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Lee HE, Cho AH, Hwang JH, Kim JW, Yang HR, Ryu T, Jung Y, Lee S. Development, High-Throughput Profiling, and Biopanning of a Large Phage Display Single-Domain Antibody Library. Int J Mol Sci 2024; 25:4791. [PMID: 38732011 PMCID: PMC11083953 DOI: 10.3390/ijms25094791] [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: 03/20/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
Immunoglobulin G-based monoclonal antibodies (mAbs) have been effective in treating various diseases, but their large molecular size can limit their penetration of tissue and efficacy in multifactorial diseases, necessitating the exploration of alternative forms. In this study, we constructed a phage display library comprising single-domain antibodies (sdAbs; or "VHHs"), known for their small size and remarkable stability, using a total of 1.6 × 109 lymphocytes collected from 20 different alpacas, resulting in approximately 7.16 × 1010 colonies. To assess the quality of the constructed library, next-generation sequencing-based high-throughput profiling was performed, analyzing approximately 5.65 × 106 full-length VHH sequences, revealing 92% uniqueness and confirming the library's diverse composition. Systematic characterization of the library revealed multiple sdAbs with high affinity for three therapeutically relevant antigens. In conclusion, our alpaca sdAb phage display library provides a versatile resource for diagnostics and therapeutics. Furthermore, the library's vast natural VHH antibody repertoire offers insights for generating humanized synthetic sdAb libraries, further advancing sdAb-based therapeutics.
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Affiliation(s)
- Hee Eon Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea; (H.E.L.); (A.H.C.); (J.H.H.); (J.W.K.); (H.R.Y.)
| | - Ah Hyun Cho
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea; (H.E.L.); (A.H.C.); (J.H.H.); (J.W.K.); (H.R.Y.)
| | - Jae Hyeon Hwang
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea; (H.E.L.); (A.H.C.); (J.H.H.); (J.W.K.); (H.R.Y.)
| | - Ji Woong Kim
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea; (H.E.L.); (A.H.C.); (J.H.H.); (J.W.K.); (H.R.Y.)
| | - Ha Rim Yang
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea; (H.E.L.); (A.H.C.); (J.H.H.); (J.W.K.); (H.R.Y.)
| | - Taehoon Ryu
- ATG Lifetech Inc., Seoul 08507, Republic of Korea; (T.R.); (Y.J.)
| | - Yushin Jung
- ATG Lifetech Inc., Seoul 08507, Republic of Korea; (T.R.); (Y.J.)
| | - Sukmook Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul 02707, Republic of Korea; (H.E.L.); (A.H.C.); (J.H.H.); (J.W.K.); (H.R.Y.)
- Department of Applied Chemistry, Kookmin University, Seoul 02707, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul 02707, Republic of Korea
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2
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Gandotra R, Wu HB, Kuo FC, Lee MS, Lee GB. Advancing the Diagnosis of Periprosthetic Joint Infections: Integrated Microfluidic Platform for Alpha-Defensins-Specific Aptamer Selection and Its Analytical Applications. ACS Sens 2024. [PMID: 38591344 DOI: 10.1021/acssensors.3c02034] [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: 04/10/2024]
Abstract
Periprosthetic joint infections (PJIs) pose a significant challenge in orthopedic surgery, particularly total joint arthroplasty (TJA), due to the potential for implant failure and increased patient morbidity. Early and accurate detection of PJIs is crucial for timely intervention and better patient prognosis. Herein, we successfully screened a high-affinity aptamer targeting alpha-defensin complex human neutrophil protein 1-3 (HNP 1-3; potential PJI biomarkers in synovial fluid [SF]) for the first time using systematic evolution of ligands by exponential enrichment (SELEX) on an integrated microfluidic platform. The compact microfluidic device enabled efficient screening, with each round completed within <2 h, comprising five rounds of positive selection, two rounds of negative selection, and one round of competitive selection. A novel one-aptamer-one-antibody assay was further developed from the optimal aptamer screened, and it could accurately quantify HNP 1-3 in SF within 3 h with only ∼50 μL of SF. The assay demonstrated strong binding affinity and specificity for the target protein in SF. Thirteen PJI SF samples were accurately diagnosed and the assay was accurate over a wide dynamic range (0.32-100 mg/L). This study has showcased a rapid and accurate diagnostic tool for PJI detection, which should see widespread use in the clinic, holding promise for potential analytical applications in orthopedic surgery and improving patient care.
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Affiliation(s)
- Rishabh Gandotra
- Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Hung-Bin Wu
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Feng-Chih Kuo
- Department of Orthopaedic Surgery, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University, Kaohsiung 83301, Taiwan
| | - Mel S Lee
- Department of Orthopaedic Surgery, Paochien Hospital, Pingtung 90064, Taiwan
| | - Gwo-Bin Lee
- Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
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3
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Seo H, Cho SH, Vo TTB, Lee A, Cho S, Kang S, Kil EJ, Byun HS, Lee MG, Kwon MH, Chung WJ, Lee YG, Lee S. M13KO7 bacteriophage enables Potato Virus Y detection. Microbiol Spectr 2023; 11:e0144623. [PMID: 37811937 PMCID: PMC10714723 DOI: 10.1128/spectrum.01446-23] [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: 04/04/2023] [Accepted: 08/07/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE In this study, we confirmed the binding of M13KO7 to Potato virus Y (PVY) using enzyme-linked immunosorbent assay. M13KO7 is a "bald" bacteriophage in which no recombinant antibody is displayed. M13KO7 is easy to propagate by using Escherichia coli, making this method more reasonable in economic perspective. Based on this study, we suggest that M13KO7 detection system has applicability as a novel biological tool for the detection of PVY.
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Affiliation(s)
- Haneul Seo
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Sang-Ho Cho
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Thuy T. B. Vo
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Ahlim Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Sungrae Cho
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Sol Kang
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Eui-Joon Kil
- Department of Plant Medicals, Andong National University, Andong, Republic of Korea
| | - Hee-Seong Byun
- Crop Protection Division, National Academy of Agricultural Science, Rural Development Administration, Wanju, Republic of Korea
| | - Mi-Gi Lee
- Biocenter, Gyeonggido Business & Science Accelerator, Suwon, Republic of Korea
| | - Myung-Hee Kwon
- Department of Microbiology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Woo-Jae Chung
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
| | - Young-Gyu Lee
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, Republic of Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, Republic of Korea
- Department of Biopharmaceutical Convergence, School of Pharmacy, Sungkyunkwan University, Seoul, Republic of Korea
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4
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Chin SE, Schindler C, Vinall L, Dodd RB, Bamber L, Legg S, Sigurdardottir A, Rees DG, Malcolm TIM, Spratley SJ, Granéli C, Sumner J, Tigue NJ. A simeprevir-inducible molecular switch for the control of cell and gene therapies. Nat Commun 2023; 14:7753. [PMID: 38012128 PMCID: PMC10682029 DOI: 10.1038/s41467-023-43484-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
Chemical inducer of dimerization (CID) modules can be used effectively as molecular switches to control biological processes, and thus there is significant interest within the synthetic biology community in identifying novel CID systems. To date, CID modules have been used primarily in engineering cells for in vitro applications. To broaden their utility to the clinical setting, including the potential to control cell and gene therapies, the identification of novel CID modules should consider factors such as the safety and pharmacokinetic profile of the small molecule inducer, and the orthogonality and immunogenicity of the protein components. Here we describe a CID module based on the orally available, approved, small molecule simeprevir and its target, the NS3/4A protease from hepatitis C virus. We demonstrate the utility of this CID module as a molecular switch to control biological processes such as gene expression and apoptosis in vitro, and show that the CID system can be used to rapidly induce apoptosis in tumor cells in a xenograft mouse model, leading to complete tumor regression.
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Affiliation(s)
- Stacey E Chin
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Lisa Vinall
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Roger B Dodd
- Biologics Engineering, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Lisa Bamber
- Biologics Engineering, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Sandrine Legg
- Biologics Engineering, Oncology R&D, AstraZeneca, Cambridge, UK
| | | | - D Gareth Rees
- Biologics Engineering, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Tim I M Malcolm
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Cecilia Granéli
- BioPharmaceuticals R&D Cell Therapy Department, Research and Early Development, Cardiovascular, Renal, and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jonathan Sumner
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Natalie J Tigue
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.
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5
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Karn SL, Gangwar M, Kumar R, Bhartiya SK, Nath G. Phage therapy: a revolutionary shift in the management of bacterial infections, pioneering new horizons in clinical practice, and reimagining the arsenal against microbial pathogens. Front Med (Lausanne) 2023; 10:1209782. [PMID: 37928478 PMCID: PMC10620811 DOI: 10.3389/fmed.2023.1209782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023] Open
Abstract
The recent approval of experimental phage therapies by the FDA and other regulatory bodies with expanded access in cases in the United States and other nations caught the attention of the media and the general public, generating enthusiasm for phage therapy. It started to alter the situation so that more medical professionals are willing to use phage therapies with conventional antibiotics. However, more study is required to fully comprehend phage therapy's potential advantages and restrictions, which is still a relatively new field in medicine. It shows promise, nevertheless, as a secure and prosperous substitute for antibiotics when treating bacterial illnesses in animals and humans. Because of their uniqueness, phage disinfection is excellent for ready-to-eat (RTE) foods like milk, vegetables, and meat products. The traditional farm-to-fork method can be used throughout the food chain to employ bacteriophages to prevent food infections at all production stages. Phage therapy improves clinical outcomes in animal models and lowers bacterial burdens in numerous preclinical investigations. The potential of phage resistance and the need to make sure that enough phages are delivered to the infection site are obstacles to employing phages in vivo. However, according to preclinical studies, phages appear to be a promising alternative to antibiotics for treating bacterial infections in vivo. Phage therapy used with compassion (a profound understanding of and empathy for another's suffering) has recently grown with many case reports of supposedly treated patients and clinical trials. This review summarizes the knowledge on the uses of phages in various fields, such as the food industry, preclinical research, and clinical settings. It also includes a list of FDA-approved bacteriophage-based products, commercial phage products, and a global list of companies that use phages for therapeutic purposes.
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Affiliation(s)
- Subhash Lal Karn
- Department of Microbiology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Mayank Gangwar
- Department of Microbiology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Rajesh Kumar
- Department of Microbiology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Satyanam Kumar Bhartiya
- Department of General Surgery, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Gopal Nath
- Department of Microbiology, Faculty of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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6
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Stepanov AV, Xie J, Zhu Q, Shen Z, Su W, Kuai L, Soll R, Rader C, Shaver G, Douthit L, Zhang D, Kalinin R, Fu X, Zhao Y, Qin T, Baran PS, Gabibov AG, Bushnell D, Neri D, Kornberg RD, Lerner RA. Control of the antitumour activity and specificity of CAR T cells via organic adapters covalently tethering the CAR to tumour cells. Nat Biomed Eng 2023:10.1038/s41551-023-01102-5. [PMID: 37798444 DOI: 10.1038/s41551-023-01102-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 08/25/2023] [Indexed: 10/07/2023]
Abstract
On-target off-tumour toxicity limits the anticancer applicability of chimaeric antigen receptor (CAR) T cells. Here we show that the tumour-targeting specificity and activity of T cells with a CAR consisting of an antibody with a lysine residue that catalytically forms a reversible covalent bond with a 1,3-diketone hapten can be regulated by the concentration of a small-molecule adapter. This adapter selectively binds to the hapten and to a chosen tumour antigen via a small-molecule binder identified via a DNA-encoded library. The adapter therefore controls the formation of a covalent bond between the catalytic antibody and the hapten, as well as the tethering of the CAR T cells to the tumour cells, and hence the cytotoxicity and specificity of the cytotoxic T cells, as we show in vitro and in mice with prostate cancer xenografts. Such small-molecule switches of T-cell cytotoxicity and specificity via an antigen-independent 'universal' CAR may enhance the control and safety profile of CAR-based cellular immunotherapies.
