1
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Schnider ST, Vigano MA, Affolter M, Aguilar G. Functionalized Protein Binders in Developmental Biology. Annu Rev Cell Dev Biol 2024; 40:119-142. [PMID: 39038471 DOI: 10.1146/annurev-cellbio-112122-025214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Developmental biology has greatly profited from genetic and reverse genetic approaches to indirectly studying protein function. More recently, nanobodies and other protein binders derived from different synthetic scaffolds have been used to directly dissect protein function. Protein binders have been fused to functional domains, such as to lead to protein degradation, relocalization, visualization, or posttranslational modification of the target protein upon binding. The use of such functionalized protein binders has allowed the study of the proteome during development in an unprecedented manner. In the coming years, the advent of the computational design of protein binders, together with further advances in scaffold engineering and synthetic biology, will fuel the development of novel protein binder-based technologies. Studying the proteome with increased precision will contribute to a better understanding of the immense molecular complexities hidden in each step along the way to generate form and function during development.
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Affiliation(s)
| | | | | | - Gustavo Aguilar
- Current affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA;
- Biozentrum, Universität Basel, Basel, Switzerland;
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2
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Li Q, Yang X, Xia X, Xia XX, Yan D. Affibody-Functionalized Elastin-like Peptide-Drug Conjugate Nanomicelle for Targeted Ovarian Cancer Therapy. Biomacromolecules 2024. [PMID: 39235966 DOI: 10.1021/acs.biomac.4c00640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024]
Abstract
Recombinant elastin-like polypeptides (ELPs) have emerged as an attractive nanoplatform for drug delivery due to their tunable genetically encoded sequence, biocompatibility, and stimuli-responsive self-assembly behaviors. Here, we designed and biosynthesized an HER2 (human epidermal growth factor receptor 2)-targeted affibody-ELP fusion protein (Z-ELP), which was subsequently conjugated with monomethyl auristatin E (MMAE) to build a protein-drug conjugate (Z-ELP-M). Due to its thermal response, Z-ELP-M can immediately self-assemble into a nanomicelle at physiological temperature. Benefiting from its active targeting and nanomorphology, Z-ELP-M exhibits enhanced cellular internalization and deep tumor penetration in vitro. Moreover, Z-ELP-M shows excellent tumor targeting and superior antitumor efficacy in HER2-positive ovarian cancer, demonstrating a relative tumor growth inhibition of 104.6%. These findings suggest that an affibody-functionalized elastin-like peptide-drug conjugate nanomicelle is an efficient strategy to improve antitumor efficacy and biosafety in cancer therapy.
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Affiliation(s)
- Qingrong Li
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Xiaoyuan Yang
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Xuelin Xia
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Xiao-Xia Xia
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Deyue Yan
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
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3
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Xia X, Yang X, Gao W, Huang W, Xia X, Yan D. A novel HER2 targeting nanoagent self-assembled from affibody-epothilone B conjugate for cancer therapy. J Nanobiotechnology 2024; 22:502. [PMID: 39169343 PMCID: PMC11337599 DOI: 10.1186/s12951-024-02754-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024] Open
Abstract
Epothilone B (Epo B), a promising antitumor compound effective against various types of cancer cells in vitro. However, its poor selectivity for tumor cells and inadequate therapeutic windows significantly limit its potential clinical application. Affibody is a class of non-immunoglobulin affinity proteins with precise targeting capability to overexpressed molecular receptors on cancer cells, has been intensively investigated due to its exceptional affinity properties. In this study, we present a targeted nanoagent self-assembled from the precursor of an affibody conjugated with Epo B via a linker containing the thioketal (tk) group that is sensitive to reactive oxygen species (ROS). The core-shell structure of the ZHER2:342-Epo B Affibody-Drug Conjugate Nanoagent (Z-E ADCN), with the cytotoxin Epo B encapsulated within the ZHER2:342 affibody corona, leads to significantly reduced side effects on normal organs. Moreover, the abundant presence of ZHER2:342 on the surface effectively enhances the targeting capacity and tumor accumulation of the drug. Z-E ADCN can be internalized by cancer cells via HER2 receptor-mediated endocytosis followed by Epo B release in response to high levels of ROS, resulting in excellent anticancer efficacy in HER2-positive tumor models.
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Affiliation(s)
- Xuelin Xia
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Xiaoyuan Yang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Wenhui Gao
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Wei Huang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Xiaoxia Xia
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Deyue Yan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
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4
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Ek M, Nilvebrant J, Nygren PÅ, Ståhl S, Lindberg H, Löfblom J. An anti-sortilin affibody-peptide fusion inhibits sortilin-mediated progranulin degradation. Front Immunol 2024; 15:1437886. [PMID: 39185427 PMCID: PMC11342335 DOI: 10.3389/fimmu.2024.1437886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 07/23/2024] [Indexed: 08/27/2024] Open
Abstract
Heterozygous loss-of-function mutations in the GRN gene are a common cause of frontotemporal dementia. Such mutations lead to decreased plasma and cerebrospinal fluid levels of progranulin (PGRN), a neurotrophic factor with lysosomal functions. Sortilin is a negative regulator of extracellular PGRN levels and has shown promise as a therapeutic target for frontotemporal dementia, enabling increased extracellular PGRN levels through inhibition of sortilin-mediated PGRN degradation. Here we report the development of a high-affinity sortilin-binding affibody-peptide fusion construct capable of increasing extracellular PGRN levels in vitro. By genetic fusion of a sortilin-binding affibody generated through phage display and a peptide derived from the progranulin C-terminus, an affinity protein (A3-PGRNC15*) with 185-pM affinity for sortilin was obtained. Treating PGRN-secreting and sortilin-expressing human glioblastoma U-251 cells with the fusion protein increased extracellular PGRN levels up to 2.5-fold, with an EC50 value of 1.3 nM. Our results introduce A3-PGRNC15* as a promising new agent with therapeutic potential for the treatment of frontotemporal dementia. Furthermore, the work highlights means to increase binding affinity through synergistic contribution from two orthogonal polypeptide units.
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Affiliation(s)
| | | | | | | | | | - John Löfblom
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
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5
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Wang J, Yin B, Lian J, Wang X. Extracellular Vesicles as Drug Delivery System for Cancer Therapy. Pharmaceutics 2024; 16:1029. [PMID: 39204374 PMCID: PMC11359799 DOI: 10.3390/pharmaceutics16081029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 07/18/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024] Open
Abstract
In recent decades, the pursuit of drug delivery systems has led to the development of numerous synthetic options aimed at enhancing drug efficacy while minimizing side effects. However, the practical application of these systems is often hindered by challenges such as inefficiency, cytotoxicity, and immunogenicity. Extracellular vesicles, natural carriers for drugs, emerge as promising alternatives with distinct advantages over synthetic carriers. Notably, EVs exhibit biocompatibility, low immunogenicity, and inherent tissue-targeting capabilities, thus opening new avenues for drug delivery strategies. This review provides an overview of EVs, including their biogenesis and absorption mechanisms. Additionally, we explore the current research efforts focusing on harnessing their potential as drug carriers, encompassing aspects such as purification techniques, drug loading, and bioengineering for targeted delivery. Finally, we discuss the existing challenges and future prospects of EVs as therapeutic agents in clinical settings. This comprehensive analysis aims to shed light on the potential of EVs as versatile and effective tools for drug delivery, particularly in the realm of cancer therapy.
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Affiliation(s)
- Jin Wang
- School of Life Sciences, Liaoning University, Shenyang 110036, China; (J.W.); (J.L.)
| | - Bohang Yin
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China;
| | - Jiabing Lian
- School of Life Sciences, Liaoning University, Shenyang 110036, China; (J.W.); (J.L.)
| | - Xia Wang
- Institute of Health Sciences, China Medical University, 77 Puhe Road, Shenyang 110122, China
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6
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Tagawa H, Saeki R, Yamamoto C, Tanito K, Tanaka C, Munekawa S, Nii T, Kishimura A, Murakami H, Mori T, Katayama Y. The effect of Fc region affinity of protein-based antibody-recruiting molecules on antibody-dependent cellular cytotoxicity. RSC Adv 2024; 14:22860-22866. [PMID: 39040702 PMCID: PMC11262565 DOI: 10.1039/d4ra03391d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 07/06/2024] [Indexed: 07/24/2024] Open
Abstract
Previously, we reported anticancer molecules, Fc-binding antibody-recruiting molecules (Fc-ARMs), which crosslink proteins on cancer cells with endogenous immunoglobulin Gs (IgGs) via their Fc region. The mobilized IgGs on cancer cells can accommodate natural killer cells to induce antibody-dependent cellular cytotoxicity (ADCC). Because previous Fc-ARMs utilized Fc-binding peptides, their affinity to IgGs is weak, which resulted in the limited induction capability of ADCC. Previous Fc-ARMs also unitized small molecular ligands to cancer cells, which limited their universal applicability to any cancer cells. A recent study reported that protein-based Fc-ARMs might overcome the issues associated with non-proteinous Fc-ARMs. Here, we examined the universality of a protein-based Fc-ARM by replacing its tumor-binding domain with a human epidermal growth factor receptor 2 (HER2)-specific affibody (ZHER2:342). We also examined the requirement of its Fc-binding domain affinity. We found that the Fc-ARMs accepted an affibody as a tumor-binding domain to induce ADCC. Furthermore, the required residence time of the complex between Fc-ARM and IgG was ∼102 min, which was comparable to that when monoclonal antibodies bind to their specific antigens. However, we found that the extent of ADCC induced by Fc-ARM was lower than that of conventional IgG-mediated ADCC, indicating that further enhancement of the affinity of the antibody-binding terminus and tumor-binding terminus of Fc-ARM may be needed to achieve ADCC equivalent to that of conventional IgG-mediated ADCC.
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Affiliation(s)
- Hiroshi Tagawa
- Graduate School of Systems Life Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Riku Saeki
- Graduate School of Systems Life Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Chihaya Yamamoto
- Graduate School of Systems Life Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Kenta Tanito
- Graduate School of Systems Life Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Chihiro Tanaka
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Shoki Munekawa
- Graduate School of Systems Life Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Teruki Nii
- Graduate School of Systems Life Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Akihiro Kishimura
- Graduate School of Systems Life Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
- Center for Future Chemistry, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
- International Research Center for Molecular Systems, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University Furo-cho, Chikusa-ku Nagoya 464-8603 Japan
| | - Takeshi Mori
- Graduate School of Systems Life Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
- Center for Future Chemistry, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
| | - Yoshiki Katayama
- Graduate School of Systems Life Sciences, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
- Center for Future Chemistry, Kyushu University 744 Motooka, Nishi-ku Fukuoka 819-0395 Japan
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7
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Yayci A, Sassmann T, Boes A, Jakob F, Töpel A, Loreth A, Rauch C, Pich A, Schwaneberg U. Adhesion Peptide-Functionalized Biobased Microgels for Controlled Delivery of Pesticides. Angew Chem Int Ed Engl 2024; 63:e202319832. [PMID: 38652238 DOI: 10.1002/anie.202319832] [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: 12/22/2023] [Revised: 04/05/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
Widespread use of plant protection agents in agriculture is a major cause of pollution. Apart from active ingredients, the environmental impact of auxiliary synthetic polymers should be minimized if they are highly persistent. An alternative to synthetic polymers is the use of natural polysaccharides, which are abundant and biodegradable. In this study, we explore pectin microgels functionalized with anchor peptides (P-MAPs) to be used as an alternative biobased pesticide delivery system. Using copper as the active ingredient, P-MAPs effectively prevented infection of grapevine plants with downy mildew under semi-field conditions on par with commercial copper pesticides. By using anchor peptides, the microgels tightly bind to the leaf surface, exhibiting excellent rain fastness and prolonged fungicidal activity. Finally, P-MAPs are shown to be easily degradable by enzymes found in nature, demonstrating their negligible long-term impact on the environment.
