1
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Niquille DL, Fitzgerald KM, Gera N. Biparatopic antibodies: therapeutic applications and prospects. MAbs 2024; 16:2310890. [PMID: 38439551 PMCID: PMC10936611 DOI: 10.1080/19420862.2024.2310890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/23/2024] [Indexed: 03/06/2024] Open
Abstract
Biparatopic antibodies (bpAbs) bind distinct, non-overlapping epitopes on an antigen. This unique binding mode enables new mechanisms of action beyond monospecific and bispecific antibodies (bsAbs) that can make bpAbs effective therapeutics for various indications, including oncology and infectious diseases. Biparatopic binding can lead to superior affinity and specificity, promote antagonism, lock target conformation, and result in higher-order target clustering. Such antibody-target complexes can elicit strong agonism, increase immune effector function, or result in rapid target downregulation and lysosomal trafficking. These are not only attractive properties for therapeutic antibodies but are increasingly being explored for other modalities such as antibody-drug conjugates, T-cell engagers and chimeric antigen receptors. Recent advances in bpAb engineering have enabled the construction of ever more sophisticated formats that are starting to show promise in the clinic.
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Affiliation(s)
| | | | - Nimish Gera
- Biologics, Mythic Therapeutics, Waltham, MA, USA
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2
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Dahlsson Leitao C, Ståhl S, Löfblom J. Bacterial Cell Display for Selection of Affibody Molecules. Methods Mol Biol 2023; 2681:99-112. [PMID: 37405645 DOI: 10.1007/978-1-0716-3279-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2023]
Abstract
This review describes the principles for generation of affibody molecules using bacterial display on the Gram-negative Escherichia coli and the Gram-positive Staphylococcus carnosus, respectively. Affibody molecules are small and robust alternative scaffold proteins that have been explored for therapeutic, diagnostic, and biotechnological applications. They typically exhibit high-stability, affinity, and specificity with high modularity of functional domains. Due to the small size of the scaffold, affibody molecules are rapidly excreted through renal filtration and can efficiently extravasate from blood and penetrate tissues. Preclinical and clinical studies have demonstrated that affibody molecules are promising and safe complements to antibodies for in vivo diagnostic imaging and therapy. Sorting of affibody libraries displayed on bacteria using fluorescence-activated cell sorting is an effective and straightforward methodology and has been used successfully to generate novel affibody molecules with high affinity for a diverse range of molecular targets.
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Affiliation(s)
| | - Stefan Ståhl
- Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - John Löfblom
- Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden.
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3
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Crook ZR, Girard EJ, Sevilla GP, Brusniak MY, Rupert PB, Friend DJ, Gewe MM, Clarke M, Lin I, Ruff R, Pakiam F, Phi TD, Bandaranayake A, Correnti CE, Mhyre AJ, Nairn NW, Strong RK, Olson JM. Ex silico engineering of cystine-dense peptides yielding a potent bispecific T cell engager. Sci Transl Med 2022; 14:eabn0402. [PMID: 35584229 PMCID: PMC10118748 DOI: 10.1126/scitranslmed.abn0402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cystine-dense peptides (CDPs) are a miniprotein class that can drug difficult targets with high affinity and low immunogenicity. Tools for their design, however, are not as developed as those for small-molecule and antibody drugs. CDPs have diverse taxonomic origins, but structural characterization is lacking. Here, we adapted Iterative Threading ASSEmbly Refinement (I-TASSER) and Rosetta protein modeling software for structural prediction of 4298 CDP scaffolds and performed in silico prescreening for CDP binders to targets of interest. Mammalian display screening of a library of docking-enriched, methionine and tyrosine scanned (DEMYS) CDPs against PD-L1 yielded binders from four distinct CDP scaffolds. One was affinity-matured, and cocrystallography yielded a high-affinity (KD = 202 pM) PD-L1-binding CDP that competes with PD-1 for PD-L1 binding. Its subsequent incorporation into a CD3-binding bispecific T cell engager produced a molecule with pM-range in vitro T cell killing potency and which substantially extends survival in two different xenograft tumor-bearing mouse models. Both in vitro and in vivo, the CDP-incorporating bispecific molecule outperformed a comparator antibody-based molecule. This CDP modeling and DEMYS technique can accelerate CDP therapeutic development.
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Affiliation(s)
- Zachary R Crook
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Blaze Bioscience Inc., Seattle, WA 98109, USA
| | - Emily J Girard
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Gregory P Sevilla
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,Blaze Bioscience Inc., Seattle, WA 98109, USA
| | - Mi-Youn Brusniak
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Peter B Rupert
- Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Della J Friend
- Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mesfin M Gewe
- Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Midori Clarke
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ida Lin
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Raymond Ruff
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Fiona Pakiam
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Ashok Bandaranayake
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Colin E Correnti
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Andrew J Mhyre
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Roland K Strong
- Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - James M Olson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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4
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Singh D, Dheer D, Samykutty A, Shankar R. Antibody drug conjugates in gastrointestinal cancer: From lab to clinical development. J Control Release 2021; 340:1-34. [PMID: 34673122 DOI: 10.1016/j.jconrel.2021.10.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/15/2022]
Abstract
The antibody-drug conjugates (ADCs) are one the fastest growing biotherapeutics in oncology and are still in their infancy in gastrointestinal (GI) cancer for clinical applications to improve patient survival. The ADC based approach is developed with tumor specific antigen, antibody carrying cytotoxic agents to precisely target and deliver chemotherapeutics at the tumor site. To date, 11 ADCs have been approved by US-FDA, and more than 80 are in the clinical development phase for different oncological indications. However, The ADCs based therapies in GI cancers are still far from having high-efficient clinical outcomes. The limited success of these ADCs and lessons learned from the past are now being used to develop a newer generation of ADC against GI cancers. In this review, we did a comprehensive assessment of the key components of ADCs, including tumor marker, antibody, cytotoxic payload, and linkage strategy, with a focus on technical improvement and some future trends in the pipeline for clinical translation. The various preclinical and clinical ADCs used in gastrointestinal malignancies, their target, composition and bioconjugation, along with preclinical and clinical outcomes, are discussed. The emphasis is also given to new generation ADCs employing novel mAb, payload, linker, and bioconjugation methods are also included.
