1
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Huhtinen O, Prince S, Lamminmäki U, Salbo R, Kulmala A. Increased stable integration efficiency in CHO cells through enhanced nuclear localization of Bxb1 serine integrase. BMC Biotechnol 2024; 24:44. [PMID: 38926833 PMCID: PMC11210126 DOI: 10.1186/s12896-024-00871-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Mammalian display is an appealing technology for therapeutic antibody development. Despite the advantages of mammalian display, such as full-length IgG display with mammalian glycosylation and its inherent ability to select antibodies with good biophysical properties, the restricted library size and large culture volumes remain challenges. Bxb1 serine integrase is commonly used for the stable genomic integration of antibody genes into mammalian cells, but presently lacks the efficiency required for the display of large mammalian display libraries. To increase the Bxb1 integrase-mediated stable integration efficiency, our study investigates factors that potentially affect the nuclear localization of Bxb1 integrase. METHODS In an attempt to enhance Bxb1 serine integrase-mediated integration efficiency, we fused various nuclear localization signals (NLS) to the N- and C-termini of the integrase. Concurrently, we co-expressed multiple proteins associated with nuclear transport to assess their impact on the stable integration efficiency of green fluorescent protein (GFP)-encoding DNA and an antibody display cassette into the genome of Chinese hamster ovary (CHO) cells containing a landing pad for Bxb1 integrase-mediated integration. RESULTS The nucleoplasmin NLS from Xenopus laevis, when fused to the C-terminus of Bxb1 integrase, demonstrated the highest enhancement in stable integration efficiency among the tested NLS fusions, exhibiting over a 6-fold improvement compared to Bxb1 integrase lacking an NLS fusion. Subsequent additions of extra NLS fusions to the Bxb1 integrase revealed an additional 131% enhancement in stable integration efficiency with the inclusion of two copies of C-terminal nucleoplasmin NLS fusions. Further improvement was achieved by co-expressing the Ran GTPase-activating protein (RanGAP). Finally, to validate the applicability of these findings to more complex proteins, the DNA encoding the membrane-bound clinical antibody abrilumab was stably integrated into the genome of CHO cells using Bxb1 integrase with two copies of C-terminal nucleoplasmin NLS fusions and co-expression of RanGAP. This approach demonstrated over 14-fold increase in integration efficiency compared to Bxb1 integrase lacking an NLS fusion. CONCLUSIONS This study demonstrates that optimizing the NLS sequence fusion for Bxb1 integrase significantly enhances the stable genomic integration efficiency. These findings provide a practical approach for constructing larger libraries in mammalian cells through the stable integration of genes into a genomic landing pad.
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Affiliation(s)
- Olli Huhtinen
- Protein & Antibody Engineering, Orion Corporation, Turku, Finland.
- Department of Life Technologies, University of Turku, Turku, Finland.
| | - Stuart Prince
- MediCity Research Laboratory, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Urpo Lamminmäki
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Rune Salbo
- Protein & Antibody Engineering, Orion Corporation, Turku, Finland
| | - Antti Kulmala
- Protein & Antibody Engineering, Orion Corporation, Turku, Finland.
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2
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Mravic M, He L, Kratochvil HT, Hu H, Nick SE, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado WF. De novo-designed transmembrane proteins bind and regulate a cytokine receptor. Nat Chem Biol 2024; 20:751-760. [PMID: 38480980 PMCID: PMC11142920 DOI: 10.1038/s41589-024-01562-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 01/25/2024] [Indexed: 05/30/2024]
Abstract
Transmembrane (TM) domains as simple as a single span can perform complex biological functions using entirely lipid-embedded chemical features. Computational design has the potential to generate custom tool molecules directly targeting membrane proteins at their functional TM regions. Thus far, designed TM domain-targeting agents have been limited to mimicking the binding modes and motifs of natural TM interaction partners. Here, we demonstrate the design of de novo TM proteins targeting the erythropoietin receptor (EpoR) TM domain in a custom binding topology competitive with receptor homodimerization. The TM proteins expressed in mammalian cells complex with EpoR and inhibit erythropoietin-induced cell proliferation. In vitro, the synthetic TM domain complex outcompetes EpoR homodimerization. Structural characterization reveals that the complex involves the intended amino acids and agrees with our designed molecular model of antiparallel TM helices at 1:1 stoichiometry. Thus, membrane protein TM regions can now be targeted in custom-designed topologies.
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Affiliation(s)
- Marco Mravic
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Li He
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Huong T Kratochvil
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
- Department of Chemistry, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Hailin Hu
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Sarah E Nick
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Weiya Bai
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Anne Edwards
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Hyunil Jo
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Yibing Wu
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT, USA.
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA.
- Yale Cancer Center, New Haven, CT, USA.
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA, USA.
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3
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Wang Y, Zhang K, Zhao Y, Li Y, Su W, Li S. Construction and Applications of Mammalian Cell-Based DNA-Encoded Peptide/Protein Libraries. ACS Synth Biol 2023; 12:1874-1888. [PMID: 37315219 DOI: 10.1021/acssynbio.3c00043] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
DNA-encoded peptide/protein libraries are the starting point for protein evolutionary modification and functional peptide/antibody selection. Different display technologies, protein directed evolution, and deep mutational scanning (DMS) experiments employ DNA-encoded libraries to provide sequence variations for downstream affinity- or function-based selections. Mammalian cells promise the inherent post-translational modification and near-to-natural conformation of exogenously expressed mammalian proteins and thus are the best platform for studying transmembrane proteins or human disease-related proteins. However, due to the current technical bottlenecks of constructing mammalian cell-based large size DNA-encoded libraries, the advantages of mammalian cells as screening platforms have not been fully exploited. In this review, we summarize the current efforts in constructing DNA-encoded libraries in mammalian cells and the existing applications of these libraries in different fields.
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Affiliation(s)
- Yi Wang
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Kaili Zhang
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Yanjie Zhao
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Yifan Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Weijun Su
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Shuai Li
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer; Key Laboratory of Cancer Prevention and Therapy, Tianjin; Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
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4
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Huhtinen O, Salbo R, Lamminmäki U, Prince S. Selection of biophysically favorable antibody variants using a modified Flp-In CHO mammalian display platform. Front Bioeng Biotechnol 2023; 11:1170081. [PMID: 37229492 PMCID: PMC10203562 DOI: 10.3389/fbioe.2023.1170081] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 04/17/2023] [Indexed: 05/27/2023] Open
Abstract
Mammalian display enables the selection of biophysically favorable antibodies from a large IgG antibody library displayed on the plasma membrane of mammalian cells. We constructed and validated a novel mammalian display platform utilizing the commercially available Flp-In CHO cell line as a starting point. We introduced a single copy of a landing pad for Bxb1 integrase-driven recombinase-mediated cassette exchange into the FRT site of the Flp-In CHO line to facilitate the efficient single-copy integration of an antibody display cassette into the genome of the cell line. We then proceeded to demonstrate the ability of our platform to select biophysically favorable antibodies from a library of 1 × 106 displayed antibodies designed to improve the biophysical properties of bococizumab via randomization of problematic hydrophobic surface residues of the antibody. Enrichment of bococizumab variants via fluorescence-activated cell sorting selections was followed by next generation sequencing and thorough characterization of biophysical properties of 10 bococizumab variants that subsequently allowed attribution of the mutations to the biophysical properties of the antibody variants. The mammalian displayed variants exhibited reduced aggregation propensity and polyreactivity, while critically retaining its target binding thereby demonstrating the utility of this valuable tool.
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Affiliation(s)
- Olli Huhtinen
- Protein and Antibody Engineering, Orion Corporation, Turku, Finland
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Rune Salbo
- Protein and Antibody Engineering, Orion Corporation, Turku, Finland
| | - Urpo Lamminmäki
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Stuart Prince
- MediCity Research Laboratory, University of Turku, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
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5
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Mravic M, He L, Kratochvil H, Hu H, Nick SE, Bai W, Edwards A, Jo H, Wu Y, DiMaio D, DeGrado WF. Designed Transmembrane Proteins Inhibit the Erythropoietin Receptor in a Custom Binding Topology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.526773. [PMID: 36824741 PMCID: PMC9949092 DOI: 10.1101/2023.02.13.526773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Transmembrane (TM) domains as simple as a single span can perform complex biological functions using entirely lipid-embedded chemical features. Computational design has potential to generate custom tool molecules directly targeting membrane proteins at their functional TM regions. Thus far, designed TM domain-targeting agents have been limited to mimicking binding modes and motifs of natural TM interaction partners. Here, we demonstrate the design of de novo TM proteins targeting the erythropoietin receptor (EpoR) TM domain in a custom binding topology competitive with receptor homodimerization. The TM proteins expressed in mammalian cells complex with EpoR and inhibit erythropoietin-induced cell proliferation. In vitro, the synthetic TM domain complex outcompetes EpoR homodimerization. Structural characterization reveals that the complex involves the intended amino acids and agrees with our designed molecular model of antiparallel TM helices at 1:1 stoichiometry. Thus, membrane protein TM regions can now be targeted in custom designed topologies.
