1
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Tsonev LI, Hirsh AG. Multiple, simultaneous, independent gradients for a versatile multidimensional liquid chromatography. Part II: Application 3 - Scouting optimization strategies for separation of monoclonal antibodies by dual simultaneous independent gradients of pH & salt on a weak cation exchange stationary phase. J Chromatogr A 2024; 1730:465065. [PMID: 38879974 DOI: 10.1016/j.chroma.2024.465065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 05/30/2024] [Accepted: 06/08/2024] [Indexed: 06/18/2024]
Abstract
In previous publications we have described the pISep dual simultaneous, independent gradients (DSIGs) liquid chromatography (LC) for uncoupling gradients of non-buffering solute (NaCl, urea or acetonitrile) from externally generated pH gradients. In DSIGs the shape and slope of the [salute] gradient does not depend on the shape and slope of the pH gradient. The technique allows in a single run true simultaneous two dimensional LC separation of complex protein mixtures on various stationary phases including anion, cation exchangers (AEX, CEX), reversed phase (RP), mixed mode and mixed bed. Using a humanized IgG1 (HIgG1) monoclonal antibody (MAb) and a variety of pH & [NaCl] DSIGs, we show that most of MAb isoforms can be successfully separated from each other. These experimental observations are supported by an initial theoretical argument presented here predicting an overall improvement of all MAb isoforms separation by DSIGs of pH & [NaCl]. Theoretical calculations predict that, in general, there exists an optimal non-zero isocratic salt concentration in a pH gradient separation that will resolve isoforms close in binding energy, but a wide range of salt concentrations will be required for acceptable resolution of all isoforms. Theory also predicts better separation of weaker rather than stronger binding isoforms. Experimentally, we have found that no one set of DSIGs LC conditions could optimally baseline resolve all identifiable MAb isoforms in a single run of reasonable duration. The versatility and simplicity of the pH & [NaCl] pISep DSIGs LC allows fast, automated scouting of protein separations over any range of pH from 2.4 to 10.8 and [NaCl] from 0 to 1 M without changing the chemistry of the buffering system. Due to the universal applicability of the pISep buffering system in IEX LC, the researcher is given a powerful tool to easily develop pH & [NaCl] DSIGs protocols that vary mobile phase compositions to achieve high resolution separations of targeted proteins.
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Affiliation(s)
- Latchezar I Tsonev
- CryoBioPhysica, Inc., 4620 N. Park Ave., #1502 w Chevy Chase, MD 20815, USA
| | - Allen G Hirsh
- CryoBioPhysica, Inc., 4620 N. Park Ave., #1502 w Chevy Chase, MD 20815, USA.
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2
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Kushnarova-Vakal A, Aalto R, Huovinen T, Wittfooth S, Lamminmäki U. Controlled labelling of tracer antibodies for time-resolved fluorescence-based immunoassays. Sci Rep 2024; 14:18113. [PMID: 39103434 PMCID: PMC11300886 DOI: 10.1038/s41598-024-69294-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 08/02/2024] [Indexed: 08/07/2024] Open
Abstract
Tracer antibodies, which are labelled with fluorescent or other type of reporter molecules, are widely employed in diagnostic immunoassays. Time-resolved fluorescence immunoassay (TRFIA), recognized as one of the most sensitive immunoassay techniques, utilizes tracers labelled with lanthanide ion (Ln) chelates. The conventional approach for conjugating isothiocyanate (ITC) Ln-chelates to antibodies involves random chemical targeting of the primary amino group of Lys residues, requiring typically overnight exposure to an elevated pH of 9-9.3 and leading to heterogeneity. Moreover, efforts to enhance the sensitivity of the assays by introducing a higher number of Ln-chelates per tracer antibody are associated with an elevated risk of targeting critical amino acid residues in the binding site, compromising the binding properties of the antibody. Herein, we report a method to precisely label recombinant antibodies with a defined number of Ln-chelates in a well-controlled manner by employing the SpyTag/SpyCatcher protein ligation technology. We demonstrate the functionality of the method with a full-length recombinant antibody (IgG) as well as an antibody fragment by producing site-specifically labelled antibodies for TRFIA for cardiac troponin I (cTnI) detection with a significant improvement in assay sensitivity compared to that with conventionally labelled tracer antibodies. Overall, our data clearly illustrates the benefits of the site-specific labelling strategy for generating high-performing tracer antibodies for TRF immunoassays.
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Affiliation(s)
- Anastasiia Kushnarova-Vakal
- Department of Life Technologies, University of Turku, 20520, Turku, Finland.
- InFLAMES Research Flagship, University of Turku, 20014, Turku, Finland.
| | - Rami Aalto
- Department of Life Technologies, University of Turku, 20520, Turku, Finland
- Tyks Laboratories, Clinical Chemistry, Turku University Hospital, 20521, Turku, Finland
| | - Tuomas Huovinen
- Department of Life Technologies, University of Turku, 20520, Turku, Finland
| | - Saara Wittfooth
- Department of Life Technologies, University of Turku, 20520, Turku, Finland
| | - Urpo Lamminmäki
- Department of Life Technologies, University of Turku, 20520, Turku, Finland.
- InFLAMES Research Flagship, University of Turku, 20014, Turku, Finland.
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3
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Shin J, Raissi S, Phelan P, Bullock PA. Rational design of a Nivolumab-based ANTI-PD-1 single chain variable fragment that blocks the interaction between PD-1 expressed on T-CELLS and PD-L1 ON CHO cells. Protein Expr Purif 2023; 202:106196. [PMID: 36280166 DOI: 10.1016/j.pep.2022.106196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/13/2022] [Accepted: 10/16/2022] [Indexed: 11/05/2022]
Abstract
Antibodies that block the interaction between PD-1 expressing T-cells and cancer cells expressing PD-L1 play a central role in contemporary immunotherapy regimes [1-3]. We previously reported the isolation of a single chain variable fragment (scFv) of the monoclonal anti-PD-1 antibody Nivolumab, that binds to purified PD-1 and blocked its interaction with PD-L1 [4]. This anti-PD-1 scFv did not, however, function in a cell-based assay designed to detect the disruption of the PD-1/PD-L1 interaction, a result likely due to its poor solubility in tissue culture media. Herein we report that following a series of structure-based rational design analyses, including Aggreescan3D, we have isolated a variant of the anti-PD-1 scFv having significantly improved solubility in tissue culture medium. Moreover, this soluble anti-PD-1 scFv variant disrupted the interaction between PD-1 expressed on Jurkat Cells and PD-L1 expressed on CHO cells. These findings are discussed in terms of the related observation that the residues mutated to form the anti-PD-1 variant are conserved in many other scFvs; thus, the properties of a range of scFvs will likely be enhanced by similar mutations of the conserved residues.
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Affiliation(s)
- Jong Shin
- Department of Pathology, New York University Grossman School of Medicine, 550 First Avenue, New York, NY, 10016, USA
| | - Siavash Raissi
- Department of Developmental, Molecular and Chemical Biology Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA, 02111, USA
| | - Paul Phelan
- Joinn Biologics, 2600 Hilltop Drive, Building L, Richmond, CA, 94806, USA
| | - Peter A Bullock
- Department of Developmental, Molecular and Chemical Biology Tufts University School of Medicine, 136 Harrison Avenue, Boston, MA, 02111, USA.
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4
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Safarzadeh Kozani P, Naseri A, Mirarefin SMJ, Salem F, Nikbakht M, Evazi Bakhshi S, Safarzadeh Kozani P. Nanobody-based CAR-T cells for cancer immunotherapy. Biomark Res 2022; 10:24. [DOI: https:/doi.org/10.1186/s40364-022-00371-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/29/2022] [Indexed: 09/15/2023] Open
Abstract
AbstractChimeric antigen receptor T-cell (CAR-T) therapy is the result of combining genetic engineering-based cancer immunotherapy with adoptive cell therapy (ACT). CAR-T therapy has been successful in treating various types of hematological cancers. CARs are receptors made of an extracellular domain, a membrane-spanning domain, and an intracellular domain. The extracellular domain of CARs harbors an antigen-targeting domain responsible for recognizing and binding cell surface-expressed target antigens. Conventionally, the single-chain fragment variable (scFv) of a monoclonal antibody (mAb) is used as the antigen-targeting domain of CARs. However, of late, researchers have exploited nanobodies for this aim based on numerous rationales including the small size of nanobodies, their stability, specificity, and high affinity, and their easy and feasible development process. Many findings have confirmed that nanobody-based CAR-Ts can be as functional as scFv-based CAR-Ts in preclinical and clinical settings. In this review, we discuss the advantages and disadvantages of scFvs and nanobodies in regards to their application as the targeting domain of CARs. Ultimately, we discuss various CAR target antigens which have been targeted using nanobody-based CAR-T cells for the treatment of different types of malignancies.
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5
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Hambach J, Mann AM, Bannas P, Koch-Nolte F. Targeting multiple myeloma with nanobody-based heavy chain antibodies, bispecific killer cell engagers, chimeric antigen receptors, and nanobody-displaying AAV vectors. Front Immunol 2022; 13:1005800. [PMID: 36405759 PMCID: PMC9668101 DOI: 10.3389/fimmu.2022.1005800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/21/2022] [Indexed: 11/29/2022] Open
Abstract
Nanobodies are well suited for constructing biologics due to their high solubility. We generated nanobodies directed against CD38, a tumor marker that is overexpressed by multiple myeloma and other hematological malignancies. We then used these CD38-specific nanobodies to construct heavy chain antibodies, bispecific killer cell engagers (BiKEs), chimeric antigen receptor (CAR)-NK cells, and nanobody-displaying AAV vectors. Here we review the utility of these nanobody-based constructs to specifically and effectively target CD38-expressing myeloma cells. The promising results of our preclinical studies warrant further clinical studies to evaluate the potential of these CD38-specific nanobody-based constructs for treatment of multiple myeloma.
