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Li SJ, Wu YL, Chen JH, Shen SY, Duan J, Xu HE. Autoimmune diseases: targets, biology, and drug discovery. Acta Pharmacol Sin 2024; 45:674-685. [PMID: 38097717 PMCID: PMC10943205 DOI: 10.1038/s41401-023-01207-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 11/20/2023] [Indexed: 03/17/2024] Open
Abstract
Autoimmune diseases (AIDs) arise from a breakdown in immunological self-tolerance, wherein the adaptive immune system mistakenly attacks healthy cells, tissues and organs. AIDs impose excessive treatment costs and currently rely on non-specific and universal immunosuppression, which only offer symptomatic relief without addressing the underlying causes. AIDs are driven by autoantigens, targeting the autoantigens holds great promise in transforming the treatment of these diseases. To achieve this goal, a comprehensive understanding of the pathogenic mechanisms underlying different AIDs and the identification of specific autoantigens are critical. In this review, we categorize AIDs based on their underlying causes and compile information on autoantigens implicated in each disease, providing a roadmap for the development of novel immunotherapy regimens. We will focus on type 1 diabetes (T1D), which is an autoimmune disease characterized by irreversible destruction of insulin-producing β cells in the Langerhans islets of the pancreas. We will discuss insulin as possible autoantigen of T1D and its role in T1D pathogenesis. Finally, we will review current treatments of TID and propose a potentially effective immunotherapy targeting autoantigens.
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Affiliation(s)
- Shu-Jie Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- Department of Traditional Chinese Medicine, Fujian Medical University Union Hospital, Fuzhou, 350000, China.
| | - Yan-Li Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Juan-Hua Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Shi-Yi Shen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jia Duan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China.
| | - H Eric Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- School of Life Science and Technology, Shanghai Tech University, Shanghai, 201210, China.
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2
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Campbell E, Luxton T, Kohl D, Goodchild SA, Walti C, Jeuken LJC. Chimeric Protein Switch Biosensors. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:1-35. [PMID: 38273207 DOI: 10.1007/10_2023_241] [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: 01/27/2024]
Abstract
Rapid detection of protein and small-molecule analytes is a valuable technique across multiple disciplines, but most in vitro testing of biological or environmental samples requires long, laborious processes and trained personnel in laboratory settings, leading to long wait times for results and high expenses. Fusion of recognition with reporter elements has been introduced to detection methods such as enzyme-linked immunoassays (ELISA), with enzyme-conjugated secondary antibodies removing one of the many incubation and wash steps. Chimeric protein switch biosensors go further and provide a platform for homogenous mix-and-read assays where long wash and incubation steps are eradicated from the process. Chimeric protein switch biosensors consist of an enzyme switch (the reporter) coupled to a recognition element, where binding of the analyte results in switching the activity of the reporter enzyme on or off. Several chimeric protein switch biosensors have successfully been developed for analytes ranging from small molecule drugs to large protein biomarkers. There are two main formats of chimeric protein switch biosensor developed, one-component and multi-component, and these formats exhibit unique advantages and disadvantages. Genetically fusing a recognition protein to the enzyme switch has many advantages in the production and performance of the biosensor. A range of immune and synthetic binding proteins have been developed as alternatives to antibodies, including antibody mimetics or antibody fragments. These are mainly small, easily manipulated proteins and can be genetically fused to a reporter for recombinant expression or manipulated to allow chemical fusion. Here, aspects of chimeric protein switch biosensors will be reviewed with a comparison of different classes of recognition elements and switching mechanisms.
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Affiliation(s)
- Emma Campbell
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Timothy Luxton
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | - Declan Kohl
- School of Biomedical Sciences, University of Leeds, Leeds, UK
| | | | - Christoph Walti
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK
| | - Lars J C Jeuken
- School of Biomedical Sciences, University of Leeds, Leeds, UK.
