.); (F.S.); (J.B.v.d.D.); (M.J.v.S.); (W.E.H.)
| | - Roland J. Pieters
- Department of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands;
| | - Bert J. C. Janssen
- Structural Biochemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.R.-E.); (B.J.C.J.)
| | - Peter M. van Hasselt
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, 3584 EA Utrecht, The Netherlands;
| | - Wim E. Hennink
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands; (X.S.); (F.S.); (J.B.v.d.D.); (M.J.v.S.); (W.E.H.)
| | - Cornelus F. van Nostrum
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CG Utrecht, The Netherlands; (X.S.); (F.S.); (J.B.v.d.D.); (M.J.v.S.); (W.E.H.)
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18
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Spatola BN, Lerner AG, Wong C, Dela Cruz T, Welch M, Fung W, Kovalenko M, Losenkova K, Yegutkin GG, Beers C, Corbin J, Soros VB. Fully human anti-CD39 antibody potently inhibits ATPase activity in cancer cells via uncompetitive allosteric mechanism. MAbs 2021; 12:1838036. [PMID: 33146056 PMCID: PMC7646477 DOI: 10.1080/19420862.2020.1838036] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The extracellular ATP/adenosine axis in the tumor microenvironment (TME) has emerged as an important immune-regulatory pathway. Nucleoside triphosphate diphosphohydrolase-1 (NTPDase1), otherwise known as CD39, is highly expressed in the TME, both on infiltrating immune cells and tumor cells across a broad set of cancer indications. CD39 processes pro-inflammatory extracellular ATP to ADP and AMP, which is then processed by Ecto-5ʹ-nucleotidase/CD73 to immunosuppressive adenosine. Directly inhibiting the enzymatic function of CD39 via an antibody has the potential to unleash an immune-mediated anti-tumor response via two mechanisms: 1) increasing the availability of immunostimulatory extracellular ATP released by damaged and/or dying cells, and 2) reducing the generation and accumulation of suppressive adenosine within the TME. Tizona Therapeutics has engineered a novel first-in-class fully human anti-CD39 antibody, TTX-030, that directly inhibits CD39 ATPase enzymatic function with sub-nanomolar potency. Further characterization of the mechanism of inhibition by TTX-030 using CD39+ human melanoma cell line SK-MEL-28 revealed an uncompetitive allosteric mechanism (α < 1). The uncompetitive mechanism of action enables TTX-030 to inhibit CD39 at the elevated ATP concentrations reported in the TME. Maximal inhibition of cellular CD39 ATPase velocity was 85%, which compares favorably to results reported for antibody inhibitors to other enzyme targets. The allosteric mechanism of TTX-030 was confirmed via mapping the epitope to a region of CD39 distant from its active site, which suggests possible models for how potent inhibition is achieved. In summary, TTX-030 is a potent allosteric inhibitor of CD39 ATPase activity that is currently being evaluated in clinical trials for cancer therapy.
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Affiliation(s)
- Bradley N Spatola
- Antibody Development, Tizona Therapeutics , South San Francisco, CA, USA
| | - Alana G Lerner
- Immunology, Tizona Therapeutics , South San Francisco, CA, USA
| | - Clifford Wong
- Antibody Development, Tizona Therapeutics , South San Francisco, CA, USA
| | - Tracy Dela Cruz
- Immunology, Tizona Therapeutics , South San Francisco, CA, USA.,Immunology, Trishula Therapeutics, South San Francisco , CA, USA
| | - Megan Welch
- Immunology, Tizona Therapeutics , South San Francisco, CA, USA
| | - Wanchi Fung
- Antibody Development, Tizona Therapeutics , South San Francisco, CA, USA
| | | | | | | | - Courtney Beers
- Immunology, Tizona Therapeutics , South San Francisco, CA, USA
| | - John Corbin
- Antibody Development, Tizona Therapeutics , South San Francisco, CA, USA
| | - Vanessa B Soros
- Antibody Development, Tizona Therapeutics , South San Francisco, CA, USA
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19
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Doyle MP, Kose N, Borisevich V, Binshtein E, Amaya M, Nagel M, Annand EJ, Armstrong E, Bombardi R, Dong J, Schey KL, Broder CC, Zeitlin L, Kuang EA, Bornholdt ZA, West BR, Geisbert TW, Cross RW, Crowe JE. Cooperativity mediated by rationally selected combinations of human monoclonal antibodies targeting the henipavirus receptor binding protein. Cell Rep 2021; 36:109628. [PMID: 34469726 PMCID: PMC8527959 DOI: 10.1016/j.celrep.2021.109628] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/25/2021] [Accepted: 08/05/2021] [Indexed: 11/25/2022] Open
Abstract
Hendra virus and Nipah virus (NiV), members of the Henipavirus (HNV) genus, are zoonotic paramyxoviruses known to cause severe disease across six mammalian orders, including humans. We isolated a panel of human monoclonal antibodies (mAbs) from the B cells of an individual with prior exposure to equine Hendra virus (HeV) vaccine, targeting distinct antigenic sites. The most potent class of cross-reactive antibodies achieves neutralization by blocking viral attachment to the host cell receptors ephrin-B2 and ephrin-B3, with a second class being enhanced by receptor binding. mAbs from both classes display synergistic activity in vitro. In a stringent hamster model of NiV Bangladesh (NiVB) infection, antibodies from both classes reduce morbidity and mortality and achieve synergistic protection in combination. These candidate mAbs might be suitable for use in a cocktail therapeutic approach to achieve synergistic potency and reduce the risk of virus escape. Doyle et al. describe two human monoclonal antibodies that target the henipavirus receptor-binding protein, HENV-103 and HENV-117, that display highly potent activity in vitro and enhanced therapeutic efficacy in vivo when delivered as a cocktail.
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Affiliation(s)
- Michael P Doyle
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Nurgun Kose
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Viktoriya Borisevich
- Department of Microbiology & Immunology, The University of Texas Medical Branch, Galveston, TX 77555, USA; Galveston National Laboratory, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Elad Binshtein
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Moushimi Amaya
- Department of Microbiology & Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Marcus Nagel
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Edward J Annand
- Sydney School of Veterinary Science and Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia; Black Mountain Laboratories & Australian Centre for Disease Preparedness, Health and Biosecurity, CSIRO, Canberra & Geelong, Australia
| | - Erica Armstrong
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robin Bombardi
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jinhui Dong
- The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kevin L Schey
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - Christopher C Broder
- Department of Microbiology & Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Larry Zeitlin
- Mapp Biopharmaceutical, Inc., San Diego, CA 92121, USA
| | - Erin A Kuang
- Mapp Biopharmaceutical, Inc., San Diego, CA 92121, USA
| | | | | | - Thomas W Geisbert
- Department of Microbiology & Immunology, The University of Texas Medical Branch, Galveston, TX 77555, USA; Galveston National Laboratory, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Robert W Cross
- Department of Microbiology & Immunology, The University of Texas Medical Branch, Galveston, TX 77555, USA; Galveston National Laboratory, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - James E Crowe
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; The Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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20
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Tahir S, Bourquard T, Musnier A, Jullian Y, Corde Y, Omahdi Z, Mathias L, Reiter E, Crépieux P, Bruneau G, Poupon A. Accurate determination of epitope for antibodies with unknown 3D structures. MAbs 2021; 13:1961349. [PMID: 34432559 PMCID: PMC8405158 DOI: 10.1080/19420862.2021.1961349] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
MAbTope is a docking-based method for the determination of epitopes. It has been used to successfully determine the epitopes of antibodies with known 3D structures. However, during the antibody discovery process, this structural information is rarely available. Although we already have evidence that homology models of antibodies could be used instead of their 3D structure, the choice of the template, the methodology for homology modeling and the resulting performance still have to be clarified. Here, we show that MAbTope has the same performance when working with homology models of the antibodies as compared to crystallographic structures. Moreover, we show that even low-quality models can be used. We applied MAbTope to determine the epitope of dupilumab, an anti- interleukin 4 receptor alpha subunit therapeutic antibody of unknown 3D structure, that we validated experimentally. Finally, we show how the MAbTope-determined epitopes for a series of antibodies targeting the same protein can be used to predict competitions, and demonstrate the accuracy with an experimentally validated example. 3D: three-dimensionalRMSD: root mean square deviationCDR: complementary-determining regionCPU: central processing unitsVH: heavy chain variable regionVL: light chain variable regionscFv: single-chain variable fragmentsVHH: single-chain antibody variable regionIL4Rα: Interleukin 4 receptor alpha chainSPR: surface plasmon resonancePDB: protein data bankHEK293: Human embryonic kidney 293 cellsEDTA: Ethylenediaminetetraacetic acidFBS: Fetal bovine serumANOVA: Analysis of varianceEGFR: Epidermal growth factor receptorPE: PhycoerythrinAPC: AllophycocyaninFSC: forward scatterSSC: side scatterWT: wild type Keywords: MAbTope, Epitope Mapping, Molecular docking, Antibody modeling, Antibody-antigen docking
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Affiliation(s)
- Shifa Tahir
- PRC, INRAE, CNRS, Université De Tours, Nouzilly, France
| | - Thomas Bourquard
- PRC, INRAE, CNRS, Université De Tours, Nouzilly, France.,MAbSilico SAS, 1 Impasse Du Palais
| | - Astrid Musnier
