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Kohnehrouz BB, Ehsasatvatan M. Redesigning amino/carboxyl ends of DARPin G3 for high thermostability and production in tobacco transplastomic plants. PLANT CELL REPORTS 2024; 43:210. [PMID: 39126530 DOI: 10.1007/s00299-024-03307-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024]
Abstract
KEY MESSAGE Redesigning the N- and C-capping repeats of the native DARPin G3 significantly improved its stability, and may facilitate its purification from the total soluble proteins of high-temperature dried leaf materials of transplastomic plants. Designed ankyrin repeat proteins (DARPins) constitute a promising class of binding molecules that can overcome the limitations of monoclonal antibodies and enable the development of novel therapeutic approaches. Despite their inherent stability, detailed studies have revealed that the original capping repeats derived from natural ankyrin repeat proteins impair the stability of the initial DARPin design. Consequently, the development of thermodynamically stabilized antibody mimetics may facilitate the development of innovative drugs in the future. In this study, we replaced the original N- and C-capping repeats with improved caps to enhance the thermostability of native DARPin G3. Computational analyses suggested that the redesigned thermostable DARPin G3 structure possessed optimal quality and stability. Molecular dynamics simulations verified the stability of the redesigned thermostable DARPin G3 at high temperatures. The redesigned thermostable DARPin G3 was expressed at high levels in tobacco transplastomic plants and subsequently purified from high-temperature dried leaf materials. Thermal denaturation results revealed that the redesigned thermostable DARPin G3 had a higher Tm value than the native DARPin G3, with a Tm of 35.51 °C greater than that of native DARPin G3. The results of the in vitro bioassays confirmed that the purified thermostable DARPin G3 from high-temperature dried leaf materials maintained its binding activity without any loss of affinity and specifically bound to the HER2 receptor on the cell surface. These findings demonstrate the successful improvement in the thermostability of DARPin G3 without compromising its biological activity.
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Affiliation(s)
- Bahram Baghban Kohnehrouz
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, 51666, Iran.
| | - Maryam Ehsasatvatan
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, 51666, Iran
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Ehsasatvatan M, Kohnehrouz BB, Gholizadeh A, Ofoghi H, Shanehbandi D. The production of the first functional antibody mimetic in higher plants: the chloroplast makes the DARPin G3 for HER2 imaging in oncology. Biol Res 2022; 55:32. [PMID: 36274167 PMCID: PMC9590205 DOI: 10.1186/s40659-022-00400-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/12/2022] [Indexed: 12/05/2022] Open
Abstract
Background Designed mimetic molecules are attractive tools in biopharmaceuticals and synthetic biology. They require mass and functional production for the assessment of upcoming challenges in the near future. The DARPin family is considered a mimetic pharmaceutical peptide group with high affinity binding to specific targets. DARPin G3 is designed to bind to the HER2 (human epidermal growth factor receptor 2) tyrosine kinase receptor. Overexpression of HER2 is common in some cancers, including breast cancer, and can be used as a prognostic and predictive tool for cancer. The chloroplasts are cost-effective alternatives, equal to, and sometimes better than, bacterial, yeast, or mammalian expression systems. This research examined the possibility of the production of the first antibody mimetic, DARPin G3, in tobacco chloroplasts for HER2 imaging in oncology. Results The chloroplast specific DARPin G3 expression cassette was constructed and transformed into N. tabacum chloroplasts. PCR and Southern blot analysis confirmed integration of transgenes as well as chloroplastic and cellular homoplasmy. The Western blot analysis and ELISA confirmed the production of DARPin G3 at the commercial scale and high dose with the rate of 20.2% in leaf TSP and 33.7% in chloroplast TSP. The functional analysis by ELISA confirmed the binding of IMAC purified chloroplast-made DARPin G3 to the extracellular domain of the HER2 receptor with highly effective picomolar affinities. The carcinoma cellular studies by flow cytometry and immunofluorescence microscopy confirmed the correct functioning by the specific binding of the chloroplast-made DARPin G3 to the HER2 receptor on the surface of HER2-positive cancer cell lines. Conclusion The efficient functional bioactive production of DARPin G3 in chloroplasts led us to introduce plant chloroplasts as the site of efficient production of the first antibody mimetic molecules. This report, as the first case of the cost-effective production of mimetic molecules, enables researchers in pharmaceuticals, synthetic biology, and bio-molecular engineering to develop tool boxes by producing new molecular substitutes for diverse purposes.