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Affiliation(s)
- Alexey V Stepanov
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA.
| | - Jia Xie
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | | | | | - Wenji Su
- WuXi AppTec Co., Ltd, Shanghai, China
| | | | | | - Christoph Rader
- Department of Immunology and Microbiology, UF Scripps Biomedical Research, University of Florida, Jupiter, FL, USA
| | - Geramie Shaver
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Lacey Douthit
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Ding Zhang
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Roman Kalinin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Xiang Fu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Yingying Zhao
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Tian Qin
- The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Phil S Baran
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Alexander G Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - David Bushnell
- Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Roger D Kornberg
- Structural Biology, School of Medicine, Stanford University, Stanford, CA, USA.
| | - Richard A Lerner
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
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7
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England E, Rees DG, Scott IC, Carmen S, Chan DTY, Chaillan Huntington CE, Houslay KF, Erngren T, Penney M, Majithiya JB, Rapley L, Sims DA, Hollins C, Hinchy EC, Strain MD, Kemp BP, Corkill DJ, May RD, Vousden KA, Butler RJ, Mustelin T, Vaughan TJ, Lowe DC, Colley C, Cohen ES. Tozorakimab (MEDI3506): an anti-IL-33 antibody that inhibits IL-33 signalling via ST2 and RAGE/EGFR to reduce inflammation and epithelial dysfunction. Sci Rep 2023; 13:9825. [PMID: 37330528 PMCID: PMC10276851 DOI: 10.1038/s41598-023-36642-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/07/2023] [Indexed: 06/19/2023] Open
Abstract
Interleukin (IL)-33 is a broad-acting alarmin cytokine that can drive inflammatory responses following tissue damage or infection and is a promising target for treatment of inflammatory disease. Here, we describe the identification of tozorakimab (MEDI3506), a potent, human anti-IL-33 monoclonal antibody, which can inhibit reduced IL-33 (IL-33red) and oxidized IL-33 (IL-33ox) activities through distinct serum-stimulated 2 (ST2) and receptor for advanced glycation end products/epidermal growth factor receptor (RAGE/EGFR complex) signalling pathways. We hypothesized that a therapeutic antibody would require an affinity higher than that of ST2 for IL-33, with an association rate greater than 107 M-1 s-1, to effectively neutralize IL-33 following rapid release from damaged tissue. An innovative antibody generation campaign identified tozorakimab, an antibody with a femtomolar affinity for IL-33red and a fast association rate (8.5 × 107 M-1 s-1), which was comparable to soluble ST2. Tozorakimab potently inhibited ST2-dependent inflammatory responses driven by IL-33 in primary human cells and in a murine model of lung epithelial injury. Additionally, tozorakimab prevented the oxidation of IL-33 and its activity via the RAGE/EGFR signalling pathway, thus increasing in vitro epithelial cell migration and repair. Tozorakimab is a novel therapeutic agent with a dual mechanism of action that blocks IL-33red and IL-33ox signalling, offering potential to reduce inflammation and epithelial dysfunction in human disease.
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Affiliation(s)
| | - D Gareth Rees
- Biologics Engineering, R&D, AstraZeneca, Cambridge, UK
| | - Ian Christopher Scott
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Sara Carmen
- Biologics Engineering, R&D, AstraZeneca, Cambridge, UK
| | | | | | - Kirsty F Houslay
- Bioscience Asthma and Skin Immunity, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Teodor Erngren
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Mark Penney
- Early Oncology DMPK, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Jayesh B Majithiya
- Bioscience Asthma and Skin Immunity, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Laura Rapley
- Bioscience Asthma and Skin Immunity, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Dorothy A Sims
- Bioscience Asthma and Skin Immunity, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, USA
| | - Claire Hollins
- Bioscience Asthma and Skin Immunity, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Elizabeth C Hinchy
- Bioscience Asthma and Skin Immunity, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | | | - Dominic J Corkill
- Bioscience In Vivo, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Richard D May
- Bioscience Asthma and Skin Immunity, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | | | - Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - David C Lowe
- Biologics Engineering, R&D, AstraZeneca, Cambridge, UK
| | | | - E Suzanne Cohen
- Bioscience Asthma and Skin Immunity, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.
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8
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Giacon N, Lo Cascio E, Davidson DS, Polêto MD, Lemkul JA, Pennacchietti V, Pagano L, Zamparelli C, Toto A, Arcovito A. Monomeric and dimeric states of human ZO1-PDZ2 are functional partners of the SARS-CoV-2 E protein. Comput Struct Biotechnol J 2023; 21:3259-3271. [PMID: 37293240 PMCID: PMC10210826 DOI: 10.1016/j.csbj.2023.05.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/10/2023] Open
Abstract
The Envelope (E) protein of SARS-CoV-2 plays a key role in virus maturation, assembly, and virulence mechanisms. The E protein is characterized by the presence of a PDZ-binding motif (PBM) at its C-terminus that allows it to interact with several PDZ-containing proteins in the intracellular environment. One of the main binding partners of the SARS-CoV-2 E protein is the PDZ2 domain of ZO1, a protein with a crucial role in the formation of epithelial and endothelial tight junctions (TJs). In this work, through a combination of analytical ultracentrifugation analysis and equilibrium and kinetic folding experiments, we show that ZO1-PDZ2 domain is able to fold in a monomeric state, an alternative form to the dimeric conformation that is reported to be functional in the cell for TJs assembly. Importantly, surface plasmon resonance (SPR) data indicate that the PDZ2 monomer is fully functional and capable of binding the C-terminal portion of the E protein of SARS-CoV-2, with a measured affinity in the micromolar range. Moreover, we present a detailed computational analysis of the complex between the C-terminal portion of E protein with ZO1-PDZ2, both in its monomeric conformation (computed as a high confidence AlphaFold2 model) and dimeric conformation (obtained from the Protein Data Bank), by using both polarizable and nonpolarizable simulations. Together, our results indicate both the monomeric and dimeric states of PDZ2 to be functional partners of the E protein, with similar binding mechanisms, and provide mechanistic and structural information about a fundamental interaction required for the replication of SARS-CoV-2.
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Affiliation(s)
- Noah Giacon
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
| | - Ettore Lo Cascio
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
| | - Darcy S. Davidson
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States
| | - Marcelo D. Polêto
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States
| | - Justin A. Lemkul
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, United States
- Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, United States
| | - Valeria Pennacchietti
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy – Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Italy
| | - Livia Pagano
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy – Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Italy
| | - Carlotta Zamparelli
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy – Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Italy
| | - Angelo Toto
- Dipartimento di Scienze Biochimiche “A. Rossi Fanelli”, Sapienza Università di Roma, P.le Aldo Moro 5, 00185, Rome, Italy – Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Italy
| | - Alessandro Arcovito
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Roma, Italy
- Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168 Roma, Italy
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9
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Gandotra R, Chen TW, Kuo FC, Lee MS, Lee GB. An aptamer-based sandwich assay for detection of alpha-defensin human neutrophil protein 1 on a microfluidic platform. Biosens Bioelectron 2023; 229:115120. [PMID: 36963324 DOI: 10.1016/j.bios.2023.115120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/26/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
The diagnosis of periprosthetic joint infection (PJI) remains a labor-intensive and challenging issue, with life-threatening complications associated with misdiagnoses. Superior diagnostic approaches are therefore urgently needed, and synovial biomarkers are gaining substantial attention in this capacity. A new aptamer-based sandwich assay was developed where the aptamer probes specific to one such biomarker, alpha-defensin human neutrophil protein 1 (HNP 1), was integrated herein into a new microfluidic platform. The magnetic beads coated with the primary aptamer probe were able to bind the target protein with high affinity and high specificity in synovial fluid and a fluorescent-labelled secondary aptamer were further used to quantify HNP 1 in a sandwich approach. Up to four clinical samples with low volume (∼50 μL each) in a much faster assay including detection within <60 min with 100% accuracy (with totally 13 clinical samples without the need of sample pretreatment) through the use of the aptamer-based sandwich assay were automatically detected on a single chip. The wide dynamic range of this compact device, 0.5-100 mg/L, highlights its utility for future PJI diagnostics in the clinic.
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Affiliation(s)
- Rishabh Gandotra
- Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan
| | - To-Wen Chen
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Feng-Chih Kuo
- Department of Orthopedic Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Mel S Lee
- Department of Orthopedic Surgery, Paochien Hospital, Pintung, Taiwan.
| | - Gwo-Bin Lee
- Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu, Taiwan; Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu, Taiwan.
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10
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Abstract
Phage display has been applied successfully for the rapid isolation of monoclonal antibodies against various targets including infectious diseases, autoantigens, cancer markers, and even small molecules. The main component in any phage display experiment is the availability of an antibody library to carry out the selection process of target-specific antibodies through an iterative process termed as biopanning. To generate human antibody libraries, the antibody repertoire can be obtained from human peripheral blood mononuclear cell (PBMC) or directly from cell-sorted B-cell populations. The choice of antibody isotype is dictated by the nature of the library. Naïve libraries would utilize IgM repertoires, whereas the IgG repertoire is commonly used for immune libraries. Antibody genes are amplified through polymerase chain reaction (PCR) and paired in a combinatorial fashion to expand the diversity of the cloned library repertoire. The protocol here describes the use of a two-step cloning method that can be applied for the construction of either a naïve or immune human antibody library in Fab format followed by the subsequent panning.
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Affiliation(s)
- Jing Yi Lai
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang, Malaysia.
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11
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Loughran ST, Walls D. Tagging Recombinant Proteins to Enhance Solubility and Aid Purification. Methods Mol Biol 2023; 2699:97-123. [PMID: 37646996 DOI: 10.1007/978-1-0716-3362-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Protein fusion technology has had a major impact on the efficient production and purification of individual recombinant proteins. The use of genetically engineered affinity and solubility-enhancing polypeptide "tags" has a long history, and there is a considerable repertoire of these that can be used to address issues related to the expression, stability, solubility, folding, and purification of their fusion partner. In the case of large-scale proteomic studies, the development of purification procedures tailored to individual proteins is not practicable, and affinity tags have become indispensable tools for structural and functional proteomic initiatives that involve the expression of many proteins in parallel. In this chapter, the rationale and applications of a range of established and more recently developed solubility-enhancing and affinity tags is described.
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Affiliation(s)
- Sinéad T Loughran
- Department of Life and Health Sciences, School of Health and Science, Dundalk Institute of Technology, Dundalk, Louth, Ireland.
| | - Dermot Walls
- School of Biotechnology, Dublin City University, Dublin, Ireland
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12
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Vollmer L, Krah S, Zielonka S, Yanakieva D. A Two-Step Golden Gate Cloning Procedure for the Generation of Natively Paired YSD Fab Libraries. Methods Mol Biol 2023; 2681:161-173. [PMID: 37405648 DOI: 10.1007/978-1-0716-3279-6_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
In vitro antibody display libraries have emerged as powerful tools for a streamlined discovery of novel antibody binders. While in vivo antibody repertoires are matured and selected as a specific pair of variable heavy and light chains (VH and VL) with optimal specificity and affinity, during the recombinant generation of in vitro libraries, the native sequence pairing is not maintained. Here we describe a cloning method that combines the flexibility and versatility of in vitro antibody display with the advantages of natively paired VH-VL antibodies. In this regard, VH-VL amplicons are cloned via a two-step Golden Gate cloning procedure, allowing the display of Fab fragments on yeast cells.