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6
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Sargunas PR, Spangler JB. Joined at the hip: The role of light chain complementarity determining region 2 in antibody self-association. Proc Natl Acad Sci U S A 2022; 119:e2208330119. [PMID: 35776537 PMCID: PMC9282379 DOI: 10.1073/pnas.2208330119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Paul R. Sargunas
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
| | - Jamie B. Spangler
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218
- Translational Tissue Engineering Center, Johns Hopkins University, Baltimore, MD 21231
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21231
- Bloomberg–Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, MD 21231
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD 21231
- Department of Ophthalmology, Johns Hopkins University, Baltimore, MD 21231
- Department of Molecular Microbiology & Immunology, Johns Hopkins University, Baltimore, MD 21231
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7
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Schardt JS, Jhajj HS, O’Meara RL, Lwo TS, Smith MD, Tessier PM. Agonist antibody discovery: Experimental, computational, and rational engineering approaches. Drug Discov Today 2022; 27:31-48. [PMID: 34571277 PMCID: PMC8714685 DOI: 10.1016/j.drudis.2021.09.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 07/19/2021] [Accepted: 09/20/2021] [Indexed: 01/03/2023]
Abstract
Agonist antibodies that activate cellular signaling have emerged as promising therapeutics for treating myriad pathologies. Unfortunately, the discovery of rare antibodies with the desired agonist functions is a major bottleneck during drug development. Nevertheless, there has been important recent progress in discovering and optimizing agonist antibodies against a variety of therapeutic targets that are activated by diverse signaling mechanisms. Herein, we review emerging high-throughput experimental and computational methods for agonist antibody discovery as well as rational molecular engineering methods for optimizing their agonist activity.
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Affiliation(s)
- John S. Schardt
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Harkamal S. Jhajj
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ryen L. O’Meara
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Timon S. Lwo
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew D. Smith
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter M. Tessier
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA,Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109, USA
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8
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Dyson MR, Masters E, Pazeraitis D, Perera RL, Syrjanen JL, Surade S, Thorsteinson N, Parthiban K, Jones PC, Sattar M, Wozniak-Knopp G, Rueker F, Leah R, McCafferty J. Beyond affinity: selection of antibody variants with optimal biophysical properties and reduced immunogenicity from mammalian display libraries. MAbs 2021; 12:1829335. [PMID: 33103593 PMCID: PMC7592150 DOI: 10.1080/19420862.2020.1829335] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The early phase of protein drug development has traditionally focused on target binding properties leading to a desired mode of therapeutic action. As more protein therapeutics pass through the development pipeline; however, it is clear that non-optimal biophysical properties can emerge, particularly as proteins are formulated at high concentrations, causing aggregation or polyreactivity. Such late-stage "developability" problems can lead to delay or failure in traversing the development process. Aggregation propensity is also correlated with increased immunogenicity, resulting in expensive, late-stage clinical failures. Using nucleases-directed integration, we have constructed large mammalian display libraries where each cell contains a single antibody gene/cell inserted at a single locus, thereby achieving transcriptional normalization. We show a strong correlation between poor biophysical properties and display level achieved in mammalian cells, which is not replicated by yeast display. Using two well-documented examples of antibodies with poor biophysical characteristics (MEDI-1912 and bococizumab), a library of variants was created based on surface hydrophobic and positive charge patches. Mammalian display was used to select for antibodies that retained target binding and permitted increased display level. The resultant variants exhibited reduced polyreactivity and reduced aggregation propensity. Furthermore, we show in the case of bococizumab that biophysically improved variants are less immunogenic than the parental molecule. Thus, mammalian display helps to address multiple developability issues during the earliest stages of lead discovery, thereby significantly de-risking the future development of protein drugs.
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Affiliation(s)
| | | | | | | | - Johanna L Syrjanen
- WM Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory , NY, USA
| | | | | | | | | | | | - Gordana Wozniak-Knopp
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences , Vienna, Austria
| | - Florian Rueker
- Department of Biotechnology, BOKU-University of Natural Resources and Life Sciences , Vienna, Austria
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9
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Wang Y, Jin R, Shen B, Li N, Zhou H, Wang W, Zhao Y, Huang M, Fang P, Wang S, Mary P, Wang R, Ma P, Li R, Tian Y, Cao Y, Li F, Schweizer L, Zhang H. High-throughput functional screening for next-generation cancer immunotherapy using droplet-based microfluidics. SCIENCE ADVANCES 2021; 7:7/24/eabe3839. [PMID: 34117053 PMCID: PMC8195480 DOI: 10.1126/sciadv.abe3839] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 04/23/2021] [Indexed: 05/08/2023]
Abstract
Currently, high-throughput approaches are lacking in the isolation of antibodies with functional readouts beyond simple binding. This situation has impeded the next generation of cancer immunotherapeutics, such as bispecific T cell engager (BiTE) antibodies or agonist antibodies against costimulatory receptors, from reaching their full potential. Here, we developed a highly efficient droplet-based microfluidic platform combining a lentivirus transduction system that enables functional screening of millions of antibodies to identify potential hits with desired functionalities. To showcase the capacity of this system, functional antibodies for CD40 agonism with low frequency (<0.02%) were identified with two rounds of screening. Furthermore, the versatility of the system was demonstrated by combining an anti-Her2 × anti-CD3 BiTE antibody library with functional screening, which enabled efficient identification of active anti-Her2 × anti-CD3 BiTE antibodies. The platform could revolutionize next-generation cancer immunotherapy drug development and advance medical research.
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Affiliation(s)
- Yuan Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Ruina Jin
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | | | - Na Li
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - He Zhou
- HiFiBiO (Shanghai) Co. Ltd., Shanghai, China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Yingjie Zhao
- Shanghai Institute of Immunology, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Pan Fang
- HiFiBiO (Shanghai) Co. Ltd., Shanghai, China
| | | | | | - Ruikun Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Ruonan Li
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Yujie Tian
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Youjia Cao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China
| | - Fubin Li
- Shanghai Institute of Immunology, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Hongkai Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China.
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
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10
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Lin CW, Lerner RA. Antibody Libraries as Tools to Discover Functional Antibodies and Receptor Pleiotropism. Int J Mol Sci 2021; 22:4123. [PMID: 33923551 PMCID: PMC8073236 DOI: 10.3390/ijms22084123] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 12/16/2022] Open
Abstract
Most antibodies currently in use have been selected based on their binding affinity. However, nowadays, antibodies that can not only bind but can also alter the function of cell surface signaling components are increasingly sought after as therapeutic drugs. Therefore, the identification of such functional antibodies from a large antibody library is the subject of intensive research. New methods applied to combinatorial antibody libraries now allow the isolation of functional antibodies in the cellular environment. These selected agonist antibodies have provided new insights into important issues of signal transduction. Notably, when certain antibodies bind to a given receptor, the cell fate induced by them may be the same or different from that induced by natural agonists. In addition, combined with phenotypic screening, this platform allows us to discover unexpected experimental results and explore various phenomena in cell biology, such as those associated with stem cells and cancer cells.
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Affiliation(s)
| | - Richard A. Lerner
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA;
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11
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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: 62] [Impact Index Per Article: 20.7] [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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12
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Hanna R, Cardarelli L, Patel N, Blazer LL, Adams JJ, Sidhu SS. A phage-displayed single-chain Fab library optimized for rapid production of single-chain IgGs. Protein Sci 2020; 29:2075-2084. [PMID: 32803886 DOI: 10.1002/pro.3931] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/25/2022]
Abstract
Phage-displayed synthetic antibody (Ab) repertoires have become a major source of affinity reagents for basic and clinical research. Specific Abs identified from such libraries are often screened as fragments antigen binding (Fabs) produced in bacteria, and those with desired biochemical characteristics are reformatted for production as full-length immunoglobulin G (IgG) in mammalian cells. The conversion of Fabs to IgGs is a cumbersome and often rate-limiting step in the development of Abs. Moreover, biochemical properties required for lead IgG development are not always shared by the Fabs, and these issues are not uncovered until a significant effort has been spent on Abs that ultimately will not be useful. Thus, there is a need for simple and rapid techniques to convert phage-displayed Fabs to IgGs at an early stage of the Ab screening process. We report the generation of a highly diverse phage-displayed synthetic single-chain Fab (scFab) library, in which the light and heavy chains were tethered with an optimized linker. Following selection, pools of scFabs were converted to single-chain IgGs (scIgGs) en masse, enabling facile screening of hundreds of phage-derived scIgGs. We show that this approach can be used to rapidly screen for and select scIgGs that target cell-surface receptors, and scIgGs behave the same as conventional IgGs.