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Affiliation(s)
- Julia Hambach
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany,Department of Diagnostic and Interventional Radiology and Nuclear Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anna Marei Mann
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Bannas
- Department of Diagnostic and Interventional Radiology and Nuclear Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany,*Correspondence: Friedrich Koch-Nolte,
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6
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Antoine D, Mohammadi M, McDermott CE, Walsh E, Johnson PA, Wawrousek KE, Wall JG. Isolation of SARS-CoV-2-blocking recombinant antibody fragments and characterisation of their binding to variant spike proteins. FRONTIERS IN NANOTECHNOLOGY 2022. [DOI: 10.3389/fnano.2022.1028186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
COVID-19 is a severe acute respiratory disease caused by SARS-CoV-2. From its initial appearance in Wuhan, China in 2019, it developed rapidly into a global pandemic. In addition to vaccines, therapeutic antibodies play an important role in immediately treating susceptible individuals to lessen severity of the disease. In this study, phage display technology was utilised to isolate human scFv antibody fragments that bind the receptor-binding domain (RBD) of SARS-CoV-2 Wuhan-Hu-1 spike protein. Of eight RBD-binding scFvs isolated, two inhibited interaction of RBD with ACE2 protein on VeroE6 cells. Both scFvs also exhibited binding to SARS-CoV-2 Delta variant spike protein but not to Omicron variant spike protein in a Raman spectroscopy immunotest. The study demonstrates the potential of recombinant antibody approaches to rapidly isolate antibody moieties with virus neutralisation potential.
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7
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Safarzadeh Kozani P, Naseri A, Mirarefin SMJ, Salem F, Nikbakht M, Evazi Bakhshi S, Safarzadeh Kozani P. Nanobody-based CAR-T cells for cancer immunotherapy. Biomark Res 2022; 10:24. [PMID: 35468841 PMCID: PMC9036779 DOI: 10.1186/s40364-022-00371-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/29/2022] [Indexed: 12/23/2022] Open
Abstract
Chimeric antigen receptor T-cell (CAR-T) therapy is the result of combining genetic engineering-based cancer immunotherapy with adoptive cell therapy (ACT). CAR-T therapy has been successful in treating various types of hematological cancers. CARs are receptors made of an extracellular domain, a membrane-spanning domain, and an intracellular domain. The extracellular domain of CARs harbors an antigen-targeting domain responsible for recognizing and binding cell surface-expressed target antigens. Conventionally, the single-chain fragment variable (scFv) of a monoclonal antibody (mAb) is used as the antigen-targeting domain of CARs. However, of late, researchers have exploited nanobodies for this aim based on numerous rationales including the small size of nanobodies, their stability, specificity, and high affinity, and their easy and feasible development process. Many findings have confirmed that nanobody-based CAR-Ts can be as functional as scFv-based CAR-Ts in preclinical and clinical settings. In this review, we discuss the advantages and disadvantages of scFvs and nanobodies in regards to their application as the targeting domain of CARs. Ultimately, we discuss various CAR target antigens which have been targeted using nanobody-based CAR-T cells for the treatment of different types of malignancies.
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Affiliation(s)
- Pouya Safarzadeh Kozani
- Department of Medical Biotechnology, Faculty of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Abdolhossein Naseri
- School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | | | - Faeze Salem
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mojtaba Nikbakht
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Sahar Evazi Bakhshi
- Department of Anatomical Sciences, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Pooria Safarzadeh Kozani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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8
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Rajasekaran N, Kaiser CM. Co-Translational Folding of Multi-Domain Proteins. Front Mol Biosci 2022; 9:869027. [PMID: 35517860 PMCID: PMC9065291 DOI: 10.3389/fmolb.2022.869027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/21/2022] [Indexed: 12/24/2022] Open
Abstract
The majority of proteins in nature are composed of multiple domains connected in a single polypeptide. How these long sequences fold into functional structures without forming toxic misfolds or aggregates is poorly understood. Their folding is inextricably linked to protein synthesis and interactions with cellular machinery, making mechanistic studies challenging. Recent progress has revealed critical features of multi-domain protein folding in isolation and in the context of translation by the ribosome. In this review, we discuss challenges and progress in understanding multi-domain protein folding, and highlight how molecular interactions shape folding and misfolding pathways. With the development of new approaches and model systems, the stage is now set for mechanistically exploring the folding of large multi-domain proteins.
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Affiliation(s)
| | - Christian M. Kaiser
- Department of Biology, Johns Hopkins University, Baltimore, MD, United States,Department of Biophysics, Johns Hopkins University, Baltimore, MD, United States,*Correspondence: Christian M. Kaiser,
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9
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CAR-NK Cells in the Treatment of Solid Tumors. Int J Mol Sci 2021; 22:ijms22115899. [PMID: 34072732 PMCID: PMC8197981 DOI: 10.3390/ijms22115899] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 02/07/2023] Open
Abstract
CAR-T (chimeric antigen receptor T) cells have emerged as a milestone in the treatment of patients with refractory B-cell neoplasms. However, despite having unprecedented efficacy against hematological malignancies, the treatment is far from flawless. Its greatest drawbacks arise from a challenging and expensive production process, strict patient eligibility criteria and serious toxicity profile. One possible solution, supported by robust research, is the replacement of T lymphocytes with NK cells for CAR expression. NK cells seem to be an attractive vehicle for CAR expression as they can be derived from multiple sources and safely infused regardless of donor-patient matching, which greatly reduces the cost of the treatment. CAR-NK cells are known to be effective against hematological malignancies, and a growing number of preclinical findings indicate that they have activity against non-hematological neoplasms. Here, we present a thorough overview of the current state of knowledge regarding the use of CAR-NK cells in treating various solid tumors.
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10
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The Application of Nanobody in CAR-T Therapy. Biomolecules 2021; 11:biom11020238. [PMID: 33567640 PMCID: PMC7914546 DOI: 10.3390/biom11020238] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/25/2021] [Accepted: 02/01/2021] [Indexed: 02/06/2023] Open
Abstract
Chimeric antigen receptor (CAR) T therapy represents a form of immune cellular therapy with clinical efficacy and a specific target. A typical chimeric antigen receptor (CAR) construct consists of an antigen binding domain, a transmembrane domain, and a cytoplasmic domain. Nanobodies have been widely applied as the antigen binding domain of CAR-T due to their small size, optimal stability, high affinity, and manufacturing feasibility. The nanobody-based CAR structure has shown a proven function in more than ten different tumor-specific targets. After being transduced in Jurkat cells, natural killer cells, or primary T cells, the resulting nanobody-based CAR-T or CAR-NK cells demonstrate anti-tumor effects both in vitro and in vivo. Interestingly, anti-BCMA CAR-T modulated by a single nanobody or bi-valent nanobody displays comparable clinical effects with that of single-chain variable fragment (scFv)-modulated CAR-T. The application of nanobodies in CAR-T therapy has been well demonstrated from bench to bedside and displays great potential in forming advanced CAR-T for more challenging tasks.
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11
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Kang TH, Seong BL. Solubility, Stability, and Avidity of Recombinant Antibody Fragments Expressed in Microorganisms. Front Microbiol 2020; 11:1927. [PMID: 33101218 PMCID: PMC7546209 DOI: 10.3389/fmicb.2020.01927] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/22/2020] [Indexed: 11/13/2022] Open
Abstract
Solubility of recombinant proteins (i.e., the extent of soluble versus insoluble expression in heterogeneous hosts) is the first checkpoint criterion for determining recombinant protein quality. However, even soluble proteins often fail to represent functional activity because of the involvement of non-functional, misfolded, soluble aggregates, which compromise recombinant protein quality. Therefore, screening of solubility and folding competence is crucial for improving the quality of recombinant proteins, especially for therapeutic applications. The issue is often highlighted especially in bacterial recombinant hosts, since bacterial cytoplasm does not provide an optimal environment for the folding of target proteins of mammalian origin. Antibody fragments, such as single-chain variable fragment (scFv), single-chain antibody (scAb), and fragment antigen binding (Fab), have been utilized for numerous applications such as diagnostics, research reagents, or therapeutics. Antibody fragments can be efficiently expressed in microorganisms so that they offer several advantages for diagnostic applications such as low cost and high yield. However, scFv and scAb fragments have generally lower stability to thermal stress than full-length antibodies, necessitating a judicious combination of designer antibodies, and bacterial hosts harnessed with robust chaperone function. In this review, we discuss efforts on not only the production of antibodies or antibody fragments in microorganisms but also scFv stabilization via (i) directed evolution of variants with increased stability using display systems, (ii) stabilization of the interface between variable regions of heavy (VH) and light (VL) chains through the introduction of a non-native covalent bond between the two chains, (iii) rational engineering of VH-VL pair, based on the structure, and (iv) computational approaches. We also review recent advances in stability design, increase in avidity by multimerization, and maintaining the functional competence of chimeric proteins prompted by various types of chaperones.
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Affiliation(s)
- Tae Hyun Kang
- Biopharmaceutical Chemistry Major, School of Applied Chemistry, Kookmin University, Seoul, South Korea
| | - Baik Lin Seong
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, South Korea.,Vaccine Innovative Technology ALliance (VITAL)-Korea, Yonsei University, Seoul, South Korea
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12
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Lee J, Der BS, Karamitros CS, Li W, Marshall NM, Lungu OI, Miklos AE, Xu J, Kang TH, Lee CH, Tan B, Hughes RA, Jung ST, Ippolito GC, Gray JJ, Zhang Y, Kuhlman B, Georgiou G, Ellington AD. Computer-based Engineering of Thermostabilized Antibody Fragments. AIChE J 2020; 66:e16864. [PMID: 32336757 PMCID: PMC7181397 DOI: 10.1002/aic.16864] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We used the molecular modeling program Rosetta to identify clusters of amino acid substitutions in antibody fragments (scFvs and scAbs) that improve global protein stability and resistance to thermal deactivation. Using this methodology, we increased the melting temperature (Tm) and resistance to heat treatment of an antibody fragment that binds to the Clostridium botulinum hemagglutinin protein (anti-HA33). Two designed antibody fragment variants with two amino acid replacement clusters, designed to stabilize local regions, were shown to have both higher Tm compared to the parental scFv and importantly, to retain full antigen binding activity after 2 hours of incubation at 70 °C. The crystal structure of one thermostabilized scFv variants was solved at 1.6 Å and shown to be in close agreement with the RosettaAntibody model prediction.
