1
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Fang XQ, Gan T, Wang LM. Clinical effect of spleen aminopeptide on improving liver function damage and immune function in children with infant hepatitis syndrome. World J Gastrointest Surg 2024; 16:1742-1748. [PMID: 38983347 PMCID: PMC11229994 DOI: 10.4240/wjgs.v16.i6.1742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 05/13/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024] Open
Abstract
BACKGROUND Infant hepatitis syndrome (IHS) is a clinical syndrome in infants less than one year of age with generalized skin jaundice, abnormal liver function, and hepatomegaly due to various etiologies such as infection. AIM To investigate the effect of IHS patients, after treatment with arsphenamine-based peptides, on patients' liver function damage and immune function. METHODS Of 110 patients with IHS treated in our hospital from January 2019 to January 2021 were grouped according to the randomized residual grouping method, with 5 cases in each group shed due to transfer, etc. Ultimately, 50 cases remained in each group. The control group was treated with reduced glutathione, and the treatment group was treated with sesquiterpene peptide based on the control group. Observe and compare the differences in indicators after treatment. RESULTS The comparison of serum total bilirubin, direct bilirubin, and serum alanine transferase after treatment was significantly different and lower in the treatment group than in the control group (P < 0.05). The comparison of CD4+, CD3+, CD4+/CD8+ after treatment was significantly different and higher in the treatment group than in the control group, and the comparison was statistically significant (P < 0.05). The complication of the two groups showed that the rash, cough and sputum, elevated platelets, and gastrointestinal reactions in the treatment group were significantly lower than those in the control group, and the differences were statistically significant by test (P < 0.05). CONCLUSION The comparative study of IHS treated with arsphenamine combined with reduced glutathione is more effective.
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Affiliation(s)
- Xiao-Qing Fang
- Department of Pediatrics, General Hospital of Central Theater Command of PLA, Wuhan 430061, Hubei Province, China
| | - Tian Gan
- Department of Pharmacy, The First People’s Hospital of Jiangxia District, Wuhan 430200, Hubei Province, China
| | - Lie-Min Wang
- Department of Neonatal, Central Hospital of Enshi, Enshi 445000, Hubei Province, China
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2
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Heier JL, Boselli DJ, Parker LL. Antibody-free time-resolved terbium luminescence assays designed for cyclin-dependent kinase 5 (CDK5). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.24.590988. [PMID: 38712268 PMCID: PMC11071522 DOI: 10.1101/2024.04.24.590988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Novel time-resolved terbium luminescence assays were developed for CDK5 and CDK2 by designing synthetic substrates which incorporate phospho-inducible terbium sensitizing motifs with kinase substrate consensus sequences. Substrates designed for CDK5 showed no phosphorylation by CDK2, opening the possibility for CDK5-specific assay development for selective drug discovery.
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3
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Gaddameedi JD, Chou T, Geller BS, Rangarajan A, Swaminathan TA, Dixon D, Long K, Golder CJ, Vuong VA, Banuelos S, Greenhouse R, Snyder MP, Lipchik AM, Gruber JJ. Acetyl-Click Screening Platform Identifies Small-Molecule Inhibitors of Histone Acetyltransferase 1 (HAT1). J Med Chem 2023; 66:5774-5801. [PMID: 37027002 PMCID: PMC10243098 DOI: 10.1021/acs.jmedchem.3c00039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
HAT1 is a central regulator of chromatin synthesis that acetylates nascent histone H4. To ascertain whether targeting HAT1 is a viable anticancer treatment strategy, we sought to identify small-molecule inhibitors of HAT1 by developing a high-throughput HAT1 acetyl-click assay. Screening of small-molecule libraries led to the discovery of multiple riboflavin analogs that inhibited HAT1 enzymatic activity. Compounds were refined by synthesis and testing of over 70 analogs, which yielded structure-activity relationships. The isoalloxazine core was required for enzymatic inhibition, whereas modifications of the ribityl side chain improved enzymatic potency and cellular growth suppression. One compound (JG-2016 [24a]) showed relative specificity toward HAT1 compared to other acetyltransferases, suppressed the growth of human cancer cell lines, impaired enzymatic activity in cellulo, and interfered with tumor growth. This is the first report of a small-molecule inhibitor of the HAT1 enzyme complex and represents a step toward targeting this pathway for cancer therapy.
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Affiliation(s)
- Jitender D. Gaddameedi
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, 48201
| | - Tristan Chou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94309
| | - Benjamin S. Geller
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94309
| | - Amithvikram Rangarajan
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94309
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158
| | - Tarun A. Swaminathan
- Department of Internal Medicine, Hematology-Oncology Division, Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX, 75235
| | - Danielle Dixon
- Department of Internal Medicine, Hematology-Oncology Division, Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX, 75235
| | - Katherine Long
- Department of Internal Medicine, Hematology-Oncology Division, Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX, 75235
| | - Caiden J. Golder
- Department of Internal Medicine, Hematology-Oncology Division, Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX, 75235
| | - Van A. Vuong
- Department of Internal Medicine, Hematology-Oncology Division, Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX, 75235
| | - Selene Banuelos
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94309
| | - Robert Greenhouse
- Department of Otolaryngology, Stanford University School of Medicine, Stanford, CA, 94309
| | - Michael P. Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94309
| | - Andrew M. Lipchik
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, 48201
| | - Joshua J. Gruber
- Department of Internal Medicine, Hematology-Oncology Division, Cecil H. and Ida Green Center for Reproductive Biology Sciences, UT Southwestern Medical Center, Dallas, TX, 75235
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4
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Chidyausiku TM, Mendes SR, Klima JC, Nadal M, Eckhard U, Roel-Touris J, Houliston S, Guevara T, Haddox HK, Moyer A, Arrowsmith CH, Gomis-Rüth FX, Baker D, Marcos E. De novo design of immunoglobulin-like domains. Nat Commun 2022; 13:5661. [PMID: 36192397 PMCID: PMC9530121 DOI: 10.1038/s41467-022-33004-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/17/2022] [Indexed: 11/21/2022] Open
Abstract
Antibodies, and antibody derivatives such as nanobodies, contain immunoglobulin-like (Ig) β-sandwich scaffolds which anchor the hypervariable antigen-binding loops and constitute the largest growing class of drugs. Current engineering strategies for this class of compounds rely on naturally existing Ig frameworks, which can be hard to modify and have limitations in manufacturability, designability and range of action. Here, we develop design rules for the central feature of the Ig fold architecture—the non-local cross-β structure connecting the two β-sheets—and use these to design highly stable Ig domains de novo, confirm their structures through X-ray crystallography, and show they can correctly scaffold functional loops. Our approach opens the door to the design of antibody-like scaffolds with tailored structures and superior biophysical properties. The immunoglobulin domain framework of antibodies has been a long standing design challenge. Here, the authors describe design rules for tailoring these domains and show they can be accurately designed, de novo, with high stability and the ability to scaffold functional loops.
