1
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Filippova TA, Masamrekh RA, Khudoklinova YY, Shumyantseva VV, Kuzikov AV. The multifaceted role of proteases and modern analytical methods for investigation of their catalytic activity. Biochimie 2024; 222:169-194. [PMID: 38494106 DOI: 10.1016/j.biochi.2024.03.006] [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: 09/25/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/19/2024]
Abstract
We discuss the diverse functions of proteases in the context of their biotechnological and medical significance, as well as analytical approaches used to determine the functional activity of these enzymes. An insight into modern approaches to studying the kinetics and specificity of proteases, based on spectral (absorption, fluorescence), mass spectrometric, immunological, calorimetric, and electrochemical methods of analysis is given. We also examine in detail electrochemical systems for determining the activity and specificity of proteases. Particular attention is given to exploring innovative electrochemical systems based on the detection of the electrochemical oxidation signal of amino acid residues, thereby eliminating the need for extra redox labels in the process of peptide synthesis. In the review, we highlight the main prospects for the further development of electrochemical systems for the study of biotechnologically and medically significant proteases, which will enable the miniaturization of the analytical process for determining the catalytic activity of these enzymes.
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Affiliation(s)
- Tatiana A Filippova
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Rami A Masamrekh
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Yulia Yu Khudoklinova
- Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Victoria V Shumyantseva
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia
| | - Alexey V Kuzikov
- Institute of Biomedical Chemistry, 10 bld. 8, Pogodinskaya str., 119121, Moscow, Russia; Pirogov Russian National Research Medical University, 1, Ostrovityanova Street, Moscow, 117513, Russia.
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2
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Tungekar AA, Ruddock LW. Design of an alternate antibody fragment format that can be produced in the cytoplasm of Escherichia coli. Sci Rep 2023; 13:14188. [PMID: 37648872 PMCID: PMC10469194 DOI: 10.1038/s41598-023-41525-3] [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: 05/23/2023] [Accepted: 08/28/2023] [Indexed: 09/01/2023] Open
Abstract
With increased accessibility and tissue penetration, smaller antibody formats such as antibody fragments (Fab) and single chain variable fragments (scFv) show potential as effective and low-cost choices to full-length antibodies. These formats derived from the modular architecture of antibodies could prove to be game changers for certain therapeutic and diagnostic applications. Microbial hosts have shown tremendous promise as production hosts for antibody fragment formats. However, low target protein yields coupled with the complexity of protein folding result in production limitations. Here, we report an alternative antibody fragment format 'FabH3' designed to overcome some key bottlenecks associated with the folding and production of Fabs. The FabH3 molecule is based on the Fab format with the constant domains replaced by engineered immunoglobulin G1 (IgG1) CH3 domains capable of heterodimerization based on the electrostatic steering approach. We show that this alternative antibody fragment format can be efficiently produced in the cytoplasm of E. coli using the catalyzed disulfide-bond formation system (CyDisCo) in a natively folded state with higher soluble yields than its Fab counterpart and a comparable binding affinity against the target antigen.
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Affiliation(s)
- Aatir A Tungekar
- Protein and Structural Biology Research Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220, Oulu, Finland
| | - Lloyd W Ruddock
- Protein and Structural Biology Research Unit, Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220, Oulu, Finland.
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3
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Wu SY, Wu FG, Chen X. Antibody-Incorporated Nanomedicines for Cancer Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2109210. [PMID: 35142395 DOI: 10.1002/adma.202109210] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/06/2022] [Indexed: 06/14/2023]
Abstract
Antibody-based cancer therapy, one of the most significant therapeutic strategies, has achieved considerable success and progress over the past decades. Nevertheless, obstacles including limited tumor penetration, short circulation half-lives, undesired immunogenicity, and off-target side effects remain to be overcome for the antibody-based cancer treatment. Owing to the rapid development of nanotechnology, antibody-containing nanomedicines that have been extensively explored to overcome these obstacles have already demonstrated enhanced anticancer efficacy and clinical translation potential. This review intends to offer an overview of the advancements of antibody-incorporated nanoparticulate systems in cancer treatment, together with the nontrivial challenges faced by these next-generation nanomedicines. Diverse strategies of antibody immobilization, formats of antibodies, types of cancer-associated antigens, and anticancer mechanisms of antibody-containing nanomedicines are provided and discussed in this review, with an emphasis on the latest applications. The current limitations and future research directions on antibody-containing nanomedicines are also discussed from different perspectives to provide new insights into the construction of anticancer nanomedicines.