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Affiliation(s)
- Jiwon Lee
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755
| | - Bryan S. Der
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | | | - Wenzong Li
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Nicholas M. Marshall
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Oana I. Lungu
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Aleksandr E. Miklos
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, APGEA, MD 21010
| | - Jianqing Xu
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MA 21218
| | - Tae Hyun Kang
- Biopharmaceutical Chemistry Major, School of Applied Chemistry, Kookmin University, Seongbuk-gu, Seoul 02707, Republic of Korea
| | - Chang-Han Lee
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Bing Tan
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Randall A. Hughes
- US Army Research Laboratory, Austin, TX 78712,Applied Research Laboratories, The University of Texas at Austin, Austin, TX 78712
| | - Sang Taek Jung
- Department of Biomedical Science, Graduate School of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Gregory C. Ippolito
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MA 21218
| | - Yan Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | - George Georgiou
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712,Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712,Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712,To whom correspondence should be addressed: George Georgiou () and Andrew D. Ellington ()
| | - Andrew D. Ellington
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712,Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712,Department of Chemistry, The University of Texas at Austin, Austin, TX 78712,To whom correspondence should be addressed: George Georgiou () and Andrew D. Ellington ()
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13
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Majumder S, Wang W, Alphonse Ignatius A. Impact of Buffers on Colloidal Property and Aggregation Propensities of a Bispecific Antibody. J Pharm Sci 2019; 108:1139-1147. [DOI: 10.1016/j.xphs.2018.10.048] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/11/2018] [Accepted: 10/22/2018] [Indexed: 11/29/2022]
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14
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Shinozaki N, Hashimoto R, Noda M, Uchiyama S. Physicochemical improvement of rabbit derived single-domain antibodies by substitutions with amino acids conserved in camelid antibodies. J Biosci Bioeng 2018; 125:654-661. [PMID: 29398547 DOI: 10.1016/j.jbiosc.2018.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/26/2017] [Accepted: 01/09/2018] [Indexed: 01/02/2023]
Abstract
Recently, we showed that immunized rabbit heavy chain variable regions (rVHs) can have strong antigen binding activity comparable to that of the camelid variable domain of the heavy chain of heavy chain antibody (VHH). These rVHs lack the light chain variable regions (rVLs), which exist in the authentic Fab format; thus, molecular surfaces at the interface region of rVHs are exposed to solvent. This physical feature may change physicochemical properties, such as causing reduced stability. By overcoming potential physicochemical issues through engineering the interface region, rVHs could become more useful as single-domain antibodies. In this study, we substituted amino acid residues conserved at the interface region of rVHs with those of VHHs. These substitutions included V37F, involving substitution of a residue in the hydrophobic core with a bulkier hydrophobic amino acid, and G44E/L45R, involving double substitutions of highly exposed residues with more hydrophilic ones. As expected, biophysical and structural characterizations showed that the V37F substitution markedly enhanced the thermal stability through increased hydrophobic packing, while G44E/L45R substitutions greatly reduced hydrophobicity of the interface. The quadruple substitutions of V37F/G44E/L45R/F91Y resulted in not only enhancements of thermal stability and reduction in hydrophobicity, both in an additive manner, but also synergistic improvement of purification yield. This quadruple mutant exhibited greatly reduced non-specific binding with improved colloidal stability owing to the reduced hydrophobicity. The approach used in this study should further enhance the utility of rVHs and promote research and development of single-domain antibodies.
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Affiliation(s)
- Naoya Shinozaki
- Modality Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd., Shinagawa R&D Center, 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan; Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ryuji Hashimoto
- Modality Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd., Shinagawa R&D Center, 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Masanori Noda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan.
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15
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Isothermal chemical denaturation of large proteins: Path-dependence and irreversibility. Anal Biochem 2017; 539:60-69. [DOI: 10.1016/j.ab.2017.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 12/16/2022]
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16
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Shinozaki N, Hashimoto R, Fukui K, Uchiyama S. Efficient generation of single domain antibodies with high affinities and enhanced thermal stabilities. Sci Rep 2017; 7:5794. [PMID: 28725057 PMCID: PMC5517631 DOI: 10.1038/s41598-017-06277-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 06/12/2017] [Indexed: 01/02/2023] Open
Abstract
Single domain antibodies (sdAbs), made of natural single variable regions of camelid or cartilaginous fish antibodies, or unpaired variable regions of mouse or human IgGs, are some of the more promising biologic modalities. However, such conventional sdAbs have difficulties of either using unwieldy animals for immunization or having high affinity deficiencies. Herein, we offer a versatile method to generate rabbit variable domain of heavy chain (rVH) derived sdAbs with high affinities (KD values of single digit nM or less) and enhanced thermal stabilities (equal to or even higher than those of camelid derived sdAbs). It was found that a variety of rVH binders, including those with high affinities, were efficiently acquired using an rVH-displaying phage library produced at a low temperature of 16 °C. By a simple method to introduce an additional disulfide bond, their unfolding temperatures were increased by more than 20 °C without severe loss of binding affinity. Differential scanning calorimetry analysis suggested that this highly efficient thermal stabilization was mainly attributed to the entropic contribution and unique thermodynamic character of the rVHs.
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Affiliation(s)
- Naoya Shinozaki
- Modality Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd., Shinagawa R&D Center, 1-2-58 Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan
| | - Ryuji Hashimoto
- Modality Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd., Shinagawa R&D Center, 1-2-58 Hiromachi, Shinagawa-ku, Tokyo, 140-8710, Japan
| | - Kiichi Fukui
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
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17
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Yang N, Yao N, Liao X, Xie X, Wu Y, Fan C, Zhao J, Li G. Effects of metal ions on the structure and activity of a human anti-cyclin D1 single-chain variable fragment AD5. Mol Med Rep 2017. [PMID: 28627625 PMCID: PMC5561975 DOI: 10.3892/mmr.2017.6756] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Cyclin D1 has become a potential target for anti-tumor therapy. Recently, a novel human anti-cyclin D1 single-chain variable fragment (AD5) was identified, which demonstrated specific binding activity to cyclin D1 and exhibited anti-tumor effects. However, the detailed characteristics of AD5 remain unclear. In the present study, the structure and activity of AD5 in the presence of copper II (Cu2+) or iron III (Fe3+) metal ions was investigated by fluorescence spectroscopy, synchronous fluorescence and enzyme-linked immunosorbent assay. Cu2+ and Fe3+ were able to bind to AD5 and quench the fluorescence intensity of AD5 primarily by static quenching, which slightly altered the conformation of AD5 at temperatures of 293, 298 and 303 K; however, these temperatures demonstrated different effects on the activity of AD5. These results may be of value for the clinical application of anti-cyclin D1 single chain antibodies in the future.
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18
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Julian MC, Lee CC, Tiller KE, Rabia LA, Day EK, Schick AJ, Tessier PM. Co-evolution of affinity and stability of grafted amyloid-motif domain antibodies. Protein Eng Des Sel 2015; 28:339-50. [PMID: 26386257 DOI: 10.1093/protein/gzv050] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 08/17/2015] [Indexed: 11/12/2022] Open
Abstract
An attractive approach for designing lead antibody candidates is to mimic natural protein interactions by grafting peptide recognition motifs into the complementarity-determining regions (CDRs). We are using this approach to generate single-domain (VH) antibodies specific for amyloid-forming proteins such as the Alzheimer's Aβ peptide. Here, we use random mutagenesis and yeast surface display to improve the binding affinity of a lead VH domain grafted with Aβ residues 33-42 in CDR3. Interestingly, co-selection for improved Aβ binding and VH display on the surface of yeast yields antibody domains with improved affinity and reduced stability. The highest affinity VH domains were strongly destabilized on the surface of yeast as well as unfolded when isolated as autonomous domains. In contrast, stable VH domains with improved affinity were reliably identified using yeast surface display by replacing the display antibody that recognizes a linear epitope tag at the terminus of both folded and unfolded VH domains with a conformational ligand (Protein A) that recognizes a discontinuous epitope on the framework of folded VH domains. Importantly, we find that selection for improved stability using Protein A without simultaneous co-selection for improved Aβ binding leads to strong enrichment for stabilizing mutations that reduce antigen binding. Our findings highlight the importance of simultaneously optimizing affinity and stability to improve the rapid isolation of well-folded and specific antibody fragments.
