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Holdgate GA, Bardelle C, Berry SK, Lanne A, Cuomo ME. Screening for molecular glues - Challenges and opportunities. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100136. [PMID: 38104659 DOI: 10.1016/j.slasd.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/03/2023] [Accepted: 12/14/2023] [Indexed: 12/19/2023]
Abstract
Molecular glues are small molecules, typically smaller than PROTACs, and usually with improved physicochemical properties that aim to stabilise the interaction between two proteins. Most often this approach is used to improve or induce an interaction between the target and an E3 ligase, but other interactions which stabilise interactions to increase activity or to inhibit binding to a natural effector have also been demonstrated. This review will describe the effects of induced proximity, discuss current methods used to identify molecular glues and introduce approaches that could be adapted for molecular glue screening.
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Affiliation(s)
| | - Catherine Bardelle
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Sophia K Berry
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Alice Lanne
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
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Stanojević M, Sollner Dolenc M, Vračko M. Development of in silico classification models for binding affinity to the glucocorticoid receptor. CHEMOSPHERE 2023:139147. [PMID: 37301514 DOI: 10.1016/j.chemosphere.2023.139147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 04/12/2023] [Accepted: 06/04/2023] [Indexed: 06/12/2023]
Abstract
The endocrine disrupting properties of chemicals acting through the glucocorticoid receptor (GR) have attracted considerable interest. Since there are few data for most chemicals on their endocrine properties in silico approaches seem to be the most appropriate tool for screening and prioritizing chemicals for planning further experiments. In this work, we developed classification models for binding affinity to the glucocorticoid receptor using the counterpropagation artificial neural network method. We considered two series of 142 and 182 compounds and their binding affinity to the glucocorticoid receptor as agonists and antagonists, respectively. The compounds belong to different chemical classes. The compounds were represented by a set of descriptors calculated with the DRAGON program. The clustering structure of sets was studied with standard principal component method. A weak separation between binders and non-binders was found. Another classification model was developed using the counterpropagation artificial neural network method (CPANN). The final classification models developed were well balanced and showed a high level of accuracy, with 85.7% of GR agonist and 78.9% of GR antagonist correctly assigned in leave-one-out cross-validation.
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Affiliation(s)
- Mark Stanojević
- Bisafe Doo, V Kladeh 11c, 1000, Ljubljana, Slovenia; University of Ljubljana, Faculty of Pharmacy, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia.
| | - Marija Sollner Dolenc
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva Cesta 7, 1000, Ljubljana, Slovenia.
| | - Marjan Vračko
- National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia.
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3
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Stanojević M, Sollner Dolenc M, Vračko M. Predictive Models for Compound Binding to Androgen and Estrogen Receptors Based on Counter-Propagation Artificial Neural Networks. TOXICS 2023; 11:486. [PMID: 37368586 DOI: 10.3390/toxics11060486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023]
Abstract
Endocrine-disrupting chemicals (EDCs) are exogenous substances that interfere with the normal function of the human endocrine system. These chemicals can affect specific nuclear receptors, such as androgen receptors (ARs) or estrogen receptors (ER) α and β, which play a crucial role in regulating complex physiological processes in humans. It is now more crucial than ever to identify EDCs and reduce exposure to them. For screening and prioritizing chemicals for further experimentation, the use of artificial neural networks (ANN), which allow the modeling of complicated, nonlinear relationships, is most appropriate. We developed six models that predict the binding of a compound to ARs, ERα, or ERβ as agonists or antagonists, using counter-propagation artificial neural networks (CPANN). Models were trained on a dataset of structurally diverse compounds, and activity data were obtained from the CompTox Chemicals Dashboard. Leave-one-out (LOO) tests were performed to validate the models. The results showed that the models had excellent performance with prediction accuracy ranging from 94% to 100%. Therefore, the models can predict the binding affinity of an unknown compound to the selected nuclear receptor based solely on its chemical structure. As such, they represent important alternatives for the safety prioritization of chemicals.
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Affiliation(s)
- Mark Stanojević
- BiSafe d.o.o., 1000 Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia
| | | | - Marjan Vračko
- National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
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4
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Chen Y, Guo Y, Liu Y, Xiang Y, Liu G, Zhang Q, Yin Y, Cai Y, Jiang G. Advances in bacterial whole-cell biosensors for the detection of bioavailable mercury: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161709. [PMID: 36682565 DOI: 10.1016/j.scitotenv.2023.161709] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/29/2022] [Accepted: 01/15/2023] [Indexed: 06/17/2023]
Abstract
Mercury (Hg) and its organic compounds, especially monomethylmercury (MeHg), cause major damage to the ecosystem and human health. In surface water or sediments, microorganisms play a crucial role in the methylation and demethylation of Hg. Given that Hg transformation processes are intracellular reactions, accurate assessment of the bioavailability of Hg(II)/MeHg in the environment, particularly for microorganisms, is of major importance. Compared with traditional analytical methods, bacterial whole-cell biosensors (BWCBs) provide a more accurate, convenient, and cost-effective strategy to assess the environmental risks of Hg(II)/MeHg. This Review summarizes recent progress in the application of BWCBs in the detection of bioavailable Hg(II)/MeHg, providing insight on current challenges and strategies. The principle and components of BWCBs for Hg(II)/MeHg bioavailability analysis are introduced. Furthermore, the impact of water chemical factors on the bioavailability of Hg is discussed as are future perspectives of BWCBs in bioavailable Hg analysis and optimization of BWCBs.
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Affiliation(s)
- Yueqian Chen
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
| | - Yingying Guo
- Laboratory of Environmental Nanotechnology and Health, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yanwei Liu
- Laboratory of Environmental Nanotechnology and Health, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yuping Xiang
- Laboratory of Environmental Nanotechnology and Health, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Guangliang Liu
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States of America
| | - Qinghua Zhang
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yongguang Yin
- School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; Laboratory of Environmental Nanotechnology and Health, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yong Cai
- Laboratory of Environmental Nanotechnology and Health, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States of America
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
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Gopu B, Kour P, Pandian R, Singh K. Insights into the drug screening approaches in leishmaniasis. Int Immunopharmacol 2023; 114:109591. [PMID: 36700771 DOI: 10.1016/j.intimp.2022.109591] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/25/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
Leishmaniasis, a tropically neglected disease, is responsible for the high mortality and morbidity ratio in poverty-stricken areas. Currently, no vaccine is available for the complete cure of the disease. Current chemotherapeutic regimens face the limitations of drug resistance and toxicity concerns indicating a great need to develop better chemotherapeutic leads that are orally administrable, potent, non-toxic, and cost-effective. The anti-leishmanial drug discovery process accelerated the desire for large-scale drug screening assays and high-throughput screening (HTS) technology to identify new chemo-types that can be used as potential drug molecules to control infection. Using the HTS approach, about one million compounds can be screened daily within the shortest possible time for biological activity using automation tools, miniaturized assay formats, and large-scale data analysis. Classical and modern in vitro screening assays have led to the progression of active compounds further to ex vivo and in vivo studies. In the present review, we emphasized on the HTS approaches employed in the leishmanial drug discovery program. Recent in vitro screening assays are widely explored to discover new chemical scaffolds. Developing appropriate experimental animal models and their related techniques is necessary to understand the pathophysiological processes and disease host responses, paving the way for unraveling novel therapies against leishmaniasis.
