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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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Kim S, Kim S, Kim S, Kim N, Lee SW, Yi H, Lee S, Sim T, Kwon Y, Lee HS. Affinity-Directed Site-Specific Protein Labeling and Its Application to Antibody-Drug Conjugates. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306401. [PMID: 38032124 PMCID: PMC10811483 DOI: 10.1002/advs.202306401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/05/2023] [Indexed: 12/01/2023]
Abstract
Chemically modified proteins have diverse applications; however, conventional chemo-selective methods often yield heterogeneously labeled products. To address this limitation, site-specific protein labeling holds significant potential, driving extensive research in this area. Nevertheless, site-specific modification of native proteins remains challenging owing to the complexity of their functional groups. Therefore, a method for site-selective labeling of intact proteins is aimed to design. In this study, a novel approach to traceless affinity-directed intact protein labeling is established, which leverages small binding proteins and genetic code expansion technology. By applying this method, a site-specific antibody labeling with a drug, which leads to the production of highly effective antibody-drug conjugates specifically targeting breast cancer cell lines is achieved. This approach enables traceless conjugation of intact target proteins, which is a critical advantage in pharmaceutical applications. Furthermore, small helical binding proteins can be easily engineered for various target proteins, thereby expanding their potential applications in diverse fields. This innovative approach represents a significant advancement in site-specific modification of native proteins, including antibodies. It also bears immense potential for facilitating the development of therapeutic agents for various diseases.
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Affiliation(s)
- Sooin Kim
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Sanggil Kim
- New Drug Development CenterOsong Medical Innovation Foundation123 Osongsaengmyeong‐ro, Heungdeok‐guCheongjuChungbuk28160Republic of Korea
| | - Sangji Kim
- School of PharmacySungkyunkwan University2066 Seobu‐ro, Jangan‐guSuwon16419Republic of Korea
| | - Namkyoung Kim
- Department of Biomedical SciencesGraduate School of Medical ScienceBrain Korea 21 ProjectYonsei University College of Medicine50 Yonsei‐ro, Seodaemun‐guSeoul03722Republic of Korea
| | - Sang Won Lee
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Hanbin Yi
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Seungeun Lee
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
| | - Taebo Sim
- Department of Biomedical SciencesGraduate School of Medical ScienceBrain Korea 21 ProjectYonsei University College of Medicine50 Yonsei‐ro, Seodaemun‐guSeoul03722Republic of Korea
| | - Yongseok Kwon
- School of PharmacySungkyunkwan University2066 Seobu‐ro, Jangan‐guSuwon16419Republic of Korea
| | - Hyun Soo Lee
- Department of ChemistrySogang University35 Baekbeom‐ro, Mapo‐guSeoul04107Republic of Korea
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3
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Song S, Shi Q. Interface-Based Design of High-Affinity Affibody Ligands for the Purification of RBD from Spike Proteins. Molecules 2023; 28:6358. [PMID: 37687186 PMCID: PMC10489752 DOI: 10.3390/molecules28176358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) has sparked an urgent demand for advanced diagnosis and vaccination worldwide. The discovery of high-affinity ligands is of great significance for vaccine and diagnostic reagent manufacturing. Targeting the receptor binding domain (RBD) from the spike protein of severe acute respiratory syndrome-coronavirus 2, an interface at the outer surface of helices on the Z domain from protein A was introduced to construct a virtual library for the screening of ZRBD affibody ligands. Molecular docking was performed using HADDOCK software, and three potential ZRBD affibodies, ZRBD-02, ZRBD-04, and ZRBD-07, were obtained. Molecular dynamics (MD) simulation verified that the binding of ZRBD affibodies to RBD was driven by electrostatic interactions. Per-residue free energy decomposition analysis further substantiated that four residues with negative-charge characteristics on helix α1 of the Z domain participated in this process. Binding affinity analysis by microscale thermophoresis showed that ZRBD affibodies had high affinity for RBD binding, and the lowest dissociation constant was 36.3 nmol/L for ZRBD-07 among the three potential ZRBD affibodies. Herein, ZRBD-02 and ZRBD-07 affibodies were selected for chromatographic verifications after being coupled to thiol-activated Sepharose 6 Fast Flow (SepFF) gel. Chromatographic experiments showed that RBD could bind on both ZRBD SepFF gels and was eluted by 0.1 mol/L NaOH. Moreover, the ZRBD-07 SepFF gel had a higher affinity for RBD. This research provided a new idea for the design of affibody ligands and validated the potential of affibody ligands in the application of RBD purification from complex feedstock.
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Affiliation(s)
- Siyuan Song
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Qinghong Shi
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
- Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin 300350, China
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4
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Improvement of specific aiming of X-ray radiotherapy on HER2-overexpressing cancerous cell lines by targeted delivery of silver nanoparticle. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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5
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Ebrahimi F, Hosseinimehr SJ. Homomultimer strategy for improvement of radiolabeled peptides and antibody fragments in tumor targeting. Curr Med Chem 2022; 29:4923-4957. [PMID: 35450521 DOI: 10.2174/0929867329666220420131836] [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: 11/23/2021] [Revised: 01/18/2022] [Accepted: 02/07/2022] [Indexed: 11/22/2022]
Abstract
A homomultimeric radioligand is composed of multiple identical ligands connected to the linker and radionuclide to detect a variety of overexpressed receptors on cancer cells. Multimer strategy holds great potential for introducing new radiotracers based on peptide and monoclonal antibody (mAb) derivatives in molecular imaging and therapy. It offers a reliable procedure for the preparation of biological-based targeting with diverse affinities and pharmacokinetics. In this context, we provide a useful summary and interpretation of the main results by a comprehensive look at multimeric radiopharmaceuticals in nuclear oncology. Therefore, there will be explanations for the strategy mechanisms and the main variables affecting the biodistribution results. The discussion is followed by highlights of recent work in the targeting of various types of receptors. The consequences are expressed based on comparing some parameters between monomer and multimer counterparts in each relevant section.
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Affiliation(s)
- Fatemeh Ebrahimi
- Department of Radiopharmacy, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Seyed Jalal Hosseinimehr
- Department of Radiopharmacy, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
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6
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Non-Antibody-Based Binders for the Enrichment of Proteins for Analysis by Mass Spectrometry. Biomolecules 2021; 11:biom11121791. [PMID: 34944435 PMCID: PMC8698613 DOI: 10.3390/biom11121791] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 02/07/2023] Open
Abstract
There is often a need to isolate proteins from body fluids, such as plasma or serum, prior to further analysis with (targeted) mass spectrometry. Although immunoglobulin or antibody-based binders have been successful in this regard, they possess certain disadvantages, which stimulated the development and validation of alternative, non-antibody-based binders. These binders are based on different protein scaffolds and are often selected and optimized using phage or other display technologies. This review focuses on several non-antibody-based binders in the context of enriching proteins for subsequent liquid chromatography-mass spectrometry (LC-MS) analysis and compares them to antibodies. In addition, we give a brief introduction to approaches for the immobilization of binders. The combination of non-antibody-based binders and targeted mass spectrometry is promising in areas, like regulated bioanalysis of therapeutic proteins or the quantification of biomarkers. However, the rather limited commercial availability of these binders presents a bottleneck that needs to be addressed.