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Affiliation(s)
- Lena Vollmer
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany
| | - Desislava Yanakieva
- Protein Engineering and Antibody Technologies (PEAT), Merck Healthcare KGaA, Darmstadt, Germany.
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13
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Li X, Jones KS, Acca FE, Chapados CD, Driscoll HA, Fuller EP, Mendez QM, Mirando G, Weiner MP, Ferguson MR. Epivolve: A Protocol for Site-Directed Antibodies. Methods Mol Biol 2023; 2702:587-601. [PMID: 37679640 PMCID: PMC10568616 DOI: 10.1007/978-1-0716-3381-6_29] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Researchers can often successfully generate antibodies to predicted epitopes. Especially when the epitopes are on the surface of a protein or in a hydrophilic loop. But it is difficult to direct recombinant antibodies to bind either to- or near a specific amino acid on a protein or peptide. We have developed a unique immune-targeting strategy, that we call "Epivolve," that enables us to make site-specific antibodies (Abs). Epivolve technology leverages a highly immunogenic modified amino acid that acts as a "pseudo-hapten" immuno-target and takes advantage of Ab affinity maturation technologies to make high-affinity site-specific antibodies. Epivolve functions by the evolution of an Ab paratope to either synonymous or especially non-synonymous amino acid (aa) binding. Here we describe the use of Epivolve technology in phage display and the protocols for developing site-specific antibodies.
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Affiliation(s)
| | | | | | | | | | - Emily P Fuller
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
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14
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Amir A, Taussig D, Bitton A, Nahary L, Vaisman-Mentesh A, Benhar I, Wine Y. Antibody Isolation from Human Synthetic Libraries of Single-Chain Antibodies and Analysis Using NGS. Methods Mol Biol 2023; 2702:347-372. [PMID: 37679629 DOI: 10.1007/978-1-0716-3381-6_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Antibody libraries came into existence 30 years ago when the accumulating sequence data of immunoglobulin genes and the advent of PCR technology made it possible to clone antibody gene repertoires. Phage display (most common) and additional display and screening technologies were applied to pan out desired binding specificities from antibody libraries. As other antibody discovery tools, phage display is not an off-the-shelf technology and not offered as a kit but rather requires experience and expertise for making it indeed very useful.Next-generation sequencing (NGS) coupled with bioinformatics is a powerful tool for analyzing large amount of DNA sequence output of the panning. Here, we demonstrate how NGS analysis of phage biopanning (phage-Seq) of complex antibody libraries can facilitate the antibody discovery process and provide insights regarding the biopanning process (see Fig. 1).
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Affiliation(s)
- Adi Amir
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - David Taussig
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | - Limor Nahary
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | | | - Itai Benhar
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Yariv Wine
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
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15
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Ruschig M, Heine PA, Fühner V, Zilkens KJK, Steinke S, Schubert M, Bertoglio F, Hust M. Construction of Human Immune and Naive scFv Phage Display Libraries. Methods Mol Biol 2023; 2702:15-37. [PMID: 37679613 DOI: 10.1007/978-1-0716-3381-6_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Antibody phage display is a widely used in vitro selection technology for the generation of human recombinant antibodies and has yielded thousands of useful antibodies for research, diagnostics, and therapy. In order to successfully generate antibodies using phage display, the basis is the construction of high-quality antibody gene libraries. Here, we describe detailed methods for the construction of such high-quality immune and naive scFv gene libraries of human origin. These protocols were used to develop human naive (e.g., HAL9/10) and immune libraries, which resulted in thousands of specific antibodies for all kinds of applications.
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Affiliation(s)
- Maximilian Ruschig
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Philip Alexander Heine
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Viola Fühner
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Stephan Steinke
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany
- Choose Life Biotech SA, Bellinzona, Switzerland
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Departments Biotechnology and Medical Biotechnology, Technische Universität Braunschweig, Braunschweig, Germany.
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16
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Huang RR, Kierny M, Volgina V, Iwashima M, Miller C, Kay BK. Construction of an Ultra-Large Phage Display Library by Kunkel Mutagenesis and Rolling Circle Amplification. Methods Mol Biol 2023; 2702:205-226. [PMID: 37679621 DOI: 10.1007/978-1-0716-3381-6_10] [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: 09/09/2023]
Abstract
An important contributor to the successful generation of recombinant affinity reagents via phage display is a large and diverse library. We describe, herein, the application of Kunkel mutagenesis and rolling circle amplification (RCA) to the construction of a 1.1 × 1011 member library, with only 26 electroporations, and isolation of low- to sub-nanomolar monobodies to a number of protein targets, including human COP9 signalosome subunit 5 (COPS5), HIV-1 Rev. binding protein-like protein (HRBL), X-ray repair cross-complementing 5/6 (Ku70/80) heterodimer, the receptor-binding domain (RBD) of SARS-CoV-2, and transforming growth factor beta 1 (TGF-β1).
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Affiliation(s)
| | | | - Veronica Volgina
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Makio Iwashima
- Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
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17
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Wang Z, Wang G, Lu H, Li H, Tang M, Tong A. Development of therapeutic antibodies for the treatment of diseases. MOLECULAR BIOMEDICINE 2022; 3:35. [PMID: 36418786 PMCID: PMC9684400 DOI: 10.1186/s43556-022-00100-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/24/2022] [Indexed: 11/25/2022] Open
Abstract
Since the first monoclonal antibody drug, muromonab-CD3, was approved for marketing in 1986, 165 antibody drugs have been approved or are under regulatory review worldwide. With the approval of new drugs for treating a wide range of diseases, including cancer and autoimmune and metabolic disorders, the therapeutic antibody drug market has experienced explosive growth. Monoclonal antibodies have been sought after by many biopharmaceutical companies and scientific research institutes due to their high specificity, strong targeting abilities, low toxicity, side effects, and high development success rate. The related industries and markets are growing rapidly, and therapeutic antibodies are one of the most important research and development areas in the field of biology and medicine. In recent years, great progress has been made in the key technologies and theoretical innovations provided by therapeutic antibodies, including antibody-drug conjugates, antibody-conjugated nuclides, bispecific antibodies, nanobodies, and other antibody analogs. Additionally, therapeutic antibodies can be combined with technologies used in other fields to create new cross-fields, such as chimeric antigen receptor T cells (CAR-T), CAR-natural killer cells (CAR-NK), and other cell therapy. This review summarizes the latest approved or in regulatory review therapeutic antibodies that have been approved or that are under regulatory review worldwide, as well as clinical research on these approaches and their development, and outlines antibody discovery strategies that have emerged during the development of therapeutic antibodies, such as hybridoma technology, phage display, preparation of fully human antibody from transgenic mice, single B-cell antibody technology, and artificial intelligence-assisted antibody discovery.
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Affiliation(s)
- Zeng Wang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Guoqing Wang
- grid.13291.380000 0001 0807 1581Department of Neurosurgery, West China Medical School, West China Hospital, Sichuan University, Chengdu, China
| | - Huaqing Lu
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hongjian Li
- grid.12527.330000 0001 0662 3178Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Mei Tang
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Aiping Tong
- grid.13291.380000 0001 0807 1581State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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18
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André AS, Moutinho I, Dias JNR, Aires-da-Silva F. In vivo Phage Display: A promising selection strategy for the improvement of antibody targeting and drug delivery properties. Front Microbiol 2022; 13:962124. [PMID: 36225354 PMCID: PMC9549074 DOI: 10.3389/fmicb.2022.962124] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
The discovery of hybridoma technology, described by Kohler and Milstein in 1975, and the resulting ability to generate monoclonal antibodies (mAbs) initiated a new era in antibody research and clinical development. However, limitations of the hybridoma technology as a routine antibody generation method in conjunction with high immunogenicity responses have led to the development of alternative approaches for the streamlined identification of most effective antibodies. Within this context, display selection technologies such as phage display, ribosome display, yeast display, bacterial display, and mammalian cell surface display have been widely promoted over the past three decades as ideal alternatives to traditional hybridoma methods. The display of antibodies on phages is probably the most widespread and powerful of these methods and, since its invention in late 1980s, significant technological advancements in the design, construction, and selection of antibody libraries have been made, and several fully human antibodies generated by phage display are currently approved or in various clinical development stages. With evolving novel disease targets and the emerging of a new generation of therapeutic antibodies, such as bispecific antibodies, antibody drug conjugates (ADCs), and chimeric antigen receptor T (CAR-T) cell therapies, it is clear that phage display is expected to continue to play a central role in antibody development. Nevertheless, for non-standard and more demanding cases aiming to generate best-in-class therapeutic antibodies against challenging targets and unmet medical needs, in vivo phage display selections by which phage libraries are directly injected into animals or humans for isolating and identifying the phages bound to specific tissues offer an advantage over conventional in vitro phage display screening procedures. Thus, in the present review, we will first summarize a general overview of the antibody therapeutic market, the different types of antibody fragments, and novel engineered variants that have already been explored. Then, we will discuss the state-of-the-art of in vivo phage display methodologies as a promising emerging selection strategy for improvement antibody targeting and drug delivery properties.
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Affiliation(s)
- Ana S. André
- Centro de Investigação Interdisciplinar em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisbon, Portugal
- Laboratório Associado para Ciência Animal e Veterinária (AL4AnimalS), Lisbon, Portugal
| | - Isa Moutinho
- Centro de Investigação Interdisciplinar em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisbon, Portugal
- Laboratório Associado para Ciência Animal e Veterinária (AL4AnimalS), Lisbon, Portugal
| | - Joana N. R. Dias
- Centro de Investigação Interdisciplinar em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisbon, Portugal
- Laboratório Associado para Ciência Animal e Veterinária (AL4AnimalS), Lisbon, Portugal
| | - Frederico Aires-da-Silva
- Centro de Investigação Interdisciplinar em Sanidade Animal (CIISA), Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisbon, Portugal
- Laboratório Associado para Ciência Animal e Veterinária (AL4AnimalS), Lisbon, Portugal
- *Correspondence: Frederico Aires-da-Silva,
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19
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Jirapongpairoj W, Nozaki R, Koiwai K, Hirono I, Kondo H. Identification of a rabbit Ig light chain recombinant protein bound to serum immunoglobulins from different marine fish species. FISH & SHELLFISH IMMUNOLOGY 2022; 127:939-947. [PMID: 35868474 DOI: 10.1016/j.fsi.2022.07.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/05/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
The structures of fish serum immunoglobulin differ among different fish species. In this study, we accidently isolated a rabbit immunoglobulin (Ig) light chain bound to serum immunoglobulin from different marine fish species using phage display. Fish Ig was separated using a protein A column. The phage library was generated from variable regions of rabbit spleen B cells immunized with bluefin tuna Thunnus orientalis Ig. Fish Ig-specific phages were enriched using two rounds of bio-panning with yellowtail Seriola quinqueradiata serum Ig, followed by two rounds of bio-panning with red seabream Pagrus major serum Ig. The enriched phages demonstrated an increase in binding specificity to the tuna, yellowtail, and red seabream Igs compared to the phages listed in the unpanned library. A recombinant protein of a single clonal phage, which encodes the rabbit Ig light chain, was produced, and the binding specificities to fish Igs were analyzed using enzyme-linked immunosorbent assay (ELISA) and western blotting. The recombinant protein exhibited binding properties to fish Igs in the ELISA. However, the recombinant protein that bound to serum protein(s), but not IgM, was detected via western blotting. The recombinant protein may provide a novel information on the common structural feature in the fish immunoglobulins.
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Affiliation(s)
- Walissara Jirapongpairoj
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Reiko Nozaki
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Keiichiro Koiwai
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Ikuo Hirono
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan
| | - Hidehiro Kondo
- Laboratory of Genome Science, Graduate School of Tokyo University of Marine Science and Technology, Konan 4-5-7, Minato-ku, Tokyo, 108-8477, Japan.