- PRC, INRAE, CNRS, Université De Tours, Nouzilly, France.,MAbSilico SAS, 1 Impasse Du Palais
| | - Yann Jullian
- MAbSilico SAS, 1 Impasse Du Palais.,CaSciModOT, UFR De Sciences Et Techniques, Université De Tours
| | | | | | | | - Eric Reiter
- PRC, INRAE, CNRS, Université De Tours, Nouzilly, France.,France Inria, Inria Saclay-Île-de-France, Palaiseau, France.,Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | - Pascale Crépieux
- PRC, INRAE, CNRS, Université De Tours, Nouzilly, France.,France Inria, Inria Saclay-Île-de-France, Palaiseau, France.,Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | | | - Anne Poupon
- PRC, INRAE, CNRS, Université De Tours, Nouzilly, France.,MAbSilico SAS, 1 Impasse Du Palais.,France Inria, Inria Saclay-Île-de-France, Palaiseau, France.,Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
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21
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Kim S, Yee E, Miller EA, Hao Y, Tay DMY, Sung KJ, Jia H, Johnson JM, Saeed M, Mace CR, Yüksel Yurt D, Sikes HD. Developing a SARS-CoV-2 Antigen Test Using Engineered Affinity Proteins. ACS APPLIED MATERIALS & INTERFACES 2021; 13:38990-39002. [PMID: 34379400 DOI: 10.1021/acsami.1c08174] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The ongoing COVID-19 pandemic has clearly established how vital rapid, widely accessible diagnostic tests are in controlling infectious diseases and how difficult and slow it is to scale existing technologies. Here, we demonstrate the use of the rapid affinity pair identification via directed selection (RAPIDS) method to discover multiple affinity pairs for SARS-CoV-2 nucleocapsid protein (N-protein), a biomarker of COVID-19, from in vitro libraries in 10 weeks. The pair with the highest biomarker sensitivity was then integrated into a 10 min, vertical-flow cellulose paper test. Notably, the as-identified affinity proteins were compatible with a roll-to-roll printing process for large-scale manufacturing of tests. The test achieved 40 and 80 pM limits of detection in 1× phosphate-buffered saline (mock swab) and saliva matrices spiked with cell-culture-generated SARS-CoV-2 viruses and is also capable of detection of N-protein from characterized clinical swab samples. Hence, this work paves the way toward the mass production of cellulose paper-based assays which can address the shortages faced due to dependence on nitrocellulose and current manufacturing techniques. Further, the results reported herein indicate the promise of RAPIDS and engineered binder proteins for the timely and flexible development of clinically relevant diagnostic tests in response to emerging infectious diseases.
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Affiliation(s)
- Seunghyeon Kim
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Emma Yee
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Eric A Miller
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Yining Hao
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Dousabel M Y Tay
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ki-Joo Sung
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Huan Jia
- Antimicrobial Resistance Integrated Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore 138602, Singapore
| | - Joseph M Johnson
- Quanterix Corporation, Billerica, Massachusetts 01821, United States
| | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, United States
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston, Massachusetts 02188, United States
| | - Charles R Mace
- Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
| | | | - Hadley D Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Antimicrobial Resistance Integrated Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore 138602, Singapore
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22
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Critical reagent generation, characterization, handling and storage workflows: impact on ligand binding assays. Bioanalysis 2021; 13:847-860. [PMID: 33890503 DOI: 10.4155/bio-2020-0252] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The foundation of pharmacokinetics and antidrug antibodies assay robustness relies on the use of high-quality reagents. Over the past decade, there has been increasing interest within the pharmaceutical industry, as well as regulators, on defining best practices and scientific approaches for generation, characterization and handling of critical reagents. In this review, we will discuss current knowledge and practices on critical reagent workflows and state-of-the-art approaches for characterization, generation, stability and storage and how each of these steps can impact ligand-binding assay robustness.
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23
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Kim S, Yee E, Miller EA, Hao Y, Tay DMY, Sung KJ, Jia H, Johnson JM, Saeed M, Mace CR, Yurt DY, Sikes HD. Developing a SARS-CoV-2 Antigen Test Using Engineered Affinity Proteins. CHEMRXIV : THE PREPRINT SERVER FOR CHEMISTRY 2021:14442785. [PMID: 34013166 PMCID: PMC8132241 DOI: 10.26434/chemrxiv.14442785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 04/19/2021] [Indexed: 11/09/2022]
Abstract
The ongoing COVID-19 pandemic has clearly established how vital rapid, widely accessible diagnostic tests are in controlling infectious diseases and how difficult and slow it is to scale existing technologies. Here, we demonstrate the use of the rapid affinity pair identification via directed selection (RAPIDS) method to discover multiple affinity pairs for SARS-CoV-2 nucleocapsid protein (N-protein), a biomarker of COVID-19, from in vitro libraries in 10 weeks. The pair with the highest biomarker sensitivity was then integrated into a 10-minute, vertical-flow cellulose paper test. Notably, the as-identified affinity proteins were compatible with a roll-to-roll printing process for large-scale manufacturing of tests. The test achieved 40 pM and 80 pM limits of detection in 1×PBS (mock swab) and saliva matrices spiked with cell-culture generated SARS-CoV-2 viruses and is also capable of detection of N-protein from characterized clinical swab samples. Hence, this work paves the way towards the mass production of cellulose paper-based assays which can address the shortages faced due to dependence on nitrocellulose and current manufacturing techniques. Further, the results reported herein indicate the promise of RAPIDS and engineered binder proteins for the timely and flexible development of clinically relevant diagnostic tests in response to emerging infectious diseases.
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Affiliation(s)
- Seunghyeon Kim
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Emma Yee
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eric A. Miller
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yining Hao
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dousabel M. Y. Tay
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ki-Joo Sung
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Huan Jia
- Antimicrobial Resistance Integrated Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore 138602, Singapore
| | | | - Mohsan Saeed
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston, MA 02188, USA
| | - Charles R. Mace
- Department of Chemistry, Tufts University, Medford, MA 02155, USA
| | | | - Hadley D. Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Antimicrobial Resistance Integrated Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore 138602, Singapore
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24
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Using multiple platforms for critical reagents selection process to support pharmacokinetic ligand-binding assay development. Bioanalysis 2021; 13:761-769. [PMID: 33769087 DOI: 10.4155/bio-2020-0257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We have evaluated the utility of epitope binning on biolayer interferometry (BLI) as a strategy to funnel the selection of candidate pairs suitable for pharmacokinetic assay development. Totally, 8 anti-Idiotypic monoclonal antibodies in 64 possible combinations were tested by BLI, ELISA and Gyrolab®. Two epitope binning approaches were utilized, in-tandem and classic sandwich. Both formats identified four mutually exclusive bins providing 31 and 25 possible antibody pair combinations, respectively. In contrast, the ELISA and Gyrolab yielded 18 and 9 positive pairs, respectively, with only a partial correlation to the BLI results. Several positive pairs by ELISA and Gyrolab, screened negative by BLI. Just over half of the pairs predicted by BLI were positive on ELISA and less than a quarter were positive on Gyrolab. This evaluation showed, in our case, that BLI was limited in its ability to predict candidate pairs that would be successful in pharmacokinetic method development.
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25
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Epitope Binning of Novel Monoclonal Anti F1 and Anti LcrV Antibodies and Their Application in a Simple, Short, HTRF Test for Clinical Plague Detection. Pathogens 2021; 10:pathogens10030285. [PMID: 33801490 PMCID: PMC8001648 DOI: 10.3390/pathogens10030285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 11/18/2022] Open
Abstract
Mouse monoclonal antibodies were raised against plague disease biomarkers: the bacterial capsular protein fraction 1 (F1) and the low-calcium response—LcrV virulence factor (Vag). A novel tandem assay, employing BioLayer Interferometry (BLI), enabled the isolation of antibodies against four different epitopes on Vag. The tandem assay was carried out with hybridoma supernatants, circumventing the need for antibody purification. The BioLayer assay was further adopted for characterization of epitope-repetitive antigens, enabling the discovery of two unique epitopes on F1. The selected antibodies were purified and applied as “oligo-clonal” reagents for the immuno-detection of both biomarkers. The developed Homogenous Time Resolved Fluorescence (HTRF) tests were short (10 min) and simple (no washing steps), allowing for detection of 10 ng/mL F1 and 2.5 ng/mL Vag. The tests were successfully applied for detection of disease biomarkers produced by various Y. pestis strains during growth in blood culture vials.