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Affiliation(s)
- Abdulkadir Yayci
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, 52056, Aachen, Germany
| | - Tim Sassmann
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, 52056, Aachen, Germany
| | - Alexander Boes
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, 52056, Aachen, Germany
| | - Felix Jakob
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, 52056, Aachen, Germany
| | - Alexander Töpel
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, 52056, Aachen, Germany
| | - Anne Loreth
- Julius-Kühn-Institute, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, 76833, Siebeldingen, Germany
| | - Carolin Rauch
- Julius-Kühn-Institute, Institute for Plant Protection in Fruit Crops and Viticulture, Geilweilerhof, 76833, Siebeldingen, Germany
| | - Andrij Pich
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, 52056, Aachen, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
- DWI - Leibniz-Institute for Interactive Materials, Forckenbeckstrasse 50, 52056, Aachen, Germany
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8
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Badenhorst M, Windhorst AD, Beaino W. Navigating the landscape of PD-1/PD-L1 imaging tracers: from challenges to opportunities. Front Med (Lausanne) 2024; 11:1401515. [PMID: 38915766 PMCID: PMC11195831 DOI: 10.3389/fmed.2024.1401515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/20/2024] [Indexed: 06/26/2024] Open
Abstract
Immunotherapy targeted to immune checkpoint inhibitors, such as the program cell death receptor (PD-1) and its ligand (PD-L1), has revolutionized cancer treatment. However, it is now well-known that PD-1/PD-L1 immunotherapy response is inconsistent among patients. The current challenge is to customize treatment regimens per patient, which could be possible if the PD-1/PD-L1 expression and dynamic landscape are known. With positron emission tomography (PET) imaging, it is possible to image these immune targets non-invasively and system-wide during therapy. A successful PET imaging tracer should meet specific criteria concerning target affinity, specificity, clearance rate and target-specific uptake, to name a few. The structural profile of such a tracer will define its properties and can be used to optimize tracers in development and design new ones. Currently, a range of PD-1/PD-L1-targeting PET tracers are available from different molecular categories that have shown impressive preclinical and clinical results, each with its own advantages and disadvantages. This review will provide an overview of current PET tracers targeting the PD-1/PD-L1 axis. Antibody, peptide, and antibody fragment tracers will be discussed with respect to their molecular characteristics and binding properties and ways to optimize them.
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Affiliation(s)
- Melinda Badenhorst
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Radiology and Nuclear Medicine, De Boelelaan, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - Albert D. Windhorst
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Radiology and Nuclear Medicine, De Boelelaan, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - Wissam Beaino
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Radiology and Nuclear Medicine, De Boelelaan, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
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9
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Chamrád I, Simerský R, Lenobel R, Novák O. Exploring affinity chromatography in proteomics: A comprehensive review. Anal Chim Acta 2024; 1306:342513. [PMID: 38692783 DOI: 10.1016/j.aca.2024.342513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
Over the past decades, the proteomics field has undergone rapid growth. Progress in mass spectrometry and bioinformatics, together with separation methods, has brought many innovative approaches to the study of the molecular biology of the cell. The potential of affinity chromatography was recognized immediately after its first application in proteomics, and since that time, it has become one of the cornerstones of many proteomic protocols. Indeed, this chromatographic technique exploiting the specific binding between two molecules has been employed for numerous purposes, from selective removal of interfering (over)abundant proteins or enrichment of scarce biomarkers in complex biological samples to mapping the post-translational modifications and protein interactions with other proteins, nucleic acids or biologically active small molecules. This review presents a comprehensive survey of this versatile analytical tool in current proteomics. To navigate the reader, the haphazard space of affinity separations is classified according to the experiment's aims and the separated molecule's nature. Different types of available ligands and experimental strategies are discussed in further detail for each of the mentioned procedures.
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Affiliation(s)
- Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic.
| | - Radim Simerský
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
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10
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Dudley JA, Park S, Cho O, Wells NGM, MacDonald ME, Blejec KM, Fetene E, Zanderigo E, Houliston S, Liddle JC, Dashnaw CM, Sabo TM, Shaw BF, Balsbaugh JL, Rocklin GJ, Smith CA. Heat-induced structural and chemical changes to a computationally designed miniprotein. Protein Sci 2024; 33:e4991. [PMID: 38757381 PMCID: PMC11099715 DOI: 10.1002/pro.4991] [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: 12/11/2023] [Revised: 03/22/2024] [Accepted: 03/28/2024] [Indexed: 05/18/2024]
Abstract
The de novo design of miniprotein inhibitors has recently emerged as a new technology to create proteins that bind with high affinity to specific therapeutic targets. Their size, ease of expression, and apparent high stability makes them excellent candidates for a new class of protein drugs. However, beyond circular dichroism melts and hydrogen/deuterium exchange experiments, little is known about their dynamics, especially at the elevated temperatures they seemingly tolerate quite well. To address that and gain insight for future designs, we have focused on identifying unintended and previously overlooked heat-induced structural and chemical changes in a particularly stable model miniprotein, EHEE_rd2_0005. Nuclear magnetic resonance (NMR) studies suggest the presence of dynamics on multiple time and temperature scales. Transiently elevating the temperature results in spontaneous chemical deamidation visible in the NMR spectra, which we validate using both capillary electrophoresis and mass spectrometry (MS) experiments. High temperatures also result in greatly accelerated intrinsic rates of hydrogen exchange and signal loss in NMR heteronuclear single quantum coherence spectra from local unfolding. These losses are in excellent agreement with both room temperature hydrogen exchange experiments and hydrogen bond disruption in replica exchange molecular dynamics simulations. Our analysis reveals important principles for future miniprotein designs and the potential for high stability to result in long-lived alternate conformational states.
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Affiliation(s)
- Joshua A. Dudley
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Sojeong Park
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Oliver Cho
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | | | | | | | - Emmanuel Fetene
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Eric Zanderigo
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
| | - Scott Houliston
- Structural Genomics ConsortiumUniversity of TorontoTorontoOntarioCanada
| | - Jennifer C. Liddle
- Proteomics and Metabolomics FacilityUniversity of ConnecticutStorrsConnecticutUSA
| | - Chad M. Dashnaw
- Department of Chemistry and BiochemistryBaylor UniversityWacoTexasUSA
| | - T. Michael Sabo
- Department of Medicine and Brown Cancer CenterUniversity of LouisvilleLouisvilleKentuckyUSA
| | - Bryan F. Shaw
- Department of Chemistry and BiochemistryBaylor UniversityWacoTexasUSA
| | - Jeremy L. Balsbaugh
- Proteomics and Metabolomics FacilityUniversity of ConnecticutStorrsConnecticutUSA
| | - Gabriel J. Rocklin
- Department of Pharmacology and Center for Synthetic BiologyNorthwestern UniversityEvanstonIllinoisUSA
| | - Colin A. Smith
- Department of ChemistryWesleyan UniversityMiddletownConnecticutUSA
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11
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Nielsen GH, Schmitz ZD, Hackel BJ. Sequence-developability mapping of affibody and fibronectin paratopes via library-scale variant characterization. Protein Eng Des Sel 2024; 37:gzae010. [PMID: 38836499 PMCID: PMC11170491 DOI: 10.1093/protein/gzae010] [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: 03/18/2024] [Revised: 05/29/2024] [Accepted: 06/04/2024] [Indexed: 06/06/2024] Open
Abstract
Protein developability is requisite for use in therapeutic, diagnostic, or industrial applications. Many developability assays are low throughput, which limits their utility to the later stages of protein discovery and evolution. Recent approaches enable experimental or computational assessment of many more variants, yet the breadth of applicability across protein families and developability metrics is uncertain. Here, three library-scale assays-on-yeast protease, split green fluorescent protein (GFP), and non-specific binding-were evaluated for their ability to predict two key developability outcomes (thermal stability and recombinant expression) for the small protein scaffolds affibody and fibronectin. The assays' predictive capabilities were assessed via both linear correlation and machine learning models trained on the library-scale assay data. The on-yeast protease assay is highly predictive of thermal stability for both scaffolds, and the split-GFP assay is informative of affibody thermal stability and expression. The library-scale data was used to map sequence-developability landscapes for affibody and fibronectin binding paratopes, which guides future design of variants and libraries.
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Affiliation(s)
- Gregory H Nielsen
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, Minneapolis, MN 55455, United States
| | - Zachary D Schmitz
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, Minneapolis, MN 55455, United States
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota, Twin Cities, Minneapolis, MN 55455, United States
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12
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Kim E, Bang J, Sung JH, Lee J, Shin DH, Kim S, Lee BC. Generation of human TMEM16F-specific affibodies using purified TMEM16F. Front Mol Biosci 2024; 10:1319251. [PMID: 38274091 PMCID: PMC10808743 DOI: 10.3389/fmolb.2023.1319251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/27/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction: TMEM16 family proteins are involved in a variety of functions, including ion transport, phospholipid scrambling, and the regulation of membrane proteins. Among them, TMEM16F has dual functions as a phospholipid scramblase and a nonselective ion channel. TMEM16F is widely expressed and functions in platelet activation during blood clotting, bone formation, and T cell activation. Despite the functional importance of TMEM16F, the modulators of TMEM16F function have not been sufficiently studied. Method: In this study, we generated TMEM16F-specific affibodies by performing phage display with brain-specific TMEM16F (hTMEM16F) variant 1 purified from GnTi- cells expressing this variant in the presence of digitonin as a detergent. Purified human TMEM16F protein, which was proficient in transporting phospholipids in a Ca2+-dependent manner in proteoliposomes, was coated onto plates and then the phage library was added to fish out TMEM16F-binding affibodies. For the validation of interaction between affibodies and TMEM16F proteins, ELISA, bio-layer interferometry, and size exclusion chromatography were conducted. Results and Discussion: As a result, the full sequences of 38 candidates were acquired from 98 binding candidates. Then, we selected 10 candidates and purified seven of them from E. coli expressing these candidates. Using various assays, we confirmed that two affibodies bound to human TMEM16F with high affinity. These affibodies can be useful for therapeutical and diagnostic applications of TMEM16F-related cancer and neurodegenerative diseases. Future studies will be required to investigate the effects of these affibodies on TMEM16F function.
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Affiliation(s)
- Eunyoung Kim
- Korea Brain Research Institute, Neurovascular Unit Research Group, Daegu, Republic of Korea
| | - Jinho Bang
- Korea Institute of Ceramic Engineering and Technology, Bio-Healthcare Materials Center, Cheongju, Republic of Korea
- College of Pharmacy, Chungbuk National University, Cheongju, Republic of Korea
| | - Ji Hye Sung
- Korea Brain Research Institute, Neurovascular Unit Research Group, Daegu, Republic of Korea
| | - Jonghwan Lee
- Korea Institute of Ceramic Engineering and Technology, Bio-Healthcare Materials Center, Cheongju, Republic of Korea
| | - Dae Hwan Shin
- College of Pharmacy, Chungbuk National University, Cheongju, Republic of Korea
| | - Sunghyun Kim
- Korea Institute of Ceramic Engineering and Technology, Bio-Healthcare Materials Center, Cheongju, Republic of Korea
| | - Byoung-Cheol Lee
- Korea Brain Research Institute, Neurovascular Unit Research Group, Daegu, Republic of Korea
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13
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Blanchard PL, Knick BJ, Whelan SA, Hackel BJ. Hyperstable Synthetic Mini-Proteins as Effective Ligand Scaffolds. ACS Synth Biol 2023; 12:3608-3622. [PMID: 38010428 PMCID: PMC10822706 DOI: 10.1021/acssynbio.3c00409] [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] [Indexed: 11/29/2023]
Abstract
Small, single-domain protein scaffolds are compelling sources of molecular binding ligands with the potential for efficient physiological transport, modularity, and manufacturing. Yet, mini-proteins require a balance between biophysical robustness and diversity to enable new functions. We tested the developability and evolvability of millions of variants of 43 designed libraries of synthetic 40-amino acid βαββ proteins with diversified sheet, loop, or helix paratopes. We discovered a scaffold library that yielded hundreds of binders to seven targets while exhibiting high stability and soluble expression. Binder discovery yielded 6-122 nM affinities without affinity maturation and Tms averaging ≥78 °C. Broader βαββ libraries exhibited varied developability and evolvability. Sheet paratopes were the most consistently developable, and framework 1 was the most evolvable. Paratope evolvability was dependent on target, though several libraries were evolvable across many targets while exhibiting high stability and soluble expression. Select βαββ proteins are strong starting points for engineering performant binders.
