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Leonard AC, Friedman AJ, Chayer R, Petersen BM, Woojuh J, Xing Z, Cutler SR, Kaar JL, Shirts MR, Whitehead TA. Rationalizing Diverse Binding Mechanisms to the Same Protein Fold: Insights for Ligand Recognition and Biosensor Design. ACS Chem Biol 2024; 19:1757-1772. [PMID: 39017707 DOI: 10.1021/acschembio.4c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The engineering of novel protein-ligand binding interactions, particularly for complex drug-like molecules, is an unsolved problem, which could enable many practical applications of protein biosensors. In this work, we analyzed two engineered biosensors, derived from the plant hormone sensor PYR1, to recognize either the agrochemical mandipropamid or the synthetic cannabinoid WIN55,212-2. Using a combination of quantitative deep mutational scanning experiments and molecular dynamics simulations, we demonstrated that mutations at common positions can promote protein-ligand shape complementarity and revealed prominent differences in the electrostatic networks needed to complement diverse ligands. MD simulations indicate that both PYR1 protein-ligand complexes bind a single conformer of their target ligand that is close to the lowest free-energy conformer. Computational design using a fixed conformer and rigid body orientation led to new WIN55,212-2 sensors with nanomolar limits of detection. This work reveals mechanisms by which the versatile PYR1 biosensor scaffold can bind diverse ligands. This work also provides computational methods to sample realistic ligand conformers and rigid body alignments that simplify the computational design of biosensors for novel ligands of interest.
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Affiliation(s)
- Alison C Leonard
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - Anika J Friedman
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - Rachel Chayer
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - Brian M Petersen
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - Janty Woojuh
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521-9800, United States
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California 92521, United States
- Center for Plant Cell Biology, University of California, Riverside, Riverside, California 92521, United States
| | - Zenan Xing
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521-9800, United States
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California 92521, United States
- Center for Plant Cell Biology, University of California, Riverside, Riverside, California 92521, United States
| | - Sean R Cutler
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521-9800, United States
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, California 92521, United States
- Center for Plant Cell Biology, University of California, Riverside, Riverside, California 92521, United States
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
| | - Timothy A Whitehead
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States
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Leonard AC, Friedman AJ, Chayer R, Petersen BM, Kaar J, Shirts MR, Whitehead TA. Rationalizing diverse binding mechanisms to the same protein fold: insights for ligand recognition and biosensor design. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.25.586677. [PMID: 38586024 PMCID: PMC10996623 DOI: 10.1101/2024.03.25.586677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The engineering of novel protein-ligand binding interactions, particularly for complex drug-like molecules, is an unsolved problem which could enable many practical applications of protein biosensors. In this work, we analyzed two engineer ed biosensors, derived from the plant hormone sensor PYR1, to recognize either the agrochemical mandipropamid or the synthetic cannabinoid WIN55,212-2. Using a combination of quantitative deep mutational scanning experiments and molecular dynamics simulations, we demonstrated that mutations at common positions can promote protein-ligand shape complementarity and revealed prominent differences in the electrostatic networks needed to complement diverse ligands. MD simulations indicate that both PYR1 protein-ligand complexes bind a single conformer of their target ligand that is close to the lowest free energy conformer. Computational design using a fixed conformer and rigid body orientation led to new WIN55,212-2 sensors with nanomolar limits of detection. This work reveals mechanisms by which the versatile PYR1 biosensor scaffold can bind diverse ligands. This work also provides computational methods to sample realistic ligand conformers and rigid body alignments that simplify the computational design of biosensors for novel ligands of interest.
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Pandey RK, Mehrotra S. Engineering high affinity antigen-binders: Beyond conventional antibodies. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 140:37-57. [PMID: 38762275 DOI: 10.1016/bs.apcsb.2023.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
For decades, antibodies have remained the archetypal binding proteins that can be rapidly produced with high affinity and specificity against virtually any target. A conventional antibody is still considered the prototype of a binding molecule. It is therefore not surprising that antibodies are routinely used in basic scientific and biomedical research, analytical workflows, molecular diagnostics etc. and represent the fastest growing sector in the field of biotechnology. However, several limitations associated with conventional antibodies, including stringent requirement of animal immunizations, mammalian cells for expression, issues on stability and aggregation, bulkier size and the overall time and cost of production has propelled evolution of concepts along alternative antigen binders. Rapidly evolving protein engineering approaches and high throughput screening platforms have further complemented the development of myriads of classes of non-conventional protein binders including antibody derived as well as non-antibody based molecular scaffolds. These non-canonical binders are finding use across disciplines of which diagnostics and therapeutics are the most noteworthy.
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Affiliation(s)
- Rajeev Kumar Pandey
- Research and Development-Protein Biology, Thermo Fisher Scientific, Bangalore, India
| | - Sanjana Mehrotra
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India.
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Huang R, Warner Jenkins G, Kim Y, Stanfield RL, Singh A, Martinez-Yamout M, Kroon GJ, Torres JL, Jackson AM, Kelley A, Shaabani N, Zeng B, Bacica M, Chen W, Warner C, Radoicic J, Joh J, Dinali Perera K, Sang H, Kim T, Yao J, Zhao F, Sok D, Burton DR, Allen J, Harriman W, Mwangi W, Chung D, Teijaro JR, Ward AB, Dyson HJ, Wright PE, Wilson IA, Chang KO, McGregor D, Smider VV. The smallest functional antibody fragment: Ultralong CDR H3 antibody knob regions potently neutralize SARS-CoV-2. Proc Natl Acad Sci U S A 2023; 120:e2303455120. [PMID: 37722054 PMCID: PMC10523490 DOI: 10.1073/pnas.2303455120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/15/2023] [Indexed: 09/20/2023] Open
Abstract
Cows produce antibodies with a disulfide-bonded antigen-binding domain embedded within ultralong heavy chain third complementarity determining regions. This "knob" domain is analogous to natural cysteine-rich peptides such as knottins in that it is small and stable but can accommodate diverse loops and disulfide bonding patterns. We immunized cattle with SARS-CoV-2 spike and found ultralong CDR H3 antibodies that could neutralize several viral variants at picomolar IC50 potencies in vitro and could protect from disease in vivo. The independent CDR H3 peptide knobs were expressed and maintained the properties of the parent antibodies. The knob interaction with SARS-CoV-2 spike was revealed by electron microscopy, X-ray crystallography, NMR spectroscopy, and mass spectrometry and established ultralong CDR H3-derived knobs as the smallest known recombinant independent antigen-binding fragment. Unlike other vertebrate antibody fragments, these knobs are not reliant on the immunoglobulin domain and have potential as a new class of therapeutics.
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Affiliation(s)
- Ruiqi Huang
- Applied Biomedical Science Institute, San Diego, CA92127
| | | | - Yunjeong Kim
- College of Veterinary Medicine, Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS66506
| | - Robyn L. Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Amrinder Singh
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Maria Martinez-Yamout
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Gerard J. Kroon
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Jonathan L. Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Abigail M. Jackson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Abigail Kelley
- Applied Biomedical Science Institute, San Diego, CA92127
| | - Namir Shaabani
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA92037
| | | | | | - Wen Chen
- Ligand Pharmaceuticals, San Diego, CA92121
| | | | | | - Joongho Joh
- School of Medicine, Department of Medicine, University of Louisville, Louisville, KY40202
| | - Krishani Dinali Perera
- College of Veterinary Medicine, Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS66506
| | - Huldah Sang
- College of Veterinary Medicine, Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS66506
| | - Tae Kim
- College of Veterinary Medicine, Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS66506
| | - Jianxiu Yao
- College of Veterinary Medicine, Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS66506
| | - Fangzhu Zhao
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA92037
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA92037
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA92037
| | - Jeff Allen
- Ligand Pharmaceuticals, San Diego, CA92121
| | | | - Waithaka Mwangi
- College of Veterinary Medicine, Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS66506
| | - Donghoon Chung
- School of Medicine, Department of Microbiology and Immunology, University of Louisville, Louisville, KY40202
| | - John R. Teijaro
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA92037
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - H. Jane Dyson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Peter E. Wright
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA92037
| | - Kyeong-Ok Chang
- College of Veterinary Medicine, Department of Diagnostic Medicine and Pathobiology, Kansas State University, Manhattan, KS66506
| | | | - Vaughn V. Smider
- Applied Biomedical Science Institute, San Diego, CA92127
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA92037
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Jolugbo P, Willott T, Lin WH, Maisey T, O'Callaghan D, Green MA, Jayne DG, Khot MI. Fluorescent imaging using novel conjugated polymeric nanoparticles-affimer probes in complex in vitro models of colorectal cancer. NANOSCALE 2023. [PMID: 37466243 DOI: 10.1039/d3nr02160b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
We developed a carcinoembryonic antigen (CEA) conjugated polymer nanoparticle (CPN510-CEA-Af) probe to target CEA-expressing CRC cells in vitro. Its efficacy was evaluated in 2D and 3D cultures of LS174T, LoVo, and HT29 CRC cell lines. CPN510-CEA-Af produced greater fluorescent signal intensity than unconjugated particles in both 2D cells and 3D spheriods, indicating its potential as a probe for image-guided colorectal cancer surgery.