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26
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McMaster M, Mohr K, Page A, Closmore A, Towne F, Brooks BD. Epitope characterization of anti-drug antibodies-a tool for discovery and health: an overview of the necessity of early epitope characterization to avoid anti-drug antibodies and promote patient health. Expert Opin Biol Ther 2021; 21:705-715. [PMID: 33317351 DOI: 10.1080/14712598.2021.1863942] [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] [Indexed: 01/07/2023]
Abstract
Introduction: The market for monoclonal antibody (mAb) therapies is growing rapidly as the pharmaceutical industry expands its development across a broad spectrum of diseases. Unfortunately, as shown in the recent failure of bococizumab by Pfizer, these treatments often stimulate the formation of problematic anti-drug antibodies (ADAs). ADAs can cause side effects and limit efficacy for many patients. To increase efficacy and decrease safety concerns from ADAs, immunogenicity characterization is needed early in the drug development process. Here, we present emerging techniques that hold promise to improve ADA assays and their potential applications to pharmaceutical development and personalized medicine.Areas covered: This manuscript outlines the importance of epitope characterization to better understand immunogenicity and describes a strategy for using this information in treating patients taking mAb therapies.Expert opinion: We propose using high-information assays to characterize epitopes to help mAb therapy engineering and potentially improve individual patient outcomes. To understand this, we will discuss three different aspects of ADAs: (1) the problem of ADAs and what is currently being done about them, (2) the current state of epitope characterization and how it is being utilized, and (3) how early epitope characterization can advance drug discovery and improve outcomes for patients taking mAb therapies.
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Affiliation(s)
- Matthew McMaster
- Department of Biomedical Sciences, Rocky Vista University, Parker, CO, USA
| | - Kelly Mohr
- Department of Biomedical Sciences, Rocky Vista University, Parker, CO, USA
| | - Austin Page
- Department of Biomedical Sciences, Rocky Vista University, Ivins, UT, USA
| | - Adam Closmore
- Department of Pharmacy, North Dakota State University, Fargo, ND, USA
| | - Francina Towne
- Department of Biomedical Sciences, Rocky Vista University, Parker, CO, USA
| | - Benjamin D Brooks
- Department of Biomedical Sciences, Rocky Vista University, Ivins, UT, USA
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27
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Localization of the Interaction Site of Herpes Simplex Virus Glycoprotein D (gD) on the Membrane Fusion Regulator, gH/gL. J Virol 2020; 94:JVI.00983-20. [PMID: 32759318 DOI: 10.1128/jvi.00983-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Abstract
A cascade of protein-protein interactions between four herpes simplex virus (HSV) glycoproteins (gD, gH/gL, and gB) drive fusion between the HSV envelope and host membrane, thereby allowing for virus entry and infection. Specifically, binding of gD to one of its receptors induces a conformational change that allows gD to bind to the regulatory complex gH/gL, which then activates the fusogen gB, resulting in membrane fusion. Using surface plasmon resonance and a panel of anti-gD monoclonal antibodies (MAbs) that sterically blocked the interaction, we previously showed that gH/gL binds directly to gD at sites distinct from the gD receptor binding site. Here, using an analogous strategy, we first evaluated the ability of a panel of uncharacterized anti-gH/gL MAbs to block binding to gD and/or inhibit fusion. We found that the epitopes of four gD-gH/gL-blocking MAbs were located within flexible regions of the gH N terminus and the gL C terminus, while the fifth was placed around gL residue 77. Taken together, our data localized the gD binding region on gH/gL to a group of gH and gL residues at the membrane distal region of the heterodimer. Surprisingly, a second set of MAbs did not block gD-gH/gL binding but instead stabilized the complex by altering the kinetic binding. However, despite this prolonged gD-gH/gL interaction, "stabilizing" MAbs also inhibited cell-cell fusion, suggesting a unique mechanism by which the fusion process is halted. Our findings support targeting the gD-gH/gL interaction to prevent fusion in both therapeutic and vaccine strategies against HSV.IMPORTANCE Key to developing a human HSV vaccine is an understanding of the virion glycoproteins involved in entry. HSV employs multiple glycoproteins for attachment, receptor interaction, and membrane fusion. Determining how these proteins function was resolved, in part, by structural biology coupled with immunological and biologic evidence. After binding, virion gD interacts with a receptor to activate the regulator gH/gL complex, triggering gB to drive fusion. Multiple questions remain, one being the physical location of each glycoprotein interaction site. Using protective antibodies with known epitopes, we documented the long-sought interaction between gD and gH/gL, detailing the region on gD important to create the gD-gH/gL triplex. Now, we have identified the corresponding gD contact sites on gH/gL. Concurrently we discovered a novel mechanism whereby gH/gL antibodies stabilize the complex and inhibit fusion progression. Our model for the gD-gH/gL triplex provides a new framework for studying fusion, which identifies targets for vaccine development.
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28
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A panel of human neutralizing mAbs targeting SARS-CoV-2 spike at multiple epitopes. Nat Commun 2020; 11:4303. [PMID: 32855401 PMCID: PMC7452893 DOI: 10.1038/s41467-020-18159-4] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/05/2020] [Indexed: 12/14/2022] Open
Abstract
The novel highly transmissible human coronavirus SARS-CoV-2 is the causative agent of the COVID-19 pandemic. Thus far, there is no approved therapeutic drug specifically targeting this emerging virus. Here we report the isolation and characterization of a panel of human neutralizing monoclonal antibodies targeting the SARS-CoV-2 receptor binding domain (RBD). These antibodies were selected from a phage display library constructed using peripheral circulatory lymphocytes collected from patients at the acute phase of the disease. These neutralizing antibodies are shown to recognize distinct epitopes on the viral spike RBD. A subset of the antibodies exert their inhibitory activity by abrogating binding of the RBD to the human ACE2 receptor. The human monoclonal antibodies described here represent a promising basis for the design of efficient combined post-exposure therapy for SARS-CoV-2 infection. Here, Noy-Porat, Makdasi et al. report the isolation of a panel of neutralizing mAbs selected against SARS-CoV-2 receptor-binding domain (RBD) from a phage display library constructed based on patient samples collected in the acute phase of the disease, which show efficient neutralizing activities against authentic virus in vitro.
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29
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Brooks BD, Closmore A, Yang J, Holland M, Cairns T, Cohen GH, Bailey-Kellogg C. Characterizing Epitope Binding Regions of Entire Antibody Panels by Combining Experimental and Computational Analysis of Antibody: Antigen Binding Competition. Molecules 2020; 25:molecules25163659. [PMID: 32796656 PMCID: PMC7464469 DOI: 10.3390/molecules25163659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 11/16/2022] Open
Abstract
Vaccines and immunotherapies depend on the ability of antibodies to sensitively and specifically recognize particular antigens and specific epitopes on those antigens. As such, detailed characterization of antibody-antigen binding provides important information to guide development. Due to the time and expense required, high-resolution structural characterization techniques are typically used sparingly and late in a development process. Here, we show that antibody-antigen binding can be characterized early in a process for whole panels of antibodies by combining experimental and computational analyses of competition between monoclonal antibodies for binding to an antigen. Experimental "epitope binning" of monoclonal antibodies uses high-throughput surface plasmon resonance to reveal which antibodies compete, while a new complementary computational analysis that we call "dock binning" evaluates antibody-antigen docking models to identify why and where they might compete, in terms of possible binding sites on the antigen. Experimental and computational characterization of the identified antigenic hotspots then enables the refinement of the competitors and their associated epitope binding regions on the antigen. While not performed at atomic resolution, this approach allows for the group-level identification of functionally related monoclonal antibodies (i.e., communities) and identification of their general binding regions on the antigen. By leveraging extensive epitope characterization data that can be readily generated both experimentally and computationally, researchers can gain broad insights into the basis for antibody-antigen recognition in wide-ranging vaccine and immunotherapy discovery and development programs.
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Affiliation(s)
- Benjamin D. Brooks
- Department of Biomedical Sciences, Rocky Vista University, Ivins, UT 84738, USA
- Inovan Inc., Fargo, ND 58102, USA
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (T.C.); (G.H.C.)
- Correspondence: ; Tel.: +1-435-222-1403
| | - Adam Closmore
- Department of Pharmacy, North Dakota State University, Fargo, ND 58102, USA;
| | - Juechen Yang
- Department of Biomedical Engineering, North Dakota State University, Fargo, ND 58102, USA; (J.Y.); (M.H.)
| | - Michael Holland
- Department of Biomedical Engineering, North Dakota State University, Fargo, ND 58102, USA; (J.Y.); (M.H.)
| | - Tina Cairns
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (T.C.); (G.H.C.)
| | - Gary H. Cohen
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; (T.C.); (G.H.C.)
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30
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Cusano AM, Aliberti A, Cusano A, Ruvo M. Detection of small DNA fragments by biolayer interferometry. Anal Biochem 2020; 607:113898. [PMID: 32777266 DOI: 10.1016/j.ab.2020.113898] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 02/07/2023]
Abstract
Small molecular weight species such as miRNAs and other nucleic acid fragments are gaining an increased interest as biomarkers for relevant diseases. Also, cheap and rapid assays for their routine detection are becoming an urgent need. We have investigated the usability and convenience of a price affordable, label free and fast technique for their detection on a laboratory scale small device based on Bio-Layer Interferometry. Using a model DNA fragment (7 kDa), we have found that the technique is effectively fast and sensitive enough for the detection of nucleic acid fragments having a MW below the stated molecular size detection limit (10 kDa). The test molecule has been detected in solution at 100 nM in a direct capture experiment and up to about 10 nM following an improved approach where an enhancing probe is used to increase the apparent molecular dimensions of the analyte. The technique, following further optimizations, can be applied for the routine, cheap and fast analysis of small nucleic acid fragments that have a relevance in diagnosis and in therapy.