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Affiliation(s)
- Mark C Julian
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Christine C Lee
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Kathryn E Tiller
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Lilia A Rabia
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Evan K Day
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Arthur J Schick
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Peter M Tessier
- Center for Biotechnology & Interdisciplinary Studies, Isermann Department of Chemical & Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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19
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Li Z, Cheng Y, Xi H, Gu T, Yuan R, Chen X, Jiang C, Kong W, Wu Y. A novel variable antibody fragment dimerized by leucine zippers with enhanced neutralizing potency against rabies virus G protein compared to its corresponding single-chain variable antibody fragment. Mol Immunol 2015; 68:168-75. [PMID: 26325475 DOI: 10.1016/j.molimm.2015.06.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/18/2015] [Accepted: 06/26/2015] [Indexed: 10/23/2022]
Abstract
Fatal rabies can be prevented effectively by post-exposure prophylactic (PEP) with rabies immunoglobulin (RIG). Single-chain variable fragments (scFv), which are composed of a variable heavy chain (VH) and a variable light chain (VL) connected by a peptide linker, can potentially be used to replace RIG. However, in our previous study, a scFv (scFV57S) specific for the rabies virus (RV) G protein showed a lower neutralizing potency than that of its parent IgG due to lower stability and altered peptide assembly pattern. In monoclonal antibodies, the VH and VL interact non-covalently, while in scFvs the VH is connected covalently with the VL by the artificial linker. In this study, we constructed and expressed two peptides 57VL-JUN-HIS and 57VH-FOS-HA in Escherichia coli. The well-known Fos and Jun leucine zippers were utilized to dimerize VH and VL similarly to the IgG counterpart. The two peptides assembled to form zipFv57S in vitro. Due to the greater similarity in structure with IgG, the zipFv57S protein showed a higher binding ability and affinity resulting in notable improvement of in vitro neutralizing activity over its corresponding scFv. The zipFv57S protein was also found to be more stable and showed similar protective rate as RIG in mice challenged with a lethal dose of RV. Our results not only indicated zipFv57S as an ideal alternative for RIG in PEP but also offered a novel and efficient hetero-dimerization pattern of VH and VL leading to enhanced neutralizing potency.
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Affiliation(s)
- Zhuang Li
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun 130012, China
| | - Yue Cheng
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun 130012, China
| | - Hualong Xi
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun 130012, China
| | - Tiejun Gu
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China
| | - Ruosen Yuan
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun 130012, China
| | - Xiaoxu Chen
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun 130012, China
| | - Chunlai Jiang
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China
| | - Wei Kong
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Yongge Wu
- National Engineering Laboratory for AIDS Vaccine, School of Life Science, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
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20
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Friedel T, Hanisch LJ, Muth A, Honegger A, Abken H, Plückthun A, Buchholz CJ, Schneider IC. Receptor-targeted lentiviral vectors are exceptionally sensitive toward the biophysical properties of the displayed single-chain Fv. Protein Eng Des Sel 2015; 28:93-106. [PMID: 25715658 DOI: 10.1093/protein/gzv005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
An increasing number of applications require the expression of single-chain variable fragments (scFv) fusion proteins in mammalian cells at the cell surface membrane. Here we assessed the CD30-specific scFv HRS3, which is used in immunotherapy, for its ability to retarget lentiviral vectors (LVs) to CD30 and to mediate selective gene transfer into CD30-positive cells. Fused to the C-terminus of the type-II transmembrane protein hemagglutinin (H) of measles virus and expressed in LV packaging cells, gene transfer mediated by the released LV particles was inefficient. A series of point mutations in the scFv framework regions addressing its biophysical properties, which substantially improved production and increased the melting temperature without impairing its kinetic binding behavior to CD30, also improved the performance of LV particles. Gene transfer into CD30-positive cells increased ∼100-fold due to improved transport of the H-scFv protein to the plasma membrane. Concomitantly, LV particle aggregation and syncytia formation in packaging cells were substantially reduced. The data suggest that syncytia formation can be triggered by trans-cellular dimerization of H-scFv proteins displayed on adjacent cells. Taken together, we show that the biophysical properties of the targeting ligand have a decisive role for the gene transfer efficiency of receptor-targeted LVs.
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Affiliation(s)
- Thorsten Friedel
- Section of Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, Paul-Ehrlich-Str. 51-59, Langen 63225, Germany
| | - Lydia J Hanisch
- Roche Pharmaceutical Research and Early Development, Protein Engineering Group, Roche Innovation Center Zürich, Schlieren 8952, Switzerland
| | - Anke Muth
- Section of Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, Paul-Ehrlich-Str. 51-59, Langen 63225, Germany
| | - Annemarie Honegger
- Department of Biochemistry, University of Zürich, Zürich 8057, Switzerland
| | - Hinrich Abken
- Center for Molecular Medicine Cologne, University of Cologne, Cologne 50931, Germany Department I of Internal Medicine, University Hospital Cologne, Cologne 50931, Germany
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Zürich 8057, Switzerland
| | - Christian J Buchholz
- Section of Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, Paul-Ehrlich-Str. 51-59, Langen 63225, Germany
| | - Irene C Schneider
- Section of Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, Paul-Ehrlich-Str. 51-59, Langen 63225, Germany
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21
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Škerlová J, Král V, Fábry M, Sedláček J, Veverka V, Řezáčová P. Optimization of the crystallizability of a single-chain antibody fragment. Acta Crystallogr F Struct Biol Commun 2014; 70:1701-6. [PMID: 25484230 PMCID: PMC4259244 DOI: 10.1107/s2053230x1402247x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 10/13/2014] [Indexed: 11/10/2022] Open
Abstract
Single-chain variable antibody fragments (scFvs) are molecules with immense therapeutic and diagnostic potential. Knowledge of their three-dimensional structure is important for understanding their antigen-binding mode as well as for protein-engineering approaches such as antibody humanization. A major obstacle to the crystallization of single-chain variable antibody fragments is their relatively poor homogeneity caused by spontaneous oligomerization. A new approach to optimization of the crystallizability of single-chain variable antibody fragments is demonstrated using a representative single-chain variable fragment derived from the anti-CD3 antibody MEM-57. A Thermofluor-based assay was utilized to screen for optimal conditions for antibody-fragment stability and homogeneity. Such an optimization of the protein storage buffer led to a significantly improved ability of the scFv MEM-57 to yield crystals.
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Affiliation(s)
- Jana Škerlová
- Institute of Molecular Genetics, ASCR, v.v.i., Vídeňská 1083, 14220 Prague 4, Czech Republic
- Institute of Organic Chemistry and Biochemistry, ASCR, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Faculty of Science, Charles University in Prague, Albertov 6, 12843 Prague 2, Czech Republic
| | - Vlastimil Král
- Institute of Molecular Genetics, ASCR, v.v.i., Vídeňská 1083, 14220 Prague 4, Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics, ASCR, v.v.i., Vídeňská 1083, 14220 Prague 4, Czech Republic
| | - Juraj Sedláček
- Institute of Molecular Genetics, ASCR, v.v.i., Vídeňská 1083, 14220 Prague 4, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry, ASCR, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Pavlína Řezáčová
- Institute of Molecular Genetics, ASCR, v.v.i., Vídeňská 1083, 14220 Prague 4, Czech Republic
- Institute of Organic Chemistry and Biochemistry, ASCR, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
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22
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Roberts CJ. Therapeutic protein aggregation: mechanisms, design, and control. Trends Biotechnol 2014; 32:372-80. [PMID: 24908382 DOI: 10.1016/j.tibtech.2014.05.005] [Citation(s) in RCA: 296] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/08/2014] [Accepted: 05/13/2014] [Indexed: 11/28/2022]
Abstract
Although it is well known that proteins are only marginally stable in their folded states, it is often less well appreciated that most proteins are inherently aggregation-prone in their unfolded or partially unfolded states, and the resulting aggregates can be extremely stable and long-lived. For therapeutic proteins, aggregates are a significant risk factor for deleterious immune responses in patients, and can form via a variety of mechanisms. Controlling aggregation using a mechanistic approach may allow improved design of therapeutic protein stability, as a complement to existing design strategies that target desired protein structures and function. Recent results highlight the importance of balancing protein environment with the inherent aggregation propensities of polypeptide chains.
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Affiliation(s)
- Christopher J Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
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23
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Abe R, Jeong HJ, Arakawa D, Dong J, Ohashi H, Kaigome R, Saiki F, Yamane K, Takagi H, Ueda H. Ultra Q-bodies: quench-based antibody probes that utilize dye-dye interactions with enhanced antigen-dependent fluorescence. Sci Rep 2014; 4:4640. [PMID: 24721819 PMCID: PMC3983608 DOI: 10.1038/srep04640] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 03/21/2014] [Indexed: 11/09/2022] Open
Abstract
Recently, we described a novel reagentless fluorescent biosensor strategy named Quenchbody, which functions via the antigen-dependent removal of the quenching effect on a fluorophore that is attached to a single-chain antibody variable region. To explore the practical utility of Quenchbodies, we prepared antibody Fab fragments that were fluorolabeled at either one or two of the N-terminal regions, using a cell-free translation-mediated position-specific protein labeling system. Unexpectedly, the Fab fragment labeled at the heavy chain N-terminal region demonstrated a deeper quenching and antigen-dependent release compared to that observed using scFv. Moreover, when the Fab was fluorolabeled at the two N-termini with either the same dye or with two different dyes, an improved response due to enhanced quenching via dye-dye interactions was observed. On the basis of this approach, several targets, including peptides, proteins, and haptens, as well as narcotics, were quantified with a higher response up to 50-fold. In addition, differentiation of osteosarcoma to osteoblasts was successfully imaged using a similarly fluorolabeled recombinant Fab protein prepared from E. coli. Due to its versatility, this "Ultra-Quenchbody" is expected to exhibit a range of applications from in vitro diagnostics to the live imaging of various targets in situ.