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Affiliation(s)
- Boobalan Gopu
- Animal House Facility, Pharmacology Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Parampreet Kour
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Ramajayan Pandian
- Animal House Facility, Pharmacology Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kuljit Singh
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Shi Z, Xia M, Xiao S, Zhang Q. Identification of nonmonotonic concentration-responses in Tox21 high-throughput screening estrogen receptor assays. Toxicol Appl Pharmacol 2022; 452:116206. [PMID: 35988584 PMCID: PMC9452481 DOI: 10.1016/j.taap.2022.116206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 10/15/2022]
Abstract
Environmental endocrine-disrupting chemicals (EDCs) interfere with the metabolism and actions of endogenous hormones. It has been well documented in numerous in vivo and in vitro studies that EDCs can exhibit nonmonotonic dose response (NMDR) behaviors. Not conforming to the conventional linear or linear-no-threshold response paradigm, these NMDR relationships pose practical challenges to the risk assessment of EDCs. In the meantime, the endocrine signaling pathways and biological mechanisms underpinning NMDR remain incompletely understood. The US Tox21 program has conducted in vitro cell-based high-throughput screening assays for estrogen receptors (ER), androgen receptors, and other nuclear receptors, and screened the 10 K-compound library for potential endocrine activities. Using 15 concentrations across several orders of magnitude of concentration range and run in both agonist and antagonist modes, these Tox21 assay datasets contain valuable quantitative information that can be explored to evaluate the nonlinear effects of EDCs and may infer potential mechanisms. In this study we analyzed the concentration-response curves (CRCs) in all 8 Tox21 ERα and ERβ assays by developing clustering and classification algorithms customized to the datasets to identify various shapes of CRCs. After excluding NMDR curves likely caused by cytotoxicity, luciferase inhibition, or autofluorescence, hundreds of compounds were identified to exhibit Bell or U-shaped CRCs. Bell-shaped CRCs are about 7 times more frequent than U-shaped ones in the Tox21 ER assays. Many compounds exhibit NMDR in at least one assay, and some EDCs well-known for their NMDRs in the literature were also identified, suggesting their nonmonotonic effects may originate at cellular levels involving transcriptional ER signaling. The developed computational methods for NMDR identification in ER assays can be adapted and applied to other high-throughput bioassays.
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Affiliation(s)
- Zhenzhen Shi
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, NIH, Bethesda, MD, USA
| | - Shuo Xiao
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, NJ, USA
| | - Qiang Zhang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
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Wang H, Xie M, Rizzi G, Li X, Tan K, Fussenegger M. Identification of Sclareol As a Natural Neuroprotective Ca v 1.3-Antagonist Using Synthetic Parkinson-Mimetic Gene Circuits and Computer-Aided Drug Discovery. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2102855. [PMID: 35040584 PMCID: PMC8895113 DOI: 10.1002/advs.202102855] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 11/30/2021] [Indexed: 05/14/2023]
Abstract
Parkinson's disease (PD) results from selective loss of substantia nigra dopaminergic (SNc DA) neurons, and is primarily caused by excessive activity-related Ca2+ oscillations. Although L-type voltage-gated calcium channel blockers (CCBs) selectively inhibiting Cav 1.3 are considered promising candidates for PD treatment, drug discovery is hampered by the lack of high-throughput screening technologies permitting isoform-specific assessment of Cav-antagonistic activities. Here, a synthetic-biology-inspired drug-discovery platform enables identification of PD-relevant drug candidates. By deflecting Cav-dependent activation of nuclear factor of activated T-cells (NFAT)-signaling to repression of reporter gene translation, they engineered a cell-based assay where reporter gene expression is activated by putative CCBs. By using this platform in combination with in silico virtual screening and a trained deep-learning neural network, sclareol is identified from a essential oils library as a structurally distinctive compound that can be used for PD pharmacotherapy. In vitro studies, biochemical assays and whole-cell patch-clamp recordings confirmed that sclareol inhibits Cav 1.3 more strongly than Cav 1.2 and decreases firing responses of SNc DA neurons. In a mouse model of PD, sclareol treatment reduced DA neuronal loss and protected striatal network dynamics as well as motor performance. Thus, sclareol appears to be a promising drug candidate for neuroprotection in PD patients.
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Affiliation(s)
- Hui Wang
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26Basel4058Switzerland
- Present address:
Lonza AGLonzastrasseVisp3930Switzerland
| | - Mingqi Xie
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26Basel4058Switzerland
- Present address:
Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityShilongshan Road 18HangzhouP. R. China
| | - Giorgio Rizzi
- BiozentrumUniversity of BaselKlingelbergstrasse 50/70Basel4056Switzerland
- Present address:
Inscopix IncEmbarcadero WayPalo AltoCA94303USA
| | - Xin Li
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26Basel4058Switzerland
- Present address:
Key Laboratory of Growth Regulation and Translational Research of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityShilongshan Road 18HangzhouP. R. China
| | - Kelly Tan
- BiozentrumUniversity of BaselKlingelbergstrasse 50/70Basel4056Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26Basel4058Switzerland
- University of BaselFaculty of ScienceMattenstrasse 26BaselCH‐4058Switzerland
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8
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Hsieh JH. Accounting for Artifacts in High-Throughput Toxicity Assays. Methods Mol Biol 2022; 2474:155-167. [PMID: 35294764 DOI: 10.1007/978-1-0716-2213-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Compound activity identification is the primary goal in high throughput screening (HTS) assays. However, assay artifacts including both systematic (e.g., compound autofluorescence) and nonsystematic (e.g., noise) complicate activity interpretation. In addition, other than the traditional potency parameter, half-maximal effect concentration [EC50], additional activity parameters (e.g., point-of-departure [POD] and weighted area-under-the-curve [wAUC]) could be derived from HTS data for activity profiling. A data analysis pipeline has been developed to handle the artifacts, and to provide compound activity characterization with either binary or continuous metrics. This chapter outlines the steps in the pipeline using Tox21 estrogen receptor (ER) β-lactamase assays, including the formats to identify either agonists or antagonists, as well as the counterscreen assays for identifying artifacts as examples. The steps can be applied to other lower throughput assays with concentration-response data.
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Affiliation(s)
- Jui-Hua Hsieh
- National Institute of Environmental Health Sciences, Durham, NC, USA.