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Affiliation(s)
- Precious Jolugbo
- Leeds Institute of Medical Research at St James', School of Medicine, St James University Hospital, University of Leeds, Leeds, LS9 7TF, UK.
| | - Thomas Willott
- Leeds Institute of Medical Research at St James', School of Medicine, St James University Hospital, University of Leeds, Leeds, LS9 7TF, UK.
| | - Wei-Hsiang Lin
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, M13 9PL, UK
| | - Thomas Maisey
- Leeds Institute of Medical Research at St James', School of Medicine, St James University Hospital, University of Leeds, Leeds, LS9 7TF, UK.
| | | | - Mark A Green
- Stream Bio Ltd, Alderley Park, Nether Alderley, Cheshire, SK10 4TG, UK
- Department of Physics, Faculty of Natural, Mathematical & Engineering Sciences, King's College London, Strand, London, WC2R 2LS, UK
| | - David G Jayne
- Leeds Institute of Medical Research at St James', School of Medicine, St James University Hospital, University of Leeds, Leeds, LS9 7TF, UK.
| | - M Ibrahim Khot
- Leeds Institute of Medical Research at St James', School of Medicine, St James University Hospital, University of Leeds, Leeds, LS9 7TF, UK.
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Ji Y, Liu D, Zhu H, Bao L, Chang R, Gao X, Yin J. Unstructured Polypeptides as a Versatile Drug Delivery Technology. Acta Biomater 2023; 164:74-93. [PMID: 37075961 DOI: 10.1016/j.actbio.2023.04.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/23/2023] [Accepted: 04/13/2023] [Indexed: 04/21/2023]
Abstract
Although polyethylene glycol (PEG), or "PEGylation" has become a widely applied approach for improving the efficiency of drug delivery, the immunogenicity and non-biodegradability of this synthetic polymer have prompted an evident need for alternatives. To overcome these caveats and to mimic PEG -or other natural or synthetic polymers- for the purpose of drug half-life extension, unstructured polypeptides are designed. Due to their tunable length, biodegradability, low immunogenicity and easy production, unstructured polypeptides have the potential to replace PEG as the preferred technology for therapeutic protein/peptide delivery. This review provides an overview of the evolution of unstructured polypeptides, starting from natural polypeptides to engineered polypeptides and discusses their characteristics. Then, it is described that unstructured polypeptides have been successfully applied to numerous drugs, including peptides, proteins, antibody fragments, and nanocarriers, for half-life extension. Innovative applications of unstructured peptides as releasable masks, multimolecular adaptors and intracellular delivery carriers are also discussed. Finally, challenges and future perspectives of this promising field are briefly presented. STATEMENT OF SIGNIFICANCE: : Polypeptide fusion technology simulating PEGylation has become an important topic for the development of long-circulating peptide or protein drugs without reduced activity, complex processes, and kidney injury caused by PEG modification. Here we provide a detailed and in-depth review of the recent advances in unstructured polypeptides. In addition to the application of enhanced pharmacokinetic performance, emphasis is placed on polypeptides as scaffolders for the delivery of multiple drugs, and on the preparation of reasonably designed polypeptides to manipulate the performance of proteins and peptides. This review will provide insight into future application of polypeptides in peptide or protein drug development and the design of novel functional polypeptides.
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Affiliation(s)
- Yue Ji
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Dingkang Liu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Haichao Zhu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Lichen Bao
- Jiangsu Key Laboratory of Neurodegeneration, Nanjing Medical University, Nanjing 210009, China
| | - Ruilong Chang
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Xiangdong Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China.
| | - Jun Yin
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals and State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China.
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Yang HH, Wang X, Li S, Liu Y, Akbar R, Fan GC. Lipocalin family proteins and their diverse roles in cardiovascular disease. Pharmacol Ther 2023; 244:108385. [PMID: 36966973 PMCID: PMC10079643 DOI: 10.1016/j.pharmthera.2023.108385] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 03/01/2023] [Accepted: 03/13/2023] [Indexed: 04/03/2023]
Abstract
The lipocalin (LCN) family members, a group of small extracellular proteins with 160-180 amino acids in length, can be detected in all kingdoms of life from bacteria to human beings. They are characterized by low similarity of amino acid sequence but highly conserved tertiary structures with an eight-stranded antiparallel β-barrel which forms a cup-shaped ligand binding pocket. In addition to bind small hydrophobic ligands (i.e., fatty acids, odorants, retinoids, and steroids) and transport them to specific cells, lipocalins (LCNs) can interact with specific cell membrane receptors to activate their downstream signaling pathways, and with soluble macromolecules to form the complex. Consequently, LCNs exhibit great functional diversity. Accumulating evidence has demonstrated that LCN family proteins exert multiple layers of function in the regulation of many physiological processes and human diseases (i.e., cancers, immune disorders, metabolic disease, neurological/psychiatric disorders, and cardiovascular disease). In this review, we firstly introduce the structural and sequence properties of LCNs. Next, six LCNs including apolipoprotein D (ApoD), ApoM, lipocalin 2 (LCN2), LCN10, retinol-binding protein 4 (RBP4), and Lipocalin-type prostaglandin D synthase (L-PGDS) which have been characterized so far are highlighted for their diagnostic/prognostic values and their potential effects on coronary artery disease and myocardial infarction injury. The roles of these 6 LCNs in cardiac hypertrophy, heart failure, diabetes-induced cardiac disorder, and septic cardiomyopathy are also summarized. Finally, their therapeutic potential for cardiovascular disease is discussed in each section.
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Affiliation(s)
- Hui-Hui Yang
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Xiaohong Wang
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Siru Li
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Yueying Liu
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Rubab Akbar
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Guo-Chang Fan
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA.
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Elarekibep (PRS-060/AZD1402), a new class of inhaled Anticalin medicine targeting IL-4Ra for type 2 endotype asthma. J Allergy Clin Immunol 2022; 151:966-975. [PMID: 36592703 DOI: 10.1016/j.jaci.2022.12.815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/20/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
BACKGROUND Type 2 endotype asthma is driven by IL-4 and IL-13 signaling via IL-4Ra, which is highly expressed on airway epithelium, airway smooth muscle, and immunocytes in the respiratory mucosa, suggesting potential advantages of an inhalable antagonist. Lipocalin 1 (Lcn1), a 16 kDa protein abundant in human periciliary fluid, has a robust drug-like structure well suited to protein engineering, but it has never been used to make an inhaled Anticalin protein therapeutic. OBJECTIVES We sought to reengineer Lcn1 into an inhalable IL-4Ra antagonist and assess its pharmacodynamic/kinetic profile. METHODS Lcn1 was systematically modified by directed protein mutagenesis yielding a high-affinity, slowly dissociating, long-acting full antagonist of IL-4Ra designated PRS-060 with properties analogous to dupilumab, competitively antagonizing IL-4Ra-dependent cell proliferation, mucus induction, and eotaxin expression in vitro. Because PRS-060 displayed exquisite specificity for human IL-4Ra, with no cross-reactivity to rodents or higher primates, we created a new triple-humanized mouse model substituting human IL-4Ra, IL-4, and IL-13 at their correct syntenic murine loci to model clinical dosing. RESULTS Inhaled PRS-060 strongly suppressed acute allergic inflammation indexes in triple-humanized mice with a duration of action longer than its bulk clearance, suggesting that it may act locally in the lung. CONCLUSION Lcn1 can be reengineered into the Anticalin antagonist PRS-060 (elarekibep), exemplifying a new class of inhaled topical, long-acting therapeutic drugs with the potential to treat type 2 endotype asthma.
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Morales-Kastresana A, Siegemund M, Haak S, Peper-Gabriel J, Neiens V, Rothe C. Anticalin®-based therapeutics: Expanding new frontiers in drug development. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2022; 369:89-106. [PMID: 35777866 DOI: 10.1016/bs.ircmb.2022.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Anticalin proteins are a novel class of clinical-stage biopharmaceuticals with high potential in various disease areas. Anticalin proteins, derived from extracellular human lipocalins are single-chain proteins, with a highly stable structure that can be engineered to bind with high specificity and potency to targets of therapeutic relevance. The small size and stable structure support their development as inhalable biologics in the field of respiratory diseases as already demonstrated for PRS-060/AZD1402, an Anticalin protein currently undergoing clinical development for the treatment of asthma. Anticalin proteins provide formatting flexibility which allows fusion with the same or other Anticalin proteins, or with other biologics to generate multivalent, multiparatopic or multispecific fusion proteins. The fusion of Anticalin proteins to antibodies allows the generation of potent therapeutic proteins with new modes of action, such as antibody-Anticalin bispecific proteins with tumor-localized activity. Cinrebafusp alfa and PRS-344/S095012 antibody-Anticalin bispecific proteins were designed to reduce potential systemic toxicity by localizing the activity to the tumor, and are currently in clinical development in immuno-oncology. Furthermore, the ease in generating bi- and multispecifics as well as the small and stable structure prompted the investigation of Anticalin proteins for the CAR T space, opening additional potential treatment options based on Anticalin protein therapies.
