1
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Liu S, Zhang Q, Zhang X, Du C, Chen J, Si S. Real-time monitoring of dephosphorylation process of phosphopeptide and rapid assay of PTP1B activity based on a 100 MHz QCM biosensing platform. Talanta 2024; 277:126399. [PMID: 38876030 DOI: 10.1016/j.talanta.2024.126399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/06/2024] [Accepted: 06/08/2024] [Indexed: 06/16/2024]
Abstract
The misregulation of protein phosphatases is a key factor in the development of many human diseases, notably cancers. Here, based on a 100 MHz quartz crystal microbalance (QCM) biosensing platform, the dephosphorylation process of phosphopeptide (P-peptide) caused by protein tyrosine phosphatase 1B (PTP1B) was monitored in real time for the first time and PTP1B activity was assayed rapidly and sensitively. The QCM chip, coated with a gold (Au) film, was used to immobilized thiol-labeled single-stranded 5'-phosphate-DNAs (P-DNA) through Au-S bond. The P-peptide, specific to PTP1B, was then connected to the P-DNA via chelation between Zr4+ and phosphate groups. When PTP1B was injected into the QCM flow cell where the P-peptide/Zr4+/MCH/P-DNA/Au chip was placed, the P-peptide was dephosphorylated and released from the Au chip surface, resulting in an increase in the frequency of the QCM Au chip. This allowed the real-time monitoring of the P-peptide dephosphorylation process and sensitive detection of PTP1B activity within 6 min with a linear detection range of 0.01-100 pM and a detection limit of 0.008 pM. In addition, the maximum inhibitory ratios of inhibitors were evaluated using this proposed 100 MHz QCM biosensor. The developed 100 MHz QCM biosensing platform shows immense potential for early diagnosis of diseases related to protein phosphatases and the development of drugs targeting protein phosphatases.
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Affiliation(s)
- Shuping Liu
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR China
| | - Qingqing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China; School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China.
| | - Xiaohua Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Cuicui Du
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Jinhua Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
| | - Shihui Si
- College of Chemistry and Chemical Engineering, Central South University, Changsha, 410083, PR China.
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2
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Muli CS, Tarasov SG, Walters KJ. High-throughput assay exploiting disorder-to-order conformational switches: application to the proteasomal Rpn10:E6AP complex. Chem Sci 2024; 15:4041-4053. [PMID: 38487241 PMCID: PMC10935766 DOI: 10.1039/d3sc06370d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/05/2024] [Indexed: 03/17/2024] Open
Abstract
Conformational switching is pervasively driven by protein interactions, particularly for intrinsically disordered binding partners. We developed a dually orthogonal fluorescence-based assay to monitor such events, exploiting environmentally sensitive fluorophores. This assay is applied to E3 ligase E6AP, as its AZUL domain induces a disorder-to-order switch in an intrinsically disordered region of the proteasome, the so-named Rpn10 AZUL-binding domain (RAZUL). By testing various fluorophores, we developed an assay appropriate for high-throughput screening of Rpn10:E6AP-disrupting ligands. We found distinct positions in RAZUL for fluorophore labeling with either acrylodan or Atto610, which had disparate spectral responses to E6AP binding. E6AP caused a hypsochromic shift with increased fluorescence of acrylodan-RAZUL while decreasing fluorescence intensity of Atto610-RAZUL. Combining RAZUL labeled with either acrylodan or Atto610 into a common sample achieved robust and orthogonal measurement of the E6AP-induced conformational switch. This approach is generally applicable to disorder-to-order (or vice versa) transitions mediated by molecular interactions.
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Affiliation(s)
- Christine S Muli
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick MD 21702 USA
| | - Sergey G Tarasov
- Biophysics Resource, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick MD 21702 USA
| | - Kylie J Walters
- Protein Processing Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health Frederick MD 21702 USA
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3
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Elsayed MSA, Blake JF, Boys ML, Brown E, Chapsal BD, Chicarelli MJ, Cook AW, Fell JB, Fischer JP, Hanson L, Lemieux C, Martinson MC, McCown J, McNulty OT, Mejia MJ, Neitzel NA, Otten JN, Rodriguez ME, Wilcox D, Wong CE, Zhou Y, Hinklin RJ. Discovery of 5-Azaquinoxaline Derivatives as Potent and Orally Bioavailable Allosteric SHP2 Inhibitors. ACS Med Chem Lett 2023; 14:1673-1681. [PMID: 38116446 PMCID: PMC10726463 DOI: 10.1021/acsmedchemlett.3c00310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 12/21/2023] Open
Abstract
SHP2 has emerged as an important target for oncology small-molecule drug discovery. As a nonreceptor tyrosine phosphatase within the MAPK pathway, it has been shown to control cell growth, differentiation, and oncogenic transformation. We used structure-based design to find a novel class of potent and orally bioavailable SHP2 inhibitors. Our efforts led to the discovery of the 5-azaquinoxaline as a new core for developing this class of compounds. Optimization of the potency and properties of this scaffold generated compound 30, that exhibited potent in vitro SHP2 inhibition and showed excellent in vivo efficacy and pharmacokinetic profile.
