1
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Liu Z, Wang H, Li Y, Meng N, Liu H, Ding K, Fu R. PIM2 kinase regulates the expression of TIGIT and energy metabolism on NK cell in multiple myeloma patients.. [DOI: 10.21203/rs.3.rs-2159151/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Abstract
Background: PIM2 kinase play a vital role in the generation of plasma cell and bone loss in multiple myeloma(MM), which highly related to the tumor progression and as a potential therapy target in MM. In immune cell,PIM2 kinase involved in the regulation of lymphocyte like T cell and B cell, However, its role in NK cells remains unclear.
Methods: Single-cell RNA sequencing data were analysed the expression of PIM2 kinase in NK cells from MM patients and healthy donors.Immune checkpoint expression, cell apoptosis, and NK cell function had been evaluated through flow cytometry.Then, NCBI, UCSC, JASPAR and GEPIA database were used to predict promoter of TIGIT.NK-92 cells with ETS-1 knockdown were established by using sh-RNA. Kinase functional assay (ADP-Glo) were used to confirm PIM2 inhibitor from 160 kinds of natural flavonoids compound.Samples treated with or without drugs were analyzed using mass spectrometry and RNA-seq. The oxygen consumption rate (OCR), and the extracellular acidification rate (ECAR) were measured by assay kit.
Result: The PIM2 kinase was highly expressed in the NK cells from MM patients based on single-cell sequencing analysis and confirmed in clinical sample by PCR and flow cytometry.Inhibition of PIM2 kinase can increase the function of NK cells and down regulation TIGIT expression. Mechanism, we confirmed that ETS-1 which was directly binding to the promoter of TIGIT was up-regulated by PIM2 kinase, which can lead the strengthened transcription of TIGIT on NK cells.Furthermore, two novel natural flavonoids compound named Kaempferol and Quercetin dihydrate as PIM2 kinase inhibitors exhibiting higher efficiency at low dose in MM cells,while influence the expression of TIGIT and energy metabolism on NK-92 cells. For in vitro experiment,PIM2 kinase inhibitors can activate NK cell killing function and decrease TIGIT expression,while promoted the apoptosis of MM cells irrespective of adding BMSCs or not in co-culture systems BMSCs.
Conclusion: PIM2 kinase involved in the regulation of NK cell.Inhibiting PIM2 kinase could down-regulate the expression of TIGIT and improve energy metabolism to enhance NK cell anti myeloma cell.
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Affiliation(s)
| | | | | | | | | | | | - Rong Fu
- Tianjin Medical University General Hospital
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2
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Abramczyk H, Imiela A, Brożek-Płuska B, Kopeć M, Surmacki J, Śliwińska A. Aberrant Protein Phosphorylation in Cancer by Using Raman Biomarkers. Cancers (Basel) 2019; 11:E2017. [PMID: 31847192 PMCID: PMC6966530 DOI: 10.3390/cancers11122017] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/03/2019] [Accepted: 12/11/2019] [Indexed: 12/30/2022] Open
Abstract
(1) Background: Novel methods are required for analysing post-translational modifications of protein phosphorylation by visualizing biochemical landscapes of proteins in human normal and cancerous tissues and cells. (2) Methods: A label-free Raman method is presented for detecting spectral changes that arise in proteins due to phosphorylation in the tissue of human breasts, small intestines, and brain tumours, as well as in the normal human astrocytes and primary glioblastoma U-87 MG cell lines. Raman spectroscopy and Raman imaging are effective tools for monitoring and analysing the vibrations of functional groups involved in aberrant phosphorylation in cancer without any phosphorecognition of tag molecules. (3) Results: Our results based on 35 fresh human cancer and normal tissues prove that the aberrant tyrosine phosphorylation monitored by the unique spectral signatures of Raman vibrations is a universal characteristic in the metabolic regulation in different types of cancers. Overexpressed tyrosine phosphorylation in the human breast, small intestine and brain tissues and in the human primary glioblastoma U-87 MG cell line was monitored by using Raman biomarkers. (4) We showed that the bands at 1586 cm-1 and 829 cm-1, corresponding to phosphorylated tyrosine, play a pivotal role as a Raman biomarker of the phosphorylation status in aggressive cancers. We found that the best Raman biomarker of phosphorylation is the 1586/829 ratio showing the statistical significance at p Values of ≤ 0.05. (5) Conclusions: Raman spectroscopy and imaging have the potential to be used as screening functional assays to detect phosphorylated target proteins and will help researchers to understand the role of phosphorylation in cellular processes and cancer progression. The abnormal and excessive high level of tyrosine phosphorylation in cancer samples compared with normal samples was found in the cancerous human tissue of breasts, small intestines and brain tumours, as well as in the mitochondria and lipid droplets of the glioblastoma U-87 MG cell line. Detailed insights are presented into the intracellular oncogenic metabolic pathways mediated by phosphorylated tyrosine.
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Affiliation(s)
- Halina Abramczyk
- Laboratory of Laser Molecular Spectroscopy, Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Wroblewskiego 15, 93-590 Lodz, Poland; (A.I.); (B.B.-P.); (M.K.); (J.S.)
| | - Anna Imiela
- Laboratory of Laser Molecular Spectroscopy, Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Wroblewskiego 15, 93-590 Lodz, Poland; (A.I.); (B.B.-P.); (M.K.); (J.S.)
| | - Beata Brożek-Płuska
- Laboratory of Laser Molecular Spectroscopy, Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Wroblewskiego 15, 93-590 Lodz, Poland; (A.I.); (B.B.-P.); (M.K.); (J.S.)
| | - Monika Kopeć
- Laboratory of Laser Molecular Spectroscopy, Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Wroblewskiego 15, 93-590 Lodz, Poland; (A.I.); (B.B.-P.); (M.K.); (J.S.)
| | - Jakub Surmacki
- Laboratory of Laser Molecular Spectroscopy, Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Wroblewskiego 15, 93-590 Lodz, Poland; (A.I.); (B.B.-P.); (M.K.); (J.S.)
| | - Agnieszka Śliwińska
- Faculty of Medicine, Medical University of Lodz, Chair of Department of Nucleic Acids Biochemistry, Pomorska 251, 92-213 Lodz, Poland;
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3
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Precise Quantification of Platelet Proteins and Their Phosphorylation States. Methods Mol Biol 2018. [PMID: 30171575 DOI: 10.1007/978-1-4939-8585-2_7] [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
Systems biology and modeling approaches require quantitative data-rich temporal experiments to better understand the dynamics and regulation of the components of the signaling pathways that governs cell biology and physiology. Here we present a modified Western blotting method to rapidly analyze and accurately quantify protein copy number, and their respective phosphorylation states at specific sites over detailed time courses.
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4
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Ahmed M, Carrascosa LG, Ibn Sina AA, Zarate EM, Korbie D, Ru KL, Shiddiky MJ, Mainwaring P, Trau M. Detection of aberrant protein phosphorylation in cancer using direct gold-protein affinity interactions. Biosens Bioelectron 2017; 91:8-14. [DOI: 10.1016/j.bios.2016.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/27/2016] [Accepted: 12/06/2016] [Indexed: 01/06/2023]
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5
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Han W, Zhu J, Wang S, Xu D. Understanding the Phosphorylation Mechanism by Using Quantum Chemical Calculations and Molecular Dynamics Simulations. J Phys Chem B 2017; 121:3565-3573. [PMID: 27976577 PMCID: PMC6138447 DOI: 10.1021/acs.jpcb.6b09421] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Phosphorylation is one of the most frequent post-translational modifications on proteins. It regulates many cellular processes by modulation of phosphorylation on protein structure and dynamics. However, the mechanism of phosphorylation-induced conformational changes of proteins is still poorly understood. Here, we report a computational study of three representative groups of tyrosine in ADP-ribosylhydrolase 1, serine in BTG2, and serine in Sp100C by using six molecular dynamics (MD) simulations and quantum chemical calculations. Added phosphorylation was found to disrupt hydrogen bond, and increase new weak interactions (hydrogen bond and hydrophobic interaction) during MD simulations, leading to conformational changes. Quantum chemical calculations further indicate that the phosphorylation on tyrosine, threonine, and serine could decrease the optical band gap energy (Egap), which can trigger electronic transitions to form or disrupt interactions easily. Our results provide an atomic and electronic description of how phosphorylation facilitates conformational and dynamic changes in proteins, which may be useful for studying protein function and protein design.
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Affiliation(s)
- Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
- Department of Computer Science, C.S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65201, USA
| | - Jingxuan Zhu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Song Wang
- Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Dong Xu
- Department of Computer Science, C.S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65201, USA
- College of Computer Science and Technology Jilin University, 2699 Qianjin Street, Changchun 130012, China
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6
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Sartori A, Portioli E, Battistini L, Calorini L, Pupi A, Vacondio F, Arosio D, Bianchini F, Zanardi F. Synthesis of Novel c(AmpRGD)-Sunitinib Dual Conjugates as Molecular Tools Targeting the α vβ 3 Integrin/VEGFR2 Couple and Impairing Tumor-Associated Angiogenesis. J Med Chem 2016; 60:248-262. [PMID: 27997164 DOI: 10.1021/acs.jmedchem.6b01266] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
On the basis of a previously discovered anti-αVβ3 integrin peptidomimetic (c(AmpRGD)) and the clinically approved antiangiogenic kinase inhibitor sunitinib, three novel dual conjugates were synthesized (compounds 1-3), featuring the covalent and robust linkage between these two active modules. In all conjugates, the ligand binding competence toward αVβ3 (using both isolated receptors and αVβ3-overexpressing endothelial progenitor EP cells) and the kinase inhibitory activity (toward both isolated kinases and EPCs) remained almost untouched and comparable to the activity of the single active units. Compounds 1-3 showed interesting antiangiogenesis properties in an in vitro tubulogenic assay; furthermore, dimeric-RGD conjugate 3 strongly inhibited in vivo angiogenesis in Matrigel plug assays in FVB mice. These results offer proof-of-concept of how the covalent conjugation of two angiogenesis-related small modules may result in novel and stable molecules, which impair tumor-related angiogenesis with equal or even superior ability as compared to the single modules or their simple combinations.