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Morcillo-Parra MÁ, Beltran G, Mas A, Torija MJ. Determination of melatonin by a whole cell bioassay in fermented beverages. Sci Rep 2019; 9:9120. [PMID: 31235891 PMCID: PMC6591416 DOI: 10.1038/s41598-019-45645-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/12/2019] [Indexed: 11/09/2022] Open
Abstract
Melatonin is a bioactive compound that is present in fermented beverages, such as wine and beer, at concentrations ranging from picograms to nanograms per mL of product. The purpose of this study was to optimize a novel fluorescent bioassay for detecting melatonin based on a cell line that contains the human melatonin receptor 1B gene and to compare these results with LC-MS/MS as a reference method. Conditions that could affect cell growth and detection (cell number per well, stimulation time, presence or absence of fetal bovine serum and adhesion of cells) were tested in the TANGO® cell line. Food matrices (wine and grape must) could not be directly used for the cell line due to low response. Therefore, for the determination of melatonin in food samples, an extraction procedure was required before conducting the assay. We demonstrated an improvement in melatonin determination by the cell-based bioassay due to increased sensitivity and specificity and improved quantification in complex matrices. Therefore, this method is a good alternative to determine melatonin content in some food samples, especially for those containing very low melatonin levels.
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Affiliation(s)
| | - Gemma Beltran
- Departament de Bioquimica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Spain
| | - Albert Mas
- Departament de Bioquimica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Spain
| | - María-Jesús Torija
- Departament de Bioquimica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, Tarragona, Spain.
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Zhu J, He M, Xu W, Li Y, Huang R, Wu S, Niu H. Development of TEM-1 β-lactamase based protein translocation assay for identification of Anaplasma phagocytophilum type IV secretion system effector proteins. Sci Rep 2019; 9:4235. [PMID: 30862835 PMCID: PMC6414681 DOI: 10.1038/s41598-019-40682-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 02/20/2019] [Indexed: 11/24/2022] Open
Abstract
Anaplasma phagocytophilum, the aetiologic agent of human granulocytic anaplasmosis (HGA) is an obligate intracellular Gram-negative bacterium with the genome size of 1.47 megabases. The intracellular life style and small size of genome suggest that A. phagocytophilum has to modulate a multitude of host cell physiological processes to facilitate its replication. One strategy employed by A. phagocytophilum is through its type IV secretion system (T4SS), which translocates bacterial effectors into target cells to disrupt normal cellular activities. In this study we developed a TEM-1 β-lactamase based protein translocation assay and applied this assay for identification of A. phagocytophilum T4SS effectors. An A. phagocytophilum hypothetical protein, APH0215 is identified as a T4SS effector protein and found interacting with trans-Golgi network in transfected cells. Hereby, this protein translocation assay developed in this study will facilitate the identification of A. phagocytophilum T4SS effectors and elucidation of HGA pathogenesis.
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Affiliation(s)
- Jiafeng Zhu
- Department of Microbiology, College of Medicine, Soochow University, Suzhou, Jiangsu Province, 215123, China
| | - Meiling He
- Department of Microbiology, College of Medicine, Soochow University, Suzhou, Jiangsu Province, 215123, China
| | - Wenting Xu
- Department of Microbiology, College of Medicine, Soochow University, Suzhou, Jiangsu Province, 215123, China
| | - Yuanyuan Li
- Department of Microbiology, College of Medicine, Soochow University, Suzhou, Jiangsu Province, 215123, China
| | - Rui Huang
- Department of Microbiology, College of Medicine, Soochow University, Suzhou, Jiangsu Province, 215123, China
| | - Shuyan Wu
- Department of Microbiology, College of Medicine, Soochow University, Suzhou, Jiangsu Province, 215123, China
| | - Hua Niu
- Department of Microbiology, College of Medicine, Soochow University, Suzhou, Jiangsu Province, 215123, China.
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A platform for discovery of functional cell-penetrating peptides for efficient multi-cargo intracellular delivery. Sci Rep 2018; 8:12538. [PMID: 30135446 PMCID: PMC6105642 DOI: 10.1038/s41598-018-30790-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 08/06/2018] [Indexed: 12/19/2022] Open
Abstract
Cell penetrating peptides (CPPs) offer great potential to deliver therapeutic molecules to previously inaccessible intracellular targets. However, many CPPs are inefficient and often leave their attached cargo stranded in the cell’s endosome. We report a versatile platform for the isolation of peptides delivering a wide range of cargos into the cytoplasm of cells. We used this screening platform to identify multiple “Phylomer” CPPs, derived from bacterial and viral genomes. These peptides are amenable to conventional sequence optimization and engineering approaches for cell targeting and half-life extension. We demonstrate potent, functional delivery of protein, peptide, and nucleic acid analog cargos into cells using Phylomer CPPs. We validate in vivo activity in the cytoplasm, through successful transport of an oligonucleotide therapeutic fused to a Phylomer CPP in a disease model for Duchenne’s muscular dystrophy. This report thus establishes a discovery platform for identifying novel, functional CPPs to expand the delivery landscape of druggable intracellular targets for biological therapeutics.
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Stone SR, Heinrich T, Juraja SM, Satiaputra JN, Hall CM, Anastasas M, Mills AD, Chamberlain CA, Winslow S, Priebatsch K, Cunningham PT, Hoffmann K, Milech N. β-Lactamase Tools for Establishing Cell Internalization and Cytosolic Delivery of Cell Penetrating Peptides. Biomolecules 2018; 8:biom8030051. [PMID: 29997382 PMCID: PMC6163455 DOI: 10.3390/biom8030051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/22/2018] [Accepted: 06/29/2018] [Indexed: 12/15/2022] Open
Abstract
The ability of cell penetrating peptides (CPPs) to deliver biologically relevant cargos into cells is becoming more important as targets in the intracellular space continue to be explored. We have developed two assays based on CPP-dependent, intracellular delivery of TEM-1 β-lactamase enzyme, a functional biological molecule comparable in size to many protein therapeutics. The first assay focuses on the delivery of full-length β-lactamase to evaluate the internalization potential of a CPP sequence. The second assay uses a split-protein system where one component of β-lactamase is constitutively expressed in the cytoplasm of a stable cell line and the other component is delivered by a CPP. The delivery of a split β-lactamase component evaluates the cytosolic delivery capacity of a CPP. We demonstrate that these assays are rapid, flexible and have potential for use with any cell type and CPP sequence. Both assays are validated using canonical and novel CPPs, with limits of detection from <500 nM to 1 µM. Together, the β-lactamase assays provide compatible tools for functional characterization of CPP activity and the delivery of biological cargos into cells.
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Affiliation(s)
- Shane R Stone
- Telethon Kids Institute, University of Western Australia, Subiaco, WA 6008, Australia.
- Phylogica Pty Ltd., Subiaco, WA 6008, Australia.
| | - Tatjana Heinrich
- Telethon Kids Institute, University of Western Australia, Subiaco, WA 6008, Australia.