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Affiliation(s)
| | - James F. Blake
- Computational
Chemistry, Pfizer-Boulder, Boulder, Colorado 80301, United States
| | - Mark L. Boys
- Medicinal
Chemistry, Pfizer-Boulder, Boulder, Colorado 80301, United States
| | - Eric Brown
- Pharmacology, Pfizer-Boulder, Boulder, Colorado 80301, United States
| | - Bruno D. Chapsal
- Medicinal
Chemistry, Pfizer-Boulder, Boulder, Colorado 80301, United States
| | - Mark J. Chicarelli
- Medicinal
Chemistry, Pfizer-Boulder, Boulder, Colorado 80301, United States
| | - Adam W. Cook
- Medicinal
Chemistry, Pfizer-Boulder, Boulder, Colorado 80301, United States
| | - Jay B. Fell
- Medicinal
Chemistry, Pfizer-Boulder, Boulder, Colorado 80301, United States
| | - John P. Fischer
- Medicinal
Chemistry, Pfizer-Boulder, Boulder, Colorado 80301, United States
| | - Lauren Hanson
- Enzymology, Pfizer-Boulder, Boulder, Colorado 80301, United States
| | - Christine Lemieux
- Cellular
Biology, Pfizer-Boulder, Boulder, Colorado 80301, United States
| | | | - Joseph McCown
- ADME
Sciences, Pfizer-Boulder, Boulder, Colorado 80301, United States
| | - Oren T. McNulty
- Medicinal
Chemistry, Pfizer-Boulder, Boulder, Colorado 80301, United States
| | - Macedonio J. Mejia
- Medicinal
Chemistry, Pfizer-Boulder, Boulder, Colorado 80301, United States
| | | | - Jennifer N. Otten
- ADME
Sciences, Pfizer-Boulder, Boulder, Colorado 80301, United States
| | | | - Daniel Wilcox
- Medicinal
Chemistry, Pfizer-Boulder, Boulder, Colorado 80301, United States
| | - Christina E. Wong
- Medicinal
Chemistry, Pfizer-Boulder, Boulder, Colorado 80301, United States
| | - Yeyun Zhou
- Structural
Biology, Pfizer-Boulder, Boulder, Colorado 80301, United States
| | - Ronald J. Hinklin
- Medicinal
Chemistry, Pfizer-Boulder, Boulder, Colorado 80301, United States
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4
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Wang N, Zhu S, Lv D, Wang Y, Khawar MB, Sun H. Allosteric modulation of SHP2: Quest from known to unknown. Drug Dev Res 2023; 84:1395-1410. [PMID: 37583266 DOI: 10.1002/ddr.22100] [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: 04/12/2023] [Revised: 07/15/2023] [Accepted: 07/25/2023] [Indexed: 08/17/2023]
Abstract
Src homology-2 domain-containing protein tyrosine phosphatase-2 (SHP2) is a key regulatory factor in the cell cycle and its activating mutations play an important role in the development of various cancers, making it an important target for antitumor drugs. Due to the highly conserved amino acid sequence and positively charged nature of the active site of SHP2, it is difficult to discover inhibitors with high affinity for the catalytic site of SHP2 and sufficient cell permeability, making it considered an "undruggable" target. However, the discovery of allosteric regulation mechanisms provides new opportunities for transforming undruggable targets into druggable ones. Given the limitations of orthosteric inhibitors, SHP2 allosteric inhibitors have become a more selective and safer research direction. In this review, we elucidate the oncogenic mechanism of SHP2 and summarize the discovery methods of SHP2 allosteric inhibitors, providing new strategies for the design and improvement of SHP2 allosteric inhibitors.
