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Mao M, Ahrens L, Luka J, Contreras F, Kurkina T, Bienstein M, Sárria Pereira de Passos M, Schirinzi G, Mehn D, Valsesia A, Desmet C, Serra MÁ, Gilliland D, Schwaneberg U. Material-specific binding peptides empower sustainable innovations in plant health, biocatalysis, medicine and microplastic quantification. Chem Soc Rev 2024; 53:6445-6510. [PMID: 38747901 DOI: 10.1039/d2cs00991a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Material-binding peptides (MBPs) have emerged as a diverse and innovation-enabling class of peptides in applications such as plant-/human health, immobilization of catalysts, bioactive coatings, accelerated polymer degradation and analytics for micro-/nanoplastics quantification. Progress has been fuelled by recent advancements in protein engineering methodologies and advances in computational and analytical methodologies, which allow the design of, for instance, material-specific MBPs with fine-tuned binding strength for numerous demands in material science applications. A genetic or chemical conjugation of second (biological, chemical or physical property-changing) functionality to MBPs empowers the design of advanced (hybrid) materials, bioactive coatings and analytical tools. In this review, we provide a comprehensive overview comprising naturally occurring MBPs and their function in nature, binding properties of short man-made MBPs (<20 amino acids) mainly obtained from phage-display libraries, and medium-sized binding peptides (20-100 amino acids) that have been reported to bind to metals, polymers or other industrially produced materials. The goal of this review is to provide an in-depth understanding of molecular interactions between materials and material-specific binding peptides, and thereby empower the use of MBPs in material science applications. Protein engineering methodologies and selected examples to tailor MBPs toward applications in agriculture with a focus on plant health, biocatalysis, medicine and environmental monitoring serve as examples of the transformative power of MBPs for various industrial applications. An emphasis will be given to MBPs' role in detecting and quantifying microplastics in high throughput, distinguishing microplastics from other environmental particles, and thereby assisting to close an analytical gap in food safety and monitoring of environmental plastic pollution. In essence, this review aims to provide an overview among researchers from diverse disciplines in respect to material-(specific) binding of MBPs, protein engineering methodologies to tailor their properties to application demands, re-engineering for material science applications using MBPs, and thereby inspire researchers to employ MBPs in their research.
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Affiliation(s)
- Maochao Mao
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Leon Ahrens
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Julian Luka
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Francisca Contreras
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Tetiana Kurkina
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Marian Bienstein
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | | | | | - Dora Mehn
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Andrea Valsesia
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Cloé Desmet
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | | | | | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
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2
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Jönsson M, Scheffel J, Larsson E, Möller M, Rossi G, Lundqvist M, Rockberg J, Uhlén M, Tegel H, Kanje S, Hober S. CaRA - A multi-purpose phage display library for selection of calcium-regulated affinity proteins. N Biotechnol 2022; 72:159-167. [PMID: 36450334 DOI: 10.1016/j.nbt.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 11/02/2022] [Accepted: 11/26/2022] [Indexed: 11/29/2022]
Abstract
Protein activity regulated by interactions with metal ions can be utilized for many different purposes, including biological therapies and bioprocessing, among others. Calcium ions are known to interact with the frequently occurring EF-hand motif, which can alter protein activity upon binding through an induced conformational change. The calcium-binding loop of the EF-hand motif has previously been introduced into a small protein domain derived from staphylococcal Protein A in a successful effort to render antibody binding dependent on calcium. Presented here, is a combinatorial library for calcium-regulated affinity, CaRA, based on this domain. CaRA is the first alternative scaffold library designed to achieve novel target specificities with metal-dependent binding. From this library, several calcium-dependent binders could be isolated through phage display campaigns towards a set of unrelated target proteins (IgE Cε3-Cε4, TNFα, IL23, scFv, tPA, PCSK9 and HER3) useful for distinct applications. Overall, these monomeric CaRA variants showed high stability and target affinities within the nanomolar range. They displayed considerably higher melting temperatures in the presence of 1 mM calcium compared to without calcium. Further, all discovered binders proved to be calcium-dependent, with the great majority showing complete lack of target binding in the absence of calcium. As demonstrated, the CaRA library is highly capable of providing protein-binding domains with calcium-dependent behavior, independent of the type of target protein. These binding domains could subsequently be of great use in gentle protein purification or as novel therapeutic modalities.
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Affiliation(s)
- Malin Jönsson
- Department of Protein Science, KTH-Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Julia Scheffel
- Department of Protein Science, KTH-Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Emma Larsson
- Department of Protein Science, KTH-Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Marit Möller
- Department of Protein Science, KTH-Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Gabriella Rossi
- Department of Protein Science, KTH-Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Magnus Lundqvist
- Department of Protein Science, KTH-Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Johan Rockberg
- Department of Protein Science, KTH-Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Mathias Uhlén
- Department of Protein Science, KTH-Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Hanna Tegel
- Department of Protein Science, KTH-Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Sara Kanje
- Department of Protein Science, KTH-Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Sophia Hober
- Department of Protein Science, KTH-Royal Institute of Technology, SE-10691 Stockholm, Sweden.
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3
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Lin WC, Tang HC, Wang HY, Kao CY, Chang YC, Li AH, Yang SB, Mou KY. Fragment-Directed Random Mutagenesis by the Reverse Kunkel Method. ACS Synth Biol 2022; 11:1658-1668. [PMID: 35324156 DOI: 10.1021/acssynbio.2c00086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Two fundamentally different approaches are routinely used for protein engineering: user-defined mutagenesis and random mutagenesis, each with its own strengths and weaknesses. Here, we invent a unique mutagenesis protocol, which combines the advantages of user-defined mutagenesis and random mutagenesis. The new method, termed the reverse Kunkel method, allows the user to create random mutations at multiple specified regions in a one-pot reaction. We demonstrated the reverse Kunkel method by mimicking the somatic hypermutation in antibodies that introduces random mutations concentrated in complementarity-determining regions. Coupling with the phage display and yeast display selections, we successfully generated dramatically improved antibodies against a model protein and a neurotransmitter peptide in terms of affinity and immunostaining performance. The reverse Kunkel method is especially suitable for engineering proteins whose activities are determined by multiple variable regions, such as antibodies and adeno-associated virus capsids, or whose functional domains are composed of several discontinuous sequences, such as Cas9 and Cas12a.
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Affiliation(s)
- Wen-Ching Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Hao-Cheng Tang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Han Ying Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Yi Kao
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Taiwan International Graduate Program in Molecular Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 11529, Taiwan
| | - You-Chiun Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Taiwan International Graduate Program in Chemical Biology and Molecular Biophysics, National Taiwan University and Academia Sinica, Taipei 11529, Taiwan
| | - Athena Hsu Li
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Yang Ming Chiao Tung University and Academia Sinica, Taipei 11529, Taiwan
| | - Shi-Bing Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Kurt Yun Mou
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
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4
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Jin S, Sun Y, Liang X, Gu X, Ning J, Xu Y, Chen S, Pan L. Emerging new therapeutic antibody derivatives for cancer treatment. Signal Transduct Target Ther 2022; 7:39. [PMID: 35132063 PMCID: PMC8821599 DOI: 10.1038/s41392-021-00868-x] [Citation(s) in RCA: 180] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 12/18/2022] Open
Abstract
Monoclonal antibodies constitute a promising class of targeted anticancer agents that enhance natural immune system functions to suppress cancer cell activity and eliminate cancer cells. The successful application of IgG monoclonal antibodies has inspired the development of various types of therapeutic antibodies, such as antibody fragments, bispecific antibodies, and antibody derivatives (e.g., antibody-drug conjugates and immunocytokines). The miniaturization and multifunctionalization of antibodies are flexible and viable strategies for diagnosing or treating malignant tumors in a complex tumor environment. In this review, we summarize antibodies of various molecular types, antibody applications in cancer therapy, and details of clinical study advances. We also discuss the rationale and mechanism of action of various antibody formats, including antibody-drug conjugates, antibody-oligonucleotide conjugates, bispecific/multispecific antibodies, immunocytokines, antibody fragments, and scaffold proteins. With advances in modern biotechnology, well-designed novel antibodies are finally paving the way for successful treatments of various cancers, including precise tumor immunotherapy, in the clinic.
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Affiliation(s)
- Shijie Jin
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Yanping Sun
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Xiao Liang
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Xinyu Gu
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Jiangtao Ning
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Yingchun Xu
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China
| | - Shuqing Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China.
- Department of Precision Medicine on Tumor Therapeutics, ZJU-Hangzhou Global Scientific and Technological Innovation Center, 311200, Hangzhou, China.
| | - Liqiang Pan
- Institute of Drug Metabolism and Pharmaceutical Analysis, College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, China.