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
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3
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Campbell E, Adamson H, Kohl D, Tiede C, Wälti C, Tomlinson DC, Jeuken LJC. Enzyme - Switch sensors for therapeutic drug monitoring of immunotherapies. Biosens Bioelectron 2023; 237:115488. [PMID: 37419072 PMCID: PMC10427837 DOI: 10.1016/j.bios.2023.115488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/19/2023] [Accepted: 06/16/2023] [Indexed: 07/09/2023]
Abstract
Therapeutic monoclonal antibodies (TmAb) have emerged as effective treatments for a number of cancers and autoimmune diseases. However, large interpatient disparities in the pharmacokinetics of TmAb treatment requires close therapeutic drug monitoring (TDM) to optimise dosage for individual patients. Here we demonstrate an approach for achieving rapid, sensitive quantification of two monoclonal antibody therapies using a previously described enzyme switch sensor platform. The enzyme switch sensor consists of a β-lactamase - β-lactamase inhibitor protein (BLA-BLIP) complex with two anti-idiotype binding proteins (Affimer proteins) as recognition elements. The BLA-BLIP sensor was engineered to detect two TmAbs (trastuzumab and ipilimumab) by developing constructs incorporating novel synthetic binding reagents to each of these mAbs. Trastuzumab and ipilimumab were successfully monitored with sub nM sensitivity in up to 1% serum, thus covering the relevant therapeutic range. Despite the modular design, the BLA-BLIP sensor was unsuccessful in detecting two further TmAbs (rituximab and adalimumab), an explanation for which was explored. In conclusion, the BLA-BLIP sensors provide a rapid biosensor for TDM of trastuzumab and ipilimumab with the potential to improve therapy. The sensitivity of this platform alongside its rapid action would be suitable for bedside monitoring in a point-of-care (PoC) setting.
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Affiliation(s)
- Emma Campbell
- School of Biomedical Science, University of Leeds, Leeds, LS2 9JT, United Kingdom; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, United Kingdom
| | - Hope Adamson
- School of Biomedical Science, University of Leeds, Leeds, LS2 9JT, United Kingdom; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, United Kingdom
| | - Declan Kohl
- School of Biomedical Science, University of Leeds, Leeds, LS2 9JT, United Kingdom; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, United Kingdom
| | - Christian Tiede
- Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, United Kingdom; School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Christoph Wälti
- School of Electronic and Electrical Engineering, University of Leeds, LS2 9JT, United Kingdom
| | - Darren C Tomlinson
- Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, United Kingdom; School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Lars J C Jeuken
- School of Biomedical Science, University of Leeds, Leeds, LS2 9JT, United Kingdom; Astbury Centre for Structural Molecular Biology, University of Leeds, LS2 9JT, United Kingdom; Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA, Leiden, the Netherlands.
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4
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Sekhon H, Ha JH, Loh SN. Engineering protein and DNA tools for creating DNA-dependent protein switches. Methods Enzymol 2022; 675:1-32. [PMID: 36220266 PMCID: PMC10314797 DOI: 10.1016/bs.mie.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Switchable proteins are capable of changing conformations from inactive (OFF) to active (ON) forms in response to inputs such as ligand binding, pH or temperature change, or light absorption. A particularly powerful class of protein switches, exemplified by the Cas nucleases of CRISPR systems, are activated by binding of specific DNA or RNA sequences. The mechanism by which oligonucleotide binding regulates biological activity is complex and highly specialized in the case of Cas enzymes, but recent advancements in protein and DNA engineering have made it possible to introduce this mode of control into other enzymes. This chapter highlights recent examples of protein switches that combine these two fields of engineering for the purpose of creating biosensors that detect pathogen and other genomic sequences. One protein engineering method-alternate frame folding-has the potential to convert many proteins into ligand-activated switches by inserting a binding protein (input domain) into an enzyme (output domain). The steps for doing so are illustrated using GCN4 as a DNA recognition domain and nanoluciferase as a luminescent reporter that changes color as a result of DNA binding. DNA engineering protocols are included for creating DNA tools (de novo designed hairpins and modified aptamers), that enable the biosensor to be activated by arbitrary DNA/RNA sequences and small molecules/proteins, respectively. These methodologies can be applied to other proteins to gain control of their functions by DNA binding.
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Affiliation(s)
- Harsimranjit Sekhon
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY, United States
| | - Jeung-Hoi Ha
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY, United States
| | - Stewart N Loh
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY, United States.