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20
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How neutron scattering techniques benefit investigating structures and dynamics of monoclonal antibody. Biochim Biophys Acta Gen Subj 2022; 1866:130206. [PMID: 35872327 DOI: 10.1016/j.bbagen.2022.130206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/16/2022] [Accepted: 07/18/2022] [Indexed: 11/23/2022]
Abstract
Over the past several decades, great progresses have been made for the pharmaceutical industry of monoclonal antibody (mAb). More and more mAb products were approved for human therapeutics. This review describes the state of art of utilizing neutron scattering to investigate mAbs, in the aspects of structures, dynamics, physicochemical stability, functionality, etc. Firstly, brief histories of mAbs and neutron scattering, as well as some basic knowledges and principles of neutron scattering were introduced. Then specific examples were demonstrated. For the structure and structural evolution investigation of in dilute and concentrated mAbs solution, in situ small angle neutron scattering (SANS) was frequently utilized. Neutron reflectometry (NR) is powerful to probe the absorption behaviors of mAbs on various surfaces and interfaces. While for dynamic investigation, quasi-elastic scattering techniques such as neutron spin echo (NSE) demonstrate the capabilities. With this review, how to utilize and take advantages of neutron scattering on investigating structures and dynamics of mAbs were demonstrated and discussed.
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21
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Hu J, Chen X, Lu X, Wu L, Yin L, Zhu L, Liang H, Xu F, Zhou Q. A spike protein S2 antibody efficiently neutralizes the Omicron variant. Cell Mol Immunol 2022; 19:644-646. [PMID: 35318422 PMCID: PMC8938633 DOI: 10.1038/s41423-022-00847-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 01/07/2023] Open
Affiliation(s)
- Jia Hu
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
| | - Xiang Chen
- Institute for Immunology, Tsinghua University, Beijing, China
| | - Xingbing Lu
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Lijuan Wu
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Liyuan Yin
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Lingling Zhu
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Liang
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Feng Xu
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qinghua Zhou
- Lung Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
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22
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A Simple Whole-Plasmid PCR Method to Construct High-Diversity Synthetic Phage Display Libraries. Mol Biotechnol 2022; 64:791-803. [PMID: 35107752 PMCID: PMC9217769 DOI: 10.1007/s12033-021-00442-4] [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: 01/25/2021] [Accepted: 12/17/2021] [Indexed: 11/03/2022]
Abstract
Phage display technology utilises peptide and antibody libraries with very high diversities to select ligands with specific binding properties. The production of such libraries can be labour intensive and technically challenging and whilst there are commercial sources of libraries, the exploitation of the resulting binders is constrained by ownership of the libraries. Here, a peptide library of ~ 1 × 109 variants for display on gene VIII was produced alongside three VHH antibody libraries with similar diversity, where 12mer, 16mer or 21mer CDR3s were introduced into the highly stable cAbBCII10 scaffold displayed on gene III. The cloning strategy used a simple whole-plasmid PCR method and type IIS restriction enzyme assembly that facilitate the seamless insertion of diversity into any suitable phage coat protein or antibody scaffold. This method reproducibly produced 1 × 109 variants from just 10 transformations and the four libraries had relatively low bias with 82 to 86% of all sequences present as single copies. The functionality of both peptide and antibody libraries were demonstrated by selection of ligands with specific binding properties by biopanning. The peptide library was used to epitope map a monoclonal antibody. The VHH libraries were pooled and used to select an antibody to recombinant human collagen type 1.
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23
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Thomas OS, Rebmann B, Tonn M, Schirmeister IC, Wehrle S, Becker J, Zea Jimenez GJ, Hook S, Jäger S, Klenzendorf M, Laskowski M, Kaier A, Pütz G, Zurbriggen MD, Weber W, Hörner M, Wagner HJ. Reversible Shielding and Immobilization of Liposomes and Viral Vectors by Tailored Antibody-Ligand Interactions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2105157. [PMID: 34859962 DOI: 10.1002/smll.202105157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/24/2021] [Indexed: 06/13/2023]
Abstract
Controlling the time and dose of nanoparticulate drug delivery by administration of small molecule drugs holds promise for efficient and safer therapies. This study describes a versatile approach of exploiting antibody-ligand interactions for the design of small molecule-responsive nanocarrier and nanocomposite systems. For this purpose, antibody fragments (scFvs) specific for two distinct small molecule ligands are designed. Subsequently, the surface of nanoparticles (liposomes or adeno-associated viral vectors, AAVs) is modified with these ligands, serving as anchor points for scFv binding. By modifying the scFvs with polymer tails, they can act as a non-covalently bound shielding layer, which is recruited to the anchor points on the nanoparticle surface and prevents interactions with cultured mammalian cells. Administration of an excess of the respective ligand triggers competitive displacement of the shielding layer from the nanoparticle surface and restores nanoparticle-cell interactions. The same principle is applied for developing hydrogel depots that can release integrated AAVs or liposomes in response to small molecule ligands. The liberated nanoparticles subsequently deliver their cargoes to cells. In summary, the utilization of different antibody-ligand interactions, different nanoparticles, and different release systems validates the versatility of the design concept described herein.
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Affiliation(s)
- Oliver S Thomas
- Faculty of Biology II, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104, Freiburg, Germany
| | - Balder Rebmann
- Faculty of Biology II, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
| | - Matthias Tonn
- Faculty of Biology II, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
| | - Ivo C Schirmeister
- Faculty of Biology II, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
| | - Sarah Wehrle
- Faculty of Biology II, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
| | - Jan Becker
- Faculty of Biology II, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
| | - Gabriel J Zea Jimenez
- Faculty of Biology II, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
| | - Sebastian Hook
- Faculty of Biology II, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
| | - Sarah Jäger
- Faculty of Biology II, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
| | - Melissa Klenzendorf
- Faculty of Biology II, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
| | - Mateo Laskowski
- Faculty of Biology II, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
| | - Alexander Kaier
- Faculty of Biology II, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
| | - Gerhard Pütz
- University Medical Center Freiburg, Institute for Clinical Chemistry, 79106, Freiburg, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Wilfried Weber
- Faculty of Biology II, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104, Freiburg, Germany
| | - Maximilian Hörner
- Faculty of Biology II, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
| | - Hanna J Wagner
- Faculty of Biology II, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
- Department of Biosystems Science and Engineering - D-BSSE, ETH Zurich, Basel, 4058, Switzerland
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24
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Ferrara F, Erasmus MF, D'Angelo S, Leal-Lopes C, Teixeira AA, Choudhary A, Honnen W, Calianese D, Huang D, Peng L, Voss JE, Nemazee D, Burton DR, Pinter A, Bradbury ARM. A pandemic-enabled comparison of discovery platforms demonstrates a naïve antibody library can match the best immune-sourced antibodies. Nat Commun 2022; 13:462. [PMID: 35075126 PMCID: PMC8786865 DOI: 10.1038/s41467-021-27799-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 12/14/2021] [Indexed: 12/02/2022] Open
Abstract
As a result of the SARS-CoV-2 pandemic numerous scientific groups have generated antibodies against a single target: the CoV-2 spike antigen. This has provided an unprecedented opportunity to compare the efficacy of different methods and the specificities and qualities of the antibodies generated by those methods. Generally, the most potent neutralizing antibodies have been generated from convalescent patients and immunized animals, with non-immune phage libraries usually yielding significantly less potent antibodies. Here, we show that it is possible to generate ultra-potent (IC50 < 2 ng/ml) human neutralizing antibodies directly from a unique semisynthetic naïve antibody library format with affinities, developability properties and neutralization activities comparable to the best from hyperimmune sources. This demonstrates that appropriately designed and constructed naïve antibody libraries can effectively compete with immunization to directly provide therapeutic antibodies against a viral pathogen, without the need for immune sources or downstream optimization. The most potent neutralizing antibodies are typically generated from convalescent patients and immunized animals. Here, the authors show it is possible to generate highly potent human neutralizing antibodies against the SARS-CoV-2 spike protein directly from a semisynthetic naïve antibody library.
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Affiliation(s)
| | | | | | - Camila Leal-Lopes
- Bioscience Division, New Mexico Consortium, Los Alamos, NM, 87544, USA
| | - André A Teixeira
- Bioscience Division, New Mexico Consortium, Los Alamos, NM, 87544, USA
| | - Alok Choudhary
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, 07103, USA
| | - William Honnen
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, 07103, USA
| | - David Calianese
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, 07103, USA
| | - Deli Huang
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Linghan Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - James E Voss
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, 92037, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Abraham Pinter
- Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, 07103, USA
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25
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Gandotra R, Wu HB, Gopinathan P, Tsai YC, Kuo FC, Lee MS, Lee GB. Aptamer selection against alpha-defensin human neutrophil peptide 1 on an integrated microfluidic system for diagnosis of periprosthetic joint infections. LAB ON A CHIP 2022; 22:250-261. [PMID: 34918728 DOI: 10.1039/d1lc00969a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Periprosthetic joint infections (PJIs) arising from joint arthroplasty are dreadful, yet difficult to diagnose in subtle cases. Definite diagnosis requires microbiological culture to confirm the causative pathogens. However, up to 40% of culture-negative PJI needs other surrogate biomarkers such as human neutrophil peptide 1 (HNP 1) to improve diagnostic accuracy or gauge therapeutic responses. To devise a diagnostic method, systematic evolution of ligands by exponential enrichment (SELEX) (five rounds) was used to screen PJI biomarkers on a compact (20 × 20 × 35 cm), integrated microfluidic system equipped with two separate Peltier devices and one magnetic control module where an aptamer with high affinity and specificity for HNP 1, which has been used as one of the synovial fluid (SF) biomarkers for detecting PJI, was identified for the first time. Two rounds of negative selection (with immunoglobulin G & human serum album) on-chip followed by one round of unique "competitive selection" with SF extracted from PJI patients validated the specificity of the HNP 1 aptamer. The dissociation constant was measured to be 19 nM. The applicability of SF HNP 1 levels for diagnosing PJI was then verified by a new aptamer-based enzyme-linked immunosorbent assay (ELISA)-like assay. It is envisioned that this new aptamer and the associated assay could be used in future clinical applications.
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Affiliation(s)
- Rishabh Gandotra
- Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Hung-Bin Wu
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Priya Gopinathan
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Yi-Cheng Tsai
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
| | - Feng-Chih Kuo
- Department of Orthopaedic Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 83301, Taiwan
| | - Mel S Lee
- Department of Orthopaedic Surgery, Paochien Hospital, Pingtung 90064, Taiwan.
| | - Gwo-Bin Lee
- Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.
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26
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Berry SK, Rust S, Caceres C, Irving L, Bartholdson Scott J, Tabor DE, Dougan G, Christie G, Warrener P, Minter R, Grant AJ. Phenotypic whole-cell screening identifies a protective carbohydrate epitope on Klebsiella pneumoniae. MAbs 2021; 14:2006123. [PMID: 34923908 PMCID: PMC8726669 DOI: 10.1080/19420862.2021.2006123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The increasing global occurrence of recalcitrant multi-drug resistant Klebsiella pneumoniae infections warrants the investigation of alternative therapy options, such as the use of monoclonal antibodies (mAbs). We used a target-agnostic phage display approach to K. pneumoniae bacteria lacking bulky, highly variable surface polysaccharides in order to isolate antibodies targeting conserved epitopes among clinically relevant strains. One antibody population contained a high proportion of unique carbohydrate binders, and biolayer interferometry revealed these antibodies bound to lipopolysaccharide (LPS). Antibodies that bound to O1 and O1/O2 LPS were identified. Antibodies were found to promote opsonophagocytic killing by human monocyte-derived macrophages and clearance of macrophage-associated bacteria when assessed using high-content imaging. One antibody, B39, was found to protect mice in a lethal model of K. pneumoniae pneumonia against both O1 and O2 strains when dosed therapeutically. High-content imaging, western blotting and fluorescence-activated cell sorting were used to determine binding to a collection of clinical K. pneumoniae O1 and O2 strains. The data suggests B39 binds to D-galactan-I and D-galactan-II of the LPS of O1 and O2 strains. Thus, we have discovered an mAb with novel binding and functional activity properties that is a promising candidate for development as a novel biotherapeutic for the treatment and prevention of K. pneumoniae infections.