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Affiliation(s)
- Paul L. Blanchard
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, MN 55455
| | - Brandon J. Knick
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, MN 55455
| | - Sarah A. Whelan
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, MN 55455
| | - Benjamin J. Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota – Twin Cities, 421 Washington Avenue SE, Minneapolis, MN 55455
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14
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Sekhon H, Ha JH, Presti MF, Procopio SB, Jarvis AR, Mirsky PO, John AM, Loh SN. Adaptable, turn-on maturation (ATOM) fluorescent biosensors for multiplexed detection in cells. Nat Methods 2023; 20:1920-1929. [PMID: 37945909 PMCID: PMC11080272 DOI: 10.1038/s41592-023-02065-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 10/04/2023] [Indexed: 11/12/2023]
Abstract
A grand challenge in biosensor design is to develop a single-molecule, fluorescent protein-based platform that can be easily adapted to recognize targets of choice. Here, we created a family of adaptable, turn-on maturation (ATOM) biosensors consisting of a monobody (circularly permuted at one of two positions) or a nanobody (circularly permuted at one of three positions) inserted into a fluorescent protein at one of three surface loops. Multiplexed imaging of live human cells coexpressing cyan, yellow and red ATOM sensors detected biosensor targets that were specifically localized to various subcellular compartments. Fluorescence activation involved ligand-dependent chromophore maturation with turn-on ratios of up to 62-fold in cells and 100-fold in vitro. Endoplasmic reticulum- and mitochondria-localized ATOM sensors detected ligands that were targeted to those organelles. The ATOM design was validated with three monobodies and one nanobody inserted into distinct fluorescent proteins, suggesting that customized ATOM sensors can be generated quickly.
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Affiliation(s)
- Harsimranjit Sekhon
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Maria F Presti
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Spencer B Procopio
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Ava R Jarvis
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Paige O Mirsky
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Anna M John
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.
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15
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Giang KA, Boxaspen T, Diao Y, Nilvebrant J, Kosugi-Kanaya M, Kanaya M, Krokeide SZ, Lehmann F, Svensson Gelius S, Malmberg KJ, Nygren PÅ. Affibody-based hBCMA x CD16 dual engagers for NK cell-mediated killing of multiple myeloma cells. N Biotechnol 2023; 77:139-148. [PMID: 37673373 DOI: 10.1016/j.nbt.2023.09.002] [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: 07/04/2023] [Revised: 08/16/2023] [Accepted: 09/03/2023] [Indexed: 09/08/2023]
Abstract
We describe the development and characterization of the (to date) smallest Natural Killer (NK) cell re-directing human B Cell Maturation Antigen (hBCMA) x CD16 dual engagers for potential treatment of multiple myeloma, based on combinations of small 58 amino acid, non-immunoglobulin, affibody affinity proteins. Affibody molecules to human CD16a were selected from a combinatorial library by phage display resulting in the identification of three unique binders with affinities (KD) for CD16a in the range of 100 nM-3 µM. The affibody exhibiting the highest affinity demonstrated insensitivity towards the CD16a allotype (158F/V) and did not interfere with IgG (Fc) binding to CD16a. For the construction of hBCMA x CD16 dual engagers, different CD16a binding arms, including bi-paratopic affibody combinations, were genetically fused to a high-affinity hBCMA-specific affibody. Such 15-23 kDa dual engager constructs showed simultaneous hBCMA and CD16a binding ability and could efficiently activate resting primary NK cells and trigger specific lysis of a panel of hBCMA-positive multiple myeloma cell lines. Hence, we report a novel class of uniquely small NK cell engagers with specific binding properties and potent functional profiles.
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Affiliation(s)
- Kim Anh Giang
- Department of Protein Science, Div. Protein Engineering, AlbaNova University Center, KTH Royal Institute of Technology, S-114 21 Stockholm, Sweden
| | - Thorstein Boxaspen
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, N-0424 Oslo, Norway; Precision Immunotherapy Alliance, Institute of Clinical Medicine, University of Oslo, N-0313 Oslo, Norway
| | - Yumei Diao
- Oncopeptides AB, S-171 48 Stockholm, Sweden
| | - Johan Nilvebrant
- Department of Protein Science, Div. Protein Engineering, AlbaNova University Center, KTH Royal Institute of Technology, S-114 21 Stockholm, Sweden
| | - Mizuha Kosugi-Kanaya
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, N-0424 Oslo, Norway; Precision Immunotherapy Alliance, Institute of Clinical Medicine, University of Oslo, N-0313 Oslo, Norway
| | - Minoru Kanaya
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, N-0424 Oslo, Norway; Precision Immunotherapy Alliance, Institute of Clinical Medicine, University of Oslo, N-0313 Oslo, Norway
| | - Silje Zandstra Krokeide
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, N-0424 Oslo, Norway; Precision Immunotherapy Alliance, Institute of Clinical Medicine, University of Oslo, N-0313 Oslo, Norway
| | | | | | - Karl-Johan Malmberg
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, N-0424 Oslo, Norway; Precision Immunotherapy Alliance, Institute of Clinical Medicine, University of Oslo, N-0313 Oslo, Norway.
| | - Per-Åke Nygren
- Department of Protein Science, Div. Protein Engineering, AlbaNova University Center, KTH Royal Institute of Technology, S-114 21 Stockholm, Sweden; Science For Life Laboratory, S-171 65 Solna, Sweden.
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16
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D’Ercole C, De March M, Veggiani G, Oloketuyi S, Svigelj R, de Marco A. Biological Applications of Synthetic Binders Isolated from a Conceptually New Adhiron Library. Biomolecules 2023; 13:1533. [PMID: 37892215 PMCID: PMC10605594 DOI: 10.3390/biom13101533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Adhirons are small (10 kDa) synthetic ligands that might represent an alternative to antibody fragments and to alternative scaffolds such as DARPins or affibodies. METHODS We prepared a conceptionally new adhiron phage display library that allows the presence of cysteines in the hypervariable loops and successfully panned it against antigens possessing different characteristics. RESULTS We recovered binders specific for membrane epitopes of plant cells by panning the library directly against pea protoplasts and against soluble C-Reactive Protein and SpyCatcher, a small protein domain for which we failed to isolate binders using pre-immune nanobody libraries. The best binders had a binding constant in the low nM range, were produced easily in bacteria (average yields of 15 mg/L of culture) in combination with different tags, were stable, and had minimal aggregation propensity, independent of the presence or absence of cysteine residues in their loops. DISCUSSION The isolated adhirons were significantly stronger than those isolated previously from other libraries and as good as nanobodies recovered from a naïve library of comparable theoretical diversity. Moreover, they proved to be suitable reagents for ELISA, flow cytometry, the western blot, and also as capture elements in electrochemical biosensors.
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Affiliation(s)
- Claudia D’Ercole
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Rožna Dolina, 5000 Nova Gorica, Slovenia; (C.D.); (M.D.M.); (S.O.)
| | - Matteo De March
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Rožna Dolina, 5000 Nova Gorica, Slovenia; (C.D.); (M.D.M.); (S.O.)
| | - Gianluca Veggiani
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Sandra Oloketuyi
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Rožna Dolina, 5000 Nova Gorica, Slovenia; (C.D.); (M.D.M.); (S.O.)
| | - Rossella Svigelj
- Department of Agrifood, Environmental and Animal Science, University of Udine, via Cotonificio 108, 33100 Udine, Italy;
| | - Ario de Marco
- Lab of Environmental and Life Sciences, University of Nova Gorica, Vipavska cesta 13, Rožna Dolina, 5000 Nova Gorica, Slovenia; (C.D.); (M.D.M.); (S.O.)
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17
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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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18
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Xu K, Han J, Yang L, Cao L, Li S, Hong Z. Tumor Site-Specific Cleavage Improves the Antitumor Efficacy of Antibody-Drug Conjugates. Int J Mol Sci 2023; 24:11011. [PMID: 37446189 DOI: 10.3390/ijms241311011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Antibody-drug conjugates (ADCs) play important roles in tumor therapy. However, traditional ADCs are limited by the extremely large molecular weight of the antibody molecules, which results in low permeability into solid tumors. The use of small ADCs may be expected to alleviate this problem, but this switch brings the new limitation of a greatly shortened blood circulation half-life. Here, we propose a new cleavable ADC design with excellent tumor tissue permeability and a long circulation half-life by fusing the small ADC ZHER2-MMAE with the Fc domain of the antibody for circulation half-life extension, and inserting a digestion sequence between them to release the small ADC inside tumors for better tumor penetration. The experimental results showed that the designed molecule Fc-U-ZHER2-MMAE has a significantly increased blood circulation half-life (7.1 h, 59-fold longer) compared to the small ADC ZHER2-MMAE, and significantly improved drug accumulation ability at tumor sites compared to the conventional full-length antibody-coupled ADC Herceptin-MMAE. These combined effects led to Fc-U-ZHER2-MMAE having significantly enhanced tumor treatment ability, as shown in mouse models of NCI-N87 gastric cancer and SK-OV-3 ovarian cancer, where Fc-U-ZHER2-MMAE treatment achieved complete regression of tumors in all or a portion of animals with no obvious side effects and an MTD exceeding 90 mg/kg. These data demonstrate the therapeutic advantages of this cleavable ADC strategy, which could provide a new approach for ADC design.
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Affiliation(s)
- Keyuan Xu
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Jiani Han
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Liu Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Li Cao
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Shuang Li
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhangyong Hong
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin 300071, China
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19
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Gabriele F, Palerma M, Ippoliti R, Angelucci F, Pitari G, Ardini M. Recent Advances on Affibody- and DARPin-Conjugated Nanomaterials in Cancer Therapy. Int J Mol Sci 2023; 24:ijms24108680. [PMID: 37240041 DOI: 10.3390/ijms24108680] [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: 03/31/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Affibodies and designed ankyrin repeat proteins (DARPins) are synthetic proteins originally derived from the Staphylococcus aureus virulence factor protein A and the human ankyrin repeat proteins, respectively. The use of these molecules in healthcare has been recently proposed as they are endowed with biochemical and biophysical features heavily demanded to target and fight diseases, as they have a strong binding affinity, solubility, small size, multiple functionalization sites, biocompatibility, and are easy to produce; furthermore, impressive chemical and thermal stability can be achieved. especially when using affibodies. In this sense, several examples reporting on affibodies and DARPins conjugated to nanomaterials have been published, demonstrating their suitability and feasibility in nanomedicine for cancer therapy. This minireview provides a survey of the most recent studies describing affibody- and DARPin-conjugated zero-dimensional nanomaterials, including inorganic, organic, and biological nanoparticles, nanorods, quantum dots, liposomes, and protein- and DNA-based assemblies for targeted cancer therapy in vitro and in vivo.