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Affiliation(s)
| | - Anna Aliberti
- Cerict Scarl, Italy; Dipartimento di Ingegneria, Università Del Sannio, Italy
| | - Andrea Cusano
- Cerict Scarl, Italy; Dipartimento di Ingegneria, Università Del Sannio, Italy
| | - Menotti Ruvo
- Istituto di Biostrutture e Bioimmagini, CNR, Italy.
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31
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Yuan TZ, Lujan Hernandez AG, Keane E, Liu Q, Axelrod F, Kailasan S, Noonan-Shueh M, Aman MJ, Sato AK, Abdiche YN. Rapid exploration of the epitope coverage produced by an Ebola survivor to guide the discovery of therapeutic antibody cocktails. Antib Ther 2020; 3:167-178. [PMID: 33912793 PMCID: PMC7454256 DOI: 10.1093/abt/tbaa016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/24/2020] [Accepted: 07/28/2020] [Indexed: 11/17/2022] Open
Abstract
Background Development of successful neutralizing antibodies is dependent upon broad epitope coverage to increase the likelihood of achieving therapeutic function. Recent advances in synthetic biology have allowed us to conduct an epitope binning study on a large panel of antibodies identified to bind to Ebola virus glycoprotein with only published sequences. Methods and Results A rapid, first-pass epitope binning experiment revealed seven distinct epitope families that overlapped with known structural epitopes from the literature. A focused set of antibodies was selected from representative clones per bin to guide a second-pass binning that revealed previously unassigned epitopes, confirmed epitopes known to be associated with neutralizing antibodies, and demonstrated asymmetric blocking of EBOV GP from allosteric effectors reported from literature. Conclusions Critically, this workflow allows us to probe the epitope landscape of EBOV GP without any prior structural knowledge of the antigen or structural benchmark clones. Incorporating epitope binning on hundreds of antibodies during early stage antibody characterization ensures access to a library’s full epitope coverage, aids in the identification of high quality reagents within the library that recapitulate this diversity for use in other studies, and ultimately enables the rational development of therapeutic cocktails that take advantage of multiple mechanisms of action such as cooperative synergistic effects to enhance neutralization function and minimize the risk of mutagenic escape. The use of high-throughput epitope binning during new outbreaks such as the current COVID-19 pandemic is particularly useful in accelerating timelines due to the large amount of information gained in a single experiment.
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Affiliation(s)
- Tom Z Yuan
- Twist Biopharma, Twist Bioscience, South San Francisco, CA 94080, USA
| | | | - Erica Keane
- Twist Biopharma, Twist Bioscience, South San Francisco, CA 94080, USA
| | - Qiang Liu
- Twist Biopharma, Twist Bioscience, South San Francisco, CA 94080, USA
| | - Fumiko Axelrod
- Twist Biopharma, Twist Bioscience, South San Francisco, CA 94080, USA
| | | | | | | | - Aaron K Sato
- Twist Biopharma, Twist Bioscience, South San Francisco, CA 94080, USA
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32
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Gauglitz G. Critical assessment of relevant methods in the field of biosensors with direct optical detection based on fibers and waveguides using plasmonic, resonance, and interference effects. Anal Bioanal Chem 2020; 412:3317-3349. [PMID: 32313998 PMCID: PMC7214504 DOI: 10.1007/s00216-020-02581-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/28/2020] [Accepted: 03/04/2020] [Indexed: 12/16/2022]
Abstract
Direct optical detection has proven to be a highly interesting tool in biomolecular interaction analysis to be used in drug discovery, ligand/receptor interactions, environmental analysis, clinical diagnostics, screening of large data volumes in immunology, cancer therapy, or personalized medicine. In this review, the fundamental optical principles and applications are reviewed. Devices are based on concepts such as refractometry, evanescent field, waveguides modes, reflectometry, resonance and/or interference. They are realized in ring resonators; prism couplers; surface plasmon resonance; resonant mirror; Bragg grating; grating couplers; photonic crystals, Mach-Zehnder, Young, Hartman interferometers; backscattering; ellipsometry; or reflectance interferometry. The physical theories of various optical principles have already been reviewed in detail elsewhere and are therefore only cited. This review provides an overall survey on the application of these methods in direct optical biosensing. The "historical" development of the main principles is given to understand the various, and sometimes only slightly modified variations published as "new" methods or the use of a new acronym and commercialization by different companies. Improvement of optics is only one way to increase the quality of biosensors. Additional essential aspects are the surface modification of transducers, immobilization strategies, selection of recognition elements, the influence of non-specific interaction, selectivity, and sensitivity. Furthermore, papers use for reporting minimal amounts of detectable analyte terms such as value of mass, moles, grams, or mol/L which are difficult to compare. Both these essential aspects (i.e., biochemistry and the presentation of LOD values) can be discussed only in brief (but references are provided) in order to prevent the paper from becoming too long. The review will concentrate on a comparison of the optical methods, their application, and the resulting bioanalytical quality.
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Affiliation(s)
- Günter Gauglitz
- Institute of Physical and Theoretical Chemistry, Eberhard Karls Universität, Auf der Morgenstelle 18, 72076, Tübingen, Germany.
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33
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Brown ME, Bedinger D, Lilov A, Rathanaswami P, Vásquez M, Durand S, Wallace-Moyer I, Zhong L, Nett JH, Burnina I, Caffry I, Lynaugh H, Sinclair M, Sun T, Bukowski J, Xu Y, Abdiche YN. Assessing the binding properties of the anti-PD-1 antibody landscape using label-free biosensors. PLoS One 2020; 15:e0229206. [PMID: 32134960 PMCID: PMC7058304 DOI: 10.1371/journal.pone.0229206] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/31/2020] [Indexed: 12/21/2022] Open
Abstract
Here we describe an industry-wide collaboration aimed at assessing the binding properties of a comprehensive panel of monoclonal antibodies (mAbs) against programmed cell death protein 1 (PD-1), an important checkpoint protein in cancer immunotherapy and validated therapeutic target, with well over thirty unique mAbs either in clinical development or market-approved in the United States, the European Union or China. The binding kinetics of the PD-1/mAb interactions were measured by surface plasmon resonance (SPR) using a Carterra LSA instrument and the results were compared to data collected on a Biacore 8K. The effect of chip type on the SPR-derived binding rate constants and affinities were explored and the results compared with solution affinities from Meso Scale Discovery (MSD) and Kinetic Exclusion Assay (KinExA) experiments. When using flat chip types, the LSA and 8K platforms yielded near-identical kinetic rate and affinity constants that matched solution phase values more closely than those produced on 3D-hydrogels. Of the anti-PD-1 mAbs tested, which included a portion of those known to be in clinical development or approved, the affinities spanned from single digit picomolar to nearly 425 nM, challenging the dynamic range of our methods. The LSA instrument was also used to perform epitope binning and ligand competition studies which revealed over ten unique competitive binding profiles within this group of mAbs.
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Affiliation(s)
- Michael E. Brown
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
- * E-mail: (MEB); (YNA)
| | | | - Asparouh Lilov
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | | | - Maximiliano Vásquez
- Department of Computational Biology, Adimab, Palo Alto, CA, United States of America
| | - Stéphanie Durand
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Ian Wallace-Moyer
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Lihui Zhong
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Juergen H. Nett
- Department of High Throughput Expression, Adimab, Lebanon, NH, United States of America
| | - Irina Burnina
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Isabelle Caffry
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Heather Lynaugh
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Melanie Sinclair
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - Tingwan Sun
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
| | - John Bukowski
- Department of Antibody Discovery, Adimab, Lebanon, NH, United States of America
| | - Yingda Xu
- Department of Protein Analytics, Adimab, Lebanon, NH, United States of America
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34
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Ching KH, Berg K, Morales J, Pedersen D, Harriman WD, Abdiche YN, Leighton PA. Expression of human lambda expands the repertoire of OmniChickens. PLoS One 2020; 15:e0228164. [PMID: 31995598 PMCID: PMC6988971 DOI: 10.1371/journal.pone.0228164] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/08/2020] [Indexed: 12/20/2022] Open
Abstract
Most of the approved monoclonal antibodies used in the clinic were initially discovered in mice. However, many targets of therapeutic interest are highly conserved proteins that do not elicit a robust immune response in mice. There is a need for non-mammalian antibody discovery platforms which would allow researchers to access epitopes that are not recognized in mammalian hosts. Recently, we introduced the OmniChicken®, a transgenic animal carrying human VH3-23 and VK3-15 at its immunoglobulin loci. Here, we describe a new version of the OmniChicken which carries VH3-23 and either VL1-44 or VL3-19 at its heavy and light chain loci, respectively. The Vλ-expressing birds showed normal B and T populations in the periphery. A panel of monoclonal antibodies demonstrated comparable epitope coverage of a model antigen compared to both wild-type and Vκ-expressing OmniChickens. Kinetic analysis identified binders in the picomolar range. The Vλ-expressing bird increases the antibody diversity available in the OmniChicken platform, further enabling discovery of therapeutic leads.