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Affiliation(s)
- Ryoji Abe
- Ushio Inc., 6409 Moto-Ishikawa-cho, Aoba-ku, Yokohama, Kanagawa 225-0004, Japan
| | - Hee-Jin Jeong
- 1] Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan [2] Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1-18, Nagatsuta-cho, Midori-ku, Yokoyama, Kanagawa 226-8503, Japan
| | - Dai Arakawa
- Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jinhua Dong
- 1] Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan [2] Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1-18, Nagatsuta-cho, Midori-ku, Yokoyama, Kanagawa 226-8503, Japan
| | - Hiroyuki Ohashi
- 1] Ushio Inc., 6409 Moto-Ishikawa-cho, Aoba-ku, Yokohama, Kanagawa 225-0004, Japan [2] Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Rena Kaigome
- Ushio Inc., 6409 Moto-Ishikawa-cho, Aoba-ku, Yokohama, Kanagawa 225-0004, Japan
| | - Fujio Saiki
- Ushio Inc., 6409 Moto-Ishikawa-cho, Aoba-ku, Yokohama, Kanagawa 225-0004, Japan
| | - Kyosuke Yamane
- 1] Ushio Inc., 6409 Moto-Ishikawa-cho, Aoba-ku, Yokohama, Kanagawa 225-0004, Japan [2] Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroaki Takagi
- Ushio Inc., 6409 Moto-Ishikawa-cho, Aoba-ku, Yokohama, Kanagawa 225-0004, Japan
| | - Hiroshi Ueda
- 1] Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan [2] Chemical Resources Laboratory, Tokyo Institute of Technology, 4259-R1-18, Nagatsuta-cho, Midori-ku, Yokoyama, Kanagawa 226-8503, Japan
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24
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Malpiedi LP, Nerli BB, Abdalla DSP, Pessoa A. Assessment of the effect of triton X-114 on the physicochemical properties of an antibody fragment. Biotechnol Prog 2014; 30:554-61. [DOI: 10.1002/btpr.1882] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 01/29/2014] [Indexed: 01/05/2023]
Affiliation(s)
- Luciana P. Malpiedi
- Biochemical and Pharmaceutical Technology Dept./FCF; University of São Paulo. Av. Prof. Lineu Prestes; 580-Bloco 16 CEP 05508-000 São Paulo Brazil
- Physical Chemistry Dept., Faculty of Biochemistry and Pharmaceutical Sciences; National University of Rosario; Suipacha 570 S2002LRK Rosario Argentina
| | - Bibiana B. Nerli
- Physical Chemistry Dept., Faculty of Biochemistry and Pharmaceutical Sciences; National University of Rosario; Suipacha 570 S2002LRK Rosario Argentina
| | | | - Adalberto Pessoa
- Biochemical and Pharmaceutical Technology Dept./FCF; University of São Paulo. Av. Prof. Lineu Prestes; 580-Bloco 16 CEP 05508-000 São Paulo Brazil
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25
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Gu J, Ghayur T. Rationale and development of multispecific antibody drugs. Expert Rev Clin Pharmacol 2014; 3:491-508. [DOI: 10.1586/ecp.10.28] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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26
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Rivera-Hernández G, Marin-Argany M, Blasco-Moreno B, Bonet J, Oliva B, Villegas S. Elongation of the C-terminal domain of an anti-amyloid β single-chain variable fragment increases its thermodynamic stability and decreases its aggregation tendency. MAbs 2013; 5:678-89. [PMID: 23924802 DOI: 10.4161/mabs.25382] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Amyloid β (Aβ) immunotherapy is considered a promising approach to Alzheimer disease treatment. In contrast to the use of complete antibodies, administration of single-chain variable fragments (scFv) has not been associated with either meningoencephalitis or cerebral hemorrhage. ScFv-h3D6 is known to preclude cytotoxicity of the Aβ 1-42 peptide by removing its oligomers from the amyloid pathway. As is the case for other scFv molecules, the recombinant production of scFv-h3D6 is limited by its folding and stability properties. Here, we show that its urea-induced unfolding pathway is characterized by the presence of an intermediate state composed of the unfolded VL domain and the folded VH domain, which suggests the VL domain as a target for thermodynamic stability redesign. The modeling of the 3D structure revealed that the VL domain, located at the C-terminal of the molecule, was ending before its latest β-strand was completed. Three elongation mutants, beyond VL-K107, showed increased thermodynamic stability and lower aggregation tendency, as determined from urea denaturation experiments and Fourier-transform infrared spectroscopy, respectively. Because the mutants maintained the capability of removing Aβ-oligomers from the amyloid pathway, we expect these traits to increase the half-life of scFv-h3D6 in vivo and, consequently, to decrease the effective doses. Our results led to the improvement of a potential Alzheimer disease treatment and may be extrapolated to other class-I scFv molecules of therapeutic interest.
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Affiliation(s)
- Geovanny Rivera-Hernández
- Protein Folding and Stability Group; Departament de Bioquímica i Biologia Molecular; Unitat de Biociències; Universitat Autònoma de Barcelona; Barcelona, Spain
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27
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Gil D, Schrum AG. Strategies to stabilize compact folding and minimize aggregation of antibody-based fragments. ADVANCES IN BIOSCIENCE AND BIOTECHNOLOGY (PRINT) 2013; 4:73-84. [PMID: 25635232 PMCID: PMC4307952 DOI: 10.4236/abb.2013.44a011] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Monoclonal antibodies (mAbs) have proven to be useful for development of new therapeutic drugs and diagnostic techniques. To overcome the difficulties posed by their complex structure and folding, reduce undesired immunogenicity, and improve pharmacokinetic properties, a plethora of different Ab fragments have been developed. These include recombinant Fab and Fv segments that can display improved properties over those of the original mAbs upon which they are based. Antibody (Ab) fragments such as Fabs, scFvs, diabodies, and nanobodies, all contain the variable Ig domains responsible for binding to specific antigenic epitopes, allowing for specific targeting of pathological cells and/or molecules. These fragments can be easier to produce, purify and refold than a full Ab, and due to their smaller size they can be well absorbed and distributed into target tissues. However, the physicochemical and structural properties of the immunoglobulin (Ig) domain, upon which the folding and conformation of all these Ab fragments is based, can limit the stability of Ab-based drugs. The Ig domain is fairly sensitive to unfolding and aggregation when produced out of the structural context of an intact Ab molecule. When unfolded, Ab fragments may lose their specificity as well as establish non-native interactions leading to protein aggregation. Aggregated antibody fragments display altered pharmacokinetic and immunogenic properties that can augment their toxicity. Therefore, much effort has been placed in understanding the factors impacting the stability of Ig folding at two different levels: 1) intrinsically, by studying the effects of the amino acid sequence on Ig folding; 2) extrinsically, by determining the environmental conditions that may influence the stability of Ig folding. In this review we will describe the structure of the Ig domain, and the factors that impact its stability, to set the context for the different approaches currently used to achieve stable recombinant Ig domains when pursuing the development of Ab fragment-based biotechnologies.
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Affiliation(s)
- Diana Gil
- Department of Immunology, Mayo Clinic College of Medicine, Rochester, USA
| | - Adam G. Schrum
- Department of Immunology, Mayo Clinic College of Medicine, Rochester, USA
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28
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Entzminger KC, Chang C, Myhre RO, McCallum KC, Maynard JA. The Skp chaperone helps fold soluble proteins in vitro by inhibiting aggregation. Biochemistry 2012; 51:4822-34. [PMID: 22650963 DOI: 10.1021/bi300412y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The periplasmic seventeen kilodalton protein (Skp) chaperone has been characterized primarily for its role in outer membrane protein (OMP) biogenesis, during which the jellyfish-like trimeric protein encapsulates partially folded OMPs, protecting them from the aqueous environment until delivery to the BAM outer membrane protein insertion complex. However, Skp is increasingly recognized as a chaperone that also assists in folding soluble proteins in the bacterial periplasm. In this capacity, Skp coexpression increases the active yields of many recombinant proteins and bacterial virulence factors. Using a panel of single-chain antibodies and a single-chain T-cell receptor (collectively termed scFvs) possessing varying stabilities and biophysical characteristics, we performed in vivo expression and in vitro folding and aggregation assays in the presence or absence of Skp. For Skp-sensitive scFvs, the presence of Skp during in vitro refolding assays reduced aggregation but did not alter the observed folding rates, resulting in a higher overall yield of active protein. Of the proteins analyzed, Skp sensitivity in all assays correlated with the presence of folding intermediates, as observed with urea denaturation studies. These results are consistent with Skp acting as a holdase, sequestering partially folded intermediates and thereby preventing aggregation. Because not all soluble proteins are sensitive to Skp coexpression, we hypothesize that the presence of a long-lived protein folding intermediate renders a protein sensitive to Skp. Improved understanding of the bacterial periplasmic protein folding machinery may assist in high-level recombinant protein expression and may help identify novel approaches to block bacterial virulence.
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Affiliation(s)
- Kevin C Entzminger
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA
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Paoletti F, Malerba F, Konarev PV, Visintin M, Scardigli R, Fasulo L, Lamba D, Svergun DI, Cattaneo A. Direct intracellular selection and biochemical characterization of a recombinant anti-proNGF single chain antibody fragment. Arch Biochem Biophys 2012; 522:26-36. [PMID: 22516657 DOI: 10.1016/j.abb.2012.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 03/30/2012] [Accepted: 04/03/2012] [Indexed: 01/06/2023]
Abstract
proNGF, the precursor of the neurotrophin NGF, is widely expressed in central and peripheral nervous system. Its physiological functions are still largely unknown, although it emerged from studies in the last decade that proNGF has additional and distinct functions with respect to NGF, besides acting chaperone-like for NGF folding during its biogenesis. The regulation of proNGF/NGF ratio represents a crucial process for homeostasis of brain and other tissues, and understanding the molecular aspects of these differences is important. We report the selection and characterization of a recombinant monoclonal anti-proNGF antibody in single chain Fv fragment (scFv) format. The selection exploited the Intracellular Antibody Capture Technology (IACT), starting from a naïve mouse SPLINT (Single Pot Library of INTracellular antibodies) library. This antibody (scFv FPro10) was expressed recombinantly in Escherichia coli, was proven to be highly soluble and stable, and thoroughly characterized from the biochemical-biophysical point of view. scFv FPro10 displays high affinity and specificity for proNGF, showing no cross-reactivity with other pro-neurotrophins. A structural model was obtained by SAXS. scFv FPro10 represents a new tool to be exploited for the selective immunoanalysis of proNGF, both in vitro and in vivo, and might help in understanding the molecular function of proNGF in neurodegeneration.