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Affiliation(s)
- Federica Gabriele
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Marta Palerma
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Rodolfo Ippoliti
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Francesco Angelucci
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Giuseppina Pitari
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Matteo Ardini
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
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20
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Bhoyar S, Foster M, Oh YH, Xu X, Traylor SJ, Guo J, Ghose S, Lenhoff AM. Engineering protein A ligands to mitigate antibody loss during high-pH washes in protein A chromatography. J Chromatogr A 2023; 1696:463962. [PMID: 37043977 DOI: 10.1016/j.chroma.2023.463962] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/30/2023] [Accepted: 04/01/2023] [Indexed: 04/05/2023]
Abstract
Protein A chromatography is a workhorse in monoclonal antibody (mAb) manufacture since it provides effective separation of mAbs from impurities such as host-cell proteins (HCPs) in a single capture step. HCP clearance can be aided by the inclusion of a wash step prior to low-pH elution. Although high-pH washes can be effective in removing additional HCPs from the loaded column, they may also contribute to a reduced mAb yield. In this work we show that this yield loss is reflected in a pH-dependent variation of the equilibrium binding capacity of the protein A resin, which is also observed for the capacity of the Fc fragments alone and therefore not a result of steric interactions involving the Fab fragments in the intact mAbs. We therefore hypothesized that the high-pH wash loss was due to protonation or deprotonation of ionizable residues on the protein A ligand. To evaluate this, we applied a rational protein engineering approach to the Z domain (the Fc-binding component of most commercial protein A ligands) and expressed engineered mutants in E. coli. Biolayer interferometry and affinity chromatography experiments showed that some of the Z domain mutants were able to mitigate wash loss at high pH while maintaining similar binding characteristics at neutral pH. These experiments enabled elucidation of the roles of specific interactions in the Z domain - Fc complex, but more importantly offer a route to ameliorating the disadvantages of high-pH washes in protein A chromatography.
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21
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Sekhon H, Ha JH, Presti MF, Procopio SB, Mirsky PO, John AM, Loh SN. Adaptable, Turn-On Monobody (ATOM) Fluorescent Biosensors for Multiplexed Detection in Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534597. [PMID: 37034669 PMCID: PMC10081266 DOI: 10.1101/2023.03.28.534597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
A grand challenge in biosensor design is to develop a single molecule, fluorescent protein-based platform that can be easily adapted to recognize targets of choice. Conceptually, this can be achieved by fusing a small, antibody-like binding domain to a fluorescent protein in such a way that target binding activates fluorescence. Although this design is simple to envision, its execution is not obvious. Here, we created a family of adaptable, turn-on monobody (ATOM) biosensors consisting of a monobody, circularly permuted at one of two positions, inserted into a fluorescent protein at one of three surface loops. Multiplexed imaging of live human cells co-expressing cyan, yellow, and red ATOM sensors detected the biosensor targets (WDR5, SH2, and hRAS proteins) that were localized to the nucleus, cytoplasm, and plasma membrane, respectively, with high specificity. ER- and mitochondria-localized ATOM sensors also detected ligands that were targeted to those organelles. Fluorescence activation involved ligand-dependent chromophore maturation with fluorescence turn-on ratios of >20-fold in cells and up to 100-fold in vitro . The sensing mechanism was validated with three arbitrarily chosen monobodies inserted into jellyfish as well as anemone lineages of fluorescent proteins, suggesting that ATOM sensors with different binding specificities and additional colors can be generated relatively quickly.
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22
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Dahlsson Leitao C, Mestre Borras A, Jonsson A, Malm M, Kronqvist N, Fleetwood F, Sandersjöö L, Uhlén M, Löfblom J, Ståhl S, Lindberg H. Display of a naïve affibody library on staphylococci for selection of binders by means of flow cytometry sorting. Biochem Biophys Res Commun 2023; 655:75-81. [PMID: 36933310 DOI: 10.1016/j.bbrc.2023.03.003] [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: 02/19/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Within the field of combinatorial protein engineering there is a great demand for robust high-throughput selection platforms that allow for unbiased protein library display, affinity-based screening, and amplification of selected clones. We have previously described the development of a staphylococcal display system used for displaying both alternative-scaffolds and antibody-derived proteins. In this study, the objective was to generate an improved expression vector for displaying and screening a high-complexity naïve affibody library, and to facilitate downstream validation of isolated clones. A high-affinity normalization tag, consisting of two ABD-moieties, was introduced to simplify off-rate screening procedures. In addition, the vector was furnished with a TEV protease substrate recognition sequence upstream of the protein library which enables proteolytic processing of the displayed construct for improved binding signal. In the library design, 13 of the 58 surface-exposed amino acid positions were selected for full randomization (except proline and cysteine) using trinucleotide technology. The genetic library was successfully transformed to Staphylococcus carnosus cells, generating a protein library exceeding 109 members. De novo selections against three target proteins (CD14, MAPK9 and the affibody ZEGFR:2377) were successfully performed using magnetic bead-based capture followed by flow-cytometric sorting, yielding affibody molecules binding their respective target with nanomolar affinity. Taken together, the results demonstrate the feasibility of the staphylococcal display system and the proposed selection procedure to generate new affibody molecules with high affinity.
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Affiliation(s)
- Charles Dahlsson Leitao
- Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Anna Mestre Borras
- Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Andreas Jonsson
- Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Magdalena Malm
- Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Nina Kronqvist
- Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Filippa Fleetwood
- Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Lisa Sandersjöö
- Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Mathias Uhlén
- Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - John Löfblom
- Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Stefan Ståhl
- Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - Hanna Lindberg
- Department of Protein Science, KTH - Royal Institute of Technology, SE-106 91, Stockholm, Sweden.
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23
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Bhaskar H, Kleinjan D, Oi C, Gidden Z, Rosser SJ, Horrocks MH, Regan L. Live-cell super-resolution imaging of actin using LifeAct-14 with a PAINT-based approach. Protein Sci 2023; 32:e4558. [PMID: 36585831 PMCID: PMC9878614 DOI: 10.1002/pro.4558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
We present direct-LIVE-PAINT, an easy-to-implement approach for the nanoscopic imaging of protein structures in live cells using labeled binding peptides. We demonstrate the feasibility of direct-LIVE-PAINT with an actin-binding peptide fused to EGFP, the location of which can be accurately determined as it transiently binds to actin filaments. We show that direct-LIVE-PAINT can be used to image actin structures below the diffraction-limit of light and have used it to observe the dynamic nature of actin in live cells. We envisage a similar approach could be applied to imaging other proteins within live mammalian cells.
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Affiliation(s)
- Haresh Bhaskar
- The School of Biological SciencesUniversity of EdinburghEdinburghUK,EaStCHEM School of ChemistryUniversity of EdinburghEdinburghUK
| | - Dirk‐Jan Kleinjan
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Curran Oi
- Department of Genome SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Zoe Gidden
- The School of Biological SciencesUniversity of EdinburghEdinburghUK,EaStCHEM School of ChemistryUniversity of EdinburghEdinburghUK
| | - Susan J. Rosser
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological SciencesUniversity of EdinburghEdinburghUK
| | | | - Lynne Regan
- The School of Biological SciencesUniversity of EdinburghEdinburghUK
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24
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Nandy S, Maranholkar VM, Crum M, Wasden K, Patil U, Goyal A, Vu B, Kourentzi K, Mo W, Henrickson A, Demeler B, Sen M, Willson RC. Expression and Characterization of Intein-Cyclized Trimer of Staphylococcus aureus Protein A Domain Z. Int J Mol Sci 2023; 24:1281. [PMID: 36674796 PMCID: PMC9865183 DOI: 10.3390/ijms24021281] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
Staphylococcus aureus protein A (SpA) is an IgG Fc-binding virulence factor that is widely used in antibody purification and as a scaffold to develop affinity molecules. A cyclized SpA Z domain could offer exopeptidase resistance, reduced chromatographic ligand leaching after single-site endopeptidase cleavage, and enhanced IgG binding properties by preorganization, potentially reducing conformational entropy loss upon binding. In this work, a Z domain trimer (Z3) was cyclized using protein intein splicing. Interactions of cyclic and linear Z3 with human IgG1 were characterized by differential scanning fluorimetry (DSF), surface plasmon resonance (SPR), and isothermal titration calorimetry (ITC). DSF showed a 5 ℃ increase in IgG1 melting temperature when bound by each Z3 variant. SPR showed the dissociation constants of linear and cyclized Z3 with IgG1 to be 2.9 nM and 3.3 nM, respectively. ITC gave association enthalpies for linear and cyclic Z3 with IgG1 of -33.0 kcal/mol and -32.7 kcal/mol, and -T∆S of association 21.2 kcal/mol and 21.6 kcal/mol, respectively. The compact cyclic Z3 protein contains 2 functional binding sites and exhibits carboxypeptidase Y-resistance. The results suggest cyclization as a potential approach toward more stable SpA-based affinity ligands, and this analysis may advance our understanding of protein engineering for ligand and drug development.
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Affiliation(s)
- Suman Nandy
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Vijay M. Maranholkar
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA
| | - Mary Crum
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Katherine Wasden
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Ujwal Patil
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA
| | - Atul Goyal
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Binh Vu
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Katerina Kourentzi
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - William Mo
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Borries Demeler
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA
| | - Mehmet Sen
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA
| | - Richard C. Willson
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, USA
- Escuela de Medicina y Ciencias de Salud, Tecnológico de Monterrey, Monterrey 64849, Nuevo León, Mexico
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25
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Imiołek M, Winssinger N. Two-Helix Supramolecular Proteomimetic Binders Assembled via PNA-Assisted Disulfide Crosslinking. Chembiochem 2023; 24:e202200561. [PMID: 36349499 DOI: 10.1002/cbic.202200561] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 11/05/2022] [Indexed: 11/10/2022]
Abstract
Peptidic motifs folded in a defined conformation are able to inhibit protein-protein interactions (PPIs) covering large interfaces and as such they are biomedical molecules of interest. Mimicry of such natural structures with synthetically tractable constructs often requires complex scaffolding and extensive optimization to preserve the fidelity of binding to the target. Here, we present a novel proteomimetic strategy based on a 2-helix binding motif that is brought together by hybridization of peptide nucleic acids (PNA) and stabilized by a rationally positioned intermolecular disulfide crosslink. Using a solid phase synthesis approach (SPPS), the building blocks are easily accessible and such supramolecular peptide-PNA helical hybrids could be further coiled using precise templated chemistry. The elaboration of the structural design afforded high affinity SARS CoV-2 RBD (receptor binding domain) binders without interference with the underlying peptide sequence, creating a basis for a new architecture of supramolecular proteomimetics.
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Affiliation(s)
- Mateusz Imiołek
- Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, University of Geneva, 1211, Geneva, Switzerland
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26
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Klint S, Feldwisch J, Gudmundsdotter L, Dillner Bergstedt K, Gunneriusson E, Höidén Guthenberg I, Wennborg A, Nyborg AC, Kamboj AP, Peloso PM, Bejker D, Frejd FY. Izokibep: Preclinical development and first-in-human study of a novel IL-17A neutralizing Affibody molecule in patients with plaque psoriasis. MAbs 2023; 15:2209920. [PMID: 37184136 PMCID: PMC10187109 DOI: 10.1080/19420862.2023.2209920] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 04/28/2023] [Indexed: 05/16/2023] Open
Abstract
Psoriasis, an immune-mediated inflammatory disease, affects nearly 125 million people globally. The interleukin (IL)-17A homodimer is a key driver of psoriasis and other autoimmune diseases, including psoriatic arthritis, axial spondyloarthritis, hidradenitis suppurativa, and uveitis. Treatment with monoclonal antibodies (mAbs) against IL-17A provides an improvement in the Psoriasis Area and Severity Index compared to conventional systemic agents. In this study, the AffibodyⓇ technology was used to identify and optimize a novel, small, biological molecule comprising three triple helical affinity domains, izokibep (previously ABY-035), for the inhibition of IL-17A signaling. Preclinical studies show that izokibep, a small 18.6 kDa IL-17 ligand trap comprising two IL-17A-specific Affibody domains and one albumin-binding domain, selectively inhibits human IL-17A in vitro and in vivo with superior potency and efficacy relative to anti-IL-17A mAbs. A Phase 1 first-in-human study was conducted to establish the safety, pharmacokinetics, and preliminary efficacy of izokibep, when administered intravenously and subcutaneously as single doses to healthy subjects, and as single intravenous and multiple subcutaneous doses to patients with psoriasis (NCT02690142; EudraCT No: 2015-004531-13). Izokibep was well tolerated with no meaningful safety concerns identified in healthy volunteers and patients with psoriasis. Rapid efficacy was seen in all psoriasis patients after one dose which further improved in patients receiving multiple doses. A therapeutic decrease in joint pain was also observed in a single patient with concurrent psoriatic arthritis. The study suggests that izokibep has the potential to safely treat IL17A-associated diseases such as psoriasis, psoriatic arthritis, axial spondyloarthritis, hidradenitis suppurativa, and uveitis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Fredrik Y. Frejd
- Affibody AB, Solna, Sweden
- Department of Immunology, Genetics and Pathology, IGP, Uppsala University, Uppsala, Sweden
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27
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Giang KA, Nygren PÅ, Nilvebrant J. Selection of Affibody Affinity Proteins from Phagemid Libraries. Methods Mol Biol 2023; 2702:373-392. [PMID: 37679630 DOI: 10.1007/978-1-0716-3381-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
Herein, we describe a general protocol for the selection of target-binding affinity protein molecules from a phagemid-encoded library. The protocol is based on our experience with phage display selections of non-immunoglobulin affibody affinity proteins but can in principle be applied to perform biopanning experiments from any phage-displayed affinity protein library available in a similar phagemid vector. The procedure begins with an amplification of the library from frozen bacterial glycerol stocks via cultivation and helper phage superinfection, followed by a step-by-step instruction of target protein preparation, selection cycles, and post-selection analyses. The described procedures in this standard protocol are relatively conservative and rely on ordinary reagents and equipment available in most molecular biology laboratories.