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Ergun Ayva C, Fiorito MM, Guo Z, Edwardraja S, Kaczmarski JA, Gagoski D, Walden P, Johnston WA, Jackson CJ, Nebl T, Alexandrov K. Exploring Performance Parameters of Artificial Allosteric Protein Switches. J Mol Biol 2022; 434:167678. [PMID: 35709893 DOI: 10.1016/j.jmb.2022.167678] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/30/2022] [Accepted: 06/06/2022] [Indexed: 10/18/2022]
Abstract
Biological information processing networks rely on allosteric protein switches that dynamically interconvert biological signals. Construction of their artificial analogues is a central goal of synthetic biology and bioengineering. Receptor domain insertion is one of the leading methods for constructing chimeric protein switches. Here we present an in vitro expression-based platform for the analysis of chimeric protein libraries for which traditional cell survival or cytometric high throughput assays are not applicable. We utilise this platform to screen a focused library of chimeras between PQQ-glucose dehydrogenase and calmodulin. Using this approach, we identified 50 chimeras (approximately 23% of the library) that were activated by calmodulin-binding peptides. We analysed performance parameters of the active chimeras and demonstrated that their dynamic range and response times are anticorrelated, pointing to the existence of an inherent thermodynamic trade-off. We show that the structure of the ligand peptide affects both the response and activation kinetics of the biosensors suggesting that the structure of a ligand:receptor complex can influence the chimera's activation pathway. In order to understand the extent of structural changes in the reporter protein induced by the receptor domains, we have analysed one of the chimeric molecules by CD spectroscopy and hydrogen-deuterium exchange mass spectrometry. We concluded that subtle ligand-induced changes in the receptor domain propagated into the GDH domain and affected residues important for substrate and cofactor binding. Finally, we used one of the identified chimeras to construct a two-component rapamycin biosensor and demonstrated that core switch optimisation translated into improved biosensor performance.
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Affiliation(s)
- Cagla Ergun Ayva
- ARC Centre of Excellence in Synthetic Biology, Australia; Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD 4001, Australia; School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Maria M Fiorito
- ARC Centre of Excellence in Synthetic Biology, Australia; Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD 4001, Australia; School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Zhong Guo
- ARC Centre of Excellence in Synthetic Biology, Australia; Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD 4001, Australia; School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Selvakumar Edwardraja
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Joe A Kaczmarski
- ARC Centre of Excellence in Synthetic Biology, Australia; Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Dejan Gagoski
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Chemistry, Columbia University, New York, NY 10027, USA
| | - Patricia Walden
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD 4001, Australia; School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Wayne A Johnston
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD 4001, Australia; School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Colin J Jackson
- ARC Centre of Excellence in Synthetic Biology, Australia; Research School of Biology, Australian National University, Canberra, ACT 2601, Australia; Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia; Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT 2601, Australia. https://twitter.com/Jackson_Lab
| | - Tom Nebl
- Biology Group, Biomedical Manufacturing Program, CSIRO, Bayview Ave/Research Way, Clayton, VIC 3168, Australia
| | - Kirill Alexandrov
- ARC Centre of Excellence in Synthetic Biology, Australia; Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD 4001, Australia; School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia; CSIRO-QUT Synthetic Biology Alliance, Brisbane, QLD 4001, Australia; Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4001, Australia.
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6
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Stephens EA, Ludwicki MB, Meksiriporn B, Li M, Ye T, Monticello C, Forsythe KJ, Kummer L, Zhou P, Plückthun A, DeLisa MP. Engineering Single Pan-Specific Ubiquibodies for Targeted Degradation of All Forms of Endogenous ERK Protein Kinase. ACS Synth Biol 2021; 10:2396-2408. [PMID: 34399052 DOI: 10.1021/acssynbio.1c00357] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Ubiquibodies (uAbs) are a customizable proteome editing technology that utilizes E3 ubiquitin ligases genetically fused to synthetic binding proteins to steer otherwise stable proteins of interest (POIs) to the 26S proteasome for degradation. The ability of engineered uAbs to accelerate the turnover of exogenous or endogenous POIs in a post-translational manner offers a simple yet robust tool for dissecting diverse functional properties of cellular proteins as well as for expanding the druggable proteome to include tumorigenic protein families that have yet-to-be successfully drugged by conventional inhibitors. Here, we describe the engineering of uAbs composed of human carboxyl-terminus of Hsc70-interacting protein (CHIP), a highly modular human E3 ubiquitin ligase, tethered to differently designed ankyrin repeat proteins (DARPins) that bind to nonphosphorylated (inactive) and/or doubly phosphorylated (active) forms of extracellular signal-regulated kinase 1 and 2 (ERK1/2). Two of the resulting uAbs were found to be global ERK degraders, pan-specifically capturing all endogenous ERK1/2 protein forms and redirecting them to the proteasome for degradation in different cell lines, including MCF7 breast cancer cells. Taken together, these results demonstrate how the substrate specificity of an E3 ubiquitin ligase can be reprogrammed to generate designer uAbs against difficult-to-drug targets, enabling a modular platform for remodeling the mammalian proteome.