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7
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Shibasaki S, Karasaki M, Matsui K, Iwasaki T. Functional Evaluation of Anti-TNF-α Affibody Molecules in Biochemical Detection and Inhibition to Signalling Pathways of a Synovial Cell. Curr Pharm Biotechnol 2021; 22:1228-1234. [PMID: 33069194 DOI: 10.2174/1389201021666201016143730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/15/2020] [Accepted: 09/21/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND An affibody molecule obtained from a bioengineered staphylococcal protein was previously shown to act as an affinity binder for a wide range of targets and develop Tumour Necrosis Factor α (TNF-α)-binding clones. METHODS In this study, we demonstrated that affibody molecules against TNF-α could bind to recombinant TNF-α on the membrane for biochemical detection. In addition, we examined whether the affibody molecules could block binding between recombinant TNF-α and its receptor on MH7A synovial cells. RESULTS When a TNF-α-binding affibody was added, the production level of inflammatory mediators IL-6 and MMP-3 in MH7A were found to decrease up to 44%. Additionally, proliferation of synovial cells was also inhibited by the addition of TNF-α to cultivation media. CONCLUSION These results suggest that affibody molecules against TNF-α could be candidate molecules for the detection of TNF-α during biochemical analysis and pharmacotherapy for rheumatoid arthritis.
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Affiliation(s)
- Seiji Shibasaki
- Department of Internal Medicine, Hyogo College of Medicine, Mukogawa-cho, Nishinomiya, 663-8501, Japan
| | - Miki Karasaki
- General Education Center, Hyogo University of Health Sciences, Minatojima 1-3-6, Kobe, 650-8530, Japan
| | - Kiyoshi Matsui
- Department of Internal Medicine, Hyogo College of Medicine, Mukogawa-cho, Nishinomiya, 663-8501, Japan
| | - Tsuyoshi Iwasaki
- Department of Internal Medicine, Hyogo College of Medicine, Mukogawa-cho, Nishinomiya, 663-8501, Japan
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8
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Abstract
The concept of engineering robust protein scaffolds for novel binding functions emerged 20 years ago, one decade after the advent of recombinant antibody technology. Early examples were the Affibody, Monobody (Adnectin), and Anticalin proteins, which were derived from fragments of streptococcal protein A, from the tenth type III domain of human fibronectin, and from natural lipocalin proteins, respectively. Since then, this concept has expanded considerably, including many other protein templates. In fact, engineered protein scaffolds with useful binding specificities, mostly directed against targets of biomedical relevance, constitute an area of active research today, which has yielded versatile reagents as laboratory tools. However, despite strong interest from basic science, only a handful of those protein scaffolds have undergone biopharmaceutical development up to the clinical stage. This includes the abovementioned pioneering examples as well as designed ankyrin repeat proteins (DARPins). Here we review the current state and clinical validation of these next-generation therapeutics.
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Affiliation(s)
| | - Arne Skerra
- Lehrstuhl für Biologische Chemie, Technische Universität München, 85354 Freising, Germany;
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9
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Shakeran Z, Javadi-Zarnaghi F, Emamzadeh R. Novel luminescent affiprobes for molecular detection of Staphylococcus aureus using flow cytometry. J Appl Microbiol 2020; 130:493-503. [PMID: 32738017 DOI: 10.1111/jam.14799] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 07/11/2020] [Accepted: 07/20/2020] [Indexed: 11/27/2022]
Abstract
AIMS Diagnosis of Staphylococcus aureus is important in various diseases from hospital-acquired infections to foodborne diseases. This work reports two new luminescent affiprobes for specific detection of S. aureus. METHODS AND RESULTS To develop advanced luminescent affiprobes, enhanced green fluorescent protein (EGFP) was flanked by single and double repeats of ZpA963 affibody using molecular biology studies. The recombinant proteins including fluorescent monomeric affibody (fA1 ) and fluorescent dimeric affibody (fA2 ) were expressed in the bacterial expression system, purified and used to identify the S. aureus. Fluorescence microscope and flow cytometry results demonstrated that the treated samples with fA1 and fA2 had relatively high fluorescent mean intensities in comparison to the untreated S. aureus cells. Moreover, it was revealed that 'fA2 ' affiprobe had lower dissociation constant value (about 25-fold) and was more effective for detection of S. aureus than the 'fA1 ' affiprobe. In addition, the binding of the affiprobes for some other pathogenic bacteria i.e. Escherichia coli, Bacillus cereus, Enterococcus faecalis and Staphylococcus saprophyticus was examined. Expectedly, no cross-reaction was observed for binding the constructed affiprobes to these bacteria, eliminating possibilities for false positive results. CONCLUSIONS The results show that 'fA1 ' affiprobe and 'fA2 ' affiprobe are two new efficient luminescent affiprobes for detecting S. aureus. SIGNIFICANCE AND IMPACT OF THE STUDY We developed a new approach for detection of Staphylococcus aureus in a simple one-step process and in low concentrations of probes. In the best of our knowledge, this is the first study to direct detection of bacterial cells by affiprobes and may be used to develop new diagnostic kits.
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Affiliation(s)
- Z Shakeran
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - F Javadi-Zarnaghi
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - R Emamzadeh
- Department of Cell and Molecular Biology & Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.,NanoBioPhotonics Lab, Department of Biological Engineering, Utah State University, Utah, United States
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10
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Zhang X, Wang Y, Zhong T, Feng X. Optimal spacer arm microenvironment for the immobilization of recombinant Protein A on heterofunctional amino-epoxy agarose supports. Process Biochem 2020. [DOI: 10.1016/j.procbio.2019.11.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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11
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Begum AA, Toth I, Hussein WM, Moyle PM. Advances in Targeted Gene Delivery. Curr Drug Deliv 2020; 16:588-608. [PMID: 31142250 DOI: 10.2174/1567201816666190529072914] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/31/2019] [Accepted: 04/03/2019] [Indexed: 02/07/2023]
Abstract
Gene therapy has the potential to treat both acquired and inherited genetic diseases. Generally, two types of gene delivery vectors are used - viral vectors and non-viral vectors. Non-viral gene delivery systems have attracted significant interest (e.g. 115 gene therapies approved for clinical trials in 2018; clinicaltrials.gov) due to their lower toxicity, lack of immunogenicity and ease of production compared to viral vectors. To achieve the goal of maximal therapeutic efficacy with minimal adverse effects, the cell-specific targeting of non-viral gene delivery systems has attracted research interest. Targeting through cell surface receptors; the enhanced permeability and retention effect, or pH differences are potential means to target genes to specific organs, tissues, or cells. As for targeting moieties, receptorspecific ligand peptides, antibodies, aptamers and affibodies have been incorporated into synthetic nonviral gene delivery vectors to fulfill the requirement of active targeting. This review provides an overview of different potential targets and targeting moieties to target specific gene delivery systems.