- Phylogica Pty Ltd., Subiaco, WA 6008, Australia.
| | - Suzy M Juraja
- Telethon Kids Institute, University of Western Australia, Subiaco, WA 6008, Australia.
- Phylogica Pty Ltd., Subiaco, WA 6008, Australia.
| | - Jiulia N Satiaputra
- Telethon Kids Institute, University of Western Australia, Subiaco, WA 6008, Australia.
- Phylogica Pty Ltd., Subiaco, WA 6008, Australia.
| | - Clinton M Hall
- Telethon Kids Institute, University of Western Australia, Subiaco, WA 6008, Australia.
- Phylogica Pty Ltd., Subiaco, WA 6008, Australia.
| | - Mark Anastasas
- Telethon Kids Institute, University of Western Australia, Subiaco, WA 6008, Australia.
- Phylogica Pty Ltd., Subiaco, WA 6008, Australia.
| | - Anna D Mills
- Telethon Kids Institute, University of Western Australia, Subiaco, WA 6008, Australia.
- Phylogica Pty Ltd., Subiaco, WA 6008, Australia.
| | - Christopher A Chamberlain
- Telethon Kids Institute, University of Western Australia, Subiaco, WA 6008, Australia.
- Phylogica Pty Ltd., Subiaco, WA 6008, Australia.
| | - Scott Winslow
- Telethon Kids Institute, University of Western Australia, Subiaco, WA 6008, Australia.
- Phylogica Pty Ltd., Subiaco, WA 6008, Australia.
| | - Kristin Priebatsch
- Telethon Kids Institute, University of Western Australia, Subiaco, WA 6008, Australia.
- Phylogica Pty Ltd., Subiaco, WA 6008, Australia.
| | - Paula T Cunningham
- Telethon Kids Institute, University of Western Australia, Subiaco, WA 6008, Australia.
- Phylogica Pty Ltd., Subiaco, WA 6008, Australia.
| | - Katrin Hoffmann
- Telethon Kids Institute, University of Western Australia, Subiaco, WA 6008, Australia.
- Phylogica Pty Ltd., Subiaco, WA 6008, Australia.
| | - Nadia Milech
- Telethon Kids Institute, University of Western Australia, Subiaco, WA 6008, Australia.
- Phylogica Pty Ltd., Subiaco, WA 6008, Australia.
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Melnikov F, Hsieh JH, Sipes NS, Anastas PT. Channel Interactions and Robust Inference for Ratiometric β-lactamase Assay Data: a Tox21 Library Analysis. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2018; 6:3233-3241. [PMID: 32461840 PMCID: PMC7252516 DOI: 10.1021/acssuschemeng.7b03394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Ratiometric β-lactamase (BLA) reporters are widely used to study transcriptional responses in a high-throughput screening (HTS) format. Typically, a ratio readout (background/target fluorescence) is used for toxicity assessment and structure-activity modeling efforts from BLA HTS data. This ratio readout may be confounded by channel-specific artifacts. To maximize the utility of BLA HTS data, we analyzed the relationship between individual channels and ratio readouts after fitting 10,000 chemical titration series screened in seven BLA stress-response assays from the Tox21 initiative. Similar to previous observations, we found that activity classifications based on BLA ratio readout alone are confounded by interference patterns for up to 85% (50 % on average) of active chemicals. Most Tox21 analyses adjust for this issue by evaluating target and ratio readout direction. In addition, we found that the potency and efficacy estimates derived from the ratio readouts may not represent the target channel effects and thus complicates chemical activity comparison. From these analyses we recommend a simpler approach using a direct evaluation of the target and background channels as well as the respective noise levels when using BLA data for toxicity assessment. This approach eliminates the channel interference issues and allows for straightforward chemical assessment and comparisons.
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Affiliation(s)
- Fjodor Melnikov
- School of Forestry and Environmental Studies, Yale University, New Haven, CT 06520, United States
| | - Jui-Hua Hsieh
- Kelly Government Solutions, 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, United States
| | - Nisha S Sipes
- National Toxicology Program / National Institute of Environmental Health Sciences (NIEHS), 111 T.W. Alexander Drive, Research Triangle Park, NC 27709, United States
| | - Paul T Anastas
- School of Forestry and Environmental Studies, Yale University, New Haven, CT 06520, United States
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT 06520, United States
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14
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Abstract
Compound activity identification is the primary goal in high-throughput screening (HTS) assays. However, assay artifacts including both systematic (e.g., compound auto-fluorescence) and nonsystematic (e.g., noise) complicate activity interpretation. In addition, other than the traditional potency parameter, half-maximal effect concentration (EC50), additional activity parameters (e.g., point-of-departure, POD) could be derived from HTS data for activity profiling. A data analysis pipeline has been developed to handle the artifacts and to provide compound activity characterization with either binary or continuous metrics. This chapter outlines the steps in the pipeline using Tox21 glucocorticoid receptor (GR) β-lactamase assays, including the formats to identify either agonists or antagonists, as well as the counter-screen assays for identifying artifacts as examples. The steps can be applied to other lower-throughput assays with concentration-response data.
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15
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Bland MJ, Ducos-Galand M, Val ME, Mazel D. An att site-based recombination reporter system for genome engineering and synthetic DNA assembly. BMC Biotechnol 2017; 17:62. [PMID: 28705159 PMCID: PMC5512741 DOI: 10.1186/s12896-017-0382-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/09/2017] [Indexed: 11/25/2022] Open
Abstract
Background Direct manipulation of the genome is a widespread technique for genetic studies and synthetic biology applications. The tyrosine and serine site-specific recombination systems of bacteriophages HK022 and ΦC31 are widely used for stable directional exchange and relocation of DNA sequences, making them valuable tools in these contexts. We have developed site-specific recombination tools that allow the direct selection of recombination events by embedding the attB site from each system within the β-lactamase resistance coding sequence (bla). Results The HK and ΦC31 tools were developed by placing the attB sites from each system into the signal peptide cleavage site coding sequence of bla. All possible open reading frames (ORFs) were inserted and tested for recombination efficiency and bla activity. Efficient recombination was observed for all tested ORFs (3 for HK, 6 for ΦC31) as shown through a cointegrate formation assay. The bla gene with the embedded attB site was functional for eight of the nine constructs tested. Conclusions The HK/ΦC31 att-bla system offers a simple way to directly select recombination events, thus enhancing the use of site-specific recombination systems for carrying out precise, large-scale DNA manipulation, and adding useful tools to the genetics toolbox. We further show the power and flexibility of bla to be used as a reporter for recombination.