- The First Affiliated Hospital, Zhejiang University School of Medicine, 310003, Hangzhou, China.
- Key Laboratory of Pancreatic Disease of Zhejiang Province, 310003, Hangzhou, China.
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5
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Shipunova VO, Deyev SM. Artificial Scaffold Polypeptides As an Efficient Tool for the Targeted Delivery of Nanostructures In Vitro and In Vivo. Acta Naturae 2022; 14:54-72. [PMID: 35441046 PMCID: PMC9013437 DOI: 10.32607/actanaturae.11545] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 12/20/2021] [Indexed: 12/22/2022] Open
Abstract
The use of traditional tools for the targeted delivery of nanostructures, such as antibodies, transferrin, lectins, or aptamers, often leads to an entire range of undesirable effects. The large size of antibodies often does not allow one to reach the required number of molecules on the surface of nanostructures during modification, and the constant domains of heavy chains, due to their effector functions, can induce phagocytosis. In the recent two decades, targeted polypeptide scaffold molecules of a non-immunoglobulin nature, antibody mimetics, have emerged as much more effective targeting tools. They are small in size (3-20 kDa), possess high affinity (from subnano- to femtomolar binding constants), low immunogenicity, and exceptional thermodynamic stability. These molecules can be effectively produced in bacterial cells, and, using genetic engineering manipulations, it is possible to create multispecific fusion proteins for the targeting of nanoparticles to cells with a given molecular portrait, which makes scaffold polypeptides an optimal tool for theranostics.
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Affiliation(s)
- V. O. Shipunova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
| | - S. M. Deyev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997 Russia
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6
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Krutty JD, Sun J, Koesser K, Murphy WL, Gopalan P. Polymer-Coated Magnetic Microspheres Conjugated with Growth Factor Receptor Binding Peptides Enable Cell Sorting. ACS Biomater Sci Eng 2021; 7:5927-5932. [PMID: 34851098 DOI: 10.1021/acsbiomaterials.1c01199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The separation and sorting of human cells is an important step in the bioprocessing of cell-based therapeutics. Heterogeneous mixtures of cells must be sorted to isolate the desired cell type and purify the final product. This process is often achieved by antibody-based sorting techniques. In this work, we demonstrate that magnetic microspheres may be functionalized with peptides that selectively bind to cells on the basis of their relative concentration of specific surface proteins. Five-micrometer-magnetic microspheres were coated with the synthetic copolymer PVG (poly(poly(ethylene glycol)methyl ether methacrylate-ran-vinyl dimethyl azlactone-ran-glycidyl methacrylate) and functionalized with the vascular endothelial growth factor receptor binding peptide (VRBP), which binds to the vascular endothelial growth factor receptor (VEGFR). These microspheres exhibited low cytotoxicity and bind to cells depending on their relative surface protein expression. Finally, coated, magnetic microspheres were used to separate heterogeneous populations of cells dependent on their VEGFR expression through magnetic-assisted cell sorting (MACS), demonstrating that peptide-based cell sorting mechanisms may be useful in the bioprocessing of human-cell-based products.
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Affiliation(s)
- John D Krutty
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jian Sun
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kevin Koesser
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - William L Murphy
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Padma Gopalan
- Department of Materials Science and Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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7
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Xi Z, Liu X, Lin R, Persons JD, Ilina TV, Li W, Dimitrov DS, Ishima R. The reduced form of the antibody CH2 domain. Protein Sci 2021; 30:1895-1903. [PMID: 34107549 DOI: 10.1002/pro.4142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 12/12/2022]
Abstract
Among the immunoglobulin domains, the CH2 domain has the lowest thermal stability, which also depends on amino acid sequence and buffer conditions. To further identify factors that influence CH2 folding and stability, we characterized the domain in the reduced form using differential scanning fluorimetry and nuclear magnetic resonance. We show that the CH2 domain can fold, similarly to the disulfide-bridged form, without forming a disulfide-bridge, even though the protein contains two Cys residues. Although the reduced form exhibits thermal stability more than 15°C lower than the disulfide-bridged form, it does not undergo immediate full oxidization. To explain this phenomenon, we compared CH2 oxidization at different conditions and demonstrate a need for significant fluctuation of the folded conformation to enhance CH2 disulfide-bridge formation. We conclude that, since CH2 can be purified as a folded, semi-stable, reduced protein that can coexist with the oxidized form, verification of the level of oxidization at each step is critical in CH2 engineering studies.
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Affiliation(s)
- Zhaoyong Xi
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Xianglei Liu
- Center for Antibody Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rui Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Department of Gastroenterology and Hepatology, Tianjin Medical University, General Hospital, Tianjin, China
| | - John D Persons
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Tatiana V Ilina
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Wei Li
- Center for Antibody Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Dimiter S Dimitrov
- Center for Antibody Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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8
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Ahmadi A, Ayyadevara VSSA, Baudry J, Roh KH. Calcium signaling on Jurkat T cells induced by microbeads coated with novel peptide ligands specific to human CD3ε. J Mater Chem B 2021; 9:1661-1675. [PMID: 33481966 DOI: 10.1039/d0tb02235g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
CD3ε is expressed on T lymphocytes as a part of the T cell receptor (TCR)-CD3 complex. Together with other CD3 molecules, CD3ε is responsible for the activation of T cells via transducing the event of antigen recognition by the TCR into intracellular signaling cascades. The present study first aims to identify a novel peptide ligand that binds to human CD3ε in a specific manner and to perform an initial evaluation of its biological efficacy on the human T cell line, Jurkat cells. We screened a phage-display peptide library against human CD3ε using a subtractive biopanning process, from which we identified 13 phage clones displaying unique peptide sequences. One dominant phage clone displaying the 7 amino acid sequence of WSLGYTG, which occupied 90% of tested plaques (18 out of 20) after the 5th round of biopanning, demonstrated a superior binding behavior to other clones in the binding assays against recombinant CD3ε on microbeads or Jurkat cells. The synthesized peptide also showed specific binding to Jurkat cells in a dose-dependent manner but not to B cell lymphoma line, 2PK3 cells. Molecular modeling and docking simulation confirmed that the selected peptide ligand in an energetically stable conformation binds to a pocket of CD3ε that is not hidden by either CD3γ or CD3δ. Lastly, magnetic microbeads conjugated with the synthesized peptide ligands showed a weak but specific association with Jurkat cells and induced the calcium flux, a hallmark indication of proximal T cell receptor signaling, which gave rise to an enhancement of IL-2 section and cell proliferation. The novel peptide ligand and its various multivalent forms have a great potential in applications related to T cell biology and T cell immunotherapy.
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Affiliation(s)
- Armin Ahmadi
- Department of Chemical & Materials Engineering, University of Alabama in Huntsville, 301 Sparkman Drive NW, Huntsville, AL 35899, USA.
| | - V S S Abhinav Ayyadevara
- Biotechnology Science and Engineering, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Jerome Baudry
- Biotechnology Science and Engineering, University of Alabama in Huntsville, Huntsville, AL 35899, USA and Department of Biological Sciences, University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Kyung-Ho Roh
- Department of Chemical & Materials Engineering, University of Alabama in Huntsville, 301 Sparkman Drive NW, Huntsville, AL 35899, USA. and Biotechnology Science and Engineering, University of Alabama in Huntsville, Huntsville, AL 35899, USA
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9
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Carrington G, Tomlinson D, Peckham M. Exploiting nanobodies and Affimers for superresolution imaging in light microscopy. Mol Biol Cell 2020; 30:2737-2740. [PMID: 31609674 PMCID: PMC6789155 DOI: 10.1091/mbc.e18-11-0694] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Antibodies have long been the main approach used for localizing proteins of interest by light microscopy. In the past 5 yr or so, and with the advent of superresolution microscopy, the diversity of tools for imaging has rapidly expanded. One main area of expansion has been in the area of nanobodies, small single-chain antibodies from camelids or sharks. The other has been the use of artificial scaffold proteins, including Affimers. The small size of nanobodies and Affimers compared with the traditional antibody provides several advantages for superresolution imaging.