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Affiliation(s)
- Anjuman A Begum
- School of Chemistry and Molecular Biosciences (SCMB), The University of Queensland, St Lucia 4072, Australia.,School of Pharmacy, The University of Queensland, Woolloongabba, 4102, Australia
| | - Istvan Toth
- School of Chemistry and Molecular Biosciences (SCMB), The University of Queensland, St Lucia 4072, Australia.,School of Pharmacy, The University of Queensland, Woolloongabba, 4102, Australia.,Institute for Molecular Bioscience (IMB), The University of Queensland, St Lucia, St Lucia 4072, Australia
| | - Waleed M Hussein
- School of Chemistry and Molecular Biosciences (SCMB), The University of Queensland, St Lucia 4072, Australia
| | - Peter M Moyle
- School of Pharmacy, The University of Queensland, Woolloongabba, 4102, Australia
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12
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Bam R, Laffey M, Nottberg K, Lown PS, Hackel BJ, Wilson KE. Affibody-Indocyanine Green Based Contrast Agent for Photoacoustic and Fluorescence Molecular Imaging of B7-H3 Expression in Breast Cancer. Bioconjug Chem 2019; 30:1677-1689. [PMID: 31082216 PMCID: PMC6745046 DOI: 10.1021/acs.bioconjchem.9b00239] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Spectroscopic photoacoustic (sPA) molecular imaging has high potential for identification of exogenous contrast agents targeted to specific markers. Antibody-dye conjugates have recently been used extensively for preclinical sPA and other optical imaging modalities for highly specific molecular imaging of breast cancer. However, antibody-based agents suffer from long circulation times that limit image specificity. Here, the efficacy of a small protein scaffold, the affibody (ABY), conjugated to indocyanine green (ICG), a near-infrared fluorescence dye, as a targeted molecular imaging probe is demonstrated. In particular, B7-H3 (CD276), a cellular receptor expressed in breast cancer, was imaged via sPA and fluorescence molecular imaging to differentiate invasive tumors from normal glands in mice. Administration of ICG conjugated to an ABY specific to B7-H3 (ABYB7-H3-ICG) showed significantly higher signal in mammary tumors compared to normal glands of mice. ABYB7-H3-ICG is a compelling scaffold for molecular sPA imaging for breast cancer detection.
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Affiliation(s)
- Rakesh Bam
- Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Makenna Laffey
- Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Katharine Nottberg
- Department of Radiology, Stanford University, Stanford, California 94305, United States
| | - Patrick S. Lown
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Benjamin J. Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Katheryne E. Wilson
- Department of Radiology, Stanford University, Stanford, California 94305, United States
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13
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Koo S, Cheley S, Bayley H. Redirecting Pore Assembly of Staphylococcal α-Hemolysin by Protein Engineering. ACS CENTRAL SCIENCE 2019; 5:629-639. [PMID: 31041382 PMCID: PMC6487460 DOI: 10.1021/acscentsci.8b00910] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Indexed: 05/03/2023]
Abstract
α-Hemolysin (αHL), a β-barrel pore-forming toxin (βPFT), is secreted as a water-soluble monomer by Staphylococcus aureus. Upon binding to receptors on target cell membranes, αHL assembles to form heptameric membrane-spanning pores. We have previously engineered αHL to create a protease-activatable toxin that is activated by site-specific proteolysis including by tumor proteases. In this study, we redesigned αHL so that it requires 2-fold activation on target cells through (i) binding to specific receptors, and (ii) extracellular proteolytic cleavage. To assess our strategy, we constructed a fusion protein of αHL with galectin-1 (αHLG1, αHL-Galectin-1 chimera). αHLG1 was cytolytic toward cells that lack a receptor for wild-type αHL. We then constructed protease-activatable mutants of αHLG1 (PAMαHLG1s). PAMαHLG1s were activated by matrix metalloproteinase 2 (MMP-2) and had approximately 50-fold higher cytolytic activity toward MMP-2 overexpressing cells (HT-1080 cells) than toward non-overexpressing cells (HL-60 cells). Our approach provides a novel strategy for tailoring pore-forming toxins for therapeutic applications.
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Affiliation(s)
- Sunwoo Koo
- Department
of Neuroscience and Experimental Therapeutics, Texas A&M University Health Science Center, 8447 Riverside Parkway, Bryan, Texas 77807, United States
- E-mail: . Phone: 1-979-436-0381
| | - Stephen Cheley
- Department
of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, T6G 2E1 Alberta, Canada
| | - Hagan Bayley
- Department
of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield
Road, Oxford, OX1 3TA England, United Kingdom
- E-mail: . Phone: +44 1865 285101
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14
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Toxin Neutralization Using Alternative Binding Proteins. Toxins (Basel) 2019; 11:toxins11010053. [PMID: 30658491 PMCID: PMC6356946 DOI: 10.3390/toxins11010053] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 01/07/2019] [Accepted: 01/12/2019] [Indexed: 12/20/2022] Open
Abstract
Animal toxins present a major threat to human health worldwide, predominantly through snakebite envenomings, which are responsible for over 100,000 deaths each year. To date, the only available treatment against snakebite envenoming is plasma-derived antivenom. However, despite being key to limiting morbidity and mortality among snakebite victims, current antivenoms suffer from several drawbacks, such as immunogenicity and high cost of production. Consequently, avenues for improving envenoming therapy, such as the discovery of toxin-sequestering monoclonal antibodies against medically important target toxins through phage display selection, are being explored. However, alternative binding protein scaffolds that exhibit certain advantages compared to the well-known immunoglobulin G scaffold, including high stability under harsh conditions and low cost of production, may pose as possible low-cost alternatives to antibody-based therapeutics. There is now a plethora of alternative binding protein scaffolds, ranging from antibody derivatives (e.g., nanobodies), through rationally designed derivatives of other human proteins (e.g., DARPins), to derivatives of non-human proteins (e.g., affibodies), all exhibiting different biochemical and pharmacokinetic profiles. Undeniably, the high level of engineerability and potentially low cost of production, associated with many alternative protein scaffolds, present an exciting possibility for the future of snakebite therapeutics and merit thorough investigation. In this review, a comprehensive overview of the different types of binding protein scaffolds is provided together with a discussion on their relevance as potential modalities for use as next-generation antivenoms.
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15
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Lagoutte P, Lugari A, Elie C, Potisopon S, Donnat S, Mignon C, Mariano N, Troesch A, Werle B, Stadthagen G. Combination of ribosome display and next generation sequencing as a powerful method for identification of affibody binders against β-lactamase CTX-M15. N Biotechnol 2019; 50:60-69. [PMID: 30634000 DOI: 10.1016/j.nbt.2019.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 01/07/2019] [Accepted: 01/07/2019] [Indexed: 01/15/2023]
Abstract
CTX-M15 is one of the most widespread, extended spectrum β-lactamases, a major determinant of antibiotic resistance representing urgent public health threats, among enterobacterial strains infecting humans and animals. Here we describe the selection of binders to CTX-M15 from a combinatorial affibody library displayed on ribosomes. Upon three increasingly selective ribosome display iterations, selected variants were identified by next generation sequencing (NGS). Nine affibody variants with high relative abundance bearing QRP and QLH amino acid motifs at residues 9-11 were produced and characterized in terms of stability, affinity and specificity. All affibodies were correctly folded, with affinities ranging from 0.04 to 2 μM towards CTX-M15, and successfully recognized CTX-M15 in bacterial lysates, culture supernatants and on whole bacteria. It was further demonstrated that the binding of affibody molecules to CTX-M15 modulated the enzyme's kinetic parameters. This work provides an approach using ribosome display coupled to NGS for the rapid generation of protein ligands of interest in diagnostic and research applications.