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Affiliation(s)
- Shun-Yu Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou Road, Nanjing, 210096, P. R. China
| | - Fu-Gen Wu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou Road, Nanjing, 210096, P. R. China
| | - Xiaoyuan Chen
- Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, Singapore, 119077, Singapore
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4
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Mehta D, Chirmade T, Tungekar AA, Gani K, Bhambure R. Cloning and expression of antibody fragment (Fab) I: Effect of expression construct and induction strategies on light and heavy chain gene expression. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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5
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Zhang L, Wang Z, Wang Z, Luo F, Guan M, Xu M, Li Y, Zhang Y, Wang Z, Wang W. A Simple and Efficient Method to Generate Dual Site-Specific Conjugation ADCs with Cysteine Residue and an Unnatural Amino Acid. Bioconjug Chem 2021; 32:1094-1104. [PMID: 34013721 DOI: 10.1021/acs.bioconjchem.1c00134] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Antibody-drug conjugates (ADCs) are complex pharmaceutical molecules that combine monoclonal antibodies with biologically active drugs through chemical linkers. ADCs are designed to specifically kill disease cells by utilizing the target specificity of antibodies and the cytotoxicity of chemical drugs. However, the traditional ADCs were only applied to a few disease targets because of some limitations such as the huge molecular weight, the uncontrollable coupling reactions, and a single mechanism of action. Here we report a simple, one-pot, successive reaction method to produce dual payload conjugates with the site-specifically engineered cysteine and p-acetyl-phenylalanine using Herceptin (trastuzumab), an anti-HER2 antibody drug widely used for breast cancer treatment, as a tool molecule. This strategy enables antibodies to conjugate with two mechanistically distinct cytotoxic drugs through different functional groups sequentially, therefore, rendering the newly designed ADCs with functional diversity and the potential to overcome drug resistance and enhance the therapeutic efficacy.
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Affiliation(s)
- Lin Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zewei Wang
- Interdisciplinary Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyuan Wang
- Interdisciplinary Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Luo
- Interdisciplinary Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingfeng Guan
- Interdisciplinary Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meimei Xu
- Interdisciplinary Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yundong Li
- Interdisciplinary Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaoyang Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaoyin Wang
- Interdisciplinary Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenyuan Wang
- Interdisciplinary Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Department of Rehabilitation Medicine, Huashan Hospital, Fudan University, Shanghai 200040, China
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Abstract
In the past 30 years, highly specific drugs, known as antibodies, have conquered the biopharmaceutical market. In addition to monoclonal antibodies (mAbs), antibody fragments are successfully applied. However, recombinant production faces challenges. Process analytical tools for monitoring and controlling production processes are scarce and time-intensive. In the downstream process (DSP), affinity ligands are established as the primary and most important step, while the application of other methods is challenging. The use of these affinity ligands as monitoring tools would enable a platform technology to monitor process steps in the USP and DSP. In this review, we highlight the current applications of affinity ligands (proteins A, G, and L) and discuss further applications as process analytical tools.
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7
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Rosenstein S, Vaisman-Mentesh A, Levy L, Kigel A, Dror Y, Wine Y. Production of F(ab') 2 from Monoclonal and Polyclonal Antibodies. ACTA ACUST UNITED AC 2020; 131:e119. [PMID: 32319727 DOI: 10.1002/cpmb.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Antibodies are widely used in therapeutic, diagnostic, and research applications, and antibody derivatives such as F(ab')2 fragments are used when only a particular antibody region is required. F(ab')2 can be produced through antibody engineering, but some applications require F(ab')2 produced from an original formulated antibody or directly from a polyclonal antibody pool. The cysteine protease immunoglobulin-degrading enzyme (IdeS) from Streptococcus pyogenes digests immunoglobulin G (IgG) specifically and efficiently to produce F(ab')2 . Here we detail the production and purification of recombinant IdeS; its utilization to digest monoclonal or polyclonal antibodies to F(ab')2 fragments; and F(ab')2 purification through consecutive affinity chromatography steps. The resultant F(ab')2 exhibit high purity, retain antigen-binding functionality, and are readily utilizable in various downstream applications. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Production and purification of F(ab')2 fragments from monoclonal and polyclonal antibodies using IdeS Alternate Protocol: Purification of polyclonal antigen-specific F(ab')2 fragments from human serum or secretions Support Protocol: Production and purification of IdeS.
