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Qiu X, Hou X, Yang Y, Fang H, Cui F, Yang X. An in-line method for high-throughput screening of protein tyrosine phosphatase receptor type O inhibitors by capillary electrophoresis based on electrophoretically mediated microanalysis. J Chromatogr A 2024; 1713:464511. [PMID: 38007841 DOI: 10.1016/j.chroma.2023.464511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/28/2023]
Abstract
Protein tyrosine phosphatase receptor type O (PTPRO) plays an important role in inflammation-related pathways and has become an emerging drug target. In this study, we developed an in-line capillary electrophoresis (CE) method for the investigation of the enzymatic activity of PTPRO, which was based on electrophoretically mediated microanalysis (EMMA). After a thorough method validation of the optimized conditions, this protocol was successfully employed to determine the kinetics of PTPRO as well as the half-maximal inhibitory concentration (IC50) of two typical PTPRO inhibitors. The final results were consistent with the values obtained through classical ultraviolet-visible (UV-vis) spectrophotometry. Our new method exhibited improved accuracy and reduced consumption, avoiding the disadvantages of traditional methods. This work provides a new strategy for PTPRO enzyme kinetic studies as well as inhibitory activity determination through capillary electrophoresis for the first time.
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Affiliation(s)
- Xueting Qiu
- Department of Pharmaceutical Analysis and Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China
| | - Xuben Hou
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China
| | - Yue Yang
- School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China
| | - Hao Fang
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China
| | - Fei Cui
- Department of Pharmaceutical Analysis and Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China
| | - Xinying Yang
- Department of Pharmaceutical Analysis and Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China.
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2
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Fontanillo M, Trebacz M, Reinkemeier CD, Avilés Huerta D, Uhrig U, Sehr P, Köhn M. Short peptide pharmacophores developed from protein phosphatase-1 disrupting peptides (PDPs). Bioorg Med Chem 2022; 65:116785. [PMID: 35525109 PMCID: PMC7613447 DOI: 10.1016/j.bmc.2022.116785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 11/28/2022]
Abstract
PP1 is a major phosphoserine/threonine-specific phosphatase that is involved in diseases such as heart insufficiency and diabetes. PP1-disrupting peptides (PDPs) are selective modulators of PP1 activity that release its catalytic subunit, which then dephosphorylates nearby substrates. Recently, PDPs enabled the creation of phosphatase-recruiting chimeras, which are bifunctional molecules that guide PP1 to a kinase to dephosphorylate and inactivate it. However, PDPs are 23mer peptides, which is not optimal for their use in therapy due to potential stability and immunogenicity issues. Therefore, we present here the sequence optimization of the 23mer PDP to a 5mer peptide, involving several attempts considering structure-based virtual screening, high throughput screening and peptide sequence optimization. We provide here a strong pharmacophore as lead structure to enable PP1 targeting in therapy or its use in phosphatase-recruiting chimeras in the future.
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Affiliation(s)
| | - Malgorzata Trebacz
- Centres for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany
| | | | | | - Ulrike Uhrig
- Chemical Biology Core Facility, EMBL, Heidelberg, Germany
| | - Peter Sehr
- Chemical Biology Core Facility, EMBL, Heidelberg, Germany
| | - Maja Köhn
- Genome Biology Unit, EMBL, Heidelberg, Germany; Centres for Biological Signalling Studies BIOSS and CIBSS, University of Freiburg, Freiburg, Germany; Faculty of Biology, University of Freiburg, Schänzlestrasse 18, 79104 Freiburg, Germany.