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Affiliation(s)
- Sophia K Berry
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.,Antibody Discovery and Protein Engineering, Biopharmaceuticals R&d, AstraZeneca, Cambridge, UK
| | - Steven Rust
- Antibody Discovery and Protein Engineering, Biopharmaceuticals R&d, AstraZeneca, Cambridge, UK
| | - Carolina Caceres
- Microbial Sciences, Biopharmaceuticals R&d, AstraZeneca, Gaithersburg, MD, USA
| | - Lorraine Irving
- Antibody Discovery and Protein Engineering, Biopharmaceuticals R&d, AstraZeneca, Cambridge, UK
| | - Josefin Bartholdson Scott
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, UK
| | - David E Tabor
- Microbial Sciences, Biopharmaceuticals R&d, AstraZeneca, Gaithersburg, MD, USA
| | - Gordon Dougan
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Graham Christie
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Paul Warrener
- Microbial Sciences, Biopharmaceuticals R&d, AstraZeneca, Gaithersburg, MD, USA
| | - Ralph Minter
- Antibody Discovery and Protein Engineering, Biopharmaceuticals R&d, AstraZeneca, Cambridge, UK.,Alchemab Therapeutics, Russel Square, London, UK
| | - Andrew J Grant
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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27
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Hanning KR, Minot M, Warrender AK, Kelton W, Reddy ST. Deep mutational scanning for therapeutic antibody engineering. Trends Pharmacol Sci 2021; 43:123-135. [PMID: 34895944 DOI: 10.1016/j.tips.2021.11.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/02/2021] [Accepted: 11/10/2021] [Indexed: 12/24/2022]
Abstract
The biophysical and functional properties of monoclonal antibody (mAb) drug candidates are often improved by protein engineering methods to increase the probability of clinical efficacy. One emerging method is deep mutational scanning (DMS) which combines the power of exhaustive protein mutagenesis and functional screening with deep sequencing and bioinformatics. The application of DMS has yielded significant improvements to the affinity, specificity, and stability of several preclinical antibodies alongside novel applications such as introducing multi-specific binding properties. DMS has also been applied directly on target antigens to precisely map antibody-binding epitopes and notably to profile the mutational escape potential of viral targets (e.g., SARS-CoV-2 variants). Finally, DMS combined with machine learning is enabling advances in the computational screening and engineering of therapeutic antibodies.
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Affiliation(s)
- Kyrin R Hanning
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand
| | - Mason Minot
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel 4058, Switzerland
| | - Annmaree K Warrender
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand
| | - William Kelton
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand.
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel 4058, Switzerland.
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28
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Kamalinia G, Grindel BJ, Takahashi TT, Millward SW, Roberts RW. Directing evolution of novel ligands by mRNA display. Chem Soc Rev 2021; 50:9055-9103. [PMID: 34165126 PMCID: PMC8725378 DOI: 10.1039/d1cs00160d] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
mRNA display is a powerful biological display platform for the directed evolution of proteins and peptides. mRNA display libraries covalently link the displayed peptide or protein (phenotype) with the encoding genetic information (genotype) through the biochemical activity of the small molecule puromycin. Selection for peptide/protein function is followed by amplification of the linked genetic material and generation of a library enriched in functional sequences. Iterative selection cycles are then performed until the desired level of function is achieved, at which time the identity of candidate peptides can be obtained by sequencing the genetic material. The purpose of this review is to discuss the development of mRNA display technology since its inception in 1997 and to comprehensively review its use in the selection of novel peptides and proteins. We begin with an overview of the biochemical mechanism of mRNA display and its variants with a particular focus on its advantages and disadvantages relative to other biological display technologies. We then discuss the importance of scaffold choice in mRNA display selections and review the results of selection experiments with biological (e.g., fibronectin) and linear peptide library architectures. We then explore recent progress in the development of "drug-like" peptides by mRNA display through the post-translational covalent macrocyclization and incorporation of non-proteogenic functionalities. We conclude with an examination of enabling technologies that increase the speed of selection experiments, enhance the information obtained in post-selection sequence analysis, and facilitate high-throughput characterization of lead compounds. We hope to provide the reader with a comprehensive view of current state and future trajectory of mRNA display and its broad utility as a peptide and protein design tool.
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Affiliation(s)
- Golnaz Kamalinia
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
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29
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Roth KDR, Wenzel EV, Ruschig M, Steinke S, Langreder N, Heine PA, Schneider KT, Ballmann R, Fühner V, Kuhn P, Schirrmann T, Frenzel A, Dübel S, Schubert M, Moreira GMSG, Bertoglio F, Russo G, Hust M. Developing Recombinant Antibodies by Phage Display Against Infectious Diseases and Toxins for Diagnostics and Therapy. Front Cell Infect Microbiol 2021; 11:697876. [PMID: 34307196 PMCID: PMC8294040 DOI: 10.3389/fcimb.2021.697876] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/21/2021] [Indexed: 12/30/2022] Open
Abstract
Antibodies are essential molecules for diagnosis and treatment of diseases caused by pathogens and their toxins. Antibodies were integrated in our medical repertoire against infectious diseases more than hundred years ago by using animal sera to treat tetanus and diphtheria. In these days, most developed therapeutic antibodies target cancer or autoimmune diseases. The COVID-19 pandemic was a reminder about the importance of antibodies for therapy against infectious diseases. While monoclonal antibodies could be generated by hybridoma technology since the 70ies of the former century, nowadays antibody phage display, among other display technologies, is robustly established to discover new human monoclonal antibodies. Phage display is an in vitro technology which confers the potential for generating antibodies from universal libraries against any conceivable molecule of sufficient size and omits the limitations of the immune systems. If convalescent patients or immunized/infected animals are available, it is possible to construct immune phage display libraries to select in vivo affinity-matured antibodies. A further advantage is the availability of the DNA sequence encoding the phage displayed antibody fragment, which is packaged in the phage particles. Therefore, the selected antibody fragments can be rapidly further engineered in any needed antibody format according to the requirements of the final application. In this review, we present an overview of phage display derived recombinant antibodies against bacterial, viral and eukaryotic pathogens, as well as microbial toxins, intended for diagnostic and therapeutic applications.
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Affiliation(s)
- Kristian Daniel Ralph Roth
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Esther Veronika Wenzel
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany.,Abcalis GmbH, Braunschweig, Germany
| | - Maximilian Ruschig
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Stephan Steinke
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Nora Langreder
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Philip Alexander Heine
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Kai-Thomas Schneider
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Rico Ballmann
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Viola Fühner
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | | | | | | | - Stefan Dübel
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany.,Abcalis GmbH, Braunschweig, Germany.,YUMAB GmbH, Braunschweig, Germany
| | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany
| | - Giulio Russo
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany.,Abcalis GmbH, Braunschweig, Germany
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Braunschweig, Germany.,YUMAB GmbH, Braunschweig, Germany
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30
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Eskafi AH, Bagheri KP, Behdani M, Yamabhai M, Shahbazzadeh D, Kazemi-Lomedasht F. Development and characterization of human single chain antibody against Iranian Macrovipera lebetina snake venom. Toxicon 2021; 197:106-113. [DOI: 10.1016/j.toxicon.2021.04.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 04/14/2021] [Accepted: 04/20/2021] [Indexed: 12/18/2022]
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31
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Bullen G, Galson JD, Hall G, Villar P, Moreels L, Ledsgaard L, Mattiuzzo G, Bentley EM, Masters EW, Tang D, Millett S, Tongue D, Brown R, Diamantopoulos I, Parthiban K, Tebbutt C, Leah R, Chaitanya K, Ergueta-Carballo S, Pazeraitis D, Surade SB, Ashiru O, Crippa L, Cowan R, Bowler MW, Campbell JI, Lee WYJ, Carr MD, Matthews D, Pfeffer P, Hufton SE, Sawmynaden K, Osbourn J, McCafferty J, Karatt-Vellatt A. Cross-Reactive SARS-CoV-2 Neutralizing Antibodies From Deep Mining of Early Patient Responses. Front Immunol 2021; 12:678570. [PMID: 34211469 PMCID: PMC8239432 DOI: 10.3389/fimmu.2021.678570] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/13/2021] [Indexed: 12/22/2022] Open
Abstract
Passive immunization using monoclonal antibodies will play a vital role in the fight against COVID-19. The recent emergence of viral variants with reduced sensitivity to some current antibodies and vaccines highlights the importance of broad cross-reactivity. This study describes deep-mining of the antibody repertoires of hospitalized COVID-19 patients using phage display technology and B cell receptor (BCR) repertoire sequencing to isolate neutralizing antibodies and gain insights into the early antibody response. This comprehensive discovery approach has yielded a panel of potent neutralizing antibodies which bind distinct viral epitopes including epitopes conserved in SARS-CoV-1. Structural determination of a non-ACE2 receptor blocking antibody reveals a previously undescribed binding epitope, which is unlikely to be affected by the mutations in any of the recently reported major viral variants including B.1.1.7 (from the UK), B.1.351 (from South Africa) and B.1.1.28 (from Brazil). Finally, by combining sequences of the RBD binding and neutralizing antibodies with the B cell receptor repertoire sequencing, we also describe a highly convergent early antibody response. Similar IgM-derived sequences occur within this study group and also within patient responses described by multiple independent studies published previously.
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Affiliation(s)
| | | | - Gareth Hall
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | | | | | | | - Giada Mattiuzzo
- National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | - Emma M Bentley
- National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Richard Cowan
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | | | | | - Wing-Yiu Jason Lee
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Mark D Carr
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | | | - Paul Pfeffer
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Simon E Hufton
- National Institute for Biological Standards and Control, Potters Bar, United Kingdom
| | | | - Jane Osbourn
- Alchemab Therapeutics Ltd., London, United Kingdom
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32
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Aloisio A, Nisticò N, Mimmi S, Maisano D, Vecchio E, Fiume G, Iaccino E, Quinto I. Phage-Displayed Peptides for Targeting Tyrosine Kinase Membrane Receptors in Cancer Therapy. Viruses 2021; 13:649. [PMID: 33918836 PMCID: PMC8070105 DOI: 10.3390/v13040649] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/04/2021] [Accepted: 04/07/2021] [Indexed: 02/06/2023] Open
Abstract
Receptor tyrosine kinases (RTKs) regulate critical physiological processes, such as cell growth, survival, motility, and metabolism. Abnormal activation of RTKs and relative downstream signaling is implicated in cancer pathogenesis. Phage display allows the rapid selection of peptide ligands of membrane receptors. These peptides can target in vitro and in vivo tumor cells and represent a novel therapeutic approach for cancer therapy. Further, they are more convenient compared to antibodies, being less expensive and non-immunogenic. In this review, we describe the state-of-the-art of phage display for development of peptide ligands of tyrosine kinase membrane receptors and discuss their potential applications for tumor-targeted therapy.
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Affiliation(s)
| | | | | | | | | | | | | | - Ileana Quinto
- Correspondence: (A.A.); (I.Q.): Tel.: +39-0961-3694057 (I.Q.)