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Affiliation(s)
- Kim Anh Giang
- Division of Protein Engineering, School of Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden
| | - Per-Åke Nygren
- Division of Protein Engineering, School of Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Solna, Sweden
| | - Johan Nilvebrant
- Division of Protein Engineering, School of Chemistry, Biotechnology and Health, Royal Institute of Technology, Stockholm, Sweden.
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28
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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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29
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Hokanson CA, Zacco E, Cappuccilli G, Odineca T, Crea R. AXL-Receptor Targeted 14FN3 Based Single Domain Proteins (Pronectins™) from 3 Synthetic Human Libraries as Components for Exploring Novel Bispecific Constructs against Solid Tumors. Biomedicines 2022; 10:biomedicines10123184. [PMID: 36551940 PMCID: PMC9775294 DOI: 10.3390/biomedicines10123184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/19/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
A highly specific AXL-receptor targeted family of non-immunoglobulin, single domain protein binders (Pronectins™) have been isolated from three (3) synthetic libraries that employ the human scaffold of the 14th domain of Fibronectin III (14FN3) and evolutionary CDRs diversity of over 25 billion loop sequences. The three libraries, each containing diversity in two loops, were designed to expand upon a human database of more than 6000 natural scaffold sequences and approximately 3000 human loop sequences. We used a bioinformatic-based approach to maximize "human" amino acid loop diversity and minimize or prevent altogether CDR immunogenicity created by the use of mutagenesis processes to generate diversity. A combination of phage display and yeast display was used to isolate 59 AXL receptor targeted Pronectins with KD ranging between 2 and 100 nM. FACS analysis with tumor cells over-expressing AXL and the use of an AXL knock-out cell line allowed us to identify Pronectin candidates with exquisite specificity for AXL receptor. Based upon several in vitro cell-based tests, we selected the best candidate, AXL54, to further characterize its in vitro cancer cells killing activity. Finally, AXL54 was used to produce the first bi-specific T cell engager protein (AXL54 [Pronectin]-linker-scFV CD3), a "new in class" protein for further testing of its anti-tumor activity in vitro and in vivo.
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Affiliation(s)
- Craig A. Hokanson
- Protelica, Inc., 26225 Eden Landing Road, Suite C, Hayward, CA 94545, USA
| | | | | | - Tatjana Odineca
- Protelica, Inc., 26225 Eden Landing Road, Suite C, Hayward, CA 94545, USA
| | - Roberto Crea
- Protelica, Inc., 26225 Eden Landing Road, Suite C, Hayward, CA 94545, USA
- Correspondence:
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30
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Wang Z, Wang G, Lu H, Li H, Tang M, Tong A. Development of therapeutic antibodies for the treatment of diseases. MOLECULAR BIOMEDICINE 2022; 3:35. [PMID: 36418786 PMCID: PMC9684400 DOI: 10.1186/s43556-022-00100-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/24/2022] [Indexed: 11/25/2022] Open
Abstract
Since the first monoclonal antibody drug, muromonab-CD3, was approved for marketing in 1986, 165 antibody drugs have been approved or are under regulatory review worldwide. With the approval of new drugs for treating a wide range of diseases, including cancer and autoimmune and metabolic disorders, the therapeutic antibody drug market has experienced explosive growth. Monoclonal antibodies have been sought after by many biopharmaceutical companies and scientific research institutes due to their high specificity, strong targeting abilities, low toxicity, side effects, and high development success rate. The related industries and markets are growing rapidly, and therapeutic antibodies are one of the most important research and development areas in the field of biology and medicine. In recent years, great progress has been made in the key technologies and theoretical innovations provided by therapeutic antibodies, including antibody-drug conjugates, antibody-conjugated nuclides, bispecific antibodies, nanobodies, and other antibody analogs. Additionally, therapeutic antibodies can be combined with technologies used in other fields to create new cross-fields, such as chimeric antigen receptor T cells (CAR-T), CAR-natural killer cells (CAR-NK), and other cell therapy. This review summarizes the latest approved or in regulatory review therapeutic antibodies that have been approved or that are under regulatory review worldwide, as well as clinical research on these approaches and their development, and outlines antibody discovery strategies that have emerged during the development of therapeutic antibodies, such as hybridoma technology, phage display, preparation of fully human antibody from transgenic mice, single B-cell antibody technology, and artificial intelligence-assisted antibody discovery.
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Affiliation(s)
- Zeng Wang
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Guoqing Wang
- Department of Neurosurgery, West China Medical School, West China Hospital, Sichuan University, Chengdu, China
| | - Huaqing Lu
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hongjian Li
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Mei Tang
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Aiping Tong
- State Key Laboratory of Biotherapy and Cancer Center, Research Unit of Gene and Immunotherapy, Chinese Academy of Medical Sciences, Collaborative Innovation Center of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.
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31
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A red light-responsive photoswitch for deep tissue optogenetics. Nat Biotechnol 2022; 40:1672-1679. [PMID: 35697806 DOI: 10.1038/s41587-022-01351-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 05/04/2022] [Indexed: 12/30/2022]
Abstract
Red light penetrates deep into mammalian tissues and has low phototoxicity, but few optogenetic tools that use red light have been developed. Here we present MagRed, a red light-activatable photoswitch that consists of a red light-absorbing bacterial phytochrome incorporating a mammalian endogenous chromophore, biliverdin and a photo-state-specific binder that we developed using Affibody library selection. Red light illumination triggers the binding of the two components of MagRed and the assembly of split-proteins fused to them. Using MagRed, we developed a red light-activatable Cre recombinase, which enables light-activatable DNA recombination deep in mammalian tissues. We also created red light-inducible transcriptional regulators based on CRISPR-Cas9 that enable an up to 378-fold activation (average, 135-fold induction) of multiple endogenous target genes. MagRed will facilitate optogenetic applications deep in mammalian organisms in a variety of biological research areas.
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32
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Zhang Q, Zhu H, Cui Z, Li Y, Zhuo J, Ye J, Zhang Z, Lian Z, Du Q, Zhao KN, Zhang L, Jiang P. The HPV16E7 Affibody as a Novel Potential Therapeutic Agent for Treating Cervical Cancer Is Likely Internalized through Dynamin and Caveolin-1 Dependent Endocytosis. Biomolecules 2022; 12:biom12081114. [PMID: 36009008 PMCID: PMC9405713 DOI: 10.3390/biom12081114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/14/2022] [Accepted: 07/21/2022] [Indexed: 12/24/2022] Open
Abstract
Affibodies targeting intracellular proteins have a great potential to function as ideal therapeutic agents. However, little is known about how the affibodies enter target cells to interact with intracellular target proteins. We have previously developed the HPV16E7 affibody (ZHPV16E7384) for HPV16 positive cervical cancer treatment. Here, we explored the underlying mechanisms of ZHPV16E7384 and found that ZHPV16E7384 significantly inhibited the proliferation of target cells and induced a G1/S phase cell cycle arrest. Furthermore, ZHPV16E7384 treatment resulted in the upregulation of retinoblastoma protein (Rb) and downregulation of phosphorylated Rb (pRb), E2F1, cyclin D1, and CDK4 in the target cells. Moreover, treatment with dynamin or the caveolin-1 inhibitor not only significantly suppressed the internalization of ZHPV16E7384 into target cells but also reversed the regulation of cell cycle factors by ZHPV16E7384. Overall, these results indicate that ZHPV16E7384 was likely internalized specifically into target cells through dynamin- and caveolin-1 mediated endocytosis. ZHPV16E7384 induced the cell cycle arrest in the G1/S phase at least partially by interrupting HPV16E7 binding to and degrading Rb, subsequently leading to the downregulation of E2F1, cyclin D1, CDK4, and pRb, which ultimately inhibited target cell proliferation. These findings provide a rationale of using ZHPV16E7384 to conduct a clinical trial for target therapy in cervical cancer.
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Affiliation(s)
- Qingyuan Zhang
- Institute of Molecular Virology and Immunology, Department of Microbiology & Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Hua Zhu
- Department of Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325035, China
| | - Zhouying Cui
- Institute of Molecular Virology and Immunology, Department of Microbiology & Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Yuxiao Li
- Institute of Molecular Virology and Immunology, Department of Microbiology & Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Jiaying Zhuo
- Institute of Molecular Virology and Immunology, Department of Microbiology & Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Jingwei Ye
- Institute of Molecular Virology and Immunology, Department of Microbiology & Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Zhihui Zhang
- Institute of Molecular Virology and Immunology, Department of Microbiology & Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Zheng Lian
- Institute of Molecular Virology and Immunology, Department of Microbiology & Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Qianqian Du
- Institute of Molecular Virology and Immunology, Department of Microbiology & Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325035, China
| | - Kong-Nan Zhao
- Institute of Molecular Virology and Immunology, Department of Microbiology & Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia 4067, Australia
- Correspondence: (K.-N.Z.); (L.Z.); (P.J.); Tel.: +61-7-34431291 (K.-N.Z.); +86-577-86689910 (L.Z.); +86-577-86699583 (P.J.)
| | - Lifang Zhang
- Institute of Molecular Virology and Immunology, Department of Microbiology & Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- Correspondence: (K.-N.Z.); (L.Z.); (P.J.); Tel.: +61-7-34431291 (K.-N.Z.); +86-577-86689910 (L.Z.); +86-577-86699583 (P.J.)
| | - Pengfei Jiang
- Institute of Molecular Virology and Immunology, Department of Microbiology & Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou 325035, China
- Correspondence: (K.-N.Z.); (L.Z.); (P.J.); Tel.: +61-7-34431291 (K.-N.Z.); +86-577-86689910 (L.Z.); +86-577-86699583 (P.J.)