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Affiliation(s)
- Erin A Stephens
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
| | - Morgan B Ludwicki
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Bunyarit Meksiriporn
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Mingji Li
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Tianzheng Ye
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Connor Monticello
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Katherine J Forsythe
- College of Arts and Sciences, Cornell University, Ithaca, New York 14853, United States
| | - Lutz Kummer
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Pengbo Zhou
- Department of Pathology and Laboratory Medicine, The Joan and Stanford I. Weill Medical College of Cornell University, New York, New York 10065, United States
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, 8057 Zürich, Switzerland
| | - Matthew P DeLisa
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, New York 14853, United States
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York 14853, United States
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7
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Ludwig SG, Kiyohara CL, Carlucci LA, Kisiela D, Sokurenko EV, Thomas WE. FimH as a scaffold for regulated molecular recognition. J Biol Eng 2021; 15:3. [PMID: 33436006 PMCID: PMC7805223 DOI: 10.1186/s13036-020-00253-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 12/17/2020] [Indexed: 11/16/2022] Open
Abstract
Background Recognition proteins are critical in many biotechnology applications and would be even more useful if their binding could be regulated. The current gold standard for recognition molecules, antibodies, lacks convenient regulation. Alternative scaffolds can be used to build recognition proteins with new functionalities, including regulated recognition molecules. Here we test the use of the bacterial adhesin FimH as a scaffold for regulated molecular recognition. FimH binds to its native small molecule target mannose in a conformation-dependent manner that can be regulated by two types of noncompetitive regulation: allosteric and parasteric. Results We demonstrate that conformational regulation of FimH can be maintained even after reengineering the binding site to recognize the non-mannosylated targets nickel or Penta-His antibody, resulting in an up to 7-fold difference in KD between the two conformations. Moreover, both the allosteric and parasteric regulatory mechanisms native to FimH can be used to regulate binding to its new target. In one mutant, addition of the native ligand mannose parasterically improves the mutant’s affinity for Penta-His 4-fold, even as their epitopes overlap. In another mutant, the allosteric antibody mab21 reduces the mutant’s affinity for Penta-His 7-fold. The advantage of noncompetitive regulation is further illustrated by the ability of this allosteric regulator to induce 98% detachment of Penta-His, even with modest differences in affinity. Conclusions This illustrates the potential of FimH, with its deeply studied conformation-dependent binding, as a scaffold for conformationally regulated binding via multiple mechanisms. Supplementary Information The online version contains supplementary material available at 10.1186/s13036-020-00253-2.
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Affiliation(s)
- Shivani Gupta Ludwig
- Department of Bioengineering, University of Washington, 3720 15th Ave NE. Foege N430P, Box 355061, Seattle, USA
| | - Casey L Kiyohara
- Department of Bioengineering, University of Washington, 3720 15th Ave NE. Foege N430P, Box 355061, Seattle, USA
| | - Laura A Carlucci
- Department of Bioengineering, University of Washington, 3720 15th Ave NE. Foege N430P, Box 355061, Seattle, USA
| | - Dagmara Kisiela
- Department of Bioengineering, University of Washington, 3720 15th Ave NE. Foege N430P, Box 355061, Seattle, USA.,Department of Microbiology, University of Washington, HSB room J267a, Box 357735, Seattle, WA, USA
| | - Evgeni V Sokurenko
- Department of Bioengineering, University of Washington, 3720 15th Ave NE. Foege N430P, Box 355061, Seattle, USA.,Department of Microbiology, University of Washington, HSB room J267a, Box 357735, Seattle, WA, USA
| | - Wendy Evelyn Thomas
- Department of Bioengineering, University of Washington, 3720 15th Ave NE. Foege N430P, Box 355061, Seattle, USA.