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Affiliation(s)
| | - Adrien Lugari
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France
| | - Céline Elie
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France
| | | | | | | | | | - Alain Troesch
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France
| | - Bettina Werle
- BIOASTER, 40 Avenue Tony Garnier, 69007 Lyon, France.
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16
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Oriented covalent immobilization of recombinant protein A on the glutaraldehyde activated agarose support. Int J Biol Macromol 2018; 120:100-108. [DOI: 10.1016/j.ijbiomac.2018.08.074] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/11/2018] [Accepted: 08/15/2018] [Indexed: 12/21/2022]
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17
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Case BA, Kruziki MA, Stern LA, Hackel BJ. Evaluation of affibody charge modification identified by synthetic consensus design in molecular PET imaging of epidermal growth factor receptor. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2018; 3:171-182. [PMID: 31467687 PMCID: PMC6715147 DOI: 10.1039/c7me00095b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Tumor overexpression of epidermal growth factor receptor (EGFR) correlates to therapeutic response in select patient populations. Thus, molecular positron emission tomography (PET) imaging of EGFR could stratify responders versus non-responders. We previously demonstrated effectiveness of a "synthetic consensus" design principle to identify six neutralizing mutations within a 58-amino acid EGFR-targeted affibody domain. Herein, we extend the approach to identify additional neutralized variants that vary net charge from -2 to either -4 or +4 while retaining high affinity (1.6 ± 1.2 nM and 2.5 ± 0.7 nM), specific binding to EGFR, secondary structure, and stability (Tm = 68 °C and 59 °C). We radiolabeled the resultant collection of five charge variants with 64Cu and evaluated PET imaging performance in murine models with subcutaneously xenografted EGFRhigh and EGFRlow tumors. All variants exhibited good EGFRhigh tumor imaging as early as 1 h, with EA35S (+3/-5) achieving 7.7 ± 1.4 %ID/g tumor at 4 h with 1.5 ± 0.3%ID/g EGFRlow tumor, 34 ± 5 tumor:muscle and 12 ± 3 tumor:blood ratios. The positively charged EA62S mutant (+6/-2) exhibited 2.2-3.3-fold higher liver signal than the other variants (p<0.01). The EA68 variant with higher charge density was more stable to human and mouse serum than neutralized variants. In a comparison of radiometal chelators, 1,4,7-triazacyclononane,1-glutaric acid-4,7-acetic acid (NODAGA) exhibited superior physiological specificity to 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA). In total, these studies comparatively evaluated a set of EGFR-targeted affibodies varying in net charge and charge density, which revealed functional variations that are useful in engineering an ideal probe for translational studies.
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Affiliation(s)
- Brett A Case
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455
| | - Max A Kruziki
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455
| | - Lawrence A Stern
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota - Twin Cities, Minneapolis, MN 55455
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18
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Woldring DR, Holec PV, Stern LA, Du Y, Hackel BJ. A Gradient of Sitewise Diversity Promotes Evolutionary Fitness for Binder Discovery in a Three-Helix Bundle Protein Scaffold. Biochemistry 2017; 56:1656-1671. [PMID: 28248518 DOI: 10.1021/acs.biochem.6b01142] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Engineered proteins provide clinically and industrially impactful molecules and utility within fundamental research, yet inefficiencies in discovering lead variants with new desired functionality, while maintaining stability, hinder progress. Improved function, which can result from a few strategic mutations, is fundamentally separate from discovering novel function, which often requires large leaps in sequence space. While a highly diverse combinatorial library covering immense sequence space would empower protein discovery, the ability to sample only a minor subset of sequence space and the typical destabilization of random mutations preclude this strategy. A balance must be reached. At library scale, compounding several destabilizing mutations renders many variants unable to properly fold and devoid of function. Broadly searching sequence space while reducing the level of destabilization may enhance evolution. We exemplify this balance with affibody, a three-helix bundle protein scaffold. Using natural ligand data sets, stability and structural computations, and deep sequencing of thousands of binding variants, a protein library was designed on a sitewise basis with a gradient of mutational levels across 29% of the protein. In direct competition of biased and uniform libraries, both with 1 × 109 variants, for discovery of 6 × 104 ligands (5 × 103 clusters) toward seven targets, biased amino acid frequency increased ligand discovery 13 ± 3-fold. Evolutionarily favorable amino acids, both globally and site-specifically, are further elucidated. The sitewise amino acid bias aids evolutionary discovery by reducing the level of mutant destabilization as evidenced by a midpoint of denaturation (62 ± 4 °C) 15 °C higher than that of unbiased mutants (47 ± 11 °C; p < 0.001). Sitewise diversification, identified by high-throughput evolution and rational library design, improves discovery efficiency.
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Affiliation(s)
- Daniel R Woldring
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities , 421 Washington Avenue Southeast, Minneapolis, Minnesota 55455, United States
| | - Patrick V Holec
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities , 421 Washington Avenue Southeast, Minneapolis, Minnesota 55455, United States
| | - Lawrence A Stern
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities , 421 Washington Avenue Southeast, Minneapolis, Minnesota 55455, United States
| | - Yang Du
- Molecular and Cellular Physiology, Stanford University , 279 Campus Drive, Stanford, California 94305, United States
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities , 421 Washington Avenue Southeast, Minneapolis, Minnesota 55455, United States
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19
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Abstract
It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.
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20
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Valliant JF. A Bridge Not Too Far: Linking Disciplines Through Molecular Imaging Probes. J Nucl Med Technol 2016; 44:173-83. [DOI: 10.2967/jnumed.109.068312] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Accepted: 04/01/2010] [Indexed: 11/16/2022] Open
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21
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Case BA, Hackel BJ. Synthetic and natural consensus design for engineering charge within an affibody targeting epidermal growth factor receptor. Biotechnol Bioeng 2016; 113:1628-38. [PMID: 26724421 PMCID: PMC5200887 DOI: 10.1002/bit.25931] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 12/19/2015] [Accepted: 12/28/2015] [Indexed: 01/10/2023]
Abstract
Protein ligand charge can impact physiological delivery with charge reduction often benefiting performance. Yet neutralizing mutations can be detrimental to protein function. Herein, three approaches are evaluated to introduce charged-to-neutral mutations of three cations and three anions within an affibody engineered to bind epidermal growth factor receptor. These approaches-combinatorial library sorting or consensus design, based on natural homologs or library-sorted mutants-are used to identify mutations with favorable affinity, stability, and recombinant yield. Consensus design, based on 942 affibody homologs, yielded a mutant of modest function (Kd = 11 ±4 nM, Tm = 62°C, and yield = 4.0 ± 0.8 mg/L as compared to 5.3 ± 1.7 nM, 71°C, and 3.5 ± 0.3 mg/L for the parental affibody). Extension of consensus design to 10 additional mutants exhibited varied performance including a substantially improved mutant (Kd = 6.9 ± 1.4 nM, Tm = 71°C, and 12.7 ± 0.9 mg/L yield). Sorting a homolog-based combinatorial library of 7 × 10(5) mutants generated a distribution of mutants with lower stability and yield, but did identify one strongly binding variant (Kd = 1.2 ± 0.3 nM, Tm = 69°C, and 6.0 ± 0.4 mg/L yield). Synthetic consensus design, based on the amino acid distribution in functional library mutants, yielded higher affinities (P = 0.05) with comparable stabilities and yields. The best of four analyzed clones had Kd = 1.7 ± 0.5 nM, Tm = 68°C, and 7.0 ± 0.5 mg/L yield. While all three approaches were effective in creating targeted affibodies with six charged-to-neutral mutations, synthetic consensus design proved to be the most robust. Synthetic consensus design provides a valuable tool for ligand engineering, particularly in the context of charge manipulation. Biotechnol. Bioeng. 2016;113: 1628-1638. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Brett A Case
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Avenue SE, 356 Amundson Hall, Minneapolis, Minnesota, 55455
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Avenue SE, 356 Amundson Hall, Minneapolis, Minnesota, 55455.