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33
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Hu X, Li D, Fu Y, Zheng J, Feng Z, Cai J, Wang P. Advances in the Application of Radionuclide-Labeled HER2 Affibody for the Diagnosis and Treatment of Ovarian Cancer. Front Oncol 2022; 12:917439. [PMID: 35785201 PMCID: PMC9240272 DOI: 10.3389/fonc.2022.917439] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/20/2022] [Indexed: 12/19/2022] Open
Abstract
Human epidermal growth factor receptor 2 (HER2) is a highly expressed tumor marker in epithelial ovarian cancer, and its overexpression is considered to be a potential factor of poor prognosis. Therefore, monitoring the expression of HER2 receptor in tumor tissue provides favorable conditions for accurate localization, diagnosis, targeted therapy, and prognosis evaluation of cancer foci. Affibody has the advantages of high affinity, small molecular weight, and stable biochemical properties. The molecular probes of radionuclide-labeled HER2 affibody have recently shown broad application prospects in the diagnosis and treatment of ovarian cancer; the aim is to introduce radionuclides into the cancer foci, display systemic lesions, and kill tumor cells through the radioactivity of the radionuclides. This process seamlessly integrates the diagnosis and treatment of ovarian cancer. Current research and development of new molecular probes of radionuclide-labeled HER2 affibody should focus on overcoming the deficiencies of non-specific uptake in the kidney, bone marrow, liver, and gastrointestinal tract, and on reducing the background of the image to improve image quality. By modifying the amino acid sequence; changing the hydrophilicity, surface charge, and lipid solubility of the affibody molecule; and using different radionuclides, chelating agents, and labeling conditions to optimize the labeling method of molecular probes, the specific uptake of molecular probes at tumor sites will be improved, while reducing radioactive retention in non-target organs and obtaining the best target/non-target value. These measures will enable the clinical use of radionuclide-labeled HER2 affibody molecular probes as soon as possible, providing a new clinical path for tumor-specific diagnosis, targeted therapy, and efficacy evaluation. The purpose of this review is to describe the application of radionuclide-labeled HER2 affibody in the imaging and treatment of ovarian cancer, including its potential clinical value and dilemmas.
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Affiliation(s)
- Xianwen Hu
- Department of Nuclear Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Dandan Li
- Department of Obstetrics, Zunyi Hospital of Traditional Chinese Medicine, Zunyi, China
| | - Yujie Fu
- Research and Development Department, Jiangsu Yuanben Biotechnology Co., Ltd., Zunyi, China
| | - Jiashen Zheng
- Department of Nuclear Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zelong Feng
- Department of Nuclear Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Jiong Cai
- Department of Nuclear Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- *Correspondence: Jiong Cai, ; Pan Wang,
| | - Pan Wang
- Department of Nuclear Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- *Correspondence: Jiong Cai, ; Pan Wang,
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Berg S, Suljovic D, Kärrberg L, Englund M, Bönisch H, Karlberg I, Van Zuydam N, Abrahamsson B, Hugerth AM, Davies N, Bergström CAS. Intestinal Absorption of FITC-Dextrans and Macromolecular Model Drugs in the Rat Intestinal Instillation Model. Mol Pharm 2022; 19:2564-2572. [PMID: 35642793 PMCID: PMC9257752 DOI: 10.1021/acs.molpharmaceut.2c00261] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
In this work, we
studied the intestinal absorption of a peptide
with a molecular weight of 4353 Da (MEDI7219) and a protein having
a molecular weight of 11 740 Da (PEP12210) in the rat intestinal
instillation model and compared their absorption to fluorescein isothiocyanate
(FITC)-labeled dextrans of similar molecular weights (4 and 10 kDa).
To increase the absorption of the compounds, the permeation enhancer
sodium caprate (C10) was included in the liquid formulations at concentrations
of 50 and 300 mM. All studied compounds displayed an increased absorption
rate and extent when delivered together with 50 mM C10 as compared
to control formulations not containing C10. The time period during
which the macromolecules maintained an increased permeability through
the intestinal epithelium was approximately 20 min for all studied
compounds at 50 mM C10. For the formulations containing 300 mM C10,
it was noted that the dextrans displayed an increased absorption rate
(compared to 50 mM C10), and their absorption continued for at least
60 min. The absorption rate of MEDI7219, on the other hand, was similar
at both studied C10 concentrations, but the duration of absorption
was extended at the higher enhancer concentration, leading to an increase
in the overall extent of absorption. The absorption of PEP12210 was
similar in terms of the rate and duration at both studied C10 concentrations.
This is likely caused by the instability of this molecule in the intestinal
lumen. The degradation decreases the luminal concentrations over time,
which in turn limits absorption at time points beyond 20 min. The
results from this study show that permeation enhancement effects cannot
be extrapolated between different types of macromolecules. Furthermore,
to maximize the absorption of a macromolecule delivered together with
C10, prolonging the duration of absorption appears to be important.
In addition, the macromolecule needs to be stable enough in the intestinal
lumen to take advantage of the prolonged absorption time window enabled
by the permeation enhancer.
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Affiliation(s)
- Staffan Berg
- The Swedish Drug Delivery Center, Department of Pharmacy, Uppsala University, BMC P.O. Box 580, Uppsala SE-751 23, Sweden.,Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Denny Suljovic
- The Swedish Drug Delivery Center, Department of Pharmacy, Uppsala University, BMC P.O. Box 580, Uppsala SE-751 23, Sweden
| | - Lillevi Kärrberg
- Animal Sciences and Technologies, Clinical Pharmacology and Safety Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Maria Englund
- Drug Metabolism and Pharmacokinetics, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | | | | | - Natalie Van Zuydam
- Data Science and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Bertil Abrahamsson
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg 431 83, Sweden
| | - Andreas Martin Hugerth
- Ferring Pharmaceuticals A/S, Product Development and Drug Delivery, Global Pharmaceutical R&D, Amager Strandvej 405, Kastrup 2770, Denmark
| | - Nigel Davies
- Advanced Drug Delivery, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg 431 83, Sweden
| | - Christel A S Bergström
- The Swedish Drug Delivery Center, Department of Pharmacy, Uppsala University, BMC P.O. Box 580, Uppsala SE-751 23, Sweden
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Transferrin Receptor Binding BBB-Shuttle Facilitates Brain Delivery of Anti-Aβ-Affibodies. Pharm Res 2022; 39:1509-1521. [PMID: 35538266 PMCID: PMC9246779 DOI: 10.1007/s11095-022-03282-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/29/2022] [Indexed: 12/13/2022]
Abstract
Affibodies targeting amyloid-beta (Aβ) could potentially be used as therapeutic and diagnostic agents in Alzheimer's disease (AD). Affibodies display suitable characteristics for imaging applications such as high stability and a short biological half-life. The aim of this study was to explore brain delivery and retention of Aβ protofibril-targeted affibodies in wild-type (WT) and AD transgenic mice and to evaluate their potential as imaging agents. Two affibodies, Z5 and Z1, were fused with the blood-brain barrier (BBB) shuttle single-chain variable fragment scFv8D3. In vitro binding of 125I-labeled affibodies with and without scFv8D3 was evaluated by ELISA and autoradiography. Brain uptake and retention of the affibodies at 2 h and 24 h post injection was studied ex vivo in WT and transgenic (tg-Swe and tg-ArcSwe) mice. At 2 h post injection, [125I]I-Z5 and [125I]I-Z1 displayed brain concentrations of 0.37 ± 0.09% and 0.46 ± 0.08% ID/g brain, respectively. [125I]I-scFv8D3-Z5 and [125I]I-scFv8D3-Z1 showed increased brain concentrations of 0.53 ± 0.16% and 1.20 ± 0.35%ID/g brain. At 24 h post injection, brain retention of [125I]I-Z1 and [125I]I-Z5 was low, while [125I]I-scFv8D3-Z1 and [125I]I-scFv8D3-Z5 showed moderate brain retention, with a tendency towards higher retention of [125I]I-scFv8D3-Z5 in AD transgenic mice. Nuclear track emulsion autoradiography showed greater parenchymal distribution of [125I]I-scFv8D3-Z5 and [125I]I-scFv8D3-Z1 compared with the affibodies without scFv8D3, but could not confirm specific affibody accumulation around Aβ deposits. Affibody-scFv8D3 fusions displayed increased brain and parenchymal delivery compared with the non-fused affibodies. However, fast brain washout and a suboptimal balance between Aβ and mTfR1 affinity resulted in low intrabrain retention around Aβ deposits.
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McNulty MJ, Schwartz A, Delzio J, Karuppanan K, Jacobson A, Hart O, Dandekar A, Giritch A, Nandi S, Gleba Y, McDonald KA. Affinity Sedimentation and Magnetic Separation With Plant-Made Immunosorbent Nanoparticles for Therapeutic Protein Purification. Front Bioeng Biotechnol 2022; 10:865481. [PMID: 35573255 PMCID: PMC9092175 DOI: 10.3389/fbioe.2022.865481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/04/2022] [Indexed: 11/20/2022] Open
Abstract
The virus-based immunosorbent nanoparticle is a nascent technology being developed to serve as a simple and efficacious agent in biosensing and therapeutic antibody purification. There has been particular emphasis on the use of plant virions as immunosorbent nanoparticle chassis for their diverse morphologies and accessible, high yield manufacturing via plant cultivation. To date, studies in this area have focused on proof-of-concept immunosorbent functionality in biosensing and purification contexts. Here we consolidate a previously reported pro-vector system into a single Agrobacterium tumefaciens vector to investigate and expand the utility of virus-based immunosorbent nanoparticle technology for therapeutic protein purification. We demonstrate the use of this technology for Fc-fusion protein purification, characterize key nanomaterial properties including binding capacity, stability, reusability, and particle integrity, and present an optimized processing scheme with reduced complexity and increased purity. Furthermore, we present a coupling of virus-based immunosorbent nanoparticles with magnetic particles as a strategy to overcome limitations of the immunosorbent nanoparticle sedimentation-based affinity capture methodology. We report magnetic separation results which exceed the binding capacity reported for current industry standards by an order of magnitude.
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Affiliation(s)
- Matthew J. McNulty
- Department of Chemical Engineering, University of California, Davis, Davis, CA, United States
| | | | - Jesse Delzio
- Department of Chemical Engineering, University of California, Davis, Davis, CA, United States
| | - Kalimuthu Karuppanan
- Department of Chemical Engineering, University of California, Davis, Davis, CA, United States
| | - Aaron Jacobson
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Olivia Hart
- Department of Chemical Engineering, University of California, Davis, Davis, CA, United States
| | - Abhaya Dandekar
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | | | - Somen Nandi
- Department of Chemical Engineering, University of California, Davis, Davis, CA, United States
- Global HealthShare® Initiative, University of California, Davis, Davis, CA, United States
| | | | - Karen A. McDonald
- Department of Chemical Engineering, University of California, Davis, Davis, CA, United States
- Global HealthShare® Initiative, University of California, Davis, Davis, CA, United States
- *Correspondence: Karen A. McDonald,
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Fay R, Törő I, Schinke AL, Simic B, Schaefer JV, Dreier B, Plückthun A, Holland JP. Sortase-Mediated Site-Specific Conjugation and 89Zr-Radiolabeling of Designed Ankyrin Repeat Proteins for PET. Mol Pharm 2022; 19:3576-3585. [DOI: 10.1021/acs.molpharmaceut.2c00136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rachael Fay
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Imre Törő
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Anna-Lena Schinke
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Branko Simic
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jonas V. Schaefer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jason P. Holland
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Gast V, Sandegren A, Dunås F, Ekblad S, Güler R, Thorén S, Tous Mohedano M, Molin M, Engqvist MKM, Siewers V. Engineering Saccharomyces cerevisiae for the production and secretion of Affibody molecules. Microb Cell Fact 2022; 21:36. [PMID: 35264156 PMCID: PMC8905840 DOI: 10.1186/s12934-022-01761-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/22/2022] [Indexed: 11/23/2022] Open
Abstract
Background Affibody molecules are synthetic peptides with a variety of therapeutic and diagnostic applications. To date, Affibody molecules have mainly been produced by the bacterial production host Escherichia coli. There is an interest in exploring alternative production hosts to identify potential improvements in terms of yield, ease of production and purification advantages. In this study, we evaluated the feasibility of Saccharomyces cerevisiae as a production chassis for this group of proteins. Results We examined the production of three different Affibody molecules in S. cerevisiae and found that these Affibody molecules were partially degraded. An albumin-binding domain, which may be attached to the Affibody molecules to increase their half-life, was identified to be a substrate for several S. cerevisiae proteases. We tested the removal of three vacuolar proteases, proteinase A, proteinase B and carboxypeptidase Y. Removal of one of these, proteinase A, resulted in intact secretion of one of the targeted Affibody molecules. Removal of either or both of the two additional proteases, carboxypeptidase Y and proteinase B, resulted in intact secretion of the two remaining Affibody molecules. The produced Affibody molecules were verified to bind their target, human HER3, as potently as the corresponding molecules produced in E. coli in an in vitro surface-plasmon resonance binding assay. Finally, we performed a fed-batch fermentation with one of the engineered protease-deficient S. cerevisiae strains and achieved a protein titer of 530 mg Affibody molecule/L. Conclusion This study shows that engineered S. cerevisiae has a great potential as a production host for recombinant Affibody molecules, reaching a high titer, and for proteins where endotoxin removal could be challenging, the use of S. cerevisiae obviates the need for endotoxin removal from protein produced in E. coli. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01761-0.