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Affiliation(s)
- Davinder Singh
- Natural Products and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Divya Dheer
- Natural Products and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Abhilash Samykutty
- Stephenson Comprehensive Cancer Center, University of Oklahoma, Oklahoma City, OK 73104, USA.
| | - Ravi Shankar
- Natural Products and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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5
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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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6
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Diamante A, Chaturbedy PK, Rowling PJE, Kumita JR, Eapen RS, McLaughlin SH, de la Roche M, Perez-Riba A, Itzhaki LS. Engineering mono- and multi-valent inhibitors on a modular scaffold. Chem Sci 2021; 12:880-895. [PMID: 33623657 PMCID: PMC7885266 DOI: 10.1039/d0sc03175e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
Here we exploit the simple, ultra-stable, modular architecture of consensus-designed tetratricopeptide repeat proteins (CTPRs) to create a platform capable of displaying both single as well as multiple functions and with diverse programmable geometrical arrangements by grafting non-helical short linear binding motifs (SLiMs) onto the loops between adjacent repeats. As proof of concept, we built synthetic CTPRs to bind and inhibit the human tankyrase proteins (hTNKS), which play a key role in Wnt signaling and are upregulated in cancer. A series of mono-valent and multi-valent hTNKS binders was assembled. To fully exploit the modular scaffold and to further diversify the multi-valent geometry, we engineered the binding modules with two different formats, one monomeric and the other trimeric. We show that the designed proteins are stable, correctly folded and capable of binding to and inhibiting the cellular activity of hTNKS leading to downregulation of the Wnt pathway. Multivalency in both the CTPR protein arrays and the hTNKS target results in the formation of large macromolecular assemblies, which can be visualized both in vitro and in the cell. When delivered into the cell by nanoparticle encapsulation, the multivalent CTPR proteins displayed exceptional activity. They are able to inhibit Wnt signaling where small molecule inhibitors have failed to date. Our results point to the tremendous potential of the CTPR platform to exploit a range of SLiMs and assemble synthetic binding molecules with built-in multivalent capabilities and precise, pre-programmed geometries.
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Affiliation(s)
- Aurora Diamante
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Piyush K Chaturbedy
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Pamela J E Rowling
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Janet R Kumita
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Rohan S Eapen
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Stephen H McLaughlin
- MRC Laboratory of Molecular Biology , Francis Crick Avenue , Cambridge Biomedical Campus , Cambridge , CB2 0QH , UK
| | - Marc de la Roche
- Department of Biochemistry , University of Cambridge , Tennis Court Road , Cambridge CB2 1GA , UK
| | - Albert Perez-Riba
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
| | - Laura S Itzhaki
- Department of Pharmacology , University of Cambridge , Tennis Court Road , Cambridge CB2 1PD , UK . ;
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7
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Güler R, Svedmark SF, Abouzayed A, Orlova A, Löfblom J. Increasing thermal stability and improving biodistribution of VEGFR2-binding affibody molecules by a combination of in silico and directed evolution approaches. Sci Rep 2020; 10:18148. [PMID: 33097752 PMCID: PMC7585445 DOI: 10.1038/s41598-020-74560-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/23/2020] [Indexed: 11/09/2022] Open
Abstract
The family of vascular endothelial growth factor (VEGF) ligands and their interactions with VEGF receptors (VEGFRs) play important roles in both pathological and physiological angiogenesis. Hence, agonistic and antagonistic ligands targeting this signaling pathway have potential for both studies on fundamental biology and for development of therapies and diagnostics. Here, we engineer VEGFR2-binding affibody molecules for increased thermostability, refolding and improved biodistribution. We designed libraries based on the original monomeric binders with the intention of reducing hydrophobicity, while retaining high affinity for VEGFR2. Libraries were displayed on bacteria and binders were isolated by fluorescence-activated cell sorting (FACS). In parallel, we used an automated sequence- and structure-based in silico algorithm to identify potentially stabilizing mutations. Monomeric variants isolated from the screening and the in silico approach, respectively, were characterized by circular dichroism spectroscopy and biosensor assays. The most promising mutations were combined into new monomeric constructs which were finally fused into a dimeric construct, resulting in a 15 °C increase in melting temperature, complete refolding capability after heat-induced denaturation, retained low picomolar affinity and improved biodistribution profile in an in vivo mouse model. These VEGFR2-binding affibody molecules show promise as candidates for further in vivo studies to assess their suitability as molecular imaging and therapeutic agents.
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Affiliation(s)
- Rezan Güler
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Siri Flemming Svedmark
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ayman Abouzayed
- Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Anna Orlova
- Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Research Centrum for Oncotheranostics, Research School of Chemistry and Applied Biomedical Sciences, Tomsk Polytechnic University, Tomsk, Russia
| | - 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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8
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Jussing E, Lu L, Grafström J, Tegnebratt T, Arnberg F, Rosik HW, Wennborg A, Holmin S, Feldwisch J, Stone-Elander S. [ 68Ga]ABY-028: an albumin-binding domain (ABD) protein-based imaging tracer for positron emission tomography (PET) studies of altered vascular permeability and predictions of albumin-drug conjugate transport. EJNMMI Res 2020; 10:106. [PMID: 32960353 PMCID: PMC7509035 DOI: 10.1186/s13550-020-00694-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 09/07/2020] [Indexed: 12/12/2022] Open
Abstract
Background Albumin is commonly used as a carrier platform for drugs to extend their circulatory half-lives and influence their uptake into tissues that have altered permeability to the plasma protein. The albumin-binding domain (ABD) protein, which binds in vivo to serum albumin with high affinity, has proven to be a versatile scaffold for engineering biopharmaceuticals with a range of binding capabilities. In this study, the ABD protein equipped with a mal-DOTA chelator (denoted ABY-028) was radiolabeled with gallium-68 (68Ga). This novel radiotracer was then used together with positron emission tomography (PET) imaging to examine variations in the uptake of the ABD-albumin conjugate with variations in endothelial permeability. Results ABY-028, produced by peptide synthesis in excellent purity and stored at − 20 °C, was stable for 24 months (end of study). [68Ga]ABY-028 could be obtained with labeling yields of > 80% and approximately 95% radiochemical purity. [68Ga]ABY-028 distributed in vivo with the plasma pool, with highest radioactivity in the heart ventricles and major vessels of the body, a gradual transport over time from the circulatory system into tissues and elimination via the kidneys. Early [68Ga]ABY-028 uptake differed in xenografts with different vascular properties: mean standard uptake values (SUVmean) were initially 5 times larger in FaDu than in A431 xenografts, but the difference decreased to 3 after 1 h. Cutaneously administered, vasoactive nitroglycerin increased radioactivity in the A431 xenografts. Heterogeneity in the levels and rates of increases of radioactivity uptake was observed in sub-regions of individual MMTV-PyMT mammary tumors and in FaDu xenografts. Higher uptake early after tracer administration could be observed in lower metabolic regions. Fluctuations in the increased permeability for the tracer across the blood-brain-barrier (BBB) direct after experimentally induced stroke were monitored by PET and the increased uptake was confirmed by ex vivo phosphorimaging. Conclusions [68Ga]ABY-028 is a promising new tracer for visualization of changes in albumin uptake due to disease- and pharmacologically altered vascular permeability and their potential effects on the passive uptake of targeting therapeutics based on the ABD protein technology.