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Affiliation(s)
- Michael J Bland
- Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Institut Pasteur, 75015, Paris, France.,UMR3525, Centre National de la Recherche Scientifique, 75015, Paris, France
| | - Magaly Ducos-Galand
- Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Institut Pasteur, 75015, Paris, France.,UMR3525, Centre National de la Recherche Scientifique, 75015, Paris, France
| | - Marie-Eve Val
- Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Institut Pasteur, 75015, Paris, France.,UMR3525, Centre National de la Recherche Scientifique, 75015, Paris, France
| | - Didier Mazel
- Unité Plasticité du Génome Bactérien, Département Génomes et Génétique, Institut Pasteur, 75015, Paris, France. .,UMR3525, Centre National de la Recherche Scientifique, 75015, Paris, France.
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16
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Mok PL, Leow SN, Koh AEH, Mohd Nizam HH, Ding SLS, Luu C, Ruhaslizan R, Wong HS, Halim WHWA, Ng MH, Idrus RBH, Chowdhury SR, Bastion CML, Subbiah SK, Higuchi A, Alarfaj AA, Then KY. Micro-Computed Tomography Detection of Gold Nanoparticle-Labelled Mesenchymal Stem Cells in the Rat Subretinal Layer. Int J Mol Sci 2017; 18:ijms18020345. [PMID: 28208719 PMCID: PMC5343880 DOI: 10.3390/ijms18020345] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 12/09/2016] [Accepted: 12/21/2016] [Indexed: 12/13/2022] Open
Abstract
Mesenchymal stem cells are widely used in many pre-clinical and clinical settings. Despite advances in molecular technology; the migration and homing activities of these cells in in vivo systems are not well understood. Labelling mesenchymal stem cells with gold nanoparticles has no cytotoxic effect and may offer suitable indications for stem cell tracking. Here, we report a simple protocol to label mesenchymal stem cells using 80 nm gold nanoparticles. Once the cells and particles were incubated together for 24 h, the labelled products were injected into the rat subretinal layer. Micro-computed tomography was then conducted on the 15th and 30th day post-injection to track the movement of these cells, as visualized by an area of hyperdensity from the coronal section images of the rat head. In addition, we confirmed the cellular uptake of the gold nanoparticles by the mesenchymal stem cells using transmission electron microscopy. As opposed to other methods, the current protocol provides a simple, less labour-intensive and more efficient labelling mechanism for real-time cell tracking. Finally, we discuss the potential manipulations of gold nanoparticles in stem cells for cell replacement and cancer therapy in ocular disorders or diseases.
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Affiliation(s)
- Pooi Ling Mok
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Genetics and Regenerative Medicine Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Sue Ngein Leow
- Department of Ophthalmology, Hospital Sultanah Aminah, 80100 Johor Bahru, Johor, Malaysia.
| | - Avin Ee-Hwan Koh
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Hairul Harun Mohd Nizam
- Department of Ophthalmology, Faculty of Medicine, UKM Medical Center, 56000 Cheras, Kuala Lumpur, Malaysia.
| | - Suet Lee Shirley Ding
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Chi Luu
- Centre for Eye Research Australia, Royal Victorian Eye & Ear Hospital, Melbourne 3002, Australia.
- Department of Surgery (Ophthalmology), The University of Melbourne, Melbourne 3002, Australia.
| | - Raduan Ruhaslizan
- Department of Ophthalmology, Faculty of Medicine, UKM Medical Center, 56000 Cheras, Kuala Lumpur, Malaysia.
| | - Hon Seng Wong
- Department of Ophthalmology, Faculty of Medicine, UKM Medical Center, 56000 Cheras, Kuala Lumpur, Malaysia.
| | | | - Min Hwei Ng
- Tissue Engineering Centre, Universiti Kebangsaan Malaysia Medical Center, 56000 Cheras, Kuala Lumpur, Malaysia.
| | - Ruszymah Binti Hj Idrus
- Department of Physiology, Universiti Kebangsaan Malaysia Medical Center, 56000 Cheras, Kuala Lumpur, Malaysia.
| | - Shiplu Roy Chowdhury
- Tissue Engineering Centre, Universiti Kebangsaan Malaysia Medical Center, 56000 Cheras, Kuala Lumpur, Malaysia.
| | - Catherine Mae-Lynn Bastion
- Department of Ophthalmology, Faculty of Medicine, UKM Medical Center, 56000 Cheras, Kuala Lumpur, Malaysia.
| | - Suresh Kumar Subbiah
- Genetics and Regenerative Medicine Research Center, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
- Department of Medical Microbiology and Parasitology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
| | - Akon Higuchi
- Department of Chemical and Materials Engineering, National Central University, Jhong-li, Taoyuan 32001, Taiwan.
- Department of Reproduction, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan.
- Department of Botany and Microbiology, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Abdullah A Alarfaj
- Department of Botany and Microbiology, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Kong Yong Then
- Department of Ophthalmology, Faculty of Medicine, UKM Medical Center, 56000 Cheras, Kuala Lumpur, Malaysia.
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17
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Nakamura M, Suzuki A, Akada J, Yarimizu T, Iwakiri R, Hoshida H, Akada R. A Novel Terminator Primer and Enhancer Reagents for Direct Expression of PCR-Amplified Genes in Mammalian Cells. Mol Biotechnol 2016; 57:767-80. [PMID: 25997599 DOI: 10.1007/s12033-015-9870-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Escherichia coli plasmids are commonly used for gene expression experiments in mammalian cells, while PCR-amplified DNAs are rarely used even though PCR is a much faster and easier method to construct recombinant DNAs. One difficulty may be the limited amount of DNA produced by PCR. For direct utilization of PCR-amplified DNA in transfection experiments, efficient transfection with a smaller amount of DNA should be attained. For this purpose, we investigated two enhancer reagents, polyethylene glycol and tRNA, for a chemical transfection method. The addition of the enhancers to a commercial transfection reagent individually and synergistically exhibited higher transfection efficiency applicable for several mammalian cell culture lines in a 96-well plate. By taking advantage of a simple transfection procedure using PCR-amplified DNA, SV40 and rabbit β-globin terminator lengths were minimized. The terminator length is short enough to design in oligonucleotides; thus, terminator primers can be used for the construction and analysis of numerous mutations, deletions, insertions, and tag-fusions at the 3'-terminus of any gene. The PCR-mediated gene manipulation with the terminator primers will transform gene expression by allowing for extremely simple and high-throughput experiments with small-scale, multi-well, and mammalian cell cultures.
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Affiliation(s)
- Mikiko Nakamura
- Innovation Center, Yamaguchi University, Tokiwadai, Ube, 755-8611, Japan,
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18
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A fluorogenic substrate of beta-lactamases and its potential as a probe to detect the bacteria resistant to the third-generation oxyimino-cephalosporins. Biosens Bioelectron 2016; 77:1026-31. [DOI: 10.1016/j.bios.2015.10.081] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 10/24/2015] [Accepted: 10/28/2015] [Indexed: 11/19/2022]
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19
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Beerepoot P, Lam VM, Salahpour A. A β-lactamase based assay to measure surface expression of membrane proteins. Methods Mol Biol 2015; 1270:107-14. [PMID: 25702112 DOI: 10.1007/978-1-4939-2309-0_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Measurement of cell surface expression is an essential part of studying membrane proteins. Traditional techniques for measuring surface expression depend on the availability of appropriate radioligands or antibodies towards extracellular epitopes of a protein of interest. The current protocol outlines the use of an assay to monitor surface expression of membrane proteins tagged with a bacterial β-lactamase in mammalian cell lines. The use of this technique allows for quick, quantitative, sensitive, and inexpensive measurement of surface expression, with the potential for high-throughput screening.