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Affiliation(s)
- Kathryn H. Ching
- Ligand Pharmaceuticals Incorporated, Emeryville, California, United States of America
| | - Kimberley Berg
- Ligand Pharmaceuticals Incorporated, Emeryville, California, United States of America
| | - Jacqueline Morales
- Ligand Pharmaceuticals Incorporated, Emeryville, California, United States of America
| | - Darlene Pedersen
- Ligand Pharmaceuticals Incorporated, Emeryville, California, United States of America
| | - William D. Harriman
- Ligand Pharmaceuticals Incorporated, Emeryville, California, United States of America
| | | | - Philip A. Leighton
- Ligand Pharmaceuticals Incorporated, Emeryville, California, United States of America
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35
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Miller EA, Sung KJ, Kongsuphol P, Baniya S, Aw-Yong HQ, Tay V, Tan Y, Kabir FM, Pang-Yeo K, Kaspriskie IG, Sikes HD. Beyond Epitope Binning: Directed in Vitro Selection of Complementary Pairs of Binding Proteins. ACS COMBINATORIAL SCIENCE 2020; 22:49-60. [PMID: 31769955 DOI: 10.1021/acscombsci.9b00176] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Many biotechnological applications require the simultaneous binding of affinity reagents to nonoverlapping target epitopes, the most prominent example being sandwich immunoassays. Typically, affinity pairs are identified via post facto functional analysis of clones that were not selected for complementarity. Here, we developed the Rapid Affinity Pair Identification via Directed Selection (RAPIDS) process, which enables the efficient identification of affinity reagents that function together as complementary pairs, from in vitro libraries of ∼109 variants. We used RAPIDS to develop highly specific affinity pairs against biomarkers of tuberculosis, Zika virus, and sepsis. Without additional trial-and-error screening, these affinity pairs exhibited utility in multiple assay formats. The RAPIDS process applies selective pressure to hundreds of thousands of potential affinity pairs to efficiently identify complementary pairs that bind to separate epitopes without binding to one another or nontargets, yielding diagnostic assays that are sensitive and specific by design.
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Affiliation(s)
- Eric A. Miller
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ki-Joo Sung
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Patthara Kongsuphol
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Singapore 138602
| | - Subha Baniya
- Department of Biochemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| | - Hui Qi Aw-Yong
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Singapore 138602
| | - Vivian Tay
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Singapore 138602
| | - Yuxuan Tan
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Singapore 138602
| | - Farah M. Kabir
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Karl Pang-Yeo
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Singapore 138602
| | - Isabel G. Kaspriskie
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hadley D. Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Singapore 138602
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36
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Tuzmen C, Cairns TM, Atanasiu D, Lou H, Saw WT, Hall BL, Cohen JB, Cohen GH, Glorioso JC. Point Mutations in Retargeted gD Eliminate the Sensitivity of EGFR/EGFRvIII-Targeted HSV to Key Neutralizing Antibodies. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 16:145-154. [PMID: 32042851 PMCID: PMC7000558 DOI: 10.1016/j.omtm.2019.12.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/26/2019] [Indexed: 11/29/2022]
Abstract
Effective oncolytic virotherapy may require systemic delivery, tumor targeting, and resistance to virus-neutralizing (VN) antibodies. Since herpes simplex virus (HSV) glycoprotein D (gD) is the viral attachment/entry protein and predominant VN target, we examined the impact of gD retargeting alone and in combination with alterations in dominant VN epitopes on virus susceptibility to VN antibodies. We compared the binding of a panel of anti-gD monoclonal antibodies (mAbs) that mimic antibody specificities in human HSV-immune sera to the purified ectodomains of wild-type and retargeted gD, revealing the retention of two prominent epitopes. Substitution of a key residue in each epitope, separately and together, revealed that both substitutions (1) blocked retargeted gD recognition by mAbs to the respective epitopes, and, in combination, caused a global reduction in mAb binding; (2) protected against fusion inhibition by VN mAbs reactive with each epitope in virus-free cell-cell fusion assays; and (3) increased the resistance of retargeted HSV-1 to these VN mAbs. Although the combined modifications of retargeted gD allowed bona fide retargeting, incorporation into virions was partially compromised. Our results indicate that stacking of epitope mutations can additively block retargeted gD recognition by VN antibodies but also that improvements in gD incorporation into virus particles may be required.
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Affiliation(s)
- Ceren Tuzmen
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Tina M Cairns
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Doina Atanasiu
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Huan Lou
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wan Ting Saw
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bonnie L Hall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Justus B Cohen
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Gary H Cohen
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph C Glorioso
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15219, USA
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37
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Surface Plasmon Resonance Reveals Direct Binding of Herpes Simplex Virus Glycoproteins gH/gL to gD and Locates a gH/gL Binding Site on gD. J Virol 2019; 93:JVI.00289-19. [PMID: 31092568 DOI: 10.1128/jvi.00289-19] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/04/2019] [Indexed: 12/23/2022] Open
Abstract
Herpes simplex virus (HSV) requires fusion between the viral envelope and host membrane. Four glycoproteins, gD, gH/gL, and gB, are essential for this process. To initiate fusion, gD binds its receptor and undergoes a conformational change that hypothetically leads to activation of gH/gL, which in turn triggers the fusion protein gB to undergo rearrangements leading to membrane fusion. Our model predicts that gD must interact with both its receptor and gH/gL to promote fusion. In support of this, we have shown that gD is structurally divided into two "faces": one for the binding receptor and the other for its presumed interaction with gH/gL. However, until now, we have been unable to demonstrate a direct interaction between gD and gH/gL. Here, we used surface plasmon resonance to show that the ectodomain of gH/gL binds directly to the ectodomain of gD when (i) gD is captured by certain anti-gD monoclonal antibodies (MAbs) that are bound to a biosensor chip, (ii) gD is bound to either one of its receptors on a chip, and (iii) gD is covalently bound to the chip surface. To localize the gH/gL binding site on gD, we used multiple anti-gD MAbs from six antigenic communities and determined which ones interfered with this interaction. MAbs from three separate communities block gD-gH/gL binding, and their epitopes encircle a geographical area on gD that we propose comprises the gH/gL binding domain. Together, our results show that gH/gL interacts directly with gD, supporting a role for this step in HSV entry.IMPORTANCE HSV entry is a multistep process that requires the actions of four glycoproteins, gD, gH/gL, and gB. Our current model predicts that gD must interact with both its receptor and gH/gL to promote viral entry. Although we know a great deal about how gD binds its receptors, until now we have been unable to demonstrate a direct interaction between gD and gH/gL. Here, we used a highly sensitive surface plasmon resonance technique to clearly demonstrate that gD and gH/gL interact. Furthermore, using multiple MAbs with defined epitopes, we have delineated a domain on gD that is independent of that used for receptor binding and which likely represents the gH/gL interaction domain. Targeting this interaction to prevent fusion may enhance both therapeutic and vaccine strategies.
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38
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Sim J, Sockolosky JT, Sangalang E, Izquierdo S, Pedersen D, Harriman W, Wibowo AS, Carter J, Madan A, Doyle L, Harrabi O, Kauder SE, Chen A, Kuo TC, Wan H, Pons J. Discovery of high affinity, pan-allelic, and pan-mammalian reactive antibodies against the myeloid checkpoint receptor SIRPα. MAbs 2019; 11:1036-1052. [PMID: 31257988 PMCID: PMC6748616 DOI: 10.1080/19420862.2019.1624123] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Targeting the CD47-signal-regulatory protein α (SIRPα) pathway represents a novel therapeutic approach to enhance anti-cancer immunity by promoting both innate and adaptive immune responses. Unlike CD47, which is expressed ubiquitously, SIRPα expression is mainly restricted to myeloid cells and neurons. Therefore, compared to CD47-targeted therapies, targeting SIRPα may result in differential safety and efficacy profiles, potentially enabling lower effective doses and improved pharmacokinetics and pharmacodynamics. The development of effective SIRPα antagonists is restricted by polymorphisms within the CD47-binding domain of SIRPα, necessitating pan-allele reactive anti-SIRPα antibodies for therapeutic intervention in diverse patient populations. We immunized wild-type and human antibody transgenic chickens with a multi-allele and multi-species SIRPα regimen in order to discover pan-allelic and pan-mammalian reactive anti-SIRPα antibodies suitable for clinical translation. A total of 200 antibodies were isolated and screened for SIRPα reactivity from which approximately 70 antibodies with diverse SIRPα binding profiles, sequence families, and epitopes were selected for further characterization. A subset of anti-SIRPα antibodies bound to both human SIRPα v1 and v2 alleles with high affinity ranging from low nanomolar to picomolar, potently antagonized the CD47/SIRPα interaction, and potentiated macrophage-mediated antibody-dependent cellular phagocytosis in vitro. X-ray crystal structures of five anti-SIRPα antigen-binding fragments, each with unique epitopes, in complex with SIRPα (PDB codes 6NMV, 6NMU, 6NMT, 6NMS, and 6NMR) are reported. Furthermore, some of the anti-SIRPα antibodies cross-react with cynomolgus SIRPα and various mouse SIRPα alleles (BALB/c, NOD, BL/6), which can facilitate preclinical to clinical development. These properties provide an attractive rationale to advance the development of these anti-SIRPα antibodies as a novel therapy for advanced malignancies. Abbreviations: ADCC: antibody-dependent cellular cytotoxicity; ADCP: antibody-dependent cellular phagocytosis; CFSE: carboxyfluorescein succinimidyl ester; Fab: fragment antigen binding; Fc: fragment crystallizable; FcγR: Fcγ receptor; Ig: immunoglobulin; IND: investigational new drug; MDM⊘: monocyte-derived macrophage; NOD: non-obese diabetic; scFv: single chain fragment variable; SCID: severe combined immunodeficiency; SIRP: signal-regulatory protein.