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Affiliation(s)
- Emma Jussing
- Department of Clinical Neuroscience, Karolinska Institutet, SE17177, Stockholm, Sweden. .,Department of Oncology and Pathology, Karolinska Institutet, SE17177, Stockholm, Sweden. .,Department of Radiopharmacy, Karolinska University Hospital, SE17176, Stockholm, Sweden.
| | - Li Lu
- Department of Clinical Neuroscience, Karolinska Institutet, SE17177, Stockholm, Sweden.,Comparative Medicine (KERIC), Karolinska University Hospital, SE17176, Stockholm, Sweden
| | - Jonas Grafström
- Department of Clinical Neuroscience, Karolinska Institutet, SE17177, Stockholm, Sweden
| | - Tetyana Tegnebratt
- Department of Clinical Neuroscience, Karolinska Institutet, SE17177, Stockholm, Sweden.,Department of Radiopharmacy, Karolinska University Hospital, SE17176, Stockholm, Sweden
| | - Fabian Arnberg
- Department of Clinical Neuroscience, Karolinska Institutet, SE17177, Stockholm, Sweden.,Department of Neuroradiology, Karolinska University Hospital, SE17176, Stockholm, Sweden
| | - Helena Wållberg Rosik
- Department of Clinical Neuroscience, Karolinska Institutet, SE17177, Stockholm, Sweden.,Affibody AB, SE17165, Solna, Sweden
| | | | - Staffan Holmin
- Department of Clinical Neuroscience, Karolinska Institutet, SE17177, Stockholm, Sweden.,Department of Neuroradiology, Karolinska University Hospital, SE17176, Stockholm, Sweden
| | | | - Sharon Stone-Elander
- Department of Clinical Neuroscience, Karolinska Institutet, SE17177, Stockholm, Sweden.,Department of Neuroradiology, Karolinska University Hospital, SE17176, Stockholm, Sweden
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9
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Samson F, Patrick AT, Fabunmi TE, Yahaya MF, Madu J, He W, Sripathi SR, Tyndall J, Raji H, Jee D, Gutsaeva DR, Jahng WJ. Oleic Acid, Cholesterol, and Linoleic Acid as Angiogenesis Initiators. ACS OMEGA 2020; 5:20575-20585. [PMID: 32832811 PMCID: PMC7439708 DOI: 10.1021/acsomega.0c02850] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/23/2020] [Indexed: 05/03/2023]
Abstract
The current study determined the natural angiogenic molecules using an unbiased metabolomics approach. A chick chorioallantoic membrane (CAM) model was used to examine pro- and antiangiogenic molecules, followed by gas chromatography-mass spectrometry (GCMS) analysis. Vessel formation was analyzed quantitatively using the angiogenic index (p < 0.05). At embryonic day one, a white streak or circle area was observed when vessel formation begins. GCMS analysis and database search demonstrated that angiogenesis may initiate when oleic, cholesterol, and linoleic acids increased in the area of angiogenic reactions. The gain of function study was conducted by the injection of cholesterol and oleic acid into a chick embryo to determine the role of each lipid in angiogenesis. We propose that oleic acid, cholesterol, and linoleic acid are natural molecules that set the platform for the initiation stage of angiogenesis before other proteins including the vascular endothelial growth factor, angiopoietin, angiotensin, and erythropoietin join as the angiome in sprout extension and vessel maturation.
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Affiliation(s)
| | - Ambrose Teru Patrick
- Department
of Petroleum Chemistry, American University
of Nigeria, Yola 640101, Nigeria
| | - Tosin Esther Fabunmi
- Department
of Petroleum Chemistry, American University
of Nigeria, Yola 640101, Nigeria
| | | | - Joshua Madu
- Department
of Petroleum Chemistry, American University
of Nigeria, Yola 640101, Nigeria
| | - Weilue He
- Department
of Biomedical Engineering, Michigan Technological
University, Houghton Michigan 49931, United
States
| | - Srinivas R. Sripathi
- Department
of Ophthalmology, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jennifer Tyndall
- Department
of Natural and Environmental Sciences, American
University of Nigeria, Yola 640101, Nigeria
| | - Hayatu Raji
- Department
of Natural and Environmental Sciences, American
University of Nigeria, Yola 640101, Nigeria
| | - Donghyun Jee
- Department
of Ophthalmology and Visual Science, St. Vincent’s Hospital,
College of Medicine, The Catholic University
of Korea, Suwon 16247, Korea
| | - Diana R. Gutsaeva
- Department
of Ophthalmology, Augusta University, Augusta, Georgia 30912, United States
| | - Wan Jin Jahng
- Department
of Petroleum Chemistry, American University
of Nigeria, Yola 640101, Nigeria
- . Phone: +234-805-550-1032
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10
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Crook ZR, Nairn NW, Olson JM. Miniproteins as a Powerful Modality in Drug Development. Trends Biochem Sci 2020; 45:332-346. [PMID: 32014389 PMCID: PMC7197703 DOI: 10.1016/j.tibs.2019.12.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/06/2019] [Accepted: 12/31/2019] [Indexed: 01/03/2023]
Abstract
Miniproteins are a diverse group of protein scaffolds characterized by small (1-10 kDa) size, stability, and versatility in drug-like roles. Coming largely from native sources, they have been widely adopted into drug development pipelines. While their structures and capabilities are diverse, the approaches to their utilization share more similarities with each other than with more widely used modalities (e.g., antibodies or small molecules). In this review, we highlight recent advances in miniprotein-based approaches to otherwise poorly addressed clinical needs, including structure-based and functional characterization. We also summarize their unique screening strategies and pharmacology considerations. Through a greater understanding of the unique properties that make them attractive for drug design, miniproteins can be effectively utilized against targets that are intractable by other approaches.