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Affiliation(s)
- Pieter Beerepoot
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
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20
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Zuverink M, Barbieri JT. From GFP to β-lactamase: advancing intact cell imaging for toxins and effectors. Pathog Dis 2015; 73:ftv097. [PMID: 26500183 DOI: 10.1093/femspd/ftv097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2015] [Indexed: 11/13/2022] Open
Abstract
Canonical reporters such as green fluorescent protein (GFP) and luciferase have assisted researchers in probing cellular pathways and processes. Prior research in pathogenesis depended on sensitivity of biochemical and biophysical techniques to identify effectors and elucidate entry mechanisms. Recently, the β-lactamase (βlac) reporter system has advanced toxin and effector reporting by permitting measurement of βlac delivery into the cytosol or host βlac expression in intact cells. βlac measurement in cells was facilitated by the development of the fluorogenic substrate, CCF2-AM, to identify novel effectors, target cells, and domains involved in bacterial pathogenesis. The assay is also adaptable for high-throughput screening of small molecule inhibitors against toxins, providing information on mechanism and potential therapeutic agents. The versatility and limitations of the βlac reporter system as applied to toxins and effectors are discussed in this review.
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Affiliation(s)
- Madison Zuverink
- Medical College of Wisconsin, Microbiology and Molecular Genetics, Milwaukee, WI 53226, USA
| | - Joseph T Barbieri
- Medical College of Wisconsin, Microbiology and Molecular Genetics, Milwaukee, WI 53226, USA
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21
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Paramonov VM, Mamaeva V, Sahlgren C, Rivero-Müller A. Genetically-encoded tools for cAMP probing and modulation in living systems. Front Pharmacol 2015; 6:196. [PMID: 26441653 PMCID: PMC4569861 DOI: 10.3389/fphar.2015.00196] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/28/2015] [Indexed: 11/19/2022] Open
Abstract
Intracellular 3′-5′-cyclic adenosine monophosphate (cAMP) is one of the principal second messengers downstream of a manifold of signal transduction pathways, including the ones triggered by G protein-coupled receptors. Not surprisingly, biochemical assays for cAMP have been instrumental for basic research and drug discovery for decades, providing insights into cellular physiology and guiding pharmaceutical industry. However, despite impressive track record, the majority of conventional biochemical tools for cAMP probing share the same fundamental shortcoming—all the measurements require sample disruption for cAMP liberation. This common bottleneck, together with inherently low spatial resolution of measurements (as cAMP is typically analyzed in lysates of thousands of cells), underpin the ensuing limitations of the conventional cAMP assays: (1) genuine kinetic measurements of cAMP levels over time in a single given sample are unfeasible; (2) inability to obtain precise information on cAMP spatial distribution and transfer at subcellular levels, let alone the attempts to pinpoint dynamic interactions of cAMP and its effectors. At the same time, tremendous progress in synthetic biology over the recent years culminated in drastic refinement of our toolbox, allowing us not only to bypass the limitations of conventional assays, but to put intracellular cAMP life-span under tight control—something, that seemed scarcely attainable before. In this review article we discuss the main classes of modern genetically-encoded tools tailored for cAMP probing and modulation in living systems. We examine the capabilities and weaknesses of these different tools in the context of their operational characteristics and applicability to various experimental set-ups involving living cells, providing the guidance for rational selection of the best tools for particular needs.
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Affiliation(s)
- Valeriy M Paramonov
- Department of Physiology, Institute of Biomedicine, University of Turku , Turku, Finland ; Turku Center for Biotechnology, University of Turku and Åbo Akademi University , Turku, Finland
| | - Veronika Mamaeva
- Department of Clinical Science, University of Bergen , Bergen, Norway
| | - Cecilia Sahlgren
- Turku Center for Biotechnology, University of Turku and Åbo Akademi University , Turku, Finland ; Department of Biomedical Engineering, Eindhoven University of Technology , Eindhoven, Netherlands
| | - Adolfo Rivero-Müller
- Department of Physiology, Institute of Biomedicine, University of Turku , Turku, Finland ; Faculty of Natural Sciences and Technology, Åbo Akademi University , Turku, Finland ; Department of Biochemistry and Molecular Biology, Medical University of Lublin , Lublin, Poland
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22
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Peng Y, Zeng W, Ye H, Han K, Dharmarajan V, Novick S, Wilson I, Griffin P, Friedman J, Lerner R. A General Method for Insertion of Functional Proteins within Proteins via Combinatorial Selection of Permissive Junctions. ACTA ACUST UNITED AC 2015; 22:1134-43. [DOI: 10.1016/j.chembiol.2015.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 06/12/2015] [Accepted: 07/06/2015] [Indexed: 10/23/2022]
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23
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Lam VM, Beerepoot P, Angers S, Salahpour A. A Novel Assay for Measurement of Membrane-Protein Surface Expression using a β-lactamase Reporter. Traffic 2013; 14:778-84. [DOI: 10.1111/tra.12073] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2012] [Revised: 04/04/2013] [Accepted: 04/09/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Vincent M. Lam
- Department of Pharmacology and Toxicology; University of Toronto; Toronto; Ontario,; Canada
| | - Pieter Beerepoot
- Department of Pharmacology and Toxicology; University of Toronto; Toronto; Ontario,; Canada
| | - Stephane Angers
- Leslie Dan Faculty of Pharmacy; University of Toronto; Toronto; Ontario,; Canada
| | - Ali Salahpour
- Department of Pharmacology and Toxicology; University of Toronto; Toronto; Ontario,; Canada
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24
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Abstract
The ability to introduce DNA sequences (e.g., genes) of interest into the germline genome has rendered the mouse a powerful and indispensable experimental model in fundamental and medical research. The DNA sequences can be integrated into the genome randomly or into a specific locus by homologous recombination, in order to: (1) delete or insert mutations into genes of interest to determine their function, (2) introduce human genes into the genome of mice to generate animal models enabling study of human-specific genes and diseases, e.g., mice susceptible to infections by human-specific pathogens of interest, (3) introduce individual genes or genomes of pathogens (such as viruses) in order to examine the contributions of such genes to the pathogenesis of the parent pathogens, (4) and last but not least introduce reporter genes that allow monitoring in vivo or ex vivo the expression of genes of interest. Furthermore, the use of recombination systems, such as Cre/loxP or FRT/FLP, enables conditional induction or suppression of gene expression of interest in a restricted period of mouse's lifetime, in a particular cell type, or in a specific tissue. In this review, we will give an updated summary of the gene targeting technology and discuss some important considerations in the design of gene-targeted mice.