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Abstract
Biological signaling pathways are underpinned by protein switches that sense and respond to molecular inputs. Inspired by nature, engineered protein switches have been designed to directly transduce analyte binding into a quantitative signal in a simple, wash-free, homogeneous assay format. As such, they offer great potential to underpin point-of-need diagnostics that are needed across broad sectors to improve access, costs, and speed compared to laboratory assays. Despite this, protein switch assays are not yet in routine diagnostic use, and a number of barriers to uptake must be overcome to realize this potential. Here, we review the opportunities and challenges in engineering protein switches for rapid diagnostic tests. We evaluate how their design, comprising a recognition element, reporter, and switching mechanism, relates to performance and identify areas for improvement to guide further optimization. Recent modular switches that enable new analytes to be targeted without redesign are crucial to ensure robust and efficient development processes. The importance of translational steps toward practical implementation, including integration into a user-friendly device and thorough assay validation, is also discussed.
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Affiliation(s)
- Hope Adamson
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Lars J. C. Jeuken
- School of Biomedical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
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Lopez‐Barbosa N, Ludwicki MB, DeLisa MP. Proteome editing using engineered proteins that hijack cellular quality control machinery. AIChE J 2019. [DOI: 10.1002/aic.16854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Natalia Lopez‐Barbosa
- Robert F. Smith School of Chemical and Biomolecular Engineering Cornell University Ithaca New York
| | - Morgan B. Ludwicki
- Robert F. Smith School of Chemical and Biomolecular Engineering Cornell University Ithaca New York
| | - Matthew P. DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering Cornell University Ithaca New York
- Nancy E. and Peter C. Meinig School of Biomedical Engineering Cornell University Ithaca New York
- Biochemistry, Molecular and Cell Biology Cornell University Ithaca New York
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10
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Adamson H, Ajayi MO, Campbell E, Brachi E, Tiede C, Tang AA, Adams TL, Ford R, Davidson A, Johnson M, McPherson MJ, Tomlinson DC, Jeuken LJC. Affimer-Enzyme-Inhibitor Switch Sensor for Rapid Wash-free Assays of Multimeric Proteins. ACS Sens 2019; 4:3014-3022. [PMID: 31578863 DOI: 10.1021/acssensors.9b01574] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Robust technology is required to underpin rapid point-of-care and in-field diagnostics to improve timely decision making across broad sectors. An attractive strategy combines target recognition and signal generating elements into an "active" enzyme-switch that directly transduces target-binding into a signal. However, approaches that are broadly applicable to diverse targets remain elusive. Here, an enzyme-inhibitor switch sensor was developed by insertion of non-immunoglobulin Affimer binding proteins, between TEM1-β-lactamase and its inhibitor protein, such that target binding disrupts the enzyme-inhibitor complex. Design principles for a successful switch architecture are illustrated by the rapid (min), simple (wash-free), and sensitive (pM) quantification of multimeric target analytes in biological samples (serum, plasma, leaf extracts), across three application areas. A therapeutic antibody (Herceptin), protein biomarker (human C-reactive protein), and plant virus (cow pea mosaic virus) were targeted, demonstrating assays for therapeutic drug monitoring, health diagnostics, and plant pathogen detection, respectively. Batch-to-batch reproducibility, shelf-life stability, and consistency with validated enzyme-linked immunosorbent assay analysis confirm that the principle of an Affimer-enzyme-inhibitor switch provides a platform for point-of-care and in-field diagnostics.