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Kosareva A, Punjabi M, Ochoa-Espinosa A, Xu L, Schaefer JV, Dreier B, Plückthun A, Kaufmann BA. Designed Ankyrin Repeat Proteins as Novel Binders for Ultrasound Molecular Imaging. ULTRASOUND IN MEDICINE & BIOLOGY 2021; 47:2664-2675. [PMID: 34144832 DOI: 10.1016/j.ultrasmedbio.2021.04.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 03/07/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
Clinical translation of ultrasound molecular imaging will depend on the development of binders that can easily be generated, manufactured and coupled, and that are compatible with in vivo use. We describe targeted microbubbles (MBs) using designed ankyrin repeat proteins (DARPins) as a novel class of such translatable binders. Candidate DARPin binders for vascular cell adhesion molecule 1, an endothelial cell adhesion molecule involved in inflammatory processes, were selected using ribosome display and coupled to MBs. Flow-chamber assays of five MBs carrying high-affinity binders showed selective retention on endothelial cells activated by tumor necrosis factor-α for two binders compared with a MB carrying a control DARPin. In vivo ultrasound molecular imaging in a murine hind-limb inflammation model demonstrated up to a fourfold signal enhancement for three of the five MBs versus control. However, there was no correlation between results from flow-chamber assays and in vivo imaging. Thus, we conclude that ultrasound molecular imaging of inflammation using DARPin binders is feasible per se, but that screening of candidates cannot be accomplished with flow-chamber assays as used in our study.
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Affiliation(s)
- Alexandra Kosareva
- Cardiovascular Molecular Imaging, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Mukesh Punjabi
- Cardiovascular Molecular Imaging, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Amanda Ochoa-Espinosa
- Cardiovascular Molecular Imaging, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Lifen Xu
- Cardiovascular Molecular Imaging, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Beat A Kaufmann
- Cardiovascular Molecular Imaging, Department of Biomedicine, University of Basel, Basel, Switzerland; Department of Cardiology, University Hospital and University of Basel, Basel, Switzerland.
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Shipunova VO, Kolesnikova OA, Kotelnikova PA, Soloviev VD, Popov AA, Proshkina GM, Nikitin MP, Deyev SM. Comparative Evaluation of Engineered Polypeptide Scaffolds in HER2-Targeting Magnetic Nanocarrier Delivery. ACS OMEGA 2021; 6:16000-16008. [PMID: 34179645 PMCID: PMC8223436 DOI: 10.1021/acsomega.1c01811] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/31/2021] [Indexed: 06/01/2023]
Abstract
Targeted drug delivery is one of the most intriguing and challenging issues in modern biomedicine. For active targeting, full-size IgG molecules (150 kDa) are usually used. Recent studies have revealed that small artificial polypeptide scaffolds such as DARPins (14 kDa) and affibodies (8 kDa) are much more promising tools for drug delivery due to their small size, artificial nature, low immunogenicity, and many other properties. However, there is no comparative information on the targeting abilities of scaffold polypeptides, which should be taken into account when developing drug delivery systems (DDSs). The present work is the first comprehensive study on the comparison of the effectiveness of different HER2-targeting proteins within the architecture of nanoparticles. Namely, we synthesized trimodal nanoparticles: magnetic, fluorescent, and directed toward HER2 oncomarker on cancer cells. The magnetic particles (MPs) were covalently modified with (i) full-size IgG, 150 kDa, (ii) DARPin_G3, 14 kDa, and (iii) affibody ZHER2:342, 8 kDa. We showed that the number of DARPin_G3 and affibody ZHER2:342 molecules conjugated to the nanoparticle surface are 10 and 40 times higher, respectively, than the corresponding value for trastuzumab. Using the methods of magnetic particle quantification (MPQ)-cytometry and confocal microscopy, we showed that all types of the obtained magnetic conjugates specifically labeled HER2-overexpressing cells. Namely, we demonstrated that particle binding to HER2-positive cells is 1113 ± 39 fg/cell for MP*trastuzumab, 1431 ± 186 fg/cell for MP*ZHER2:342, and 625±21 fg/cell for MP*DARPin_G3, which are 2.77, 2.75, and 2.30 times higher than the corresponding values for control HER2-negative cells. Thus, we showed that the smallest HER2-recognizing polypeptide affibody ZHER2:342 is more effective in terms of specificity and selectivity in nanoparticle-mediated cell labeling.