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Affiliation(s)
- Andrea Sartori
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27A, 43124 Parma, Italy
| | - Elisabetta Portioli
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27A, 43124 Parma, Italy
| | - Lucia Battistini
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27A, 43124 Parma, Italy
| | - Lido Calorini
- Dipartimento di Scienze Biomediche, Sperimentali e Cliniche "Mario Serio", Università degli Studi di Firenze , Viale G. B. Morgagni 50, 50134 Firenze, Italy
| | - Alberto Pupi
- Dipartimento di Scienze Biomediche, Sperimentali e Cliniche "Mario Serio", Università degli Studi di Firenze , Viale G. B. Morgagni 50, 50134 Firenze, Italy.,Centro Interdipartimentale per lo Sviluppo Preclinico dell'Imaging Molecolare (CISPIM), Università degli Studi di Firenze , Viale G. B. Morgagni 50, 50134 Firenze, Italy
| | - Federica Vacondio
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27A, 43124 Parma, Italy
| | - Daniela Arosio
- Istituto di Scienze e Tecnologie Molecolari, Consiglio Nazionale delle Ricerche , Via Golgi 19, 20133 Milano, Italy
| | - Francesca Bianchini
- Dipartimento di Scienze Biomediche, Sperimentali e Cliniche "Mario Serio", Università degli Studi di Firenze , Viale G. B. Morgagni 50, 50134 Firenze, Italy.,Centro Interdipartimentale per lo Sviluppo Preclinico dell'Imaging Molecolare (CISPIM), Università degli Studi di Firenze , Viale G. B. Morgagni 50, 50134 Firenze, Italy
| | - Franca Zanardi
- Dipartimento di Farmacia, Università degli Studi di Parma , Parco Area delle Scienze 27A, 43124 Parma, Italy
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7
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Choi H, Choi B, Seo JT, Lee KJ, Gye MC, Kim YP. Rapid Detection of Glycogen Synthase Kinase-3 Activity in Mouse Sperm Using Fluorescent Gel Shift Electrophoresis. SENSORS 2016; 16:s16040551. [PMID: 27092510 PMCID: PMC4851065 DOI: 10.3390/s16040551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2016] [Revised: 03/30/2016] [Accepted: 04/13/2016] [Indexed: 12/17/2022]
Abstract
Assaying the glycogen synthase kinase-3 (GSK3) activity in sperm is of great importance because it is closely implicated in sperm motility and male infertility. While a number of studies on GSK3 activity have relied on labor-intensive immunoblotting to identify phosphorylated GSK3, here we report the simple and rapid detection of GSK3 activity in mouse sperm using conventional agarose gel electrophoresis and a fluorescent peptide substrate. When a dye-tethered and prephosphorylated (primed) peptide substrate for GSK3 was employed, a distinct mobility shift in the fluorescent bands on the agarose was observed by GSK3-induced phosphorylation of the primed peptides. The GSK3 activity in mouse testes and sperm were quantifiable by gel shift assay with low sample consumption and were significantly correlated with the expression levels of GSK3 and p-GSK3. We suggest that our assay can be used for reliable and rapid detection of GSK3 activity in cells and tissue extracts.
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Affiliation(s)
- Hoseok Choi
- Department of Life Science, Hanyang University, Seoul 04763, Korea.
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea.
| | - Bomi Choi
- Department of Life Science, Hanyang University, Seoul 04763, Korea.
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea.
| | - Ju Tae Seo
- Department of Urology, College of Medicine, Dankook University, Cheil General Hospital, Seoul 04619, Korea.
| | - Kyung Jin Lee
- Department of Convergence Medicine, Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea.
| | - Myung Chan Gye
- Department of Life Science, Hanyang University, Seoul 04763, Korea.
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea.
| | - Young-Pil Kim
- Department of Life Science, Hanyang University, Seoul 04763, Korea.
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea.
- Institute of Nano Science and Technology, Hanyang University, Seoul 04763, Korea.
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Korea.
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8
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Dong M, Liu X, Dang Q, Qi H, Huang Y, Gao Q, Zhang C. Sensitive and versatile electrogenerated chemiluminescence biosensing platform for protein kinase based on Ru(bpy)32+ functionalized gold nanoparticles mediated signal transduction. Anal Chim Acta 2016; 906:72-79. [DOI: 10.1016/j.aca.2015.11.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/19/2015] [Accepted: 11/25/2015] [Indexed: 01/10/2023]
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9
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Abstract
Cell-based assays have the potential and advantage to identify cell-permeable modulators of kinase function, and hence provide an alternative to the conventional enzymatic activity-driven discovery approaches that rely on purified recombinant kinase catalytic domains. Here, we describe a domain-based high-content biosensor approach to study endogenous EGFR activity whereby EGF-induced receptor activation, subsequent trafficking, and internalization are imaged and quantified using time-dependent granule formation in cells. This method can readily be used to search for EGFR modulators in both chemical and RNAi screening; with potential applicability to other receptor tyrosine kinases.
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10
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Wang H, Duan Y, Zhong W. ZrO2 Nanofiber as a Versatile Tool for Protein Analysis. ACS APPLIED MATERIALS & INTERFACES 2015; 7:26414-20. [PMID: 26571083 DOI: 10.1021/acsami.5b09348] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Phosphorylation is one of the most important post-translational modifications in proteins. Their essential roles in the regulation of cellular processes and alteration of protein-protein interaction networks have been actively studied. However, phosphorylated proteins are present at low abundance in cells, and ionization of the modified peptides is often suppressed by the more abundant species in mass spectrometry. Effective enrichment techniques are needed to remove the unmodified peptides and concentrate the phosphorylated ones before their identification and quantification. Herein, we prepared ZrO2 nanofibers by electrospinning, a straightforward and easy fabrication technique, and applied them to enrich phosphorylated peptides and proteins. The fibers showed good size homogeneity and porosity and could specifically bind to the phosphorylated peptides and proteins, allowing their separation from the unmodified analogues when present in either simple protein digests or highly complex cell lysates. The enrichment performance was superior to that of the commercially available nanoparticles. Moreover, modifying the solution pH could lead to selective adsorption of proteins with different pI values, suggesting the fibers' potential applicability in charge-based protein fractionation. Our results support that the electrospun ZrO2 nanofibers can serve as a versatile tool for protein analysis with great ease in preparation and handling.
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Affiliation(s)
- Hui Wang
- Department of Chemistry, University of California , Riverside, California, United States
| | - Yaokai Duan
- Department of Chemistry, University of California , Riverside, California, United States
| | - Wenwan Zhong
- Department of Chemistry, University of California , Riverside, California, United States
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11
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Mazet F, Dunster JL, Jones CI, Vaiyapuri S, Tindall MJ, Fry MJ, Gibbins JM. A high-density immunoblotting methodology for quantification of total protein levels and phosphorylation modifications. Sci Rep 2015; 5:16995. [PMID: 26592927 PMCID: PMC4655314 DOI: 10.1038/srep16995] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/22/2015] [Indexed: 01/04/2023] Open
Abstract
The components of many signaling pathways have been identified and there is now a need to conduct quantitative data-rich temporal experiments for systems biology and modeling approaches to better understand pathway dynamics and regulation. Here we present a modified Western blotting method that allows the rapid and reproducible quantification and analysis of hundreds of data points per day on proteins and their phosphorylation state at individual sites. The approach is of particular use where samples show a high degree of sample-to-sample variability such as primary cells from multiple donors. We present a case study on the analysis of >800 phosphorylation data points from three phosphorylation sites in three signaling proteins over multiple time points from platelets isolated from ten donors, demonstrating the technique's potential to determine kinetic and regulatory information from limited cell numbers and to investigate signaling variation within a population. We envisage the approach being of use in the analysis of many cellular processes such as signaling pathway dynamics to identify regulatory feedback loops and the investigation of potential drug/inhibitor responses, using primary cells and tissues, to generate information about how a cell's physiological state changes over time.