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Affiliation(s)
- Rachel Hanna
- Department of Molecular Genetics, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Lia Cardarelli
- Department of Molecular Genetics, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Nish Patel
- Department of Molecular Genetics, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Levi L Blazer
- Department of Molecular Genetics, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Jarrett J Adams
- Department of Molecular Genetics, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Sachdev S Sidhu
- Department of Molecular Genetics, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
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13
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Tao P, Kuang Y, Li Y, Li W, Gao Z, Liu L, Qiang M, Zha Z, Fan K, Ma P, Friedman JM, Yang G, Lerner RA. Selection of a Full Agonist Combinatorial Antibody that Rescues Leptin Deficiency In Vivo. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2000818. [PMID: 32832353 PMCID: PMC7435230 DOI: 10.1002/advs.202000818] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/19/2020] [Indexed: 05/15/2023]
Abstract
Growth factor deficiency in adulthood constitutes a distinct clinical syndrome with significant morbidities including abnormal body composition, reduced energy, affective disturbances, dyslipidemia, and increased cardiovascular risk. Protein replacement therapies using recombinant proteins or enzymes represent the only approved treatment. Combinatorial antibodies have shown great promise as a new class of therapeutic molecules because they act as "mechanism-based antibodies" with both agonist and antagonist activities. Using leptin, a key hormone in energy metabolism, as an example, a function-guided approach is developed to select combinatorial antibodies with high potency and full agonist activity that substitute natural growth factors in vivo. The identified antibody shows identical biochemical properties and cellular profiles as leptin, and rescues leptin-deficiency in ob/ob mice. Remarkably, the antibody activates leptin receptors that are otherwise nonfunctional because of mutations (L372A and A409E). Combinatorial antibodies have significant advantages over recombinant proteins for chronical usage in terms of immunological tolerance and biological stability.
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Affiliation(s)
- Pingdong Tao
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
- School of Life Science and Technology
ShanghaiTech UniversityShanghai201210China
- Institute of Biochemistry and Cell BiologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yuanyuan Kuang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
- School of Life Science and Technology
ShanghaiTech UniversityShanghai201210China
- Institute of Biochemistry and Cell BiologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
| | - Yu Li
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
- School of Life Science and Technology
ShanghaiTech UniversityShanghai201210China
- Institute of Biochemistry and Cell BiologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
| | - Wenping Li
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
- School of Life Science and Technology
ShanghaiTech UniversityShanghai201210China
- Institute of Biochemistry and Cell BiologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
| | - Zibei Gao
- School of Life Science and Technology
ShanghaiTech UniversityShanghai201210China
| | - Lili Liu
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Min Qiang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Zhao Zha
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Kun Fan
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
- School of Life Science and Technology
ShanghaiTech UniversityShanghai201210China
- Institute of Biochemistry and Cell BiologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai200031China
- University of Chinese Academy of SciencesBeijing100049China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
| | - Jeffrey M. Friedman
- Laboratory of Molecular GeneticsHoward Hughes Medical InstituteThe Rockefeller UniversityNew YorkNY10065USA
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical StudiesShanghaiTech UniversityShanghai201210China
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14
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A Potent Anti-SpuE Antibody Allosterically Inhibits Type III Secretion System and Attenuates Virulence of Pseudomonas Aeruginosa. J Mol Biol 2019; 431:4882-4896. [DOI: 10.1016/j.jmb.2019.10.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 10/12/2019] [Accepted: 10/20/2019] [Indexed: 01/12/2023]
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15
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Spangler JB, Moraga I, Jude KM, Savvides CS, Garcia KC. A strategy for the selection of monovalent antibodies that span protein dimer interfaces. J Biol Chem 2019; 294:13876-13886. [PMID: 31387945 PMCID: PMC6755802 DOI: 10.1074/jbc.ra119.009213] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/15/2019] [Indexed: 11/06/2022] Open
Abstract
Ligand-induced dimerization is the predominant mechanism through which secreted proteins activate cell surface receptors to transmit essential biological signals. Cytokines are a large class of soluble proteins that dimerize transmembrane receptors into precise signaling topologies, but there is a need for alternative, engineerable ligand scaffolds that specifically recognize and stabilize these protein interactions. Recombinant antibodies can potentially serve as robust and versatile platforms for cytokine complex stabilization, and their specificity allows for tunable modulation of dimerization equilibrium. Here, we devised an evolutionary strategy to isolate monovalent antibody fragments that bridge together two different receptor subunits in a cytokine-receptor complex, precisely as the receptors are disposed in their natural signaling orientations. To do this, we screened a naive antibody library against a stabilized ligand-receptor ternary complex that acted as a "molecular cast" of the natural receptor dimer conformation. Our selections elicited "stapler" single-chain variable fragments (scFvs) of antibodies that specifically engage the interleukin-4 receptor heterodimer. The 3.1 Å resolution crystal structure of one such stapler revealed that, as intended, this scFv recognizes a composite epitope between the two receptors as they are positioned in the complex. Extending our approach, we evolved a stapler scFv that specifically binds to and stabilizes the interface between the interleukin-2 cytokine and one of its receptor subunits, leading to a 15-fold enhancement in interaction affinity. This demonstration that scFvs can be selected to recognize epitopes that span protein interfaces presents new opportunities to engineer structurally defined antibodies for a broad range of research and therapeutic applications.
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Affiliation(s)
- Jamie B Spangler
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305 .,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218
| | - Ignacio Moraga
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
| | - Kevin M Jude
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
| | - Christina S Savvides
- Department of Biology, Stanford University School of Medicine, Stanford, California 94305
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California 94305 .,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305.,Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305
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16
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Ziraldo G, Buratto D, Kuang Y, Xu L, Carrer A, Nardin C, Chiani F, Salvatore AM, Paludetti G, Lerner RA, Yang G, Zonta F, Mammano F. A Human-Derived Monoclonal Antibody Targeting Extracellular Connexin Domain Selectively Modulates Hemichannel Function. Front Physiol 2019; 10:392. [PMID: 31263420 PMCID: PMC6584803 DOI: 10.3389/fphys.2019.00392] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 03/21/2019] [Indexed: 11/30/2022] Open
Abstract
Connexin hemichannels, which are plasma membrane hexameric channels (connexons) composed of connexin protein protomers, have been implicated in a host of physiological processes and pathological conditions. A number of single point pathological mutations impart a “leaky” character to the affected hemichannels, i.e., make them more active or hyperactive, suggesting that normal physiological condition could be recovered using selective hemichannel inhibitors. Recently, a human-derived monoclonal antibody named abEC1.1 has been shown to inhibit both wild type and hyperactive hemichannels composed of human (h) connexin 26 (hCx26) subunits. The aims of this work were (1) to characterize further the ability of abEC1.1 to selectively modulate connexin hemichannel function and (2) to assess its in vitro stability in view of future translational applications. In silico analysis of abEC1.1 interaction with the hCx26 hemichannel identified critically important extracellular domain amino acids that are conserved in connexin 30 (hCx30) and connexin 32 (hCx32). Patch clamp experiments performed in HeLa DH cells confirmed the inhibition efficiency of abEC1.1 was comparable for hCx26, hCx30 and hCx32 hemichannels. Of note, even a single amino acid difference in the putative binding region reduced drastically the inhibitory effects of the antibody on all the other tested hemichannels, namely hCx30.2/31.3, hCx30.3, hCx31, hCx31.1, hCx37, hCx43 and hCx45. Plasma membrane channels composed of pannexin 1 were not affected by abEC1.1. Finally, size exclusion chromatography assays showed the antibody does not aggregate appreciably in vitro. Altogether, these results indicate abEC1.1 is a promising tool for further translational studies.
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Affiliation(s)
- Gaia Ziraldo
- CNR Institute of Cell Biology and Neurobiology, Monterotondo, Italy.,Institute of Otolaryngology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Damiano Buratto
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Yuanyuan Kuang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Liang Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Andrea Carrer
- CNR Institute of Cell Biology and Neurobiology, Monterotondo, Italy.,Department of Physics and Astronomy "G. Galilei", University of Padova, Padua, Italy
| | - Chiara Nardin
- CNR Institute of Cell Biology and Neurobiology, Monterotondo, Italy.,Department of Physics and Astronomy "G. Galilei", University of Padova, Padua, Italy
| | - Francesco Chiani
- CNR Institute of Cell Biology and Neurobiology, Monterotondo, Italy
| | | | - Gaetano Paludetti
- Institute of Otolaryngology, Università Cattolica del Sacro Cuore, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Richard A Lerner
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Francesco Zonta
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Fabio Mammano
- CNR Institute of Cell Biology and Neurobiology, Monterotondo, Italy.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.,Department of Physics and Astronomy "G. Galilei", University of Padova, Padua, Italy
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17
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Phenotypic selection with an intrabody library reveals an anti-apoptotic function of PKM2 requiring Mitofusin-1. PLoS Biol 2019; 17:e2004413. [PMID: 31181072 PMCID: PMC6586363 DOI: 10.1371/journal.pbio.2004413] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 06/20/2019] [Accepted: 05/21/2019] [Indexed: 12/22/2022] Open
Abstract
Bcl-2 family proteins control a decisive apoptotic event: mitochondrial outer membrane permeabilization (MOMP). To discover MOMP-regulating proteins, we expressed a library of intracellular single-chain variable fragments (scFvs) (“intrabodies”) and selected for those rescuing cells from apoptosis induced by BimS (the short isoform of Bim). One anti-apoptotic intrabody, intrabody 5 (IB5), recognized pyruvate kinase M2 (PKM2), which is expressed in cancer cells. PKM2 deletion ablated this clonogenic rescue; thus, IB5 activated a latent cytoprotective function of PKM2. This resulted not from pyruvate kinase activity per se but rather from the formation of an active tetrameric conformation of PKM2. A stably tetrameric PKM2 mutant, K422R, promoted cell survival even in the absence of IB5, and IB5 further increased survival. Mitochondria isolated from IB5-expressing cells were relatively resistant to MOMP in vitro. In cells, IB5 expression up-regulated Mitofusin-1 (Mfn1) and increased mitochondrial length. Importantly, Mfn1 deficiency abrogated IB5’s cytoprotective effect. PKM2’s anti-apoptotic function could help explain its preferential expression in human cancer. Proteins belonging to the Bcl-2 family regulate a common form of cell death known as apoptosis. Typically, these proteins function in apoptosis by controlling the formation of large pores in the mitochondrial outer membrane (MOM). While many proteins that regulate apoptosis have been identified over the years, some may still be unknown. Here, we used an unbiased approach in which we first expressed in cultured tumor cells a library of intracellular single-chain antibodies termed “intrabodies.” We then selected for intrabodies that allowed cells to evade apoptosis. We identified pyruvate kinase isoform M2 (PKM2), a major glycolytic enzyme that has been linked to cancer development, as the specific target of one such anti-apoptotic intrabody. We showed that the PKM2-specific intrabody promoted cell survival not by neutralizing its target but rather by activating an anti-apoptotic function of PKM2. While this cell survival function of PKM2 was not related to changes in the levels of Bcl-2 family proteins or to effects on the enzymatic activity of PKM2, we found that cell survival requires the increased expression of a MOM protein, Mitofusin-1 (Mfn1), known to regulate mitochondrial fusion. We conclude that this cell survival function of PKM2 could contribute to a role in cancer progression for this protein.