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Affiliation(s)
- Zachary R Crook
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Room D4-100, Seattle, WA 98109, USA
| | - Natalie W Nairn
- Blaze Bioscience, Inc, 530 Fairview Ave N., Suite 1400, Seattle, WA 98109, USA
| | - James M Olson
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N., Room D4-100, Seattle, WA 98109, USA.
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11
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Miller EA, Sung KJ, Kongsuphol P, Baniya S, Aw-Yong HQ, Tay V, Tan Y, Kabir FM, Pang-Yeo K, Kaspriskie IG, Sikes HD. Beyond Epitope Binning: Directed in Vitro Selection of Complementary Pairs of Binding Proteins. ACS COMBINATORIAL SCIENCE 2020; 22:49-60. [PMID: 31769955 DOI: 10.1021/acscombsci.9b00176] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Many biotechnological applications require the simultaneous binding of affinity reagents to nonoverlapping target epitopes, the most prominent example being sandwich immunoassays. Typically, affinity pairs are identified via post facto functional analysis of clones that were not selected for complementarity. Here, we developed the Rapid Affinity Pair Identification via Directed Selection (RAPIDS) process, which enables the efficient identification of affinity reagents that function together as complementary pairs, from in vitro libraries of ∼109 variants. We used RAPIDS to develop highly specific affinity pairs against biomarkers of tuberculosis, Zika virus, and sepsis. Without additional trial-and-error screening, these affinity pairs exhibited utility in multiple assay formats. The RAPIDS process applies selective pressure to hundreds of thousands of potential affinity pairs to efficiently identify complementary pairs that bind to separate epitopes without binding to one another or nontargets, yielding diagnostic assays that are sensitive and specific by design.
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Affiliation(s)
- Eric A. Miller
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ki-Joo Sung
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Patthara Kongsuphol
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Singapore 138602
| | - Subha Baniya
- Department of Biochemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| | - Hui Qi Aw-Yong
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Singapore 138602
| | - Vivian Tay
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Singapore 138602
| | - Yuxuan Tan
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Singapore 138602
| | - Farah M. Kabir
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Karl Pang-Yeo
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Singapore 138602
| | - Isabel G. Kaspriskie
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hadley D. Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Singapore 138602
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12
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Akiba H, Takayanagi K, Kusano-Arai O, Iwanari H, Hamakubo T, Tsumoto K. Generation of biparatopic antibody through two-step targeting of fragment antibodies on antigen using SpyTag and SpyCatcher. ACTA ACUST UNITED AC 2020; 25:e00418. [PMID: 31993343 PMCID: PMC6976922 DOI: 10.1016/j.btre.2020.e00418] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 01/03/2020] [Accepted: 01/03/2020] [Indexed: 12/25/2022]
Abstract
Biparatopic fragment antibodies can overcome deficiencies in avidity of conventional antibody fragments. Here, we describe a technology for generating biparatopic antibodies through two-step targeting using a pair of polypeptides, SpyTag and SpyCatcher, that spontaneously react to form a covalent bond between antibody fragments. In this method, two antibody fragments, each targeting different epitopes of the antigen, are fused to SpyTag and to SpyCatcher. When the two polypeptides are serially added to the antigen, their proximity on the antigen results in covalent bond formation and generation of a biparatopic antibody. We validated the system with purified recombinant antigen. Results in antigen-overexpressing cells were promising although further optimization will be required. Because this strategy results in high-affinity targeting with a bipartite molecule that has considerably lower molecular weight than an antibody, this technology is potentially useful for diverse applications.
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Affiliation(s)
- Hiroki Akiba
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kensuke Takayanagi
- Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Osamu Kusano-Arai
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Hiroko Iwanari
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Takao Hamakubo
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.,Department of Protein-protein Interaction Research, Institute for Advanced Medical Sciences, Nippon Medical School, 1-396 Kosugimachi, Nakahara-ku, Kawasaki, 211-8533, Japan
| | - Kouhei Tsumoto
- Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan.,Department of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
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13
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Mazigi O, Schofield P, Langley DB, Christ D. Protein A superantigen: structure, engineering and molecular basis of antibody recognition. Protein Eng Des Sel 2019; 32:359-366. [PMID: 31641749 DOI: 10.1093/protein/gzz026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/02/2019] [Accepted: 07/11/2019] [Indexed: 12/22/2022] Open
Abstract
Staphylococcus aureus interacts with the human immune system through the production of secreted factors. Key among these is protein A, a B-cell superantigen capable of interacting with both antibody Fc and VH regions. Here, we review structural and molecular features of this important example of naturally occurring bacterial superantigens, as well as engineered variants and their application in biotechnology.