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Affiliation(s)
- F Mazet
- The University of Reading, Whiteknights, Reading, RG6 6AS, UK
| | - J L Dunster
- The University of Reading, Whiteknights, Reading, RG6 6AS, UK
| | - C I Jones
- The University of Reading, Whiteknights, Reading, RG6 6AS, UK
| | - S Vaiyapuri
- The University of Reading, Whiteknights, Reading, RG6 6AS, UK
| | - M J Tindall
- The University of Reading, Whiteknights, Reading, RG6 6AS, UK
| | - M J Fry
- The University of Reading, Whiteknights, Reading, RG6 6AS, UK
| | - J M Gibbins
- The University of Reading, Whiteknights, Reading, RG6 6AS, UK
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12
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MacConaghy KI, Chadly DM, Stoykovich MP, Kaar JL. Optically diffracting hydrogels for screening kinase activity in vitro and in cell lysate: impact of material and solution properties. Anal Chem 2015; 87:3467-75. [PMID: 25714913 DOI: 10.1021/acs.analchem.5b00442] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Optically diffracting films based on hydrogel-encapsulated crystalline colloidal arrays have considerable utility as sensors for detecting enzymaticphosphorylation and, thus, in screening small molecule modulators of kinases. In this work, we have investigated the impact of hydrogel properties, as well as the role of the ionic character of the surrounding environment, on the optical sensitivity of kinase responsive crystalline colloidal array-containing hydrogels. In agreement with a model of hydrogel swelling, the optical sensitivity of such materials increased as the shear modulus and the Flory-Huggins interaction parameter between polymer and solvent decreased. Additionally, elimination of extraneous charges in the polymer backbone by exploiting azide-alkyne click chemistry to functionalize the hydrogels with a peptide substrate for protein kinase A further enhanced the sensitivity of the optically diffracting films. Increasing peptide concentration and, in turn, immobilized charge within the hydrogel network was shown to increase the optical response over a range of ionic strength conditions. Ultimately, we showed that, by tuning the hydrogel and solution properties, as little as 0.1 U/μL protein kinase A could be detected in short reaction times (i.e., 2 h), which is comparable to conventional biochemical kinase assays. We further showed that this approach can be used to detect protein kinase A activity in lysate from HEK293 cells. The sensitivity of the resulting films, coupled with the advantages of photonic crystal based sensors (e.g., label free detection), makes this approach highly attractive for screening enzymatic phosphorylation.
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Affiliation(s)
- Kelsey I MacConaghy
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, Colorado 80309, United States
| | - Duncan M Chadly
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, Colorado 80309, United States
| | - Mark P Stoykovich
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, Colorado 80309, United States
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 596, Boulder, Colorado 80309, United States
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13
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Wang N, She Z, Lin YC, Martić S, Mann DJ, Kraatz HB. Clickable 5′-γ-Ferrocenyl Adenosine Triphosphate Bioconjugates in Kinase-Catalyzed Phosphorylations. Chemistry 2015; 21:4988-99. [DOI: 10.1002/chem.201405510] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Indexed: 11/07/2022]
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14
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Tang S, Hu Y, Shen Q, Fang H, Li W, Nie Z, Yao S. Cyclic-AMP-dependent protein kinase (PKA) activity assay based on FRET between cationic conjugated polymer and chromophore-labeled peptide. Analyst 2014; 139:4710-6. [DOI: 10.1039/c4an00814f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Liu X, Li Y, Xu X, Li P, Nie Z, Huang Y, Yao S. Nanomaterial-based tools for protein kinase bioanalysis. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2014.01.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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16
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Spry C, Saliba KJ, Strauss E. A miniaturized assay for measuring small molecule phosphorylation in the presence of complex matrices. Anal Biochem 2014; 451:76-8. [DOI: 10.1016/j.ab.2013.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/03/2013] [Accepted: 12/06/2013] [Indexed: 11/15/2022]
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17
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Quantification and kinetic analysis of Grb2-EGFR interaction on micro-patterned surfaces for the characterization of EGFR-modulating substances. PLoS One 2014; 9:e92151. [PMID: 24658383 PMCID: PMC3962377 DOI: 10.1371/journal.pone.0092151] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 02/17/2014] [Indexed: 11/25/2022] Open
Abstract
The identification of the epidermal growth factor receptor (EGFR) as an oncogene has led to the development of several anticancer therapeutics directed against this receptor tyrosine kinase. However, drug resistance and low efficacy remain a severe challenge, and have led to a demand for novel systems for an efficient identification and characterization of new substances. Here we report on a technique which combines micro-patterned surfaces and total internal reflection fluorescence (TIRF) microscopy (μ-patterning assay) for the quantitative analysis of EGFR activity. It does not simply measure the phosphorylation of the receptor, but instead quantifies the interaction of the key signal transmitting protein Grb2 (growth factor receptor-bound protein 2) with the EGFR in a live cell context. It was possible to demonstrate an EGF dependent recruitment of Grb2 to the EGFR, which was significantly inhibited in the presence of clinically tested EGFR inhibitors, including small tyrosine kinase inhibitors and monoclonal antibodies targeting the EGF binding site. Importantly, in addition to its potential use as a screening tool, our experimental setup offers the possibility to provide insight into the molecular mechanisms of bait-prey interaction. Recruitment of the EGFR together with Grb2 to clathrin coated pits (CCPs) was found to be a key feature in our assay. Application of bleaching experiments enabled calculation of the Grb2 exchange rate, which significantly changed upon stimulation or the presence of EGFR activity inhibiting drugs.
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18
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Hoffmann BR, Wagner JR, Prisco AR, Janiak A, Greene AS. Vascular endothelial growth factor-A signaling in bone marrow-derived endothelial progenitor cells exposed to hypoxic stress. Physiol Genomics 2013; 45:1021-34. [PMID: 24022223 PMCID: PMC3841787 DOI: 10.1152/physiolgenomics.00070.2013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 09/09/2013] [Indexed: 01/13/2023] Open
Abstract
Bone marrow-derived endothelial progenitor cells (BM-EPCs) are stimulated by vascular endothelial growth factor-A (VEGF-A) and other potent proangiogenic factors. During angiogenesis, an increase in VEGF-A expression stimulates BM-EPCs to enhance endothelial tube formation and contribute to an increase in microvessel density. Hypoxia is known to produce an enhanced angiogenic response and heightened levels of VEGF-A have been seen in oxygen deprived epithelial and endothelial cells, yet the pathways for VEGF-A signaling in BM-EPCs have not been described. This study explores the influence of hypoxia on VEGF-A signaling in rat BM-EPCs utilizing a novel proteomic strategy to directly identify interacting downstream components of the combined VEGF receptor(s) signaling pathways, gene expression analysis, and functional phenotyping. VEGF-A signaling network analysis following liquid chromatographic separation and tandem mass spectrometry revealed proteins related to inositol/calcium signaling, nitric oxide signaling, cell survival, cell migration, and inflammatory responses. Alterations in BM-EPC expression of common angiogenic genes and tube formation in response to VEGF-A during hypoxia were measured and combined with the proteomic analysis to enhance and support the signaling pathways detected. BM-EPC tube formation assays in response to VEGF-A exhibited little tube formation; however, a cell projection/migratory phenotype supported the signaling data. Additionally, a novel assay measuring BM-EPC incorporation into preformed endothelial cell tubes indicated a significant increase of incorporated BM-EPCs after pretreatment with VEGF-A during hypoxia. This study verifies known VEGF-A pathway components and reveals several unidentified mechanisms of VEGF-A signaling in BM-EPCs during hypoxia that may be important for migration to sites of vascular regeneration.
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Affiliation(s)
- Brian R Hoffmann
- Biotechnology and Bioengineering Center, Medical College of Wisconsin, Milwaukee, Wisconsin; and
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19
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Bai J, Zhao Y, Wang Z, Liu C, Wang Y, Li Z. Dual-readout fluorescent assay of protein kinase activity by use of TiO2-coated magnetic microspheres. Anal Chem 2013; 85:4813-21. [PMID: 23581884 DOI: 10.1021/ac400799w] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A simple, highly sensitive, and dual-readout fluorescent assay is developed for the detection of protein kinase activity based on the specific recognition utility of TiO2-coated Fe3O4/SiO2 magnetic microspheres (TMSPs) for kinase-induced phosphopeptides. When the fluorophore-labeled substrate peptides are phosphorylated by the kinase reaction, they can bind specifically to the TiO2 layer of TMSPs by means of phosphate groups, resulting in fluorophore enrichment on the TMSP surfaces. The accumulated fluorophores on the TMSPs are proportional to the kinase activity, and the fluorescence signal readout could be run through either direct fluorescent imaging of the TMSPs or measurement of the fluorescence intensity by simply detaching the fluorescent phosphopeptides into the solution. The TMSPs exhibit extremely high selectivity for capturing phosphorylated peptides over the nonphosphorylated ones, resulting in an ultrahigh fluorescence signal-to-background ratio of 42, which is the highest fluorescence change thus far in fluorescent assays for detection of protein kinase activities. Therefore, the proposed fluorescent assay presents high sensitivity, low detection limit of 0.1 milliunit/μL, and wide dynamic range from 0.5 milliunit/μL to 0.5 unit/μL with protein kinase A (PKA) as a model target. Moreover, the TMSP-based fluorescent assay can simultaneously quantify multiple kinase activities with their specific peptides labeled with different dyes. This new strategy is also successfully applied to monitoring drug-triggered PKA activation in cell lysates. Therefore, the TMSP-based fluorescent assay is very promising in high-throughput screening of kinase inhibitors and in highly sensitive detection of kinase activity, and thus it is a valuable tool for development of targeted therapy, clinical diagnosis, and studies of fundamental life science.