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18
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Parthiban K, Perera RL, Sattar M, Huang Y, Mayle S, Masters E, Griffiths D, Surade S, Leah R, Dyson MR, McCafferty J. A comprehensive search of functional sequence space using large mammalian display libraries created by gene editing. MAbs 2019; 11:884-898. [PMID: 31107136 PMCID: PMC6601556 DOI: 10.1080/19420862.2019.1618673] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The construction of large libraries in mammalian cells allows the direct screening of millions of molecular variants for binding properties in a cell type relevant for screening or production. We have created mammalian cell libraries of up to 10 million clones displaying a repertoire of IgG-formatted antibodies on the cell surface. TALE nucleases or CRISPR/Cas9 were used to direct the integration of the antibody genes into a single genomic locus, thereby rapidly achieving stable expression and transcriptional normalization. The utility of the system is illustrated by the affinity maturation of a PD-1-blocking antibody through the systematic mutation and functional survey of 4-mer variants within a 16 amino acid paratope region. Mutating VH CDR3 only, we identified a dominant "solution" involving substitution of a central tyrosine to histidine. This appears to be a local affinity maximum, and this variant was surpassed by a lysine substitution when light chain variants were introduced. We achieve this comprehensive and quantitative interrogation of sequence space by combining high-throughput oligonucleotide synthesis with mammalian display and flow cytometry operating at the multi-million scale.
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19
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Ministro J, Manuel AM, Goncalves J. Therapeutic Antibody Engineering and Selection Strategies. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 171:55-86. [PMID: 31776591 DOI: 10.1007/10_2019_116] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Antibody drugs became an increasingly important element of the therapeutic landscape. Their accomplishment has been driven by many unique properties, in particular by their very high specificity and selectivity, in contrast to the off-target liabilities of small molecules (SMs). Antibodies can bring additional functionality to the table with their ability to interact with the immune system, and this can be further manipulated with advances in antibody engineering.The expansion of strategies related to discovery technologies of monoclonal antibodies (mAbs) (phage display, yeast display, ribosome display, bacterial display, mammalian cell surface display, mRNA display, DNA display, transgenic animal, and human B cell derived) opened perspectives for the screening and the selection of therapeutic antibodies for, theoretically, any target from any kind of organism. Moreover, antibody engineering technologies were developed and explored to obtain chosen characteristics of selected leading candidates such as high affinity, low immunogenicity, improved functionality, improved protein production, improved stability, and others. This chapter contains an overview of discovery technologies, mainly display methods and antibody humanization methods for the selection of therapeutic humanized and human mAbs that appeared along the development of these technologies and thereafter. The increasing applications of these technologies will be highlighted in the antibody engineering area (affinity maturation, guided selection to obtain human antibodies) giving promising perspectives for the development of future therapeutics.
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Affiliation(s)
| | - Ana Margarida Manuel
- iMed - Research Institute for Medicines, Faculty of Pharmacy at University of Lisbon, Lisbon, Portugal
| | - Joao Goncalves
- iMed - Research Institute for Medicines, Faculty of Pharmacy at University of Lisbon, Lisbon, Portugal.
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20
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Ferrao RD, Wallweber HJ, Lupardus PJ. Receptor-mediated dimerization of JAK2 FERM domains is required for JAK2 activation. eLife 2018; 7:38089. [PMID: 30044226 PMCID: PMC6078494 DOI: 10.7554/elife.38089] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/24/2018] [Indexed: 12/11/2022] Open
Abstract
Cytokines and interferons initiate intracellular signaling via receptor dimerization and activation of Janus kinases (JAKs). How JAKs structurally respond to changes in receptor conformation induced by ligand binding is not known. Here, we present two crystal structures of the human JAK2 FERM and SH2 domains bound to Leptin receptor (LEPR) and Erythropoietin receptor (EPOR), which identify a novel dimeric conformation for JAK2. This 2:2 JAK2/receptor dimer, observed in both structures, identifies a previously uncharacterized receptor interaction essential to dimer formation that is mediated by a membrane-proximal peptide motif called the ‘switch’ region. Mutation of the receptor switch region disrupts STAT phosphorylation but does not affect JAK2 binding, indicating that receptor-mediated formation of the JAK2 FERM dimer is required for kinase activation. These data uncover the structural and molecular basis for how a cytokine-bound active receptor dimer brings together two JAK2 molecules to stimulate JAK2 kinase activity.
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Affiliation(s)
- Ryan D Ferrao
- Department of Structural Biology, Genentech, Inc., South San Francisco, United States
| | - Heidi Ja Wallweber
- Department of Structural Biology, Genentech, Inc., South San Francisco, United States
| | - Patrick J Lupardus
- Department of Structural Biology, Genentech, Inc., South San Francisco, United States
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21
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Abstract
The unique class of heavy chain-only antibodies, present in Camelidae, can be shrunk to just the variable region of the heavy chain to yield VHHs, also called nanobodies. About one-tenth the size of their full-size counterparts, nanobodies can serve in applications similar to those for conventional antibodies, but they come with a number of signature advantages that find increasing application in biology. They not only function as crystallization chaperones but also can be expressed inside cells as such, or fused to other proteins to perturb the function of their targets, for example, by enforcing their localization or degradation. Their small size also affords advantages when applied in vivo, for example, in imaging applications. Here we review such applications, with particular emphasis on those areas where conventional antibodies would face a more challenging environment.
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Affiliation(s)
- Jessica R Ingram
- Department of Cancer Immunology and Virology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA
| | - Florian I Schmidt
- Institute of Innate Immunity, University of Bonn, 53127 Bonn, Germany
| | - Hidde L Ploegh
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, Massachusetts 02115, USA;
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22
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Migration-based selections of antibodies that convert bone marrow into trafficking microglia-like cells that reduce brain amyloid β. Proc Natl Acad Sci U S A 2018; 115:E372-E381. [PMID: 29295920 PMCID: PMC5777004 DOI: 10.1073/pnas.1719259115] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A migration-based selection system is used to identify antibodies from combinatorial libraries that induce stem cells to both differentiate and selectively traffic to different tissues in adult animals. Significantly, a single agonist antibody induces microglia-like cells, which have the capacity to migrate to the brain and decrease amyloid beta deposition in the brain. One goal of regenerative medicine is to repair damaged tissue. This requires not only generating new cells of the proper phenotype, but also selecting for those that properly integrate into sites of injury. In our laboratory we are using a cell-migration–based in vivo selection system to generate antibodies that induce cells to both differentiate and selectively localize to different tissues. Here we describe an antibody that induces bone marrow stem cells to differentiate into microglia-like cells that traffic to the brain where they organize into typical networks. Interestingly, in the APP/PS1 Alzheimer’s disease mouse model, these induced microglia-like cells are found at sites of plaque formation and significantly reduce their number. These results raise the intriguing question as to whether one can use such antibody-induced differentiation of stem cells to essentially recapitulate embryogenesis in adults to discover cells that can regenerate damaged organ systems.
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23
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Kim HS, Dunshee DR, Yee A, Tong RK, Kim I, Farahi F, Hongo JA, Ernst JA, Sonoda J, Spiess C. Tethered-variable CL bispecific IgG: an antibody platform for rapid bispecific antibody screening. Protein Eng Des Sel 2017; 30:627-637. [PMID: 28985411 PMCID: PMC5914367 DOI: 10.1093/protein/gzx034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/26/2017] [Indexed: 12/31/2022] Open
Abstract
Bispecific antibodies offer a clinically validated platform for drug discovery. In generating functionally active bispecific antibodies, it is necessary to identify a unique parental antibody pair to merge into a single molecule. However, technologies that allow high-throughput production of bispecific immunoglobulin Gs (BsIgGs) for screening purposes are limited. Here, we describe a novel bispecific antibody format termed tethered-variable CLBsIgG (tcBsIgG) that allows robust production of intact BsIgG in a single cell line, concurrently ensuring cognate light chain pairing and preserving key antibody structural and functional properties. This technology is broadly applicable in the generation of BsIgG from a variety of antibody isotypes, including human BsIgG1, BsIgG2 and BsIgG4. The practicality of the tcBsIgG platform is demonstrated by screening BsIgGs generated from FGF21-mimetic anti-Klotho-β agonistic antibodies in a combinatorial manner. This screen identified multiple biepitopic combinations with enhanced agonistic activity relative to the parental monoclonal antibodies, thereby demonstrating that biepitopic antibodies can acquire enhanced functionality compared to monospecific parental antibodies. By design, the tcBsIgG format is amenable to high-throughput production of large panels of bispecific antibodies and thus can facilitate the identification of rare BsIgG combinations to enable the discovery of molecules with improved biological function.