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22
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Huang R, Gorman KT, Vinci CR, Dobrovetsky E, Gräslund S, Kay BK. Streamlining the Pipeline for Generation of Recombinant Affinity Reagents by Integrating the Affinity Maturation Step. Int J Mol Sci 2015; 16:23587-603. [PMID: 26437402 PMCID: PMC4632715 DOI: 10.3390/ijms161023587] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 09/18/2015] [Accepted: 09/23/2015] [Indexed: 12/26/2022] Open
Abstract
Often when generating recombinant affinity reagents to a target, one singles out an individual binder, constructs a secondary library of variants, and affinity selects a tighter or more specific binder. To enhance the throughput of this general approach, we have developed a more integrated strategy where the "affinity maturation" step is part of the phage-display pipeline, rather than a follow-on process. In our new schema, we perform two rounds of affinity selection, followed by error-prone PCR on the pools of recovered clones, generation of secondary libraries, and three additional rounds of affinity selection, under conditions of off-rate competition. We demonstrate the utility of this approach by generating low nanomolar fibronectin type III (FN3) monobodies to five human proteins: ubiquitin-conjugating enzyme E2 R1 (CDC34), COP9 signalosome complex subunit 5 (COPS5), mitogen-activated protein kinase kinase 5 (MAP2K5), Splicing factor 3A subunit 1 (SF3A1) and ubiquitin carboxyl-terminal hydrolase 11 (USP11). The affinities of the resulting monobodies are typically in the single-digit nanomolar range. We demonstrate the utility of two binders by pulling down the targets from a spiked lysate of HeLa cells. This integrated approach should be applicable to directed evolution of any phage-displayed affinity reagent scaffold.
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Affiliation(s)
- Renhua Huang
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607, USA.
| | - Kevin T Gorman
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607, USA.
| | - Chris R Vinci
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607, USA.
| | - Elena Dobrovetsky
- Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, ON M5G1L7, Canada.
| | - Susanne Gräslund
- Structural Genomics Consortium, University of Toronto, 101 College St., Toronto, ON M5G1L7, Canada.
| | - Brian K Kay
- Department of Biological Sciences, University of Illinois at Chicago, 900 S. Ashland Ave., Chicago, IL 60607, USA.
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23
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Vazquez-Lombardi R, Phan TG, Zimmermann C, Lowe D, Jermutus L, Christ D. Challenges and opportunities for non-antibody scaffold drugs. Drug Discov Today 2015; 20:1271-83. [PMID: 26360055 DOI: 10.1016/j.drudis.2015.09.004] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 08/06/2015] [Accepted: 09/01/2015] [Indexed: 12/22/2022]
Abstract
The first candidates from the promising class of small non-antibody protein scaffolds are now moving into clinical development and practice. Challenges remain, and scaffolds will need to be further tailored toward applications where they provide real advantages over established therapeutics to succeed in a rapidly evolving drug development landscape.
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Affiliation(s)
- Rodrigo Vazquez-Lombardi
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia; The University of New South Wales, Faculty of Medicine, St Vincent's Clinical School, Darlinghurst, Sydney, NSW 2010, Australia
| | - Tri Giang Phan
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia; The University of New South Wales, Faculty of Medicine, St Vincent's Clinical School, Darlinghurst, Sydney, NSW 2010, Australia
| | - Carsten Zimmermann
- University of San Diego, School of Business Administration, 5998 Alcala Park, San Diego, CA 92110, USA
| | - David Lowe
- MedImmune Ltd., Granta Park, Cambridge CB21 6GH, UK
| | - Lutz Jermutus
- MedImmune Ltd., Granta Park, Cambridge CB21 6GH, UK; Trinity Hall, University of Cambridge, Trinity Lane CB2 1TJ, UK.
| | - Daniel Christ
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia; The University of New South Wales, Faculty of Medicine, St Vincent's Clinical School, Darlinghurst, Sydney, NSW 2010, Australia.
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24
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25
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26
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Raina M, Sharma R, Deacon SE, Tiede C, Tomlinson D, Davies AG, McPherson MJ, Wälti C. Antibody mimetic receptor proteins for label-free biosensors. Analyst 2015; 140:803-10. [DOI: 10.1039/c4an01418a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Small synthetic antibody mimetic receptor proteins which offer high stability, specificity and affinity are presented as capture molecules in solid-state electro-chemical biosensors.
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Affiliation(s)
- M. Raina
- Bioelectronics
- School of Electronic and Electrical Engineering
- University of Leeds
- Leeds
- UK
| | - R. Sharma
- Bioelectronics
- School of Electronic and Electrical Engineering
- University of Leeds
- Leeds
- UK
| | - S. E. Deacon
- School of Molecular and Cellular Biology
- University of Leeds
- Leeds
- UK
| | - C. Tiede
- School of Molecular and Cellular Biology
- University of Leeds
- Leeds
- UK
| | - D. Tomlinson
- School of Molecular and Cellular Biology
- University of Leeds
- Leeds
- UK
- Astbury Centre for Structural Molecular Biology
| | - A. G. Davies
- Bioelectronics
- School of Electronic and Electrical Engineering
- University of Leeds
- Leeds
- UK
| | - M. J. McPherson
- School of Molecular and Cellular Biology
- University of Leeds
- Leeds
- UK
- Astbury Centre for Structural Molecular Biology
| | - C. Wälti
- Bioelectronics
- School of Electronic and Electrical Engineering
- University of Leeds
- Leeds
- UK
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27
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Lindborg M, Dubnovitsky A, Olesen K, Bjorkman T, Abrahmsen L, Feldwisch J, Hard T. High-affinity binding to staphylococcal protein A by an engineered dimeric Affibody molecule. Protein Eng Des Sel 2013; 26:635-44. [DOI: 10.1093/protein/gzt038] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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28
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Gilbreth RN, Koide S. Structural insights for engineering binding proteins based on non-antibody scaffolds. Curr Opin Struct Biol 2012; 22:413-20. [PMID: 22749196 DOI: 10.1016/j.sbi.2012.06.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 05/25/2012] [Accepted: 06/01/2012] [Indexed: 11/18/2022]
Abstract
Engineered binding proteins derived from non-antibody scaffolds constitute an increasingly prominent class of reagents in both research and therapeutic applications. The growing number of crystal structures of these 'alternative' scaffold-based binding proteins in complex with their targets illustrate the mechanisms of molecular recognition that are common among these systems and those unique to each. This information is useful for critically assessing and improving/expanding engineering strategies. Furthermore, the structural features of these synthetic proteins produced under tightly controlled, directed evolution deepen our understanding of the underlying principles governing molecular recognition.