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Affiliation(s)
- Glenn Carrington
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Darren Tomlinson
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Michelle Peckham
- School of Molecular and Cellular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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10
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Imaging using radiolabelled targeted proteins: radioimmunodetection and beyond. EJNMMI Radiopharm Chem 2020; 5:16. [PMID: 32577943 PMCID: PMC7311618 DOI: 10.1186/s41181-020-00094-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 04/14/2020] [Indexed: 12/18/2022] Open
Abstract
The use of radiolabelled antibodies was proposed in 1970s for staging of malignant tumours. Intensive research established chemistry for radiolabelling of proteins and understanding of factors determining biodistribution and targeting properties. The use of radioimmunodetection for staging of cancer was not established as common practice due to approval and widespread use of [18F]-FDG, which provided a more general diagnostic use than antibodies or their fragments. Expanded application of antibody-based therapeutics renewed the interest in radiolabelled antibodies. RadioimmunoPET emerged as a powerful tool for evaluation of pharmacokinetics of and target engagement by biotherapeutics. In addition to monoclonal antibodies, new radiolabelled engineered proteins have recently appeared, offering high-contrast imaging of expression of therapeutic molecular targets in tumours shortly after injection. This creates preconditions for noninvasive determination of a target expression level and stratification of patients for targeted therapies. Radiolabelled proteins hold great promise to play an important role in development and implementation of personalised targeted treatment of malignant tumours. This article provides an overview of biodistribution and tumour-seeking features of major classes of targeting proteins currently utilized for molecular imaging. Such information might be useful for researchers entering the field of the protein-based radionuclide molecular imaging.
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11
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Shetab Boushehri MA, Dietrich D, Lamprecht A. Nanotechnology as a Platform for the Development of Injectable Parenteral Formulations: A Comprehensive Review of the Know-Hows and State of the Art. Pharmaceutics 2020; 12:pharmaceutics12060510. [PMID: 32503171 PMCID: PMC7356945 DOI: 10.3390/pharmaceutics12060510] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 05/24/2020] [Indexed: 12/11/2022] Open
Abstract
Within recent decades, the development of nanotechnology has made a significant contribution to the progress of various fields of study, including the domains of medical and pharmaceutical sciences. A substantially transformed arena within the context of the latter is the development and production of various injectable parenteral formulations. Indeed, recent decades have witnessed a rapid growth of the marketed and pipeline nanotechnology-based injectable products, which is a testimony to the remarkability of the aforementioned contribution. Adjunct to the ability of nanomaterials to deliver the incorporated payloads to many different targets of interest, nanotechnology has substantially assisted to the development of many further facets of the art. Such contributions include the enhancement of the drug solubility, development of long-acting locally and systemically injectable formulations, tuning the onset of the drug’s release through the endowment of sensitivity to various internal or external stimuli, as well as adjuvancy and immune activation, which is a desirable component for injectable vaccines and immunotherapeutic formulations. The current work seeks to provide a comprehensive review of all the abovementioned contributions, along with the most recent advances made within each domain. Furthermore, recent developments within the domains of passive and active targeting will be briefly debated.
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Affiliation(s)
- Maryam A. Shetab Boushehri
- Department of Pharmaceutics, Faculty of Pharmacy, University of Bonn, 53121 Bonn, Germany;
- Correspondence: ; Tel.: +49-228-736428; Fax: +49-228-735268
| | - Dirk Dietrich
- Department of Neurosurgery, University Clinic of Bonn, 53105 Bonn, Germany;
| | - Alf Lamprecht
- Department of Pharmaceutics, Faculty of Pharmacy, University of Bonn, 53121 Bonn, Germany;
- PEPITE EA4267, Institute of Pharmacy, University Bourgogne Franche-Comté, 25000 Besançon, France
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12
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Abstract
The advent of biologic therapies, particularly antibody therapeutics, has revolutionized the pharmacological treatment of many rheumatic diseases. Antibody discovery began with the immunization of mice for the production of rodent immunoglobulins, but advances in protein and genetic engineering have now made it possible to generate fully human antibodies, which are better tolerated by patients. For most clinical applications in rheumatology, antibodies have been used as blocking agents capable of neutralizing the function of pro-inflammatory proteins, such as TNF. The latest strategies involve antibody products armed with effector moieties, such as anti-inflammatory drugs or cytokines, or antibody products that are specific for multiple targets for the selective inhibition of inflammation at sites of disease. Antibodies are some of the best-selling drugs in the world, and with further advances in antibody development, engineering of armed antibodies and bispecific products will have an important role in the treatment of rheumatic diseases.
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13
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McCord JP, Grove TZ. Engineering repeat proteins of the immune system. Biopolymers 2020; 111:e23348. [PMID: 32031681 DOI: 10.1002/bip.23348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 08/30/2019] [Accepted: 09/06/2019] [Indexed: 11/06/2022]
Abstract
Limitations associated with immunoglobulins have motivated the search for novel binding scaffolds. Repeat proteins have emerged as one promising class of scaffolds, but often are limited to binding protein and peptide targets. An exception is the repeat proteins of the immune system, which have in recent years served as an inspiration for binding scaffolds which can bind glycans and other classes of biomolecule. Like other repeat proteins, these proteins can be very stable and have a monomeric mode of binding, with elongated and highly variable binding surfaces. The ability to target glycans and glycoproteins fill an important gap in current tools for research and biomedical applications.
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Affiliation(s)
- Jennifer P McCord
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, U.S.A
| | - Tijana Z Grove
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, U.S.A.,Zarkovic Grove Consulting, LLC, Blacksburg, VA, U.S.A
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14
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Deyev SM, Vorobyeva A, Schulga A, Abouzayed A, Günther T, Garousi J, Konovalova E, Ding H, Gräslund T, Orlova A, Tolmachev V. Effect of a radiolabel biochemical nature on tumor-targeting properties of EpCAM-binding engineered scaffold protein DARPin Ec1. Int J Biol Macromol 2019; 145:216-225. [PMID: 31863835 DOI: 10.1016/j.ijbiomac.2019.12.147] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/17/2019] [Accepted: 12/17/2019] [Indexed: 12/27/2022]
Abstract
Radionuclide-based imaging of molecular therapeutic targets might facilitate stratifying patients for specific biotherapeutics. New type of imaging probes, based on designed ankyrin repeat proteins (DARPins), have demonstrated excellent contrast of imaging of human epidermal growth factor type 2 (HER2) expression in preclinical models. We hypothesized that labeling approaches, which result in lipophilic radiometabolites (non-residualizing labels), would provide the best imaging contrast for DARPins that internalize slowly after binding to cancer cells. The hypothesis was tested using DARPin Ec1 that binds to epithelial cell adhesion molecule (EpCAM). EpCAM is a promising therapeutic target. Ec1 was labeled with 125I using two methods to obtain the non-residualizing labels, while residualizing labels were obtained by labeling it with 99mTc. All labeled Ec1 variants preserved target specificity and picomolar binding affinity to EpCAM-expressing pancreatic adenocarcinoma BxPC-3 cells. In murine models, all the variants provided similar tumor uptake. However, 125I-PIB-H6-Ec1 had noticeably lower retention in normal tissues, which provided appreciably higher tumor-to-organ ratios. Furthermore, 125I-PIB-H6-Ec1 demonstrated the highest imaging contrast in preclinical models than any other EpCAM-imaging agent tested so far. In conclusion, DARPin Ec1 in combination with a non-residualizing label is a promising probe for imaging EpCAM expression a few hours after injection.