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Affiliation(s)
- Tamuka M Chidyausiku
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.,Novartis Institutes for BioMedical Research Inc., San Diego, CA, 92121, USA
| | - Soraia R Mendes
- Proteolysis Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Jason C Klima
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.,Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA.,Encodia, Inc., San Diego, CA, 92121, USA
| | - Marta Nadal
- Protein Design and Modeling Lab, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Ulrich Eckhard
- Proteolysis Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Jorge Roel-Touris
- Protein Design and Modeling Lab, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Scott Houliston
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Tibisay Guevara
- Proteolysis Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain
| | - Hugh K Haddox
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Adam Moyer
- Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - F Xavier Gomis-Rüth
- Proteolysis Laboratory, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain.
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA. .,Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA. .,Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
| | - Enrique Marcos
- Protein Design and Modeling Lab, Department of Structural and Molecular Biology, Molecular Biology Institute of Barcelona (IBMB-CSIC), Baldiri Reixac 15, 08028, Barcelona, Spain.
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5
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Wang J, Jin Y, Li M, Liu S, Lo KKW, Zhao Q. Time-Resolved Luminescent Sensing and Imaging for Enzyme Catalytic Activity Based on Responsive Probes. Chem Asian J 2022; 17:e202200429. [PMID: 35819359 DOI: 10.1002/asia.202200429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/11/2022] [Indexed: 11/07/2022]
Abstract
Enzymes, as a kind of biomacromolecules, play an important role in many physiological processes and relate directly to various diseases. Developing an efficient detection method for enzyme activity is important to achieve early diagnosis of enzyme-relevant diseases and high throughput screening of potential enzyme-relevant drugs. Time-resolved luminescence assay provide a high accuracy and signal-to-noise ratios detection methods for enzyme activity, which has been widely used in high throughput screening of enzyme-relevant drugs and diagnosis of enzyme-relevant diseases. Inspired by these advantages, various responsive probes based on metal complexes and metal-free organic compounds have been developed for time-resolved bioimaging and biosensing of enzyme activity owing to their long luminescence lifetimes, high quantum yields and photostability. In this review, we comprehensively reviewed metal complex- and metal-free organic compound-based responsive probes applied to detect enzyme activity through time-resolved imaging, including their design strategies and sensing principles. Current challenges and future prospects in this rapidly growing field are also discussed.
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Affiliation(s)
- Jiawei Wang
- Nanjing University of Posts and Telecommunications, Institute of Advanced Materials, 9 Wenyuan Road, 210023, Nanjing, CHINA
| | - Yibiao Jin
- Nanjing University of Posts and Telecommunications, Institute of Advanced Materials, 9 Wenyuan Road, 210023, Nanjing, CHINA
| | - Mingdang Li
- Nanjing University of Posts and Telecommunications, Institute of Advanced Materials, 9 Wenyuan Road, 210023, Nanjing, CHINA
| | - Shujuan Liu
- Nanjing University of Posts and Telecommunications, Institute of Advanced Materials, 9 Wenyuan Road, 210023, Nanjing, CHINA
| | - Kenneth Kam-Wing Lo
- City University of Hong Kong, Department of Chemistry, Tat Chee Avenue, Hong Kong, CHINA
| | - Qiang Zhao
- Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, 210023, Nanjing, CHINA
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6
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Widstrom NE, Perez M, Pratt ED, Heier JL, Blankenhorn JF, Breidenbach L, Peterson H, Parker LL. Novel Bruton's Tyrosine Kinase (BTK) Substrates for Time-Resolved Luminescence Assays. ACS Chem Biol 2022; 17:1328-1333. [PMID: 35653784 PMCID: PMC10041687 DOI: 10.1021/acschembio.2c00106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bruton's tyrosine kinase (BTK) is a well-documented target for cancer therapeutics due to its role in B-cell signaling pathways. However, inhibitor design is hindered by lack of tools to assess kinase activity. We used in vitro phosphoproteomics to determine BTK's substrate preferences and applied this information to our updated data processing pipeline, KINATEST-ID 2.1.0. This pipeline generates a position-specific scoring matrix for BTK and a list of candidate synthetic substrates, each given a score. Characterization of selected synthetic substrates demonstrated a correlation between KINATEST-ID 2.1.0 score and biochemical performance in in vitro kinase assays. Additionally, by incorporating a known terbium-chelation motif, we adapted synthetic substrates for use in an antibody-free time-resolved terbium luminescence assay. This assay has applications in high-throughput inhibitor screening.