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Affiliation(s)
- Ryan N Gilbreth
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.
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29
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Noel JK, Schug A, Verma A, Wenzel W, Garcia AE, Onuchic JN. Mirror images as naturally competing conformations in protein folding. J Phys Chem B 2012; 116:6880-8. [PMID: 22497217 DOI: 10.1021/jp212623d] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Evolution has selected a protein's sequence to be consistent with the native state geometry, as this configuration must be both thermodynamically stable and kinetically accessible to prevent misfolding and loss of function. In simple protein geometries, such as coiled-coil helical bundles, symmetry produces a competing, globally different, near mirror image with identical secondary structure and similar native contact interactions. Experimental techniques such as circular dichroism, which rely on probing secondary structure content, cannot readily distinguish these folds. Here, we want to clarify whether the native fold and mirror image are energetically competitive by investigating the free energy landscape of three-helix bundles. To prevent a bias from a specific computational approach, the present study employs the structure prediction forcefield PFF01/02, explicit solvent replica exchange molecular dynamics (REMD) with the Amber94 forcefield, and structure-based simulations based on energy landscape theory. We observe that the native fold and its mirror image have a similar enthalpic stability and are thermodynamically competitive. There is evidence that the mirror fold has faster folding kinetics and could function as a kinetic trap. All together, our simulations suggest that mirror images might not just be a computational annoyance but are competing folds that might switch depending on environmental conditions or functional considerations.
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Affiliation(s)
- Jeffrey K Noel
- Center for Theoretical Biological Physics and Department of Physics, Rice University, Houston, Texas 77005, USA
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30
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Zhang Y, Cai W. Molecular imaging of insulin-like growth factor 1 receptor in cancer. AMERICAN JOURNAL OF NUCLEAR MEDICINE AND MOLECULAR IMAGING 2012; 2:248-259. [PMID: 23066521 PMCID: PMC3477732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 03/22/2012] [Indexed: 06/01/2023]
Abstract
Insulin-like growth factor 1 receptor (IGF1R) plays an important role in proliferation, apoptosis, angiogenesis, and tumor invasion. Histology and in situ hybridization studies have revealed that IGF1R was significantly up-regulated at the protein and mRNA level in many types of cancer. Since measuring IGF1R expression with immunohistochemistry has many limitations, non-invasive imaging of IGF1R can allow for more accurate patient stratification (e.g. selecting the right patient population for IGF1R-targeted therapy) and more effective monitoring of the therapeutic responses in cancer patients. In this review, we will summarize the current status of imaging IGF1R expression in cancer, which includes single-photon emission computed tomography, positron emission tomography, fluorescence, and γ-camera imaging. The four major classes of ligands that have been developed for non-invasive visualization of IGF1R will be discussed: proteins, antibodies, peptides, and affibodies. To date, molecular imaging of IGF1R expression is understudied and more research effort is needed in the future.
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Affiliation(s)
- Yin Zhang
- Department of Medical Physics, School of Medicine and Public Health, University of Wisconsin - MadisonWI, USA
| | - Weibo Cai
- Department of Medical Physics, School of Medicine and Public Health, University of Wisconsin - MadisonWI, USA
- Department of Radiology, School of Medicine and Public Health, University of Wisconsin - MadisonWI, USA
- University of Wisconsin Carbone Cancer CenterMadison, WI, USA
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31
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Govindarajan S, Sivakumar J, Garimidi P, Rangaraj N, Kumar JM, Rao NM, Gopal V. Targeting human epidermal growth factor receptor 2 by a cell-penetrating peptide–affibody bioconjugate. Biomaterials 2012; 33:2570-82. [DOI: 10.1016/j.biomaterials.2011.12.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 12/02/2011] [Indexed: 11/24/2022]
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32
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Cavalli A, Montalvao RW, Vendruscolo M. Using Chemical Shifts to Determine Structural Changes in Proteins upon Complex Formation. J Phys Chem B 2011; 115:9491-4. [DOI: 10.1021/jp202647q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Andrea Cavalli
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Rinaldo W. Montalvao
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, U.K
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33
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Wållberg H, Löfdahl PÅ, Tschapalda K, Uhlén M, Tolmachev V, Nygren PÅ, Ståhl S. Affinity recovery of eight HER2-binding affibody variants using an anti-idiotypic affibody molecule as capture ligand. Protein Expr Purif 2011; 76:127-35. [DOI: 10.1016/j.pep.2010.10.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 10/19/2010] [Accepted: 10/19/2010] [Indexed: 10/18/2022]
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34
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Gopal V, Guruprasad K. Structure prediction and validation of an affibody engineered for cell-specific nucleic acid targeting. SYSTEMS AND SYNTHETIC BIOLOGY 2011; 4:293-7. [PMID: 22132056 DOI: 10.1007/s11693-011-9074-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 11/23/2010] [Accepted: 02/03/2011] [Indexed: 12/18/2022]
Abstract
Cell-penetrating peptides comprising cloned epitopes that contribute to membrane transduction, DNA-binding and cell targeting functions are known to facilitate nucleic acid delivery. Using the ITASSER software, we predicted the 3-D structure of a well characterized and efficient transfecting cell-penetrating peptide, namely TAT-Mu and its derivative TAT-Mu-AF protein that harbors a targeting ligand, the HER2-binding affibody. Our model predicts TAT-Mu-AF fusion protein as primarily comprising α-helices. The affibody in TAT-Mu-AF is predicted as a 3-helical domain that is distinct from the TAT-Mu domain. Its positioning in three-dimensional structure is oriented in a manner that possibly favors interactions with receptor and facilitates transport to the target site. The linker region between TAT-Mu and the affibody is also predicted as a helix that is likely to stabilize the overall fold of the TAT-Mu-AF complex. Further, the evaluation of secondary structure of the designed TAT-Mu-AF fusion protein by circular dichroism is in support of our predictions.