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Affiliation(s)
- Sergey M Deyev
- Molecular Immunology Laboratory, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Research School of Chemistry and Applied Biomedical Sciences, Research Tomsk Polytechnic University, Tomsk, Russia; Center of Biomedical Engineering, Sechenov University, Moscow, Russia
| | - Anzhelika Vorobyeva
- Research School of Chemistry and Applied Biomedical Sciences, Research Tomsk Polytechnic University, Tomsk, Russia; Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Alexey Schulga
- Molecular Immunology Laboratory, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia; Research School of Chemistry and Applied Biomedical Sciences, Research Tomsk Polytechnic University, Tomsk, Russia
| | - Ayman Abouzayed
- Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Tyran Günther
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Javad Garousi
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Elena Konovalova
- Molecular Immunology Laboratory, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Haozhong Ding
- Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Torbjörn Gräslund
- Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anna Orlova
- Research School of Chemistry and Applied Biomedical Sciences, Research Tomsk Polytechnic University, Tomsk, Russia; Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Vladimir Tolmachev
- Research School of Chemistry and Applied Biomedical Sciences, Research Tomsk Polytechnic University, Tomsk, Russia; Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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15
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Gebauer M, Skerra A. Engineering of binding functions into proteins. Curr Opin Biotechnol 2019; 60:230-241. [DOI: 10.1016/j.copbio.2019.05.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/07/2019] [Indexed: 12/13/2022]
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16
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Influence of Molecular Design on the Targeting Properties of ABD-Fused Mono- and Bi-Valent Anti-HER3 Affibody Therapeutic Constructs. Cells 2018; 7:cells7100164. [PMID: 30314301 PMCID: PMC6210767 DOI: 10.3390/cells7100164] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 09/23/2018] [Accepted: 10/08/2018] [Indexed: 01/26/2023] Open
Abstract
Overexpression of human epidermal growth factor receptor type 3 (HER3) is associated with tumour cell resistance to HER-targeted therapies. Monoclonal antibodies (mAbs) targeting HER3 are currently being investigated for treatment of various types of cancers. Cumulative evidence suggests that affibody molecules may be appropriate alternatives to mAbs. We previously reported a fusion construct (3A3) containing two HER3-targeting affibody molecules flanking an engineered albumin-binding domain (ABD035) included for the extension of half-life in circulation. The 3A3 fusion protein (19.7 kDa) was shown to delay tumour growth in mice bearing HER3-expressing xenografts and was equipotent to the mAb seribantumab. Here, we have designed and explored a series of novel formats of anti-HER3 affibody molecules fused to the ABD in different orientations. All constructs inhibited heregulin-induced phosphorylation in HER3-expressing BxPC-3 and DU-145 cell lines. Biodistribution studies demonstrated extended the half-life of all ABD-fused constructs, although at different levels. The capacity of our ABD-fused proteins to accumulate in HER3-expressing tumours was demonstrated in nude mice bearing BxPC-3 xenografts. Formats where the ABD was located on the C-terminus of affibody binding domains (3A, 33A, and 3A3) provided the best tumour targeting properties in vivo. Further development of these promising candidates for treatment of HER3-overexpressing tumours is therefore justified.
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A dimeric form of a small-sized protein binder exhibits enhanced anti-tumor activity through prolonged blood circulation. J Control Release 2018; 279:282-291. [DOI: 10.1016/j.jconrel.2018.04.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/27/2018] [Accepted: 04/18/2018] [Indexed: 12/24/2022]
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18
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Computational screening of potential non-immunoglobulin scaffolds using overlapped conserved residues (OCR)-based fingerprints. KOREAN J CHEM ENG 2018. [DOI: 10.1007/s11814-017-0350-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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19
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Könning D, Kolmar H. Beyond antibody engineering: directed evolution of alternative binding scaffolds and enzymes using yeast surface display. Microb Cell Fact 2018; 17:32. [PMID: 29482656 PMCID: PMC6389260 DOI: 10.1186/s12934-018-0881-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/22/2018] [Indexed: 01/08/2023] Open
Abstract
Pioneered exactly 20 years ago, yeast surface display (YSD) continues to take a major role in protein engineering among the high-throughput display methodologies that have been developed to date. The classical yeast display technology relies on tethering an engineered protein to the cell wall by genetic fusion to one subunit of a dimeric yeast-mating agglutination receptor complex. This method enables an efficient genotype-phenotype linkage while exploiting the benefits of a eukaryotic expression machinery. Over the past two decades, a plethora of protein engineering efforts encompassing conventional antibody Fab and scFv fragments have been reported. In this review, we will focus on the versatility of YSD beyond conventional antibody engineering and, instead, place the focus on alternative scaffold proteins and enzymes which have successfully been tailored for purpose with regard to improving binding, activity or specificity.
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Affiliation(s)
- Doreen Könning
- Antibody-Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287 Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287 Darmstadt, Germany
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20
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De A, Kuppusamy G, Karri VVSR. Affibody molecules for molecular imaging and targeted drug delivery in the management of breast cancer. Int J Biol Macromol 2017; 107:906-919. [PMID: 28935537 DOI: 10.1016/j.ijbiomac.2017.09.059] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 09/09/2017] [Accepted: 09/17/2017] [Indexed: 12/29/2022]
Abstract
Breast cancer is one of the leading reasons for the morbidity and mortality of cancer related death globally. The modern therapies are basically the combination of the breast-preserving surgeries or ablation with or without node biopsy or destroying the carcinoma cells adjuvant with chemotherapy, radiotherapy, hormonal or biological therapies depending upon the nature of the receptor of the cancerous cells, nature of the lymph node, as well as the tendency of the recurrence. For decade's carcinoma management suffered by the limitation of imagining, targeting and penetrability problem associated with management and cure of this deadly disease leads to unwanted chemo-toxicity and side effects. Alike other antibody mimetics, affibodies are designed with the combinatorial protein engineering approaches which are small and robust protein scaffolds retaining the favorable folding and stability. Affibody is one of the significantly important tools for imaging and diagnosis of the affinity specific over expressed proteins in the breast cancer management. The review summarizes the various affibody strategies uses in the management of breast cancer.
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Affiliation(s)
- Anindita De
- JSS College of Pharmacy, Ootacamund, Jagadguru Sri Shivarathreeshwara University, Mysuru, Karnataka, India.
| | - Gowthamarajan Kuppusamy
- JSS College of Pharmacy, Ootacamund, Jagadguru Sri Shivarathreeshwara University, Mysuru, Karnataka, India.
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21
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Armenta S, Moreno-Mendieta S, Sánchez-Cuapio Z, Sánchez S, Rodríguez-Sanoja R. Advances in molecular engineering of carbohydrate-binding modules. Proteins 2017; 85:1602-1617. [PMID: 28547780 DOI: 10.1002/prot.25327] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 05/04/2017] [Accepted: 05/20/2017] [Indexed: 11/06/2022]
Abstract
Carbohydrate-binding modules (CBMs) are non-catalytic domains that are generally appended to carbohydrate-active enzymes. CBMs have a broadly conserved structure that allows recognition of a notable variety of carbohydrates, in both their soluble and insoluble forms, as well as in their alpha and beta conformations and with different types of bonds or substitutions. This versatility suggests a high functional plasticity that is not yet clearly understood, in spite of the important number of studies relating protein structure and function. Several studies have explored the flexibility of these systems by changing or improving their specificity toward substrates of interest. In this review, we examine the molecular strategies used to identify CBMs with novel or improved characteristics. The impact of the spatial arrangement of the functional amino acids of CBMs is discussed in terms of unexpected new functions that are not related to the original biological roles of the enzymes. Proteins 2017; 85:1602-1617. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Silvia Armenta
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Silvia Moreno-Mendieta
- CONACYT, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Zaira Sánchez-Cuapio
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Sergio Sánchez
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
| | - Romina Rodríguez-Sanoja
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Circuito Mario de la Cueva s/n Ciudad Universitaria, Ciudad de México, 04510, México
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22
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Zhao N, Spencer J, Schmitt MA, Fisk JD. Hyperthermostable binding molecules on phage: Assay components for point-of-care diagnostics for active tuberculosis infection. Anal Biochem 2017; 521:59-71. [DOI: 10.1016/j.ab.2016.12.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/25/2016] [Accepted: 12/23/2016] [Indexed: 11/24/2022]
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23
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Wang Y, Ballou B, Schmidt BF, Andreko S, St Croix CM, Watkins SC, Bruchez MP. Affibody-targeted fluorogen activating protein for in vivo tumor imaging. Chem Commun (Camb) 2017; 53:2001-2004. [PMID: 28120951 PMCID: PMC5340305 DOI: 10.1039/c6cc09137g] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Molecular imaging using near-infrared (NIR) fluorescence is useful for intraoperative imaging and real-time margin identification. Directly conjugated IR dyes possess useful properties for in vivo imaging, but conjugation often substantially alters the circulation dynamics of targeting moieties. We developed and characterized a new tumor-targeting probe, affiFAP, which consists of a protein that specifically binds EGFR (affibody) and a fluorogen activating protein (FAP). This compact molecular recognition reagent can reversibly bind and activate fluorescence of otherwise nonfluorescent dyes and allows tumor visualization with low nonspecific tissue staining. We demonstrate molecular pre-targeting of affiFAPs and subsequent systemic or topical application of fluorogenic dye to achieve high contrast, fast clearance, and good tissue penetration that may be used in clinical settings to molecularly define tumor margins.