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Affiliation(s)
- Shai Rosenstein
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Anna Vaisman-Mentesh
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Limor Levy
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Aya Kigel
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Yael Dror
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Yariv Wine
- School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
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8
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Canovas C, Bellaye PS, Moreau M, Romieu A, Denat F, Goncalves V. Site-specific near-infrared fluorescent labelling of proteins on cysteine residues with meso-chloro-substituted heptamethine cyanine dyes. Org Biomol Chem 2019; 16:8831-8836. [PMID: 30411777 DOI: 10.1039/c8ob02646g] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Near-infrared (NIR) fluorescence imaging is a promising new medical imaging modality. Associated with a targeting molecule, NIR fluorophores can accumulate selectively in tissues of interest and become valuable tools for the diagnosis and therapy of various pathologies. To facilitate the design of targeted NIR imaging agents, it is important to identify simple and affordable fluorescent probes, allowing rapid labelling of biovectors such as proteins, ideally in a site-specific manner. Here, we demonstrate that heptamethine cyanine based fluorophores, such as IR-783, that contain a chloro-cyclohexyl moiety within their polymethine chain can react selectively, at neutral pH, with cysteine residues in proteins to give stable, site-specifically labelled conjugates, that emit in the NIR spectral window. This reaction is exemplified with the labelling of peptides and two protein models: albumin and a Fab' antibody fragment. The resulting fluorescent proteins are stable and suitable for in vivo NIR imaging applications, as shown on a mice model. This straightforward one-step procedure, that does not require the prior derivatisation of the fluorophore with a bioconjugatable handle, should facilitate the production and use of near-infrared labelled proteins in life sciences.
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Affiliation(s)
- Coline Canovas
- Institut de Chimie Moléculaire de l'Université de Bourgogne, UMR6302, CNRS, Université Bourgogne Franche-Comté, 9 avenue Alain Savary, 21000, Dijon, France.
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9
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Assessment of the higher order structure of Humira®, Remicade®, Avastin®, Rituxan®, Herceptin®, and Enbrel® by 2D-NMR fingerprinting. J Pharm Biomed Anal 2018; 163:144-152. [PMID: 30296716 DOI: 10.1016/j.jpba.2018.09.056] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 09/26/2018] [Accepted: 09/30/2018] [Indexed: 01/14/2023]
Abstract
The advent of monoclonal antibody biosimilar products has stimulated the development of analytical methods that can better characterize an important quality attribute, namely the higher order structure (HOS). Here, we propose a simple approach based on heteronuclear 2D NMR techniques at natural abundance for generating spectral fingerprints of the HOS at high resolution. We show that the proposed method can assess the HOS of six therapeutic products, adalimumab (Humira®), bevacizumab (Avastin®), infliximab (Remicade®), rituximab (Rituxan®), trastuzumab (Herceptin®), and Etanercept (Enbrel®). After treatment with immobilized papain, the purified fragments (Fab and Fc) were analyzed by 2D proton-nitrogen and proton-carbon NMR correlations. All Fab and Fc fragments produced high-resolution 2D-NMR spectra from which assessment of their higher order structure can be performed in the context of comparability studies. In particular, the two different sequences of Fc fragments could be unambiguously distinguished. The results show that it is possible to obtain structurally dependent information at amino acid resolution of these important therapeutic agents.