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Affiliation(s)
- Victoria O. Shipunova
- Shemyakin−Ovchinnikov
Institute of Bioorganic Chemistry, Russian
Academy of Sciences, 16/10 Miklukho-Maklaya Street, Moscow 117997, Russia
- Moscow
Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny 141701, Russia
- MEPhI
(Moscow Engineering Physics Institute), Institute of Engineering Physics for Biomedicine (PhysBio), 31 Kashirskoe Shosse, Moscow 115409, Russia
- Sirius
University of Science and Technology, 1 Olympic Avenue, Sochi 354340, Russia
| | - Olga A. Kolesnikova
- Shemyakin−Ovchinnikov
Institute of Bioorganic Chemistry, Russian
Academy of Sciences, 16/10 Miklukho-Maklaya Street, Moscow 117997, Russia
| | - Polina A. Kotelnikova
- Shemyakin−Ovchinnikov
Institute of Bioorganic Chemistry, Russian
Academy of Sciences, 16/10 Miklukho-Maklaya Street, Moscow 117997, Russia
| | - Vladislav D. Soloviev
- Shemyakin−Ovchinnikov
Institute of Bioorganic Chemistry, Russian
Academy of Sciences, 16/10 Miklukho-Maklaya Street, Moscow 117997, Russia
- Sirius
University of Science and Technology, 1 Olympic Avenue, Sochi 354340, Russia
| | - Anton A. Popov
- MEPhI
(Moscow Engineering Physics Institute), Institute of Engineering Physics for Biomedicine (PhysBio), 31 Kashirskoe Shosse, Moscow 115409, Russia
| | - Galina M. Proshkina
- Shemyakin−Ovchinnikov
Institute of Bioorganic Chemistry, Russian
Academy of Sciences, 16/10 Miklukho-Maklaya Street, Moscow 117997, Russia
| | - Maxim P. Nikitin
- Shemyakin−Ovchinnikov
Institute of Bioorganic Chemistry, Russian
Academy of Sciences, 16/10 Miklukho-Maklaya Street, Moscow 117997, Russia
- Moscow
Institute of Physics and Technology, 9 Institutskiy per., Dolgoprudny 141701, Russia
- Sirius
University of Science and Technology, 1 Olympic Avenue, Sochi 354340, Russia
| | - Sergey M. Deyev
- Shemyakin−Ovchinnikov
Institute of Bioorganic Chemistry, Russian
Academy of Sciences, 16/10 Miklukho-Maklaya Street, Moscow 117997, Russia
- MEPhI
(Moscow Engineering Physics Institute), Institute of Engineering Physics for Biomedicine (PhysBio), 31 Kashirskoe Shosse, Moscow 115409, Russia
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5
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Chockalingam K, Peng Z, Vuong CN, Berghman LR, Chen Z. Golden Gate assembly with a bi-directional promoter (GBid): A simple, scalable method for phage display Fab library creation. Sci Rep 2020; 10:2888. [PMID: 32076016 PMCID: PMC7031318 DOI: 10.1038/s41598-020-59745-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 02/03/2020] [Indexed: 11/09/2022] Open
Abstract
Fabs offer an attractive platform for monoclonal antibody discovery/engineering, but library construction can be cumbersome. We report a simple method – Golden Gate assembly with a bi-directional promoter (GBid) – for constructing phage display Fab libraries. In GBid, the constant domains of the Fabs are located in the backbone of the phagemid vector and the library insert comprises only the variable regions of the antibodies and a central bi-directional promoter. This vector design reduces the process of Fab library construction to “scFv-like” simplicity and the double promoter ensures robust expression of both constituent chains. To maximize the library size, the 3 fragments comprising the insert – two variable chains and one bi-directional promoter – are assembled via a 3-fragment overlap extension PCR and the insert is incorporated into the vector via a high-efficiency one-fragment, one-pot Golden Gate assembly. The reaction setup requires minimal preparatory work and enzyme quantities, making GBid highly scalable. Using GBid, we constructed a chimeric chicken-human Fab phage display library comprising 1010 variants targeting the multi-transmembrane protein human CD20 (hCD20). Selection/counter-selection on transfected whole cells yielded hCD20-specific antibodies in four rounds of panning. The simplicity and scalability of GBid makes it a powerful tool for the discovery/engineering of Fabs and IgGs.
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Affiliation(s)
- Karuppiah Chockalingam
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas, 77843, USA
| | - Zeyu Peng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas, 77843, USA.,Biosion, Inc., Nanjing, 210061, China
| | - Christine N Vuong
- Department of Poultry Science, Texas A&M University, College Station, Texas, 77843, USA.,Department of Poultry Science, University of Arkansas, Fayetteville, Arkansas, 72703, USA
| | - Luc R Berghman
- Department of Poultry Science, Texas A&M University, College Station, Texas, 77843, USA
| | - Zhilei Chen
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, Texas, 77843, USA.