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Affiliation(s)
- Hok Seon Kim
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Diana Ronai Dunshee
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Angie Yee
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Raymond K Tong
- Department of Protein Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Ingrid Kim
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Farzam Farahi
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jo-Anne Hongo
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - James A Ernst
- Department of Protein Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Junichiro Sonoda
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Christoph Spiess
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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24
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Xu L, Carrer A, Zonta F, Qu Z, Ma P, Li S, Ceriani F, Buratto D, Crispino G, Zorzi V, Ziraldo G, Bruno F, Nardin C, Peres C, Mazzarda F, Salvatore AM, Raspa M, Scavizzi F, Chu Y, Xie S, Yang X, Liao J, Liu X, Wang W, Wang S, Yang G, Lerner RA, Mammano F. Design and Characterization of a Human Monoclonal Antibody that Modulates Mutant Connexin 26 Hemichannels Implicated in Deafness and Skin Disorders. Front Mol Neurosci 2017; 10:298. [PMID: 29018324 PMCID: PMC5615210 DOI: 10.3389/fnmol.2017.00298] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/05/2017] [Indexed: 12/21/2022] Open
Abstract
Background: Mutations leading to changes in properties, regulation, or expression of connexin-made channels have been implicated in 28 distinct human hereditary diseases. Eight of these result from variants of connexin 26 (Cx26), a protein critically involved in cell-cell signaling in the inner ear and skin. Lack of non-toxic drugs with defined mechanisms of action poses a serious obstacle to therapeutic interventions for diseases caused by mutant connexins. In particular, molecules that specifically modulate connexin hemichannel function without affecting gap junction channels are considered of primary importance for the study of connexin hemichannel role in physiological as well as pathological conditions. Monoclonal antibodies developed in the last three decades have become the most important class of therapeutic biologicals. Recombinant methods permit rapid selection and improvement of monoclonal antibodies from libraries with large diversity. Methods: By screening a combinatorial library of human single-chain fragment variable (scFv) antibodies expressed in phage, we identified a candidate that binds an extracellular epitope of Cx26. We characterized antibody action using a variety of biochemical and biophysical assays in HeLa cells, organotypic cultures of mouse cochlea and human keratinocyte-derived cells. Results: We determined that the antibody is a remarkably efficient, non-toxic, and completely reversible inhibitor of hemichannels formed by connexin 26 and does not affect direct cell-cell communication via gap junction channels. Importantly, we also demonstrate that the antibody efficiently inhibits hyperative mutant Cx26 hemichannels implicated in autosomal dominant non-syndromic hearing impairment accompanied by keratitis and hystrix-like ichthyosis-deafness (KID/HID) syndrome. We solved the crystal structure of the antibody, identified residues that are critical for binding and used molecular dynamics to uncover its mechanism of action. Conclusions: Although further studies will be necessary to validate the effect of the antibody in vivo, the methodology described here can be extended to select antibodies against hemichannels composed by other connexin isoforms and, consequently, to target other pathologies associated with hyperactive hemichannels. Our study highlights the potential of this approach and identifies connexins as therapeutic targets addressable by screening phage display libraries expressing human randomized antibodies.
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Affiliation(s)
- Liang Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China.,Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of SciencesShanghai, China
| | - Andrea Carrer
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy.,Department of Physics and Astronomy "G. Galilei,", University of PadovaPadova, Italy
| | - Francesco Zonta
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China.,CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy
| | - Zhihu Qu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China
| | - Peixiang Ma
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China
| | - Sheng Li
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China
| | - Federico Ceriani
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy.,Department of Physics and Astronomy "G. Galilei,", University of PadovaPadova, Italy
| | - Damiano Buratto
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy.,Department of Physics and Astronomy "G. Galilei,", University of PadovaPadova, Italy
| | - Giulia Crispino
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy.,Department of Physics and Astronomy "G. Galilei,", University of PadovaPadova, Italy.,Venetian Institute of Molecular MedicinePadova, Italy
| | - Veronica Zorzi
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy.,Institute of Otolaryngology, Catholic University School of MedicineRome, Italy
| | - Gaia Ziraldo
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy.,Department of Physics and Astronomy "G. Galilei,", University of PadovaPadova, Italy.,Institute of Otolaryngology, Catholic University School of MedicineRome, Italy
| | - Francesca Bruno
- Department of Physics and Astronomy "G. Galilei,", University of PadovaPadova, Italy.,Venetian Institute of Molecular MedicinePadova, Italy
| | - Chiara Nardin
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy.,Department of Science, Roma Tre UniversityRome, Italy
| | - Chiara Peres
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy
| | - Flavia Mazzarda
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy.,Department of Science, Roma Tre UniversityRome, Italy
| | - Anna M Salvatore
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy
| | - Marcello Raspa
- CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy
| | | | - Youjun Chu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China
| | - Sichun Xie
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China
| | - Xuemei Yang
- School of Life Science and Technology, Shanghai Tech UniversityShanghai, China
| | - Jun Liao
- School of Life Science and Technology, Shanghai Tech UniversityShanghai, China
| | - Xiao Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China.,Institute of Biochemistry and Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of SciencesShanghai, China.,University of Chinese Academy of SciencesBeijing, China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China
| | - Shanshan Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China
| | - Guang Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China
| | - Richard A Lerner
- Department of Cell and Molecular Biology, The Scripps Research InstituteLa Jolla, CA, United States
| | - Fabio Mammano
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech UniversityShanghai, China.,CNR Institute of Cell Biology and NeurobiologyMonterotondo, Italy.,Department of Physics and Astronomy "G. Galilei,", University of PadovaPadova, Italy.,Venetian Institute of Molecular MedicinePadova, Italy
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25
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Replacing reprogramming factors with antibodies selected from combinatorial antibody libraries. Nat Biotechnol 2017; 35:960-968. [PMID: 28892074 DOI: 10.1038/nbt.3963] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 08/16/2017] [Indexed: 01/12/2023]
Abstract
The reprogramming of differentiated cells into induced pluripotent stem cells (iPSCs) is usually achieved by exogenous induction of transcription by factors acting in the nucleus. In contrast, during development, signaling pathways initiated at the membrane induce differentiation. The central idea of this study is to identify antibodies that can catalyze cellular de-differentiation and nuclear reprogramming by acting at the cell surface. We screen a lentiviral library encoding ∼100 million secreted and membrane-bound single-chain antibodies and identify antibodies that can replace either Sox2 and Myc (c-Myc) or Oct4 during reprogramming of mouse embryonic fibroblasts into iPSCs. We show that one Sox2-replacing antibody antagonizes the membrane-associated protein Basp1, thereby de-repressing nuclear factors WT1, Esrrb and Lin28a (Lin28) independent of Sox2. By manipulating this pathway, we identify three methods to generate iPSCs. Our results establish unbiased selection from autocrine combinatorial antibody libraries as a robust method to discover new biologics and uncover membrane-to-nucleus signaling pathways that regulate pluripotency and cell fate.
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26
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27
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Kennedy PJ, Oliveira C, Granja PL, Sarmento B. Monoclonal antibodies: technologies for early discovery and engineering. Crit Rev Biotechnol 2017; 38:394-408. [PMID: 28789584 DOI: 10.1080/07388551.2017.1357002] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Antibodies are essential in modern life sciences biotechnology. Their architecture and diversity allow for high specificity and affinity to a wide array of biochemicals. Combining monoclonal antibody (mAb) technology with recombinant DNA and protein expression links antibody genotype with phenotype. Yet, the ability to select and screen for high affinity binders from recombinantly-displayed, combinatorial libraries unleashes the true power of mAbs and a flood of clinical applications. The identification of novel antibodies can be accomplished by a myriad of in vitro display technologies from the proven (e.g. phage) to the emerging (e.g. mammalian cell and cell-free) based on affinity binding as well as function. Lead candidates can be further engineered for increased affinity and half-life, reduced immunogenicity and/or enhanced manufacturing, and storage capabilities. This review begins with antibody biology and how the structure and genetic machinery relate to function, diversity, and in vivo affinity maturation and follows with the general requirements of (therapeutic) antibody discovery and engineering with an emphasis on in vitro display technologies. Throughout, we highlight where antibody biology inspires technology development and where high-throughput, "big data" and in silico strategies are playing an increasing role. Antibodies dominate the growing class of targeted therapeutics, alone or as bioconjugates. However, their versatility extends to research, diagnostics, and beyond.