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Affiliation(s)
- Jie Bai
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, College of Chemistry and Environmental Science, Hebei University, Baoding 071002, Hebei Province, People's Republic of China
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20
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Khawaja X, Dunlop J, Kowal D. Scintillation proximity assay in lead discovery. Expert Opin Drug Discov 2013; 3:1267-80. [PMID: 23496165 DOI: 10.1517/17460441.3.11.1267] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Scintillation proximity assay (SPA) is a homogeneous scintillant bead-based platform for the measurement of biological processes and plays an important role in the identification of active chemical entities in drug discovery. OBJECTIVE The design and development of solid-phase SPA approaches are examined and compared with alternative non-radiometric fluorescence-based technologies. METHODS This review provides background on the principle of SPA and its application to biomolecular interactions from a variety of biological sources. CONCLUSION The SPA approach is well suited to the demands of commercial high volume automation and assay miniaturization for target-based high-throughput screening campaigns on synthetic and natural product libraries as well as for benchtop characterization and confirmation studies. In the near future, innovations in the way SPA and fluorescence-based screening strategies are multiplexed will improve our comprehensive understanding of cellular system biology and dramatically advance the lead discovery process for the treatment of complex target-related disorders.
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Affiliation(s)
- Xavier Khawaja
- Depression and Anxiety, Neuroscience Discovery Research, Wyeth Research, Princeton, NJ 08543, USA +1 732 274 4382 ; +1 732 274 4020 ;
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21
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Martić S, Gabriel M, Turowec JP, Litchfield DW, Kraatz HB. Versatile Strategy for Biochemical, Electrochemical and Immunoarray Detection of Protein Phosphorylations. J Am Chem Soc 2012; 134:17036-45. [DOI: 10.1021/ja302586q] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Sanela Martić
- Department of Physical and Environmental
Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada, and Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Michelle Gabriel
- Department of Biochemistry,
Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Jacob P. Turowec
- Department of Biochemistry,
Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - David W. Litchfield
- Department of Biochemistry,
Schulich School of Medicine and Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental
Sciences, University of Toronto Scarborough, Toronto, Ontario M1C 1A4, Canada, and Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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22
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Tognolini M, Incerti M, Mohamed IH, Giorgio C, Russo S, Bruni R, Lelli B, Bracci L, Noberini R, Pasquale EB, Barocelli E, Vicini P, Mor M, Lodola A. Structure-activity relationships and mechanism of action of Eph-ephrin antagonists: interaction of cholanic acid with the EphA2 receptor. ChemMedChem 2012; 7:1071-83. [PMID: 22529030 PMCID: PMC3677030 DOI: 10.1002/cmdc.201200102] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Revised: 03/23/2012] [Indexed: 01/08/2023]
Abstract
The Eph-ephrin system, including the EphA2 receptor and the ephrinA1 ligand, plays a critical role in tumor and vascular functions during carcinogenesis. We previously identified (3α,5β)-3-hydroxycholan-24-oic acid (lithocholic acid) as an Eph-ephrin antagonist that is able to inhibit EphA2 receptor activation; it is therefore potentially useful as a novel EphA2 receptor-targeting agent. Herein we explore the structure-activity relationships of a focused set of lithocholic acid derivatives based on molecular modeling investigations and displacement binding assays. Our exploration shows that while the 3-α-hydroxy group of lithocholic acid has a negligible role in recognition of the EphA2 receptor, its carboxylate group is critical for disrupting the binding of ephrinA1 to EphA2. As a result of our investigation, we identified (5β)-cholan-24-oic acid (cholanic acid) as a novel compound that competitively inhibits the EphA2-ephrinA1 interaction with higher potency than lithocholic acid. Surface plasmon resonance analysis indicates that cholanic acid binds specifically and reversibly to the ligand binding domain of EphA2, with a steady-state dissociation constant (K(D) ) in the low micromolar range. Furthermore, cholanic acid blocks the phosphorylation of EphA2 as well as cell retraction and rounding in PC3 prostate cancer cells, two effects that depend on EphA2 activation by the ephrinA1 ligand. These findings suggest that cholanic acid can be used as a template structure for the design of effective EphA2 antagonists, and may have potential impact in the elucidation of the role played by this receptor in pathological conditions.
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Affiliation(s)
- Massimiliano Tognolini
- Dipartimento di Scienze Farmacologiche, Biologiche e Chimiche applicate, Università degli Studi di Parma, V.le delle Scienze 27/A, 43124 Parma, Italy
| | - Matteo Incerti
- Dipartimento Farmaceutico, Università degli Studi di Parma, V.le delle Scienze 27/A, 43124 Parma, Italy
| | - Iftiin Hassan Mohamed
- Dipartimento di Scienze Farmacologiche, Biologiche e Chimiche applicate, Università degli Studi di Parma, V.le delle Scienze 27/A, 43124 Parma, Italy
| | - Carmine Giorgio
- Dipartimento di Scienze Farmacologiche, Biologiche e Chimiche applicate, Università degli Studi di Parma, V.le delle Scienze 27/A, 43124 Parma, Italy
| | - Simonetta Russo
- Dipartimento Farmaceutico, Università degli Studi di Parma, V.le delle Scienze 27/A, 43124 Parma, Italy
| | - Renato Bruni
- Dipartimento di Biologia Evolutiva e Funzionale, Viale delle Scienze 11/A, 43124, Università degli Studi di Parma, Italy
| | - Barbara Lelli
- Dipartimento di Biotecnologie, Via Fiorentina 1, 53100, Università degli Studi di Siena, Italy
| | - Luisa Bracci
- Dipartimento di Biotecnologie, Via Fiorentina 1, 53100, Università degli Studi di Siena, Italy
| | - Roberta Noberini
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Elena B. Pasquale
- Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Elisabetta Barocelli
- Dipartimento di Scienze Farmacologiche, Biologiche e Chimiche applicate, Università degli Studi di Parma, V.le delle Scienze 27/A, 43124 Parma, Italy
| | - Paola Vicini
- Dipartimento Farmaceutico, Università degli Studi di Parma, V.le delle Scienze 27/A, 43124 Parma, Italy
| | - Marco Mor
- Dipartimento Farmaceutico, Università degli Studi di Parma, V.le delle Scienze 27/A, 43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento Farmaceutico, Università degli Studi di Parma, V.le delle Scienze 27/A, 43124 Parma, Italy
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23
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Syed F, Thomas AN, Singh S, Kolluru V, Emeigh Hart SG, Bayat A. In vitro study of novel collagenase (XIAFLEX®) on Dupuytren's disease fibroblasts displays unique drug related properties. PLoS One 2012; 7:e31430. [PMID: 22384021 PMCID: PMC3286458 DOI: 10.1371/journal.pone.0031430] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 01/08/2012] [Indexed: 11/19/2022] Open
Abstract
Dupuytren's disease (DD) is a benign, fibroproliferative disease of the palmar fascia, with excessive extracellular matrix (ECM) deposition and over-production of cytokines and growth factors, resulting in digital fixed flexion contractures limiting hand function and patient quality of life. Surgical fasciectomy is the gold standard treatment but is invasive and has associated morbidity without limiting disease recurrence. Injectable Collagenase Clostridium histolyticum (CCH)--Xiaflex®--is a novel, nonsurgical option with clinically proven in vivo reduction of DD contractures but with limited in vitro data demonstrating its cellular and molecular effects. The aim of this study was to delineate the effects of CCH on primary fibroblasts isolated from DD and non-DD anatomical sites (using RTCA, LDH, WST-1, FACS, qRT-PCR, ELISA and In-Cell Quantitative Western Blotting) to compare the efficacy of varying concentrations of Xiaflex® against a reagent grade Collagenase, Collagenase A. Results demonstrated that DD nodule and cord fibroblasts had greater proliferation than those from fat and skin. Xiaflex® exposure resulted in dose- and time-dependent inhibition of cellular spreading, attachment and proliferation, with cellular recovery after enzyme removal. Unlike Collagenase A, Xiaflex® did not cause apoptosis. Collagen expression patterns were significantly (p<0.05) different in DD fibroblasts across anatomical sites - the highest levels of collagen I and III were detected in DD nodule, with DD cord and fat fibroblasts demonstrating a smaller increase in both collagen expression relative to DD skin. Xiaflex® significantly (p<0.05) down-regulated ECM components, cytokines and growth factors in a dose-dependent manner. An in vitro scratch wound assay model demonstrated that, at low concentrations, Xiaflex® enabled a faster fibroblast reparatory migration into the wound, whereas, at high concentrations, this process was significantly (p<0.05) inhibited. This is the first report elucidating potential mechanisms of action of Xiaflex® on Dupuytren fibroblasts, offering a greater insight and a better understanding of its effect in DD.