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Jankauskaite J, Jiménez-García B, Dapkunas J, Fernández-Recio J, Moal IH. SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation. Bioinformatics 2019; 35:462-469. [PMID: 30020414 PMCID: PMC6361233 DOI: 10.1093/bioinformatics/bty635] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/17/2018] [Indexed: 11/18/2022] Open
Abstract
Motivation Understanding the relationship between the sequence, structure, binding energy, binding kinetics and binding thermodynamics of protein–protein interactions is crucial to understanding cellular signaling, the assembly and regulation of molecular complexes, the mechanisms through which mutations lead to disease, and protein engineering. Results We present SKEMPI 2.0, a major update to our database of binding free energy changes upon mutation for structurally resolved protein–protein interactions. This version now contains manually curated binding data for 7085 mutations, an increase of 133%, including changes in kinetics for 1844 mutations, enthalpy and entropy changes for 443 mutations, and 440 mutations, which abolish detectable binding. Availability and implementation The database is available as supplementary data and at https://life.bsc.es/pid/skempi2/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Justina Jankauskaite
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Brian Jiménez-García
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Justas Dapkunas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Juan Fernández-Recio
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Institut de Biologia Molecular de Barcelona (IBMB), CSIC, Barcelona, Spain
| | - Iain H Moal
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK
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Stüber JC, Kast F, Plückthun A. High-Throughput Quantification of Surface Protein Internalization and Degradation. ACS Chem Biol 2019; 14:1154-1163. [PMID: 31050891 DOI: 10.1021/acschembio.9b00016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cell surface proteins are key regulators of fundamental cellular processes and, therefore, often at the root of human diseases. Thus, a large number of targeted drugs which are approved or under development act upon cell surface proteins. Although down-regulation of surface proteins by many natural ligands is well-established, the ability of drug candidates to cause internalization or degradation of the target is only recently moving into focus. This property is important both for the pharmacokinetics and pharmacodynamics of the drug but may also constitute a potential resistance mechanism. The enormous numbers of drug candidates targeting cell surface molecules, comprising small molecules, antibodies, or alternative protein scaffolds, necessitate methods for the investigation of internalization and degradation in high throughput. Here, we present a generic high-throughput assay protocol, which allows the simultaneous and independent quantification of internalization and degradation of surface proteins on a single-cell level. Because we fuse a HaloTag to the cell surface protein of interest and exploit the differential cell permeability of two fluorescent HaloTag ligands, no labeling of the molecules to be screened is required. In contrast to previously described approaches, our homogeneous assay is performed with adherent live cells in a 96-well format. Through channel rescaling, we are furthermore able to obtain true relative abundances of surface and internal protein. We demonstrate the applicability of our procedure to three major drug targets, EGFR, HER2, and EpCAM, examining a selection of well-investigated but also novel small molecule ligands and protein affinity reagents.
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Affiliation(s)
- Jakob C. Stüber
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Florian Kast
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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8
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Advances in the Application of Designed Ankyrin Repeat Proteins (DARPins) as Research Tools and Protein Therapeutics. Methods Mol Biol 2018; 1798:307-327. [PMID: 29868969 DOI: 10.1007/978-1-4939-7893-9_23] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Nonimmunoglobulin scaffolds have been developed to overcome the limitations of monoclonal antibodies with regard to stability and size. Of these scaffolds, the class of designed ankyrin repeat proteins (DARPins) has advanced the most in biochemical and biomedical applications. This review focuses on the recent progress in DARPin technology, highlighting the scaffold's potential and possibilities.
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9
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Li DL, Tan JE, Tian Y, Huang S, Sun PH, Wang M, Han YJ, Li HS, Wu HB, Zhang XM, Xu YK, Wang QS. Multifunctional superparamagnetic nanoparticles conjugated with fluorescein-labeled designed ankyrin repeat protein as an efficient HER2-targeted probe in breast cancer. Biomaterials 2017; 147:86-98. [PMID: 28938164 DOI: 10.1016/j.biomaterials.2017.09.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 08/13/2017] [Accepted: 09/07/2017] [Indexed: 12/14/2022]
Abstract
Based on the discordance of human epidermal growth factor receptor-2 (HER2) expression between primary and metastatic/recurrent breast cancer, HER2 molecular imaging, which had potential to systemically assess and dynamically monitor HER2 expression, might improve the selection of patients for anti-HER2 therapy. In this study, designed ankyrin repeat protein (DARPin) G3, a novel binding protein with picomolar affinity for HER2, was used and multifunctional superparamagnetic nanoparticles modified with fluorescein-5-maleimide-labeled DARPin G3 (SPIO-G3-5MF) were developed for HER2 imaging. Our results showed that SPIO-G3-5MF nanoparticles, which possessed uniform size of about 100 nm, favorable dispersity and low cytotoxicity, could selectively bind to HER2-positive breast cancer cells even in the presence of trastuzumab. Biodistribution assay demonstrated that abundant accumulation and long retention of SPIO-G3-5MF were observed in HER2-positive transplantation breast tumors although a portion of SPIO-G3-5MF nanoparticles were unavoidably captured by liver and spleen. Further MR imaging revealed that SPIO-G3-5MF could selectively image HER2-positive transplantation breast tumors, yielding remarkable T2 signal reduction (50.33 ± 2.90% at 6 h and 47.29 ± 9.36% at 24 h). Our study suggested that SPIO-G3-5MF might be a promising MR molecular probe for diagnosing and monitoring HER2 expression state of breast cancer in the future.