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Affiliation(s)
- Francesca Paoletti
- EBRI-European Brain Research Institute, Via del Fosso di Fiorano 64, 00143 Rome, Italy
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30
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Abstract
The ability of antibodies to bind to target molecules with high affinity and specificity has led to their widespread use in diagnostic and therapeutic applications. Nevertheless, a limitation of antibodies is their propensity to self-associate and aggregate at high concentrations and elevated temperatures. The large size and multidomain architecture of full-length monoclonal antibodies have frustrated systematic analysis of how antibody sequence and structure regulate antibody solubility. In contrast, analysis of single and multidomain antibody fragments that retain the binding activity of mono-clonal antibodies has provided valuable insights into the determinants of antibody aggregation. Here we review advances in engineering antibody frameworks, domain interfaces, and antigen-binding loops to prevent aggregation of natively and nonnatively folded antibody fragments. We also highlight advances and unmet challenges in developing robust strategies for engineering large, multidomain antibodies to resist aggregation.
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Affiliation(s)
- Joseph M Perchiacca
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA
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31
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Abstract
ScFv fragments are popular recombinant antibody formats but often suffer from limited stability. Phage display is a powerful tool in antibody engineering and applicable also for stability selection. ScFv variants with improved stability can be selected from large randomly mutated phage displayed libraries with a specific antigen after the unstable variants have been inactivated by heat or GdmCl. Irreversible scFv denaturation, which is a prerequisite for efficient selection, is achieved by combining denaturation with reduction of the intradomain disulfide bonds. Repeated selection cycles of increasing stringency result in enrichment of stabilized scFv fragments. Procedures for constructing a randomly mutated scFv library by error-prone PCR and phage display selection for enrichment of stable scFv antibodies from the library are described here.
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Abstract
Proteolytic release from the cell surface is an essential activation event for many growth factors and cytokines. TNF-α converting enzyme (TACE) is a membrane-bound metalloprotease responsible for solubilizing many pathologically significant membrane substrates and is an attractive therapeutic target for the treatment of cancer and arthritis. Prior attempts to antagonize cell-surface TACE activity have focused on small-molecule inhibition of the metalloprotease active site. Given the highly conserved nature of metalloprotease active sites, this paradigm has failed to produce a truly specific TACE inhibitor and continues to obstruct the clinical investigation of TACE activity. We report the bespoke development of a specific TACE inhibitory human antibody using "two-step" phage display. This approach combines calculated selection conditions with antibody variable-domain exchange to direct individual antibody variable domains to desired epitopes. The resulting "cross-domain" human antibody is a previously undescribed selective TACE antagonist and provides a unique alternative to small-molecule metalloprotease inhibition.
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Salinas BA, Sathish HA, Shah AU, Carpenter JF, Randolph TW. Buffer-dependent fragmentation of a humanized full-length monoclonal antibody. J Pharm Sci 2010; 99:2962-74. [PMID: 20091831 PMCID: PMC3938388 DOI: 10.1002/jps.22056] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
During storage stability studies of a monoclonal antibody (mAb) it was determined that the primary route of degradation involved fragmentation into lower molecular weight species. The fragmentation was characterized with size-exclusion high performance liquid chromatography (SE-HPLC), SDS-PAGE, and matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry. Fragmentation proceeded via hydrolysis, likely catalyzed by trace metal ions, of a peptide bond in the hinge region of the mAb's heavy chain, which produced two prominent low molecular weight species during storage: a single, free Fab fragment and a Fab + Fc fragment. The fragmentation is observed in phosphate-buffered solutions at two ionic strengths but not in histidine-buffered solutions at identical ionic strengths. Chaotrope-induced and thermally induced unfolding studies of the mAb indicated differences in the unfolding pathways between the two buffer solutions. The folding intermediate observed during chaotrope-induced unfolding was further characterized by intrinsic fluorescence quenching, which suggested that a small portion of the molecule is resistant to chaotrope-induced unfolding in histidine buffer systems. The thermally induced unfolding indicates a reduction in cooperativity of the unfolding process in the presence of histidine relative to phosphate. A relationship between the histidine-induced effects on unfolding pathway and the relative resistance to fragmentation is suggested.
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Affiliation(s)
- Branden A Salinas
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado, USA.
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Igawa T, Tsunoda H, Kikuchi Y, Yoshida M, Tanaka M, Koga A, Sekimori Y, Orita T, Aso Y, Hattori K, Tsuchiya M. VH/VL interface engineering to promote selective expression and inhibit conformational isomerization of thrombopoietin receptor agonist single-chain diabody. Protein Eng Des Sel 2010; 23:667-77. [DOI: 10.1093/protein/gzq034] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Hur BU, Choi HJ, Yoon JB, Cha SH. Expression of a Functional zipFv Antibody Fragment and Its Fusions with Alkaline Phosphatase in the Cytoplasm of an Escherichia coli. Immune Netw 2010; 10:35-45. [PMID: 20532123 PMCID: PMC2881423 DOI: 10.4110/in.2010.10.2.35] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 03/15/2010] [Accepted: 03/19/2010] [Indexed: 12/01/2022] Open
Abstract
Background Expression of recombinant antibodies and their derivatives fused with other functional molecules such as alkaline phosphatase in Escherichia coli is important in the development of molecular diagnostic reagents for biomedical research. Methods We investigated the possibility of applying a well-known Fos-Jun zipper to dimerize VH and VL fragments originated from the Fab clone (SP 112) that recognizes pyruvate dehydrogenase complex-E2 (PDC-E2), and demonstrated that the functional zipFv-112 and its alkaline phosphatase fusion molecules (zipFv-AP) can be produced in the cytoplasm of Origami(DE3) trxB gor mutant E. coli strain. Results The zipFv-AP fusion molecules exhibited higher antigen-binding signals than the zipFv up to a 10-fold under the same experimental conditions. However, conformation of the zipFv-AP seemed to be influenced by the location of an AP domain at the C-terminus of VH or VL domain [zipFv-112(H-AP) or zipFv-112(L-AP)], and inclusion of an AraC DNA binding domain at the C-terminus of VH of the zipFv-112(L-AP), termed zipFv-112(H-AD/L-AP), was also beneficial. Cytoplasmic co-expression of disulfide-binding isomerase C (DsbC) helped proper folding of the zipFv-112(H-AD/L-AP) but not significantly. Conclusion We believe that our zipFv constructs may serve as an excellent antibody format bi-functional antibody fragments that can be produced stably in the cytoplasm of E. coli.
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Affiliation(s)
- Byung-Ung Hur
- Division of Molecular & Medical Biotechnology, College of Biomedical Science, Kangwon National University, Chuncheon 200-701, Korea
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36
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Use of high-capacity surface with oriented recombinant antibody fragments in a 5-min immunoassay for thyroid-stimulating hormone. Anal Biochem 2010; 396:242-9. [DOI: 10.1016/j.ab.2009.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 09/29/2009] [Accepted: 10/02/2009] [Indexed: 10/20/2022]
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Padiolleau-Lefevre S, Alexandrenne C, Dkhissi F, Clement G, Essono S, Blache C, Couraud JY, Wijkhuisen A, Boquet D. Expression and detection strategies for an scFv fragment retaining the same high affinity than Fab and whole antibody: Implications for therapeutic use in prion diseases. Mol Immunol 2007; 44:1888-96. [PMID: 17140664 DOI: 10.1016/j.molimm.2006.09.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Accepted: 09/29/2006] [Indexed: 11/26/2022]
Abstract
Since antibodies currently constitute the most rapidly growing class of human therapeutics, the high-yield production of recombinant antibodies and antibody fragments is a real challenge. Using as model a monoclonal antibody directed against the human prion protein that we prepared previously and tested for its therapeutic value, we describe here experimental conditions allowing the production of large quantities (up to 35 mg/l of bacterial culture) of correctly refolded and totally functional single chain fragment variable (scFv). These quantities were sufficient to characterize the binding properties of this small recombinant fragment through in vitro and ex vivo approaches. Interestingly, this scFv retains full binding capacity for its antigen, i.e. the human prion protein, when compared with the corresponding Fab or whole antibody, and recognizes soluble, solid-phase-adsorbed, and membrane-bound prion protein. This strongly suggests that from the mAb cloning step to the refolding of the recombinant fragment, each stage is well controlled, leading to almost 100% functional scFv. These results are of interest not only in view of possible immunotherapy for prion diseases, but also more generally in emphasizing the great promise of these small recombinant molecules in the context of targeted therapies.
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Affiliation(s)
- Séverine Padiolleau-Lefevre
- Commissariat à l'Energie Atomique (CEA) Saclay, Service de Pharmacologie et d'Immunologie, Bat 136, 91191 Gif sur Yvette Cedex, France
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38
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Yesylevskyy SO, Kharkyanen VN, Demchenko AP. Dynamic protein domains: identification, interdependence, and stability. Biophys J 2006; 91:670-85. [PMID: 16632509 PMCID: PMC1483087 DOI: 10.1529/biophysj.105.078584] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Existing methods of domain identification in proteins usually provide no information about the degree of domain independence and stability. However, this information is vital for many areas of protein research. The recently developed hierarchical clustering of correlation patterns (HCCP) technique provides machine-based domain identification in a computationally simple and physically consistent way. Here we present the modification of this technique, which not only allows determination of the most plausible number of dynamic domains but also makes it possible to estimate the degree of their independence (the extent of correlated motion) and stability (the range of environmental conditions, where domains remain intact). With this technique we provided domain assignments and calculated intra- and interdomain correlations and interdomain energies for >2500 test proteins. It is shown that mean intradomain correlation of motions can serve as a quantitative criterion of domain independence, and the HCCP stability gap is a measure of their stability. Our data show that the motions of domains with high stability are usually independent. In contrast, the domains with moderate stability usually exhibit a substantial degree of correlated motions. It is shown that in multidomain proteins the domains are most stable if they are of similar size, and this correlates with the observed abundance of such proteins.
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Affiliation(s)
- Semen O Yesylevskyy
- Department of Physics of Biological Systems, Institute of Physics, National Academy of Sciences of Ukraine, Kiev, Ukraine.