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Affiliation(s)
- Naomi E Widstrom
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics, 420 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| | - Minervo Perez
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics, 420 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| | - Erica D Pratt
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics, 420 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| | - Jason L Heier
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics, 420 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| | - John F Blankenhorn
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics, 420 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| | - Lindsay Breidenbach
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics, 420 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| | - Hannah Peterson
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics, 420 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
| | - Laurie L Parker
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics, 420 Washington Avenue SE, Minneapolis, Minnesota 55455, United States
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7
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Hu J, Li G. Recent Progress in Fluorescent Chemosensors for Protein Kinases. Chem Asian J 2022; 17:e202200182. [PMID: 35486328 DOI: 10.1002/asia.202200182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/21/2022] [Indexed: 11/10/2022]
Abstract
Protein kinases are involved in almost all biological activities. The activities of different kinases reflect the normal or abnormal status of the human body. Therefore, detecting the activities of different kinases is important for disease diagnosis and drug discovery. Fluorescent probes offer opportunities for studying kinase behaviors at different times and spatial locations. In this review, we summarize different kinds of fluorescent chemosensors that have been used to detect the activities of many different kinases.
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Affiliation(s)
- Jun Hu
- Fujian Agriculture and Forestry University, College of Life Sciences, No.15 Shangxiadian Road, Cangshan District, 350002, Fuzhou, CHINA
| | - Gao Li
- Minjiang University, College of Material and Chemical Engineering, CHINA
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8
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Morris MC. A Toolbox of Fluorescent Peptide Biosensors to Highlight Protein Kinases in Complex Samples : focus on cyclin‐dependent kinases. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- May Catherine Morris
- IBMM-UMR5247 Peptide & Proteins Faculté de Pharmacie,15 Av. Charles Flahault 34093 Montpellier FRANCE
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9
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Shining Light on Protein Kinase Biomarkers with Fluorescent Peptide Biosensors. Life (Basel) 2022; 12:life12040516. [PMID: 35455007 PMCID: PMC9026840 DOI: 10.3390/life12040516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 11/23/2022] Open
Abstract
Protein kinases (PKs) are established gameplayers in biological signalling pathways, and a large body of evidence points to their dysregulation in diseases, in particular cancer, where rewiring of PK networks occurs frequently. Fluorescent biosensors constitute attractive tools for probing biomolecules and monitoring dynamic processes in complex samples. A wide variety of genetically encoded and synthetic biosensors have been tailored to report on PK activities over the last decade, enabling interrogation of their function and insight into their behaviour in physiopathological settings. These optical tools can further be used to highlight enzymatic alterations associated with the disease, thereby providing precious functional information which cannot be obtained through conventional genetic, transcriptomic or proteomic approaches. This review focuses on fluorescent peptide biosensors, recent developments and strategies that make them attractive tools to profile PK activities for biomedical and diagnostic purposes, as well as insights into the challenges and opportunities brought by this unique toolbox of chemical probes.
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10
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Jia C, Bai J, Liu Z, Gao S, Han Y, Yan H. Application of a titanium-based metal-organic framework to protein kinase activity detection and inhibitor screening. Anal Chim Acta 2020; 1128:99-106. [DOI: 10.1016/j.aca.2020.06.065] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 05/31/2020] [Accepted: 06/25/2020] [Indexed: 02/07/2023]
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11
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Urmey AR, Zondlo NJ. Cysteine oxidation to the sulfinic acid induces oxoform-specific lanthanide binding and fluorescence in a designed peptide. Free Radic Biol Med 2020; 152:166-174. [PMID: 32097680 DOI: 10.1016/j.freeradbiomed.2020.02.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/30/2020] [Accepted: 02/19/2020] [Indexed: 10/24/2022]
Abstract
Cysteine sulfinic acid (Cys-SO2-) is a protein post-translational modification that is formed reversibly under oxidative conditions. A short, encodable peptide was developed whose metal binding and terbium luminescence are dependent on cysteine (Cys) oxidation to the sulfinic acid. The protein design is based on the modification of a key metal-binding aspartate (Asp) in a canonical EF-Hand motif (DKDADGWISPAEAK) to Cys. In this design, Cys in the thiol oxidation state does not mimic the native Asp, and thus the peptide binds terbium(III) (Tb3+) poorly and exhibits weak terbium luminescence (fluorescence). In contrast, when Cys is oxidized to the Cys sulfinic acid oxoform, the Cys sulfinate effectively mimics Asp, resulting in a significant increase in terbium affinity and luminescence. Asp residues at positions 1, 3, and 5 of the EF-Hand motif were examined as potential sites for Cys oxidation-responsive metal binding. The peptide with Cys at residue 1 exhibited the highest Tb3+ affinity in both oxidation states. The peptide with Cys at residue 3 exhibited a 4.2-fold distinction in affinity between the oxidation states. Most significantly, the peptide with Cys at residue 5 had only modest Tb3+ affinity as the Cys thiol, but exhibited a 30-fold increase in Tb3+ affinity and an 18-fold increase in Tb3+ luminescence on Cys oxidation to the sulfinic acid. This peptide (Ac-DKDACGWISPAEAK-NH2) exhibited selective Tb3+ binding via Cys-SO2- over the thiol, S-glutathionyl, S-nitrosyl, and sulfonic acid oxoforms, indicating substantially greater Lewis basicity of the sulfinate than the sulfonate. NMR spectroscopy and quantum homology modeling indicated that the designed peptide binds metal with an overall geometry similar to that of an EF-Hand motif, with the Cys sulfinate effectively replacing Asp as a metal-binding ligand. This peptide was applied to detect Cys oxidation to the sulfinic acid by fluorescence spectroscopy, suggesting its broader application in understanding Cys sulfinic acid biology.
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Affiliation(s)
- Andrew R Urmey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States.