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Affiliation(s)
- Janet Sim
- a ALX Oncology, Departments of Protein Sciences and Translational Biology , Burlingame , CA , USA
| | - Jonathan T Sockolosky
- a ALX Oncology, Departments of Protein Sciences and Translational Biology , Burlingame , CA , USA
| | - Emma Sangalang
- a ALX Oncology, Departments of Protein Sciences and Translational Biology , Burlingame , CA , USA
| | | | | | | | | | | | - Anup Madan
- d Covance Genomics Laboratory , Redmond , WA , USA
| | - Laura Doyle
- a ALX Oncology, Departments of Protein Sciences and Translational Biology , Burlingame , CA , USA
| | - Ons Harrabi
- a ALX Oncology, Departments of Protein Sciences and Translational Biology , Burlingame , CA , USA
| | - Steven E Kauder
- a ALX Oncology, Departments of Protein Sciences and Translational Biology , Burlingame , CA , USA
| | - Amy Chen
- a ALX Oncology, Departments of Protein Sciences and Translational Biology , Burlingame , CA , USA
| | - Tracy C Kuo
- a ALX Oncology, Departments of Protein Sciences and Translational Biology , Burlingame , CA , USA
| | - Hong Wan
- a ALX Oncology, Departments of Protein Sciences and Translational Biology , Burlingame , CA , USA
| | - Jaume Pons
- a ALX Oncology, Departments of Protein Sciences and Translational Biology , Burlingame , CA , USA
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39
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Gui X, Deng M, Song H, Chen Y, Xie J, Li Z, He L, Huang F, Xu Y, Anami Y, Yu H, Yu C, Li L, Yuan Z, Xu X, Wang Q, Chai Y, Huang T, Shi Y, Tsuchikama K, Liao XC, Xia N, Gao GF, Zhang N, Zhang CC, An Z. Disrupting LILRB4/APOE Interaction by an Efficacious Humanized Antibody Reverses T-cell Suppression and Blocks AML Development. Cancer Immunol Res 2019; 7:1244-1257. [PMID: 31213474 DOI: 10.1158/2326-6066.cir-19-0036] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/29/2019] [Accepted: 06/12/2019] [Indexed: 11/16/2022]
Abstract
Therapeutic strategies are urgently needed for patients with acute myeloid leukemia (AML). Leukocyte immunoglobulin-like receptor B4 (LILRB4), which suppresses T-cell activation and supports tissue infiltration of AML cells, represents an attractive drug target for anti-AML therapeutics. Here, we report the identification and development of an LILRB4-specific humanized mAb that blocks LILRB4 activation. This mAb, h128-3, showed potent activity in blocking the development of monocytic AML in various models including patient-derived xenograft mice and syngeneic immunocompetent AML mice. MAb h128-3 enhanced the anti-AML efficacy of chemotherapy treatment by stimulating mobilization of leukemia cells. Mechanistic studies revealed four concordant modes of action for the anti-AML activity of h128-3: (i) reversal of T-cell suppression, (ii) inhibition of monocytic AML cell tissue infiltration, (iii) antibody-dependent cellular cytotoxicity, and (iv) antibody-dependent cellular phagocytosis. Therefore, targeting LILRB4 with antibody represents an effective therapeutic strategy for treating monocytic AML.
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Affiliation(s)
- Xun Gui
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas
| | - Mi Deng
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Hao Song
- Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Yuanzhi Chen
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas.,School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - Jingjing Xie
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas.,Taishan Immunology Program, Basic Medicine School, Binzhou Medical University, Yantai, China
| | - Zunling Li
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas.,Taishan Immunology Program, Basic Medicine School, Binzhou Medical University, Yantai, China
| | - Licai He
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas.,Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medical and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Fangfang Huang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas.,Department of Hematology, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Yixiang Xu
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas
| | - Yasuaki Anami
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas
| | - Hai Yu
- School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - Chenyi Yu
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas.,School of Xiangya Medicine, Central South University, Changsha, Hunan, China
| | - Leike Li
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas
| | - Zihao Yuan
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas
| | - Xiaoying Xu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qihui Wang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas.,CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yan Chai
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Tao Huang
- Immune-Onc Therapeutics, Inc., Palo Alto, California
| | - Yi Shi
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Kyoji Tsuchikama
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas
| | | | - Ningshao Xia
- School of Public Health, Xiamen University, Xiamen, Fujian, China
| | - George F Gao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing, China
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas.
| | - Cheng Cheng Zhang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas.
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, Texas.
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40
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Wollacott AM, Robinson LN, Ramakrishnan B, Tissire H, Viswanathan K, Shriver Z, Babcock GJ. Structural prediction of antibody-APRIL complexes by computational docking constrained by antigen saturation mutagenesis library data. J Mol Recognit 2019; 32:e2778. [DOI: 10.1002/jmr.2778] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/21/2018] [Accepted: 12/06/2018] [Indexed: 12/29/2022]
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41
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Van Blarcom T, Rossi A, Foletti D, Sundar P, Pitts S, Melton Z, Telman D, Zhao L, Cheung WL, Berka J, Zhai W, Strop P, Pons J, Rajpal A, Chaparro-Riggers J. Epitope Mapping Using Yeast Display and Next Generation Sequencing. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2019; 1785:89-118. [PMID: 29714014 DOI: 10.1007/978-1-4939-7841-0_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Monoclonal antibodies are the largest class of therapeutic proteins due in part to their ability to bind an antigen with a high degree of affinity and specificity. A precise determination of their epitope is important for gaining insights into their therapeutic mechanism of action and to help differentiate antibodies that bind the same antigen. Here, we describe a method to precisely and efficiently map the epitopes of multiple antibodies in parallel over the course of just several weeks. This approach is based on a combination of rational library design, yeast surface display, and next generation DNA sequencing and provides quantitative insights into the epitope residues most critical for the antibody-antigen interaction. As an example, we will use this method to map the epitopes of several antibodies that neutralize alpha toxin from Staphylococcus aureus.
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Affiliation(s)
| | - Andrea Rossi
- Rinat, Pfizer Inc., South San Francisco, CA, USA
| | - Davide Foletti
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,23andMe Inc., South San Francisco, CA, USA
| | | | - Steven Pitts
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,23andMe Inc., South San Francisco, CA, USA
| | - Zea Melton
- Rinat, Pfizer Inc., South San Francisco, CA, USA
| | | | - Lora Zhao
- Rinat, Pfizer Inc., South San Francisco, CA, USA
| | - Wai Ling Cheung
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,Princeton University, Princeton, NJ, USA
| | - Jan Berka
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,Roche Sequencing Solutions, Pleasanton, CA, USA
| | - Wenwu Zhai
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,NGM Biopharmaceuticals Inc., South San Francisco, CA, USA
| | - Pavel Strop
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,Bristol-Myers Squibb Inc., Redwood City, CA, USA
| | - Jaume Pons
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,Alexo Therapeutics Inc., South San Francisco, CA, USA
| | - Arvind Rajpal
- Rinat, Pfizer Inc., South San Francisco, CA, USA.,Bristol-Myers Squibb Inc., Redwood City, CA, USA
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42
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Tang F, LeBlanc ME, Wang W, Liang D, Chen P, Chou TH, Tian H, Li W. Anti-secretogranin III therapy of oxygen-induced retinopathy with optimal safety. Angiogenesis 2019; 22:369-382. [PMID: 30644010 DOI: 10.1007/s10456-019-09662-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 01/07/2019] [Indexed: 12/17/2022]
Abstract
Retinopathy of prematurity (ROP) with pathological retinal neovascularization is the most common cause of blindness in children. ROP is currently treated with laser therapy or cryotherapy, both of which may adversely affect the peripheral vision with limited efficacy. Owing to the susceptibility of the developing retina and vasculatures to pharmacological intervention, there is currently no approved drug therapy for ROP in preterm infants. Secretogranin III (Scg3) was recently discovered as a highly disease-restricted angiogenic factor, and a Scg3-neutralizing monoclonal antibody (mAb) was reported with high efficacy to alleviate oxygen-induced retinopathy (OIR) in mice, a surrogate model of ROP. Herein we independently investigated the efficacy of anti-Scg3 mAb in OIR mice and characterized its safety in neonatal mice. We developed a new Scg3-neutralizing mAb recognizing a distinct epitope and independently established the therapeutic activity of anti-Scg3 therapy to alleviate OIR-induced pathological retinal neovascularization in mice. Importantly, anti-Scg3 mAb showed no detectable adverse effects on electroretinography and developing retinal vasculature. Furthermore, systemic anti-Scg3 mAb induced no renal tubular injury or abnormality in kidney vessel development and body weight gain of neonatal mice. In contrast, anti-vascular endothelial growth factor drug aflibercept showed significant side effects in neonatal mice. These results suggest that anti-Scg3 mAb may have the safety and efficacy profiles required for ROP therapy.