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Affiliation(s)
- Ohan Mazigi
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia.,Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Darlinghurst, Sydney, NSW 2010, Australia
| | - Peter Schofield
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia.,Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Darlinghurst, Sydney, NSW 2010, Australia
| | - David B Langley
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia
| | - Daniel Christ
- Department of Immunology, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia.,Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Darlinghurst, Sydney, NSW 2010, Australia
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14
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Güler R, Thatikonda N, Ghani HA, Hedhammar M, Löfblom J. VEGFR2-Specific Ligands Based on Affibody Molecules Demonstrate Agonistic Effects when Tetrameric in the Soluble Form or Immobilized via Spider Silk. ACS Biomater Sci Eng 2019; 5:6474-6484. [PMID: 33417800 DOI: 10.1021/acsbiomaterials.9b00994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Strategies to promote vascularization are being developed in order to improve long-term survival of artificial tissue constructs. Vascular endothelial growth factor A (VEGFA) has an important role in both pathological and physiological angiogenesis, mediated by binding to VEGF receptors (VEGFRs). In nature, signaling can be modulated by presentation of growth factors in either soluble form or bound to the extracellular matrix. Herein, a previously reported VEGFR2-binding antagonistic affibody heterodimer (di-ZVEGFR2) was formatted into a tetrameric construct (tetra-ZVEGFR2) with the intention of generating artificial agonistic ligands for VEGFR2 signaling. In vitro cell assays demonstrated that tetra-ZVEGFR2 induced VEGFR2 phosphorylation and increased cell proliferation, in contrast to di-ZVEGFR2. In order to simulate matrix-bound factors, both constructs were fused at the genetic level to a partial spider silk protein, 4RepCT. Assembly of the silk fusion proteins onto a solid surface was verified by quartz crystal microbalance with dissipation analysis. Moreover, surface plasmon resonance studies demonstrated retained VEGFR2 binding ability of di-ZVEGFR2-silk and tetra-ZVEGFR2-silk after silk-mediated immobilization. Cell culture studies demonstrated that VEGFR2-overexpressing cells adhered to di-ZVEGFR2-silk and tetra-ZVEGFR2-silk and had activated VEGFR2 signaling. Altogether, we demonstrate the potential of especially tetra-ZVEGFR2-silk to promote angiogenesis in tissue-engineering applications. The results from the study also show that molecules can obtain completely new functions when presented on materials, and verifying the biological effects after functionalizing materials is thus always recommended.
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Affiliation(s)
- Rezan Güler
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Centre, SE-10691 Stockholm, Sweden
| | - Naresh Thatikonda
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Centre, SE-10691 Stockholm, Sweden
| | - Hawraa Ali Ghani
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Centre, SE-10691 Stockholm, Sweden
| | - My Hedhammar
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Centre, SE-10691 Stockholm, Sweden
| | - John Löfblom
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Centre, SE-10691 Stockholm, Sweden
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15
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Jing L, Liu J, Cui D, Li Y, Liu Z, Tao L, Zhao Q, Diao A. Screening and production of an affibody inhibiting the interaction of the PD-1/PD-L1 immune checkpoint. Protein Expr Purif 2019; 166:105520. [PMID: 31644959 DOI: 10.1016/j.pep.2019.105520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/14/2019] [Accepted: 10/18/2019] [Indexed: 12/20/2022]
Abstract
An affibody is a 58 amino acids peptide derived from the Z domain of staphylococcal protein A and generally applied in areas such as imaging diagnosis, clinical therapeutics and biotechnology research. To screen for an affibody targeting the immune checkpoint PD-L1, a combinatorial affibody library was generated in yeast using degenerate overlap PCR primers and In-fusion technology. Z-j1 and Z-j2 affibodies targeting the Ig-like V domain of PD-L1 were screened and identified from this combinatorial library using the yeast two hybrid system. The Z-j1 and Z-j2 recombinant affibody proteins were over produced in E.coli and purified. ELISA and GST pull-down assays showed that recombinant Z-j1 and Z-j2 affibody proteins bound with high affinity to PD-L1 and inhibited the interaction of PD-1/PD-L1. Thus, novel affibodies targeting the immune checkpoint PD-1/PD-L1 were identified and produced in this study and have the potential to be used in cancer immunotherapy.
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Affiliation(s)
- Lei Jing
- School of Biotechnology, Tianjin University of Science and Technology, Key Lab of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin, 300457, China
| | - Juanjuan Liu
- School of Biotechnology, Tianjin University of Science and Technology, Key Lab of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin, 300457, China
| | - Dongxu Cui
- School of Biotechnology, Tianjin University of Science and Technology, Key Lab of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin, 300457, China
| | - Yuyin Li
- School of Biotechnology, Tianjin University of Science and Technology, Key Lab of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin, 300457, China
| | - Zhenxing Liu
- School of Biotechnology, Tianjin University of Science and Technology, Key Lab of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin, 300457, China
| | - Li Tao
- School of Biotechnology, Tianjin University of Science and Technology, Key Lab of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin, 300457, China
| | - Qing Zhao
- School of Biotechnology, Tianjin University of Science and Technology, Key Lab of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin, 300457, China; Tianjin Engineering Research Center of Safety Control Technology in Food Processing, 300457, Tianjin, China; Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, 300457, Tianjin, China.
| | - Aipo Diao
- School of Biotechnology, Tianjin University of Science and Technology, Key Lab of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin, 300457, China.