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Affiliation(s)
- Patrick J Kennedy
- a i3S - Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal.,b INEB - Instituto de Engenharia Biomédica , Universidade do Porto , Porto , Portugal.,c IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto , Porto , Portugal.,d ICBAS - Instituto de Ciências Biomédicas Abel Salazar , Universidade do Porto , Porto , Portugal
| | - Carla Oliveira
- a i3S - Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal.,c IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto , Porto , Portugal
| | - Pedro L Granja
- a i3S - Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal.,b INEB - Instituto de Engenharia Biomédica , Universidade do Porto , Porto , Portugal.,d ICBAS - Instituto de Ciências Biomédicas Abel Salazar , Universidade do Porto , Porto , Portugal.,e Departmento de Engenharia Metalúrgica e de Materiais , FEUP - Faculdade de Engenharia da Universidade do Porto , Porto , Portugal
| | - Bruno Sarmento
- a i3S - Instituto de Investigação e Inovação em Saúde , Universidade do Porto , Porto , Portugal.,b INEB - Instituto de Engenharia Biomédica , Universidade do Porto , Porto , Portugal.,f CESPU , Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde & Instituto Universitário de Ciências da Saúde , Gandra , Portugal
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28
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Liu T, Jia P, Ma H, Reed SA, Luo X, Larman HB, Schultz PG. Construction and Screening of a Lentiviral Secretome Library. Cell Chem Biol 2017; 24:767-771.e3. [PMID: 28602759 DOI: 10.1016/j.chembiol.2017.05.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Revised: 04/11/2017] [Accepted: 05/15/2017] [Indexed: 12/22/2022]
Abstract
Over 2,000 human proteins are predicted to be secreted, but the biological function of the many of these proteins is still unknown. Moreover, a number of these proteins may act as new therapeutic agents or be targets for the development of therapeutic antibodies. To further explore the extracellular proteome, we have developed a secretome-enriched open reading frame (ORF) library that can be readily screened for autocrine activity in cell-based phenotypic or reporter assays. Next-generation sequencing (NGS) and database analysis predict that the library contains approximately 900 ORFs encoding known secreted proteins (accounting for 77.8% of the library), as well as genes encoding potentially unknown secreted proteins. In a proof-of-principle study, human TF-1 cells were screened for proliferative factors, and the known cytokine GMCSF was identified as a dominant hit. This library offers a relatively low-cost and straightforward approach for functional autocrine screens of secreted proteins.
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Affiliation(s)
- Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China.
| | - Panpan Jia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Huailei Ma
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing 100191, China
| | - Sean A Reed
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaozhou Luo
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - H Benjamin Larman
- Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Peter G Schultz
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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29
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Minter RR, Sandercock AM, Rust SJ. Phenotypic screening-the fast track to novel antibody discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2017. [PMID: 28647091 DOI: 10.1016/j.ddtec.2017.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The majority of antibody therapeutics have been isolated from target-led drug discovery, where many years of target research preceded drug program initiation. However, as the search for validated targets becomes more challenging and target space becomes increasingly competitive, alternative strategies, such as phenotypic drug discovery, are gaining favour. This review highlights successful examples of antibody phenotypic screens that have led to clinical drug candidates. We also review the requirements for performing an effective antibody phenotypic screen, including antibody enrichment and target identification strategies. Finally, the future impact of phenotypic drug discovery on antibody drug pipelines will be discussed.
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Affiliation(s)
- Ralph R Minter
- Department of Antibody Discovery and Protein Engineering, MedImmune, Milstein Building, Granta Park, Cambridge CB21 6GH, UK
| | - Alan M Sandercock
- Department of Antibody Discovery and Protein Engineering, MedImmune, Milstein Building, Granta Park, Cambridge CB21 6GH, UK
| | - Steven J Rust
- Department of Antibody Discovery and Protein Engineering, MedImmune, Milstein Building, Granta Park, Cambridge CB21 6GH, UK.
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30
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Antibodies from combinatorial libraries use functional receptor pleiotropism to regulate cell fates. Q Rev Biophys 2016; 48:389-94. [PMID: 26537396 DOI: 10.1017/s0033583515000049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To date, most antibodies from combinatorial libraries have been selected purely on the basis of binding. However, new methods now allow selection on the basis of function in animal cells. These selected agonist antibodies have given new insights into the important problem of signal transduction. Remarkably, when some antibodies bind to a given receptor they induce a cell fate that is different than that induced by the natural agonist to the same receptor. The fact that receptors can be functionally pleiotropic may yield new insights into the important problem of signal transduction.
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31
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Zhang H, Du M, Xie J, Liu X, Sun J, Wang W, Xin X, Possani LD, Yea K, Lerner RA. Autocrine‐Based Selection of Drugs That Target Ion Channels from Combinatorial Venom Peptide Libraries. Angew Chem Int Ed Engl 2016; 55:9306-10. [DOI: 10.1002/anie.201603052] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 04/18/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Hongkai Zhang
- Department of Molecular and Cellular BiologyThe Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Mingjuan Du
- The institute for Advanced Immunochemical StudiesShanghai Tech University 99 Haike Road, Pudong Shanghai 201210 P.R.China
| | - Jia Xie
- Department of Molecular and Cellular BiologyThe Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Xiao Liu
- The institute for Advanced Immunochemical StudiesShanghai Tech University 99 Haike Road, Pudong Shanghai 201210 P.R.China
| | - Jingying Sun
- The institute for Advanced Immunochemical StudiesShanghai Tech University 99 Haike Road, Pudong Shanghai 201210 P.R.China
| | - Wei Wang
- The institute for Advanced Immunochemical StudiesShanghai Tech University 99 Haike Road, Pudong Shanghai 201210 P.R.China
| | - Xiu Xin
- The institute for Advanced Immunochemical StudiesShanghai Tech University 99 Haike Road, Pudong Shanghai 201210 P.R.China
| | - Lourival D. Possani
- Departamento de Medicina Molecular y BioprocesosInstituto de BiotecnologíaUniversidad Nacional Autónoma de México Apartado Postal 510-3 Cuernavaca, Morelos 62250 México
| | - Kyungmoo Yea
- Department of Molecular and Cellular BiologyThe Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Richard A. Lerner
- Department of Molecular and Cellular BiologyThe Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
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32
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Zhang H, Du M, Xie J, Liu X, Sun J, Wang W, Xin X, Possani LD, Yea K, Lerner RA. Autocrine‐Based Selection of Drugs That Target Ion Channels from Combinatorial Venom Peptide Libraries. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Hongkai Zhang
- Department of Molecular and Cellular BiologyThe Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Mingjuan Du
- The institute for Advanced Immunochemical StudiesShanghai Tech University 99 Haike Road, Pudong Shanghai 201210 P.R.China
| | - Jia Xie
- Department of Molecular and Cellular BiologyThe Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Xiao Liu
- The institute for Advanced Immunochemical StudiesShanghai Tech University 99 Haike Road, Pudong Shanghai 201210 P.R.China
| | - Jingying Sun
- The institute for Advanced Immunochemical StudiesShanghai Tech University 99 Haike Road, Pudong Shanghai 201210 P.R.China
| | - Wei Wang
- The institute for Advanced Immunochemical StudiesShanghai Tech University 99 Haike Road, Pudong Shanghai 201210 P.R.China
| | - Xiu Xin
- The institute for Advanced Immunochemical StudiesShanghai Tech University 99 Haike Road, Pudong Shanghai 201210 P.R.China
| | - Lourival D. Possani
- Departamento de Medicina Molecular y BioprocesosInstituto de BiotecnologíaUniversidad Nacional Autónoma de México Apartado Postal 510-3 Cuernavaca, Morelos 62250 México
| | - Kyungmoo Yea
- Department of Molecular and Cellular BiologyThe Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Richard A. Lerner
- Department of Molecular and Cellular BiologyThe Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
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33
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Combinatorial antibody libraries: new advances, new immunological insights. Nat Rev Immunol 2016; 16:498-508. [DOI: 10.1038/nri.2016.67] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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34
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Agonist antibody that induces human malignant cells to kill one another. Proc Natl Acad Sci U S A 2015; 112:E6158-65. [PMID: 26487683 DOI: 10.1073/pnas.1519079112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
An attractive, but as yet generally unrealized, approach to cancer therapy concerns discovering agents that change the state of differentiation of the cancer cells. Recently, we discovered a phenomenon that we call "receptor pleiotropism" in which agonist antibodies against known receptors induce cell fates that are very different from those induced by the natural agonist to the same receptor. Here, we show that one can take advantage of this phenomenon to convert acute myeloblastic leukemic cells into natural killer cells. Upon induction with the antibody, these leukemic cells enter into a differentiation cascade in which as many as 80% of the starting leukemic cells can be differentiated. The antibody-induced killer cells make large amounts of perforin, IFN-γ, and granzyme B and attack and kill other members of the leukemic cell population. Importantly, induction of killer cells is confined to transformed cells, in that normal bone marrow cells are not induced to form killer cells. Thus, it seems possible to use agonist antibodies to change the differentiation state of cancer cells into those that attack and kill other members of the malignant clone from which they originate.