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Affiliation(s)
- Hicham Bouabe
- Laboratory of Lymphocyte Signalling and Development, Babraham Institute, Cambridge, UK
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25
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Moss SJ, Stanley-Smith AE, Schell U, Coates NJ, Foster TA, Gaisser S, Gregory MA, Martin CJ, Nur-e-Alam M, Piraee M, Radzom M, Suthar D, Thexton DG, Warneck TD, Zhang MQ, Wilkinson B. Novel FK506 and FK520 analogues via mutasynthesis: mutasynthon scope and product characteristics. MEDCHEMCOMM 2013. [DOI: 10.1039/c2md20266b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel FK506 and FK520 analogues were generated via biosynthetic engineering in order to generate analogue compounds with equal potency but improved pharmacological profiles compared to FK506.
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26
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Abstract
IL-10 is one of the key cytokines preventing inflammation-mediated tissue damage. In an attempt to identify IL-10-producing cells in vivo, several groups have recently developed IL-10 reporter mouse strains. Up until now, in total, eight IL-10 reporter strains have been published. This incomparable interest in IL-10 reporter mice emphasizes the importance and difficulties in tracking and subsequently investigating the role of IL-10-producing cells in infectious, inflammatory, autoimmune and cancer diseases. In this review, I summarize and compare the properties of those published IL-10 reporter mouse models. I also discuss the necessity to develop new strategies to generate 'multi-cytokine' reporter mouse models enabling highly sensitive in/ex vivo detection of many cytokines in the same single cell. Such 'multi-cytokine' reporter mice will enable to reconsider the dichotomy 'T-effector versus T-regulatory' paradigm and to provide an accurate revised model for cellular sources of cytokines. Finally, I propose to launch cooperative, international initiatives to promote and coordinate the generation of accurate, combinatorial, reporter mice for every individual murine cytokine.
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Affiliation(s)
- H Bouabe
- Department of Bacteriology, Max von Pettenkofer Institute, Munich, Germany.
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27
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Schürer SC, Vempati U, Smith R, Southern M, Lemmon V. BioAssay ontology annotations facilitate cross-analysis of diverse high-throughput screening data sets. ACTA ACUST UNITED AC 2011; 16:415-26. [PMID: 21471461 DOI: 10.1177/1087057111400191] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
High-throughput screening data repositories, such as PubChem, represent valuable resources for the development of small-molecule chemical probes and can serve as entry points for drug discovery programs. Although the loose data format offered by PubChem allows for great flexibility, important annotations, such as the assay format and technologies employed, are not explicitly indexed. The authors have previously developed a BioAssay Ontology (BAO) and curated more than 350 assays with standardized BAO terms. Here they describe the use of BAO annotations to analyze a large set of assays that employ luciferase- and β-lactamase-based technologies. They identified promiscuous chemotypes pertaining to different subcategories of assays and specific mechanisms by which these chemotypes interfere in reporter gene assays. Results show that the data in PubChem can be used to identify promiscuous compounds that interfere nonspecifically with particular technologies. Furthermore, they show that BAO is a valuable toolset for the identification of related assays and for the systematic generation of insights that are beyond the scope of individual assays or screening campaigns.
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Affiliation(s)
- Stephan C Schürer
- Center for Computational Science, University of Miami, Miami, Florida 33136, USA.
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28
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Murthy TV, Kroncke D, Bonin PD. Adding precise nanoliter volume capabilities to liquid-handling automation for compound screening experimentation. ACTA ACUST UNITED AC 2011; 16:221-8. [PMID: 21609705 DOI: 10.1016/j.jala.2010.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Indexed: 01/17/2023]
Abstract
Miniaturizing experimental sample volumes to the nanoliter volume range is one of the most economical ways to perform mid- and high-throughput compound screening experiments. Existing automation platforms for nanoliter fluid handling can be bulky, expensive, and require periodic calibration to provide consistent liquid dispensing. In addition, even with frequent calibration, significant instrument-to-instrument variation in low-volume dispensing can occur between different instrument platforms. Many of these issues can be addressed by the use of PocketTips. PocketTips are tips with a defined internal pocket designed to hold specific nanoliter volumes of compound dissolved in dimethylsulfoxide. Although the overall liquid-handling process with PocketTips uses the aspirate/dispense features of the specific liquid-handling device being used, the dispensed nanoliter volume is solely based on the dimensions of the pocket of the PocketTip and thus, the liquid-handling device itself need not have nanoliter dispensing capabilities. In this report, we demonstrate the performance of PocketTips on different automation platforms. In addition, we used a cell-based ß-lactamase reporter assay system to demonstrate that compound delivery by PocketTips compares favorably with a standard compound addition technique.
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Affiliation(s)
- Tal V Murthy
- Applications Laboratories, Thermo Fisher Scientific, Hudson, NH 03051, USA.
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29
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Shukla GS, Krag DN. Phage-displayed combinatorial peptide libraries in fusion to beta-lactamase as reporter for an accelerated clone screening: Potential uses of selected enzyme-linked affinity reagents in downstream applications. Comb Chem High Throughput Screen 2010; 13:75-87. [PMID: 20214576 DOI: 10.2174/138620710790218258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Phage-display selection of combinatorial libraries is a powerful technique for identifying binding ligands against desired targets. Evaluation of target binding capacity of multiple clones recovered from phage display selection to a specific target is laborious, time-consuming, and a rate-limiting step. We constructed phage-display combinatorial peptide libraries in fusion with a beta-lactamase enzyme, which acts as a reporter. Linear dodecapeptide and cysteine-constrained decapeptide libraries were created at the amino-terminus of the Enterobacter cloacae P99 cephalosporinase molecule (P99 beta-lactamase). The overall and positional diversity of amino acids in both libraries was similar to other phage-display systems. The libraries were selected against the extracellular domain of ErbB2 receptor (ErbB2(ECD)). The target-selected clones were already conjugated to an enzyme reporter, therefore, did not require subcloning or any other post-panning modifications. We used beta-lactamase enzyme activity-based assays for sample normalizations and clone binding evaluation. Clones were identified that bound to purified ErbB2(ECD) and ErbB2-overexpressing cell-lines. The peptide sequences of the selected binding clones shared significant motifs with several rationally designed peptide mimetics and phage-display derived peptides that have been reported to bind ErbB2(ECD). beta-Lactamase fusion to peptides saved time and resources otherwise required by the phage-ELISA of a typical phage display screening protocol. The beta-lactamase enzyme assay protocols is a one-step process that does not require secondary proteins, several steps of lengthy incubations, or washings and can be finished in a few minutes instead of hours. The clone screening protocol can be adopted for a high throughput platform. Target-specific beta-lactamase-linked affinity reagents selected by this procedure can be produced in bulk, purified, and used, without any modification, for a variety of downstream applications, including targeted prodrug therapy.