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39
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Sulchek TA, Friddle RW, Langry K, Lau EY, Albrecht H, Ratto TV, DeNardo SJ, Colvin ME, Noy A. Dynamic force spectroscopy of parallel individual Mucin1-antibody bonds. Proc Natl Acad Sci U S A 2005; 102:16638-43. [PMID: 16269547 PMCID: PMC1276867 DOI: 10.1073/pnas.0505208102] [Citation(s) in RCA: 153] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2005] [Indexed: 01/15/2023] Open
Abstract
We used atomic force microscopy to measure the binding forces between Mucin1 (MUC1) peptide and a single-chain variable fragment (scFv) antibody selected from a scFv library screened against MUC1. This binding interaction is central to the design of molecules used for targeted delivery of radioimmunotherapeutic agents for prostate and breast cancer treatment. Our experiments separated the specific binding interaction from nonspecific interactions by tethering the antibody and MUC1 molecules to the atomic force microscope tip and sample surface with flexible polymer spacers. Rupture force magnitude and elastic characteristics of the spacers allowed identification of the rupture events corresponding to different numbers of interacting proteins. We used dynamic force spectroscopy to estimate the intermolecular potential widths and equivalent thermodynamic off rates for monovalent, bivalent, and trivalent interactions. Measured interaction potential parameters agree with the results of molecular docking simulation. Our results demonstrate that an increase of the interaction valency leads to a precipitous decline in the dissociation rate. Binding forces measured for monovalent and multivalent interactions match the predictions of a Markovian model for the strength of multiple uncorrelated bonds in a parallel configuration. Our approach is promising for comparison of the specific effects of molecular modifications as well as for determination of the best configuration of antibody-based multivalent targeting agents.
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Affiliation(s)
- Todd A Sulchek
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
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40
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Monsellier E, Bedouelle H. Quantitative measurement of protein stability from unfolding equilibria monitored with the fluorescence maximum wavelength. Protein Eng Des Sel 2005; 18:445-56. [PMID: 16087653 DOI: 10.1093/protein/gzi046] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The fluorescence of tryptophan is used as a signal to monitor the unfolding of proteins, in particular the intensity of fluorescence and the wavelength of its maximum lambda(max). The law of the signal is linear with respect to the concentrations of the reactants for the intensity but not for lambda(max). Consequently, the stability of a protein and its variation upon mutation cannot be deduced directly from measurements made with lambda(max). Here, we established a rigorous law of the signal for lambda(max). We then compared the stability DeltaG(H(2)O) and coefficient of cooperativity m for a two-state equilibrium of unfolding, monitored with lambda(max), when the rigorous and empirical linear laws of the signal are applied. The corrective terms involve the curvature of the emission spectra at their lambda(max) and can be determined experimentally. The rigorous and empirical values of the cooperativity coefficient m are equal within the experimental error for this parameter. In contrast, the rigorous and empirical values of the stability DeltaG(H(2)O) generally differ. However, they are equal within the experimental error if the curvatures of the spectra for the native and unfolded states are identical. We validated this analysis experimentally using domain 3 of the envelope glycoprotein of the dengue virus and the single-chain variable fragment (scFv) of antibody mAbD1.3, directed against lysozyme.
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Affiliation(s)
- Elodie Monsellier
- Unit of Molecular Prevention and Therapy of Human Diseases (CNRS FRE 2849), Institut Pasteur, 28 rue Docteur Roux, 75724 Paris Cedex 15, France
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41
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Nishi K, Ishiuchi M, Morimune K, Ohkawa H. Molecular and immunochemical characteristics of monoclonal and recombinant antibodies selective for the triazine herbicide simetryn and application to environmental analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2005; 53:5096-104. [PMID: 15969481 DOI: 10.1021/jf050246t] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
A monoclonal antibody (mab) selective for the thiomethyl-s-triazine herbicide simetryn was obtained and characterized in enzyme-linked immunosorbent assay (ELISA). An IC(50) value for simetryn was 8.5 ng/mL, and the detection range extended from 1.1 to 70 ng/mL in ELISA. The cDNAs encoding variable heavy chain (VH) and variable light chain (VL) of the mab were cloned to produce various recombinant antibodies. Single-chain variable fragment (scFv) antibodies derived from the mab were characterized in ELISA and showed similar reactivities and specificities to the parent mab. A urea denaturation test revealed that the scFv antibodies bound to simetryn were more stable than those in the absence of antigen. A sandwich ELISA based on VH and VL fragments of the mab was successfully developed and showed similar sensitivity to those based on the mab and scFv antibodies in ELISA. In the recovery experiments using spiked environmental samples, the results obtained in ELISA based on the mab were favorably correlated with those by HPLC.
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Affiliation(s)
- Kosuke Nishi
- Research Center for Environmental Genomics, Kobe University, Japan.
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42
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Brockmann EC, Cooper M, Strömsten N, Vehniäinen M, Saviranta P. Selecting for antibody scFv fragments with improved stability using phage display with denaturation under reducing conditions. J Immunol Methods 2005; 296:159-70. [PMID: 15680160 DOI: 10.1016/j.jim.2004.11.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2004] [Revised: 10/27/2004] [Accepted: 11/11/2004] [Indexed: 11/27/2022]
Abstract
Stability of single-chain Fvs (scFvs) can be improved by mutagenesis followed by phage display selection where the unstable variants are first inactivated by, for example, denaturing treatment. Here we describe a modified strategy for the selection of stabilized antibody fragments by phage display, based on denaturation under reducing conditions. This strategy was applied to an anti-thyroid-stimulating hormone (TSH) scFv fragment which refolded remarkably during the selection if denaturation was carried out in conventionally used non-reducing conditions. Refolding was, however, efficiently prevented by combining denaturation with reduction of the intra-domain disulfide bridges, which created favourable conditions for selection of clones with improved stability. Using this strategy, scFv mutants with 8-9 degrees C improved thermal stability and 0.8-0.9 M improved stability for guanidinium chloride were found after 4-5 enrichment cycles. The most stable mutants selected contained either Lys(H)66Arg or Asn(H)52aSer mutations, which are known to stabilize other scFvs. Periplasmic expression level of the mutants was also improved.
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Affiliation(s)
- Eeva-Christine Brockmann
- Department of Biotechnology, University of Turku, Tykistökatu 6A 6th floor, FIN-20520 Turku, Finland.
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43
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Petrov K, Dion M, Hoffmann L, Dintinger T, Defontaine A, Tellier C. Bivalent Fv antibody fragments obtained by substituting the constant domains of a fab fragment with heterotetrameric molybdopterin synthase. J Mol Biol 2004; 341:1039-48. [PMID: 15328616 DOI: 10.1016/j.jmb.2004.06.075] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2004] [Revised: 06/16/2004] [Accepted: 06/18/2004] [Indexed: 11/30/2022]
Abstract
The antibody Fv fragment is the smallest functional unit of an antibody but for practical use, the VH/VL interface requires stabilization, which is usually accomplished by a peptide linker that joins the two variable domains to form a single chain Fv fragment (scFv). An alternative format to scFv is proposed that (i) allows stabilization of the Fv fragment, and (ii) restores the bivalency of the antibody as a pseudo-F(ab')2 format. This new antibody fragment was constructed by replacing the CHI and CL domains of the Fab fragment with heterotetrameric molybdopterin synthase (MPTS). We found that this format, named MoaFv, improved significantly the cytoplasmic expression of the Fv as a soluble protein in BL21 or Origami Escherichia coli strains. This MoaFv format is expressed as a homogeneous heterotetrameric protein with a Mr value of 110 kDa containing two functional binding sites as revealed by active site titration. In its native condition at 37 degrees C or in the presence of urea, this format was nearly as stable as the corresponding scFv, indicating that non-covalent interactions between the MPTS subunits can replace the covalent peptide linker in scFv. Finally, this MoaFv construct could be a useful format when bivalency is desirable to improve the functional avidity.
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Affiliation(s)
- Kliment Petrov
- UMR-CNRS n degrees 6204, Biotechnoligie, Biocatalyse et Bioréegulation, Nates cedex, France
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44
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Colby DW, Garg P, Holden T, Chao G, Webster JM, Messer A, Ingram VM, Wittrup KD. Development of a Human Light Chain Variable Domain (VL) Intracellular Antibody Specific for the Amino Terminus of Huntingtin via Yeast Surface Display. J Mol Biol 2004; 342:901-12. [PMID: 15342245 DOI: 10.1016/j.jmb.2004.07.054] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2004] [Revised: 07/16/2004] [Accepted: 07/16/2004] [Indexed: 11/26/2022]
Abstract
Intracellular antibodies (intrabodies) provide an attractive means for manipulating intracellular protein function, both for research and potentially for therapy. A challenge in the isolation of effective intrabodies is the ability to find molecules that exhibit sufficient binding affinity and stability when expressed in the reducing environment of the cytoplasm. Here, we have used yeast surface display of proteins to isolate novel scFv clones against huntingtin from a non-immune human antibody library. We then applied yeast surface display to affinity mature this scFv pool and analyze the location of the binding site of the mutant with the highest affinity. Interestingly, the paratope was mapped exclusively to the variable light chain domain of the scFv. A single domain antibody was constructed consisting solely of this variable light chain domain, and was found to retain full binding activity to huntingtin. Cytoplasmic expression levels in yeast of the single domain were at least fivefold higher than the scFv. The ability of the single-domain intrabody to inhibit huntingtin aggregation, which has been implicated in the pathogenesis of Huntington's disease (HD), was confirmed in a cell-free in vitro assay as well as in a mammalian cell culture model of HD. Significantly, a single-domain intrabody that is functionally expressable in the cytoplasm was derived from a non-functional scFv by performing affinity maturation and binding site analysis on the yeast cell surface, despite the differences between the cytoplasmic and extracellular environment. This approach may find application in the development of intrabodies to a wide variety of intracellular targets.