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3
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Yang Y, Zhang L, Tian J, Ye F, Xiao Z. Integrated Approach to Identify Selective PTP1B Inhibitors Targeting the Allosteric Site. J Chem Inf Model 2021; 61:4720-4732. [PMID: 34521197 DOI: 10.1021/acs.jcim.1c00357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is an intractable target for drug discovery due to its conservative and cationic catalytic site. Targeting alternative allosteric sites of PTP1B is a promising strategy to achieve specificity and bioavailability. A hierarchical virtual screening based on a previously identified allosteric site was applied to search for potential PTP1B inhibitors with better pharmacological profiles. Four potent PTP1B inhibitors (H1, H3, H7, and H9) with structures distinct from known inhibitors were identified. Among them, H3 and H9 demonstrated evident selectivity to PTP1B over homologous T-cell protein tyrosine phosphatase (TCPTP) and SHP2. Molecular dynamics simulations and molecular mechanics-generalized Born surface area (MM-GBSA) calculations recognized Phe280, Phe196, Leu192, and Asn193 as key residues responsible for potent allosteric inhibition and excellent PTP selectivity. The results not only expand the structural diversity but also aid the future molecular design of PTP1B allosteric inhibitors.
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Affiliation(s)
- Ying Yang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
| | - Lei Zhang
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
| | - Jinying Tian
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P. R. China
| | - Fei Ye
- Beijing Key Laboratory of New Drug Mechanisms and Pharmacological Evaluation Study, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, P. R. China
| | - Zhiyan Xiao
- Beijing Key Laboratory of Active Substance Discovery and Druggability Evaluation, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, P. R. China
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4
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Liu S, Zheng S, Chu J. Cationic Polythiophene-based Colorimetric Assay for Probing the Activity of Protein Kinase A. ANAL SCI 2021; 37:1039-1043. [PMID: 33250451 DOI: 10.2116/analsci.20n034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this work, a novel colorimetric assay based on polythiophene derivative (PMNT) was designed for the detection of protein kinase A (PKA). PKA can catalyze the phosphorylation of peptide, leading to the conformation change of PMNT from random-coil to planar, with the disappearance of absorption peaks above 500 nm and a color change from pink to yellow. The fabricated assay exhibits a wide linear range of 0.05 - 20 U/mL with a detection limit of 0.02 U/mL for PKA activity detection. The proposed protocol has promising prospects for use in clinical diagnosis related to PKA activity.
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Affiliation(s)
- Shanshan Liu
- Hubei Key Laboratory of Processing and Application of Catalytic Materials, College of Chemistry and Chemical Engineering, Huanggang Normal University
| | - Sitian Zheng
- Hubei Key Laboratory of Processing and Application of Catalytic Materials, College of Chemistry and Chemical Engineering, Huanggang Normal University
| | - Jing Chu
- Hubei Key Laboratory of Processing and Application of Catalytic Materials, College of Chemistry and Chemical Engineering, Huanggang Normal University
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5
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Suo T, Sohail M, Xie S, Li B, Chen Y, Zhang L, Zhang X. DNA nanotechnology: A recent advancement in the monitoring of microcystin-LR. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123418. [PMID: 33265072 DOI: 10.1016/j.jhazmat.2020.123418] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/24/2020] [Accepted: 07/05/2020] [Indexed: 06/12/2023]
Abstract
The Microcystin-Leucine-Arginine (MC-LR) is the most toxic and widely distributed microcystin, which originates from cyanobacteria produced by water eutrophication. The MC-LR has deleterious effects on the aquatic lives and agriculture, and this highly toxic chemical could severely endanger human health when the polluted food was intaken. Therefore, the monitoring of MC-LR is of vital importance in the fields including environment, food, and public health. Utilizing the complementary base pairing between DNA molecules, DNA nanotechnology can realize the programmable and predictable regulation of DNA molecules. In analytical applications, DNA nanotechnology can be used to detect targets via target-induced conformation change and the nano-assemblies of nucleic acids. Compared with the conventional analytical technologies, DNA nanotechnology has the advantages of sensitive, versatile, and high potential in real-time and on-site applications. According to the molecular basis for recognizing MC-LR, the strategies of applying DNA nanotechnology in the MC-LR monitoring are divided into two categories in this review: DNA as a recognition element and DNA-assisted signal processing. This paper introduces state-of-the-art analytical methods for the detection of MC-LR based on DNA nanotechnology and provides critical perspectives on the challenges and development in this field.