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Affiliation(s)
- Yi Wang
- The Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA. and The Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Byron Ballou
- The Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Brigitte F Schmidt
- The Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Sue Andreko
- The Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Claudette M St Croix
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Simon C Watkins
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Marcel P Bruchez
- The Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA. and The Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213, USA and The Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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24
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Lomonosova AV, Ulitin AB, Kazakov AS, Mirzabekov TA, Permyakov EA, Permyakov SE. Derivative of Extremophilic 50S Ribosomal Protein L35Ae as an Alternative Protein Scaffold. PLoS One 2017; 12:e0170349. [PMID: 28103321 PMCID: PMC5245882 DOI: 10.1371/journal.pone.0170349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/03/2017] [Indexed: 12/01/2022] Open
Abstract
Small antibody mimetics, or alternative binding proteins (ABPs), extend and complement antibody functionality with numerous applications in research, diagnostics and therapeutics. Given the superiority of ABPs, the last two decades have witnessed development of dozens of alternative protein scaffolds (APSs) for the design of ABPs. Proteins from extremophiles with their high structural stability are especially favorable for APS design. Here, a 10X mutant of the 50S ribosomal protein L35Ae from hyperthermophilic archaea Pyrococcus horikoshii has been probed as an APS. A phage display library of L35Ae 10X was generated by randomization of its three CDR-like loop regions (repertoire size of 2×108). Two L35Ae 10X variants specific to a model target, the hen egg-white lysozyme (HEL), were isolated from the resulting library using phage display. The affinity of these variants (L4 and L7) to HEL ranges from 0.10 μM to 1.6 μM, according to surface plasmon resonance data. While L4 has 1-2 orders of magnitude lower affinity to HEL homologue, bovine α-lactalbumin (BLA), L7 is equally specific to HEL and BLA. The reference L35Ae 10X is non-specific to both HEL and BLA. L4 and L7 are more resistant to denaturation by guanidine hydrochloride compared to the reference L35Ae 10X (mid-transition concentration is higher by 0.1-0.5 M). Chemical crosslinking experiments reveal an increased propensity of L4 and L7 to multimerization. Overall, the CDR-like loop regions of L35Ae 10X represent a proper interface for generation of functional ABPs. Hence, L35Ae is shown to extend the growing family of protein scaffolds dedicated to the design of novel binding proteins.
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Affiliation(s)
- Anna V. Lomonosova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, Russia
| | | | - Alexei S. Kazakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, Russia
| | - Tajib A. Mirzabekov
- Antherix, Pushchino, Moscow region, Russia
- Biomirex Inc., Watertown, Massachusetts, United States of America
| | - Eugene A. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, Russia
| | - Sergei E. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow region, Russia
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25
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Andersson KG, Oroujeni M, Garousi J, Mitran B, Ståhl S, Orlova A, Löfblom J, Tolmachev V. Feasibility of imaging of epidermal growth factor receptor expression with ZEGFR:2377 affibody molecule labeled with 99mTc using a peptide-based cysteine-containing chelator. Int J Oncol 2016; 49:2285-2293. [PMID: 27748899 PMCID: PMC5118000 DOI: 10.3892/ijo.2016.3721] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 08/30/2016] [Indexed: 12/13/2022] Open
Abstract
The epidermal growth factor receptor (EGFR) is overexpressed in a number of malignant tumors and is a molecular target for several specific anticancer antibodies and tyrosine kinase inhibitors. The overexpression of EGFR is a predictive biomarker for response to several therapy regimens. Radionuclide molecular imaging might enable detection of EGFR overexpression by a non-invasive procedure and could be used repeatedly. Affibody molecules are engineered scaffold proteins, which could be selected to have a high affinity and selectivity to predetermined targets. The anti-EGFR ZEGFR:2377 affibody molecule is a potential imaging probe for EGFR detection. The use of the generator-produced radionuclide 99mTc should facilitate clinical translation of an imaging probe due to its low price, availability and favorable dosimetry of the radionuclide. In the present study, we evaluated feasibility of ZEGFR:2377 labeling with 99mTc using a peptide-based cysteine-containing chelator expressed at the C-terminus of ZEGFR:2377. The label was stable in vitro under cysteine challenge. In addition, 99mTc-ZEGFR:2377 was capable of specific binding to EGFR-expressing cells with high affinity (274 pM). Studies in BALB/C nu/nu mice bearing A431 xenografts demonstrated that 99mTc-ZEGFR:2377 accumulates in tumors in an EGFR-specific manner. The tumor uptake values were 3.6±1 and 2.5±0.4% ID/g at 3 and 24 h after injection, respectively. The corresponding tumor-to-blood ratios were 1.8±0.4 and 8±3. The xenografts were clearly visualized at both time-points. This study demonstrated the potential of 99mTc-labeled ZEGFR:2377 for imaging of EGFR in vivo.
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Affiliation(s)
- Ken G Andersson
- Division of Protein Technology, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Maryam Oroujeni
- Institute of Immunology, Genetic and Pathology, Uppsala University, SE-75185 Uppsala, Sweden
| | - Javad Garousi
- Institute of Immunology, Genetic and Pathology, Uppsala University, SE-75185 Uppsala, Sweden
| | - Bogdan Mitran
- Division of Molecular Imaging, Department of Medicinal Chemistry, Uppsala University, SE-75183 Uppsala, Sweden
| | - Stefan Ståhl
- Division of Protein Technology, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Anna Orlova
- Division of Molecular Imaging, Department of Medicinal Chemistry, Uppsala University, SE-75183 Uppsala, Sweden
| | - John Löfblom
- Division of Protein Technology, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden
| | - Vladimir Tolmachev
- Institute of Immunology, Genetic and Pathology, Uppsala University, SE-75185 Uppsala, Sweden
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26
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Lomonosova AV, Ovchinnikova EV, Kazakov AS, Denesyuk AI, Sofin AD, Mikhailov RV, Ulitin AB, Mirzabekov TA, Permyakov EA, Permyakov SE. Extremophilic 50S Ribosomal RNA-Binding Protein L35Ae as a Basis for Engineering of an Alternative Protein Scaffold. PLoS One 2015; 10:e0134906. [PMID: 26247602 PMCID: PMC4527664 DOI: 10.1371/journal.pone.0134906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/15/2015] [Indexed: 01/05/2023] Open
Abstract
Due to their remarkably high structural stability, proteins from extremophiles are particularly useful in numerous biological applications. Their utility as alternative protein scaffolds could be especially valuable in small antibody mimetic engineering. These artificial binding proteins occupy a specific niche between antibodies and low molecular weight substances, paving the way for development of innovative approaches in therapeutics, diagnostics, and reagent use. Here, the 50S ribosomal RNA-binding protein L35Ae from the extremophilic archaea Pyrococcus horikoshii has been probed for its potential to serve as a backbone in alternative scaffold engineering. The recombinant wild type L35Ae has a native-like secondary structure, extreme thermal stability (mid-transition temperature of 90°C) and a moderate resistance to the denaturation by guanidine hydrochloride (half-transition at 2.6 M). Chemical crosslinking and dynamic light scattering data revealed that the wild type L35Ae protein has a propensity for multimerization and aggregation correlating with its non-specific binding to a model cell surface of HEK293 cells, as evidenced by flow cytometry. To suppress these negative features, a 10-amino acid mutant (called L35Ae 10X) was designed, which lacks the interaction with HEK293 cells, is less susceptible to aggregation, and maintains native-like secondary structure and thermal stability. However, L35Ae 10X also shows lowered resistance to guanidine hydrochloride (half-transition at 2.0M) and is more prone to oligomerization. This investigation of an extremophile protein’s scaffolding potential demonstrates that lowered resistance to charged chemical denaturants and increased propensity to multimerization may limit the utility of extremophile proteins as alternative scaffolds.