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Affiliation(s)
- Dong-Li Li
- Medical Imaging Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Jian-Er Tan
- Nanfang PET Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Ying Tian
- Nanfang PET Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Shun Huang
- Nanfang PET Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Peng-Hui Sun
- Nanfang PET Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Meng Wang
- Nanfang PET Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Yan-Jiang Han
- Nanfang PET Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Hong-Sheng Li
- Nanfang PET Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Hu-Bing Wu
- Nanfang PET Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Xing-Mei Zhang
- Department of Neurobiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Yi-Kai Xu
- Medical Imaging Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Quan-Shi Wang
- Nanfang PET Center, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China.
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A Tri-part Protein Complementation System Using Antibody-Small Peptide Fusions Enables Homogeneous Immunoassays. Sci Rep 2017; 7:8186. [PMID: 28811487 PMCID: PMC5557857 DOI: 10.1038/s41598-017-07569-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 06/19/2017] [Indexed: 11/08/2022] Open
Abstract
Protein-fragment complementation is a valuable tool for monitoring protein interactions. In complementation assays, the reporter fragments are directly fused to the interacting proteins, eliminating the possibility of monitoring native interactions. In principle, complementation could be achieved by placing the reporter fragments on antibodies which bind to the proteins of interest, enabling the monitoring of endogenous protein interactions or detection of a single protein in a homogeneous immunoassay. Previous reports have demonstrated proof-of-concept of this approach; however, current complementation systems have not met the practical requirements as suitable fusion partners for antibodies while providing the sensitivity needed for immunoassays. To surmount these challenges, we created a first-in-class, tri-part split luciferase consisting of two 11-residue peptides that are used as the antibody appendages. As an initial proof-of-concept, we used antibody-peptide fusions and found them to be capable of quantifying pg/mL concentrations of soluble or cell-bound HER2, proving this unique complementation system overcomes previous limitations and transforms this approach from merely possible to practical and useful. As shown herein, this dual-peptide system provides a rapid, simple, and sensitive "add-and-read" homogeneous immunoassay platform that can be broadly adapted as an alternative to traditional immunoassays, and in the future should enable complementation to be expanded to monitoring endogenous protein interactions.
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11
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Jost C, Stüber JC, Honegger A, Wu Y, Batyuk A, Plückthun A. Rigidity of the extracellular part of HER2: Evidence from engineering subdomain interfaces and shared-helix DARPin-DARPin fusions. Protein Sci 2017. [PMID: 28639341 DOI: 10.1002/pro.3216] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The second member of the human ErbB family of receptor tyrosine kinases, HER2/hErbB2, is regarded as an exceptional case: The four extracellular subdomains could so far only be found in one fixed overall conformation, designated "open" and resembling the ligand-bound form of the other ErbB receptors. It thus appears to be different from the extracellular domains of the other family members that show inter-subdomain flexibility and exist in a "tethered" form in the absence of ligand. For HER2, there was so far no direct evidence for such a tethered conformation on the cell surface. Nonetheless, alternative conformations of HER2 in vivo could so far not be excluded. We now demonstrate the rigidity of HER2 on the surface of tumor cells by employing two orthogonal approaches of protein engineering: To directly test the potential of the extracellular domain of HER2 to adopt a pseudo-tethered conformation on the cell surface, we first designed HER2 variants with a destabilized interface between extracellular subdomains I and III that would favor deviation from the "open" conformation. Secondly, we used differently shaped versions of a Designed Ankyrin Repeat Protein (DARPin) fusion, recognizing subdomain I of HER2, devised to work as probes for a putative pseudo-tethered extracellular domain of HER2. Combining our approaches, we exclude, on live cells and in vitro, that significant proportions of HER2 deviate from the "open" conformation.