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Affiliation(s)
- Farhatullah Syed
- Plastic and Reconstructive Surgery Research, School of Translational Medicine, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
- Inflammation Sciences Group, School of Translational Medicine, University of Manchester, Manchester, United Kingdom
| | - Alexis N. Thomas
- Plastic and Reconstructive Surgery Research, School of Translational Medicine, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
| | - Subir Singh
- Plastic and Reconstructive Surgery Research, School of Translational Medicine, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
| | - Venkatesh Kolluru
- Plastic and Reconstructive Surgery Research, School of Translational Medicine, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
| | | | - Ardeshir Bayat
- Plastic and Reconstructive Surgery Research, School of Translational Medicine, Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom
- Inflammation Sciences Group, School of Translational Medicine, University of Manchester, Manchester, United Kingdom
- Department of Plastic and Reconstructive Surgery, University Hospital South Manchester NHS Foundation Trust, Wythenshawe Hospital, Manchester, United Kingdom
- Manchester Academic Health Science Centre, University Hospital South Manchester NHS Foundation Trust, Wythenshawe Hospital, University of Manchester, Manchester, United Kingdom
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24
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Carmi C, Galvani E, Vacondio F, Rivara S, Lodola A, Russo S, Aiello S, Bordi F, Costantino G, Cavazzoni A, Alfieri RR, Ardizzoni A, Petronini PG, Mor M. Irreversible Inhibition of Epidermal Growth Factor Receptor Activity by 3-Aminopropanamides. J Med Chem 2012; 55:2251-64. [DOI: 10.1021/jm201507x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Caterina Carmi
- Dipartimento
Farmaceutico, Università degli Studi di Parma, V.le G.P. Usberti
27/A, I-43124 Parma, Italy
| | - Elena Galvani
- Dipartimento di Medicina Sperimentale, Università degli Studi di Parma, Via Volturno
39, I-43125 Parma, Italy
| | - Federica Vacondio
- Dipartimento
Farmaceutico, Università degli Studi di Parma, V.le G.P. Usberti
27/A, I-43124 Parma, Italy
| | - Silvia Rivara
- Dipartimento
Farmaceutico, Università degli Studi di Parma, V.le G.P. Usberti
27/A, I-43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento
Farmaceutico, Università degli Studi di Parma, V.le G.P. Usberti
27/A, I-43124 Parma, Italy
| | - Simonetta Russo
- Dipartimento
Farmaceutico, Università degli Studi di Parma, V.le G.P. Usberti
27/A, I-43124 Parma, Italy
| | - Stefania Aiello
- Dipartimento di Scienze e Tecnologie
Molecolari e Biomolecolari, Università degli Studi di Palermo, Via Archirafi 32, I-90123 Palermo, Italy
| | - Fabrizio Bordi
- Dipartimento
Farmaceutico, Università degli Studi di Parma, V.le G.P. Usberti
27/A, I-43124 Parma, Italy
| | - Gabriele Costantino
- Dipartimento
Farmaceutico, Università degli Studi di Parma, V.le G.P. Usberti
27/A, I-43124 Parma, Italy
| | - Andrea Cavazzoni
- Dipartimento di Medicina Sperimentale, Università degli Studi di Parma, Via Volturno
39, I-43125 Parma, Italy
| | - Roberta R. Alfieri
- Dipartimento di Medicina Sperimentale, Università degli Studi di Parma, Via Volturno
39, I-43125 Parma, Italy
| | - Andrea Ardizzoni
- Oncologia Medica, Azienda Ospedaliero-Universitaria di Parma, V.le Gramsci
14, I-43125 Parma, Italy
| | - Pier Giorgio Petronini
- Dipartimento di Medicina Sperimentale, Università degli Studi di Parma, Via Volturno
39, I-43125 Parma, Italy
| | - Marco Mor
- Dipartimento
Farmaceutico, Università degli Studi di Parma, V.le G.P. Usberti
27/A, I-43124 Parma, Italy
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25
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Antczak C, Bermingham A, Calder P, Malkov D, Song K, Fetter J, Djaballah H. Domain-based biosensor assay to screen for epidermal growth factor receptor modulators in live cells. Assay Drug Dev Technol 2012; 10:24-36. [PMID: 22280060 DOI: 10.1089/adt.2011.423] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Traditional drug discovery efforts have resulted in the approval of a handful of receptor tyrosine kinase (RTK) inhibitors; however, their discovery relied solely on screening recombinant kinases, often with poor cellular activity outcome. The ability to screen RTKs in their natural environment is sought as an alternative approach. We have adapted a novel strategy utilizing a green fluorescent protein-labeled SRC homology 2 domain-based biosensor as a surrogate reporter of endogenous epidermal growth factor receptor (EGFR) activity in A549 cells. Upon activation of the receptor, EGFR function in live cells is measured by the number of green granules that form. Here we describe assay miniaturization and demonstrate specificity for EGFR through its chemical inhibition and RNAi-dependent knockdown resulting in complete abrogation of granule formation. Gefitinib and PD 153035 were identified as hits in a pilot screen. This approach allows for the identification of novel EGFR modulators in high-throughput formats for screening chemical and RNAi libraries.
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Affiliation(s)
- Christophe Antczak
- HTS Core Facility, Molecular Pharmacology & Chemistry Program, Memorial Sloan-Kettering Cancer Center , New York, New York 10065, USA
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26
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Martić S, Labib M, Kraatz HB. Electrochemical investigations of sarcoma-related protein kinase inhibition. Electrochim Acta 2011. [DOI: 10.1016/j.electacta.2011.05.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Tarantino G, Caputi A. JNKs, insulin resistance and inflammation: A possible link between NAFLD and coronary artery disease. World J Gastroenterol 2011; 17:3785-94. [PMID: 21987620 PMCID: PMC3181439 DOI: 10.3748/wjg.v17.i33.3785] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Revised: 02/19/2011] [Accepted: 02/26/2011] [Indexed: 02/06/2023] Open
Abstract
The incidence of obesity has dramatically increased in recent years. Consequently, obesity and associated disorders such as nonalcoholic fatty liver disease constitute a serious problem. Therefore, the contribution of adipose tissue to metabolic homeostasis has become a focus of interest. In this review, we discuss the latest discoveries that support the role of lipids in nonalcoholic fatty liver disease. We describe the common mechanisms (c-Jun amino-terminal kinases, endoplasmic reticulum stress, unfolded protein response, ceramide, low-grade chronic inflammation) by which lipids and their derivatives impair insulin responsiveness and contribute to inflammatory liver and promote plaque instability in the arterial wall. Presenting the molecular mechanism of lipid activation of pro-inflammatory pathways, we attempt to find a link between nonalcoholic fatty liver disease, metabolic syndrome and cardiovascular diseases. Describing the common mechanisms by which lipid derivatives, through modulation of macrophage function, promote plaque instability in the arterial wall, impair insulin responsiveness and contribute to inflammatory liver and discussing the molecular mechanism of lipid activation of pro-inflammatory pathways, the key roles played by the proliferator-activated receptor and liver X receptor α, nuclear receptors-lipid sensors that link lipid metabolism and inflammation, should be emphasized. Further studies are warranted of anti-inflammatory drugs such as aspirin, anti-interleukin-6 receptors, immune-modulators (calcineurin inhibitors), substances enhancing the expression of heat shock proteins (which protect cells from endoplasmic reticulum stress-induced apoptosis), and anti- c-Jun amino-terminal kinases in well-designed trials to try to minimize the high impact of these illnesses, and the different expressions of the diseases, on the whole population.
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28
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Zhang HX, Goutsias J. Reducing experimental variability in variance-based sensitivity analysis of biochemical reaction systems. J Chem Phys 2011; 134:114105. [PMID: 21428605 DOI: 10.1063/1.3563539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Sensitivity analysis is a valuable task for assessing the effects of biological variability on cellular behavior. Available techniques require knowledge of nominal parameter values, which cannot be determined accurately due to experimental uncertainty typical to problems of systems biology. As a consequence, the practical use of existing sensitivity analysis techniques may be seriously hampered by the effects of unpredictable experimental variability. To address this problem, we propose here a probabilistic approach to sensitivity analysis of biochemical reaction systems that explicitly models experimental variability and effectively reduces the impact of this type of uncertainty on the results. The proposed approach employs a recently introduced variance-based method to sensitivity analysis of biochemical reaction systems [Zhang et al., J. Chem. Phys. 134, 094101 (2009)] and leads to a technique that can be effectively used to accommodate appreciable levels of experimental variability. We discuss three numerical techniques for evaluating the sensitivity indices associated with the new method, which include Monte Carlo estimation, derivative approximation, and dimensionality reduction based on orthonormal Hermite approximation. By employing a computational model of the epidermal growth factor receptor signaling pathway, we demonstrate that the proposed technique can greatly reduce the effect of experimental variability on variance-based sensitivity analysis results. We expect that, in cases of appreciable experimental variability, the new method can lead to substantial improvements over existing sensitivity analysis techniques.