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10
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Bruce VJ, Ta AN, McNaughton BR. Minimalist Antibodies and Mimetics: An Update and Recent Applications. Chembiochem 2016; 17:1892-1899. [DOI: 10.1002/cbic.201600303] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Virginia J. Bruce
- Department of Chemistry; Colorado State University; Fort Collins CO 80523 USA
| | - Angeline N. Ta
- Department of Chemistry; Colorado State University; Fort Collins CO 80523 USA
| | - Brian R. McNaughton
- Department of Chemistry; Colorado State University; Fort Collins CO 80523 USA
- Department of Biochemistry and Molecular Biology; Colorado State University; Fort Collins CO 80523 USA
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11
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Jiang L, Yang M, Zhang X, Bao S, Ma L, Fan D, Zhou Y, Xiong D, Zhen Y. A novel antibody-drug conjugate anti-CD19(Fab)-LDM in the treatment of B-cell non-Hodgkin lymphoma xenografts with enhanced anticancer activity. J Drug Target 2015. [PMID: 26204323 DOI: 10.3109/1061186x.2015.1055568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Rituximab is widely used in clinical setting for the treatment of B malignant lymphoma and has achieved remarkable success. However, in most patients, the disease ultimately relapses and become resistant to rituximab. To overcome the limitation, there is still a need to find novel strategy for improving therapeutic efficacy. OBJECTIVE To construct genetically engineered antibody anti-CD19(Fab)-LDM, and verify the anticancer activity targeted toward B-lymphoma. METHODS The anticancer activity of anti-CD19(Fab)-LDM in vitro and in vivo was examined. In vitro, the binding activity and internalization of anti-CD19(Fab)-LDP were measured. Using comet assay and apoptosis, the cytotoxicity of energized fusion proteins was observed. From in vivo experiments, targeting of therapeutic effect and anticancer efficacy bythe fusion protein was verified. RESULTS Data showed that anti-CD19(Fab)-LDM does not only binding the cell surface but is also internalized into the cell. The energized fusion proteins anti-CD19(Fab)-LDM can induce DNA damage. Furthermore, significant in vivo therapeutic efficacy was observed. CONCLUSION The present study demonstrated that the genetically engineered antibody anti-CD19(Fab)-LDM exhibited enhanced cytotoxicity compared to LDM alone. One of the most powerful advantages of anti-CD19(Fab)-LDM, however, is that it can be internalized within the cells and carry out cytotoxic effects. Therefore, anti-CD19(Fab)-LDM may be as a useful targeted therapy for B-cell lymphoma.
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Affiliation(s)
- Linlin Jiang
- a State key Laboratory of Experimental Hematology, Institute of Hematology and Hospital of Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College , China and
| | - Ming Yang
- a State key Laboratory of Experimental Hematology, Institute of Hematology and Hospital of Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College , China and
| | - Xiaoyun Zhang
- a State key Laboratory of Experimental Hematology, Institute of Hematology and Hospital of Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College , China and
| | - Shiqi Bao
- a State key Laboratory of Experimental Hematology, Institute of Hematology and Hospital of Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College , China and
| | - Li Ma
- a State key Laboratory of Experimental Hematology, Institute of Hematology and Hospital of Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College , China and
| | - Dongmei Fan
- a State key Laboratory of Experimental Hematology, Institute of Hematology and Hospital of Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College , China and
| | - Yuan Zhou
- a State key Laboratory of Experimental Hematology, Institute of Hematology and Hospital of Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College , China and
| | - Dongsheng Xiong
- a State key Laboratory of Experimental Hematology, Institute of Hematology and Hospital of Blood Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College , China and
| | - Yongsu Zhen
- b Department of Oncology , Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College , China
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12
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Research applications of proteolytic enzymes in molecular biology. Biomolecules 2013; 3:923-42. [PMID: 24970197 PMCID: PMC4030975 DOI: 10.3390/biom3040923] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 11/04/2013] [Accepted: 11/06/2013] [Indexed: 01/04/2023] Open
Abstract
Proteolytic enzymes (also termed peptidases, proteases and proteinases) are capable of hydrolyzing peptide bonds in proteins. They can be found in all living organisms, from viruses to animals and humans. Proteolytic enzymes have great medical and pharmaceutical importance due to their key role in biological processes and in the life-cycle of many pathogens. Proteases are extensively applied enzymes in several sectors of industry and biotechnology, furthermore, numerous research applications require their use, including production of Klenow fragments, peptide synthesis, digestion of unwanted proteins during nucleic acid purification, cell culturing and tissue dissociation, preparation of recombinant antibody fragments for research, diagnostics and therapy, exploration of the structure-function relationships by structural studies, removal of affinity tags from fusion proteins in recombinant protein techniques, peptide sequencing and proteolytic digestion of proteins in proteomics. The aim of this paper is to review the molecular biological aspects of proteolytic enzymes and summarize their applications in the life sciences.