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Affiliation(s)
- Christian Jost
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Jakob C Stüber
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Annemarie Honegger
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Yufan Wu
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Alexander Batyuk
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
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12
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Siegler E, Li S, Kim YJ, Wang P. Designed Ankyrin Repeat Proteins as Her2 Targeting Domains in Chimeric Antigen Receptor-Engineered T Cells. Hum Gene Ther 2017; 28:726-736. [PMID: 28796529 DOI: 10.1089/hum.2017.021] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chimeric antigen receptor (CAR) engineering is a branch of cancer immunotherapy that equips immune cells to target tumor antigens expressed on the cell surface using antibody-derived single-chain variable fragments (scFvs). However, other antibody mimetics, such as designed ankyrin repeat proteins (DARPins), can also serve as antigen-binding domains in CARs. This study shows that CAR-engineered T (CAR-T) cells utilizing Her2-targeting DARPins G3 and 929 can target human epidermal growth factor receptor 2 (Her2)-overexpressing cancer cells as effectively as CAR-T cells with the scFv 4D5 in vitro, and G3 CAR-T cells can slow or eliminate tumor growth in vivo as effectively as 4D5 CAR-T cells. Some DARPins may offer an attractive alternative to scFv usage in CARs, as they are smaller, thermodynamically stable, poorly immunogenic, and can be generated with different binding properties from DARPin libraries.
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Affiliation(s)
- Elizabeth Siegler
- 1 Department of Biomedical Engineering, University of Southern California , Los Angeles, California
| | - Si Li
- 2 Department of Pharmacology and Pharmaceutical Sciences, University of Southern California , Los Angeles, California
| | - Yu Jeong Kim
- 2 Department of Pharmacology and Pharmaceutical Sciences, University of Southern California , Los Angeles, California
| | - Pin Wang
- 1 Department of Biomedical Engineering, University of Southern California , Los Angeles, California.,2 Department of Pharmacology and Pharmaceutical Sciences, University of Southern California , Los Angeles, California.,3 Mork Family Department of Chemical Engineering and Materials Science, University of Southern California , Los Angeles, California
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Wisitponchai T, Shoombuatong W, Lee VS, Kitidee K, Tayapiwatana C. AnkPlex: algorithmic structure for refinement of near-native ankyrin-protein docking. BMC Bioinformatics 2017; 18:220. [PMID: 28424069 PMCID: PMC5395911 DOI: 10.1186/s12859-017-1628-6] [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: 06/30/2016] [Accepted: 04/07/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Computational analysis of protein-protein interaction provided the crucial information to increase the binding affinity without a change in basic conformation. Several docking programs were used to predict the near-native poses of the protein-protein complex in 10 top-rankings. The universal criteria for discriminating the near-native pose are not available since there are several classes of recognition protein. Currently, the explicit criteria for identifying the near-native pose of ankyrin-protein complexes (APKs) have not been reported yet. RESULTS In this study, we established an ensemble computational model for discriminating the near-native docking pose of APKs named "AnkPlex". A dataset of APKs was generated from seven X-ray APKs, which consisted of 3 internal domains, using the reliable docking tool ZDOCK. The dataset was composed of 669 and 44,334 near-native and non-near-native poses, respectively, and it was used to generate eleven informative features. Subsequently, a re-scoring rank was generated by AnkPlex using a combination of a decision tree algorithm and logistic regression. AnkPlex achieved superior efficiency with ≥1 near-native complexes in the 10 top-rankings for nine X-ray complexes compared to ZDOCK, which only obtained six X-ray complexes. In addition, feature analysis demonstrated that the van der Waals feature was the dominant near-native pose out of the potential ankyrin-protein docking poses. CONCLUSION The AnkPlex model achieved a success at predicting near-native docking poses and led to the discovery of informative characteristics that could further improve our understanding of the ankyrin-protein complex. Our computational study could be useful for predicting the near-native poses of binding proteins and desired targets, especially for ankyrin-protein complexes. The AnkPlex web server is freely accessible at http://ankplex.ams.cmu.ac.th .
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Affiliation(s)
- Tanchanok Wisitponchai
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand
| | - Vannajan Sanghiran Lee
- Thailand Center of Excellence in Physics, Commission on Higher Education, Bangkok, 10400, Thailand.,Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Kuntida Kitidee
- Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand. .,Center for Research and Innovation, Faculty of Medical Technology, Mahidol University, Bangkok, 10700, Thailand.
| | - Chatchai Tayapiwatana
- Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand. .,Center of Biomolecular Therapy and Diagnostic, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200, Thailand.