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Affiliation(s)
- Veronica Gast
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | | | | | | | | | - Marta Tous Mohedano
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Mikael Molin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Martin K M Engqvist
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden.
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Zhang D, Wang Z, Hu S, Chan NY, Liew HT, Lescar J, Tam JP, Liu CF. Asparaginyl Endopeptidase-Mediated Protein C-Terminal Hydrazinolysis for the Synthesis of Bioconjugates. Bioconjug Chem 2022; 33:238-247. [PMID: 34985285 DOI: 10.1021/acs.bioconjchem.1c00551] [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: 11/28/2022]
Abstract
Asparaginyl endopeptidases (AEPs) are cysteinyl enzymes naturally catalyzing the hydrolysis and transpeptidation reactions at Asx-Xaa bonds. These reactions go by a common acyl-enzyme thioester intermediate, which is either attacked by water (for a protease-AEP) or by a peptidic amine nucleophile (for a ligase-AEP) to form the respective hydrolysis or aminolysis product. Herein, we show that hydrazine and hydroxylamine, two α-effect nucleophiles, are capable of resolving the thioester intermediate to yield peptide and protein products containing a C-terminal hydrazide and hydroxamic acid functionality, respectively. The hydrazinolysis reaction exhibits very high efficiency and can be completed in minutes at a low enzyme-to-substrate ratio. We further show the utility of the so-formed asparaginyl hydrazide in native chemical ligation and hydrazone conjugation. Using an EGFR-targeting affibody as a model protein, we have showcased our methodology in the preparation of a number of protein ligation or conjugation products, which are decorated with various functional moieties. The ZEGFR affibody-doxorubicin conjugate shows high selective binding and cytotoxicity toward the EGFR-positive A431 cells. Our results demonstrate the advantages of AEP-mediated protein hydrazinolysis as a simple and straightforward strategy for the precision manufacturing of protein bioconjugates.
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Affiliation(s)
- Dingpeng Zhang
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Zhen Wang
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Side Hu
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Ning-Yu Chan
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Heng Tai Liew
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Julien Lescar
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - James P Tam
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Chuan-Fa Liu
- School of Biological Science, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
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Tolmachev VM, Chernov VI, Deyev SM. Targeted nuclear medicine. Seek and destroy. RUSSIAN CHEMICAL REVIEWS 2022. [DOI: 10.1070/rcr5034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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41
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Xia X, Yang X, Huang W, Xia X, Yan D. Self-Assembled Nanomicelles of Affibody-Drug Conjugate with Excellent Therapeutic Property to Cure Ovary and Breast Cancers. NANO-MICRO LETTERS 2021; 14:33. [PMID: 34902075 PMCID: PMC8669081 DOI: 10.1007/s40820-021-00762-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 10/14/2021] [Indexed: 05/06/2023]
Abstract
Affibody molecules are small non-immunoglobulin affinity proteins, which can precisely target to some cancer cells with specific overexpressed molecular signatures. However, the relatively short in vivo half-life of them seriously limited their application in drug targeted delivery for cancer therapy. Here an amphiphilic affibody-drug conjugate is self-assembled into nanomicelles to prolong circulation time for targeted cancer therapy. As an example of the concept, the nanoagent was prepared through molecular self-assembly of the amphiphilic conjugate of ZHER2:342-Cys with auristatin E derivate, where the affibody used is capable of binding to the human epidermal growth factor receptor 2 (HER2). Such a nanodrug not only increased the blood circulation time, but also enhanced the tumor targeting capacity (abundant affibody arms on the nanoagent surface) and the drug accumulation in tumor. As a result, this affibody-based nanoagent showed excellent antitumor activity in vivo to HER2-positive ovary and breast tumor models, which nearly eradicated both small solid tumors (about 100 mm3) and large established tumors (exceed 500 mm3). The relative tumor proliferation inhibition ratio reaches 99.8% for both models.
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Affiliation(s)
- Xuelin Xia
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Xiaoyuan Yang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Wei Huang
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Xiaoxia Xia
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Deyue Yan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
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A Panel of Engineered Ubiquitin Variants Targeting the Family of Domains Found in Ubiquitin Specific Proteases (DUSPs). J Mol Biol 2021; 433:167300. [PMID: 34666042 DOI: 10.1016/j.jmb.2021.167300] [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] [Received: 07/26/2021] [Revised: 09/16/2021] [Accepted: 10/04/2021] [Indexed: 11/21/2022]
Abstract
Domains found in ubiquitin specific proteases (DUSPs) occur in seven members of the ubiquitin specific protease (USP) family. DUSPs are defined by a distinct structural fold but their functions remain largely unknown, although studies with USP4 suggest that its DUSP enhances deubiquitination activity. We used phage-displayed libraries of ubiquitin variants (UbVs) to derive protein-based tools to target DUSP family members with high affinity and specificity. We designed a UbV library based on insights from the structure of a previously identified UbV bound to the DUSP of USP15. The new library yielded 33 unique UbVs that bound to DUSPs from five different USPs (USP4, USP11, USP15, USP20 and USP33). For each USP, we were able to identify at least one DUSP that bound with high affinity and absolute specificity relative to the other DUSPs. We showed that UbVs targeting the DUSPs of USP15, USP11 and USP20 inhibited the catalytic activity of the enzyme, despite the fact that the DUSP is located outside of the catalytic domain. These findings provide an alternative means of inhibiting USP activity by targeting DUSPs, and this mechanism could be potentially extended other DUSP-containing USPs.
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Palacio-Castañeda V, Oude Egberink R, Sait A, Andrée L, Sala BM, Hassani Besheli N, Oosterwijk E, Nilvebrant J, Leeuwenburgh SCG, Brock R, Verdurmen WPR. Mimicking the Biology of Engineered Protein and mRNA Nanoparticle Delivery Using a Versatile Microfluidic Platform. Pharmaceutics 2021; 13:pharmaceutics13111944. [PMID: 34834361 PMCID: PMC8624409 DOI: 10.3390/pharmaceutics13111944] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 12/24/2022] Open
Abstract
To investigate the delivery of next-generation macromolecular drugs, such as engineered proteins and mRNA-containing nanoparticles, there is an increasing push towards the use of physiologically relevant disease models that incorporate human cells and do not face ethical dilemmas associated with animal use. Here, we illustrate the versatility and ease of use of a microfluidic platform for studying drug delivery using high-resolution microscopy in 3D. Using this microfluidic platform, we successfully demonstrate the specific targeting of carbonic anhydrase IX (CAIX) on cells overexpressing the protein in a tumor-mimicking chip system using affibodies, with CAIX-negative cells and non-binding affibodies as controls. Furthermore, we demonstrate this system’s feasibility for testing mRNA-containing biomaterials designed to regenerate bone defects. To this end, peptide- and lipid-based mRNA formulations were successfully mixed with colloidal gelatin in microfluidic devices, while translational activity was studied by the expression of a green fluorescent protein. This microfluidic platform enables the testing of mRNA delivery from colloidal biomaterials of relatively high densities, which represents a first important step towards a bone-on-a-chip platform. Collectively, by illustrating the ease of adaptation of our microfluidic platform towards use in distinct applications, we show that our microfluidic chip represents a powerful and flexible way to investigate drug delivery in 3D disease-mimicking culture systems that recapitulate key parameters associated with in vivo drug application.
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Affiliation(s)
- Valentina Palacio-Castañeda
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands; (V.P.-C.); (R.O.E.); (A.S.)
| | - Rik Oude Egberink
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands; (V.P.-C.); (R.O.E.); (A.S.)
| | - Arbaaz Sait
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands; (V.P.-C.); (R.O.E.); (A.S.)
| | - Lea Andrée
- Department of Dentistry—Regenerative Biomaterials, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Philips van Leydenlaan 25, 6525 EX Nijmegen, The Netherlands; (L.A.); (N.H.B.); (S.C.G.L.)
| | - Benedetta Maria Sala
- Division of Protein Engineering, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology, SE-100 44 Stockholm, Sweden; (B.M.S.); (J.N.)
| | - Negar Hassani Besheli
- Department of Dentistry—Regenerative Biomaterials, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Philips van Leydenlaan 25, 6525 EX Nijmegen, The Netherlands; (L.A.); (N.H.B.); (S.C.G.L.)
| | - Egbert Oosterwijk
- Department of Urology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 26/28, 6525 GA Nijmegen, The Netherlands;
| | - Johan Nilvebrant
- Division of Protein Engineering, Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, AlbaNova University Center, Royal Institute of Technology, SE-100 44 Stockholm, Sweden; (B.M.S.); (J.N.)
| | - Sander C. G. Leeuwenburgh
- Department of Dentistry—Regenerative Biomaterials, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Philips van Leydenlaan 25, 6525 EX Nijmegen, The Netherlands; (L.A.); (N.H.B.); (S.C.G.L.)
| | - Roland Brock
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands; (V.P.-C.); (R.O.E.); (A.S.)
- Department of Medical Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama 329, Bahrain
- Correspondence: (R.B.); (W.P.R.V.)
| | - Wouter P. R. Verdurmen
- Department of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands; (V.P.-C.); (R.O.E.); (A.S.)
- Correspondence: (R.B.); (W.P.R.V.)
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Affibody Functionalized Beads for the Highly Sensitive Detection of Cancer Cell-Derived Exosomes. Int J Mol Sci 2021; 22:ijms222112014. [PMID: 34769444 PMCID: PMC8584739 DOI: 10.3390/ijms222112014] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 10/29/2021] [Accepted: 11/04/2021] [Indexed: 12/14/2022] Open
Abstract
Exosomes belong to the class of extracellular vesicles of endocytic origin, which are regarded as a promising source of cancer biomarkers in liquid biopsy. As a result, an accurate, sensitive, and specific quantification of these nano-sized particles is of significant importance. Affinity-based approaches are recognized as the most valuable technique for exosome isolation and characterization. Indeed, Affibody biomolecules are a type of protein scaffold engineered with small size and enjoy the features of high thermal stability, affinity, and specificity. While the utilization of antibodies, aptamers, and other biologically active substances for exosome detection has been reported widely, there are no reports describing Affibody molecules’ usage for exosome detection. In this study, for the first time, we have proposed a novel strategy of using Affibody functionalized microbeads (AffiBeads) for exosome detection with a high degree of efficiency. As a proof-of-concept, anti-EGFR-AffiBeads were fabricated and applied to capture and detect human lung A549 cancer cell-derived EGFR-positive exosomes using flow cytometry and fluorescent microscopy. Moreover, the capture efficiency of the AffiBeads were compared with its counterpart antibody. Our results showed that the Affibody probe had a detection limit of 15.6 ng exosomes per mL (~12 exosomes per AffiBead). The approach proposed in the current study can be used for sensitive detection of low expression level markers on tumor-derived exosomes, providing a basis for early-stage cancer diagnosis.
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Concepts in Oncolytic Adenovirus Therapy. Int J Mol Sci 2021; 22:ijms221910522. [PMID: 34638863 PMCID: PMC8508870 DOI: 10.3390/ijms221910522] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/23/2021] [Accepted: 09/24/2021] [Indexed: 02/07/2023] Open
Abstract
Oncolytic adenovirus therapy is gaining importance as a novel treatment option for the management of various cancers. Different concepts of modification within the adenovirus vector have been identified that define the mode of action against and the interaction with the tumour. Adenoviral vectors allow for genetic manipulations that restrict tumour specificity and also the expression of specific transgenes in order to support the anti-tumour effect. Additionally, replication of the virus and reinfection of neighbouring tumour cells amplify the therapeutic effect. Another important aspect in oncolytic adenovirus therapy is the virus induced cell death which is a process that activates the immune system against the tumour. This review describes which elements in adenovirus vectors have been identified for modification not only to utilize oncolytic adenovirus vectors into conditionally replicating adenoviruses (CRAds) that allow replication specifically in tumour cells but also to confer specific characteristics to these viruses. These advances in development resulted in clinical trials that are summarized based on the conceptual design.