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Affiliation(s)
- Vijaya Gopal
- Centre for Cellular and Molecular Biology, (Council for Scientific and Industrial Research), Uppal Road, Hyderabad, Andhra Pradesh 500007 India
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35
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Lindborg M, Cortez E, Höidén-Guthenberg I, Gunneriusson E, von Hage E, Syud F, Morrison M, Abrahmsén L, Herne N, Pietras K, Frejd FY. Engineered high-affinity affibody molecules targeting platelet-derived growth factor receptor β in vivo. J Mol Biol 2011; 407:298-315. [PMID: 21277312 DOI: 10.1016/j.jmb.2011.01.033] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 11/20/2010] [Accepted: 01/14/2011] [Indexed: 12/13/2022]
Abstract
Platelet-derived growth factor receptor (PDGFR) β is a marker of stromal pericytes and fibroblasts and represents an interesting target for both diagnosis and therapy of solid tumors. A receptor-specific imaging agent would be a useful tool for further understanding the prognostic role of this receptor in vivo. Affibody molecules constitute a class of very small binding proteins that are highly suited for in vivo imaging applications and that can be selected to specifically recognize a desired target protein. Here we describe the isolation of PDGFRβ-specific Affibody molecules with subnanomolar affinity. First-generation Affibody molecules were generated from a large naive library using phage display selection. Subsequently, sequences from binders having a desired selectivity profile and competing with the natural ligand for binding were used in the design of an affinity maturation library, which was created using a single partially randomized oligonucleotide. From this second-generation library, Affibody molecules with a 10-fold improvement in affinity (K(d)=0.4-0.5 nM) for human PDGFRβ and a 4-fold improvement in affinity (K(d)=6-7 nM) for murine PDGFRβ were isolated and characterized. Complete reversible folding after heating to 90 °C, as demonstrated by circular dichroism analysis, supports tolerance to labeling conditions for molecular imaging. The binders were highly specific, as verified by dot blot showing staining reactivity only with human and murine PDGFRβ, but not with human PDGFRα, or a panel of control proteins including 16 abundant human serum proteins. The final binder recognized the native conformation of PDGFRβ expressed in murine NIH-3T3 fibroblasts and human AU565 cells, and inhibited ligand-induced receptor phosphorylation in PDGFRβ-transfected porcine aortic endothelial cells. The PDGFRβ-specific Affibody molecule also accumulated around tumoral blood vessels in a model of spontaneous insulinoma, confirming a potential for in vivo targeting.
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36
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Protein stability, flexibility and function. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1814:969-76. [PMID: 21094283 DOI: 10.1016/j.bbapap.2010.11.005] [Citation(s) in RCA: 156] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 09/24/2010] [Accepted: 11/11/2010] [Indexed: 02/08/2023]
Abstract
Proteins rely on flexibility to respond to environmental changes, ligand binding and chemical modifications. Potentially, a perturbation that changes the flexibility of a protein may interfere with its function. Millions of mutations have been performed on thousands of proteins in quests for a delineation of the molecular details of their function. Several of these mutations interfered with the binding of a specific ligand with a concomitant effect on the stability of the protein scaffold. It has been ambiguous and not straightforward to recognize if any relationships exist between the stability of a protein and the affinity for its ligand. In this review, we present examples of proteins where changes in stability results in changes in affinity and of proteins where stability and affinity are uncorrelated. We discuss the possibility for a relationship between stability and binding. From the data presented is it clear that there are specific sites (flexibility hotspots) in proteins that are important for both binding and stability. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.
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Structural basis for high-affinity HER2 receptor binding by an engineered protein. Proc Natl Acad Sci U S A 2010; 107:15039-44. [PMID: 20696930 DOI: 10.1073/pnas.1005025107] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human epidermal growth factor receptor 2 (HER2) is specifically overexpressed in tumors of several cancers, including an aggressive form of breast cancer. It is therefore a target for both cancer diagnostics and therapy. The 58 amino acid residue Zher2 affibody molecule was previously engineered as a high-affinity binder of HER2. Here we determined the structure of Zher2 in solution and the crystal structure of Zher2 in complex with the HER2 extracellular domain. Zher2 binds to a conformational epitope on HER2 that is distant from those recognized by the therapeutic antibodies trastuzumab and pertuzumab. Its small size and lack of interference may provide Zher2 with advantages for diagnostic use or even for delivery of therapeutic agents to HER2-expressing tumors when trastuzumab or pertuzumab are already employed. Biophysical characterization shows that Zher2 is thermodynamically stable in the folded state yet undergoing conformational interconversion on a submillisecond time scale. The data suggest that it is the HER2-binding conformation that is formed transiently prior to binding. Still, binding is very strong with a dissociation constant K(D) = 22 pM, and perfect conformational homogeneity is therefore not necessarily required in engineered binding proteins. A comparison of the original Z domain scaffold to free and bound Zher2 structures reveals how high-affinity binding has evolved during selection and affinity maturation and suggests how a compromise between binding surface optimization and stability and dynamics of the unbound state has been reached.
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Grimm S, Lundberg E, Yu F, Shibasaki S, Vernet E, Skogs M, Nygren PÅ, Gräslund T. Selection and characterisation of affibody molecules inhibiting the interaction between Ras and Raf in vitro. N Biotechnol 2010; 27:766-73. [PMID: 20674812 DOI: 10.1016/j.nbt.2010.07.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Revised: 07/16/2010] [Accepted: 07/23/2010] [Indexed: 10/19/2022]
Abstract
Development of molecules with the ability to selectively inhibit particular protein-protein interactions is important in providing tools for understanding cell biology. In this work, we describe efforts to select small Ras- and Raf-specific three-helix bundle affibody binding proteins capable of inhibiting the interaction between H-Ras and Raf-1, from a combinatorial library displayed on bacteriophage. Target-specific variants with typically high nanomolar or low micromolar affinities (K(D)) could be selected successfully against both proteins, as shown by dot blot, ELISA and real-time biospecific interaction analyses. Affibody molecule variants selected against H-Ras were shown to bind epitopes overlapping each other at a site that differed from that at which H-Ras interacts with Raf-1. In contrast, an affibody molecule isolated during selection against Raf-1 was shown to effectively inhibit the interaction between H-Ras and Raf-1 in a dose-dependent manner. Possible intracellular applications of the selected affibody molecules are discussed.
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Affiliation(s)
- Sebastian Grimm
- Division of Molecular Biotechnology, Royal Institute of Technology, Stockholm, Sweden
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Alm T, Yderland L, Nilvebrant J, Halldin A, Hober S. A small bispecific protein selected for orthogonal affinity purification. Biotechnol J 2010; 5:605-17. [DOI: 10.1002/biot.201000041] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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40
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Feldwisch J, Tolmachev V, Lendel C, Herne N, Sjöberg A, Larsson B, Rosik D, Lindqvist E, Fant G, Höidén-Guthenberg I, Galli J, Jonasson P, Abrahmsén L. Design of an optimized scaffold for affibody molecules. J Mol Biol 2010; 398:232-47. [PMID: 20226194 DOI: 10.1016/j.jmb.2010.03.002] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 02/26/2010] [Accepted: 03/03/2010] [Indexed: 12/15/2022]
Abstract
Affibody molecules are non-immunoglobulin-derived affinity proteins based on a three-helical bundle protein domain. Here, we describe the design process of an optimized Affibody molecule scaffold with improved properties and a surface distinctly different from that of the parental scaffold. The improvement was achieved by applying an iterative process of amino acid substitutions in the context of the human epidermal growth factor receptor 2 (HER2)-specific Affibody molecule Z(HER2:342). Replacements in the N-terminal region, loop 1, helix 2 and helix 3 were guided by extensive structural modeling using the available structures of the parent Z domain and Affibody molecules. The effect of several single substitutions was analyzed followed by combination of up to 11 different substitutions. The two amino acid substitutions N23T and S33K accounted for the most dramatic improvements, including increased thermal stability with elevated melting temperatures of up to +12 degrees C. The optimized scaffold contains 11 amino acid substitutions in the nonbinding surface and is characterized by improved thermal and chemical stability, as well as increased hydrophilicity, and enables generation of identical Affibody molecules both by chemical peptide synthesis and by recombinant bacterial expression. A HER2-specific Affibody tracer, [MMA-DOTA-Cys61]-Z(HER2:2891)-Cys (ABY-025), was produced by conjugating MMA-DOTA (maleimide-monoamide-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) to the peptide produced either chemically or in Escherichia coli. ABY-025 showed high affinity and specificity for HER2 (equilibrium dissociation constant, K(D), of 76 pM) and detected HER2 in tissue sections of SKOV-3 xenograft and human breast tumors. The HER2-binding capacity was fully retained after three cycles of heating to 90 degrees C followed by cooling to room temperature. Furthermore, the binding surfaces of five Affibody molecules targeting other proteins (tumor necrosis factor alpha, insulin, Taq polymerase, epidermal growth factor receptor or platelet-derived growth factor receptor beta) were grafted onto the optimized scaffold, resulting in molecules with improved thermal stability and a more hydrophilic nonbinding surface.