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35
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Gonzalez-Munoz AL, Minter RR, Rust SJ. Phenotypic screening: the future of antibody discovery. Drug Discov Today 2015; 21:150-156. [PMID: 26440132 DOI: 10.1016/j.drudis.2015.09.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 09/22/2015] [Accepted: 09/29/2015] [Indexed: 10/22/2022]
Abstract
Most antibody therapeutics have been isolated from high throughput target-based screening. However, as the number of validated targets diminishes and the target space becomes increasingly competitive, alternative strategies, such as phenotypic screening, are gaining momentum. Here, we review successful phenotypic screens, including those used to isolate antibodies against cancer and infectious agents. We also consider exciting advances in the expression and phenotypic screening of antibody repertoires in single cell autocrine systems. As technologies continue to develop, we believe that antibody phenotypic screening will increase further in popularity and has the potential to provide the next generation of therapeutic antibodies.
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Affiliation(s)
- Andrea L Gonzalez-Munoz
- Department of Antibody Discovery and Protein Engineering, MedImmune, Milstein Building, Granta Park, Cambridge CB21 6GH, UK
| | - Ralph R Minter
- Department of Antibody Discovery and Protein Engineering, MedImmune, Milstein Building, Granta Park, Cambridge CB21 6GH, UK
| | - Steven J Rust
- Department of Antibody Discovery and Protein Engineering, MedImmune, Milstein Building, Granta Park, Cambridge CB21 6GH, UK.
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36
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Peng Y, Zeng W, Ye H, Han K, Dharmarajan V, Novick S, Wilson I, Griffin P, Friedman J, Lerner R. A General Method for Insertion of Functional Proteins within Proteins via Combinatorial Selection of Permissive Junctions. ACTA ACUST UNITED AC 2015; 22:1134-43. [DOI: 10.1016/j.chembiol.2015.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 06/12/2015] [Accepted: 07/06/2015] [Indexed: 10/23/2022]
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37
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Identification of optimal protein binders through the use of large genetically encoded display libraries. Curr Opin Chem Biol 2015; 26:16-24. [DOI: 10.1016/j.cbpa.2015.01.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 01/08/2015] [Indexed: 01/05/2023]
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38
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Moraga I, Wernig G, Wilmes S, Gryshkova V, Richter CP, Hong WJ, Sinha R, Guo F, Fabionar H, Wehrman TS, Krutzik P, Demharter S, Plo I, Weissman IL, Minary P, Majeti R, Constantinescu SN, Piehler J, Garcia KC. Tuning cytokine receptor signaling by re-orienting dimer geometry with surrogate ligands. Cell 2015; 160:1196-208. [PMID: 25728669 PMCID: PMC4766813 DOI: 10.1016/j.cell.2015.02.011] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/22/2015] [Accepted: 02/03/2015] [Indexed: 01/07/2023]
Abstract
Most cell-surface receptors for cytokines and growth factors signal as dimers, but it is unclear whether remodeling receptor dimer topology is a viable strategy to "tune" signaling output. We utilized diabodies (DA) as surrogate ligands in a prototypical dimeric receptor-ligand system, the cytokine Erythropoietin (EPO) and its receptor (EpoR), to dimerize EpoR ectodomains in non-native architectures. Diabody-induced signaling amplitudes varied from full to minimal agonism, and structures of these DA/EpoR complexes differed in EpoR dimer orientation and proximity. Diabodies also elicited biased or differential activation of signaling pathways and gene expression profiles compared to EPO. Non-signaling diabodies inhibited proliferation of erythroid precursors from patients with a myeloproliferative neoplasm due to a constitutively active JAK2V617F mutation. Thus, intracellular oncogenic mutations causing ligand-independent receptor activation can be counteracted by extracellular ligands that re-orient receptors into inactive dimer topologies. This approach has broad applications for tuning signaling output for many dimeric receptor systems.
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Affiliation(s)
- Ignacio Moraga
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Gerlinde Wernig
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Pathology, Division of Hematopathology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Stephan Wilmes
- Division of Biophysics, Department of Biology, University of Osnabrück, 49076, Germany
| | - Vitalina Gryshkova
- Ludwig Institute For Cancer Research and de Duve Institute, Université catholique de Louvain, B-1200 Brussels, Belgium
| | | | - Wan-Jen Hong
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Internal Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Rahul Sinha
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Feng Guo
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Hyna Fabionar
- DiscoveRx, 42501 Albrae St, Fremont, California, 94538, USA
| | - Tom S. Wehrman
- Primity Bio, 3350 Scott blvd ste 6101, Santa Clara, CA 95054
| | - Peter Krutzik
- Primity Bio, 3350 Scott blvd ste 6101, Santa Clara, CA 95054
| | - Samuel Demharter
- Department of Computer Science Wolfson Building, University of Oxford, Oxford OX1 3QD, United Kingdom
| | - Isabelle Plo
- Institut Gustave Roussy, INSERM U1009, 94805, Villejuif, France
| | - Irving L. Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Peter Minary
- Department of Computer Science Wolfson Building, University of Oxford, Oxford OX1 3QD, United Kingdom
| | - Ravindra Majeti
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Internal Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA
| | - Stefan N. Constantinescu
- Ludwig Institute For Cancer Research and de Duve Institute, Université catholique de Louvain, B-1200 Brussels, Belgium
| | - Jacob Piehler
- Division of Biophysics, Department of Biology, University of Osnabrück, 49076, Germany
| | - K. Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California, 94305-5345, USA,Correspondence to:
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39
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Yea K, Xie J, Zhang H, Zhang W, Lerner RA. Selection of multiple agonist antibodies from intracellular combinatorial libraries reveals that cellular receptors are functionally pleiotropic. Curr Opin Chem Biol 2015; 26:1-7. [PMID: 25621729 DOI: 10.1016/j.cbpa.2015.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/08/2015] [Indexed: 11/16/2022]
Abstract
The main purpose of this perspective is to build on the unexpected outcomes of previous laboratory experiments using antibody agonists to raise questions concerning how activation of a given receptor can be involved in inducing differentiation of cells along different pathways some of which may even derive from different lineages. While not yet answered, the question illustrates how the advent of agonists not present in nature may give a different dimension to the important problem of signal transduction. Thus, if one studies a natural agonist-receptor system one can learn details about its signal transduction pathway. However, if one has a set of orthogonal agonists, one may learn about the yet undiscovered potential of the system that, in the end, may necessitate refinements to the currently used models. Thus, we wonder why receptors conventionally linked to a given pathway induce a different pattern of differentiation when agonized in another way.
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Affiliation(s)
- Kyungmoo Yea
- Shanghai Institute for Advanced Immunological Studies, ShanghaiTech University, Shanghai 200031, China
| | - Jia Xie
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hongkai Zhang
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Wei Zhang
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Richard A Lerner
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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40
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Zhang Y, Zou H, Wang Y, Caballero D, Gonzalez J, Chao E, Welzel G, Shen W, Wang D, Schultz PG, Wang F. Rational design of a humanized glucagon-like peptide-1 receptor agonist antibody. Angew Chem Int Ed Engl 2014; 54:2126-30. [PMID: 25556336 DOI: 10.1002/anie.201410049] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Indexed: 11/09/2022]
Abstract
Bovine antibody BLV1H12 possesses a unique "stalk-knob" architecture in its ultralong heavy chain CDR3, allowing substitutions of the "knob" domain with protein agonists to generate functional antibody chimeras. We have generated a humanized glucagon-like peptide-1 (GLP-1) receptor agonist antibody by first introducing a coiled-coil "stalk" into CDR3H of the antibody herceptin. Exendin-4 (Ex-4), a GLP-1 receptor agonist, was then fused to the engineered stalk with flexible linkers, and a Factor Xa cleavage site was inserted immediately in front of Ex-4 to allow release of the N-terminus of the fused peptide. The resulting clipped herceptin-Ex-4 fusion protein is more potent in vitro in activating GLP-1 receptors than the Ex-4 peptide. The clipped herceptin-Ex-4 has an extended plasma half-life of approximately four days and sustained control of blood glucose levels for more than a week in mice. This work provides a novel approach to the development of human or humanized agonist antibodies as therapeutics.
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Affiliation(s)
- Yong Zhang
- California Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines Road, La Jolla, CA 92037 (USA)
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Zhang Y, Zou H, Wang Y, Caballero D, Gonzalez J, Chao E, Welzel G, Shen W, Wang D, Schultz PG, Wang F. Rational Design of a Humanized Glucagon-Like Peptide-1 Receptor Agonist Antibody. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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42
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Zhang H, Xie J, Lerner RA. A proximity based general method for identification of ligand and receptor interactions in living cells. Biochem Biophys Res Commun 2014; 454:251-5. [PMID: 25451250 DOI: 10.1016/j.bbrc.2014.10.085] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 10/19/2014] [Indexed: 10/24/2022]
Abstract
Autocrine based selections from intracellular combinatorial antibody and peptide libraries have proven to be a powerful method for selection of agonists and identification of new therapeutic targets. However, success requires a case-by-case construction of a robust selection system which is a process that can be time consuming and expensive. Here we report a general system that takes advantage of the chemical rate acceleration caused by approximation of a membrane tethered ligand and its receptor. The system uses an artificial signal transduction and is, thus, agnostic to the endogenous signal transduction of the receptor-ligand system. This method allows analysis of receptor-ligand interactions and selection of molecules from large libraries that interact with receptors when they are in their natural milieu.
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Affiliation(s)
- Hongkai Zhang
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, United States.
| | - Jia Xie
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, United States
| | - Richard A Lerner
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, United States.