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12
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Gao F, Thornley BS, Tressler CM, Naduthambi D, Zondlo NJ. Phosphorylation-dependent protein design: design of a minimal protein kinase-inducible domain. Org Biomol Chem 2019; 17:3984-3995. [PMID: 30942803 PMCID: PMC6668337 DOI: 10.1039/c9ob00502a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein kinases and phosphatases modulate protein structure and function, which in turn regulate cellular activities. The development of novel proteins and protein motifs that are responsive to protein phosphorylation provides new ways to probe the functions of individual protein kinases and the intracellular effects of their activation and downregulation. Herein we develop a minimal motif that is responsive to protein phosphorylation, termed a minimal protein kinase-inducible domain. The encodable protein motif comprises a 7- or 8-residue sequence (DKDADXW or DKDADXXW), derived from EF-Hand calcium-binding domains, that is necessary but not sufficient for binding terbium, combined with a protein phosphorylation site (Ser or Thr at residue 9) that, upon phosphorylation, completes the metal-binding motif. Thus, the motif binds metal poorly and exhibits weak terbium luminescence when not phosphorylated. Upon phosphorylation, the peptide binds metal with significantly higher affinity and exhibits robust terbium luminescence. Phosphorylation results in up to a 23× increase in terbium luminescence. Minimal phosphorylation-dependent motifs as small as 9 residues (DKDADGWIS) were developed. NMR spectroscopy on this lanthanum(iii)·phosphopeptide complex confirmed that binding occurs in a manner similar to that in an EF-Hand, despite the absence of the conserved Glu12 typically present in an EF-Hand. By combining molecular design with known protein kinase recognition sequences, minimal protein kinase-inducible domains were developed that were responsive to phosphorylation by Protein Kinase A (PKA: DKDADRRW(S/pS)IIAK), Protein Kinase C (PKC: DKDADGWI(T/pT)FRRKA), and Casein Kinase 1 (CK1: DKDADDWA(S/pS)I). Phosphorylation by PKA was quantified in HeLa cell extracts, with a 4.4× increase in fluorescence (terbium luminescence) observed at 544 nm. The optimized minimal motif includes alternating aspartate residues at positions 1, 3, and 5, plus binding through the main-chain carbonyl at position 7; a lysine at position 2 to provide electrostatic balance and reduce binding in the absence of phosphorylation; an alanine at residue 4 to promote the αL conformation observed at that position of the EF Hand; a tryptophan at residue 7 or 8 to sensitize terbium luminescence; and a phosphorylation site with serine or threonine at residue 9. Residues at positions 6; 7 or 8; and 10 or later may be changed to provide kinase specificity. In the CK1-responsive peptide, the acidic residues in the proto-terbium-binding motif are employed as part of the kinase recognition sequence. This work thus presents fundamental rules for the design of compact phosphorylation-responsive terbium-binding motifs, with potential further application to motifs responsive to other protein post-translational modifications.
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Affiliation(s)
- Feng Gao
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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13
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Scheuermann MJ, Forbes CR, Zondlo NJ. Redox-Responsive Protein Design: Design of a Small Protein Motif Dependent on Glutathionylation. Biochemistry 2018; 57:6956-6963. [PMID: 30511831 DOI: 10.1021/acs.biochem.8b00973] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cysteine S-glutathionylation is a protein post-translational modification that promotes cellular responses to changes in oxidative conditions. The design of protein motifs that directly depend on defined changes to protein side chains provides new methods for probing diverse protein post-translational modifications. A canonical, 12-residue EF-hand motif was redesigned to be responsive to cysteine glutathionylation. The key design principle was the replacement of the metal-binding Glu12 carboxylate of an EF-hand with a motif capable of metal binding via a free carboxylate in the glutathione-conjugated peptide. In the optimized peptide (DKDADGWCG), metal binding and terbium luminescence were dependent on glutathionylation, with weaker metal binding in the presence of reduced cysteine but increased metal affinity and a 3.5-fold increase in terbium luminescence at 544 nm when cysteine was glutathionylated. Nuclear magnetic resonance spectroscopy indicated that the structure at all residues of the glutathionylated peptide changed in the presence of metal, with chemical shift changes consistent with the adoption of an EF-hand-like structure in the metal-bound glutathionylated peptide. This small protein motif consists of canonical amino acids and is thus genetically encodable, for its potential use as a localized tag to probe protein glutathionylation.
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Affiliation(s)
- Michael J Scheuermann
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Christina R Forbes
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
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14
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Hewitt SH, Butler SJ. Application of lanthanide luminescence in probing enzyme activity. Chem Commun (Camb) 2018; 54:6635-6647. [PMID: 29790500 DOI: 10.1039/c8cc02824a] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Enzymes play critical roles in the regulation of cellular function and are implicated in numerous disease conditions. Reliable and practicable assays are required to study enzyme activity, to facilitate the discovery of inhibitors and activators of enzymes related to disease. In recent years, a variety of enzyme assays have been devised that utilise luminescent lanthanide(iii) complexes, taking advantage of their high detection sensitivities, long luminescence lifetimes, and line-like emission spectra that permit ratiometric and time-resolved analyses. In this Feature article, we focus on recent progress in the development of enzyme activity assays based on lanthanide(iii) luminescence, covering a variety of strategies including Ln(iii)-labelled antibodies and proteins, Ln(iii) ion encapsulation within defined peptide sequences, reactivity-based Ln(iii) probes, and discrete Ln(iii) complexes. Emerging approaches for monitoring enzyme activity are discussed, including the use of anion responsive lanthanide(iii) complexes, capable of molecular recognition and luminescence signalling of polyphosphate anions.
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Affiliation(s)
- Sarah H Hewitt
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, UK.