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Affiliation(s)
- Tiying Suo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Muhammad Sohail
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Siying Xie
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China.
| | - Yue Chen
- School of Nursing, Nanjing Medical University, Nanjing 211166, China.
| | - Lihui Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China.
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China.
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Camacho-Muñoz D, Lawton LA, Edwards C. Degradation of okadaic acid in seawater by UV/TiO 2 photocatalysis - Proof of concept. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 733:139346. [PMID: 32447082 PMCID: PMC7298613 DOI: 10.1016/j.scitotenv.2020.139346] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/16/2020] [Accepted: 05/09/2020] [Indexed: 06/11/2023]
Abstract
The consumption of contaminated shellfish with marine toxins causes adverse socioeconomical, environmental and health impacts. The marine toxin okadaic acid (OA) provokes diarrhetic shellfish poisoning (DSP) syndrome characterized by severe gastrointestinal symptoms. Therefore, there is increasing interest in removing these toxins from the marine environment to protect shellfish harvesting sites. Photocatalysis is proposed as an efficient method to detoxify the marine environment. In this study, Prorocentrum lima was used to produce high purity DSP toxins, in particular OA, for degradation studies. The profiling, characterization and quantification of DSP toxins in the culture of P. lima were achieved by ultrahigh performance liquid chromatography coupled to quadrupole-time of flight mass spectrometry (UPLC-QTOF-MSE) for accurate-mass full spectrum acquisition data. The effectiveness of UV/TiO2 system to degrade OA in seawater was assessed in lab-scale experiments and identification of transformation products was proposed based on the data obtained during analysis by UPLC-QTOF-MSE. The detoxification potential of the UV/TiO2 system was investigated using the phosphatase inhibition assay. Sufficient amount of high-purity OA (25 mg, >90% purity) was produced in-house for use in photocatalysis experiments by simple reversed-phase flash chromatography. Complete degradation of OA was observed in seawater after 30 min and 7.5 min in deionized water. The rate constants fitted with the pseudo-first order kinetic model (R2 > 0.96). High-resolution mass spectrometry analysis of the photocatalyzed OA allowed tentative identification of four transformation products. Detoxification was achieved in parallel with the degradation of OA in deionized water and artificial ocean water (≤20 min) but not for seawater. Overall, results suggest that UV/TiO2 photocatalysis can be an effective approach for degrading OA and their TPs in the marine environment. To the best of our knowledge, this is the first report on the use of photocatalysis to degrade marine toxins and its promising potential to protect shellfish harvesting sites.
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Affiliation(s)
- Dolores Camacho-Muñoz
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen AB10 7GJ, UK.
| | - Linda Ann Lawton
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen AB10 7GJ, UK
| | - Christine Edwards
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen AB10 7GJ, UK
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7
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Clausse V, Tao D, Debnath S, Fang Y, Tagad HD, Wang Y, Sun H, LeClair CA, Mazur SJ, Lane K, Shi ZD, Vasalatiy O, Eells R, Baker LK, Henderson MJ, Webb MR, Shen M, Hall MD, Appella E, Appella DH, Coussens NP. Physiologically relevant orthogonal assays for the discovery of small-molecule modulators of WIP1 phosphatase in high-throughput screens. J Biol Chem 2019; 294:17654-17668. [PMID: 31481464 PMCID: PMC6873202 DOI: 10.1074/jbc.ra119.010201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/30/2019] [Indexed: 01/07/2023] Open
Abstract
WT P53-Induced Phosphatase 1 (WIP1) is a member of the magnesium-dependent serine/threonine protein phosphatase (PPM) family and is induced by P53 in response to DNA damage. In several human cancers, the WIP1 protein is overexpressed, which is generally associated with a worse prognosis. Although WIP1 is an attractive therapeutic target, no potent, selective, and bioactive small-molecule modulator with favorable pharmacokinetics has been reported. Phosphatase enzymes are among the most challenging targets for small molecules because of the difficulty of achieving both modulator selectivity and bioavailability. Another major obstacle has been the availability of robust and physiologically relevant phosphatase assays that are suitable for high-throughput screening. Here, we describe orthogonal biochemical WIP1 activity assays that utilize phosphopeptides from native WIP1 substrates. We optimized an MS assay to quantify the enzymatically dephosphorylated peptide reaction product in a 384-well format. Additionally, a red-shifted fluorescence assay was optimized in a 1,536-well format to enable real-time WIP1 activity measurements through the detection of the orthogonal reaction product, Pi. We validated these two optimized assays by quantitative high-throughput screening against the National Center for Advancing Translational Sciences (NCATS) Pharmaceutical Collection and used secondary assays to confirm and evaluate inhibitors identified in the primary screen. Five inhibitors were further tested with an orthogonal WIP1 activity assay and surface plasmon resonance binding studies. Our results validate the application of miniaturized physiologically relevant and orthogonal WIP1 activity assays to discover small-molecule modulators from high-throughput screens.