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Affiliation(s)
- Hong-Xuan Zhang
- Procter & Gamble Co., Miami Valley Innovation Center, Cincinnati, Ohio 45253, USA
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29
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Bi K, Lebakken CS, Vogel KW. Transformation ofin vitrotools for kinase profiling: keeping an eye over the off-target liabilities. Expert Opin Drug Discov 2011; 6:701-12. [DOI: 10.1517/17460441.2011.575776] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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30
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Giorgio C, Hassan Mohamed I, Flammini L, Barocelli E, Incerti M, Lodola A, Tognolini M. Lithocholic acid is an Eph-ephrin ligand interfering with Eph-kinase activation. PLoS One 2011; 6:e18128. [PMID: 21479221 PMCID: PMC3068151 DOI: 10.1371/journal.pone.0018128] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 02/25/2011] [Indexed: 12/03/2022] Open
Abstract
Eph-ephrin system plays a central role in a large variety of human cancers. In
fact, alterated expression and/or de-regulated function of Eph-ephrin system
promotes tumorigenesis and development of a more aggressive and metastatic
tumour phenotype. In particular EphA2 upregulation is correlated with tumour
stage and progression and the expression of EphA2 in non-trasformed cells
induces malignant transformation and confers tumorigenic potential. Based on
these evidences our aim was to identify small molecules able to modulate
EphA2-ephrinA1 activity through an ELISA-based binding screening. We identified
lithocholic acid (LCA) as a competitive and reversible ligand inhibiting
EphA2-ephrinA1 interaction (Ki = 49 µM). Since each
ephrin binds many Eph receptors, also LCA does not discriminate between
different Eph-ephrin binding suggesting an interaction with a highly conserved
region of Eph receptor family. Structurally related bile acids neither inhibited
Eph-ephrin binding nor affected Eph phosphorylation. Conversely, LCA inhibited
EphA2 phosphorylation induced by ephrinA1-Fc in PC3 and HT29 human prostate and
colon adenocarcinoma cell lines (IC50 = 48 and
66 µM, respectively) without affecting cell viability or other receptor
tyrosine-kinase (EGFR, VEGFR, IGFR1β, IRKβ) activity. LCA did not
inhibit the enzymatic kinase activity of EphA2 at 100 µM (LANCE method)
confirming to target the Eph-ephrin protein-protein interaction. Finally, LCA
inhibited cell rounding and retraction induced by EphA2 activation in PC3 cells.
In conclusion, our findings identified a hit compound useful for the development
of molecules targeting ephrin system. Moreover, as ephrin signalling is a key
player in the intestinal cell renewal, our work could provide an interesting
starting point for further investigations about the role of LCA in the
intestinal homeostasis.
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Affiliation(s)
- Carmine Giorgio
- Dipartimento di Scienze Farmacologiche,
Biologiche e Chimiche Applicate, Università di Parma, Parma,
Italy
| | - Iftiin Hassan Mohamed
- Dipartimento di Scienze Farmacologiche,
Biologiche e Chimiche Applicate, Università di Parma, Parma,
Italy
| | - Lisa Flammini
- Dipartimento di Scienze Farmacologiche,
Biologiche e Chimiche Applicate, Università di Parma, Parma,
Italy
| | - Elisabetta Barocelli
- Dipartimento di Scienze Farmacologiche,
Biologiche e Chimiche Applicate, Università di Parma, Parma,
Italy
| | - Matteo Incerti
- Dipartimento Farmaceutico, Università
di Parma, Parma, Italy
| | - Alessio Lodola
- Dipartimento Farmaceutico, Università
di Parma, Parma, Italy
| | - Massimiliano Tognolini
- Dipartimento di Scienze Farmacologiche,
Biologiche e Chimiche Applicate, Università di Parma, Parma,
Italy
- * E-mail:
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31
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Iliuk A, Martinez JS, Hall MC, Tao WA. Phosphorylation assay based on multifunctionalized soluble nanopolymer. Anal Chem 2011; 83:2767-74. [PMID: 21395237 DOI: 10.1021/ac2000708] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantitative phosphorylation analysis is essential to understanding cellular signal transductions. Here we present a novel technology for the highly efficient assay of protein phosphorylation in high-throughput format without the use of phospho-specific antibodies. The technique is based on a water-soluble, nanosize polymer, termed pIMAGO, that is multifunctionalized with titanium(IV) ions for specific binding to phosphoproteins and with biotin groups that allow for enzyme-linked spectrometric detection. The sensitivity, specificity, and quantitative nature of pIMAGO for phosphorylation assays were examined with standard phosphoproteins and with purified phosphoproteins from whole cell extracts. As low as 100 pg of phosphoprotein can be measured quantitatively with the pIMAGO chemiluminescence assay. The pIMAGO assay was applied to an in vitro kinase assay, kinase inhibitor screening, and measurement of endogenous phosphorylation events. The technique provides a universal, quantitative method for global phosphorylation analysis with high sensitivity and specificity.
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Affiliation(s)
- Anton Iliuk
- Department of Biochemistry and Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, USA
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32
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Moerke NJ, Hoffman GR. Development of In‐Cell Western Assays Using Far‐Red Fluorophores. ACTA ACUST UNITED AC 2011; 3:39-52. [DOI: 10.1002/9780470559277.ch100153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Nathan J. Moerke
- Harvard Medical School, ICCB‐Longwood Screening Facility Boston Massachusetts
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33
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Andresen H, Gupta S, Stevens MM. Kinetic investigation of bioresponsive nanoparticle assembly as a function of ligand design. NANOSCALE 2011; 3:383-386. [PMID: 20730206 DOI: 10.1039/c0nr00469c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Homogeneous and heterogeneous nanoparticle (NP) assembly induced by ligand-specific immunorecognition is commonly used for biosensing applications. We investigated how the structural design of the peptide ligands used to functionalise gold NPs affected the kinetics of NP assembly and hence biodetection. We observed that aggregation rates varied up to 20-fold for the surface binding and 120-fold for the solution-phase assembly of NPs as a function of peptide design. Our results show how the fundamental difference in NP assembly on surfaces and in solution requires different optimised ligand designs. This increased understanding of the specifics of ligand-triggered NP aggregation should help in the design of faster and more efficient bioassays in the future.
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Affiliation(s)
- Heiko Andresen
- Imperial College London, Department of Materials and Institute for Biomedical Engineering, Prince Consort Road, London, SW7 2AZ, UK
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Zhou G, Yan X, Wu D, Kron SJ. Photocleavable peptide-conjugated magnetic beads for protein kinase assays by MALDI-TOF MS. Bioconjug Chem 2011; 21:1917-24. [PMID: 20860375 DOI: 10.1021/bc1003058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptides were immobilized onto superparamagnetic beads via photocleavable linkers. This enabled simple, rapid, and label-free protein kinase assays via MALDI-TOF MS detection of substrate peptide phosphorylation. Abltide, a model substrate for the Abl protein tyrosine kinase model, was coupled onto amine-terminated beads, incubated with ATP and recombinant c-Abl kinase, and released and further detected to determine phosphorylation. Abltide phosphorylation was found to depend significantly on the length and composition of linkers to the bead surface. Inserting a diblock spacer of poly(glycine) and poly(ethylene glycol) segments markedly enhanced phosphorylation. To validate the assay, the activity of two small-molecule kinase inhibitors, imatinib and dasatinib, which target the oncogenic mutant tyrosine kinase Bcr-Abl to treat chronic myeloid leukemia (CML), was tested. Examining inhibition of the purified c-Abl or Bcr-Abl in K562 CML cell extracts, IC(50) values were determined to be consistent with the literature. This simple, label-free, MALDI-based protein kinase assay can be readily adapted to allow multiplexed assays of multiple peptide substrates and/or analysis of alternative post-translational modifications as a tool for drug discovery and clinical testing.
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Affiliation(s)
- Guangchang Zhou
- Ludwig Center for Metastasis Research, The University of Chicago, Chicago, Illinois 60637, USA
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Wu D, Sylvester JE, Parker LL, Zhou G, Kron SJ. Peptide reporters of kinase activity in whole cell lysates. Biopolymers 2010; 94:475-86. [PMID: 20593469 DOI: 10.1002/bip.21401] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Kinase assays are used to screen for small-molecule inhibitors that may show promise as targeted pharmaceutical therapies. Using cell lysates instead of purified kinases provides a more accurate estimate of inhibitor sensitivity and selectivity in a biological setting. This review summarizes the range of homogeneous (solution-phase) and heterogeneous (solid-supported) formats available for using peptide substrates to monitor kinase activities in cell lysates. With a focus on heterogeneous kinase assays, the peptide substrate Abltide is used as a model to optimize presentation geometries and the modular arrangement of short sequences for kinase recognition. We present results from peptides immobilized on two- and three-dimensional surfaces such as hydrogels on 96-well plates and glass slides, and fluorescent Luminex beads. We discuss methods to increase assay sensitivity using chemifluorescent ELISAs, antibody-based recognition, and label-free mass spectrometry. Monitoring the activity of specific kinases in cell lysates presents challenges that can be overcome by manipulating peptide substrates to optimize assay conditions. In particular, signal-to-background ratios were improved by (1) adding long branched hydrophilic linkers between the substrate and the surface, (2) changing the orientation of peptides relative to the surface, and (3) including peptide ligands in cis or in trans to recruit kinases to the surface. By improving the accessibility of immobilized peptide substrates to kinases in solution, the apparent rate of phosphorylation increased and assays were more sensitive to changes in endogenous kinase activities. These strategies can be generalized to improve the reactivity of most peptide substrates used in heterogeneous kinase assays with cell lysates.
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Affiliation(s)
- Ding Wu
- Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL 60637, USA
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Ghadiali JE, Cohen BE, Stevens MM. Protein kinase-actuated resonance energy transfer in quantum dot--peptide conjugates. ACS NANO 2010; 4:4915-4919. [PMID: 20731464 DOI: 10.1021/nn101293s] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Bioconjugates of quantum dot nanocrystals possess unique optical properties that allow them to serve as exceptional biological imaging and sensing reagents. Protein kinases are an important family of enzymes that phosphorylate serine, threonine, or tyrosine side chains and are critical in cell signaling and cancer biology, but despite their biomedical and pharmaceutical significance, their activity has been little explored using quantum dot technology. We demonstrate that self-assembled peptide-quantum dot conjugates can serve as surrogate substrates in a simple homogeneous assay for protein kinase activity. Enzymatic phosphorylation of the peptide-conjugates is detected by means of a complementary FRET-acceptor labeled antiphosphotyrosine antibody, with formation of the immunocomplex resulting in energy transfer between the quantum dot and FRET acceptor molecules. This approach should facilitate the development of new assays for protein kinases and other enzymes based on quantum dot FRET donors.