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16
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Hober S, Lindbo S, Nilvebrant J. Bispecific applications of non-immunoglobulin scaffold binders. Methods 2019; 154:143-152. [DOI: 10.1016/j.ymeth.2018.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/24/2018] [Accepted: 09/28/2018] [Indexed: 12/13/2022] Open
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17
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Mitran B, Güler R, Roche FP, Lindström E, Selvaraju RK, Fleetwood F, Rinne SS, Claesson-Welsh L, Tolmachev V, Ståhl S, Orlova A, Löfblom J. Radionuclide imaging of VEGFR2 in glioma vasculature using biparatopic affibody conjugate: proof-of-principle in a murine model. Theranostics 2018; 8:4462-4476. [PMID: 30214632 PMCID: PMC6134937 DOI: 10.7150/thno.24395] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 04/21/2018] [Indexed: 01/09/2023] Open
Abstract
Vascular endothelial growth factor receptor-2 (VEGFR2) is a key mediator of angiogenesis and therefore a promising therapeutic target in malignancies including glioblastoma multiforme (GBM). Molecular imaging of VEGFR2 expression may enable patient stratification for antiangiogenic therapy. The goal of the current study was to evaluate the capacity of the novel anti-VEGFR2 biparatopic affibody conjugate (ZVEGFR2-Bp2) for in vivo visualization of VEGFR2 expression in GBM. Methods: ZVEGFR2-Bp2 coupled to a NODAGA chelator was generated and radiolabeled with indium-111. The VEGFR2-expressing murine endothelial cell line MS1 was used to evaluate in vitro binding specificity and affinity, cellular processing and targeting specificity in mice. Further tumor targeting was studied in vivo in GL261 glioblastoma orthotopic tumors. Experimental imaging was performed. Results: [111In]In-NODAGA-ZVEGFR2-Bp2 bound specifically to VEGFR2 (KD=33±18 pM). VEGFR2-mediated accumulation was observed in liver, spleen and lungs. The tumor-to-organ ratios 2 h post injection for mice bearing MS1 tumors were approximately 11 for blood, 15 for muscles and 78 for brain. Intracranial GL261 glioblastoma was visualized using SPECT/CT. The activity uptake in tumors was significantly higher than in normal brain tissue. The tumor-to-cerebellum ratios after injection of 4 µg [111In]In-NODAGA-ZVEGFR2-Bp2 were significantly higher than the ratios observed for the 40 µg injected dose and for the non-VEGFR2 binding size-matched conjugate, demonstrating target specificity. Microautoradiography of cryosectioned CNS tissue was in good agreement with the SPECT/CT images. Conclusion: The anti-VEGFR2 affibody conjugate [111In]In-NODAGA-ZVEGFR2-Bp2 specifically targeted VEGFR2 in vivo and visualized its expression in a murine GBM orthotopic model. Tumor-to-blood ratios for [111In]In-NODAGA-ZVEGFR2-Bp2 were higher compared to other VEGFR2 imaging probes. [111In]In-NODAGA-ZVEGFR2-Bp2 appears to be a promising probe for in vivo noninvasive visualization of tumor angiogenesis in glioblastoma.
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18
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Verdino P, Atwell S, Demarest SJ. Emerging trends in bispecific antibody and scaffold protein therapeutics. Curr Opin Chem Eng 2018. [DOI: 10.1016/j.coche.2018.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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19
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Löfblom J, Rosenstein R, Nguyen MT, Ståhl S, Götz F. Staphylococcus carnosus: from starter culture to protein engineering platform. Appl Microbiol Biotechnol 2017; 101:8293-8307. [PMID: 28971248 PMCID: PMC5694512 DOI: 10.1007/s00253-017-8528-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 02/04/2023]
Abstract
Since the 1950s, Staphylococcus carnosus is used as a starter culture for sausage fermentation where it contributes to food safety, flavor, and a controlled fermentation process. The long experience with S. carnosus has shown that it is a harmless and "food grade" species. This was confirmed by the genome sequence of S. carnosus TM300 that lacks genes involved in pathogenicity. Since the development of a cloning system in TM300, numerous genes have been cloned, expressed, and characterized and in particular, virulence genes that could be functionally validated in this non-pathogenic strain. A secretion system was developed for production and secretion of industrially important proteins and later modified to also enable display of heterologous proteins on the surface. The display system has been employed for various purposes, such as development of live bacterial delivery vehicles as well as microbial biocatalysts or bioadsorbents for potential environmental or biosensor applications. Recently, this surface display system has been utilized for display of peptide and protein libraries for profiling of protease substrates and for generation of various affinity proteins, e.g., Affibody molecules and scFv antibodies. In addition, by display of fragmented antigen-encoding genes, the surface expression system has been successfully used for epitope mapping of antibodies. Reviews on specific applications of S. carnosus have been published earlier, but here we provide a more extensive overview, covering a broad range of areas from food fermentation to sophisticated methods for protein-based drug discovery, which are all based on S. carnosus.
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Affiliation(s)
- John Löfblom
- Division of Protein Technology, School of Biotechnology, KTH-Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, 106 91, Stockholm, Sweden
| | - Ralf Rosenstein
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine and Infection Medicine (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Minh-Thu Nguyen
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine and Infection Medicine (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Stefan Ståhl
- Division of Protein Technology, School of Biotechnology, KTH-Royal Institute of Technology, AlbaNova University Center, Roslagstullsbacken 21, 106 91, Stockholm, Sweden.
| | - Friedrich Götz
- Microbial Genetics, Interfaculty Institute of Microbiology and Infection Medicine and Infection Medicine (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany.
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20
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Tiede C, Bedford R, Heseltine SJ, Smith G, Wijetunga I, Ross R, AlQallaf D, Roberts APE, Balls A, Curd A, Hughes RE, Martin H, Needham SR, Zanetti-Domingues LC, Sadigh Y, Peacock TP, Tang AA, Gibson N, Kyle H, Platt GW, Ingram N, Taylor T, Coletta LP, Manfield I, Knowles M, Bell S, Esteves F, Maqbool A, Prasad RK, Drinkhill M, Bon RS, Patel V, Goodchild SA, Martin-Fernandez M, Owens RJ, Nettleship JE, Webb ME, Harrison M, Lippiat JD, Ponnambalam S, Peckham M, Smith A, Ferrigno PK, Johnson M, McPherson MJ, Tomlinson DC. Affimer proteins are versatile and renewable affinity reagents. eLife 2017; 6:e24903. [PMID: 28654419 PMCID: PMC5487212 DOI: 10.7554/elife.24903] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 06/07/2017] [Indexed: 12/11/2022] Open
Abstract
Molecular recognition reagents are key tools for understanding biological processes and are used universally by scientists to study protein expression, localisation and interactions. Antibodies remain the most widely used of such reagents and many show excellent performance, although some are poorly characterised or have stability or batch variability issues, supporting the use of alternative binding proteins as complementary reagents for many applications. Here we report on the use of Affimer proteins as research reagents. We selected 12 diverse molecular targets for Affimer selection to exemplify their use in common molecular and cellular applications including the (a) selection against various target molecules; (b) modulation of protein function in vitro and in vivo; (c) labelling of tumour antigens in mouse models; and (d) use in affinity fluorescence and super-resolution microscopy. This work shows that Affimer proteins, as is the case for other alternative binding scaffolds, represent complementary affinity reagents to antibodies for various molecular and cell biology applications.