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41
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Holm L, Moody P, Howarth M. Electrophilic affibodies forming covalent bonds to protein targets. J Biol Chem 2009; 284:32906-13. [PMID: 19759009 DOI: 10.1074/jbc.m109.034322] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Antibody affinity limits sensitivity of detection in many areas of biology and medicine. High affinity usually depends on achieving the optimal combination of the natural 20 amino acids in the antibody binding site. Here, we investigate the effect on recognition of protein targets of placing an unnatural electrophile adjacent to the target binding site. We positioned a weak electrophile, acrylamide, near the binding site between an affibody, a non-immunoglobulin binding scaffold, and its protein target. The proximity between cysteine, lysine, or histidine on the target protein drove covalent bond formation to the electrophile on the affibody. Covalent bonds did not form to a non-interacting point mutant of the target, and there was minimal cross-reactivity with serum, cell lysate, or when imaging at the cell surface. Electrophilic affibodies showed more stable protein imaging at the surface of mammalian cells, and the sensitivity of protein detection in an immunoassay improved by two orders of magnitude. Thus electrophilic affibodies combined good specificity with improved detection of protein targets.
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Affiliation(s)
- Lotta Holm
- Department of Biochemistry, Oxford University, South Parks Road, Oxford OX1 3QU, United Kingdom
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42
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Engineered protein scaffolds as next-generation antibody therapeutics. Curr Opin Chem Biol 2009; 13:245-55. [DOI: 10.1016/j.cbpa.2009.04.627] [Citation(s) in RCA: 269] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Accepted: 04/20/2009] [Indexed: 12/26/2022]
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43
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Webster JM, Zhang R, Gambhir SS, Cheng Z, Syud FA. Engineered Two-Helix Small Proteins for Molecular Recognition. Chembiochem 2009; 10:1293-6. [DOI: 10.1002/cbic.200900062] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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44
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Boschek CB, Apiyo DO, Soares TA, Engelmann HE, Pefaur NB, Straatsma TP, Baird CL. Engineering an ultra-stable affinity reagent based on Top7. Protein Eng Des Sel 2009; 22:325-32. [DOI: 10.1093/protein/gzp007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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45
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Grönwall C, Ståhl S. Engineered affinity proteins—Generation and applications. J Biotechnol 2009; 140:254-69. [DOI: 10.1016/j.jbiotec.2009.01.014] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2008] [Revised: 12/05/2008] [Accepted: 01/26/2009] [Indexed: 12/11/2022]
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46
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Hatch DM, Weiss AA, Kale RR, Iyer SS. Biotinylated Bi- and Tetra-antennary Glycoconjugates forEscherichia coliDetection. Chembiochem 2008; 9:2433-42. [DOI: 10.1002/cbic.200800188] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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47
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Sennhauser G, Grütter MG. Chaperone-assisted crystallography with DARPins. Structure 2008; 16:1443-53. [PMID: 18940601 DOI: 10.1016/j.str.2008.08.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Revised: 08/14/2008] [Accepted: 08/18/2008] [Indexed: 11/29/2022]
Abstract
The structure of proteins that are difficult to crystallize can often be solved by forming a noncovalent complex with a helper protein--a crystallization "chaperone." Although several such applications have been described to date, their handling usually is still very laborious. A valuable addition to the present repertoire of binding proteins is the recently developed designed ankyrin repeat protein (DARPin) technology. DARPins are built based on the natural ankyrin repeat protein fold with randomized surface residue positions allowing specific binding to virtually any target protein. The broad potential of these binding proteins for X-ray crystallography is illustrated by five cocrystal structures that have been determined recently comprising target proteins from distinct families, namely a sugar binding protein, two kinases, a caspase, and a membrane protein. This article reviews the opportunities of this technology for structural biology and the structural aspects of the DARPin-protein complexes.
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Affiliation(s)
- Gaby Sennhauser
- Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
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Nygren PÅ. Alternative binding proteins: Affibody binding proteins developed from a small three-helix bundle scaffold. FEBS J 2008; 275:2668-76. [DOI: 10.1111/j.1742-4658.2008.06438.x] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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49
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Hoyer W, Härd T. Interaction of Alzheimer’s Aβ Peptide with an Engineered Binding Protein—Thermodynamics and Kinetics of Coupled Folding–Binding. J Mol Biol 2008; 378:398-411. [DOI: 10.1016/j.jmb.2008.02.040] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 02/20/2008] [Accepted: 02/21/2008] [Indexed: 12/20/2022]
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50
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Stabilization of a beta-hairpin in monomeric Alzheimer's amyloid-beta peptide inhibits amyloid formation. Proc Natl Acad Sci U S A 2008; 105:5099-104. [PMID: 18375754 DOI: 10.1073/pnas.0711731105] [Citation(s) in RCA: 338] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
According to the amyloid hypothesis, the pathogenesis of Alzheimer's disease is triggered by the oligomerization and aggregation of the amyloid-beta (Abeta) peptide into protein plaques. Formation of the potentially toxic oligomeric and fibrillar Abeta assemblies is accompanied by a conformational change toward a high content of beta-structure. Here, we report the solution structure of Abeta(1-40) in complex with the phage-display selected affibody protein Z(Abeta3), a binding protein of nanomolar affinity. Bound Abeta(1-40) features a beta-hairpin comprising residues 17-36, providing the first high-resolution structure of Abeta in beta conformation. The positions of the secondary structure elements strongly resemble those observed for fibrillar Abeta. Z(Abeta3) stabilizes the beta-sheet by extending it intermolecularly and by burying both of the mostly nonpolar faces of the Abeta hairpin within a large hydrophobic tunnel-like cavity. Consequently, Z(Abeta3) acts as a stoichiometric inhibitor of Abeta fibrillation. The selected Abeta conformation allows us to suggest a structural mechanism for amyloid formation based on soluble oligomeric hairpin intermediates.
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