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33
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Valldorf B, Hinz SC, Russo G, Pekar L, Mohr L, Klemm J, Doerner A, Krah S, Hust M, Zielonka S. Antibody display technologies: selecting the cream of the crop. Biol Chem 2021; 403:455-477. [PMID: 33759431 DOI: 10.1515/hsz-2020-0377] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 03/05/2021] [Indexed: 02/07/2023]
Abstract
Antibody display technologies enable the successful isolation of antigen-specific antibodies with therapeutic potential. The key feature that facilitates the selection of an antibody with prescribed properties is the coupling of the protein variant to its genetic information and is referred to as genotype phenotype coupling. There are several different platform technologies based on prokaryotic organisms as well as strategies employing higher eukaryotes. Among those, phage display is the most established system with more than a dozen of therapeutic antibodies approved for therapy that have been discovered or engineered using this approach. In recent years several other technologies gained a certain level of maturity, most strikingly mammalian display. In this review, we delineate the most important selection systems with respect to antibody generation with an emphasis on recent developments.
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Affiliation(s)
- Bernhard Valldorf
- Chemical and Pharmaceutical Development, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Steffen C Hinz
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287Darmstadt, Germany
| | - Giulio Russo
- Abcalis GmbH, Inhoffenstrasse 7, D-38124Braunschweig, Germany.,Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106Braunschweig, Germany
| | - Lukas Pekar
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Laura Mohr
- Institute of Cell Biology and Neuroscience and Buchmann Institute for Molecular Life Sciences, University of Frankfurt, Max-von-Laue-Strasse 13, D-60438Frankfurt am Main, Germany
| | - Janina Klemm
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287Darmstadt, Germany
| | - Achim Doerner
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Simon Krah
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106Braunschweig, Germany
| | - Stefan Zielonka
- Protein Engineering and Antibody Technologies, Merck KGaA, Frankfurter Strasse 250, D-64293Darmstadt, Germany
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A single donor is sufficient to produce a highly functional in vitro antibody library. Commun Biol 2021; 4:350. [PMID: 33742103 PMCID: PMC7979914 DOI: 10.1038/s42003-021-01881-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/19/2021] [Indexed: 01/31/2023] Open
Abstract
Antibody complementarity determining region diversity has been considered to be the most important metric for the production of a functional antibody library. Generally, the greater the antibody library diversity, the greater the probability of selecting a diverse array of high affinity leads. According to this paradigm, the primary means of elevating library diversity has been by increasing the number of donors. In the present study we explored the possibility of creating an in vitro antibody library from a single healthy individual, showing that the number of lymphocytes, rather than the number of donors, is the key criterion in the production of a diverse and functional antibody library. We describe the construction of a high-quality phage display library comprising 5 × 109 human antibodies by applying an efficient B cell extraction protocol from a single donor and a targeted V-gene amplification strategy favoring specific antibody families for their improved developability profiles. Each step of the library generation process was followed and validated by next generation sequencing to monitor the library quality and diversity. The functionality of the library was tested using several therapeutically relevant targets for which a vast number of different antibodies with desired biophysical properties were obtained.
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Affinity maturation: highlights in the application of in vitro strategies for the directed evolution of antibodies. Emerg Top Life Sci 2021; 5:601-608. [PMID: 33660765 PMCID: PMC8726058 DOI: 10.1042/etls20200331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/16/2021] [Accepted: 02/23/2021] [Indexed: 01/04/2023]
Abstract
Affinity maturation is a key technique in protein engineering which is used to improve affinity and binding interactions in vitro, a process often required to fulfil the therapeutic potential of antibodies. There are many available display technologies and maturation methods developed over the years, which have been instrumental in the production of therapeutic antibodies. However, due to the inherent limitations in display capacity of these technologies, accommodation of expansive and complex library builds is still a challenge. In this article, we discuss our recent efforts in the affinity maturation of a difficult antibody lineage using an unbiased approach, which sought to explore a larger sequence space through the application of DNA recombination and shuffling techniques across the entire antibody region and selections using ribosome display. We also highlight the key features of several display technologies and diversification methods, and discuss the strategies devised by different groups in response to different challenges. Particular attention is drawn to examples which are aimed at the expansion of sequence, structural or experimental diversity through different means and approaches. Here, we provide our perspectives on these methodologies and the considerations involved in the design of effective strategies for the directed evolution of antibodies.
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Nagano K, Tsutsumi Y. Phage Display Technology as a Powerful Platform for Antibody Drug Discovery. Viruses 2021; 13:178. [PMID: 33504115 PMCID: PMC7912188 DOI: 10.3390/v13020178] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/06/2021] [Accepted: 01/21/2021] [Indexed: 12/18/2022] Open
Abstract
Antibody drugs with a high affinity and specificity are effective and safe for intractable diseases, such as cancers and autoimmune diseases. Furthermore, they have played a central role in drug discovery, currently accounting for eight of the top 20 pharmaceutical products worldwide by sales. Forty years ago, clinical trials on antibody drugs that were thought to be a magic bullet failed, partly due to the immunogenicity of monoclonal antibodies produced in mice. The recent breakthrough in antibody drugs is largely because of the contribution of phage display technology. Here, we reviewed the importance of phage display technology as a powerful platform for antibody drug discovery from various perspectives, such as the development of human monoclonal antibodies, affinity enhancement of monoclonal antibodies, and the identification of therapeutic targets for antibody drugs.
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MESH Headings
- Animals
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/metabolism
- Antibodies, Monoclonal/pharmacology
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Monoclonal, Humanized/immunology
- Antibodies, Monoclonal, Humanized/metabolism
- Antibodies, Monoclonal, Humanized/pharmacology
- Antibodies, Monoclonal, Humanized/therapeutic use
- Antibody Affinity
- Autoantibodies/immunology
- Cell Surface Display Techniques
- Drug Discovery
- High-Throughput Screening Assays
- Humans
- Mice
- Peptide Library
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Affiliation(s)
- Kazuya Nagano
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
- Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yasuo Tsutsumi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
- Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- The Center for Advanced Medical Engineering and Informatics, Osaka University, 1-6, Yamadaoka, Suita, Osaka 565-0871, Japan
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Kang SH, Lee CH. Development of Therapeutic Antibodies and Modulating the Characteristics of Therapeutic Antibodies to Maximize the Therapeutic Efficacy. BIOTECHNOL BIOPROC E 2021; 26:295-311. [PMID: 34220207 PMCID: PMC8236339 DOI: 10.1007/s12257-020-0181-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 02/06/2023]
Abstract
Monoclonal antibodies (mAb) have been used as therapeutic agents for various diseases, and immunoglobulin G (IgG) is mainly used among antibody isotypes due to its structural and functional properties. So far, regardless of the purpose of the therapeutic antibody, wildtype IgG has been mainly used, but recently, the engineered antibodies with various strategies according to the role of the therapeutic antibody have been used to maximize the therapeutic efficacy. In this review paper, first, the overall structural features and functional characteristics of antibody IgG, second, the old and new techniques for antibody discovery, and finally, several antibody engineering strategies for maximizing therapeutic efficacy according to the role of a therapeutic antibody will be introduced.
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Affiliation(s)
- Seung Hyun Kang
- grid.31501.360000 0004 0470 5905Department of Pharmacology, Seoul National University College of Medicine, Seoul, 03080 Korea
| | - Chang-Han Lee
- grid.31501.360000 0004 0470 5905Department of Pharmacology, Seoul National University College of Medicine, Seoul, 03080 Korea ,grid.31501.360000 0004 0470 5905Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080 Korea ,Hongcheon, 25159 Korea ,grid.31501.360000 0004 0470 5905SNU Dementia Research Center, Seoul National University College of Medicine, Seoul, 03080 Korea
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38
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Jarsch IK, Gadsby JR, Nuccitelli A, Mason J, Shimo H, Pilloux L, Marzook B, Mulvey CM, Dobramysl U, Bradshaw CR, Lilley KS, Hayward RD, Vaughan TJ, Dobson CL, Gallop JL. A direct role for SNX9 in the biogenesis of filopodia. J Cell Biol 2020; 219:151579. [PMID: 32328641 PMCID: PMC7147113 DOI: 10.1083/jcb.201909178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/24/2020] [Accepted: 01/31/2020] [Indexed: 12/13/2022] Open
Abstract
Filopodia are finger-like actin-rich protrusions that extend from the cell surface and are important for cell-cell communication and pathogen internalization. The small size and transient nature of filopodia combined with shared usage of actin regulators within cells confounds attempts to identify filopodial proteins. Here, we used phage display phenotypic screening to isolate antibodies that alter the actin morphology of filopodia-like structures (FLS) in vitro. We found that all of the antibodies that cause shorter FLS interact with SNX9, an actin regulator that binds phosphoinositides during endocytosis and at invadopodia. In cells, we discover SNX9 at specialized filopodia in Xenopus development and that SNX9 is an endogenous component of filopodia that are hijacked by Chlamydia entry. We show the use of antibody technology to identify proteins used in filopodia-like structures, and a role for SNX9 in filopodia.
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Affiliation(s)
- Iris K Jarsch
- Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jonathan R Gadsby
- Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Annalisa Nuccitelli
- Antibody Discovery and Protein Engineering, AstraZeneca, Granta Park, Cambridge, UK
| | - Julia Mason
- Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Hanae Shimo
- Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Ludovic Pilloux
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Bishara Marzook
- Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Claire M Mulvey
- Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Ulrich Dobramysl
- Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Charles R Bradshaw
- Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Kathryn S Lilley
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Tristan J Vaughan
- Antibody Discovery and Protein Engineering, AstraZeneca, Granta Park, Cambridge, UK
| | - Claire L Dobson
- Antibody Discovery and Protein Engineering, AstraZeneca, Granta Park, Cambridge, UK
| | - Jennifer L Gallop
- Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
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Kim D, Hong J, Choi Y, Han J, Kim S, Jo G, Yoon JY, Chae H, Yoon H, Lee C, Hong HJ. Generation and Characterization of Monoclonal Antibodies to the Ogawa Lipopolysaccharide of Vibrio cholerae O1 from Phage-Displayed Human Synthetic Fab Library. J Microbiol Biotechnol 2020; 30:1760-1768. [PMID: 32876069 PMCID: PMC9728160 DOI: 10.4014/jmb.2005.05046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/20/2020] [Accepted: 08/22/2020] [Indexed: 12/15/2022]
Abstract
Vibrio cholerae, cause of the life-threatening diarrheal disease cholera, can be divided into different serogroups based on the structure of its lipopolysaccharide (LPS), which consists of lipid-A, corepolysaccharide and O-antigen polysaccharide (O-PS). The O1 serogroup, the predominant cause of cholera, includes two major serotypes, Inaba and Ogawa. These serotypes are differentiated by the presence of a single 2-O-methyl group in the upstream terminal perosamine of the Ogawa O-PS, which is absent in the Inaba O-PS. To ensure the consistent quality and efficacy of the current cholera vaccines, accurate measurement and characterization of each of these two serotypes is highly important. In this study, we efficiently screened a phage-displayed human synthetic Fab library by bio-panning against Ogawa LPS and finally selected three unique mAbs (D9, E11, and F7) that specifically react with Ogawa LPS. The mAbs bound to Vibrio cholerae vaccine in a dose-dependent fashion. Sequence and structure analyses of antibody paratopes suggest that IgG D9 might have the same fine specificity as that of the murine mAbs, which were shown to bind to the upstream terminal perosamine of Ogawa O-PS, whereas IgGs F7 and E11 showed some different characteristics in the paratopes. To our knowledge, this study is the first to demonstrate the generation of Ogawa-specific mAbs using phage display technology. The mAbs will be useful for identification and quantification of Ogawa LPS in multivalent V. cholerae vaccines.