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Affiliation(s)
| | | | - Stefan Haak
- Pieris Pharmaceuticals GmbH, Hallbergmoos, Germany
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Nassiri M, Behnam-Rasouli R, Vakili-Azghandi M, Gopalan V, Dolati P, Nourmohammadi R. Refined immunoRNases for the efficient targeting and selective killing of tumour cells: A novel strategy. Life Sci 2022; 289:120222. [PMID: 34902436 DOI: 10.1016/j.lfs.2021.120222] [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: 09/19/2021] [Revised: 11/13/2021] [Accepted: 12/05/2021] [Indexed: 11/18/2022]
Abstract
In order to overcome limitations of conventional cancer therapy methods, immunotoxins with the capability of target-specific action have been designed and evaluated pre-clinically, and some of them are in clinical studies. Targeting cancer cells via antibodies specific for tumour-associated surface proteins is a new biomedical approach that could provide the selectivity that is lacking in conventional cancer therapy methods such as radiotherapy and chemotherapy. A successful example of an approved immunotoxin is represented by immunoRNases. ImmunoRNases are fusion proteins in which the toxin has been replaced by a ribonuclease. Conjugation of RNase molecule to monoclonal antibody or antibody fragment was shown to enhance specific cell-killing by several orders of magnitude, both in vitro and in animal models. There are several RNases obtained from different mammalian cells that are expected to be less immunogenic and systemically toxic. In fact, RNases are pro-toxins which become toxic only upon their internalization in target cells mediated by the antibody moiety. The structure and large size of the antibody molecules assembled with the immunoRNases have always been a challenge in the application of immunoRNases as an antitoxin. To overcome this obstacle, we have offered a new strategy for the application of immunoRNases as a promising approach for upgrading immunoRNAses with maximum affinity and high stability in the cell, which can ultimately act as an effective large-scale cancer treatment. In this review, we introduce the optimized antibody-like molecules with small size, approximately 10 kD, which are presumed to significantly enhance RNase activity and be a suitable agent with the potential for anti-cancer functionality. In addition, we also discuss new molecular entities such as monobody, anticalin, nonobody and affilin as refined versions in the development of immunoRNases. These small molecules express their functionality with the suitable small size as well as with low immunogenicity in the cell, as a part of immunoRNases.
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Affiliation(s)
- Mohammadreza Nassiri
- Recombinant Proteins Research Group, The Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran; School of Life and Environmental Sciences, The University of Sydney, Sydney 2006, NSW, Australia.
| | - Reihane Behnam-Rasouli
- Recombinant Proteins Research Group, The Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Vinod Gopalan
- Cancer Molecular Pathology, School of Medicine, Griffith University, Gold Coast, Queensland 4222, Australia
| | - Peyman Dolati
- Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, Hobart, Tasmania, Australia
| | - Rouhollah Nourmohammadi
- Department of Animal Science, College of Agriculture, Lorestan University, Khorramabad, Lorestan 68137-17133, Iran
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Non-Antibody-Based Binders for the Enrichment of Proteins for Analysis by Mass Spectrometry. Biomolecules 2021; 11:biom11121791. [PMID: 34944435 PMCID: PMC8698613 DOI: 10.3390/biom11121791] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 02/07/2023] Open
Abstract
There is often a need to isolate proteins from body fluids, such as plasma or serum, prior to further analysis with (targeted) mass spectrometry. Although immunoglobulin or antibody-based binders have been successful in this regard, they possess certain disadvantages, which stimulated the development and validation of alternative, non-antibody-based binders. These binders are based on different protein scaffolds and are often selected and optimized using phage or other display technologies. This review focuses on several non-antibody-based binders in the context of enriching proteins for subsequent liquid chromatography-mass spectrometry (LC-MS) analysis and compares them to antibodies. In addition, we give a brief introduction to approaches for the immobilization of binders. The combination of non-antibody-based binders and targeted mass spectrometry is promising in areas, like regulated bioanalysis of therapeutic proteins or the quantification of biomarkers. However, the rather limited commercial availability of these binders presents a bottleneck that needs to be addressed.
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12
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Siegemund M, Oak P, Hansbauer EM, Allersdorfer A, Utschick K, Winter A, Grasmüller C, Galler G, Mayer JP, Weiche B, Prassler J, Kontermann RE, Rothe C. Pharmacokinetic Engineering of OX40-Blocking Anticalin Proteins Using Monomeric Plasma Half-Life Extension Domains. Front Pharmacol 2021; 12:759337. [PMID: 34759826 PMCID: PMC8573339 DOI: 10.3389/fphar.2021.759337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/04/2021] [Indexed: 12/26/2022] Open
Abstract
Anticalin® proteins have been proven as versatile clinical stage biotherapeutics. Due to their small size (∼20 kDa), they harbor a short intrinsic plasma half-life which can be extended, e.g., by fusion with IgG or Fc. However, for antagonism of co-immunostimulatory Tumor Necrosis Factor Receptor Superfamily (TNFRSF) members in therapy of autoimmune and inflammatory diseases, a monovalent, pharmacokinetically optimized Anticalin protein format that avoids receptor clustering and therefore potential activation is favored. We investigated the suitability of an affinity-improved streptococcal Albumin-Binding Domain (ABD) and the engineered Fab-selective Immunoglobulin-Binding Domain (IgBD) SpGC3Fab for plasma Half-Life Extension (HLE) of an OX40-specific Anticalin and bispecific Duocalin proteins, neutralizing OX40 and a second co-immunostimulatory TNFRSF member. The higher affinity of ABD fusion proteins to human serum albumin (HSA) and Mouse Serum Albumin (MSA), with a 4 to 5-order of magnitude lower KD compared with the binding affinity of IgBD fusions to human/mouse IgG, translated into longer terminal plasma half-lives (t1/2). Hence, the anti-OX40 Anticalin-ABD protein reached t1/2 values of ∼40 h in wild-type mice and 110 h in hSA/hFcRn double humanized mice, in contrast to ∼7 h observed for anti-OX40 Anticalin-IgBD in wild-type mice. The pharmacokinetics of an anti-OX40 Anticalin-Fc fusion protein was the longest in both models (t1/2 of 130 h and 146 h, respectively). Protein formats composed of two ABDs or IgBDs instead of one single HLE domain clearly showed longer presence in the circulation. Importantly, Anticalin-ABD and -IgBD fusions showed OX40 receptor binding and functional competition with OX40L-induced cellular reactivity in the presence of albumin or IgG, respectively. Our results suggest that fusion to ABD or IgBD can be a versatile platform to tune the plasma half-life of Anticalin proteins in response to therapeutic needs.
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Affiliation(s)
- Martin Siegemund
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Prajakta Oak
- Pieris Pharmaceuticals GmbH, Hallbergmoos, Germany
| | | | | | | | | | | | | | | | | | | | - Roland E Kontermann
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany.,Stuttgart Research Center Systems Biology, University of Stuttgart, Stuttgart, Germany
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13
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Frutiger A, Tanno A, Hwu S, Tiefenauer RF, Vörös J, Nakatsuka N. Nonspecific Binding-Fundamental Concepts and Consequences for Biosensing Applications. Chem Rev 2021; 121:8095-8160. [PMID: 34105942 DOI: 10.1021/acs.chemrev.1c00044] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nature achieves differentiation of specific and nonspecific binding in molecular interactions through precise control of biomolecules in space and time. Artificial systems such as biosensors that rely on distinguishing specific molecular binding events in a sea of nonspecific interactions have struggled to overcome this issue. Despite the numerous technological advancements in biosensor technologies, nonspecific binding has remained a critical bottleneck due to the lack of a fundamental understanding of the phenomenon. To date, the identity, cause, and influence of nonspecific binding remain topics of debate within the scientific community. In this review, we discuss the evolution of the concept of nonspecific binding over the past five decades based upon the thermodynamic, intermolecular, and structural perspectives to provide classification frameworks for biomolecular interactions. Further, we introduce various theoretical models that predict the expected behavior of biosensors in physiologically relevant environments to calculate the theoretical detection limit and to optimize sensor performance. We conclude by discussing existing practical approaches to tackle the nonspecific binding challenge in vitro for biosensing platforms and how we can both address and harness nonspecific interactions for in vivo systems.