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Affiliation(s)
- Victor Clausse
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Subrata Debnath
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Harichandra D Tagad
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Yuhong Wang
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Hongmao Sun
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Christopher A LeClair
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Sharlyn J Mazur
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Kelly Lane
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Zhen-Dan Shi
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Olga Vasalatiy
- Imaging Probe Development Center, NHLBI, National Institutes of Health, Rockville, Maryland 20850
| | - Rebecca Eells
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, Pennsylvania 19355
| | - Lynn K Baker
- Reaction Biology Corporation, 1 Great Valley Parkway, Suite 2, Malvern, Pennsylvania 19355
| | - Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Martin R Webb
- Francis Crick Institute, 1 Midland Road, London NW1 AT, United Kingdom
| | - Min Shen
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
| | - Ettore Appella
- Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892
| | - Daniel H Appella
- Synthetic Bioactive Molecules Section, Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Nathan P Coussens
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850
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8
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Xue W, Tian J, Wang XS, Xia J, Wu S. Discovery of potent PTP1B inhibitors via structure-based drug design, synthesis and in vitro bioassay of Norathyriol derivatives. Bioorg Chem 2019; 86:224-234. [PMID: 30716620 DOI: 10.1016/j.bioorg.2019.01.059] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 01/11/2019] [Accepted: 01/27/2019] [Indexed: 12/11/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) has recently been identified as a potential target of Norathyriol. Unfortunately, Norathyriol is not a potent PTP1B inhibitor, which somewhat hinders its further application. Based on the fact that no study on the relationship of chemical structure and PTP1B inhibitory activity of Norathyriol has been reported so far, we attempted to perform structural optimization so as to improve the potency for PTP1B. Via structure-based drug design (SBDD), a rational strategy based on the binding mode of Norathyriol to PTP1B, we designed 26 derivatives with substitutions at the four phenolic hydroxyl groups of Norathyriol. By chemical synthesis and in vitro bioassay, we identified seven PTP1B inhibitors that were more potent than Norathyriol, of which XWJ24 showed the highest potency (IC50: 0.6 μM). We also found out that XWJ24 was a competitive inhibitor and showed the 4.5-fold selectivity over its close homolog, TC-PTP. Through molecular docking of XWJ24 against PTP1B, we highlighted the essential role of its hydrogen bond with Asp181 for PTP1B inhibition and identified a potential halogen bond with Asp48 that was not observed for Norathyriol. The current data indicate that our SBDD strategy is effective to discover potent PTP1B-targeted Norathyriol derivatives, and XWJ24 is a promising lead compound for further development.