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Affiliation(s)
- Dain Kim
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 2434, Republic of Korea
| | - Jisu Hong
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 2434, Republic of Korea
| | - Yoonjoo Choi
- Medical Research Center, Chonnam National University Medical School, Hwasun 5818, Republic of Korea
| | - Jemin Han
- Eubiologics Co., Ltd., Chuncheon 2422, Republic of Korea
| | - Sangkyu Kim
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 2434, Republic of Korea
| | - Gyunghee Jo
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 2434, Republic of Korea
| | - Jun-Yeol Yoon
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 2434, Republic of Korea
| | - Heesu Chae
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 2434, Republic of Korea
| | - Hyeseon Yoon
- Eubiologics Co., Ltd., Chuncheon 2422, Republic of Korea
| | - Chankyu Lee
- Eubiologics Co., Ltd., Chuncheon 2422, Republic of Korea,Corresponding authors H.J.Hong Phone: 82-33-250-8381 Fax: 82-33-259-5643 E-mail:
| | - Hyo Jeong Hong
- Department of Systems Immunology, College of Biomedical Science, Kangwon National University, Chuncheon 2434, Republic of Korea,Scripps Korea Antibody Institute, Chuncheon 231, Republic of Korea,Corresponding authors H.J.Hong Phone: 82-33-250-8381 Fax: 82-33-259-5643 E-mail:
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40
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Kopruszinski CM, Thornton P, Arnold J, Newton P, Lowne D, Navratilova E, Swiokla J, Dodick DW, Dobson C, Gurrell I, Chessell IP, Porreca F. Characterization and preclinical evaluation of a protease activated receptor 2 (PAR2) monoclonal antibody as a preventive therapy for migraine. Cephalalgia 2020; 40:1535-1550. [PMID: 33131305 DOI: 10.1177/0333102420966581] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
AIM Migraine pain is thought to result from activation of meningeal nociceptors that might involve dural mast cell degranulation and release of proteases and pronociceptive mediators. Tryptase, the most abundant dural mast cell protease, has been demonstrated to stimulate dural mast cells, as well as trigeminal nociceptors by activating the protease activated receptor 2. Mast cell or neuronal protease activated receptors 2 may therefore represent a novel target for migraine treatment. In this study, we characterized and evaluated a novel protease activated receptor 2 monoclonal antibody as a preventive anti-migraine pain therapy in preclinical models. METHODS Flow cytometry, immunocytochemistry, calcium imaging, Homogeneous Time Resolved Technology (HTRF) epitope competition assay and serum pharmacokinetic (PK) assay in rats were performed to confirm the activity, specificity and in vivo stability of PAR650097, a novel anti- protease activated receptor 2 monoclonal antibody. In vivo assessment was performed in female C57BL/6J mice by evaluation of PAR650097 in preventing cutaneous allodynia elicited by (a) supradural injection of the protease activated receptor 2 agonist, Ser-Leu-Ile-Gly-Arg-Leu-amide trifluoroacetate (SLIGRL), or calcitonin gene-related (CGRP) peptide, and (b) induction of latent sensitization by priming with three daily episodes of restraint stress followed by challenge with a subthreshold inhalational exposure to umbellulone (UMB), a transient receptor potential ankyrin 1 (TRPA1) agonist. PAR650097 was administered as a pretreatment prior to the first restraint stress, umbellulone exposure, SLIGRL or calcitonin gene-related peptide injection. Additionally, fremanezumab, a calcitonin gene-related peptide antibody was administered as pre-treatment prior to supradural administration of calcitonin gene-related peptide or SLIGRL. RESULTS In vitro, PAR650097 demonstrated rapid interaction with protease activated receptor 2, enabling it to fully inhibit protease-induced protease activated receptor 2 activation, in human and mouse cells, with high potency. Furthermore, PAR650097 was highly selective for protease activated receptor 2, demonstrating no affinity for protease activated receptor 1 protein and no functional effect on the activation of cellular protease activated receptor 1 with thrombin. In addition, PAR650097 had an acceptable PK profile, compatible with testing the effects of selective protease activated receptor 2 inhibition in vivo. In vivo, PAR650097 blocked cutaneous allodynia induced by either supradural SLIGRL or calcitonin gene-related peptide. Fremanezumab abolished cutaneous allodynia induced by supradural CGRP, and partially attenuated cutaneous allodynia induced by SLIGRL. Administration of PAR650097, before the first restraint stress episode, did not prevent the acute stress-induced cutaneous allodynia or restraint stress priming revealed by cutaneous allodynia induced by inhalational umbellulone. In contrast, PAR650097 prevented expression of cutaneous allodynia when given before the umbellulone challenge in restraint stress-primed animals. CONCLUSION PAR650097 specifically inhibits endogenously expressed protease activated receptor 2 in human and mouse cells with high potency. This antibody has an acceptable PK profile in rodents and effectively blocked SLIGR-induced cutaneous allodynia. PAR650097 additionally prevented cutaneous allodynia induced by supradural calcitonin gene-related peptide, indicating that the protease activated receptor 2 receptor is a downstream consequence of calcitonin gene-related peptide actions. Fremanezumab effectively blocked calcitonin gene-related peptide-induced cutaneous allodynia and only partially reduced cutaneous allodynia induced by a protease activated receptor 2 activator, suggesting both calcitonin gene-related peptide-dependent and -independent mechanisms in promoting migraine pain. While PAR650097 did not prevent stress-induced cutaneous allodynia or priming, it effectively prevented cutaneous allodynia induced by a TRPA1 agonist in animals with latent sensitization. Activation of protease activated receptor 2, therefore, contributes to both calcitonin gene-related peptide-dependent and -independent mechanisms in promoting migraine-like pain. Therapeutic targeting of protease activated receptor 2 receptors may represent an anti-migraine pain strategy with a potentially broad efficacy profile.
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Affiliation(s)
| | - Peter Thornton
- Neuroscience, R&D BioPharmaceuticals, AstraZeneca, Cambridge, UK
| | - Joanne Arnold
- ADPE, R&D BioPharmaceuticals, AstraZeneca, Cambridge, UK
| | - Philip Newton
- ADPE, R&D BioPharmaceuticals, AstraZeneca, Cambridge, UK
| | - David Lowne
- ADPE, R&D BioPharmaceuticals, AstraZeneca, Cambridge, UK
| | - Edita Navratilova
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, USA
| | - Juliana Swiokla
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, USA
| | | | - Claire Dobson
- ADPE, R&D BioPharmaceuticals, AstraZeneca, Cambridge, UK
| | - Ian Gurrell
- Neuroscience, R&D BioPharmaceuticals, AstraZeneca, Cambridge, UK
| | | | - Frank Porreca
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, USA.,Department of Neurology, Mayo Clinic, Phoenix, AZ, USA
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41
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Photoswitchable CAR-T Cell Function In Vitro and In Vivo via a Cleavable Mediator. Cell Chem Biol 2020; 28:60-69.e7. [PMID: 33113407 DOI: 10.1016/j.chembiol.2020.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/07/2020] [Accepted: 10/07/2020] [Indexed: 01/20/2023]
Abstract
Chimeric antigen receptor (CAR)-T-based therapeutics are a breakthrough in cancer treatment; however, they are hampered by constitutive activation, which leads to worrisome side effects. Engineering CAR-T cells to be as tightly controllable as possible remains a topic of ongoing investigation. Here, we report a photoswitchable approach that uses a mediator for the at-will regulation of CAR-T cells. This mediator carries dual folate and fluorescein isothiocyanate moieties tethered by an ortho-nitrobenzyl ester photocleavable linker. CAR-T cells were shown to be highly cytotoxic to targeted cells only in the presence of the mediator and acted in a dose-dependent manner. The toxicity of CAR-T cells can be rapidly terminated by cleavage of the mediator, and the effects of CAR-T cells can be activated again by resupplementation with the mediator without compromising tumor therapy. The approach described here provides a direction for enhancing the controllability of CAR-T cells and can likely be applied in other immunotherapies.
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42
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Zhao Z, Ukidve A, Kim J, Mitragotri S. Targeting Strategies for Tissue-Specific Drug Delivery. Cell 2020; 181:151-167. [PMID: 32243788 DOI: 10.1016/j.cell.2020.02.001] [Citation(s) in RCA: 368] [Impact Index Per Article: 92.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/30/2020] [Accepted: 01/31/2020] [Indexed: 12/19/2022]
Abstract
Off-target effects of systemically administered drugs have been a major hurdle in designing therapies with desired efficacy and acceptable toxicity. Developing targeting strategies to enable site-specific drug delivery holds promise in reducing off-target effects, decreasing unwanted toxicities, and thereby enhancing a drug's therapeutic efficacy. Over the past three decades, a large body of literature has focused on understanding the biological barriers that hinder tissue-specific drug delivery and strategies to overcome them. These efforts have led to several targeting strategies that modulate drug delivery in both the preclinical and clinical settings, including small molecule-, nucleic acid-, peptide-, antibody-, and cell-based strategies. Here, we discuss key advances and emerging concepts for tissue-specific drug delivery approaches and their clinical translation.
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Affiliation(s)
- Zongmin Zhao
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, MA 02138, USA; Wyss Institute of Biologically Inspired Engineering at Harvard University, Boston, MA 02115, USA
| | - Anvay Ukidve
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, MA 02138, USA; Wyss Institute of Biologically Inspired Engineering at Harvard University, Boston, MA 02115, USA
| | - Jayoung Kim
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, MA 02138, USA; Wyss Institute of Biologically Inspired Engineering at Harvard University, Boston, MA 02115, USA
| | - Samir Mitragotri
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, MA 02138, USA; Wyss Institute of Biologically Inspired Engineering at Harvard University, Boston, MA 02115, USA.
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43
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Emerging Strategies for Therapeutic Antibody Discovery from Human B Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020. [PMID: 32949403 DOI: 10.1007/978-981-15-4494-1_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Monoclonal antibodies from human sources are being increasingly recognized as valuable options in many therapeutic areas. These antibodies can show exquisite specificity and high potency while maintaining a desirable safety profile, having been matured and tolerized within human patients. However, the discovery of these antibodies presents important challenges, since the B cells encoding therapeutic antibodies can be rare in a typical blood draw and are short-lived ex vivo. Furthermore, the unique pairing of VH and VL domains in each B cell contributes to specificity and function; therefore, maintaining antibody chain pairing presents a throughput limitation. This work will review the various approaches aimed at addressing these challenges with an eye to next-generation methods for high-throughput discovery from the human B-cell repertoire.
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44
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Alfaleh MA, Alsaab HO, Mahmoud AB, Alkayyal AA, Jones ML, Mahler SM, Hashem AM. Phage Display Derived Monoclonal Antibodies: From Bench to Bedside. Front Immunol 2020; 11:1986. [PMID: 32983137 PMCID: PMC7485114 DOI: 10.3389/fimmu.2020.01986] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022] Open
Abstract
Monoclonal antibodies (mAbs) have become one of the most important classes of biopharmaceutical products, and they continue to dominate the universe of biopharmaceutical markets in terms of approval and sales. They are the most profitable single product class, where they represent six of the top ten selling drugs. At the beginning of the 1990s, an in vitro antibody selection technology known as antibody phage display was developed by John McCafferty and Sir. Gregory Winter that enabled the discovery of human antibodies for diverse applications, particularly antibody-based drugs. They created combinatorial antibody libraries on filamentous phage to be utilized for generating antigen specific antibodies in a matter of weeks. Since then, more than 70 phage–derived antibodies entered clinical studies and 14 of them have been approved. These antibodies are indicated for cancer, and non-cancer medical conditions, such as inflammatory, optical, infectious, or immunological diseases. This review will illustrate the utility of phage display as a powerful platform for therapeutic antibodies discovery and describe in detail all the approved mAbs derived from phage display.