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Affiliation(s)
- Christian Tiede
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Robert Bedford
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Sophie J Heseltine
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Gina Smith
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Imeshi Wijetunga
- Leeds Institute of Cancer Studies and Pathology, University of Leeds, Leeds, United Kingdom
| | - Rebecca Ross
- Leeds Institute of Cancer Studies and Pathology, University of Leeds, Leeds, United Kingdom
| | - Danah AlQallaf
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | | | - Alexander Balls
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Alistair Curd
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Ruth E Hughes
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Heather Martin
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Sarah R Needham
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot, United Kingdom
| | - Laura C Zanetti-Domingues
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot, United Kingdom
| | | | | | - Anna A Tang
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Naomi Gibson
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Hannah Kyle
- Avacta Life Sciences, Wetherby, United Kingdom
| | | | - Nicola Ingram
- Leeds Institute of Cancer Studies and Pathology, University of Leeds, Leeds, United Kingdom
| | - Thomas Taylor
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Louise P Coletta
- Leeds Institute of Cancer Studies and Pathology, University of Leeds, Leeds, United Kingdom
| | - Iain Manfield
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Margaret Knowles
- Leeds Institute of Cancer Studies and Pathology, University of Leeds, Leeds, United Kingdom
| | - Sandra Bell
- Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | - Filomena Esteves
- Leeds Institute of Cancer Studies and Pathology, University of Leeds, Leeds, United Kingdom
| | - Azhar Maqbool
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Raj K Prasad
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Mark Drinkhill
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | - Robin S Bon
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, United Kingdom
| | | | | | - Marisa Martin-Fernandez
- Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot, United Kingdom
| | - Ray J Owens
- Oxford Protein Production Facility UK, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot, United Kingdom
| | - Joanne E Nettleship
- Oxford Protein Production Facility UK, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Didcot, United Kingdom
| | - Michael E Webb
- School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Michael Harrison
- School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
| | - Jonathan D Lippiat
- School of Biomedical Sciences, University of Leeds, Leeds, United Kingdom
| | - Sreenivasan Ponnambalam
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Michelle Peckham
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | | | | | | | - Michael J McPherson
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
| | - Darren Charles Tomlinson
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
- Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, United Kingdom
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21
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Ståhl S, Gräslund T, Eriksson Karlström A, Frejd FY, Nygren PÅ, Löfblom J. Affibody Molecules in Biotechnological and Medical Applications. Trends Biotechnol 2017; 35:691-712. [PMID: 28514998 DOI: 10.1016/j.tibtech.2017.04.007] [Citation(s) in RCA: 225] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 04/18/2017] [Accepted: 04/20/2017] [Indexed: 01/08/2023]
Abstract
Affibody molecules are small (6.5-kDa) affinity proteins based on a three-helix bundle domain framework. Since their introduction 20 years ago as an alternative to antibodies for biotechnological applications, the first therapeutic affibody molecules have now entered clinical development and more than 400 studies have been published in which affibody molecules have been developed and used in a variety of contexts. In this review, we focus primarily on efforts over the past 5 years to explore the potential of affibody molecules for medical applications in oncology, neurodegenerative, and inflammation disorders, including molecular imaging, receptor signal blocking, and delivery of toxic payloads. In addition, we describe recent examples of biotechnological applications, in which affibody molecules have been exploited as modular affinity fusion partners.
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Affiliation(s)
- Stefan Ståhl
- Division of Protein Technology, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden.
| | - Torbjörn Gräslund
- Division of Protein Technology, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | | | - Fredrik Y Frejd
- Unit of Biomedical Radiation Sciences, Uppsala University, SE-751 85 Uppsala, Sweden; Affibody AB, Gunnar Asplunds Allé 24, SE-171 69 Solna, Sweden
| | - Per-Åke Nygren
- Division of Protein Technology, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden
| | - John Löfblom
- Division of Protein Technology, KTH Royal Institute of Technology, SE-106 91, Stockholm, Sweden
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22
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Abstract
Affibody molecules can be used as tools for molecular recognition in diagnostic and therapeutic applications. There are several preclinical studies reported on diagnostic and therapeutic use of this molecular class of alternative scaffolds, and early clinical evidence is now beginning to accumulate that suggests the Affibody molecules to be efficacious and safe in man. The small size and ease of engineering make Affibody molecules suitable for use in multispecific constructs where AffiMabs is one such that offers the option to potentiate antibodies for use in complex disease.
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23
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Boonstra MC, de Geus SWL, Prevoo HAJM, Hawinkels LJAC, van de Velde CJH, Kuppen PJK, Vahrmeijer AL, Sier CFM. Selecting Targets for Tumor Imaging: An Overview of Cancer-Associated Membrane Proteins. BIOMARKERS IN CANCER 2016; 8:119-133. [PMID: 27721658 PMCID: PMC5040425 DOI: 10.4137/bic.s38542] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 09/05/2016] [Accepted: 09/06/2016] [Indexed: 12/30/2022]
Abstract
Tumor targeting is a booming business: The global therapeutic monoclonal antibody market accounted for more than $78 billion in 2012 and is expanding exponentially. Tumors can be targeted with an extensive arsenal of monoclonal antibodies, ligand proteins, peptides, RNAs, and small molecules. In addition to therapeutic targeting, some of these compounds can also be applied for tumor visualization before or during surgery, after conjugation with radionuclides and/or near-infrared fluorescent dyes. The majority of these tumor-targeting compounds are directed against cell membrane-bound proteins. Various categories of targetable membrane-bound proteins, such as anchoring proteins, receptors, enzymes, and transporter proteins, exist. The functions and biological characteristics of these proteins determine their location and distribution on the cell membrane, making them more, or less, accessible, and therefore, it is important to understand these features. In this review, we evaluate the characteristics of cancer-associated membrane proteins and discuss their overall usability for cancer targeting, especially focusing on imaging applications.