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Affiliation(s)
- Girja S Shukla
- Department of Surgery and Vermont Cancer Center, University of Vermont College of Medicine, Burlington, 05405, USA.
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30
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Suzuki G, Kawamoto H, Ohta H. Development of a β-Lactamase Reporter Gene Assay for Metabotropic Glutamate Receptor 1 by Using Coexpression of Glutamate Transporter. ACTA ACUST UNITED AC 2010; 15:148-58. [DOI: 10.1177/1087057109356982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
mGluR1 antagonists have been postulated to be novel CNS drugs, including antipsychotics. Toward this end, the authors developed a β-lactamase reporter assay to identify mGluR1 antagonists. β-Lactamase has several interesting features for high-throughput screening, including very high sensitivity and less well-to-well variation than other reporter enzymes. mGluR1-expressing Chinese hamster ovary (CHO) cells with the β-lactamase gene under control of the nuclear factor of activated T cells (NFAT) promoter (CHO-NFAT-bla-hmGluR1b) exhibited very high basal activity, resulting in an inadequate signal-to-basal (S/B) ratio. Coexpression of glutamate/aspartate transporter (GLAST) with mGluR1 in the cell line (CHO-NFAT-bla-hmGluR1b-GLAST) dramatically decreased basal activity and improved the S/B ratio (from 2- to 20-fold). The contribution of GLAST to lowering basal activity and increasing the S/B ratio was validated by the expression level of GLAST mRNA and by a GLAST inhibitor. Antagonistic activities of known mGluR1 antagonists in the β-lactamase reporter assay were comparable with those in the conventional Ca2+ mobilization assay. The Z′ factor of the β-lactamase reporter assay was 0.89 under optimized conditions. Taken together, the β-lactamase reporter assay with CHO-NFAT-bla-hmGluR1b-GLAST could be a novel high-throughput assay for mGluR1 antagonist screening. This is the first description of a successful β-lactamase reporter assay among all mGluR subtypes.
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Affiliation(s)
- Gentaroh Suzuki
- Tsukuba Research Institute, Banyu Pharmaceutical Co., Ltd., Tsukuba, Ibaraki, Japan
- Department of Molecular and System Pharmacology, Graduate School of Pharmaceutical Sciences, Kyushu University, Higashi, Fukuoka, Japan
- Central Pharmaceutical Research Institute, Japan Tobacco, Inc., Osaka, Japan
- Central Pharmaceutical Research Institute, Japan Tobacco, Inc., Osaka, Japan
| | - Hiroshi Kawamoto
- Tsukuba Research Institute, Banyu Pharmaceutical Co., Ltd., Tsukuba, Ibaraki, Japan
| | - Hisashi Ohta
- Tsukuba Research Institute, Banyu Pharmaceutical Co., Ltd., Tsukuba, Ibaraki, Japan
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Foit L, Morgan GJ, Kern MJ, Steimer LR, von Hacht AA, Titchmarsh J, Warriner SL, Radford SE, Bardwell JC. Optimizing protein stability in vivo. Mol Cell 2009; 36:861-71. [PMID: 20005848 PMCID: PMC2818778 DOI: 10.1016/j.molcel.2009.11.022] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Revised: 08/04/2009] [Accepted: 10/24/2009] [Indexed: 11/23/2022]
Abstract
Identifying mutations that stabilize proteins is challenging because most substitutions are destabilizing. In addition to being of immense practical utility, the ability to evolve protein stability in vivo may indicate how evolution has formed today's protein sequences. Here we describe a genetic selection that directly links the in vivo stability of proteins to antibiotic resistance. It allows the identification of stabilizing mutations within proteins. The large majority of mutants selected for improved antibiotic resistance are stabilized both thermodynamically and kinetically, indicating that similar principles govern stability in vivo and in vitro. The approach requires no prior structural or functional knowledge and allows selection for stability without a need to maintain function. Mutations that enhance thermodynamic stability of the protein Im7 map overwhelmingly to surface residues involved in binding to colicin E7, showing how the evolutionary pressures that drive Im7-E7 complex formation have compromised the stability of the isolated Im7 protein.
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Affiliation(s)
- Linda Foit
- Howard Hughes Medical Institute University of Michigan, Ann Arbor, MI 48109, USA
- Institute for Chemistry and Pharmacy, University of Münster, 48149 Münster, Germany
| | - Gareth J. Morgan
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, UK
- Institute for Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Maximilian J. Kern
- Howard Hughes Medical Institute University of Michigan, Ann Arbor, MI 48109, USA
| | - Lenz R. Steimer
- Howard Hughes Medical Institute University of Michigan, Ann Arbor, MI 48109, USA
| | | | - James Titchmarsh
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, UK
- School of Chemistry, University of Leeds, LS2 9JT UK
| | - Stuart L. Warriner
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, UK
- School of Chemistry, University of Leeds, LS2 9JT UK
| | - Sheena E. Radford
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, UK
- Institute for Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - James C.A. Bardwell
- Howard Hughes Medical Institute University of Michigan, Ann Arbor, MI 48109, USA
- Department of Molecular, Cellular and Developmental Biology University of Michigan, Ann Arbor, MI 48109, USA
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Cui M, Chung F, Donahue CJ. Development of a robust GABABcalcium signaling cell line using β‐lactamase technology and sorting. Cytometry A 2008; 73:761-6. [DOI: 10.1002/cyto.a.20591] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Vandevenne M, Gaspard G, Yilmaz N, Giannotta F, Frère JM, Galleni M, Filée P. Rapid and easy development of versatile tools to study protein/ligand interactions. Protein Eng Des Sel 2008; 21:443-51. [PMID: 18456870 DOI: 10.1093/protein/gzn021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The system described here allows the expression of protein fragments into a solvent-exposed loop of a carrier protein, the beta-lactamase BlaP. When using Escherichia coli constitutive expression vectors, a positive selection of antibioresistant bacteria expressing functional hybrid beta-lactamases is achieved in the presence of beta-lactams making further screening of correctly folded and secreted hybrid beta-lactamases easier. Protease-specific recognition sites have been engineered on both sides of the beta-lactamase permissive loop in order to cleave off the exogenous protein fragment from the carrier protein by an original two-step procedure. According to our data, this approach constitutes a suitable alternative for production of difficult to express protein domains. This work demonstrates that the use of BlaP as a carrier protein does not alter the biochemical activity and the native disulphide bridge formation of the inserted chitin binding domain of the human macrophage chitotriosidase. We also report that the beta-lactamase activity of the hybrid protein can be used to monitor interactions between the inserted protein fragments and its ligands and to screen neutralizing molecules.
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Affiliation(s)
- M Vandevenne
- Macromolécules biologiques, Centre d'Ingénierie des Protéines, Université de Liège, Sart-Tilman, Liège, Belgium
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