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Affiliation(s)
| | | | | | | | | | | | | | - Robert Ford
- Avacta Life Sciences Limited, Unit 20, Ash Way, Thorp Arch Estate, Wetherby LS23 7FA, U.K
| | - Alex Davidson
- Avacta Life Sciences Limited, Unit 20, Ash Way, Thorp Arch Estate, Wetherby LS23 7FA, U.K
| | - Matt Johnson
- Avacta Life Sciences Limited, Unit 20, Ash Way, Thorp Arch Estate, Wetherby LS23 7FA, U.K
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11
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Bragina OD, Chernov VI, Zeltchan RV, Sinilkin IG, Medvedeva AA, Larkina MS. Alternative scaffolds in radionuclide diagnosis of malignancies. BULLETIN OF SIBERIAN MEDICINE 2019. [DOI: 10.20538/1682-0363-2019-3-125-133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review discusses a relatively new class of targeted molecules that is being actively studied for radionuclide diagnosis and treatment of malignancies. The full-size antibodies used so far have non-optimal pharmacological properties, slow distribution in the body, poor penetration into the tissue and kidney excretion, and high immunogenicity, which significantly complicates their use in clinical practice. Over the past decade, a new class of targeted molecules, called “non-immunoglobulin scaffolds” have become popular; they have all the requirements for optimal delivery of a radionuclide to tumor cells. Scaffolds usually are smaller in size in comparison with antibodies, but they are larger than peptides, and are characterized by high affinity and optimal biochemical, biophysical, biological, and economic features. The advantages of such proteins are their stable structure, good penetration into tissues, the possibility of additional functionalization and expression in the bacterial system, which ensures low production costs.The results of preclinical and clinical studies for diagnosis of malignancies using such proteins as affibody, adnectin, DARPins, etc., have demonstrated their high specificity, affinity, good tolerance and low immunogenicity.
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Affiliation(s)
- O. D. Bragina
- Cancer Research Institute, Tomsk National Research Medical Center (NRMC), Russian Academy of Science
| | - V. I. Chernov
- Cancer Research Institute, Tomsk National Research Medical Center (NRMC), Russian Academy of Science;
National Research Tomsk Polytechnic University
| | - R. V. Zeltchan
- Cancer Research Institute, Tomsk National Research Medical Center (NRMC), Russian Academy of Science
| | - I. G. Sinilkin
- Cancer Research Institute, Tomsk National Research Medical Center (NRMC), Russian Academy of Science
| | - A. A. Medvedeva
- Cancer Research Institute, Tomsk National Research Medical Center (NRMC), Russian Academy of Science
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12
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Ligand-induced conformational switch in an artificial bidomain protein scaffold. Sci Rep 2019; 9:1178. [PMID: 30718544 PMCID: PMC6362204 DOI: 10.1038/s41598-018-37256-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 11/28/2018] [Indexed: 11/15/2022] Open
Abstract
Artificial proteins binding any predefined “target” protein can now be efficiently generated using combinatorial libraries based on robust protein scaffolds. αRep is such a family of artificial proteins, based on an α-solenoid protein repeat scaffold. The low aggregation propensity of the specific “binders” generated from this library opens new protein engineering opportunities such as the creation of biosensors within multidomain constructions. Here, we have explored the properties of two new types of artificial bidomain proteins based on αRep structures. Their structural and functional properties are characterized in detail using biophysical methods. The results clearly show that both bidomain proteins adopt a closed bivalve shell-like conformation, in the ligand free form. However, the presence of ligands induces a conformational transition, and the proteins adopt an open form in which each domain can bind its cognate protein partner. The open/closed equilibria alter the affinities of each domain and induce new cooperative effects. The binding-induced relative domain motion was monitored by FRET. Crystal structures of the chimeric proteins indicate that the conformation of each constituting domain is conserved but that their mutual interactions explain the emergent properties of these artificial bidomain proteins. The ligand-induced structural transition observed in these bidomain proteins should be transferable to other αRep proteins with different specificity and could provide the basis of a new generic biosensor design.
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Wu F, Bethke JH, Wang M, You L. Quantitative and synthetic biology approaches to combat bacterial pathogens. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2018; 4:116-126. [PMID: 30263975 DOI: 10.1016/j.cobme.2017.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Antibiotic resistance is one of the biggest threats to public health. The rapid emergence of resistant bacterial pathogens endangers the efficacy of current antibiotics and has led to increasing mortality and economic burden. This crisis calls for more rapid and accurate diagnosis to detect and identify pathogens, as well as to characterize their response to antibiotics. Building on this foundation, treatment options also need to be improved to use current antibiotics more effectively and develop alternative strategies that complement the use of antibiotics. We here review recent developments in diagnosis and treatment of bacterial pathogens with a focus on quantitative biology and synthetic biology approaches.