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13
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Nettleship JE, Ren J, Scott DJ, Rahman N, Hatherley D, Zhao Y, Stuart DI, Barclay AN, Owens RJ. Crystal structure of signal regulatory protein gamma (SIRPγ) in complex with an antibody Fab fragment. BMC STRUCTURAL BIOLOGY 2013; 13:13. [PMID: 23826770 PMCID: PMC3716694 DOI: 10.1186/1472-6807-13-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 06/24/2013] [Indexed: 11/28/2022]
Abstract
BACKGROUND Signal Regulatory Protein γ (SIRPγ) is a member of a closely related family of three cell surface receptors implicated in modulating immune/inflammatory responses. SIRPγ is expressed on T lymphocytes where it appears to be involved in the integrin-independent adhesion of lymphocytes to antigen-presenting cells. Here we describe the first full length structure of the extracellular region of human SIRPγ. RESULTS We obtained crystals of SIRPγ by making a complex of the protein with the Fab fragment of the anti-SIRP antibody, OX117, which also binds to SIRPα and SIRPβ. We show that the epitope for FabOX117 is formed at the interface of the first and second domains of SIRPγ and comprises residues which are conserved between all three SIRPs. The FabOX117 binding site is distinct from the region in domain 1 which interacts with CD47, the physiological ligand for both SIRPγ and SIRPα but not SIRPβ. Comparison of the three domain structures of SIRPγ and SIRPα showed that these receptors can adopt different overall conformations due to the flexibility of the linker between the first two domains. SIRPγ in complex with FabOX117 forms a dimer in the crystal. Binding to the Fab fixes the position of domain 1 relative to domains 2/3 exposing a surface which favours formation of a homotypic dimer. However, the interaction appears to be relatively weak since only monomers of SIRPγ were observed in sedimentation velocity analytical ultracentrifugation of the protein alone. Studies of complex formation by equilibrium ultracentrifugation showed that only a 1:1 complex of SIRPγ: FabOX117 was formed with a dissociation constant in the low micromolar range (Kd = 1.2 +/- 0.3 μM). CONCLUSION The three-domain extracellular regions of SIRPs are structurally conserved but show conformational flexibility in the disposition of the amino terminal ligand-binding Ig domain relative to the two membrane proximal Ig domains. Binding of a cross-reactive anti-SIRP Fab fragment to SIRPγ stabilises a conformation that favours SIRP dimer formation in the crystal structure, though this interaction does not appear sufficiently stable to be observed in solution.