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Affiliation(s)
- Martin C Boonstra
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | - Susanna W L de Geus
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Lukas J A C Hawinkels
- Department of Gastroenterology, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Peter J K Kuppen
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands.; Antibodies for Research Applications BV, Gouda, the Netherlands
| | | | - Cornelis F M Sier
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands.; Antibodies for Research Applications BV, Gouda, the Netherlands
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Fleetwood F, Güler R, Gordon E, Ståhl S, Claesson-Welsh L, Löfblom J. Novel affinity binders for neutralization of vascular endothelial growth factor (VEGF) signaling. Cell Mol Life Sci 2016; 73:1671-83. [PMID: 26552422 PMCID: PMC11108507 DOI: 10.1007/s00018-015-2088-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/19/2015] [Accepted: 11/03/2015] [Indexed: 02/06/2023]
Abstract
Angiogenesis denotes the formation of new blood vessels from pre-existing vasculature. Progression of diseases such as cancer and several ophthalmological disorders may be promoted by excess angiogenesis. Novel therapeutics to inhibit angiogenesis and diagnostic tools for monitoring angiogenesis during therapy, hold great potential for improving treatment of such diseases. We have previously generated so-called biparatopic Affibody constructs with high affinity for the vascular endothelial growth factor receptor-2 (VEGFR2), which recognize two non-overlapping epitopes in the ligand-binding site on the receptor. Affibody molecules have previously been demonstrated suitable for imaging purposes. Their small size also makes them attractive for applications where an alternative route of administration is beneficial, such as topical delivery using eye drops. In this study, we show that decreasing linker length between the two Affibody domains resulted in even slower dissociation from the receptor. The new variants of the biparatopic Affibody bound to VEGFR2-expressing cells, blocked VEGFA binding, and inhibited VEGFA-induced signaling of VEGFR2 over expressing cells. Moreover, the biparatopic Affibody inhibited sprout formation of endothelial cells in an in vitro angiogenesis assay with similar potency as the bivalent monoclonal antibody ramucirumab. This study demonstrates that the biparatopic Affibody constructs show promise for future therapeutic as well as in vivo imaging applications.
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Affiliation(s)
- Filippa Fleetwood
- Division of Protein Technology, School of Biotechnology, KTH, Royal Institute of Technology, AlbaNova University Center, 106 91, Stockholm, Sweden
| | - Rezan Güler
- Division of Protein Technology, School of Biotechnology, KTH, Royal Institute of Technology, AlbaNova University Center, 106 91, Stockholm, Sweden
| | - Emma Gordon
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjöldsv. 20, Uppsala, Sweden
| | - Stefan Ståhl
- Division of Protein Technology, School of Biotechnology, KTH, Royal Institute of Technology, AlbaNova University Center, 106 91, Stockholm, Sweden
| | - Lena Claesson-Welsh
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjöldsv. 20, Uppsala, Sweden
| | - John Löfblom
- Division of Protein Technology, School of Biotechnology, KTH, Royal Institute of Technology, AlbaNova University Center, 106 91, Stockholm, Sweden.
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Vazquez-Lombardi R, Phan TG, Zimmermann C, Lowe D, Jermutus L, Christ D. Challenges and opportunities for non-antibody scaffold drugs. Drug Discov Today 2015; 20:1271-83. [PMID: 26360055 DOI: 10.1016/j.drudis.2015.09.004] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 08/06/2015] [Accepted: 09/01/2015] [Indexed: 12/22/2022]
Abstract
The first candidates from the promising class of small non-antibody protein scaffolds are now moving into clinical development and practice. Challenges remain, and scaffolds will need to be further tailored toward applications where they provide real advantages over established therapeutics to succeed in a rapidly evolving drug development landscape.
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Affiliation(s)
- Rodrigo Vazquez-Lombardi
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia; The University of New South Wales, Faculty of Medicine, St Vincent's Clinical School, Darlinghurst, Sydney, NSW 2010, Australia
| | - Tri Giang Phan
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia; The University of New South Wales, Faculty of Medicine, St Vincent's Clinical School, Darlinghurst, Sydney, NSW 2010, Australia
| | - Carsten Zimmermann
- University of San Diego, School of Business Administration, 5998 Alcala Park, San Diego, CA 92110, USA
| | - David Lowe
- MedImmune Ltd., Granta Park, Cambridge CB21 6GH, UK
| | - Lutz Jermutus
- MedImmune Ltd., Granta Park, Cambridge CB21 6GH, UK; Trinity Hall, University of Cambridge, Trinity Lane CB2 1TJ, UK.
| | - Daniel Christ
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia; The University of New South Wales, Faculty of Medicine, St Vincent's Clinical School, Darlinghurst, Sydney, NSW 2010, Australia.
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Kruziki MA, Bhatnagar S, Woldring DR, Duong VT, Hackel BJ. A 45-Amino-Acid Scaffold Mined from the PDB for High-Affinity Ligand Engineering. ACTA ACUST UNITED AC 2015; 22:946-56. [PMID: 26165154 DOI: 10.1016/j.chembiol.2015.06.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 05/08/2015] [Accepted: 06/04/2015] [Indexed: 12/20/2022]
Abstract
Small protein ligands can provide superior physiological distribution compared with antibodies, and improved stability, production, and specific conjugation. Systematic evaluation of the PDB identified a scaffold to push the limits of small size and robust evolution of stable, high-affinity ligands: 45-residue T7 phage gene 2 protein (Gp2) contains an α helix opposite a β sheet with two adjacent loops amenable to mutation. De novo ligand discovery from 10(8) mutants and directed evolution toward four targets yielded target-specific binders with affinities as strong as 200 ± 100 pM, Tms from 65 °C ± 3 °C to 80°C ± 1 °C, and retained activity after thermal denaturation. For cancer targeting, a Gp2 domain for epidermal growth factor receptor was evolved with 18 ± 8 nM affinity, receptor-specific binding, and high thermal stability with refolding. The efficiency of evolving new binding function and the size, affinity, specificity, and stability of evolved domains render Gp2 a uniquely effective ligand scaffold.
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Affiliation(s)
- Max A Kruziki
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sumit Bhatnagar
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Daniel R Woldring
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Vandon T Duong
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | - Benjamin J Hackel
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA.
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