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Affiliation(s)
- Andreas Frutiger
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Alexander Tanno
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Stephanie Hwu
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Raphael F Tiefenauer
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - János Vörös
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
| | - Nako Nakatsuka
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zürich, Zürich CH-8092, Switzerland
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14
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Bogen JP, Grzeschik J, Jakobsen J, Bähre A, Hock B, Kolmar H. Treating Bladder Cancer: Engineering of Current and Next Generation Antibody-, Fusion Protein-, mRNA-, Cell- and Viral-Based Therapeutics. Front Oncol 2021; 11:672262. [PMID: 34123841 PMCID: PMC8191463 DOI: 10.3389/fonc.2021.672262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/11/2021] [Indexed: 01/02/2023] Open
Abstract
Bladder cancer is a frequent malignancy and has a clinical need for new therapeutic approaches. Antibody and protein technologies came a long way in recent years and new engineering approaches were applied to generate innovative therapeutic entities with novel mechanisms of action. Furthermore, mRNA-based pharmaceuticals recently reached the market and CAR-T cells and viral-based gene therapy remain a major focus of biomedical research. This review focuses on the engineering of biologics, particularly therapeutic antibodies and their application in preclinical development and clinical trials, as well as approved monoclonal antibodies for the treatment of bladder cancer. Besides, newly emerging entities in the realm of bladder cancer like mRNA, gene therapy or cell-based therapeutics are discussed and evaluated. As many discussed molecules exhibit unique mechanisms of action based on innovative protein engineering, they reflect the next generation of cancer drugs. This review will shed light on the engineering strategies applied to develop these next generation treatments and provides deeper insights into their preclinical profiles, clinical stages, and ongoing trials. Furthermore, the distribution and expression of the targeted antigens and the intended mechanisms of action are elucidated.
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Affiliation(s)
- Jan P Bogen
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany.,Ferring Darmstadt Laboratory, Biologics Technology and Development, Darmstadt, Germany
| | - Julius Grzeschik
- Ferring Darmstadt Laboratory, Biologics Technology and Development, Darmstadt, Germany
| | - Joern Jakobsen
- Ferring Pharmaceuticals, International PharmaScience Center, Copenhagen, Denmark
| | - Alexandra Bähre
- Ferring Pharmaceuticals, International PharmaScience Center, Copenhagen, Denmark
| | - Björn Hock
- Global Pharmaceutical Research and Development, Ferring International Center S.A., Saint-Prex, Switzerland
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
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15
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Zhang S, Li X, Zhao S, Drobizhev M, Ai HW. A fast, high-affinity fluorescent serotonin biosensor engineered from a tick lipocalin. Nat Methods 2021; 18:258-261. [PMID: 33633410 DOI: 10.1038/s41592-021-01078-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 01/25/2021] [Indexed: 11/09/2022]
Abstract
Serotonin (5-HT) is an important signaling monoamine and neurotransmitter. We report structure-guided engineering of a green fluorescent, genetically encoded serotonin sensor (G-GESS) from a 5-HT-binding lipocalin in the soft tick Argas monolakensis. G-GESS shows fast response kinetics and high affinity, specificity, brightness and photostability. We used G-GESS to image 5-HT dynamics in cultured cells, brain slices and behaving mice.
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Affiliation(s)
- Shen Zhang
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA, USA.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.,Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Xinyu Li
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA, USA.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| | - Shengyu Zhao
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA, USA.,Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Mikhail Drobizhev
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, USA
| | - Hui-Wang Ai
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA, USA. .,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA. .,Department of Chemistry, University of Virginia, Charlottesville, VA, USA. .,The UVA Cancer Center, University of Virginia, Charlottesville, VA, USA.
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16
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Selection and characterisation of Affimers specific for CEA recognition. Sci Rep 2021; 11:744. [PMID: 33436840 PMCID: PMC7804248 DOI: 10.1038/s41598-020-80354-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023] Open
Abstract
Carcinoembryonic antigen (CEA) is the only blood based protein biomarker at present, used for preoperative screening of advanced colorectal cancer (CRC) patients to determine the appropriate curative treatments and post-surveillance screening for tumour recurrence. Current diagnostics for CRC detection have several limitations and development of a highly sensitive, specific and rapid diagnostic device is required. The majority of such devices developed to date are antibody-based and suffer from shortcomings including multimeric binding, cost and difficulties in mass production. To circumvent antibody-derived limitations, the present study focused on the development of Affimer proteins as a novel alternative binding reagent for CEA detection. Here, we describe the selection, from a phage display library, of Affimers specific to CEA protein. Characterization of three anti-CEA Affimers reveal that these bind specifically and selectively to protein epitopes of CEA from cell culture lysate and on fixed cells. Kinetic binding analysis by SPR show that the Affimers bind to CEA with high affinity and within the nM range. Therefore, they have substantial potential for used as novel affinity reagents in diagnostic imaging, targeted CRC therapy, affinity purification and biosensor applications.
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17
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Carrasco-López C, Zhao EM, Gil AA, Alam N, Toettcher JE, Avalos JL. Development of light-responsive protein binding in the monobody non-immunoglobulin scaffold. Nat Commun 2020; 11:4045. [PMID: 32792484 PMCID: PMC7427095 DOI: 10.1038/s41467-020-17837-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 07/13/2020] [Indexed: 12/24/2022] Open
Abstract
Monobodies are synthetic non-immunoglobulin customizable protein binders invaluable to basic and applied research, and of considerable potential as future therapeutics and diagnostic tools. The ability to reversibly control their binding activity to their targets on demand would significantly expand their applications in biotechnology, medicine, and research. Here we present, as proof-of-principle, the development of a light-controlled monobody (OptoMB) that works in vitro and in cells and whose affinity for its SH2-domain target exhibits a 330-fold shift in binding affinity upon illumination. We demonstrate that our αSH2-OptoMB can be used to purify SH2-tagged proteins directly from crude E. coli extract, achieving 99.8% purity and over 40% yield in a single purification step. By virtue of their ability to be designed to bind any protein of interest, OptoMBs have the potential to find new powerful applications as light-switchable binders of untagged proteins with the temporal and spatial precision afforded by light.
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Affiliation(s)
- César Carrasco-López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Evan M Zhao
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Agnieszka A Gil
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Nathan Alam
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA
| | - Jared E Toettcher
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, 08544, USA.
- Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, 08544, USA.
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18
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Pletneva NV, Goryacheva EA, Artemyev IV, Arkhipova SF, Pletnev VZ. Fluorescent Tags in Biology: Three-Dimensional Structure. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020040160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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A conformation-specific ON-switch for controlling CAR T cells with an orally available drug. Proc Natl Acad Sci U S A 2020; 117:14926-14935. [PMID: 32554495 PMCID: PMC7334647 DOI: 10.1073/pnas.1911154117] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Molecular ON-switches in which a chemical compound induces protein-protein interactions can allow cellular function to be controlled with small molecules. ON-switches based on clinically applicable compounds and human proteins would greatly facilitate their therapeutic use. Here, we developed an ON-switch system in which the human retinol binding protein 4 (hRBP4) of the lipocalin family interacts with engineered hRBP4 binders in a small molecule-dependent manner. Two different protein scaffolds were engineered to bind to hRBP4 when loaded with the orally available small molecule A1120. The crystal structure of an assembled ON-switch shows that the engineered binder specifically recognizes the conformational changes induced by A1120 in two loop regions of hRBP4. We demonstrate that this conformation-specific ON-switch is highly dependent on the presence of A1120, as demonstrated by an ∼500-fold increase in affinity upon addition of the small molecule drug. Furthermore, the ON-switch successfully regulated the activity of primary human CAR T cells in vitro. We anticipate that lipocalin-based ON-switches have the potential to be broadly applied for the safe pharmacological control of cellular therapeutics.
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20
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Generating therapeutic monoclonal antibodies to complex multi-spanning membrane targets: Overcoming the antigen challenge and enabling discovery strategies. Methods 2020; 180:111-126. [PMID: 32422249 DOI: 10.1016/j.ymeth.2020.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/21/2020] [Accepted: 05/13/2020] [Indexed: 12/17/2022] Open
Abstract
Complex integral membrane proteins, which are embedded in the cell surface lipid bilayer by multiple transmembrane spanning helices, encompass families of proteins which are important target classes for drug discovery. These protein families include G protein-coupled receptors, ion channels and transporters. Although these proteins have typically been targeted by small molecule drugs and peptides, the high specificity of monoclonal antibodies offers a significant opportunity to selectively modulate these target proteins. However, it remains the case that isolation of antibodies with desired pharmacological function(s) has proven difficult due to technical challenges in preparing membrane protein antigens suitable to support antibody drug discovery. In this review recent progress in defining strategies for generation of membrane protein antigens is outlined. We also highlight antibody isolation strategies which have generated antibodies which bind the membrane protein and modulate the protein function.