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MESH Headings
- Antigen-Antibody Complex/chemistry
- Antigen-Antibody Complex/metabolism
- Antigens, Differentiation/chemistry
- Antigens, Differentiation/genetics
- Antigens, Differentiation/metabolism
- Binding Sites
- Crystallography, X-Ray
- Dimerization
- HEK293 Cells
- Humans
- Immunoglobulin Fab Fragments/chemistry
- Immunoglobulin Fab Fragments/genetics
- Immunoglobulin Fab Fragments/immunology
- Immunoglobulin Fab Fragments/metabolism
- Protein Structure, Tertiary
- Receptors, Cell Surface/chemistry
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/metabolism
- Receptors, Immunologic/chemistry
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Recombinant Proteins/biosynthesis
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Ultracentrifugation
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Affiliation(s)
- Joanne E Nettleship
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- OPPF-UK, The Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Oxfordshire OX11 0FA, UK
| | - Jingshan Ren
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - David J Scott
- The Research Complex at Harwell and ISIS Neutron and Muon source, Rutherford Appleton Laboratory, Harwell Oxford, Oxfordshire OX11 0FA, UK
- The School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire LE12 5RD, UK
| | - Nahid Rahman
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- OPPF-UK, The Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Oxfordshire OX11 0FA, UK
| | - Deborah Hatherley
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Yuguang Zhao
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - David I Stuart
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Diamond Light Sources, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - A Neil Barclay
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Raymond J Owens
- Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- OPPF-UK, The Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Oxfordshire OX11 0FA, UK
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14
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Recombinant Proteins and Immunotherapeutics. Mol Pharmacol 2012. [DOI: 10.1002/9781118451908.ch12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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15
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Kierny MR, Cunningham TD, Kay BK. Detection of biomarkers using recombinant antibodies coupled to nanostructured platforms. NANO REVIEWS 2012; 3:NANO-3-17240. [PMID: 22833780 PMCID: PMC3404449 DOI: 10.3402/nano.v3i0.17240] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 05/30/2012] [Accepted: 06/09/2012] [Indexed: 12/14/2022]
Abstract
The utility of biomarker detection in tomorrow's personalized health care field will mean early and accurate diagnosis of many types of human physiological conditions and diseases. In the search for biomarkers, recombinant affinity reagents can be generated to candidate proteins or post-translational modifications that differ qualitatively or quantitatively between normal and diseased tissues. The use of display technologies, such as phage-display, allows for manageable selection and optimization of affinity reagents for use in biomarker detection. Here we review the use of recombinant antibody fragments, such as scFvs and Fabs, which can be affinity-selected from phage-display libraries, to bind with both high specificity and affinity to biomarkers of cancer, such as Human Epidermal growth factor Receptor 2 (HER2) and Carcinoembryonic antigen (CEA). We discuss how these recombinant antibodies can be fabricated into nanostructures, such as carbon nanotubes, nanowires, and quantum dots, for the purpose of enhancing detection of biomarkers at low concentrations (pg/mL) within complex mixtures such as serum or tissue extracts. Other sensing technologies, which take advantage of 'Surface Enhanced Raman Scattering' (gold nanoshells), frequency changes in piezoelectric crystals (quartz crystal microbalance), or electrical current generation and sensing during electrochemical reactions (electrochemical detection), can effectively provide multiplexed platforms for detection of cancer and injury biomarkers. Such devices may soon replace the traditional time consuming ELISAs and Western blots, and deliver rapid, point-of-care diagnostics to market.
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Affiliation(s)
- Michael R Kierny
- Department of Biological Sciences, University of Illinois at Chicago (UIC), Chicago, IL, USA
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16
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Abstract
Antibody fragments (Fab's) represent important structure for creating new therapeutics. Compared to full antibodies Fab' fragments possess certain advantages, including higher mobility and tissue penetration, ability to bind antigen monovalently and lack of fragment crystallizable (Fc) region-mediated functions such as antibody-dependent cell mediated cytotoxicity (ADCC) or complement-dependent cytotoxicity (CDC). The main drawback for the use of Fab's in clinical applications is associated with their short half-life in vivo, which is a consequence of no longer having the Fc region. To exert meaningful clinical effects, the half-life of Fab's need to be extended, which has been achieved by postproduction chemical attachment of polyethylene glycol (PEG) chain to protein using PEGylation technology. The most suitable approach employs PEG-maleimide attachment to cysteines, either to the free hinge cysteine or to C-terminal cysteines involved in interchain disulfide linkage of the heavy and light chain. Hence, protocols for mono-PEGylation of Fab via free cysteine in the hinge region and di-PEGylation of Fab via interchain disulfide bridge are provided in this chapter.
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Affiliation(s)
- Simona Jevševar
- Sandoz Biopharmaceuticals, Mengeš, Lek Pharmaceuticals d.d, Mengeš, Slovenia.