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Kamara S, Guo Y, Mao S, Ye X, Li Q, Zheng M, Zhu J, Zhang J, Du W, Chen J, Zhu S, Zhang L. Novel EBV LMP1 C-terminal domain binding affibody molecules as potential agents for in vivo molecular imaging diagnosis of nasopharyngeal carcinoma. Appl Microbiol Biotechnol 2021; 105:7283-7293. [PMID: 34505914 DOI: 10.1007/s00253-021-11559-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 10/20/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is consistently associated with Epstein-Barr virus (EBV) latent infection and is common in Southern China and Southeast Asia. The viral latent membrane proteins LMP1 and LMP2 are persistently expressed in NPC tissues; the cytoplasmic domain of LMP1 (LMP1 C-terminal) and LMP2A (LMP2A N-terminal) proteins is essential for maintenance of latency and can alter host cell signaling to facilitate tumor growth and progression. Thus, targeting LMP1 or LMP2 oncoprotein has been an increasing interest for diagnosis and targeted therapy of NPC. Affibody molecules, a new class of small-affinity engineered scaffold proteins, have demonstrated high potential for therapeutics, diagnostics, and biotechnological applications. More recently, radiolabelled HER2-specific affibody molecules have demonstrated to be useful in imaging of HER2 expressing tumor. In this study, we report three novel EBV LMP1 C-terminal (EBV LMP1-C) domain affibody molecules (ZLMP1-C15, ZLMP1-C114, and ZLMP1-C277) were selected by biopanning from a random-peptide displayed phage library and used for molecular imaging in tumor-bearing nude mice. Surface plasmon resonance (SPR), indirect immunofluorescence, and immunohistochemistry (IHC) clearly showed that all three selected affibody molecules have high affinity and specificity in binding to EBV LMP1 protein. Moreover, in vivo tumor imaging revealed that Dylight-755-labeled affibody molecules accumulated rapidly in tumor site after injection (1 h) and then were continuously maintained for 24 h in EBV-positive NPC xenograft mice model. In conclusion, our findings highlight the potential use of ZLMP1-C affibody molecules as tumor-specific molecular imaging agents of EBV-associated NPC.Key points• We screened three novel affibody molecules (ZLMP1-C15, ZLMP1-C114, and ZLMP1-C277) targeting EBV LMP1-C terminal domain• ZLMP1-C recognize the recombinant and native LMP1-C with high affinity and specificity• ZLMP1-C can be used for molecular imaging.
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Affiliation(s)
- Saidu Kamara
- Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Yanru Guo
- Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Shanshan Mao
- Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Xiaoxian Ye
- Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Qingfeng Li
- Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Maolin Zheng
- Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Jinshun Zhu
- Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Jing Zhang
- Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Wangqi Du
- Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Jun Chen
- Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Shanli Zhu
- Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, People's Republic of China
| | - Lifang Zhang
- Institute of Molecular Virology and Immunology, Department of Microbiology and Immunology, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, People's Republic of China.
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Kondo T, Eguchi M, Tsuzuki N, Murata N, Fujino T, Hayashi G, Murakami H. Construction of a Highly Diverse mRNA Library for in vitro Selection of Monobodies. Bio Protoc 2021; 11:e4125. [PMID: 34541043 DOI: 10.21769/bioprotoc.4125] [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: 01/03/2021] [Revised: 05/07/2021] [Accepted: 05/16/2021] [Indexed: 11/02/2022] Open
Abstract
Recently, we developed transcription/translation coupled with the association of puromycin linker (TRAP) display as a quick in vitro selection method to obtain antibody-like proteins. For the in vitro selection, it is important to prepare mRNA libraries among which the diversity is high. Here, we describe a method for the preparation of monobody mRNA libraries with greater than 1013 theoretical diversity. First, we synthesized two long single-stranded DNAs that corresponded to fragments of monobody DNA, with random codons in the BC and FG loops. These oligonucleotides were ligated by T4 DNA ligase with the support of guide oligonucleotides containing 3' ends that were protected by a modification. After amplifying the product DNAs by PCR, one end of each DNA fragment was digested with the type II restriction enzyme BsaI, and the resulting DNA fragments were ligated using T4 DNA ligase. After amplification of the DNA product, mRNAs were synthesized by T7 RNA polymerase. This method is simple and could be used for the preparation of mRNA libraries for various antibody-like proteins. Graphic abstract: Construction of a highly diverse mRNA library.
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Affiliation(s)
- Taishi Kondo
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Minori Eguchi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Nariaki Tsuzuki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Naoya Murata
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Tomoshige Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Gosuke Hayashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.,Japan Science and Technology Agency (JST), PRESTO, Japan
| | - Hiroshi Murakami
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan.,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan
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Shipunova VO, Sogomonyan AS, Zelepukin IV, Nikitin MP, Deyev SM. PLGA Nanoparticles Decorated with Anti-HER2 Affibody for Targeted Delivery and Photoinduced Cell Death. Molecules 2021; 26:molecules26133955. [PMID: 34203547 PMCID: PMC8271481 DOI: 10.3390/molecules26133955] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 11/18/2022] Open
Abstract
The effect of enhanced permeability and retention is often not sufficient for highly effective cancer therapy with nanoparticles, and the development of active targeted drug delivery systems based on nanoparticles is probably the main direction of modern cancer medicine. To meet the challenge, we developed polymer PLGA nanoparticles loaded with fluorescent photosensitive xanthene dye, Rose Bengal, and decorated with HER2-recognizing artificial scaffold protein, affibody ZHER2:342. The obtained 170 nm PLGA nanoparticles possess both fluorescent and photosensitive properties. Namely, under irradiation with the green light of 540 nm nanoparticles, they produced reactive oxygen species leading to cancer cell death. The chemical conjugation of PLGA with anti-HER2 affibody resulted in the selective binding of nanoparticles only to HER2-overexpressing cancer cells. HER2 is a receptor tyrosine kinase that belongs to the EGFR/ERbB family and is overexpressed in 30% of breast cancers, thus serving as a clinically relevant oncomarker. However, the standard targeting molecules such as full-size antibodies possess serious drawbacks, such as high immunogenicity and the need for mammalian cell production. We believe that the developed affibody-decorated targeted photosensitive PLGA nanoparticles will provide new solutions for ongoing problems in cancer diagnostics and treatment, as well in cancer theranostics.
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Affiliation(s)
- Victoria Olegovna Shipunova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia; (A.S.S.); (I.V.Z.); (M.P.N.); (S.M.D.)
- Institute of Engineering Physics for Biomedicine (PhysBio), MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoe Shosse, 115409 Moscow, Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy per., 141701 Dolgoprudny, Russia
- Department of Nanobiomedicine, Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
- Correspondence: ; Tel.: +7-985-2519909
| | - Anna Samvelovna Sogomonyan
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia; (A.S.S.); (I.V.Z.); (M.P.N.); (S.M.D.)
- Institute of Engineering Physics for Biomedicine (PhysBio), MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoe Shosse, 115409 Moscow, Russia
| | - Ivan Vladimirovich Zelepukin
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia; (A.S.S.); (I.V.Z.); (M.P.N.); (S.M.D.)
- Institute of Engineering Physics for Biomedicine (PhysBio), MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoe Shosse, 115409 Moscow, Russia
- Moscow Institute of Physics and Technology, 9 Institutskiy per., 141701 Dolgoprudny, Russia
| | - Maxim Petrovich Nikitin
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia; (A.S.S.); (I.V.Z.); (M.P.N.); (S.M.D.)
- Moscow Institute of Physics and Technology, 9 Institutskiy per., 141701 Dolgoprudny, Russia
- Department of Nanobiomedicine, Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russia
| | - Sergey Mikhailovich Deyev
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., 117997 Moscow, Russia; (A.S.S.); (I.V.Z.); (M.P.N.); (S.M.D.)
- Institute of Engineering Physics for Biomedicine (PhysBio), MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoe Shosse, 115409 Moscow, Russia
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Ahmadi MKB, Mohammadi SA, Makvandi M, Mamouei M, Rahmati M, Dehghani H, Wood DW. Recent Advances in the Scaffold Engineering of Protein Binders. Curr Pharm Biotechnol 2021; 22:878-891. [PMID: 32838715 DOI: 10.2174/1389201021999200824101035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/08/2020] [Accepted: 08/10/2020] [Indexed: 11/22/2022]
Abstract
In recent years, extensive attention has been given to the generation of new classes of ligand- specific binding proteins to supplement monoclonal antibodies. A combination of protein engineering and display technologies has been used to manipulate non-human antibodies for humanization and stabilization purposes or even the generation of new binding proteins. Engineered protein scaffolds can now be directed against therapeutic targets to treat cancer and immunological disorders. Although very few of these scaffolds have successfully passed clinical trials, their remarkable properties such as robust folding, high solubility, and small size motivate their employment as a tool for biology and applied science studies. Here, we have focused on the generation of new non-Ig binding proteins and single domain antibody manipulation, with a glimpse of their applications.
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Affiliation(s)
- Mohammad K B Ahmadi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyed A Mohammadi
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Manoochehr Makvandi
- Department of Virology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Morteza Mamouei
- Department of Animal Science, Ramin Agricultural and Natural Resources University, Ahvaz, Iran
| | - Mohammad Rahmati
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hesam Dehghani
- Stem Cells Regenerative Research Group, Ressearch Institute of Biotechnology, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran
| | - David W Wood
- Department of Chemical and Biomolecular Engineering, The Ohio State University, 151 W. Woodruff Ave., Columbus, OH 43210, United States
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Wagner HJ, Weber W, Fussenegger M. Synthetic Biology: Emerging Concepts to Design and Advance Adeno-Associated Viral Vectors for Gene Therapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004018. [PMID: 33977059 PMCID: PMC8097373 DOI: 10.1002/advs.202004018] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/18/2020] [Indexed: 05/28/2023]
Abstract
Three recent approvals and over 100 ongoing clinical trials make adeno-associated virus (AAV)-based vectors the leading gene delivery vehicles in gene therapy. Pharmaceutical companies are investing in this small and nonpathogenic gene shuttle to increase the therapeutic portfolios within the coming years. This prospect of marking a new era in gene therapy has fostered both investigations of the fundamental AAV biology as well as engineering studies to enhance delivery vehicles. Driven by the high clinical potential, a new generation of synthetic-biologically engineered AAV vectors is on the rise. Concepts from synthetic biology enable the control and fine-tuning of vector function at different stages of cellular transduction and gene expression. It is anticipated that the emerging field of synthetic-biologically engineered AAV vectors can shape future gene therapeutic approaches and thus the design of tomorrow's gene delivery vectors. This review describes and discusses the recent trends in capsid and vector genome engineering, with particular emphasis on synthetic-biological approaches.
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Affiliation(s)
- Hanna J. Wagner
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26Basel4058Switzerland
- Faculty of BiologyUniversity of FreiburgSchänzlestraße 1Freiburg79104Germany
- Signalling Research Centres BIOSS and CIBSSUniversity of FreiburgSchänzlestraße 18Freiburg79104Germany
| | - Wilfried Weber
- Faculty of BiologyUniversity of FreiburgSchänzlestraße 1Freiburg79104Germany
- Signalling Research Centres BIOSS and CIBSSUniversity of FreiburgSchänzlestraße 18Freiburg79104Germany
| | - Martin Fussenegger
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26Basel4058Switzerland
- Faculty of ScienceUniversity of BaselKlingelbergstrasse 50Basel4056Switzerland
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