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Affiliation(s)
- Wenjie Xue
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Jinlong Tian
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Xiang Simon Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, Howard University, Washington DC 20059, USA
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Department of New Drug Research and Development, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
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9
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Wang Y, Hoermann B, Pavic K, Trebacz M, Rios P, Köhn M. Interrogating PP1 Activity in the MAPK Pathway with Optimized PP1-Disrupting Peptides. Chembiochem 2018; 20:66-71. [PMID: 30338897 PMCID: PMC6471087 DOI: 10.1002/cbic.201800541] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Indexed: 12/22/2022]
Abstract
Protein phosphatase‐1 (PP1)‐disrupting peptides (PDPs) are selective chemical modulators of PP1 that liberate the active PP1 catalytic subunit from regulatory proteins; thus allowing the dephosphorylation of nearby substrates. We have optimized the original cell‐active PDP3 for enhanced stability, and obtained insights into the chemical requirements for stabilizing this 23‐mer peptide for cellular applications. The optimized PDP‐Nal was used to dissect the involvement of PP1 in the MAPK signaling cascade. Specifically, we have demonstrated that, in human osteosarcoma (U2OS) cells, phosphoMEK1/2 is a direct substrate of PP1, whereas dephosphorylation of phosphoERK1/2 is indirect and likely mediated through enhanced tyrosine phosphatase activity after PDP‐mediated PP1 activation. Thus, as liberators of PP1 activity, PDPs represent a valuable tool for identifying the substrates of PP1 and understanding its role in diverse signaling cascades.
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Affiliation(s)
- Yansong Wang
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Bernhard Hoermann
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Faculty of Biology and BIOSS-Centre for Biological Signalling Studies, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany.,Collaboration for joint PhD degree between EMBL and, Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Karolina Pavic
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Malgorzata Trebacz
- Faculty of Biology and BIOSS-Centre for Biological Signalling Studies, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany
| | - Pablo Rios
- Faculty of Biology and BIOSS-Centre for Biological Signalling Studies, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany
| | - Maja Köhn
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.,Faculty of Biology and BIOSS-Centre for Biological Signalling Studies, Albert-Ludwigs-University of Freiburg, Schänzlestrasse 18, 79104, Freiburg, Germany
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10
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Gengenbach BB, Müschen CR, Buyel JF. Expression and purification of human phosphatase and actin regulator 1 (PHACTR1) in plant-based systems. Protein Expr Purif 2018; 151:46-55. [PMID: 29894805 DOI: 10.1016/j.pep.2018.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 05/31/2018] [Accepted: 06/07/2018] [Indexed: 12/21/2022]
Abstract
Cardiovascular diseases are a prevalent cause of morbidity and mortality especially in industrialized countries. The human phosphatase and actin regulator 1 (PHACTR1) may be involved in such diseases, but its precise regulatory function remains unclear due to the large number of potential interaction partners. The same phenomenon makes this protein difficult to express in mammalian cells, but it is also an intrinsically disordered protein that likely aggregates when expressed in bacteria due to the absence of chaperones. We therefore used a design of experiments approach to test the suitability of three plant-based systems for the expression of satisfactory quantities of recombinant PHACTR1, namely transient expression in tobacco (Nicotiana tabacum) BY-2 plant cell packs (PCPs), whole N. benthamiana leaves and BY-2 cell lysate (BYL). The highest yield was achieved using the BYL: up to 120 mg product kg-1 biomass equivalent within 48 h of translation. This was 1.3-fold higher than transient expression in N. benthamiana together with the silencing inhibitor p19, and 6-fold higher than the PCP system. The presence of Triton X-100 in the extraction buffer increased the recovery of PHACTR1 by 2-200-fold depending on the conditions. PHACTR1 was incompatible with biomass blanching and was stable for less than 16 h in raw plant extracts. Purification using a DDK-tag proved inefficient whereas 15% purity was achieved by immobilized metal affinity chromatography.
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Affiliation(s)
- B B Gengenbach
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstraße 6, 52074, Aachen, Germany.
| | - C R Müschen
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstraße 6, 52074, Aachen, Germany.
| | - J F Buyel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstraße 6, 52074, Aachen, Germany; Institute for Molecular Biotechnology, Worringerweg 1, RWTH Aachen University, 52074, Aachen, Germany.