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17
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Hofer T, Skeffington LR, Chapman CM, Rader C. Molecularly defined antibody conjugation through a selenocysteine interface. Biochemistry 2010; 48:12047-57. [PMID: 19894757 DOI: 10.1021/bi901744t] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Antibody conjugates have broad utility in basic, preclinical, and clinical applications. Conventional antibody conjugation through the amine group of lysine or the thiol group of cysteine residues yields heterogeneous products of undefined stoichiometry and considerable batch-to-batch variability. To preserve the two hallmarks of the antibody molecule, precision and predictability, methods that enable site-specific antibody conjugation are in high demand. On the basis of a mammalian cell expression system, we describe the utilization of the 21st natural amino acid selenocysteine for the generation of IgG and Fab molecules with unique nucleophilic reactivity that affords site-specific conjugation to electrophilic derivatives of biotin, fluorescein, and poly(ethylene glycol). The resulting antibody conjugates were found to fully retain their antigen binding capability and, in the case of IgG, the ability to mediate effector functions. Gain of function was demonstrated in vitro and in vivo. While these antibody conjugates are relevant for a variety of proteomic, diagnostic, and therapeutic applications, they also constitute a proof of principle for the generation of molecularly defined antibody-drug conjugates and radioimmunoconjugates. Compared to other site-specific antibody conjugation methods, selenocysteine interface technology (i) only involves a minor modification at the C-terminus that does not interfere with disulfide bridges, (ii) does not require activation, and (iii) generates unique 1:1 stoichiometries of biological and chemical components. Collectively, our method affords the generation of highly defined antibody conjugates with broad utility from proteomic applications to therapeutic intervention.
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Affiliation(s)
- Thomas Hofer
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-1203, USA
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Stahl SJ, Watts NR, Rader C, DiMattia MA, Mage RG, Palmer I, Kaufman JD, Grimes JM, Stuart DI, Steven AC, Wingfield PT. Generation and characterization of a chimeric rabbit/human Fab for co-crystallization of HIV-1 Rev. J Mol Biol 2010; 397:697-708. [PMID: 20138059 DOI: 10.1016/j.jmb.2010.01.061] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 01/25/2010] [Accepted: 01/26/2010] [Indexed: 11/30/2022]
Abstract
Rev is a key regulatory protein of human immunodeficiency virus type 1. Its function is to bind to viral transcripts and effect export from the nucleus of unspliced mRNA, thereby allowing the synthesis of structural proteins. Despite its evident importance, the structure of Rev has remained unknown, primarily because Rev's proclivity for polymerization and aggregation is an impediment to crystallization. Monoclonal antibody antigen-binding domains (Fabs) have proven useful for the co-crystallization of other refractory proteins. In the present study, a chimeric rabbit/human anti-Rev Fab was selected by phage display, expressed in a bacterial secretion system, and purified from the media. The Fab readily solubilized polymeric Rev. The resulting Fab/Rev complex was purified by metal ion affinity chromatography and characterized by analytical ultracentrifugation, which demonstrated monodispersity and indicated a 1:1 molar stoichiometry. The Fab binds with very high affinity, as determined by surface plasmon resonance, to a conformational epitope in the N-terminal half of Rev. The complex forms crystals suitable for structure determination. The ability to serve as a crystallization aid is a new application of broad utility for chimeric rabbit/human Fab. The corresponding single-chain antibody (scFv) was also prepared, offering the potential of intracellular antibody therapeutics against human immunodeficiency virus type 1.
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Affiliation(s)
- Stephen J Stahl
- Protein Expression Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892-2775, USA
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Enever C, Batuwangala T, Plummer C, Sepp A. Next generation immunotherapeutics--honing the magic bullet. Curr Opin Biotechnol 2009; 20:405-11. [PMID: 19709876 DOI: 10.1016/j.copbio.2009.07.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Accepted: 07/14/2009] [Indexed: 10/20/2022]
Abstract
Most therapeutic antibodies in the clinic today are based on fully humanised immunoglobulins. They have proven to be outstandingly effective, especially for the treatment of cancer, autoimmune and inflammatory diseases where the target is a single, well-defined and accessible molecule. Many diseases however are complex, involving multiple mediators or signalling pathways that could be targeted simultaneously to maximise clinical benefit. There is also a wealth of validated intracellular and CNS-based targets which are currently inaccessible to monoclonal antibody therapy. A spectrum of next generation immunotherapeutics is in development to address these issues and a number of them have also entered clinical trials.
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Affiliation(s)
- Carrie Enever
- Domantis Ltd, 315 Science Park, Cambridge CB4 0WG, UK.
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