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Affiliation(s)
- Fen Tang
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL, USA
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Michelle E LeBlanc
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL, USA
| | - Weiwen Wang
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL, USA
| | - Dan Liang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Ping Chen
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL, USA
- Department of Ophthalmology, Renji Hospital of Shanghai Jiaotong University, Shanghai, China
| | - Tsung-Han Chou
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL, USA
| | - Hong Tian
- Everglades Biopharma, LLC, Miami, FL, USA
| | - Wei Li
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami School of Medicine, Miami, FL, USA.
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43
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Ross GMS, Bremer MGEG, Wichers JH, van Amerongen A, Nielen MWF. Rapid Antibody Selection Using Surface Plasmon Resonance for High-Speed and Sensitive Hazelnut Lateral Flow Prototypes. BIOSENSORS 2018; 8:E130. [PMID: 30558252 PMCID: PMC6316566 DOI: 10.3390/bios8040130] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/06/2018] [Accepted: 12/12/2018] [Indexed: 12/20/2022]
Abstract
Lateral Flow Immunoassays (LFIAs) allow for rapid, low-cost, screening of many biomolecules such as food allergens. Despite being classified as rapid tests, many LFIAs take 10⁻20 min to complete. For a really high-speed LFIA, it is necessary to assess antibody association kinetics. By using a label-free optical technique such as Surface Plasmon Resonance (SPR), it is possible to screen crude monoclonal antibody (mAb) preparations for their association rates against a target. Herein, we describe an SPR-based method for screening and selecting crude anti-hazelnut antibodies based on their relative association rates, cross reactivity and sandwich pairing capabilities, for subsequent application in a rapid ligand binding assay. Thanks to the SPR selection process, only the fast mAb (F-50-6B12) and the slow (S-50-5H9) mAb needed purification for labelling with carbon nanoparticles to exploit high-speed LFIA prototypes. The kinetics observed in SPR were reflected in LFIA, with the test line appearing within 30 s, almost two times faster when F-50-6B12 was used, compared with S-50-5H9. Additionally, the LFIAs have demonstrated their future applicability to real life samples by detecting hazelnut in the sub-ppm range in a cookie matrix. Finally, these LFIAs not only provide a qualitative result when read visually, but also generate semi-quantitative data when exploiting freely downloadable smartphone apps.
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Affiliation(s)
- Georgina M S Ross
- RIKILT, Wageningen University & Research. P.O Box 230, 6700 AE Wageningen, The Netherlands.
| | - Maria G E G Bremer
- RIKILT, Wageningen University & Research. P.O Box 230, 6700 AE Wageningen, The Netherlands.
| | - Jan H Wichers
- Wageningen Food & Biobased Research, BioSensing & Diagnostics, Wageningen University & Research, P.O Box 17, 6700 AA, Wageningen, The Netherlands.
| | - Aart van Amerongen
- Wageningen Food & Biobased Research, BioSensing & Diagnostics, Wageningen University & Research, P.O Box 17, 6700 AA, Wageningen, The Netherlands.
| | - Michel W F Nielen
- RIKILT, Wageningen University & Research. P.O Box 230, 6700 AE Wageningen, The Netherlands.
- Wageningen University, Laboratory of Organic Chemistry, Helix Building 124, Stippeneng 4. 6708 WE Wageningen, The Netherlands.
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44
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Challenges in the Structural-Functional Characterization of Multidomain, Partially Disordered Proteins CBP and p300: Preparing Native Proteins and Developing Nanobody Tools. Methods Enzymol 2018; 611:607-675. [PMID: 30471702 DOI: 10.1016/bs.mie.2018.09.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The structural and functional characterization of large multidomain signaling proteins containing long disordered linker regions represents special methodological and conceptual challenges. These proteins show extreme structural heterogeneity and have complex posttranslational modification patterns, due to which traditional structural biology techniques provide results that are often difficult to interpret. As demonstrated through the example of two such multidomain proteins, CREB-binding protein (CBP) and its paralogue, p300, even the expression and purification of such proteins are compromised by their extreme proteolytic sensitivity and structural heterogeneity. In this chapter, we describe the effective expression of CBP and p300 in a eukaryotic host, Sf9 insect cells, followed by their tandem affinity purification based on two terminal tags to ensure their structural integrity. The major focus of this chapter is on the development of novel accessory tools, single-domain camelid antibodies (nanobodies), for structural-functional characterization. Specific nanobodies against full-length CBP and p300 can specifically target their different regions and can be used for their marking, labeling, and structural stabilization in a broad range of in vitro and in vivo studies. Here, we describe four high-affinity nanobodies binding to the KIX and the HAT domains, either mimicking known interacting partners or revealing new functionally relevant conformations. As immunization of llamas results in nanobody libraries with a great sequence variation, deep sequencing and interaction analysis with different regions of the proteins provide a novel approach toward developing a panel of specific nanobodies.
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Tomilov A, Allen S, Hui CK, Bettaieb A, Cortopassi G. Idebenone is a cytoprotective insulin sensitizer whose mechanism is Shc inhibition. Pharmacol Res 2018; 137:89-103. [PMID: 30290222 DOI: 10.1016/j.phrs.2018.09.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 01/04/2023]
Abstract
When insulin binds insulin receptor, IRS1 signaling is stimulated to trigger the maximal insulin response. p52Shc protein competes directly with IRS1, thus damping and diverting maximal insulin response. Genetic reduction of p52Shc minimizes competition with IRS1, and improves insulin signaling and glucose control in mice, and improves pathophysiological consequences of hyperglycemia. Given the multiple benefits of Shc reduction in vivo, we investigated whether any of 1680 drugs used in humans may function as Shc inhibitors, and thus potentially serve as novel anti-diabetics. Of the 1680, 30 insulin sensitizers were identified by screening in vitro, and of these 30 we demonstrated that 7 bound Shc protein. Of the 7 drugs, idebenone dose-dependently bound Shc protein in the 50-100 nM range, and induced insulin sensitivity and cytoprotection in this same 100 nM range that clinically dosed idebenone reaches in human plasma. By contrast we observe mitochondrial effects of idebenone in the 5,000 nM range that are not reached in human dosing. Multiple assays of target engagement demonstrate that idebenone physically interacts with Shc protein. Idebenone sensitizes mice to insulin in two different mouse models of prediabetes. Genetic depletion of idebenone's target eliminates idebenone's ability to insulin-sensitize in vivo. Thus, idebenone is the first-in-class member of a novel category of insulin-sensitizing and cytoprotective agents, the Shc inhibitors. Idebenone is an approved drug and could be considered for other indications such as type 2 diabetes and fatty liver disease, in which insulin resistance occurs.
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Affiliation(s)
- Alexey Tomilov
- Department of Molecular Biosciences, 1089 Veterinary Medicine Dr., VM3B, UC Davis, CA, 95616, USA.
| | - Sonia Allen
- Department of Molecular Biosciences, 1089 Veterinary Medicine Dr., VM3B, UC Davis, CA, 95616, USA.
| | - Chun Kiu Hui
- Department of Molecular Biosciences, 1089 Veterinary Medicine Dr., VM3B, UC Davis, CA, 95616, USA.
| | - Ahmed Bettaieb
- Department of Nutrition, The University of Tennessee, 1215 W. Cumberland Ave, Knoxville, TN, 37996-1920, USA.
| | - Gino Cortopassi
- Department of Molecular Biosciences, 1089 Veterinary Medicine Dr., VM3B, UC Davis, CA, 95616, USA.
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Guo Z, Wilson JR, York IA, Stevens J. Biosensor-based epitope mapping of antibodies targeting the hemagglutinin and neuraminidase of influenza A virus. J Immunol Methods 2018; 461:23-29. [PMID: 30053389 DOI: 10.1016/j.jim.2018.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/21/2018] [Accepted: 07/23/2018] [Indexed: 01/04/2023]
Abstract
Characterization of the epitopes on antigen recognized by monoclonal antibodies (mAb) is useful for the development of therapeutic antibodies, diagnostic tools, and vaccines. Epitope mapping also provides functional information for sequence-based repertoire analysis of antibody response to pathogen infection and/or vaccination. However, development of mapping strategies has lagged behind mAb discovery. We have developed a site-directed mutagenesis approach that can be used in conjunction with bio-layer interferometry (BLI) biosensors to map mAb epitopes. By generating a panel of single point mutants in the recombinant hemagglutinin (HA) and neuraminidase (NA) proteins of influenza A viruses, we have characterized the epitopes of hundreds of mAbs targeting the H1 and H3 subtypes of HA and the N9 subtype of NA.