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15
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Jiang C, Li Y, Liu C, Qiu L, Li Z. A general and versatile fluorescence turn-on assay for detecting the activity of protein tyrosine kinases based on phosphorylation-inhibited tyrosyl oxidation. Chem Commun (Camb) 2018; 52:12570-12573. [PMID: 27711350 DOI: 10.1039/c6cc07035c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A simple, homogeneous and generic method for detecting protein tyrosine (Tyr) kinase activity is developed based on a tyrosinase-assisted fluorescence turn-on strategy. The tyrosinase-mediated oxidation of the Tyr residue in a fluorescently-labeled peptide may lead to efficient fluorescence quenching, while the tyrosine kinase-catalyzed phosphorylation of the peptide can prevent the Tyr oxidation and thus maintain strong fluorescence.
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Affiliation(s)
- Chao Jiang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, P. R. China.
| | - Ya Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, P. R. China.
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, P. R. China.
| | - Liying Qiu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, P. R. China.
| | - Zhengping Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, Shaanxi Province, P. R. China.
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16
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Zhang KY, Yu Q, Wei H, Liu S, Zhao Q, Huang W. Long-Lived Emissive Probes for Time-Resolved Photoluminescence Bioimaging and Biosensing. Chem Rev 2018; 118:1770-1839. [DOI: 10.1021/acs.chemrev.7b00425] [Citation(s) in RCA: 479] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Kenneth Yin Zhang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Qi Yu
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Huanjie Wei
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Shujuan Liu
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Qiang Zhao
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
| | - Wei Huang
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, P. R. China
- Shaanxi
Institute of Flexible Electronics (SIFE), Northwestern Polytechnical University (NPU), Xi’an 710072, P. R. China
- Key
Laboratory of Flexible Electronics (KLOFE) and Institute of Advanced
Materials (IAM), Jiangsu National Synergetic Innovation Center for
Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), Nanjing 211800, P. R. China
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17
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Atomic force microscopy characterization of kinase-mediated phosphorylation of a peptide monolayer. Sci Rep 2016; 6:36793. [PMID: 27841355 PMCID: PMC5107921 DOI: 10.1038/srep36793] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 10/18/2016] [Indexed: 11/08/2022] Open
Abstract
We describe the detailed microscopic changes in a peptide monolayer following kinase-mediated phosphorylation. A reversible electrochemical transformation was observed using square wave voltammetry (SWV) in the reversible cycle of peptide phosphorylation by ERK2 followed by dephosphorylation by alkaline phosphatase. A newly developed method for analyzing local roughness, measured by atomic force microscope (AFM), showed a bimodal distribution. This may indicate either a hole-formation mechanism and/or regions on the surface in which the peptide changed its conformation upon phosphorylation, resulting in increased roughness and current. Our results provide the mechanistic basis for developing biosensors for detecting kinase-mediated phosphorylation in disease.
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18
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Cui W, Parker LL. Modular, Antibody-free Time-Resolved LRET Kinase Assay Enabled by Quantum Dots and Tb(3+)-sensitizing Peptides. Sci Rep 2016; 6:28971. [PMID: 27426233 PMCID: PMC4947905 DOI: 10.1038/srep28971] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/13/2016] [Indexed: 11/26/2022] Open
Abstract
Fluorescent drug screening assays are essential for tyrosine kinase inhibitor discovery. Here we demonstrate a flexible, antibody-free TR-LRET kinase assay strategy that is enabled by the combination of streptavidin-coated quantum dot (QD) acceptors and biotinylated, Tb(3+) sensitizing peptide donors. By exploiting the spectral features of Tb(3+) and QD, and the high binding affinity of the streptavidin-biotin interaction, we achieved multiplexed detection of kinase activity in a modular fashion without requiring additional covalent labeling of each peptide substrate. This strategy is compatible with high-throughput screening, and should be adaptable to the rapidly changing workflows and targets involved in kinase inhibitor discovery.
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Affiliation(s)
- Wei Cui
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 7-194 MCB Building, 420 Washington Ave SE, Minneapolis, MN 55455 USA
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907 USA
| | - Laurie L. Parker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 7-194 MCB Building, 420 Washington Ave SE, Minneapolis, MN 55455 USA
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19
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Selective Sensing of Tyrosine Phosphorylation in Peptides Using Terbium(III) Complexes. Int J Anal Chem 2016; 2016:3216523. [PMID: 27375742 PMCID: PMC4916314 DOI: 10.1155/2016/3216523] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/28/2016] [Indexed: 11/18/2022] Open
Abstract
Phosphorylation of tyrosine residues in proteins, as well as their dephosphorylation, is closely related to various diseases. However, this phosphorylation is usually accompanied by more abundant phosphorylation of serine and threonine residues in the proteins and covers only 0.05% of the total phosphorylation. Accordingly, highly selective detection of phosphorylated tyrosine in proteins is an urgent subject. In this review, recent developments in this field are described. Monomeric and binuclear Tb(III) complexes, which emit notable luminescence only in the presence of phosphotyrosine (pTyr), have been developed. There, the benzene ring of pTyr functions as an antenna and transfers its photoexcitation energy to the Tb(III) ion as the emission center. Even in the coexistence of phosphoserine (pSer) and phosphothreonine (pThr), pTyr can be efficintly detected with high selectivity. Simply by adding these Tb(III) complexes to the solutions, phosphorylation of tyrosine in peptides by protein tyrosine kinases and dephosphorylation by protein tyrosine phosphatases can be successfully visualized in a real-time fashion. Furthermore, the activities of various inhibitors on these enzymes are quantitatively evaluated, indicating a strong potential of the method for efficient screening of eminent inhibitors from a number of candidates.
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20
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Penas C, Mascareñas JL, Vázquez ME. Coupling the folding of a β-hairpin with chelation-enhanced luminescence of Tb(III) and Eu(III) ions for specific sensing of a viral RNA. Chem Sci 2016; 2016:2674-2678. [PMID: 27293537 PMCID: PMC4898589 DOI: 10.1039/c5sc04501k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/10/2016] [Indexed: 12/25/2022] Open
Abstract
Rational modification of a natural RNA-binding peptide with a lanthanide EDTA chelator, and a phenanthroline ligand yields a highly selective luminescent sensor. The sensing mechanism relies on the RNA-triggered folding of the peptide into a β-hairpin, which promotes the coordination of the phenanthroline sensitizer, and the efficient sensitization of complexed lanthanide ions.