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Abstract
In this issue of Chemistry & Biology, Xie and colleagues describe a "phenotype directed" approach to identify antibodies that protect cells from death caused by rhinovirus infection. The cellular antibody library of 10(8) clones yielded two antibodies that prevented cell death via the same viral target: rhinovirus 3C protease.
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Affiliation(s)
- John McCafferty
- IONTAS Ltd., Hopkins Building, Tennis Court Road, Cambridge CB2 1QW, UK.
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Liu T, Liu Y, Wang Y, Hull M, Schultz PG, Wang F. Rational design of CXCR4 specific antibodies with elongated CDRs. J Am Chem Soc 2014; 136:10557-60. [PMID: 25041362 PMCID: PMC4120998 DOI: 10.1021/ja5042447] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Indexed: 11/29/2022]
Abstract
The bovine antibody (BLV1H12) which has an ultralong heavy chain complementarity determining region 3 (CDRH3) provides a novel scaffold for antibody engineering. By substituting the extended CDRH3 of BLV1H12 with modified CXCR4 binding peptides that adopt a β-hairpin conformation, we generated antibodies specifically targeting the ligand binding pocket of CXCR4 receptor. These engineered antibodies selectively bind to CXCR4 expressing cells with binding affinities in the low nanomolar range. In addition, they inhibit SDF-1-dependent signal transduction and cell migration in a transwell assay. Finally, we also demonstrate that a similar strategy can be applied to other CDRs and show that a CDRH2-peptide fusion binds CXCR4 with a K(d) of 0.9 nM. This work illustrates the versatility of scaffold-based antibody engineering and could greatly expand the antibody functional repertoire in the future.
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Affiliation(s)
- Tao Liu
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Yan Liu
- California
Institute for Biomedical Research (Calibr), La Jolla, California 92037, United States
| | - Ying Wang
- California
Institute for Biomedical Research (Calibr), La Jolla, California 92037, United States
| | - Mitchell Hull
- California
Institute for Biomedical Research (Calibr), La Jolla, California 92037, United States
| | - Peter G. Schultz
- Department
of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, United States
- California
Institute for Biomedical Research (Calibr), La Jolla, California 92037, United States
| | - Feng Wang
- California
Institute for Biomedical Research (Calibr), La Jolla, California 92037, United States
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Marsden CJ, Eckersley S, Hebditch M, Kvist AJ, Milner R, Mitchell D, Warwicker J, Marley AE. The Use of Antibodies in Small-Molecule Drug Discovery. ACTA ACUST UNITED AC 2014; 19:829-38. [PMID: 24695620 DOI: 10.1177/1087057114527770] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 12/08/2013] [Indexed: 12/17/2022]
Abstract
Antibodies are powerful research tools that can be used in many areas of biology to probe, measure, and perturb various biological structures. Successful drug discovery is dependent on the correct identification of a target implicated in disease, coupled with the successful selection, optimization, and development of a candidate drug. Because of their specific binding characteristics, with regard to specificity, affinity, and avidity, coupled with their amenability to protein engineering, antibodies have become a key tool in drug discovery, enabling the quantification, localization, and modulation of proteins of interest. This review summarizes the application of antibodies and other protein affinity reagents as specific research tools within the drug discovery process.
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Zhang H, Yea K, Xie J, Ruiz D, Wilson IA, Lerner RA. Selecting agonists from single cells infected with combinatorial antibody libraries. ACTA ACUST UNITED AC 2013; 20:734-41. [PMID: 23706638 DOI: 10.1016/j.chembiol.2013.04.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 04/12/2013] [Accepted: 04/24/2013] [Indexed: 10/26/2022]
Abstract
We describe a system for direct selection of antibodies that are receptor agonists. Combinatorial antibody libraries in lentiviruses are used to infect eukaryotic cells that contain a fluorescent reporter system coupled to the receptor for which receptor agonist antibodies are sought. In this embodiment of the method, very large numbers of candidate antibodies expressing lentivirus and eukaryotic reporter cells are packaged together in a format where each is capable of replication, thereby forging a direct link between genotype and phenotype. Following infection, cells that fluoresce are sorted and the integrated genes encoding the agonist antibodies recovered. We validated the system by illustrating its ability to generate rapidly potent antibody agonists that are complete thrombopoietin phenocopies. The system should be generalizable to any pathway where its activation can be linked to production of a selectable phenotype.
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Affiliation(s)
- Hongkai Zhang
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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47
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Adams JJ, Sidhu SS. Synthetic antibody technologies. Curr Opin Struct Biol 2013; 24:1-9. [PMID: 24721448 DOI: 10.1016/j.sbi.2013.11.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 11/10/2013] [Indexed: 11/19/2022]
Abstract
Synthetic antibody technologies enable the rapid production of affinity reagents through in vitro selections. The production of synthetic antibodies relies on sophisticated design strategies to produce combinatorial diversity libraries that encode antibody populations optimized for molecular recognition. The technology takes advantage of display technologies that enable amplification, selection and manipulation of antibodies in vitro. The rapid yet highly controlled nature of these methods has opened new avenues in basic and clinical research. Here we review recent advances in structural biology facilitated by synthetic antibodies, as well as advances in library designs and selection methods.
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Affiliation(s)
- Jarrett J Adams
- Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Donnelly CCBR, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Sachdev S Sidhu
- Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Donnelly CCBR, 160 College Street, Toronto, Ontario M5S 3E1, Canada.
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Doerner A, Rhiel L, Zielonka S, Kolmar H. Therapeutic antibody engineering by high efficiency cell screening. FEBS Lett 2013; 588:278-87. [PMID: 24291259 DOI: 10.1016/j.febslet.2013.11.025] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 11/17/2013] [Accepted: 11/18/2013] [Indexed: 12/11/2022]
Abstract
In recent years, several cell-based screening technologies for the isolation of antibodies with prescribed properties emerged. They rely on the multi-copy display of antibodies or antibody fragments on a cell surface in functional form followed by high through put screening and isolation of cell clones that carry an antibody variant with the desired affinity, specificity, and stability. Particularly yeast surface display in combination with high-throughput fluorescence-activated cell sorting has proven successful in the last fifteen years as a very powerful technology that has some advantages over classical generation of monoclonals using the hybridoma technology or bacteriophage-based antibody display and screening. Cell-based screening harbours the benefit of single-cell online and real-time analysis and characterisation of individual library candidates. Moreover, when using eukaryotic expression hosts, intrinsic quality control machineries for proper protein folding and stability exist that allow for co-selection of high-level expression and stability simultaneously to the binding functionality. Recently, promising technologies emerged that directly rely on antibody display on higher eukaryotic cell lines using lentiviral transfection or direct screening on B-cells. The combination of immunisation, B-cell screening and next generation sequencing may open new avenues for the isolation of therapeutic antibodies with prescribed physicochemical and functional characteristics.
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Affiliation(s)
- Achim Doerner
- Protein Engineering and Antibody Technologies, Merck Serono, Merck KGaA, Frankfurter Straße 250, D-64293 Darmstadt, Germany
| | - Laura Rhiel
- Protein Engineering and Antibody Technologies, Merck Serono, Merck KGaA, Frankfurter Straße 250, D-64293 Darmstadt, Germany
| | - Stefan Zielonka
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany.
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49
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Zhang Y, Wang D, Welzel G, Wang Y, Schultz PG, Wang F. An antibody CDR3-erythropoietin fusion protein. ACS Chem Biol 2013; 8:2117-21. [PMID: 23941200 DOI: 10.1021/cb4004749] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
X-ray crystallographic analysis of a bovine antibody (BLV1H12) revealed a unique scaffold in its ultralong heavy chain complementarity determining region 3 (CDR3H) that folds into a solvent exposed, antiparallel β-stranded "stalk" fused with a disulfide cross-linked "knob" domain. This unusual variable region motif provides a novel approach for generating chimeric antibodies with novel activities. Toward this end, human erythropoietin (hEPO) was substituted for the "knob" domain in this antibody to afford an antibody-hEPO (Ab-hEPO) fusion protein that efficiently expresses in mammalian cells. Ab-hEPO proliferated TF-1 cells with a potency comparable to that of hEPO (EC50 ∼ 0.03 nM) and exhibits a significantly extended plasma half-life (>6 days) in mice relative to hEPO (∼4 h). Mice treated with the Ab-hEPO fusion protein show sustained elevated hematocrit for more than two weeks. This work demonstrates the utility of BLV1H12 CDR3 fusions as a novel approach for generating potent polypeptides with enhanced pharmacological properties.
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Affiliation(s)
- Yong Zhang
- Department
of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines
Road, La Jolla, California
92037, United States
| | - Danling Wang
- Californial Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines
Road, La Jolla, California 92037, United States
| | - Gus Welzel
- Californial Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines
Road, La Jolla, California 92037, United States
| | - Ying Wang
- Californial Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines
Road, La Jolla, California 92037, United States
| | - Peter G. Schultz
- Department
of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines
Road, La Jolla, California
92037, United States
- Californial Institute for Biomedical Research (Calibr), 11119 N. Torrey Pines
Road, La Jolla, California 92037, United States
| | - Feng Wang
- Department
of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines
Road, La Jolla, California
92037, United States
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