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21
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McCord JP, Grove TZ. Engineering repeat proteins of the immune system. Biopolymers 2020; 111:e23348. [PMID: 32031681 DOI: 10.1002/bip.23348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 08/30/2019] [Accepted: 09/06/2019] [Indexed: 11/06/2022]
Abstract
Limitations associated with immunoglobulins have motivated the search for novel binding scaffolds. Repeat proteins have emerged as one promising class of scaffolds, but often are limited to binding protein and peptide targets. An exception is the repeat proteins of the immune system, which have in recent years served as an inspiration for binding scaffolds which can bind glycans and other classes of biomolecule. Like other repeat proteins, these proteins can be very stable and have a monomeric mode of binding, with elongated and highly variable binding surfaces. The ability to target glycans and glycoproteins fill an important gap in current tools for research and biomedical applications.
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Affiliation(s)
- Jennifer P McCord
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, U.S.A
| | - Tijana Z Grove
- Department of Chemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, U.S.A.,Zarkovic Grove Consulting, LLC, Blacksburg, VA, U.S.A
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22
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Harnessing anti-idiotypic antibody alternatives to advance biotherapeutic pharmacokinetic assays. Bioanalysis 2020; 12:125-128. [DOI: 10.4155/bio-2019-0291] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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23
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Mazzarella L, Duso BA, Trapani D, Belli C, D'Amico P, Ferraro E, Viale G, Curigliano G. The evolving landscape of ‘next-generation’ immune checkpoint inhibitors: A review. Eur J Cancer 2019; 117:14-31. [DOI: 10.1016/j.ejca.2019.04.035] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 04/23/2019] [Accepted: 04/26/2019] [Indexed: 12/14/2022]
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24
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Thaler M, Luppa PB. Highly sensitive immunodiagnostics at the point of care employing alternative recognition elements and smartphones: hype, trend, or revolution? Anal Bioanal Chem 2019; 411:7623-7635. [PMID: 31236649 DOI: 10.1007/s00216-019-01974-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 05/31/2019] [Accepted: 06/11/2019] [Indexed: 10/26/2022]
Abstract
Immunodiagnostic tests performed at the point of care (POC) today usually employ antibodies for biorecognition and are read out either visually or with specialized equipment. Availability of alternative biorecognition elements with promising features as well as smartphone-based approaches for signal readout, however, challenge the described established configuration in terms of analytical performance and practicability. Assessing these developments' clinical relevance and their impact on POC immunodiagnostics is demanding. The first part of this review will therefore give an overview on suitable diagnostic biosensors based on alternative recognition elements (such as nucleic acid-based aptamers or engineered binding proteins) and exemplify advantages and drawbacks of these biomolecules on the base of selected assays. The second part of the review then focuses on smartphone-connected diagnostics and discusses the indispensable considerations required for successful future clinical POCT implementation. Together, the joint depiction of two of the most innovative and exciting developments in the field will enable the reader to cast a glance into the distant future of POC immunodiagnostics.
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Affiliation(s)
- Markus Thaler
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar der TU München, Ismaninger Str. 22, 81675, Munich, Germany
| | - Peter B Luppa
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar der TU München, Ismaninger Str. 22, 81675, Munich, Germany.
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25
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Hinner MJ, Aiba RSB, Jaquin TJ, Berger S, Dürr MC, Schlosser C, Allersdorfer A, Wiedenmann A, Matschiner G, Schüler J, Moebius U, Rothe C, Matis L, Olwill SA. Tumor-Localized Costimulatory T-Cell Engagement by the 4-1BB/HER2 Bispecific Antibody-Anticalin Fusion PRS-343. Clin Cancer Res 2019; 25:5878-5889. [DOI: 10.1158/1078-0432.ccr-18-3654] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 03/14/2019] [Accepted: 05/22/2019] [Indexed: 11/16/2022]
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26
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Agrawal N, Lehtonen SI, Uusi-Mäkelä M, Jain P, Viitala S, Määttä JAE, Kähkönen N, Azizi L, Riihimäki TA, Kulomaa MS, Johnson MS, Hytönen VP, Airenne TT. Molecular features of steroid-binding antidins and their use for assaying serum progesterone. PLoS One 2019; 14:e0212339. [PMID: 30785944 PMCID: PMC6382169 DOI: 10.1371/journal.pone.0212339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 01/31/2019] [Indexed: 11/23/2022] Open
Abstract
Chicken avidin (Avd) and streptavidin from Streptomyces avidinii are extensively used in bionanotechnology due to their extremely tight binding to biotin (Kd ~ 10−15 M for chicken Avd). We previously reported engineered Avds known as antidins, which have micro- to nanomolar affinities for steroids, non-natural ligands of Avd. Here, we report the 2.8 Å X-ray structure of the sbAvd-2 (I117Y) antidin co-crystallized with progesterone. We describe the creation of new synthetic phage display libraries and report the experimental as well as computational binding analysis of progesterone-binding antidins. We introduce a next-generation antidin with 5 nM binding affinity for progesterone, and demonstrate the use of antidins for measuring progesterone in serum samples. Our data give insights on how to engineer and alter the binding preferences of Avds and to develop better molecular tools for modern bionanotechnological applications.
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Affiliation(s)
- Nitin Agrawal
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Soili I. Lehtonen
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Meri Uusi-Mäkelä
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Purvi Jain
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sari Viitala
- University of Eastern Finland, School of Pharmacy, Kuopio, Finland
| | - Juha A. E. Määttä
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Niklas Kähkönen
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Latifeh Azizi
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Tiina A. Riihimäki
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Markku S. Kulomaa
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Mark S. Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Vesa P. Hytönen
- BioMediTech Institute and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Fimlab Laboratories, Tampere, Finland
- * E-mail: (TTA); (VPH)
| | - Tomi T. Airenne
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
- * E-mail: (TTA); (VPH)
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27
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Toxin Neutralization Using Alternative Binding Proteins. Toxins (Basel) 2019; 11:toxins11010053. [PMID: 30658491 PMCID: PMC6356946 DOI: 10.3390/toxins11010053] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 01/07/2019] [Accepted: 01/12/2019] [Indexed: 12/20/2022] Open
Abstract
Animal toxins present a major threat to human health worldwide, predominantly through snakebite envenomings, which are responsible for over 100,000 deaths each year. To date, the only available treatment against snakebite envenoming is plasma-derived antivenom. However, despite being key to limiting morbidity and mortality among snakebite victims, current antivenoms suffer from several drawbacks, such as immunogenicity and high cost of production. Consequently, avenues for improving envenoming therapy, such as the discovery of toxin-sequestering monoclonal antibodies against medically important target toxins through phage display selection, are being explored. However, alternative binding protein scaffolds that exhibit certain advantages compared to the well-known immunoglobulin G scaffold, including high stability under harsh conditions and low cost of production, may pose as possible low-cost alternatives to antibody-based therapeutics. There is now a plethora of alternative binding protein scaffolds, ranging from antibody derivatives (e.g., nanobodies), through rationally designed derivatives of other human proteins (e.g., DARPins), to derivatives of non-human proteins (e.g., affibodies), all exhibiting different biochemical and pharmacokinetic profiles. Undeniably, the high level of engineerability and potentially low cost of production, associated with many alternative protein scaffolds, present an exciting possibility for the future of snakebite therapeutics and merit thorough investigation. In this review, a comprehensive overview of the different types of binding protein scaffolds is provided together with a discussion on their relevance as potential modalities for use as next-generation antivenoms.
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28
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Using backbone-cyclized Cys-rich polypeptides as molecular scaffolds to target protein-protein interactions. Biochem J 2019; 476:67-83. [PMID: 30635453 DOI: 10.1042/bcj20180792] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/07/2018] [Accepted: 12/11/2018] [Indexed: 12/23/2022]
Abstract
The use of disulfide-rich backbone-cyclized polypeptides, as molecular scaffolds to design a new generation of bioimaging tools and drugs that are potent and specific, and thus might have fewer side effects than traditional small-molecule drugs, is gaining increasing interest among the scientific and in the pharmaceutical industries. Highly constrained macrocyclic polypeptides are exceptionally more stable to chemical, thermal and biological degradation and show better biological activity when compared with their linear counterparts. Many of these relatively new scaffolds have been also found to be highly tolerant to sequence variability, aside from the conserved residues forming the disulfide bonds, able to cross cellular membranes and modulate intracellular protein-protein interactions both in vitro and in vivo These properties make them ideal tools for many biotechnological applications. The present study provides an overview of the new developments on the use of several disulfide-rich backbone-cyclized polypeptides, including cyclotides, θ-defensins and sunflower trypsin inhibitor peptides, in the development of novel bioimaging reagents and therapeutic leads.