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11
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Zhang H, Xiao P, Wong YT, Shen W, Chhabra M, Peltier R, Jiang Y, He Y, He J, Tan Y, Xie Y, Ho D, Lam YW, Sun J, Sun H. Construction of an alkaline phosphatase-specific two-photon probe and its imaging application in living cells and tissues. Biomaterials 2017; 140:220-229. [DOI: 10.1016/j.biomaterials.2017.06.032] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 06/08/2017] [Accepted: 06/22/2017] [Indexed: 01/09/2023]
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12
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Gul S. Epigenetic assays for chemical biology and drug discovery. Clin Epigenetics 2017; 9:41. [PMID: 28439316 PMCID: PMC5399855 DOI: 10.1186/s13148-017-0342-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 04/12/2017] [Indexed: 12/27/2022] Open
Abstract
The implication of epigenetic abnormalities in many diseases and the approval of a number of compounds that modulate specific epigenetic targets in a therapeutically relevant manner in cancer specifically confirms that some of these targets are druggable by small molecules. Furthermore, a number of compounds are currently in clinical trials for other diseases including cardiovascular, neurological and metabolic disorders. Despite these advances, the approved treatments for cancer only extend progression-free survival for a relatively short time and being associated with significant side effects. The current clinical trials involving the next generation of epigenetic drugs may address the disadvantages of the currently approved epigenetic drugs. The identification of chemical starting points of many drugs often makes use of screening in vitro assays against libraries of synthetic or natural products. These assays can be biochemical (using purified protein) or cell-based (using for example, genetically modified, cancer cell lines or primary cells) and performed in microtiter plates, thus enabling a large number of samples to be tested. A considerable number of such assays are available to monitor epigenetic target activity, and this review provides an overview of drug discovery and chemical biology and describes assays that monitor activities of histone deacetylase, lysine-specific demethylase, histone methyltransferase, histone acetyltransferase and bromodomain. It is of critical importance that an appropriate assay is developed and comprehensively validated for a given drug target prior to screening in order to improve the probability of the compound progressing in the drug discovery value chain.
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Affiliation(s)
- Sheraz Gul
- Fraunhofer Institute for Molecular Biology and Applied Ecology - ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
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Fontanillo M, Zemskov I, Häfner M, Uhrig U, Salvi F, Simon B, Wittmann V, Köhn M. Synthesis of Highly Selective Submicromolar Microcystin-Based Inhibitors of Protein Phosphatase (PP)2A over PP1. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606449] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Miriam Fontanillo
- Genome Biology Unit; European Molecular Biology Laboratory; Meyerhofstrasse 1 69117 Heidelberg Germany
| | - Ivan Zemskov
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB); University of Konstanz; Fach 709 78457 Konstanz Germany
| | - Maximilian Häfner
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB); University of Konstanz; Fach 709 78457 Konstanz Germany
| | - Ulrike Uhrig
- Chemical Biology Core Facility; European Molecular Biology Laboratory; Meyerhofstrasse 1 69117 Heidelberg Germany
| | - Francesca Salvi
- Genome Biology Unit; European Molecular Biology Laboratory; Meyerhofstrasse 1 69117 Heidelberg Germany
| | - Bernd Simon
- Structural and Computational Biology Unit; European Molecular Biology Laboratory; Meyerhofstrasse 1 69117 Heidelberg Germany
| | - Valentin Wittmann
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB); University of Konstanz; Fach 709 78457 Konstanz Germany
| | - Maja Köhn
- Genome Biology Unit; European Molecular Biology Laboratory; Meyerhofstrasse 1 69117 Heidelberg Germany
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14
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Fontanillo M, Zemskov I, Häfner M, Uhrig U, Salvi F, Simon B, Wittmann V, Köhn M. Synthesis of Highly Selective Submicromolar Microcystin-Based Inhibitors of Protein Phosphatase (PP)2A over PP1. Angew Chem Int Ed Engl 2016; 55:13985-13989. [PMID: 27723199 PMCID: PMC5113787 DOI: 10.1002/anie.201606449] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 08/19/2016] [Indexed: 12/20/2022]
Abstract
Research and therapeutic targeting of the phosphoserine/threonine phosphatases PP1 and PP2A is hindered by the lack of selective inhibitors. The microcystin (MC) natural toxins target both phosphatases with equal potency, and their complex synthesis has complicated structure–activity relationship studies in the past. We report herein the synthesis and biochemical evaluation of 11 MC analogues, which was accomplished through an efficient strategy combining solid‐ and solution‐phase approaches. Our approach led to the first MC analogue with submicromolar inhibitory potency that is strongly selective for PP2A over PP1 and does not require the complex lipophilic Adda group. Through mutational and structural analyses, we identified a new key element for binding, as well as reasons for the selectivity. This work gives unprecedented insight into how selectivity between these phosphatases can be achieved with MC analogues.