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Affiliation(s)
- Cristina Penas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
;
| | - José L. Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
;
| | - M. Eugenio Vázquez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS)
, Departamento de Química Orgánica
, Universidade de Santiago de Compostela
,
15782 Santiago de Compostela
, Spain
.
;
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21
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Luminescent silica nanoparticles for sensing acetylcholinesterase-catalyzed hydrolysis of acetylcholine. Biosens Bioelectron 2016; 77:871-8. [DOI: 10.1016/j.bios.2015.10.059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/01/2015] [Accepted: 10/20/2015] [Indexed: 11/21/2022]
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22
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Li T, Liu X, Liu D, Wang Z. The Peptide Microarray-Based Resonance Light Scattering Assay for Sensitively Detecting Intracellular Kinase Activity. Methods Mol Biol 2016; 1352:85-96. [PMID: 26490469 DOI: 10.1007/978-1-4939-3037-1_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The peptide microarray technology is a robust, reliable, and efficient technique for large-scale determination of enzyme activities, and high-throughput profiling of substrate/inhibitor specificities of enzymes. Here, the activities of cyclic adenosine monophosphate (cAMP)-dependent protein kinase A (PKA) in different cell lysates have been detected by a peptide microarray-based resonance light scattering (RLS) assay with gold nanoparticle (GNP) probes. Highly sensitive detection of PKA activity in 0.1 μg total cell proteins of SHG-44 (human glioma cell) cell lysate (corresponding to 200 cells) is achieved by a selected peptide substrate. The experimental results also demonstrate that the RLS assay can be employed to evaluate the chemical regulation of intracellular kinase activity.
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Affiliation(s)
- Tao Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Xia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Dianjun Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Zhenxin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China.
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23
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Snir E, Amit E, Friedler A, Yitzchaik S. A highly sensitive square wave voltammetry based biosensor for kinase activity measurements. Biopolymers 2015; 104:515-20. [DOI: 10.1002/bip.22653] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 03/11/2015] [Accepted: 03/30/2015] [Indexed: 02/03/2023]
Affiliation(s)
- Elza Snir
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Einav Amit
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Assaf Friedler
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
| | - Shlomo Yitzchaik
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology; The Hebrew University of Jerusalem; Jerusalem 91904 Israel
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24
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Han Y, Li H, Hu Y, Li P, Wang H, Nie Z, Yao S. Time-Resolved Luminescence Biosensor for Continuous Activity Detection of Protein Acetylation-Related Enzymes Based on DNA-Sensitized Terbium(III) Probes. Anal Chem 2015; 87:9179-85. [DOI: 10.1021/acs.analchem.5b01338] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yitao Han
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People’s Republic of China
| | - Hao Li
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People’s Republic of China
| | - Yufang Hu
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People’s Republic of China
| | - Pei Li
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People’s Republic of China
| | - Huixia Wang
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People’s Republic of China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People’s Republic of China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing
and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People’s Republic of China
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25
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Lipchik AM, Perez M, Cui W, Parker LL. Multicolored, Tb³⁺-Based Antibody-Free Detection of Multiple Tyrosine Kinase Activities. Anal Chem 2015. [PMID: 26207839 DOI: 10.1021/acs.analchem.5b02233] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Kinase signaling is a major mechanism driving many cancers. While many inhibitors have been developed and are employed in the clinic, resistance due to crosstalk and pathway reprogramming is an emerging problem. High-throughput assays to detect multiple pathway kinases simultaneously could better model these complex relationships and enable drug development to combat this type of resistance. We developed a strategy to take advantage of time-resolved luminescence of Tb(3+)-chelated phosphotyrosine-containing peptides, which facilitated efficient energy transfer to small molecule fluorophores conjugated to the peptides to produce orthogonally colored biosensors for two different kinases. This enabled multiplexed detection with high signal-to-noise in a high-throughput-compatible format. This proof-of-concept study provides a platform that could be applied to other lanthanide metal and fluorophore combinations to achieve even greater multiplexing without the need for phosphospecific antibodies.
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Affiliation(s)
- Andrew M Lipchik
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy and Purdue Center for Cancer Research, Purdue University, 201 S. University Street, West Lafayette, Indiana 47907, United States
| | - Minervo Perez
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy and Purdue Center for Cancer Research, Purdue University, 201 S. University Street, West Lafayette, Indiana 47907, United States
| | - Wei Cui
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy and Purdue Center for Cancer Research, Purdue University, 201 S. University Street, West Lafayette, Indiana 47907, United States
| | - Laurie L Parker
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy and Purdue Center for Cancer Research, Purdue University, 201 S. University Street, West Lafayette, Indiana 47907, United States
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26
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Amit E, Obena R, Wang YT, Zhuravel R, Reyes AJF, Elbaz S, Rotem D, Porath D, Friedler A, Chen YJ, Yitzchaik S. Integrating proteomics with electrochemistry for identifying kinase biomarkers. Chem Sci 2015; 6:4756-4766. [PMID: 29142712 PMCID: PMC5667508 DOI: 10.1039/c5sc00560d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 05/22/2015] [Indexed: 12/25/2022] Open
Abstract
We present an integrated approach for highly sensitive identification and validation of substrate-specific kinases as cancer biomarkers. Our approach combines phosphoproteomics for high throughput cancer-related biomarker discovery from patient tissues and an impedimetric kinase activity biosensor for sensitive validation. Using non-small-cell lung cancer (NSCLC) as a proof-of-concept study, label-free quantitative phosphoproteomic analysis of a pair of cancerous and its adjacent normal tissues revealed 198 phosphoproteins that are over-phosphorylated in NSCLC. Among the differentially regulated phosphorylation sites, the most significant alteration was in residue S165 in the Hepatoma Derived Growth Factor (HDGF) protein. Hence, HDGF was selected as a model system for the electrochemical studies. Further motif-based analysis of this altered phosphorylation site revealed that extracellular-signal-regulated kinase 1/2 (ERK1/2) are most likely to be the corresponding kinases. For validation of the kinase-substrate pair, densely packed peptide monolayers corresponding to the HDGF phosphorylation site were coupled to a gold electrode. Phosphorylation of the monolayer by ERK2 and dephosphorylation by alkaline phosphatase (AP) were detected by electrochemical impedance spectroscopy (EIS) and surface roughness analysis. Compared to other methods for quantification of kinase concentration, this label-free electrochemical assay offers the advantages of ultra-sensitivity as well as higher specificity for the detection of cancer-related kinase-substrate pair. With implementation of multiple kinase-substrate biomarker pairs, we expect this integrated approach to become a high throughput platform for discovery and validation of phosphorylation-mediated biomarkers.