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Affiliation(s)
- Anna V. Lomonosova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Elena V. Ovchinnikova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Alexei S. Kazakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Alexander I. Denesyuk
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
- Department of Biosciences, Åbo Akademi University, Turku, 20520, Finland
| | - Alexander D. Sofin
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Roman V. Mikhailov
- Antherix, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Andrei B. Ulitin
- Antherix, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Tajib A. Mirzabekov
- Antherix, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
- Biomirex Inc., 304 Pleasant Street, Watertown, Massachusetts, 02472, United States of America
| | - Eugene A. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
| | - Sergei E. Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Institutskaya str., 7, Pushchino, Moscow region, 142290, Russia
- * E-mail:
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Deyev SM, Lebedenko EN, Petrovskaya LE, Dolgikh DA, Gabibov AG, Kirpichnikov MP. Man-made antibodies and immunoconjugates with desired properties: function optimization using structural engineering. RUSSIAN CHEMICAL REVIEWS 2015. [DOI: 10.1070/rcr4459] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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28
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Strand J, Varasteh Z, Eriksson O, Abrahmsen L, Orlova A, Tolmachev V. Gallium-68-labeled affibody molecule for PET imaging of PDGFRβ expression in vivo. Mol Pharm 2014; 11:3957-64. [PMID: 24972112 DOI: 10.1021/mp500284t] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Platelet-derived growth factor receptor β (PDGFRβ) is a transmembrane tyrosine kinase receptor involved, for example, in angiogenesis. Overexpression and excessive signaling of PDGFRβ has been observed in multiple malignant tumors and fibrotic diseases, making this receptor a pharmaceutical target for monoclonal antibodies and tyrosine kinase inhibitors. Successful targeted therapy requires identification of responding patients. Radionuclide molecular imaging would enable determination of the PDGFRβ status in all lesions using a single noninvasive repeatable procedure. Recently, we have demonstrated that the affibody molecule Z09591 labeled with (111)In can specifically target PDGFRβ-expressing tumors in vivo. The use of positron emission tomography (PET) as an imaging technique would provide superior resolution, sensitivity, and quantitation accuracy. In this study, a DOTA-conjugated Z09591 was labeled with the generator-produced positron emitting radionuclide (68)Ga (T1/2 = 67.6 min, Eβ + max = 1899 keV, 89% β(+)). (68)Ga-DOTA-Z09591 retained the capacity to specifically bind to PDGFRβ-expressing U-87 MG glioma cells. The half-maximum inhibition concentration (IC50) of (68)Ga-DOTA-Z09591 (6.6 ± 1.4 nM) was somewhat higher than that of (111)In-DOTA-Z09591 (1.4 ± 1.2 nM). (68)Ga-DOTA-Z09591 demonstrated specific (saturable) targeting of U-87 MG xenografts in immunodeficient mice. The tumor uptake at 2 h after injection was 3.7 ± 1.7% IA/g, which provided a tumor-to-blood ratio of 8.0 ± 3.1. The only organ with higher accumulation of radioactivity was the kidney. MicroPET imaging provided high-contrast imaging of U-87 MG xenografts. In conclusion, the (68)Ga-labeled affibody molecule Z09591 is a promising candidate for further development as a probe for imaging PDGFRβ expression in vivo using PET.
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Affiliation(s)
- Joanna Strand
- Biomedical Radiation Sciences, Rudbeck Laboratory, Uppsala University , Uppsala, Sweden
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Wållberg H, Ståhl S. Design and evaluation of radiolabeled tracers for tumor imaging. Biotechnol Appl Biochem 2014; 60:365-83. [PMID: 24033592 DOI: 10.1002/bab.1111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 02/20/2013] [Indexed: 12/22/2022]
Abstract
The growing understanding of tumor biology and the identification of tumor-specific genetic and molecular alterations, such as the overexpression of membrane receptors and other proteins, allows for personalization of patient management using targeted therapies. However, this puts stringent demands on the diagnostic tools used to identify patients who are likely to respond to a particular treatment. Radionuclide molecular imaging is a promising noninvasive method to visualize and characterize the expression of such targets. A number of different proteins, from full-length antibodies and their derivatives to small scaffold proteins and peptide receptor-ligands, have been applied to molecular imaging, each demonstrating strengths and weaknesses. Here, we discuss the concept of molecular targeting and, in particular, molecular imaging of cancer-associated targets. Additionally, we describe important biotechnological considerations and desired features when designing and developing tracers for radionuclide molecular imaging.
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Affiliation(s)
- Helena Wållberg
- Division of Molecular Biotechnology, School of Biotechnology, AlbaNova University Center, KTH Royal Institute of Technology, Stockholm, Sweden
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Steemson JD, Baake M, Rakonjac J, Arcus VL, Liddament MT. Tracking molecular recognition at the atomic level with a new protein scaffold based on the OB-fold. PLoS One 2014; 9:e86050. [PMID: 24465865 PMCID: PMC3896448 DOI: 10.1371/journal.pone.0086050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/05/2013] [Indexed: 11/19/2022] Open
Abstract
The OB-fold is a small, versatile single-domain protein binding module that occurs in all forms of life, where it binds protein, carbohydrate, nucleic acid and small-molecule ligands. We have exploited this natural plasticity to engineer a new class of non-immunoglobulin alternatives to antibodies with unique structural and biophysical characteristics. We present here the engineering of the OB-fold anticodon recognition domain from aspartyl tRNA synthetase taken from the thermophile Pyrobaculum aerophilum. For this single-domain scaffold we have coined the term OBody. Starting from a naïve combinatorial library, we engineered an OBody with 3 nM affinity for hen egg-white lysozyme, by optimising the affinity of a naïve OBody 11,700-fold over several affinity maturation steps, using phage display. At each maturation step a crystal structure of the engineered OBody in complex with hen egg-white lysozyme was determined, showing binding elements in atomic detail. These structures have given us an unprecedented insight into the directed evolution of affinity for a single antigen on the molecular scale. The engineered OBodies retain the high thermal stability of the parental OB-fold despite mutation of up to 22% of their residues. They can be expressed in soluble form and also purified from bacteria at high yields. They also lack disulfide bonds. These data demonstrate the potential of OBodies as a new scaffold for the engineering of specific binding reagents and provide a platform for further development of future OBody-based applications.
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Affiliation(s)
- John D. Steemson
- Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
| | - Matthias Baake
- Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
| | - Jasna Rakonjac
- Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand
| | - Vickery L. Arcus
- Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
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Nong RY, Gu J, Darmanis S, Kamali-Moghaddam M, Landegren U. DNA-assisted protein detection technologies. Expert Rev Proteomics 2014; 9:21-32. [DOI: 10.1586/epr.11.78] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Cai W, Naimuddin M, Inagaki H, Kameyama K, Ishida N, Kubo T. Directed evolution of three-finger toxin to produce serine protease inhibitors. J Recept Signal Transduct Res 2013; 34:154-61. [PMID: 24308378 DOI: 10.3109/10799893.2013.865747] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Directed evolution is a very popular strategy for improving biophysical properties and even for generating proteins with novel functions. Recent advances in combinatorial protein engineering mean it is now possible to develop protein scaffolds that could substitute for whole antibody-associated properties as emerging therapeutic proteins. In particular, disulfide-rich proteins are attractive templates for directed evolution in the search for novel molecules because they can regulate the activities of receptors, enzymes, and other molecules. Previously, we demonstrated that functional regulatory molecules against interleukin-6 receptor (IL-6R) could be obtained by directed evolution of the three-finger toxin (3F) scaffold. In the present study, trypsin was selected as a target for directed evolution to further explore the potential use of the 3F cDNA display library. After seven rounds of selection, the DNA sequences converged. The recombinant proteins produced by the selected candidates had inhibitory activity against trypsin (Ki of 33-450 nM). Three of the six groups had Ki values that were comparable to bovine pancreatic trypsin inhibitor and soybean trypsin inhibitor. Two of the candidates also had inhibitory effects against chymotrypsin and kallikrein. This study suggests that 3F protein is suitable for the preparation of high-diversity libraries that can be utilized to obtain protease inhibitors. In addition to our previous successful targeting of IL-6R, the technique developed in our studies may have wide applications in the generation of regulatory molecules for targets of interest, such as receptors, enzymes for research, diagnostic applications, and therapeutic uses.
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Affiliation(s)
- Weiyan Cai
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba, Ibaraki , Japan
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Kuchař M, Vaňková L, Petroková H, Cerný J, Osička R, Pelák O, Sípová H, Schneider B, Homola J, Sebo P, Kalina T, Malý P. Human interleukin-23 receptor antagonists derived from an albumin-binding domain scaffold inhibit IL-23-dependent ex vivo expansion of IL-17-producing T-cells. Proteins 2013; 82:975-89. [PMID: 24549990 PMCID: PMC4285857 DOI: 10.1002/prot.24472] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 10/30/2013] [Accepted: 11/04/2013] [Indexed: 12/12/2022]
Abstract
Engineered combinatorial libraries derived from small protein scaffolds represent a powerful tool for generating novel binders with high affinity, required specificity and designed inhibitory function. This work was aimed to generate a collection of recombinant binders of human interleukin-23 receptor (IL-23R), which is a key element of proinflammatory IL-23-mediated signaling. A library of variants derived from the three-helix bundle scaffold of the albumin-binding domain (ABD) of streptococcal protein G and ribosome display were used to select for high-affinity binders of recombinant extracellular IL-23R. A collection of 34 IL-23R-binding proteins (called REX binders), corresponding to 18 different sequence variants, was used to identify a group of ligands that inhibited binding of the recombinant p19 subunit of IL-23, or the biologically active human IL-23 cytokine, to the recombinant IL-23R or soluble IL-23R-IgG chimera. The strongest competitors for IL-23R binding in ELISA were confirmed to recognize human IL-23R-IgG in surface plasmon resonance experiments, estimating the binding affinity in the sub- to nanomolar range. We further demonstrated that several REX variants bind to human leukemic cell lines K-562, THP-1 and Jurkat, and this binding correlated with IL-23R cell-surface expression. The REX125, REX009 and REX128 variants competed with the p19 protein for binding to THP-1 cells. Moreover, the presence of REX125, REX009 and REX115 variants significantly inhibited the IL-23-driven expansion of IL-17-producing primary human CD4+ T-cells. Thus, we conclude that unique IL-23R antagonists derived from the ABD scaffold were generated that might be useful in designing novel anti-inflammatory biologicals. Proteins 2014; 82:975–989.