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Affiliation(s)
- Feilun Wu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Jonathan H Bethke
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA
| | - Meidi Wang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, 27708, USA
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14
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DeRosa JR, Moyer BS, Lumen E, Wolfe AJ, Sleeper MB, Bianchi AH, Crawford A, McGuigan C, Wortel D, Fisher C, Moody KJ, Blanden AR. RPtag as an Orally Bioavailable, Hyperstable Epitope Tag and Generalizable Protein Binding Scaffold. Biochemistry 2018; 57:3036-3049. [PMID: 29722979 DOI: 10.1021/acs.biochem.8b00170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antibodies are the most prolific biologics in research and clinical environments because of their ability to bind targets with high affinity and specificity. However, antibodies also carry liabilities. A significant portion of the life-science reproducibility crisis is driven by inconsistent performance of research-grade antibodies, and clinical antibodies are often unstable and require costly cold-chain management to reach their destinations in active form. In biotechnology, antibodies are also limited by difficulty integrating them in many recombinant systems due to their size and structural complexity. A switch to small, stable, sequence-verified binding scaffolds may overcome these barriers. Here we present such a scaffold, RPtag, based on a ribose-binding protein (RBP) from extremophile Caldanaerobacter subterraneus. RPtag binds an optimized peptide with pM affinity, is stable to extreme temperature, pH, and protease treatment, readily refolds after denaturation, is effective in common laboratory applications, was rationally engineered to bind bioactive PDGF-β, and was formulated as a gut-stable orally bioavailable preparation.
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Affiliation(s)
- Jennifer R DeRosa
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Brandon S Moyer
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Ellie Lumen
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Aaron J Wolfe
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Meegan B Sleeper
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Anthony H Bianchi
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Ashleigh Crawford
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Connor McGuigan
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Danique Wortel
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Cheyanne Fisher
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Kelsey J Moody
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
| | - Adam R Blanden
- Ichor Therapeutics, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States.,RecombiPure, Inc. , 2521 US-11 , Lafayette , New York 13084 , United States
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15
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Creation of Antigen-Dependent β-Lactamase Fusion Protein Tethered by Circularly Permuted Antibody Variable Domains. Methods Mol Biol 2017. [PMID: 28293886 DOI: 10.1007/978-1-4939-6940-1_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Antibody-based molecular switches that are able to recognize a range of exogenous antigens can be highly useful as a versatile biosensor. However, regulating the catalytic activity of enzymes by antibodies is still hard to achieve. Here, we describe a design method of unique antibody variable region Fv introduced with two circular permutations, called Clampbody. By tethering the Clampbody to a circularly permuted TEM-1 β-lactamase (BLA), we successfully constructed a genetically encoded molecular switch Cbody-cpBLA that shows antigen-dependent catalytic activity.
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16
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Abstract
Synthetic protein switches with tailored response functions are finding increasing applications as tools in basic research and biotechnology. With a number of successful design strategies emerging, the construction of synthetic protein switches still frequently necessitates an integrated approach that combines detailed biochemical and biophysical characterization in combination with high-throughput screening to construct tailored synthetic protein switches. This is increasingly complemented by computational strategies that aim to reduce the need for costly empirical optimization and thus facilitate the protein design process. Successful computational design approaches range from analyzing phylogenetic data to infer useful structural, biophysical, and biochemical information to modeling the structure and function of proteins ab initio. The following chapter provides an overview over the theoretical considerations and experimental approaches that have been successful applied in the construction of synthetic protein switches.
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Affiliation(s)
- Viktor Stein
- Fachbereich Biologie, Technische Universität Darmstadt, 64287, Darmstadt, Germany.
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17
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Ribeiro LF, Warren TD, Ostermeier M. Construction of Protein Switches by Domain Insertion and Directed Evolution. Methods Mol Biol 2017; 1596:43-55. [PMID: 28293879 DOI: 10.1007/978-1-4939-6940-1_3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A protein switch is a protein that changes between inactive ("off") and active ("on") states in response to a biomolecule or physical signal. These switches can be created by fusing two domains in such a way that the activity of the output domain is regulated by the input domain's recognition of an input signal (such as the binding of a molecule, recognition of light). Here, we describe several methods for randomly fusing two domains to create domain insertion libraries from which protein switches can be identified by selections and/or screens.
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Affiliation(s)
- Lucas F Ribeiro
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD, 21218, USA
| | - Tiana D Warren
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD, 21218, USA
| | - Marc Ostermeier
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD, 21218, USA.
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