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Affiliation(s)
- Einav Amit
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology , the Hebrew University of Jerusalem , Safra Campus, Givat Ram , Jerusalem 91904 , Israel . ;
| | - Rofeamor Obena
- Institute of Chemistry , Academia Sinica , Taipei , Taiwan .
| | - Yi-Ting Wang
- Institute of Chemistry , Academia Sinica , Taipei , Taiwan .
| | - Roman Zhuravel
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology , the Hebrew University of Jerusalem , Safra Campus, Givat Ram , Jerusalem 91904 , Israel . ;
| | - Aaron James F Reyes
- Institute of Chemistry , Academia Sinica , Taipei , Taiwan .
- Molecular Science and Technology Program , Taiwan International Graduate Program , Taipei , Taiwan
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan
| | - Shir Elbaz
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology , the Hebrew University of Jerusalem , Safra Campus, Givat Ram , Jerusalem 91904 , Israel . ;
| | - Dvir Rotem
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology , the Hebrew University of Jerusalem , Safra Campus, Givat Ram , Jerusalem 91904 , Israel . ;
| | - Danny Porath
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology , the Hebrew University of Jerusalem , Safra Campus, Givat Ram , Jerusalem 91904 , Israel . ;
| | - Assaf Friedler
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology , the Hebrew University of Jerusalem , Safra Campus, Givat Ram , Jerusalem 91904 , Israel . ;
| | - Yu-Ju Chen
- Institute of Chemistry , Academia Sinica , Taipei , Taiwan .
| | - Shlomo Yitzchaik
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology , the Hebrew University of Jerusalem , Safra Campus, Givat Ram , Jerusalem 91904 , Israel . ;
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27
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Yin C, Wang M, Lei C, Wang Z, Li P, Li Y, Li W, Huang Y, Nie Z, Yao S. Phosphorylation-Mediated Assembly of a Semisynthetic Fluorescent Protein for Label-Free Detection of Protein Kinase Activity. Anal Chem 2015; 87:6311-8. [DOI: 10.1021/acs.analchem.5b01160] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Chao Yin
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Ming Wang
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Zhen Wang
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Pei Li
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Yong Li
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Wang Li
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
| | - Shouzhuo Yao
- State Key Laboratory of Chemo/Biosensing & Chemometrics, College of Chemistry & Chemical Engineering, Hunan University, Changsha, P. R. China
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28
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Akiba H, Sumaoka J, Tsumoto K, Komiyama M. Click Conjugation of a Binuclear Terbium(III) Complex for Real-Time Detection of Tyrosine Phosphorylation. Anal Chem 2015; 87:3834-40. [DOI: 10.1021/ac5045466] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hiroki Akiba
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department
of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and
| | - Jun Sumaoka
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Life
Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8577, Japan
| | - Kouhei Tsumoto
- Department
of Bioengineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, and
| | - Makoto Komiyama
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Life
Science Center of Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Ten-noudai, Tsukuba, Ibaraki 305-8577, Japan
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29
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Lipchik AM, Perez M, Bolton S, Dumrongprechachan V, Ouellette SB, Cui W, Parker LL. KINATEST-ID: a pipeline to develop phosphorylation-dependent terbium sensitizing kinase assays. J Am Chem Soc 2015; 137:2484-94. [PMID: 25689372 DOI: 10.1021/ja507164a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nonreceptor protein tyrosine kinases (NRTKs) are essential for cellular homeostasis and thus are a major focus of current drug discovery efforts. Peptide substrates that can enhance lanthanide ion luminescence upon tyrosine phosphorylation enable rapid, sensitive screening of kinase activity, however design of suitable substrates that can distinguish between tyrosine kinase families is a huge challenge. Despite their different substrate preferences, many NRTKs are structurally similar even between families. Furthermore, the development of lanthanide-based kinase assays is hampered by incomplete understanding of how to integrate sequence selectivity with metal ion binding, necessitating laborious iterative substrate optimization. We used curated proteomic data from endogenous kinase substrates and known Tb(3+)-binding sequences to build a generalizable in silico pipeline with tools to generate, screen, align, and select potential phosphorylation-dependent Tb(3+)-sensitizing substrates that are most likely to be kinase specific. We demonstrated the approach by developing several substrates that are selective within kinase families and amenable to high-throughput screening (HTS) applications. Overall, this strategy represents a pipeline for developing efficient and specific assays for virtually any tyrosine kinase that use HTS-compatible lanthanide-based detection. The tools provided in the pipeline also have the potential to be adapted to identify peptides for other purposes, including other enzyme assays or protein-binding ligands.