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Affiliation(s)
- James E Ghadiali
- Department of Materials, Imperial College London, Exhibition Road, London, UK
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Development of an online p38α mitogen-activated protein kinase binding assay and integration of LC-HR-MS. Anal Bioanal Chem 2010; 398:1771-80. [PMID: 20730527 PMCID: PMC2943585 DOI: 10.1007/s00216-010-4087-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 07/28/2010] [Accepted: 08/02/2010] [Indexed: 11/19/2022]
Abstract
A high-resolution screening method was developed for the p38α mitogen-activated protein kinase to detect and identify small-molecule binders. Its central role in inflammatory diseases makes this enzyme a very important drug target. The setup integrates separation by high-performance liquid chromatography with two parallel detection techniques. High-resolution mass spectrometry gives structural information to identify small molecules while an online enzyme binding detection method provides data on p38α binding. The separation step allows the individual assessment of compounds in a mixture and links affinity and structure information via the retention time. Enzyme binding detection was achieved with a competitive binding assay based on fluorescence enhancement which has a simple principle, is inexpensive, and is easy to interpret. The concentrations of p38α and the fluorescence tracer SK&F86002 were optimized as well as incubation temperature, formic acid content of the LC eluents, and the material of the incubation tubing. The latter notably improved the screening of highly lipophilic compounds. For optimization and validation purposes, the known kinase inhibitors BIRB796, TAK715, and MAPKI1 were used among others. The result is a high-quality assay with Z′ factors around 0.8, which is suitable for semi-quantitative affinity measurements and applicable to various binding modes. Furthermore, the integrated approach gives affinity data on individual compounds instead of averaged ones for mixtures. P38 α online screening platform ![]()
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Markvicheva KN, Bilan DS, Mishina NM, Gorokhovatsky AY, Vinokurov LM, Lukyanov S, Belousov VV. A genetically encoded sensor for H2O2 with expanded dynamic range. Bioorg Med Chem 2010; 19:1079-84. [PMID: 20692175 DOI: 10.1016/j.bmc.2010.07.014] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 06/30/2010] [Accepted: 07/07/2010] [Indexed: 11/30/2022]
Abstract
Hydrogen peroxide is an important second messenger controlling intracellular signaling cascades by selective oxidation of redox active thiolates in proteins. Changes in intracellular [H(2)O(2)] can be tracked in real time using HyPer, a ratiometric genetically encoded fluorescent probe. Although HyPer is sensitive and selective for H(2)O(2) due to the properties of its sensing domain derived from the Escherichia coli OxyR protein, many applications may benefit from an improvement of the indicator's dynamic range. We here report HyPer-2, a probe that fills this demand. Upon saturating [H(2)O(2)] exposure, HyPer-2 undergoes an up to sixfold increase of the ratio F500/F420 versus a threefold change in HyPer. HyPer-2 was generated by a single point mutation A406V from HyPer corresponding to A233V in wtOxyR. This mutation was previously shown to destabilize interface between monomers in OxyR dimers. However, in HyPer-2, the A233V mutation stabilizes the dimer and expands the dynamic range of the probe.
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Affiliation(s)
- Kseniya N Markvicheva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, RAS, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
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Gupta S, Andresen H, Ghadiali JE, Stevens MM. Kinase-actuated immunoaggregation of Peptide-conjugated gold nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2010; 6:1509-1513. [PMID: 20578112 DOI: 10.1002/smll.201000099] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- Shalini Gupta
- Department of Materials and Institute for Biomedical Engineering Imperial College London London, UK
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Palmieri M, Nowell CJ, Condron M, Gardiner J, Holmes AB, Desai J, Burgess AW, Catimel B. Analysis of cellular phosphatidylinositol (3,4,5)-trisphosphate levels and distribution using confocal fluorescent microscopy. Anal Biochem 2010; 406:41-50. [PMID: 20599646 DOI: 10.1016/j.ab.2010.06.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 06/18/2010] [Accepted: 06/22/2010] [Indexed: 11/29/2022]
Abstract
We have developed an immunocytochemistry method for the semiquantitative detection of phosphatidylinositol (3,4,5)-trisphosphate (PI(3,4,5)P3) at the cell plasma membrane. This protocol combines the use of a glutathione S-transferase-tagged pleckstrin homology (PH) domain of the general phosphoinositides-1 receptor (GST-GRP1PH) with fluorescence confocal microscopy and image segmentation using cell mask software analysis. This methodology allows the analysis of PI(3,4,5)P3 subcellular distribution in resting and epidermal growth factor (EGF)-stimulated HEK293T cells and in LIM1215 (wild-type phosphoinositide 3-kinase (PI3K)) and LIM2550 (H1047R mutation in PI3K catalytic domain) colonic carcinoma cells. Formation of PI(3,4,5)P3 was observed 5min following EGF stimulation and resulted in an increase of the membrane/cytoplasm fluorescence ratio from 1.03 to 1.53 for HEK293T cells and from 2.2 to 3.3 for LIM1215 cells. Resting LIM2550 cells stained with GST-GRP1PH had an elevated membrane/cytoplasm fluorescence ratio of 9.8, suggesting constitutive PI3K activation. The increase in the membrane/cytoplasm fluorescent ratio was inhibited in a concentration-dependent manner by the PI3K inhibitor LY294002. This cellular confocal imaging assay can be used to directly assess the effects of PI3K mutations in cancer cell lines and to determine the potential specificity and effectiveness of PI3K inhibitors in cancer cells.
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Affiliation(s)
- Michelle Palmieri
- Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victsoria, Australia
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Lilienthal E, Kolanowski K, Becker W. Development of a sensitive non-radioactive protein kinase assay and its application for detecting DYRK activity in Xenopus laevis oocytes. BMC BIOCHEMISTRY 2010; 11:20. [PMID: 20487523 PMCID: PMC2885986 DOI: 10.1186/1471-2091-11-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Accepted: 05/20/2010] [Indexed: 12/27/2022]
Abstract
BACKGROUND Although numerous non-radioactive methods are in use to measure the catalytic activity of protein kinases, most require specialized equipment and reagents and are not sufficiently sensitive for the detection of endogenous kinase activity in biological samples. Kinases of the DYRK family have important functions in developmental and pathophysiological processes in eukaryotic organisms including mammals. We aimed to develop a highly sensitive, low-tech assay suitable to determine the activity of DYRK family kinases in tissues or cells from diverse sources. RESULTS Phosphorylation-site specific antibodies can be used to monitor the accumulation of the phosphorylated product in kinase assays. We present a modified configuration of an enzyme-linked immunosorbent assay (ELISA)-based kinase assay by using the phosphospecific antibody as the capture antibody. This assay format allowed the detection of small amounts of phosphopeptide in mixtures with an excess of the unphosphorylated substrate peptide (10 fmol phosphorylated peptide over a background of 50 pmol unphosphorylated peptide). Consequently, low substrate turnover rates can be determined. We applied this method to the measurement of endogenous DYRK1A activity in mouse heart tissue by immunocomplex kinase assay. Furthermore, we detected DYRK1-like kinase activity in Xenopus laevis oocytes and identified this kinase as a DYRK1 isoform distinct from the Xenopus DYRK1A ortholog. CONCLUSION We present a non-radioactive and highly sensitive method for the measurement of endogenous activities of DYRKs in biological samples. Xenopus laevis oocytes contain an active DYRK1-related protein kinase more similar to mammalian DYRK1B than DYRK1A.
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Affiliation(s)
- Eva Lilienthal
- Institute of Pharmacology and Toxicology, Medical Faculty of the RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
| | - Katharina Kolanowski
- Institute of Pharmacology and Toxicology, Medical Faculty of the RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
| | - Walter Becker
- Institute of Pharmacology and Toxicology, Medical Faculty of the RWTH Aachen University, Wendlingweg 2, 52074 Aachen, Germany
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Bisubstrate fluorescent probes and biosensors in binding assays for HTS of protein kinase inhibitors. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:541-6. [DOI: 10.1016/j.bbapap.2009.10.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 10/18/2009] [Accepted: 10/21/2009] [Indexed: 11/20/2022]
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Eglen RM, Reisine T. Human kinome drug discovery and the emerging importance of atypical allosteric inhibitors. Expert Opin Drug Discov 2010; 5:277-90. [PMID: 22823023 DOI: 10.1517/17460441003636820] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
IMPORTANCE OF THE FIELD Protein kinases are important targets for drug discovery because they possess critical roles in many human diseases. Several protein kinase inhibitors have entered clinical development with others having already been approved for treating a host of diseases. However, many kinase inhibitors suffer from non-selectivity because they interact with the ATP binding region which has similar structures amongst the protein kinases and this non-selectivity sometimes can cause side effects. As a consequence, there is much interest in developing drugs that inhibit kinases through non-classical mechanisms with the hope of avoiding the side effects of previous kinase drugs. AREAS COVERED IN THIS REVIEW This review covers emerging information on kinase biology and discusses new approaches to design selective inhibitors that do not compete with ATP. WHAT THE READER WILL GAIN The reader will gain a better understanding of the importance of the field of allosteric inhibitor drug discovery and how this has required the adoption of a new generation of high-throughput screening techniques. TAKE HOME MESSAGE Discovery and development of allosteric modulators will result in a family of novel kinase therapies with greater selectivity and more varied ways to control activity of disease causing kinase targets.