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29
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Bauvois B, Susin SA. Revisiting Neutrophil Gelatinase-Associated Lipocalin (NGAL) in Cancer: Saint or Sinner? Cancers (Basel) 2018; 10:cancers10090336. [PMID: 30231474 PMCID: PMC6162539 DOI: 10.3390/cancers10090336] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 09/13/2018] [Accepted: 09/15/2018] [Indexed: 12/13/2022] Open
Abstract
Human neutrophil gelatinase-associated lipocalin (NGAL) is a glycoprotein present in a wide variety of tissues and cell types. NGAL exists as a 25 kDa monomer, a 46 kDa homodimer (the most abundant form in healthy subjects) and a 130 kDa disulfide-linked heterodimer bound to latent matrix metalloproteinase-9. Dysregulated expression of NGAL in human malignancies suggests its value as a clinical marker. A growing body of evidence is highlighting NGAL’s paradoxical (i.e., both beneficial and detrimental) effects on cellular processes associated with tumor development (proliferation, survival, migration, invasion, and multidrug resistance). At least two distinct cell surface receptors are identified for NGAL. This review (i) summarizes our current knowledge of NGAL’s expression profiles in solid tumors and leukemias, and (ii) critically evaluates the beneficial and detrimental activities of NGAL having been documented in a diverse range of cancer-derived cell lines. A better understanding of the causal relationships between NGAL dysregulation and tumor development will require a fine analysis of the molecular aspects and biological role(s) of NGAL both in primary tumors and at different stages of disease. Having an accurate picture of NGAL’s contribution to tumor progression is a prerequisite for attempting to modulate this protein as a putative therapeutic target.
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Affiliation(s)
- Brigitte Bauvois
- INSERM UMRS 1138, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Centre de Recherche des Cordeliers, 75006 Paris, France.
- Sorbonne Universités Paris Cité, F-75006 Paris, France.
- Université Paris Descartes, F-75005 Paris, France.
| | - Santos A Susin
- INSERM UMRS 1138, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Centre de Recherche des Cordeliers, 75006 Paris, France.
- Sorbonne Universités Paris Cité, F-75006 Paris, France.
- Université Paris Descartes, F-75005 Paris, France.
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30
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Könning D, Kolmar H. Beyond antibody engineering: directed evolution of alternative binding scaffolds and enzymes using yeast surface display. Microb Cell Fact 2018; 17:32. [PMID: 29482656 PMCID: PMC6389260 DOI: 10.1186/s12934-018-0881-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/22/2018] [Indexed: 01/08/2023] Open
Abstract
Pioneered exactly 20 years ago, yeast surface display (YSD) continues to take a major role in protein engineering among the high-throughput display methodologies that have been developed to date. The classical yeast display technology relies on tethering an engineered protein to the cell wall by genetic fusion to one subunit of a dimeric yeast-mating agglutination receptor complex. This method enables an efficient genotype-phenotype linkage while exploiting the benefits of a eukaryotic expression machinery. Over the past two decades, a plethora of protein engineering efforts encompassing conventional antibody Fab and scFv fragments have been reported. In this review, we will focus on the versatility of YSD beyond conventional antibody engineering and, instead, place the focus on alternative scaffold proteins and enzymes which have successfully been tailored for purpose with regard to improving binding, activity or specificity.
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Affiliation(s)
- Doreen Könning
- Antibody-Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287 Darmstadt, Germany
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Alarich-Weiss-Strasse 4, 64287 Darmstadt, Germany
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31
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Masuda Y, Yamaguchi S, Suzuki C, Aburatani T, Nagano Y, Miyauchi R, Suzuki E, Yamamura N, Nagatomo K, Ishihara H, Okuno K, Nara F, Matschiner G, Hashimoto R, Takahashi T, Nishizawa T. Generation and Characterization of a Novel Small Biologic Alternative to Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) Antibodies, DS-9001a, Albumin Binding Domain–Fused Anticalin Protein. J Pharmacol Exp Ther 2018; 365:368-378. [DOI: 10.1124/jpet.117.246652] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 02/15/2018] [Indexed: 01/06/2023] Open
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32
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Abstract
Antibodies have proved to be a valuable mode of therapy for numerous diseases, mainly owing to their high target binding affinity and specificity. Unfortunately, antibodies are also limited in several respects, chief amongst those being the extremely high cost of manufacture. Therefore, non-antibody binding proteins have long been sought after as alternative therapies. New binding protein scaffolds are constantly being designed or discovered with some already approved for human use by the FDA. This review focuses on protein scaffolds that are either already being used in humans or are currently being evaluated in clinical trials. Although not all are expected to be approved, the significant benefits ensure that these molecules will continue to be investigated and developed as therapeutic alternatives to antibodies. Based on the location of the amino acids that mediate ligand binding, we place all the protein scaffolds under clinical development into two general categories: scaffolds with ligand-binding residues located in exposed flexible loops, and those with the binding residues located in protein secondary structures, such as α-helices. Scaffolds that fall under the first category include adnectins, anticalins, avimers, Fynomers, Kunitz domains, and knottins, while those belonging to the second category include affibodies, β-hairpin mimetics, and designed ankyrin repeat proteins (DARPins). Most of these scaffolds are thermostable and can be easily produced in microorganisms or completely synthesized chemically. In addition, many of these scaffolds derive from human proteins and thus possess very low immunogenic potential. Additional advantages and limitations of these protein scaffolds as therapeutics compared to antibodies will be discussed.
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Affiliation(s)
- Rudo Simeon
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, TX, 77845, USA
| | - Zhilei Chen
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, TX, 77845, USA.
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33
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Synthetic integrin-binding immune stimulators target cancer cells and prevent tumor formation. Sci Rep 2017; 7:17592. [PMID: 29242512 PMCID: PMC5730604 DOI: 10.1038/s41598-017-17627-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 11/28/2017] [Indexed: 01/03/2023] Open
Abstract
Immuno-oncology approaches mainly utilize monoclonal antibodies or protein-based scaffolds that bind with high affinity to cancer cells and can generate an immune response. Peptides can also bind with high affinity to cancer cells and are intermediate in size between antibodies and small molecules. They are also synthetically accessible and therefore easily modified to optimize their stability, binding affinity and selectivity. Here we describe the design of immune system engagers (ISErs), a novel class of synthetic peptide-based compounds that bind specifically to cancer cells and stimulate the immune system. A prototype, Y9, targets integrin α3, which is overexpressed on several cancer cells, and activates the immune system via a formyl methionine-containing effector peptide. Injection of Y9 leads to immune cell infiltration into tissue and prevents tumor formation in a guinea pig model. The anti-tumor activity and synthetic accessibility of Y9 illustrate that ISErs could be applied to a wide variety of targets and diseases.
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34
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Friedrich L, Kornberger P, Mendler CT, Multhoff G, Schwaiger M, Skerra A. Selection of an Anticalin® against the membrane form of Hsp70 via bacterial surface display and its theranostic application in tumour models. Biol Chem 2017; 399:235-252. [DOI: 10.1515/hsz-2017-0207] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/23/2017] [Indexed: 01/08/2023]
Abstract
Abstract
We describe the selection of Anticalins against a common tumour surface antigen, human Hsp70, using functional display on live Escherichia coli cells as fusion with a truncated EspP autotransporter. While found intracellularly in normal cells, Hsp70 is frequently exposed in a membrane-bound state on the surface of tumour cells and, even more pronounced, in metastases or after radiochemotherapy. Employing a recombinant Hsp70 fragment comprising residues 383-548 as the target, Anticalins were selected from a naïve bacterial library. The Anticalin with the highest affinity (K
D=13 nm), as determined towards recombinant full-length Hsp70 by real-time surface plasmon resonance analysis, was improved to K
D=510 pm by doped random mutagenesis and another cycle of E. coli surface display, followed by rational combination of mutations. This Anticalin, which recognises a linear peptide epitope located in the interdomain linker of Hsp70, was demonstrated to specifically bind Hsp70 in its membrane-associated form in immunofluorescence microscopy and via flow cytometry using the FaDu cell line, which is positive for surface Hsp70. The radiolabelled and PASylated Anticalin revealed specific tumour accumulation in xenograft mice using positron emission tomography (PET) imaging. Furthermore, after enzymatic coupling to the protein toxin gelonin, the Anticalin showed potent cytotoxicity on FaDu cells in vitro.