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Affiliation(s)
- David W Colby
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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45
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Kipriyanov SM, Moldenhauer G, Braunagel M, Reusch U, Cochlovius B, Le Gall F, Kouprianova OA, Von der Lieth CW, Little M. Effect of domain order on the activity of bacterially produced bispecific single-chain Fv antibodies. J Mol Biol 2003; 330:99-111. [PMID: 12818205 DOI: 10.1016/s0022-2836(03)00526-6] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bispecific single-chain Fv antibodies comprise four covalently linked immunoglobulin variable (VH and VL) domains of two different specificities. Depending on the order of the VH and VL domains and on the length of peptides separating them, the single-chain molecule either forms two single-chain Fv (scFv) modules from the adjacent domains of the same specificity, a so-called scFv-scFv tandem [(scFv)(2)], or folds head-to-tail with the formation of a diabody-like structure, a so-called bispecific single-chain diabody (scBsDb). We generated a number of four-domain constructs composed of the same VH and VL domains specific either for human CD19 or CD3, but arranged in different orders. When expressed in bacteria, all (scFv)(2) variants appeared to be only half-functional, binding to CD19 and demonstrating no CD3-binding activity. Only the diabody-like scBsDb could bind both antigens. Comparison of the scBsDb with a structurally similar non-covalent dimer (diabody) demonstrated a stabilizing effect of the linker in the middle of the scBsDb molecule. We demonstrated that the mechanism of inactivation of CD19xCD3 diabody under physiological conditions is initiated by a dissociation of the weaker (anti-CD3) VH/VL interface followed by domain swapping with the formation of non-active homodimers. The instability of one homodimer makes the process of diabody dissociation/reassociation irreversible, thus gradually decreasing the fraction of active molecules. The structural parameters influencing the formation of functional bispecific single-chain antibodies are indicated and ways of making relatively stable bispecific molecules are proposed.
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Affiliation(s)
- Sergey M Kipriyanov
- Recombinant Antibody Research Group, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany.
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46
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Ewert S, Honegger A, Plückthun A. Structure-based improvement of the biophysical properties of immunoglobulin VH domains with a generalizable approach. Biochemistry 2003; 42:1517-28. [PMID: 12578364 DOI: 10.1021/bi026448p] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In a systematic study of V gene families carried out with consensus V(H) and V(L) domains alone and in combinations in the scFv format, we found comparatively low expression yields and lower cooperativity in equilibrium unfolding in antibody fragments containing V(H) domains of human germline families 2, 4, and 6. From an analysis of the packing of the hydrophobic core, the completeness of charge clusters, the occurrence of unsatisfied hydrogen bonds, and residues with low beta-sheet propensities, positive Phi angles, and exposed hydrophobic side chains, we pinpointed residues potentially responsible for the unsatisfactory properties of these germline-encoded sequences. Several of those are in common between the domains of the even-numbered subgroups, but do not occur in the odd-numbered ones. In this study, we have systematically exchanged those residues alone and in combination in two different scFvs using the V(H)6 framework, and we describe their effect on equilibrium stability and folding yield. We improved the stability by 20.9 kJ/mol and the expression yield by a factor of 4 and can now use these data to rationally engineer antibodies derived from this and similar germline families for better biophysical properties. Furthermore, we provide an improved design for libraries exploiting the significant additional diversity provided by these frameworks. Both antibodies studied here completely retain their binding affinity, demonstrating that the CDR conformations were not affected.
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Affiliation(s)
- Stefan Ewert
- Biochemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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Abstract
There are great demands on the stability, expression yield and resistance to aggregation of antibody fragments. To untangle intrinsic domain effects from domain interactions, we present first a systematic evaluation of the isolated human immunoglobulin variable heavy (V(H)) and light (V(L)) germline family consensus domains and then a systematic series of V(H)-V(L) combinations in the scFv format. The constructs were evaluated in terms of their expression behavior, oligomeric state in solution and denaturant-induced unfolding equilibria under non-reducing conditions. The seven V(H) and seven V(L) domains represent the consensus sequences of the major human germline subclasses, derived from the Human Combinatorial Antibody Library (HuCAL). The isolated V(H) and V(L) domains with the highest thermodynamic stability and yield of soluble protein were V(H)3 and V(kappa)3, respectively. Similar measurements on all domain combinations in scFv fragments allowed the scFv fragments to be classified according to thermodynamic stability and in vivo folding yield. The scFv fragments containing the variable domain combinations H3kappa3, H1bkappa3, H5kappa3 and H3kappa1 show superior properties concerning yield and stability. Domain interactions diminish the intrinsic differences of the domains. ScFv fragments containing V(lambda) domains show high levels of stability, even though V(lambda) domains are surprisingly unstable by themselves. This is due to a strong interaction with the V(H) domain and depends on the amino acid sequence of the CDR-L3. On the basis of these analyses and model structures, we suggest possibilities for further improvement of the biophysical properties of individual frameworks and give recommendations for library design.
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Affiliation(s)
- Stefan Ewert
- Biochemisches Institut, Universität Zürich, Winterthurerstr 190, CH-8057 Zürich, Switzerland
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Pedroso I, Irún MP, Machicado C, Sancho J. Four-state equilibrium unfolding of an scFv antibody fragment. Biochemistry 2002; 41:9873-84. [PMID: 12146953 DOI: 10.1021/bi025742e] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The conformational stability of a single-chain Fv antibody fragment against a hepatitis B surface antigen (anti-HBsAg scFv) has been studied by urea and temperature denaturation followed by fluorescence and circular dichroism. At neutral pH and low protein concentration, it is a well-folded monomer, and its urea and thermal denaturations are reversible. The noncoincidence of the fluorescence and circular dichroism transitions indicates the accumulation in the urea denaturation of an intermediate (I(1)) not previously described in scFv molecules. In addition, at higher urea concentrations, a red-shift in the fluorescence emission maximum reveals an additional intermediate (I(2)), already reported in the denaturation of other scFvs. The urea equilibrium unfolding of the anti-HBsAg scFv is thus four-state. A similar four-state behavior is observed in the thermal unfolding although the intermediates involved are not identical to those found in the urea denaturation. Global analysis of the thermal unfolding data suggests that the first intermediate displays substantial secondary structure and some well-defined tertiary interactions while the second one lacks well-defined tertiary interactions but is compact and unfolds at higher temperature in a noncooperative fashion. Global analysis of the urea unfolding data (together with the modeled structure of the scFv) provides insights into the conformation of the chemical denaturation intermediates and allows calculation of the N-I(1), I(1)-I(2), and I(2)-D free energy differences. Interestingly, although the N-D free energy difference is very large, the N-I(1) one, representing the "relevant" conformational stability of the scFv, is small.
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Affiliation(s)
- Idolka Pedroso
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain
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Hoyer W, Ramm K, Plückthun A. A kinetic trap is an intrinsic feature in the folding pathway of single-chain Fv fragments. Biophys Chem 2002; 96:273-84. [PMID: 12034446 DOI: 10.1016/s0301-4622(02)00022-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have studied the equilibrium unfolding and the kinetics of folding and unfolding of an antibody scFv fragment devoid of cis-prolines. An anti-GCN4 scFv fragment carrying a VL lambda domain, obtained by ribosome display, served as the model system together with an engineered destabilized mutant in VH carrying the R66K exchange. Kinetic and equilibrium unfolding experiments indicate that the VH mutation also affects VL unfolding, possibly by partially destabilizing the interface provided by VH, even though the mutation is distant from the interface. Upon folding of the scFv fragment, a kinetic trap is populated whose escape rate is much faster with the more stable VH domain. The formation of the trap can be avoided if refolding is carried out stepwise, with VH folding first. These results show that antibody scFv fragments do not fold by the much faster independent domain folding, but instead form a kinetically trapped off-pathway intermediate, which slows down folding under native conditions. This intermediate is characterized by premature interaction of the unfolded domains, and particularly involving unfolded VH, independent of proline cis-trans isomerization in VL. This work also implies that VH should be a prime target in engineering well behaving antibody fragments.
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Affiliation(s)
- Wolfgang Hoyer
- Biochemisches Institut, Universität Zürich, Zürich, Switzerland
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Ewert S, Cambillau C, Conrath K, Plückthun A. Biophysical properties of camelid V(HH) domains compared to those of human V(H)3 domains. Biochemistry 2002; 41:3628-36. [PMID: 11888279 DOI: 10.1021/bi011239a] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Camelidae possess an unusual form of antibodies lacking the light chains. The variable domain of these heavy chain antibodies (V(HH)) is not paired, while the V(H) domain of all other antibodies forms a heterodimer with the variable domain of the light chain (V(L)), held together by a hydrophobic interface. Here, we analyzed the biophysical properties of four camelid V(HH) fragments (H14, AMD9, RN05, and CA05) and two human consensus V(H)3 domains with different CDR3 loops to gain insight into factors determining stability and aggregation of immunoglobulin domains. We show by denaturant-induced unfolding equilibria that the free energies of unfolding of V(HH) fragments are characterized by Delta G(N-U) values between 21.1 and 35.0 kJ/mol and thus lie in the upper range of values for V(H) fragments from murine and human antibodies. Nevertheless, the V(HH) fragments studied here did not reach the high values between 39.7 and 52.7 kJ/mol of the human consensus V(H)3 domains with which they share the highest degree of sequence similarity. Temperature-induced unfolding of the V(HH) fragments that were studied proved to be reversible, and the binding affinity after cooling was fully retained. The melting temperatures were determined to be between 60.1 and 66.7 degrees C. In contrast, the studied V(H)3 domains aggregated during temperature-induced denaturation at 63-65 degrees C. In summary, the camelid V(HH) fragments are characterized by a favorable but not unusually high stability. Their hallmark is the ability to reversibly melt without aggregation, probably mediated by the surface mutations characterizing the V(HH) domains, which allow them to regain binding activity after heat renaturation.
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Affiliation(s)
- Stefan Ewert
- Biochemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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