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Affiliation(s)
- Richard M Eglen
- Bio-discovery, PerkinElmer Life and Analytical Sciences, 940 Winter St., Waltham, MA, USA +1 781 663 5599 ; +1 781 663 5984 ;
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Carmi C, Cavazzoni A, Vezzosi S, Bordi F, Vacondio F, Silva C, Rivara S, Lodola A, Alfieri RR, La Monica S, Galetti M, Ardizzoni A, Petronini PG, Mor M. Novel Irreversible Epidermal Growth Factor Receptor Inhibitors by Chemical Modulation of the Cysteine-Trap Portion. J Med Chem 2010; 53:2038-50. [DOI: 10.1021/jm901558p] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Caterina Carmi
- Dipartimento Farmaceutico, Università degli Studi di Parma, V.le G.P. Usberti 27/A, I-43124 Parma, Italy
| | - Andrea Cavazzoni
- Dipartimento di Medicina Sperimentale, Università degli Studi di Parma, Via Volturno 39, I-43125 Parma, Italy
| | - Stefano Vezzosi
- Dipartimento Farmaceutico, Università degli Studi di Parma, V.le G.P. Usberti 27/A, I-43124 Parma, Italy
| | - Fabrizio Bordi
- Dipartimento Farmaceutico, Università degli Studi di Parma, V.le G.P. Usberti 27/A, I-43124 Parma, Italy
| | - Federica Vacondio
- Dipartimento Farmaceutico, Università degli Studi di Parma, V.le G.P. Usberti 27/A, I-43124 Parma, Italy
| | - Claudia Silva
- Dipartimento Farmaceutico, Università degli Studi di Parma, V.le G.P. Usberti 27/A, I-43124 Parma, Italy
| | - Silvia Rivara
- Dipartimento Farmaceutico, Università degli Studi di Parma, V.le G.P. Usberti 27/A, I-43124 Parma, Italy
| | - Alessio Lodola
- Dipartimento Farmaceutico, Università degli Studi di Parma, V.le G.P. Usberti 27/A, I-43124 Parma, Italy
| | - Roberta R. Alfieri
- Dipartimento di Medicina Sperimentale, Università degli Studi di Parma, Via Volturno 39, I-43125 Parma, Italy
| | - Silvia La Monica
- Dipartimento di Medicina Sperimentale, Università degli Studi di Parma, Via Volturno 39, I-43125 Parma, Italy
| | - Maricla Galetti
- Dipartimento di Medicina Sperimentale, Università degli Studi di Parma, Via Volturno 39, I-43125 Parma, Italy
| | - Andrea Ardizzoni
- Oncologia Medica, Azienda Ospedaliero—Universitaria di Parma, V.le Gramsci 14, I-43126 Parma, Italy
| | - Pier Giorgio Petronini
- Dipartimento di Medicina Sperimentale, Università degli Studi di Parma, Via Volturno 39, I-43125 Parma, Italy
| | - Marco Mor
- Dipartimento Farmaceutico, Università degli Studi di Parma, V.le G.P. Usberti 27/A, I-43124 Parma, Italy
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Han X, Katayama Y. A peptide microarray for detecting protein kinase activity in cell lysates. Methods Mol Biol 2010; 669:183-194. [PMID: 20857367 DOI: 10.1007/978-1-60761-845-4_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Protein kinases (PKs) are widely recognized as valuable targets for disease diagnosis and drug discovery. For this reason, we have developed a sensitive peptide microarray for detecting intracellular PK activity. Peptides are immobilized on a glutaraldehyde-premodified high-amino terminal glass slide, by spotting 2 nL volumes of substrate peptide solutions with an automated microarray spotter. After the peptides are phosphorylated by cell lysates, phosphorylation is specifically recognized by a fluorescence-labeled antiphosphotyrosine antibody for tyrosine kinases, or Phos-tag biotin (a biotinylated phosphate-specific ligand based on Zn(2+) complex), which is subsequently bound with fluorescence-labeled streptavidin, for serine/threonine kinases. The fluorescence signal is then detected by an automatic microarray scanner. The peptide microarray system involves simple peptide immobilization, requires low sample volumes and provides a high density array. Importantly, it provides high sensitivity for detecting PK activities in cell lysates. Thus, the peptide microarray system is expected to be useful for a high-throughput kinase assay to investigate intracellular kinase activity and has potential applications in disease diagnosis and drug discovery.
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Affiliation(s)
- Xiaoming Han
- Graduate School of System Life Sciences, Kyushu University, Fukuoka, Japan
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Klüter S, Grütter C, Naqvi T, Rabiller M, Simard JR, Pawar V, Getlik M, Rauh D. Displacement Assay for the Detection of Stabilizers of Inactive Kinase Conformations. J Med Chem 2009; 53:357-67. [DOI: 10.1021/jm901297e] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Sabine Klüter
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Christian Grütter
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Tabassum Naqvi
- DiscoveRx Corporation, 42501 Albrae Street, Fremont, California 94538
| | - Matthias Rabiller
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Jeffrey R. Simard
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Vijaykumar Pawar
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Matthäus Getlik
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Daniel Rauh
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
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Yagi YI, Abe K, Ikebukuro K, Sode K. Kinetic Mechanism and Inhibitor Characterization of WNK1 Kinase. Biochemistry 2009; 48:10255-66. [DOI: 10.1021/bi900666n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yukiko I. Yagi
- Tokyo University of Agriculture and Technology, 2-24-16 Naka-machi, Koganei, Tokyo, Japan
| | - Koichi Abe
- Tokyo University of Agriculture and Technology, 2-24-16 Naka-machi, Koganei, Tokyo, Japan
| | - Kazunori Ikebukuro
- Tokyo University of Agriculture and Technology, 2-24-16 Naka-machi, Koganei, Tokyo, Japan
| | - Koji Sode
- Tokyo University of Agriculture and Technology, 2-24-16 Naka-machi, Koganei, Tokyo, Japan
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Smyth LA, Collins I. Measuring and interpreting the selectivity of protein kinase inhibitors. J Chem Biol 2009; 2:131-51. [PMID: 19568781 PMCID: PMC2725273 DOI: 10.1007/s12154-009-0023-9] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 05/08/2009] [Accepted: 05/15/2009] [Indexed: 12/23/2022] Open
Abstract
Protein kinase inhibitors are a well-established class of clinically useful drugs, particularly for the treatment of cancer. Achieving inhibitor selectivity for particular protein kinases often remains a significant challenge in the development of new small molecules as drugs or as tools for chemical biology research. This review summarises the methodologies available for measuring kinase inhibitor selectivity, both in vitro and in cells. The interpretation of kinase inhibitor selectivity data is discussed, particularly with reference to the structural biology of the protein targets. Measurement and prediction of kinase inhibitor selectivity will be important for the development of new multi-targeted kinase inhibitors.
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Affiliation(s)
- Lynette A Smyth
- Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK,
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Moreira TJTP, Pierre K, Maekawa F, Repond C, Cebere A, Liljequist S, Pellerin L. Enhanced cerebral expression of MCT1 and MCT2 in a rat ischemia model occurs in activated microglial cells. J Cereb Blood Flow Metab 2009; 29:1273-83. [PMID: 19401710 DOI: 10.1038/jcbfm.2009.50] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Monocarboxylate transporters (MCTs) are essential for the use of lactate, an energy substrate known to be overproduced in brain during an ischemic episode. The expression of MCT1 and MCT2 was investigated at 48 h of reperfusion from focal ischemia induced by unilateral extradural compression in Wistar rats. Increased MCT1 mRNA expression was detected in the injured cortex and hippocampus of compressed animals compared to sham controls. In the contralateral, uncompressed hemisphere, increases in MCT1 mRNA level in the cortex and MCT2 mRNA level in the hippocampus were noted. Interestingly, strong MCT1 and MCT2 protein expression was found in peri-lesional macrophages/microglia and in an isolectin B4+/S100beta+ cell population in the corpus callosum. In vitro, MCT1 and MCT2 protein expression was observed in the N11 microglial cell line, whereas an enhancement of MCT1 expression by tumor necrosis factor-alpha (TNF-alpha) was shown in these cells. Modulation of MCT expression in microglia suggests that these transporters may help sustain microglial functions during recovery from focal brain ischemia. Overall, our study indicates that changes in MCT expression around and also away from the ischemic area, both at the mRNA and protein levels, are a part of the metabolic adaptations taking place in the brain after ischemia.
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50
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Eglen RM, Reisine T. The Current Status of Drug Discovery Against the Human Kinome. Assay Drug Dev Technol 2009; 7:22-43. [DOI: 10.1089/adt.2008.164] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Richard M. Eglen
- Bio-discovery, PerkinElmer Life and Analytical Sciences, Waltham, Massachusetts
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