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Affiliation(s)
- Lars Friedrich
- Munich Center for Integrated Protein Science, CIPS-M, and Lehrstuhl für Biologische Chemie , Technische Universität München , D-85354 Freising (Weihenstephan) , Germany
| | - Petra Kornberger
- Munich Center for Integrated Protein Science, CIPS-M, and Lehrstuhl für Biologische Chemie , Technische Universität München , D-85354 Freising (Weihenstephan) , Germany
| | - Claudia T. Mendler
- Munich Center for Integrated Protein Science, CIPS-M, and Lehrstuhl für Biologische Chemie , Technische Universität München , D-85354 Freising (Weihenstephan) , Germany
| | - Gabriele Multhoff
- Department of Radiation Oncology , Klinikum rechts der Isar, Technische Universität München , D-81675 München , Germany
| | - Markus Schwaiger
- Department of Nuclear Medicine, Klinikum rechts der Isar , Technische Universität München , D-81675 München , Germany
| | - Arne Skerra
- Munich Center for Integrated Protein Science, CIPS-M, and Lehrstuhl für Biologische Chemie , Technische Universität München , D-85354 Freising (Weihenstephan) , Germany
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35
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Recent advances in the development of novel protein scaffolds based therapeutics. Int J Biol Macromol 2017; 102:630-641. [DOI: 10.1016/j.ijbiomac.2017.04.045] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 12/21/2022]
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36
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Koch J, Tesar M. Recombinant Antibodies to Arm Cytotoxic Lymphocytes in Cancer Immunotherapy. Transfus Med Hemother 2017; 44:337-350. [PMID: 29070979 PMCID: PMC5649249 DOI: 10.1159/000479981] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 08/01/2017] [Indexed: 12/18/2022] Open
Abstract
Immunotherapy has the potential to support and expand the body's own armamentarium of immune effector functions, which have been circumvented during malignant transformation and establishment of cancer and is presently considered to be the most promising treatment option for cancer patients. Recombinant antibody technologies have led to a multitude of novel antibody formats, which are in clinical development and hold great promise for future therapies. Among these formats, bispecific antibodies are extremely versatile due to their high efficacy to recruit and activate anti-tumoral immune effector cells, their excellent safety profile, and the opportunity for use in combination with cellular therapies. This review article summarizes the latest developments in cancer immunotherapy using immuno-engagers for recruiting T cells and NK cells to the tumor site. In addition to antibody formats, malignant cell targets, and immune cell targets, opportunities for combination therapies, including check point inhibitors, cytokines and adoptive transfer of immune cells, will be summarized and discussed.
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Affiliation(s)
- Joachim Koch
- Affimed GmbH, Technologiepark, Heidelberg, Germany
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37
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Bozhanova NG, Baranov MS, Klementieva NV, Sarkisyan KS, Gavrikov AS, Yampolsky IV, Zagaynova EV, Lukyanov SA, Lukyanov KA, Mishin AS. Protein labeling for live cell fluorescence microscopy with a highly photostable renewable signal. Chem Sci 2017; 8:7138-7142. [PMID: 29147545 PMCID: PMC5676496 DOI: 10.1039/c7sc01628j] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/01/2017] [Indexed: 11/21/2022] Open
Abstract
A novel method of protein labeling uses the highly dynamic reversible association of a cell-permeable fluorogenic dye and lipocalin Blc mutants.
We present protein-PAINT – the implementation of the general principles of PAINT (Point Accumulation for Imaging in Nanoscale Topography) for live-cell protein labeling. Our method employs the specific binding of cell-permeable fluorogenic dyes to genetically encoded protein tags. We engineered three mutants of the bacterial lipocalin Blc that possess different affinities to a fluorogenic dye and exhibit a strong increase in fluorescence intensity upon binding. This allows for rapid labeling and washout of intracellular targets on a time scale from seconds to a few minutes. We demonstrate an order of magnitude higher photostability of the fluorescence signal in comparison with spectrally similar fluorescent proteins. Protein-PAINT ensures prolonged super-resolution fluorescence microscopy of living cells in both single molecule detection and stimulated emission depletion regimes.
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Affiliation(s)
- Nina G Bozhanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia
| | - Mikhail S Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia .
| | | | - Karen S Sarkisyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Centre for Genomic Regulation (CRG) , The Barcelona Institute for Science and Technology , Dr Aiguader 88 , 08003 Barcelona , Spain
| | - Alexey S Gavrikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia .
| | - Ilia V Yampolsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Pirogov Russian National Research Medical University , Moscow , Russia
| | | | - Sergey A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia.,Pirogov Russian National Research Medical University , Moscow , Russia
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Moscow , Russia . .,Nizhny Novgorod State Medical Academy , Nizhny Novgorod , Russia
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38
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Khan KH, Himeno A, Kosugi S, Nakashima Y, Rafique A, Imamura A, Hatanaka T, Kato DI, Ito Y. IgY-binding peptide screened from a random peptide library as a ligand for IgY purification. J Pept Sci 2017; 23:790-797. [PMID: 28758361 PMCID: PMC5637892 DOI: 10.1002/psc.3027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/22/2017] [Accepted: 07/01/2017] [Indexed: 01/29/2023]
Abstract
Chicken egg yolk immunoglobulin (IgY) is a functional substitute for mammalian IgG for antigen detection. Traditional IgY purification methods involve multi-step procedures resulting in low purity and recovery of IgY. In this study, we developed a simple IgY purification system using IgY-specific peptides identified by T7 phage display technology. From disulfide-constrained random peptide libraries constructed on a T7 phage, we identified three specific binding clones (Y4-4, Y5-14, and Y5-55) through repeated biopanning. The synthetic peptides showed high binding specificity to IgY-Fc and moderate affinity for IgY-Fc (Kd : Y4-4 = 7.3 ± 0.2 μM and Y5-55 = 4.4 ± 0.1 μM) by surface plasmon resonance analysis. To evaluate the ability to purify IgY, we performed immunoprecipitation and affinity high-performance liquid chromatography using IgY-binding peptides; the result indicated that these peptides can be used as affinity ligands for IgY purification. We then used a peptide-conjugated column to purify IgY from egg yolks pre-treated using an optimized delipidation technique. Here, we report the construction of a cost-effective, one-step IgY purification system, with high purity and recovery. © 2017 The Authors. Journal of Peptide Science published by European Peptide Society and John Wiley & Sons Ltd.
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Affiliation(s)
- Kamrul Hasan Khan
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Arisa Himeno
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Shouhei Kosugi
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Yosuke Nakashima
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Abdur Rafique
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Ayana Imamura
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Takaaki Hatanaka
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Dai-Ichiro Kato
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
| | - Yuji Ito
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima, 890-0065, Japan
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39
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Abstract
Biosensors that depend on a physical or chemical measurement can be adversely affected by non-specific interactions. For example, a biosensor designed to measure specifically the levels of a rare analyte can give false positive results if there is even a small amount of interaction with a highly abundant but irrelevant molecule. To overcome this limitation, the biosensor community has frequently turned to antibody molecules as recognition elements because they are renowned for their exquisite specificity. Unfortunately antibodies can often fail when immobilised on inorganic surfaces, and alternative biological recognition elements are needed. This article reviews the available non-antibody-binding proteins that have been successfully used in electrical and micro-mechanical biosensor platforms.
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40
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Burgess RR. Gentle antibody-mimetic affinity chromatography with polyol-responsive nanoCLAMPs. Protein Expr Purif 2017. [PMID: 28633910 DOI: 10.1016/j.pep.2017.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Richard R Burgess
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, United States
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41
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Development of polyol-responsive antibody mimetics for single-step protein purification. Protein Expr Purif 2017; 134:114-124. [DOI: 10.1016/j.pep.2017.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 04/13/2017] [Accepted: 04/15/2017] [Indexed: 12/11/2022]
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42
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Shafaei Z, Ghalandari B, Vaseghi A, Divsalar A, Haertlé T, Saboury AA, Sawyer L. β-Lactoglobulin: An efficient nanocarrier for advanced delivery systems. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2017; 13:1685-1692. [PMID: 28343017 DOI: 10.1016/j.nano.2017.03.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 02/18/2017] [Accepted: 03/14/2017] [Indexed: 01/10/2023]
Abstract
Thanks to the progress of nanotechnology there are several agent-delivery systems that can be selected to achieve rapid and specific delivery of a wide variety of biologically active agents. Consequently, the manipulation and engineering of biopolymers has become one of the most exciting subjects for those who study delivery systems on the nanoscale. In this regard, both nanoparticle formation and a carrier role have been observed in the case of the globular milk whey protein, β-lactoglobulin (β-LG), setting it apart from many other proteins. To date, many efforts adopting different approaches have created β-LG nanoparticles useful in forming delivery systems for various agents with specific targets. In this review, the potential of β-LG to play the role of an efficient and diverse carrier protein, as well as its ability to form a well-targeted nano-scale delivery system is discussed.
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Affiliation(s)
- Zahra Shafaei
- Department of Cell and Molecular Biology' Faculty of Biological Sciences' Kharazmi University, Tehran, Iran
| | - Behafarid Ghalandari
- Applied Biophotonics Research Center, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Akbar Vaseghi
- Department of Biotechnology, Faculty of Advanced Science and Technologies of Isfahan, Isfahan, Iran
| | - Adeleh Divsalar
- Department of Cell and Molecular Biology' Faculty of Biological Sciences' Kharazmi University, Tehran, Iran.
| | - Thomas Haertlé
- FIP, BIA UR1268, Institut National de la Recherche Agronomique, Nantes, France
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics' University of Tehran, Tehran, Iran; Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran
| | - Lindsay Sawyer
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
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43
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Abstract
In spite of their widespread applications as therapeutic, diagnostic, and detection agents, the limitations of polyclonal and monoclonal antibodies have enthused scientists to plan for next-generation biomedical agents, the so-called antibody mimetics, which offer many advantages compared to traditional antibodies. Antibody mimetics could be designed through protein-directed evolution or fusion of complementarity-determining regions with intervening framework regions. In the recent decade, extensive progress has been made in exploiting human, butterfly (Pieris brassicae), and bacterial systems to design and select mimetics using display technologies. Notably, some of the mimetics have made their way to market. Numerous limitations lie ahead in developing mimetics for different biomedical usage, particularly for which conventional antibodies are ineffective. This chapter presents a brief overview of the current characteristics, construction, and applications of antibody mimetics.