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Hammill JA, VanSeggelen H, Helsen CW, Denisova GF, Evelegh C, Tantalo DGM, Bassett JD, Bramson JL. Designed ankyrin repeat proteins are effective targeting elements for chimeric antigen receptors. J Immunother Cancer 2015; 3:55. [PMID: 26673402 PMCID: PMC4678647 DOI: 10.1186/s40425-015-0099-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/23/2015] [Indexed: 11/29/2022] Open
Abstract
Background Adoptive cell transfer of tumor-specific T lymphocytes (T cells) is proving to be an effective strategy for treating established tumors in cancer patients. One method of generating these cells is accomplished through engineering bulk T cell populations to express chimeric antigen receptors (CARs), which are specific for tumor antigens. Traditionally, these CARs are targeted against tumor antigens using single-chain antibodies (scFv). Here we describe the use of a designed ankyrin repeat protein (DARPin) as the tumor-antigen targeting domain. Methods We prepared second generation anti-HER2 CARs that were targeted to the tumor antigen by either a DARPin or scFv. The CARs were engineered into human and murine T cells. We then compared the ability of CARs to trigger cytokine production, degranulation and cytotoxicity. Results The DARPin CARs displayed reduced surface expression relative to scFv CARs in murine cells but both CARs were expressed equally well on human T cells, suggesting that there may be a processing issue with the murine variants. In both the murine and human systems, the DARPin CARs were found to be highly functional, triggering cytokine and cytotoxic responses that were similar to those triggered by the scFv CARs. Conclusions These findings demonstrate the utility of DARPins as CAR-targeting agents and open up an avenue for the generation of CARs with novel antigen binding attributes.
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Affiliation(s)
- Joanne A Hammill
- Department Pathology and Molecular Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, ON Canada
| | - Heather VanSeggelen
- Department Pathology and Molecular Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, ON Canada
| | - Christopher W Helsen
- Department Pathology and Molecular Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, ON Canada
| | - Galina F Denisova
- Department Pathology and Molecular Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, ON Canada
| | - Carole Evelegh
- Department Pathology and Molecular Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, ON Canada
| | - Daniela G M Tantalo
- Department Pathology and Molecular Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, ON Canada
| | - Jennifer D Bassett
- Department Pathology and Molecular Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, ON Canada
| | - Jonathan L Bramson
- Department Pathology and Molecular Medicine, McMaster Immunology Research Centre, McMaster University, Hamilton, ON Canada
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Goldstein R, Sosabowski J, Livanos M, Leyton J, Vigor K, Bhavsar G, Nagy-Davidescu G, Rashid M, Miranda E, Yeung J, Tolner B, Plückthun A, Mather S, Meyer T, Chester K. Development of the designed ankyrin repeat protein (DARPin) G3 for HER2 molecular imaging. Eur J Nucl Med Mol Imaging 2015; 42:288-301. [PMID: 25391547 PMCID: PMC4315530 DOI: 10.1007/s00259-014-2940-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/09/2014] [Indexed: 01/07/2023]
Abstract
PURPOSE Human epidermal growth factor receptor-2 (HER2) overexpression is a predictor of response to anti-HER2 therapy in breast and gastric cancer. Currently, HER2 status is assessed by tumour biopsy, but this may not be representative of the larger tumour mass or other metastatic sites, risking misclassification and selection of suboptimal therapy. The designed ankyrin repeat protein (DARPin) G3 binds HER2 with high affinity at an epitope that does not overlap with trastuzumab and is biologically inert. We hypothesized that radiolabelled DARPin G3 would be capable of selectively imaging HER2-positive tumours, and aimed to identify a suitable format for clinical application. METHODS G3 DARPins tagged with hexahistidine (His6) or with histidine glutamate (HE)3 and untagged G3 DARPins were manufactured using a GMP-compatible Pichia pastoris protocol and radiolabelled with (125)I, or with (111)In via DOTA linked to a C-terminal cysteine. BALB/c mice were injected with radiolabelled G3 and tissue biodistribution was evaluated by gamma counting. The lead construct ((HE)3-G3) was assessed in mice bearing HER2-positive human breast tumour (BT474) xenografts. RESULTS For both isotopes, (HE)3-G3 had significantly lower liver uptake than His6-G3 and untagged G3 counterparts in non-tumour-bearing mice, and there was no significantly different liver uptake between His6-G3 and untagged G3. (HE)3-G3 was taken forward for evaluation in mice bearing HER2-positive tumour xenografts. The results demonstrated that radioactivity from (111)In-(HE)3-G3 was better maintained in tumours and cleared faster from serum than radioactivity from (125)I-(HE)3-G3, achieving superior tumour-to-blood ratios (343.7 ± 161.3 vs. 22.0 ± 11.3 at 24 h, respectively). On microSPECT/CT, (111)In-labelled and (125)I-labelled (HE)3-G3 could image HER2-positive tumours at 4 h after administration, but there was less normal tissue uptake of radioactivity with (111)In-(HE)3-G3. Preadministration of trastuzumab did not affect the uptake of (HE)3-G3 by HER2-positive tumours. CONCLUSION Radiolabelled DARPin (HE)3-G3 is a versatile radioligand with potential to allow the acquisition of whole-body HER2 scans on the day of administration.