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Affiliation(s)
- Milan Kuchař
- Laboratory of Ligand Engineering, Institute of Biotechnology AS CR, v. v. i., Vídeňská 1083, 142 20 Prague, Czech Republic
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Honarvar H, Jokilaakso N, Andersson K, Malmberg J, Rosik D, Orlova A, Karlström AE, Tolmachev V, Järver P. Evaluation of backbone-cyclized HER2-binding 2-helix Affibody molecule for In Vivo molecular imaging. Nucl Med Biol 2013; 40:378-86. [DOI: 10.1016/j.nucmedbio.2012.12.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 12/13/2012] [Accepted: 12/17/2012] [Indexed: 01/22/2023]
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Combination of Phage Display and Molecular Grafting Generates Highly Specific Tumor-Targeting Miniproteins. Angew Chem Int Ed Engl 2012; 51:13136-9. [DOI: 10.1002/anie.201203857] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Revised: 08/22/2012] [Indexed: 11/07/2022]
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36
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Zoller F, Markert A, Barthe P, Zhao W, Weichert W, Askoxylakis V, Altmann A, Mier W, Haberkorn U. Combination of Phage Display and Molecular Grafting Generates Highly Specific Tumor-Targeting Miniproteins. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203857] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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37
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Ren G, Webster JM, Liu Z, Zhang R, Miao Z, Liu H, Gambhir SS, Syud FA, Cheng Z. In vivo targeting of HER2-positive tumor using 2-helix affibody molecules. Amino Acids 2012; 43:405-13. [PMID: 21984380 PMCID: PMC4172459 DOI: 10.1007/s00726-011-1096-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Accepted: 09/19/2011] [Indexed: 10/17/2022]
Abstract
Molecular imaging of human epidermal growth factor receptor type 2 (HER2) expression has drawn significant attention because of the unique role of the HER2 gene in diagnosis, therapy and prognosis of human breast cancer. In our previous research, a novel cyclic 2-helix small protein, MUT-DS, was discovered as an anti-HER2 Affibody analog with high affinity through rational protein design and engineering. MUT-DS was then evaluated for positron emission tomography (PET) of HER2-positive tumor by labeling with two radionuclides, 68Ga and 18F, with relatively short half-life (t1/2<2 h). In order to fully study the in vivo behavior of 2-helix small protein and demonstrate that it could be a robust platform for labeling with a variety of radionuclides for different applications, in this study, MUT-DS was further radiolabeled with 64Cu or 111In and evaluated for in vivo targeting of HER2-positive tumor in mice. Design 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) conjugated MUT-DS (DOTA-MUT-DS) was chemically synthesized using solid phase peptide synthesizer and I2 oxidation. DOTA-MUT-DS was then radiolabeled with 64Cu or 111In to prepare the HER2 imaging probe (64Cu/111In-DOTA-MUT-DS). Both biodistribution and microPET imaging of the probe were evaluated in nude mice bearing subcutaneous HER2-positive SKOV3 tumors. DOTA-MUT-DS could be successfully synthesized and radiolabeled with 64Cu or 111In. Biodistribution study showed that tumor uptake value of 64Cu or 111In-labeled DOTA-MUT-DS was 4.66±0.38 or 2.17±0.15%ID/g, respectively, in nude mice bearing SKOV3 xenografts (n=3) at 1 h post-injection (p.i.). Tumor-to-blood and tumor-to-muscle ratios for 64Cu-DOTA-MUT-DS were attained to be 3.05 and 3.48 at 1 h p.i., respectively, while for 111In-DOTA-MUT-DS, they were 2.04 and 3.19, respectively. Co-injection of the cold Affibody molecule ZHER2:342 with 64Cu-DOTA-MUT-DS specifically reduced the SKOV3 tumor uptake of the probe by 48%. 111In-DOTA-MUT-DS displayed lower liver uptake at all the time points investigated and higher tumor to blood ratios at 4 and 20 h p.i., when compared with 64Cu-DOTA-MUT-DS. This study demonstrates that the 2-helix protein based probes, 64Cu/111In DOTA-MUT-DS, are promising molecular probes for imaging HER2-positive tumor. Two-helix small protein scaffold holds great promise as a novel and robust platform for imaging and therapy applications.
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Affiliation(s)
- Gang Ren
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology and Bio-X Program, Stanford University, California, Stanford, CA 94305-5344, USA
| | - Jack M. Webster
- General Electric Company, Global Research Center, Niskayuna, NY 12309, USA
| | - Zhe Liu
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology and Bio-X Program, Stanford University, California, Stanford, CA 94305-5344, USA
| | - Rong Zhang
- General Electric Company, Global Research Center, Niskayuna, NY 12309, USA
| | - Zheng Miao
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology and Bio-X Program, Stanford University, California, Stanford, CA 94305-5344, USA
| | - Hongguang Liu
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology and Bio-X Program, Stanford University, California, Stanford, CA 94305-5344, USA
| | - Sanjiv S. Gambhir
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology and Bio-X Program, Stanford University, California, Stanford, CA 94305-5344, USA
| | - Faisal A. Syud
- General Electric Company, Global Research Center, Niskayuna, NY 12309, USA
| | - Zhen Cheng
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology and Bio-X Program, Stanford University, California, Stanford, CA 94305-5344, USA
- Molecular Imaging Program at Stanford, Departments of Radiology, Stanford University, 1201 Welch Road, Lucas Expansion, P020A, Stanford, CA 94305, USA
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38
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Gong R, Chen W, Dimitrov DS. Expression, purification, and characterization of engineered antibody CH2 and VH domains. Methods Mol Biol 2012; 899:85-102. [PMID: 22735948 PMCID: PMC6959533 DOI: 10.1007/978-1-61779-921-1_6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Most of the FDA-approved therapeutic monoclonal antibodies are full-size IgG molecules with a molecular weight of about 150 kDa. A major problem for such large molecules is their poor penetration into tissues (e.g., solid tumors) and poor or absent binding to regions on the surface of some molecules (e.g., on the HIV envelope glycoprotein) which are fully accessible only by molecules of smaller size. Therefore, much work especially during the last decade has been aimed at developing novel scaffolds of much smaller size and high stability. Immunoglobulin-based scaffolds including Fab (∼50 kD), ScFv (∼30 kD), and VH domain (termed domain antibody, dAb) (∼15 kD) have been well established. Recently, a new scaffold based on human IgG1 CH2 domain (∼15 kD) was also proposed (termed nanoantibody, nAb). Binders based on a CH2 scaffold could also confer some effector functions. Here, we describe the design, expression, purification, and characterization of engineered CH2 and VH domains.
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Affiliation(s)
- Rui Gong
- Protein Interactions Group, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
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39
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Mascini M, Palchetti I, Tombelli S. Nucleic acid and peptide aptamers: fundamentals and bioanalytical aspects. Angew Chem Int Ed Engl 2011; 51:1316-32. [PMID: 22213382 DOI: 10.1002/anie.201006630] [Citation(s) in RCA: 244] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Indexed: 12/11/2022]
Abstract
In recent years new nucleic acid and protein-based combinatorial molecules have attracted the attention of researchers working in various areas of science, ranging from medicine to analytical chemistry. These molecules, called aptamers, have been proposed as alternatives to antibodies in many different applications. The aim of this Review is to illustrate the peculiarities of these combinatorial molecules which have initially been explored for their importance in molecular medicine, but have enormous potential in other biotechnological fields historically dominated by antibodies, such as bioassays. A description of these molecules is given, and the methods for their selection and production are also summarized. Moreover, critical aspects related to these molecules are discussed.