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Affiliation(s)
- Mohamed A Alfaleh
- Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia.,Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hashem O Alsaab
- Department of Pharmaceutics and Pharmaceutical Technology, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Ahmad Bakur Mahmoud
- College of Applied Medical Sciences, Taibah University, Medina, Saudi Arabia
| | - Almohanad A Alkayyal
- Department of Medical Laboratory Technology, University of Tabuk, Tabuk, Saudi Arabia
| | - Martina L Jones
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia.,Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Stephen M Mahler
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia.,Australian Research Council Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Anwar M Hashem
- Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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Vaisman-Mentesh A, Gutierrez-Gonzalez M, DeKosky BJ, Wine Y. The Molecular Mechanisms That Underlie the Immune Biology of Anti-drug Antibody Formation Following Treatment With Monoclonal Antibodies. Front Immunol 2020; 11:1951. [PMID: 33013848 PMCID: PMC7461797 DOI: 10.3389/fimmu.2020.01951] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/20/2020] [Indexed: 12/25/2022] Open
Abstract
Monoclonal antibodies (mAbs) are a crucial asset for human health and modern medicine, however, the repeated administration of mAbs can be highly immunogenic. Drug immunogenicity manifests in the generation of anti-drug antibodies (ADAs), and some mAbs show immunogenicity in up to 70% of patients. ADAs can alter a drug's pharmacokinetic and pharmacodynamic properties, reducing drug efficacy. In more severe cases, ADAs can neutralize the drug's therapeutic effects or cause severe adverse events to the patient. While some contributing factors to ADA formation are known, the molecular mechanisms of how therapeutic mAbs elicit ADAs are not completely clear. Accurate ADA detection is necessary to provide clinicians with sufficient information for patient monitoring and clinical intervention. However, ADA assays present unique challenges because both the analyte and antigen are antibodies, so most assays are cumbersome, costly, time consuming, and lack standardization. This review will discuss aspects related to ADA formation following mAb drug administration. First, we will provide an overview of the prevalence of ADA formation and the available diagnostic tools for their detection. Next, we will review studies that support possible molecular mechanisms causing the formation of ADA. Finally, we will summarize recent approaches used to decrease the propensity of mAbs to induce ADAs.
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Affiliation(s)
- Anna Vaisman-Mentesh
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | | | - Brandon J. DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Department of Chemical and Petroleum Engineering, The University of Kansas, Lawrence, KS, United States
| | - Yariv Wine
- George S. Wise Faculty of Life Sciences, School of Molecular Cell Biology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
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Rapid Evaluation of Antibody Fragment Endocytosis for Antibody Fragment-Drug Conjugates. Biomolecules 2020; 10:biom10060955. [PMID: 32630402 PMCID: PMC7355425 DOI: 10.3390/biom10060955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 06/12/2020] [Accepted: 06/23/2020] [Indexed: 12/31/2022] Open
Abstract
Antibody-drug conjugates (ADCs) have emerged as the most promising strategy in targeted cancer treatment. Recent strategies for the optimization ADCs include the development of antibody fragment-drug conjugates (FDCs). The critical factor in the successful development of ADCs and FDCs is the identification of tumor antigen-specific and internalizing antibodies (Abs). However, systematic comparison or correlation studies of internalization rates with different antibody formats have not been reported previously. In this study, we generated a panel of scFv-phage Abs using phage display technology and their corresponding scFv and scFv-Fc fragments and evaluated their relative internalization kinetics in relation to their antibody forms. We found that the relative rates and levels of internalization of scFv-phage antibodies positively correlate with their scFv and scFv-Fc forms. Our systematic study demonstrates that endocytosis of scFv-phage can serve as a predictive indicator for the assessment of Ab fragment internalization. Additionally, the present study demonstrates that endocytic antibodies can be rapidly screened and selected from phage antibody libraries prior to the conversion of phage antibodies for the generation of the conventional antibody format. Our strategic approach for the identification and evaluation of endocytic antibodies would expedite the selection for optimal antibodies and antibody fragments and be broadly applicable to ADC and FDC development.
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Strobel B, Düchs MJ, Blazevic D, Rechtsteiner P, Braun C, Baum-Kroker KS, Schmid B, Ciossek T, Gottschling D, Hartig JS, Kreuz S. A Small-Molecule-Responsive Riboswitch Enables Conditional Induction of Viral Vector-Mediated Gene Expression in Mice. ACS Synth Biol 2020; 9:1292-1305. [PMID: 32427483 DOI: 10.1021/acssynbio.9b00410] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Adeno-associated viral (AAV) vector-mediated gene therapy holds great potential for future medical applications. However, to facilitate safer and broader applicability and to enable patient-centric care, therapeutic protein expression should be controllable, ideally by an orally administered drug. The use of protein-based systems is considered rather undesirable, due to potential immunogenicity and the limited coding space of AAV. Ligand-dependent riboswitches, in contrast, are small and characterized by an attractive mode-of-action based on mRNA-self-cleavage, independent of coexpressed foreign protein. While a promising approach, switches available to date have only shown moderate potency in animals. In particular, ON-switches that induce transgene expression upon ligand administration so far have achieved rather disappointing results. Here we present the utilization of the previously described tetracycline-dependent ribozyme K19 for controlling AAV-mediated transgene expression in mice. Using this tool switch, we provide first proof for the feasibility of clinically desired key features, including multiorgan functionality, potent regulation (up to 15-fold induction), reversibility, and the possibility to fine-tune and repeatedly induce expression. The systematic assessment of ligand and reporter protein plasma levels further enabled the characterization of pharmacokinetic-pharmacodynamic relationships. Thus, our results strongly support future efforts to develop engineered riboswitches for applications in clinical gene therapy.
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Affiliation(s)
- Benjamin Strobel
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, 88397, Germany
| | - Matthias J. Düchs
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, 88397, Germany
| | - Dragica Blazevic
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, 88397, Germany
| | - Philipp Rechtsteiner
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, 88397, Germany
| | - Clemens Braun
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, 88397, Germany
| | - Katja S. Baum-Kroker
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, 88397, Germany
| | - Bernhard Schmid
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, 88397, Germany
| | - Thomas Ciossek
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, 88397, Germany
| | - Dirk Gottschling
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, 88397, Germany
| | - Jörg S. Hartig
- Department of Chemistry, University of Konstanz, Konstanz, 78464, Germany
| | - Sebastian Kreuz
- Research Beyond Borders, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, 88397, Germany
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Upregulation of annexin A1 protein expression in the intratumoral vasculature of human non-small-cell lung carcinoma and rodent tumor models. PLoS One 2020; 15:e0234268. [PMID: 32497150 PMCID: PMC7272081 DOI: 10.1371/journal.pone.0234268] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 05/21/2020] [Indexed: 12/23/2022] Open
Abstract
Annexin A1 (anxA1) is an immunomodulatory protein that has been proposed as a tumor vascular target for antitumor biologic agents, yet to date the vascular expression of anxA1 in specific tumor indications has not been systematically assessed. Attempts to evaluate vascular anxA1 expression by immunohistochemistry are complicated by a lack of available antibodies that are both specific for anxA1 and bind the N-terminal–truncated form of anxA1 that has previously been identified in tumor vasculature. To study the vascular expression pattern of anxA1 in non–small-cell lung carcinoma (NSCLC), we isolated an antibody capable of binding N-terminal–truncated anxA127-346 and employed it in immunohistochemical studies of human lung specimens. Lung tumor specimens evaluated with this antibody revealed vascular (endothelial) anxA1 expression in five of eight tumor samples studied, but no vascular anxA1 expression was observed in normal lung tissue. Tumor microarray analysis further demonstrated positive vascular staining for anxA1 in 30 of 80 NSCLC samples, and positive staining of neoplastic cells was observed in 54 of 80 samples. No correlation was observed between vascular and parenchymal anxA1 expression. Two rodent tumor models, B16-F10 and Py230, were determined to have upregulated anxA1 expression in the intratumoral vasculature. These data validate anxA1 as a potential vascular anti-tumor target in a subset of human lung tumors and identify rodent models which demonstrate anxA1 expression in tumor vasculature.
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Zarei B, Javidan Z, Fatemi E, Rahimi Jamnani F, Khatami S, Khalaj V. Targeting c-Met on gastric cancer cells through a fully human fab antibody isolated from a large naive phage antibody library. Daru 2020; 28:221-235. [PMID: 32193747 PMCID: PMC7238820 DOI: 10.1007/s40199-020-00334-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/14/2020] [Indexed: 12/17/2022] Open
Abstract
PURPOSE The aberrant Hepatocyte growth factor (HGF)/ mesenchymal-epithelial transition factor (c-Met) signaling pathway in various malignancies and its correlation with tumor invasion and poor prognosis has validated c-Met as a compelling therapeutic target. Up to now, several monoclonal antibodies and small molecule inhibitors targeting c-Met have been introduced with different outcomes, none are yet clinically approved. Toward the generation of novel fully human anti-c-Met molecules, we generated a large naïve Fab antibody library using phage display technology, which subsequently screened for novel Fabs against c-Met. METHODS A phage library, with a functional size of 5.5 × 1010 individual antibody clones, was prepared using standard protocols and screened for c-Met-specific Fabs by successive rounds of panning. A panel of Fabs targeting c-Met were isolated, from which four clones were selected and further characterized by DNA sequencing. The c-Met binding ability of our selected Fabs was evaluated by c-Met ELISA assay and flow cytometry techniques. RESULTS Among the confirmed anti-c-Met Fabs, clone C16, showed the highest affinity (Kaff: 0.3 × 109 M-1), and 63% binding to MKN45 cells (a human gastric adenocarcinoma cell-line) as compared to c-Met negative T47D cell-line (9.03%). CONCLUSION Together, our study presents a single-pot antibody library, as a valuable source for finding a range of antigen-specific Fab antibodies, and also, a fully human, high affinity and specific anti c-Met Fab antibody, C16, which has the potential of developing as a therapeutic or chemotherapeutic delivery agent for killing c-Met-positive tumor cells.
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Affiliation(s)
- Bahareh Zarei
- Medical Biotechnology Department, Biotechnology
Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Zahra Javidan
- Medical Biotechnology Department, Biotechnology
Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Elnaz Fatemi
- Medical Biotechnology Department, Biotechnology
Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Rahimi Jamnani
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
- Department of Mycobacteriology and Pulmonary Research,
Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Shohreh Khatami
- Biochemistry Department, Pasteur Institute of Iran, Tehran, Iran
| | - Vahid Khalaj
- Medical Biotechnology Department, Biotechnology
Research Center, Pasteur Institute of Iran, Tehran, Iran
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Development of novel detection system for sweet potato leaf curl virus using recombinant scFv. Sci Rep 2020; 10:8039. [PMID: 32415170 PMCID: PMC7228925 DOI: 10.1038/s41598-020-64996-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/11/2020] [Indexed: 12/03/2022] Open
Abstract
Sweet potato leaf curl virus (SPLCV) causes yield losses in sweet potato cultivation. Diagnostic techniques such as serological detection have been developed because these plant viruses are difficult to treat. Serological assays have been used extensively with recombinant antibodies such as whole immunoglobulin or single-chain variable fragments (scFv). An scFv consists of variable heavy (VH) and variable light (VL) chains joined with a short, flexible peptide linker. An scFv can serve as a diagnostic application using various combinations of variable chains. Two SPLCV-specific scFv clones, F7 and G7, were screened by bio-panning process with a yeast cell which expressed coat protein (CP) of SPLCV. The scFv genes were subcloned and expressed in Escherichia coli. The binding affinity and characteristics of the expressed proteins were confirmed by enzyme-linked immunosorbent assay using SPLCV-infected plant leaves. Virus-specific scFv selection by a combination of yeast-surface display and scFv-phage display can be applied to detection of any virus.
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