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Affiliation(s)
- Miriam Fontanillo
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Ivan Zemskov
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Fach 709, 78457, Konstanz, Germany
| | - Maximilian Häfner
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Fach 709, 78457, Konstanz, Germany
| | - Ulrike Uhrig
- Chemical Biology Core Facility, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Francesca Salvi
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Bernd Simon
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Valentin Wittmann
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Fach 709, 78457, Konstanz, Germany
| | - Maja Köhn
- Genome Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany.
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15
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Irani S, Yogesha SD, Mayfield J, Zhang M, Zhang Y, Matthews WL, Nie G, Prescott NA, Zhang YJ. Structure of Saccharomyces cerevisiae Rtr1 reveals an active site for an atypical phosphatase. Sci Signal 2016; 9:ra24. [PMID: 26933063 DOI: 10.1126/scisignal.aad4805] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Changes in the phosphorylation status of the carboxyl-terminal domain (CTD) of RNA polymerase II (RNAPII) correlate with the process of eukaryotic transcription. The yeast protein regulator of transcription 1 (Rtr1) and the human homolog RNAPII-associated protein 2 (RPAP2) may function as CTD phosphatases; however, crystal structures of Kluyveromyces lactis Rtr1 lack a consensus active site. We identified a phosphoryl transfer domain in Saccharomyces cerevisiae Rtr1 by obtaining and characterizing a 2.6 Å resolution crystal structure. We identified a putative substrate-binding pocket in a deep groove between the zinc finger domain and a pair of helices that contained a trapped sulfate ion. Because sulfate mimics the chemistry of a phosphate group, this structural data suggested that this groove represents the phosphoryl transfer active site. Mutagenesis of the residues lining this groove disrupted catalytic activity of the enzyme assayed in vitro with a fluorescent chemical substrate, and expression of the mutated Rtr1 failed to rescue growth of yeast lacking Rtr1. Characterization of the phosphatase activity of RPAP2 and a mutant of the conserved putative catalytic site in the same chemical assay indicated a conserved reaction mechanism. Our data indicated that the structure of the phosphoryl transfer domain and reaction mechanism for the phosphoryl transfer activity of Rtr1 is distinct from those of other phosphatase families.