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Affiliation(s)
- Robert Goldstein
- UCL Cancer Institute, Paul O’Gorman Building, 72 Huntley St, WC1E 6DD London, UK
| | - Jane Sosabowski
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Maria Livanos
- UCL Cancer Institute, Paul O’Gorman Building, 72 Huntley St, WC1E 6DD London, UK
| | - Julius Leyton
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Kim Vigor
- Biotherapeutics Development Unit, Cancer Research UK, Clare Hall Laboratories, Blanche Lane, South Mimms, EN6 3LD UK
| | - Gaurav Bhavsar
- UCL Cancer Institute, Paul O’Gorman Building, 72 Huntley St, WC1E 6DD London, UK
| | | | - Mohammed Rashid
- UCL Cancer Institute, Paul O’Gorman Building, 72 Huntley St, WC1E 6DD London, UK
| | - Enrique Miranda
- UCL Cancer Institute, Paul O’Gorman Building, 72 Huntley St, WC1E 6DD London, UK
| | - Jenny Yeung
- UCL Cancer Institute, Paul O’Gorman Building, 72 Huntley St, WC1E 6DD London, UK
- UCL Institute of Child Health, 30 Guilford Street, London, WC1N 1EH UK
| | - Berend Tolner
- UCL Cancer Institute, Paul O’Gorman Building, 72 Huntley St, WC1E 6DD London, UK
| | - Andreas Plückthun
- Biochemisches Institut, Universität Zürich, Winterthurerstr. 190, 8057 Zürich, Switzerland
| | - Stephen Mather
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ UK
| | - Tim Meyer
- UCL Cancer Institute, Paul O’Gorman Building, 72 Huntley St, WC1E 6DD London, UK
| | - Kerry Chester
- UCL Cancer Institute, Paul O’Gorman Building, 72 Huntley St, WC1E 6DD London, UK
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Park K, Shen BW, Parmeggiani F, Huang PS, Stoddard BL, Baker D. Control of repeat-protein curvature by computational protein design. Nat Struct Mol Biol 2015; 22:167-74. [PMID: 25580576 PMCID: PMC4318719 DOI: 10.1038/nsmb.2938] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 11/25/2014] [Indexed: 01/07/2023]
Abstract
Shape complementarity is an important component of molecular recognition, and the ability to precisely adjust the shape of a binding scaffold to match a target of interest would greatly facilitate the creation of high-affinity protein reagents and therapeutics. Here we describe a general approach to control the shape of the binding surface on repeat-protein scaffolds and apply it to leucine-rich-repeat proteins. First, self-compatible building-block modules are designed that, when polymerized, generate surfaces with unique but constant curvatures. Second, a set of junction modules that connect the different building blocks are designed. Finally, new proteins with custom-designed shapes are generated by appropriately combining building-block and junction modules. Crystal structures of the designs illustrate the power of the approach in controlling repeat-protein curvature.
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Affiliation(s)
- Keunwan Park
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Betty W. Shen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Fabio Parmeggiani
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Po-Ssu Huang
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Institute for Protein Design, University of Washington, Seattle, WA 98195, USA
| | - Barry L. Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA, Institute for Protein Design, University of Washington, Seattle, WA 98195, USA,Correspondence:
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A transcription blocker isolated from a designed repeat protein combinatorial library by in vivo functional screen. Sci Rep 2015; 5:8070. [PMID: 25627011 PMCID: PMC4308713 DOI: 10.1038/srep08070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 01/02/2015] [Indexed: 12/31/2022] Open
Abstract
A highly diverse DNA library coding for ankyrin seven-repeat proteins (ANK-N5C) was designed and constructed by a PCR-based combinatorial assembly strategy. A bacterial melibiose fermentation assay was adapted for in vivo functional screen. We isolated a transcription blocker that completely inhibits the melibiose-dependent expression of α-galactosidase (MelA) and melibiose permease (MelB) of Escherichiacoli by specifically preventing activation of the melAB operon. High-resolution crystal structural determination reveals that the designed ANK-N5C protein has a typical ankyrin fold, and the specific transcription blocker, ANK-N5C-281, forms a domain-swapped dimer. Functional tests suggest that the activity of MelR, a DNA-binding transcription activator and a member of AraC family of transcription factors, is inhibited by ANK-N5C-281 protein. All ANK-N5C proteins are expected to have a concave binding area with negative surface potential, suggesting that the designed ANK-N5C library proteins may facilitate the discovery of binders recognizing structural motifs with positive surface potential, like in DNA-binding proteins. Overall, our results show that the established library is a useful tool for the discovery of novel bioactive reagents.
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