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44
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Traxlmayr MW, Kiefer JD, Srinivas RR, Lobner E, Tisdale AW, Mehta NK, Yang NJ, Tidor B, Wittrup KD. Strong Enrichment of Aromatic Residues in Binding Sites from a Charge-neutralized Hyperthermostable Sso7d Scaffold Library. J Biol Chem 2016; 291:22496-22508. [PMID: 27582495 PMCID: PMC5077188 DOI: 10.1074/jbc.m116.741314] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 08/23/2016] [Indexed: 11/06/2022] Open
Abstract
The Sso7d protein from the hyperthermophilic archaeon Sulfolobus solfataricus is an attractive binding scaffold because of its small size (7 kDa), high thermal stability (Tm of 98 °C), and absence of cysteines and glycosylation sites. However, as a DNA-binding protein, Sso7d is highly positively charged, introducing a strong specificity constraint for binding epitopes and leading to nonspecific interaction with mammalian cell membranes. In the present study, we report charge-neutralized variants of Sso7d that maintain high thermal stability. Yeast-displayed libraries that were based on this reduced charge Sso7d (rcSso7d) scaffold yielded binders with low nanomolar affinities against mouse serum albumin and several epitopes on human epidermal growth factor receptor. Importantly, starting from a charge-neutralized scaffold facilitated evolutionary adaptation of binders to differentially charged epitopes on mouse serum albumin and human epidermal growth factor receptor, respectively. Interestingly, the distribution of amino acids in the small and rigid binding surface of enriched rcSso7d-based binders is very different from that generally found in more flexible antibody complementarity-determining region loops but resembles the composition of antibody-binding energetic hot spots. Particularly striking was a strong enrichment of the aromatic residues Trp, Tyr, and Phe in rcSso7d-based binders. This suggests that the rigidity and small size of this scaffold determines the unusual amino acid composition of its binding sites, mimicking the energetic core of antibody paratopes. Despite the high frequency of aromatic residues, these rcSso7d-based binders are highly expressed, thermostable, and monomeric, suggesting that the hyperstability of the starting scaffold and the rigidness of the binding surface confer a high tolerance to mutation.
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Affiliation(s)
- Michael W Traxlmayr
- From the Koch Institute for Integrative Cancer Research and .,Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 and
| | | | | | - Elisabeth Lobner
- Department of Chemistry, Division of Biochemistry, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Alison W Tisdale
- From the Koch Institute for Integrative Cancer Research and.,Departments of Biological Engineering and
| | - Naveen K Mehta
- From the Koch Institute for Integrative Cancer Research and.,Departments of Biological Engineering and
| | - Nicole J Yang
- From the Koch Institute for Integrative Cancer Research and.,Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 and
| | | | - K Dane Wittrup
- From the Koch Institute for Integrative Cancer Research and .,Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 and.,Departments of Biological Engineering and
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45
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Iron deficiency or anemia of inflammation? : Differential diagnosis and mechanisms of anemia of inflammation. Wien Med Wochenschr 2016; 166:411-423. [PMID: 27557596 PMCID: PMC5065583 DOI: 10.1007/s10354-016-0505-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 05/30/2016] [Indexed: 02/08/2023]
Abstract
Iron deficiency and immune activation are the two most frequent causes of anemia, both of which are based on disturbances of iron homeostasis. Iron deficiency anemia results from a reduction of the body’s iron content due to blood loss, inadequate dietary iron intake, its malabsorption, or increased iron demand. Immune activation drives a diversion of iron fluxes from the erythropoietic bone marrow, where hemoglobinization takes place, to storage sites, particularly the mononuclear phagocytes system in liver and spleen. This results in iron-limited erythropoiesis and anemia. This review summarizes current diagnostic and pathophysiological concepts of iron deficiency anemia and anemia of inflammation, as well as combined conditions, and provides a brief outlook on novel therapeutic options.
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46
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Abstract
Advances in protein engineering tools, both computational and experimental, has afforded many new protein structures and functions. Here, we present a snapshot of repeat-protein engineering efforts towards new, versatile, alternative binding scaffolds for use in analytical sensors and as imaging agents. Analytical assays, sensors and imaging agents based on the direct binding of analyte are increasingly important for research and diagnostics in medicine, food safety, and national security.
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47
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Huang R, Kiss MM, Batonick M, Weiner MP, Kay BK. Generating Recombinant Antibodies to Membrane Proteins through Phage Display. Antibodies (Basel) 2016; 5:antib5020011. [PMID: 31557992 PMCID: PMC6698964 DOI: 10.3390/antib5020011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 04/21/2016] [Accepted: 04/21/2016] [Indexed: 01/03/2023] Open
Abstract
One of the most important classes of proteins in terms of drug targets is cell surface membrane proteins, and yet it is a challenging set of proteins for generating high-quality affinity reagents. In this review, we focus on the use of phage libraries, which display antibody fragments, for generating recombinant antibodies to membrane proteins. Such affinity reagents generally have high specificity and affinity for their targets. They have been used for cell staining, for promoting protein crystallization to solve three-dimensional structures, for diagnostics, and for treating diseases as therapeutics. We cover publications on this topic from the past 10 years, with a focus on the various formats of membrane proteins for affinity selection and the diverse affinity selection strategies used. Lastly, we discuss the challenges faced in this field and provide possible directions for future efforts.
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Affiliation(s)
- Renhua Huang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607-7060, USA.
| | - Margaret M Kiss
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Melissa Batonick
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Michael P Weiner
- AxioMx Inc., a subsidiary of Abcam Plc, Branford, CT 06405, USA.
| | - Brian K Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607-7060, USA.
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Huang R, Fang P, Hao Z, Kay BK. Directed Evolution of a Highly Specific FN3 Monobody to the SH3 Domain of Human Lyn Tyrosine Kinase. PLoS One 2016; 11:e0145872. [PMID: 26731115 PMCID: PMC4701441 DOI: 10.1371/journal.pone.0145872] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 12/09/2015] [Indexed: 11/26/2022] Open
Abstract
Affinity reagents of high affinity and specificity are very useful for studying the subcellular locations and quantities of individual proteins. To generate high-quality affinity reagents for human Lyn tyrosine kinase, a phage display library of fibronectin type III (FN3) monobodies was affinity selected with a recombinant form of the Lyn SH3 domain. While a highly specific monobody, TA8, was initially isolated, we chose to improve its affinity through directed evolution. A secondary library of 1.2 × 109 variants was constructed and screened by affinity selection, yielding three variants, two of which have affinities of ~ 40 nM, a 130-fold increase over the original TA8 monobody. One of the variants, 2H7, displayed high specificity to the Lyn SH3 domain, as shown by ELISA and probing arrays of 150 SH3 domains. Furthermore, the 2H7 monobody was able to pull down endogenous Lyn from a lysate of Burkitt's lymphoma cells, thereby demonstrating its utility as an affinity reagent for detecting Lyn in a complex biological mixture.
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Affiliation(s)
- Renhua Huang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail: (RH); (BK)
| | - Pete Fang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Zengping Hao
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Brian K. Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail: (RH); (BK)
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Engineered β-Lactoglobulin Produced in E. coli: Purification, Biophysical and Structural Characterisation. Mol Biotechnol 2016; 58:605-618. [PMID: 27380951 PMCID: PMC5035327 DOI: 10.1007/s12033-016-9960-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Functional recombinant bovine β-lactoglobulin has been produced by expression in E. coli using an engineered protein gene and purified to homogeneity by applying a new protocol. Mutations L1A/I2S introduced into the protein sequence greatly facilitate in vivo cleavage of the N-terminal methionine, allowing correctly folded and soluble protein suitable for biochemical, biophysical and structural studies to be obtained. The use of gel filtration on Sephadex G75 at the last purification step enables protein without endogenous ligand to be obtained. The physicochemical properties of recombinant β-lactoglobulin such as CD spectra, ligand binding (n, K a, ΔH, TΔS, ΔG), chemical and thermal stability (ΔG D, C mid) and crystal structure confirmed that the protein obtained is almost identical to the natural one. The substitutions of N-terminal residues did not influence the binding properties of the recombinant protein so that the lactoglobulin produced and purified according to our protocol is a good candidate for further engineering and potential use in pharmacology and medicine.
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Bieli D, Alborelli I, Harmansa S, Matsuda S, Caussinus E, Affolter M. Development and Application of Functionalized Protein Binders in Multicellular Organisms. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2016; 325:181-213. [DOI: 10.1016/bs.ircmb.2016.02.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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