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Affiliation(s)
- Zhu Guo
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jason R Wilson
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, USA; CNI Advantage, LLC, Norman, OK, USA
| | - Ian A York
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - James Stevens
- Influenza Division, National Center for Immunization and Respiratory Disease, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Chan BM, Badh A, Berry KA, Grauer SA, King CT. Flow Cytometry-Based Epitope Binning Using Competitive Binding Profiles for the Characterization of Monoclonal Antibodies against Cellular and Soluble Protein Targets. SLAS DISCOVERY 2018; 23:613-623. [DOI: 10.1177/2472555218774334] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A key step in the therapeutic antibody drug discovery process is early identification of diverse candidate molecules. Information comparing antibody binding epitopes can be used to classify antibodies within a large panel, guiding rational lead molecule selection. We describe a novel epitope binning method utilizing high-throughput flow cytometry (HTFC) that leverages cellular barcoding or spectrally distinct beads to multiplex samples to characterize antibodies raised against cell membrane receptor or soluble protein targets. With no requirement for sample purification or direct labeling, the method is suited for early characterization of antibody candidates. This method generates competitive binding profiles of each antibody against a defined set of known or unknown reference antibodies for binding to epitopes of an antigen. Antibodies with closely related competitive binding profiles indicate similar epitopes and are classified in the same bin. These large, high-throughput, multiplexed experiments can yield epitope bins or clusters for the entire antibody panel, from which a conceptual map of the epitope space for each antibody can be created. Combining this valuable epitope information with other data, such as functional activity, sequence, and selectivity of binding to orthologs and paralogs, enables us to advance the best epitope-diverse candidates for further development.
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Affiliation(s)
| | - Anita Badh
- Amgen Discovery Research, Burnaby, BC, Canada
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Bednenko J, Harriman R, Mariën L, Nguyen HM, Agrawal A, Papoyan A, Bisharyan Y, Cardarelli J, Cassidy-Hanley D, Clark T, Pedersen D, Abdiche Y, Harriman W, van der Woning B, de Haard H, Collarini E, Wulff H, Colussi P. A multiplatform strategy for the discovery of conventional monoclonal antibodies that inhibit the voltage-gated potassium channel Kv1.3. MAbs 2018; 10:636-650. [PMID: 29494279 PMCID: PMC5973702 DOI: 10.1080/19420862.2018.1445451] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Identifying monoclonal antibodies that block human voltage-gated ion channels (VGICs) is a challenging endeavor exacerbated by difficulties in producing recombinant ion channel proteins in amounts that support drug discovery programs. We have developed a general strategy to address this challenge by combining high-level expression of recombinant VGICs in Tetrahymena thermophila with immunization of phylogenetically diverse species and unique screening tools that allow deep-mining for antibodies that could potentially bind functionally important regions of the protein. Using this approach, we targeted human Kv1.3, a voltage-gated potassium channel widely recognized as a therapeutic target for the treatment of a variety of T-cell mediated autoimmune diseases. Recombinant Kv1.3 was used to generate and recover 69 full-length anti-Kv1.3 mAbs from immunized chickens and llamas, of which 10 were able to inhibit Kv1.3 current. Select antibodies were shown to be potent (IC50<10 nM) and specific for Kv1.3 over related Kv1 family members, hERG and hNav1.5.
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Affiliation(s)
| | - Rian Harriman
- b Department of Immunology , Crystal Bioscience , Emeryville , California , USA
| | | | - Hai M Nguyen
- d Department of Pharmacology , University of California , Davis , California , USA
| | - Alka Agrawal
- a TetraGenetics Inc , Arlington , Massachusetts , USA
| | - Ashot Papoyan
- a TetraGenetics Inc , Arlington , Massachusetts , USA
| | | | | | - Donna Cassidy-Hanley
- e Department of Immunology and Microbiology , Cornell University , Ithaca , New York , USA
| | - Ted Clark
- a TetraGenetics Inc , Arlington , Massachusetts , USA.,e Department of Immunology and Microbiology , Cornell University , Ithaca , New York , USA
| | | | | | | | | | | | | | - Heike Wulff
- d Department of Pharmacology , University of California , Davis , California , USA
| | - Paul Colussi
- a TetraGenetics Inc , Arlington , Massachusetts , USA
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Adler AS, Bedinger D, Adams MS, Asensio MA, Edgar RC, Leong R, Leong J, Mizrahi RA, Spindler MJ, Bandi SR, Huang H, Tawde P, Brams P, Johnson DS. A natively paired antibody library yields drug leads with higher sensitivity and specificity than a randomly paired antibody library. MAbs 2018; 10:431-443. [PMID: 29376776 PMCID: PMC5916548 DOI: 10.1080/19420862.2018.1426422] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Deep sequencing and single-chain variable fragment (scFv) yeast display methods are becoming more popular for discovery of therapeutic antibody candidates in mouse B cell repertoires. In this study, we compare a deep sequencing and scFv display method that retains native heavy and light chain pairing with a related method that randomly pairs heavy and light chain. We performed the studies in a humanized mouse, using interleukin 21 receptor (IL-21R) as a test immunogen. We identified 44 high-affinity binder scFv with the native pairing method and 100 high-affinity binder scFv with the random pairing method. 30% of the natively paired scFv binders were also discovered with the randomly paired method, and 13% of the randomly paired binders were also discovered with the natively paired method. Additionally, 33% of the scFv binders discovered only in the randomly paired library were initially present in the natively paired pre-sort library. Thus, a significant proportion of “randomly paired” scFv were actually natively paired. We synthesized and produced 46 of the candidates as full-length antibodies and subjected them to a panel of binding assays to characterize their therapeutic potential. 87% of the antibodies were verified as binding IL-21R by at least one assay. We found that antibodies with native light chains were more likely to bind IL-21R than antibodies with non-native light chains, suggesting a higher false positive rate for antibodies from the randomly paired library. Additionally, the randomly paired method failed to identify nearly half of the true natively paired binders, suggesting a higher false negative rate. We conclude that natively paired libraries have critical advantages in sensitivity and specificity for antibody discovery programs.
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Affiliation(s)
- Adam S Adler
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Daniel Bedinger
- b Carterra Inc. , 825 N 300 W, Suite C309, Salt Lake City , UT USA
| | - Matthew S Adams
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Michael A Asensio
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Robert C Edgar
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Renee Leong
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Jackson Leong
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Rena A Mizrahi
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | - Matthew J Spindler
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
| | | | - Haichun Huang
- c Bristol-Myers Squibb , 700 Bay Road, Redwood City , CA USA
| | - Pallavi Tawde
- c Bristol-Myers Squibb , 700 Bay Road, Redwood City , CA USA
| | - Peter Brams
- c Bristol-Myers Squibb , 700 Bay Road, Redwood City , CA USA
| | - David S Johnson
- a GigaGen Inc., One Tower Place , Suite 750, South San Francisco , CA USA
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Li M, Guo X, Li H, Zuo X, Hao R, Song H, Aldalbahi A, Ge Z, Li J, Li Q, Song S, Li S, Shao N, Fan C, Wang L. Epitope Binning Assay Using an Electron Transfer-Modulated Aptamer Sensor. ACS APPLIED MATERIALS & INTERFACES 2018; 10:341-349. [PMID: 29241329 DOI: 10.1021/acsami.7b17324] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Surface plasmon resonance and quartz crystal microbalance are workhorses of protein-DNA interaction research for over 20 years, providing ways to quantitatively determine the protein-DNA binding. However, the cost, necessary technical expertise, and severe nonspecific adsorption poses barriers to their use. Convenient and effective techniques for the measurement of protein-DNA binding affinity and the epitope binning between DNA and proteins for developing highly sensitive detection platform remain challenging. Here, we develop a binding-induced alteration in electron transfer kinetics of the redox reporter labeled (methylene blue) on DNA aptamer to measure the binding affinity between prostate-specific antigen (PSA) and aptamer. We demonstrate that the binding of PSA to aptamer decreases the electron transfer rate of methylene blue for ∼45%. Further, we identify the best pairwise selection of aptamers for developing sandwich assay by sorting from 10 pairwise modes with the PSA detection limit of 500 ng/mL. Our study provides promising ways to analyze the binding affinity between ligand and receptor and to sort pairwise between aptamers or antibodies for the development of highly sensitive sandwich immunoassays.
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Affiliation(s)
- Min Li
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Xudong Guo
- Institute of Disease Control and Prevention, AMMS , Beijing 100071, China
| | - Hui Li
- Beijing Institute of Basic Medical Sciences , Beijing 100850, China
| | - Xiaolei Zuo
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Rongzhang Hao
- Institute of Disease Control and Prevention, AMMS , Beijing 100071, China
| | - Hongbin Song
- Institute of Disease Control and Prevention, AMMS , Beijing 100071, China
| | - Ali Aldalbahi
- Chemistry Department, King Saud University , Riyadh 11451, Saudi Arabia
| | - Zhilei Ge
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Jiang Li
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Qian Li
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Shiping Song
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Shaohua Li
- Beijing Institute of Basic Medical Sciences , Beijing 100850, China
| | - Ningsheng Shao
- Beijing Institute of Basic Medical Sciences , Beijing 100850, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
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