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Affiliation(s)
- Marco Mascini
- Dipartimento di Chimica Ugo Schiff, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
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Mascini M, Palchetti I, Tombelli S. Nucleinsäure- und Peptidaptamere: Grundlagen und bioanalytische Aspekte. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006630] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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41
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Zoller F, Schwaebel T, Markert A, Haberkorn U, Mier W. Engineering and functionalization of the disulfide-constrained miniprotein min-23 as a scaffold for diagnostic application. ChemMedChem 2011; 7:237-47. [PMID: 22213706 DOI: 10.1002/cmdc.201100497] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 11/25/2011] [Indexed: 11/06/2022]
Abstract
Miniproteins are scaffolds for the development of alternative non-immunoglobin binding agents for medical applications. This peptide format features high tolerance to sequence mutagenesis, excellent proteolytic stability, and fast blood pool clearance. Herein we present the total chemical synthesis of the disulfide-constrained scaffold Min-23 and its functionalization for in vitro and in vivo application. Optimized solid-phase peptide chemistry and oxidative folding strategies were developed to engineer this miniprotein with native-like disulfide configuration. High levels of serum stability and proteolytic resistance, as well as a beneficial pharmacokinetic profile for diagnostic imaging, were determined by using radiolabeling techniques such as positron emission tomography. The reported achievements highlight Min-23 as a promising scaffold for the development of novel recognition molecules for medical application.
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Affiliation(s)
- Frederic Zoller
- German Cancer Research Center (DKFZ), Clinical Cooperation Unit Nuclear Medicine, INF 280, 69120 Heidelberg, Germany
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42
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Engineering of a phosphorylatable tag for specific protein binding on zirconium phosphonate based microarrays. J Biol Inorg Chem 2011; 17:399-407. [DOI: 10.1007/s00775-011-0863-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 11/15/2011] [Indexed: 10/14/2022]
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43
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Boersma YL, Plückthun A. DARPins and other repeat protein scaffolds: advances in engineering and applications. Curr Opin Biotechnol 2011; 22:849-57. [DOI: 10.1016/j.copbio.2011.06.004] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 04/27/2011] [Accepted: 06/01/2011] [Indexed: 10/18/2022]
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Ahmad JN, Li J, Biedermannová L, Kuchař M, Šípová H, Semerádtová A, Černý J, Petroková H, Mikulecký P, Polínek J, Staněk O, Vondrášek J, Homola J, Malý J, Osička R, Šebo P, Malý P. Novel high-affinity binders of human interferon gamma derived from albumin-binding domain of protein G. Proteins 2011; 80:774-89. [DOI: 10.1002/prot.23234] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/05/2011] [Accepted: 10/17/2011] [Indexed: 12/24/2022]
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Abstract
Antibodies are the most successful affinity tools used today, in both fundamental and applied research (diagnostics, purification and therapeutics). Nonetheless, antibodies do have their limitations, including high production costs and low stability. Alternative affinity tools based on nucleic acids (aptamers), polypeptides (engineered binding proteins) and inorganic matrices (molecular imprinted polymers) have received considerable attention. A major advantage of these alternatives concerns the efficient (microbial) production and in vitro selection procedures. The latter approach allows for the high-throughput optimization of aptamers and engineered binding proteins, e.g. aiming at enhanced chemical and physical stability. This has resulted in a rapid development of the fields of nucleic acid- and protein-based affinity tools and, although they are certainly not as widely used as antibodies, the number of their applications has steadily increased in recent years. In the present review, we compare the properties of the more conventional antibodies with these innovative affinity tools. Recent advances of affinity tool developments are described, both in a medical setting (e.g. diagnostics, therapeutics and drug delivery) and in several niche areas for which antibodies appear to be less attractive. Furthermore, an outlook is provided on anticipated future developments.
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46
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Miao Z, Levi J, Cheng Z. Protein scaffold-based molecular probes for cancer molecular imaging. Amino Acids 2011; 41:1037-47. [PMID: 20174842 PMCID: PMC2914822 DOI: 10.1007/s00726-010-0503-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Accepted: 01/25/2010] [Indexed: 01/18/2023]
Abstract
Protein scaffold molecules are powerful reagents for targeting various cell signal receptors, enzymes, cytokines and other cancer-related molecules. They belong to the peptide and small protein platform with distinct properties. For the purpose of development of new generation molecular probes, various protein scaffold molecules have been labeled with imaging moieties and evaluated both in vitro and in vivo. Among the evaluated probes Affibody molecules and analogs, cystine knot peptides, and nanobodies have shown especially good characteristics as protein scaffold platforms for development of in vivo molecular probes. Quantitative data obtained from positron emission tomography, single photon emission computed tomography/CT, and optical imaging together with biodistribution studies have shown high tumor uptakes and high tumor-to-blood ratios for these probes. High tumor contrast imaging has been obtained within 1 h after injection. The success of those molecular probes demonstrates the adequacy of protein scaffold strategy as a general approach in molecular probe development.
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Affiliation(s)
- Zheng Miao
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, CA 94305-5344, USA
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47
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Affiliation(s)
- Per-Ake Nygren
- Division of Molecular Biotechnology, School of Biotechnology, Royal Institute of Technology (KTH), SE-106 91 Stockholm, Sweden
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48
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Grimm S, Salahshour S, Nygren PÅ. Monitored whole gene in vitro evolution of an anti-hRaf-1 affibody molecule towards increased binding affinity. N Biotechnol 2011; 29:534-42. [PMID: 22027369 DOI: 10.1016/j.nbt.2011.10.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 10/11/2011] [Accepted: 10/12/2011] [Indexed: 01/02/2023]
Abstract
The use of library technologies for the generation of affinity proteins often includes an affinity maturation step, based on the construction of secondary libraries from which second generation variants with improved affinities are selected. Here, we describe for the first time the affinity maturation of affibody molecules based on step-wise in vitro molecular evolution, involving cycles of error-prone PCR (epPCR) amplification for the introduction of diversity over the entire 58-residue three-helix bundle structure and ribosome display (RD) for the selection of improved variants. The model affibody molecule for the process was Z(RAF322), binding with a 1.9μm equilibrium dissociation constant (K(D)) to human Raf-1 (hRaf-1), a protein kinase of central importance in the MAPK/ERK proliferation pathway. The molecular evolution process was followed on both gene and protein levels via DNA sequencing and a biosensor-based binding analysis of pools of selected variants. After two cycles of diversification and selection, a significant increase in binding response of selected pools was seen. DNA sequencing showed that a dominant alanine to valine substitution had been effectively enriched, and was found in 83% of all selected clones, either alone or in combination with other enriched substitutions. The evolution procedure resulted in variants showing up to 26-fold increases in affinity to the hRaf-1 target. Noteworthy, for the two variants showing the highest affinities, substitutions were also found in affibody framework positions, corresponding to regions of the protein domain not addressed by traditional affibody molecule affinity maturation strategies. Interestingly, thermal melting point (T(m)) analyses showed that an increased affinity could be associated with both higher and lower T(m) values. All investigated variants showed excellent refolding properties and selective binding to hRaf-1, as analysed using a multiplexed bead-based binding assay, making them potentially valuable affinity reagents for cell biology studies.
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Affiliation(s)
- Sebastian Grimm
- Division of Molecular Biotechnology, Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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49
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Ribosome display selection of a murine IgG₁ Fab binding affibody molecule allowing species selective recovery of monoclonal antibodies. Mol Biotechnol 2011; 48:263-76. [PMID: 21197589 PMCID: PMC3115053 DOI: 10.1007/s12033-010-9367-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Affinity reagents recognizing constant parts of antibody molecules are invaluable tools in immunotechnology applications, including purification, immobilization, and detection of immunoglobulins. In this article, murine IgG1, the primary isotype of monoclonal antibodies (mAbs) was used as target for selection of novel binders from a combinatorial ribosome display (RD) library of 1011 affibody molecules. Four rounds of selection using three different mouse IgG1 mAbs as alternating targets resulted in the identification of binders with broad mIgG1 recognition and dissociation constants (KD) in the low nanomolar to low micromolar range. For one of the binders, denoted Zmab25, competition in binding to full length mIgG1 by a streptococcal protein G (SPG) fragment and selective affinity capture of mouse IgG1 Fab fragments after papain cleavage of a full mAb suggest that an epitope functionally overlapping with the SPG-binding site in the CH1 domain of mouse IgG1 had been addressed. Interestingly, biosensor-based binding experiments showed that neither human IgG1 nor bovine Ig, the latter present in fetal bovine serum (FBS) was recognized by Zmab25. This selective binding profile towards murine IgG1 was successfully exploited in species selective recovery of two different mouse mAbs from complex samples containing FBS, resembling a hybridoma culture supernatant.
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50
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Petrovskaya LE, Shingarova LN, Dolgikh DA, Kirpichnikov MP. Alternative scaffold proteins. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:581-91. [DOI: 10.1134/s1068162011050141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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