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Affiliation(s)
- Seema Irani
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - S D Yogesha
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Joshua Mayfield
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Mengmeng Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yong Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Wendy L Matthews
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Grace Nie
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Nicholas A Prescott
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yan Jessie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
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Stadlbauer S, Rios P, Ohmori K, Suzuki K, Köhn M. Procyanidins Negatively Affect the Activity of the Phosphatases of Regenerating Liver. PLoS One 2015; 10:e0134336. [PMID: 26226290 PMCID: PMC4520450 DOI: 10.1371/journal.pone.0134336] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 07/08/2015] [Indexed: 01/10/2023] Open
Abstract
Natural polyphenols like oligomeric catechins (procyanidins) derived from green tea and herbal medicines are interesting compounds for pharmaceutical research due to their ability to protect against carcinogenesis in animal models. It is nevertheless still unclear how intracellular pathways are modulated by polyphenols. Monomeric polyphenols were shown to affect the activity of some protein phosphatases (PPs). The three phosphatases of regenerating liver (PRLs) are close relatives and promising therapeutic targets in cancer. In the present study we show that several procyanidins inhibit the activity of all three members of the PRL family in the low micromolar range, whereas monomeric epicatechins show weak inhibitory activity. Increasing the number of catechin units in procyanidins to more than three does not further enhance the potency. Remarkably, the tested procyanidins showed selectivity in vitro when compared to other PPs, and over 10-fold selectivity toward PRL-1 over PRL-2 and PRL-3. As PRL overexpression induces cell migration compared to control cells, the effect of procyanidins on this phenotype was studied. Treatment with procyanidin C2 led to a decrease in cell migration of PRL-1- and PRL-3-overexpressing cells, suggesting the compound-dependent inhibition of PRL-promoted cell migration. Treatment with procyanidin B3 led to selective suppression of PRL-1 overexpressing cells, thereby corroborating the selectivity toward PRL-1- over PRL-3 in vitro. Together, our results show that procyanidins negatively affect PRL activity, suggesting that PRLs could be targets in the polypharmacology of natural polyphenols. Furthermore, they are interesting candidates for the development of PRL-1 inhibitors due to their low cellular toxicity and the selectivity within the PRL family.
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Affiliation(s)
- Sven Stadlbauer
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117, Heidelberg, Germany
- * E-mail: (SS); (MK)
| | - Pablo Rios
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Ken Ohmori
- Tokyo Institute of Technology, Department of Chemistry, O-okayama, Meguro-ku, Tokyo, 152–8551, Japan
| | - Keisuke Suzuki
- Tokyo Institute of Technology, Department of Chemistry, O-okayama, Meguro-ku, Tokyo, 152–8551, Japan
| | - Maja Köhn
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, 69117, Heidelberg, Germany
- * E-mail: (SS); (MK)
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17
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Lee JO, Kim EJ, Lim B, Kim TW, Kim YP. Rapid detection of protein phosphatase activity using Zn(II)-coordinated gold nanosensors based on His-tagged phosphopeptides. Anal Chem 2015; 87:1257-65. [PMID: 25521387 DOI: 10.1021/ac5039412] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We report a rapid colorimetric assay to detect protein phosphatase (PP) activity based on the controlled assembly and disassembly of gold nanoparticles (AuNPs) via Zn(II)-specific coordination in the presence of His6-tagged phosphopeptides. Among divalent metal ions including Ni(II), Cu(II), Co(II), Mg(II), Mn(II), and Zn(II), only Zn(II) triggered a strong association between phosphopeptides with hexahistidine at a single end and nitrilotriacetic acid (NTA)-modified AuNPs (21.3 nm in core diameter), leading to the self-assembly of AuNPs and consequently changes in color of the AuNP solution. In contrast, unphosphorylated peptides and His6-deficient phosphopeptides did not change the color of the AuNP solution. As a result, protein phosphatase 1 (PP1) activity and its inhibition were easily quantified with high sensitivity by determining the extinction ratio (E520/E700) of colloidal AuNPs. Most importantly, this method was capable of detecting protein phosphatase 2A (PP2A) activity in immunoprecipitated plant extracts. Because PPs play pivotal roles in mediating diverse signal transduction pathways as primary effectors of protein dephosphorylation, we anticipate that our method will be applied as a rapid format method to analyze the activities of various PPs and their inhibition.
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Affiliation(s)
- Jin Oh Lee
- Department of Life Science, Hanyang University , Seoul 133-791, Republic of Korea
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Development of phosphatase inhibitor-1 peptides acting as indirect activators of phosphatase 1. Naunyn Schmiedebergs Arch Pharmacol 2014; 388:283-93. [DOI: 10.1007/s00210-014-1065-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 11/04/2014] [Indexed: 01/21/2023]
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