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Affiliation(s)
- Andrew M Lipchik
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Center for Cancer Research, Purdue University , West Lafayette, Indiana 47907
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30
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Duodu E, Kraskouskaya D, Campbell J, Graca-Lima G, Gunning PT. Selective detection of tyrosine-containing proximally phosphorylated motifs using an antenna-free Tb3+ luminescent sensor. Chem Commun (Camb) 2015; 51:6675-7. [DOI: 10.1039/c5cc00679a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Tb(iii) can be used for sensing proximally phosphorylated tyrosine-containing peptide sequences.
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Affiliation(s)
- Eugenia Duodu
- University of Toronto Mississauga
- Mississauga
- L5L 1C6 Canada
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31
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Cui W, Parker LL. A time-resolved luminescence biosensor assay for anaplastic lymphoma kinase (ALK) activity. Chem Commun (Camb) 2014; 51:362-5. [PMID: 25406835 DOI: 10.1039/c4cc07453j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A novel time-resolved luminescence biosensor assay for anaplastic lymphoma kinase (ALK) was developed. We used a straightforward strategy to modify a known ALK substrate into a peptide biosensor that can accommodate terbium luminescence sensitization upon its phosphorylation by ALK. Since this strategy is generalizable, this high-throughput screening compatible assay serves as an example for development of other kinase assays that employ terbium luminescence as a read-out.
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Affiliation(s)
- Wei Cui
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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32
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Yamada K, Takaki S, Komuro N, Suzuki K, Citterio D. An antibody-free microfluidic paper-based analytical device for the determination of tear fluid lactoferrin by fluorescence sensitization of Tb3+. Analyst 2014; 139:1637-43. [PMID: 24482793 DOI: 10.1039/c3an01926h] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
An inkjet-printed microfluidic paper-based analytical device (μPAD) for the detection of lactoferrin has been developed. The analyte concentration dependent fluorescence emission, caused by the sensitization of pre-deposited terbium (Tb(3+)) upon complexation with lactoferrin on the paper device, is captured using a digital camera. The dynamic response range (0.5-3 mg mL(-1)) and the limit of detection (0.30 mg mL(-1)) of the μPAD are suitable for the analysis of normal human tears and the detection of eye disorders. Finally, lactoferrin concentrations in human tear samples were analyzed by the μPADs and the assay results corresponded within 6% error to those obtained by an immunoassay (ELISA). The μPADs provide a simple, rapid and accurate method for lactoferrin detection in tear fluid. Results are obtained within 15 min of a single application of 2.5 μL of sample. To the best of our knowledge, this is the first report of a device for lactoferrin quantification relying neither on an immunoassay nor on high cost analytical instrumentation.
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Affiliation(s)
- Kentaro Yamada
- Department of Applied Chemistry, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
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Akiba H, Sumaoka J, Hamakubo T, Komiyama M. Conjugation-free, visual, and quantitative evaluation of inhibitors on protein tyrosine kinases and phosphatases with a luminescent Tb(III) complex. Anal Bioanal Chem 2014; 406:2957-64. [PMID: 24652149 DOI: 10.1007/s00216-014-7707-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 02/14/2014] [Accepted: 02/19/2014] [Indexed: 10/25/2022]
Abstract
A straightforward and visual method to assess inhibitors on protein tyrosine kinases (PTKs) and phosphatases (PTPs) has been developed. These enzymes play critical roles in a number of diseases and, thus, their inhibitors are important for effective therapy. With the use of the long-life luminescence emitted from a binuclear Tb(III) complex, enzymatic reactions of PTKs and PTPs were monitored in real-time, and the inhibitor activity was quantitatively evaluated in terms of the decrease in the rate of luminescence change. No conjugation of the probe to a substrate peptide was necessary. The IC50 values of four inhibitors on three kinds of PTKs [Src, Fyn, and epidermal growth factor receptor (EGFR)] were determined. For example, gefitinib, which is a selective inhibitor on EGFR, inhibited this PTK with IC50 of 22 nM. Towards Src and Fyn (non-targeted PTK), however, IC50 of this inhibitor was greater than 20 μM as expected. Inhibition of two kinds of PTPs (Shp-1 and PTP1B) by two inhibitors was also assayed, providing completely consistent results on their known selectivity. Furthermore, the system where both PTK and PTP are active was monitored and the reactions were visualized with the present Tb(III) complex-based method. High potential of the present method to a variety of systems has been evidenced.
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Affiliation(s)
- Hiroki Akiba
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Meguro-ku, Tokyo, 153-8904, Japan
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Pazos E, Vázquez ME. Advances in lanthanide-based luminescent peptide probes for monitoring the activity of kinase and phosphatase. Biotechnol J 2013; 9:241-52. [DOI: 10.1002/biot.201300203] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Revised: 08/27/2013] [Accepted: 09/25/2013] [Indexed: 01/16/2023]
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Li T, Liu X, Liu D, Wang Z. Sensitive detection of protein kinase A activity in cell lysates by peptide microarray-based assay. Anal Chem 2013; 85:7033-7. [PMID: 23855559 DOI: 10.1021/ac4010502] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In the present work, the activities of protein kinase A (PKA) in cell lysates have been detected by a peptide microarray-based resonance light scattering assay with gold nanoparticle probes. Highly sensitive detection of PKA activity in 0.1 μg total cell proteins of SHG-44 cell lysate (corresponding to 200 cells) is achieved by a selected peptide substrate. The experimental results also demonstrate that the assay can be employed to evaluate expression levels of PKA activity in different cell lines and chemical (e.g., Forskolin )-mediated PKA activity fluctuation in living cells. In addition, PKA inhibition by the inhibitor (H89) is shown, suggesting the potential for screening PKA inhibitors at the living cell level.
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Affiliation(s)
- Tao Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P R China
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36
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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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