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Affiliation(s)
- Ning Wang
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, China
| | - Shilin Zhu
- Department of Oncology, Haian Hospital of Traditional Chinese Medicine, Haian, China
| | - Dan Lv
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, China
- School of Life Sciences, Anqing Normal University, Anqing, China
| | - Yajun Wang
- Department of Oncology, Haian Hospital of Traditional Chinese Medicine, Haian, China
| | - Muhammad B Khawar
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, China
- Applied Molecular Biology and Biomedicine Lab, Department of Zoology, University of Narowal, Narowal, Pakistan
| | - Haibo Sun
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou, China
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5
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Maccari R, Ottanà R. Can Allostery Be a Key Strategy for Targeting PTP1B in Drug Discovery? A Lesson from Trodusquemine. Int J Mol Sci 2023; 24:ijms24119621. [PMID: 37298571 DOI: 10.3390/ijms24119621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/29/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is an enzyme crucially implicated in aberrations of various signaling pathways that underlie the development of different human pathologies, such as obesity, diabetes, cancer, and neurodegenerative disorders. Its inhibition can prevent these pathogenetic events, thus providing a useful tool for the discovery of novel therapeutic agents. The search for allosteric PTP1B inhibitors can represent a successful strategy to identify drug-like candidates by offering the opportunity to overcome some issues related to catalytic site-directed inhibitors, which have so far hampered the development of drugs targeting this enzyme. In this context, trodusquemine (MSI-1436), a natural aminosterol that acts as a non-competitive PTP1B inhibitor, appears to be a milestone. Initially discovered as a broad-spectrum antimicrobial agent, trodusquemine exhibited a variety of unexpected properties, ranging from antidiabetic and anti-obesity activities to effects useful to counteract cancer and neurodegeneration, which prompted its evaluation in several preclinical and clinical studies. In this review article, we provide an overview of the main findings regarding the activities and therapeutic potential of trodusquemine and their correlation with PTP1B inhibition. We also included some aminosterol analogues and related structure-activity relationships that could be useful for further studies aimed at the discovery of new allosteric PTP1B inhibitors.
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Affiliation(s)
- Rosanna Maccari
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Rosaria Ottanà
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
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6
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Zhang Q, Yang H, Du C, Liu S, Zhang X, Chen J. Bifunctional Magnetic Fe 3O 4@Cu 2O@TiO 2 Nanosphere-Mediated Dual-Mode Assay of PTP1B Activity Based on Photocurrent Polarity Switching and Nanozyme-Engineered Biocatalytic Precipitation Strategies. Anal Chem 2022; 94:13342-13349. [PMID: 36129464 DOI: 10.1021/acs.analchem.2c01575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Dysregulation of protein phosphatases is associated with the progression of various human diseases and cancers. Herein, a photoelectrochemical (PEC)-quartz crystal microbalance (QCM) dual-mode sensing platform was developed for protein tyrosine phosphatase 1B (PTP1B) activity assay based on bifunctional magnetic Fe3O4@Cu2O@TiO2 nanosphere-mediated PEC photocurrent polarity switching and QCM signal amplification strategies. The PTP1B-specific phosphopeptide (P-peptide) with a cysteine end was designed and immobilized onto the QCM Au chip via the Au-S bond. Subsequently, the Fe3O4@Cu2O@TiO2 nanosphere was connected to the P-peptide via the specific interaction between the phosphate group on the P-peptide and TiO2. After incubation with PTP1B, the dephosphorylation of the P-peptide occurred, causing some Fe3O4@Cu2O@TiO2 nanospheres to be released from the chip surface. The released magnetic Fe3O4@Cu2O@TiO2 nanospheres (labeled as R-Fe3O4@Cu2O@TiO2) were quickly separated via magnetic separation technology and attached to the Bi2S3-decorated magnetic indium-tin oxide (Bi2S3/MITO) electrode by magnetic force, inducing the switch of the photocurrent polarity of the electrode from anodic current (the Bi2S3/MITO electrode) to cathodic current (the R-Fe3O4@Cu2O@TiO2/Bi2S3/MITO electrode). Also, the nondephosphorylated P-peptide linked Fe3O4@Cu2O@TiO2 nanospheres as nanozymes with horseradish peroxidase activity to catalyze the formation of precipitation on the surface of the Au chip, leading to a frequency change of the QCM. Thus, the proposed PEC-QCM dual-mode sensing platform achieved accurate and reliable assay of PTP1B activity because of the different mechanisms and independent signal transductions. In addition, this dual-mode sensing platform can be easily extended for other protein phosphatase activity analysis and shows great potential in the early diagnosis of the protein phosphatase-related diseases and the protein phosphatase-targeted drug discovery.
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Affiliation(s)
- Qingqing Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Haokun Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Cuicui Du
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Suying Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Xiaohua Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
| | - Jinhua Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P.R. China
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7
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Faria AVS, Andrade SS, Peppelenbosch MP, Ferreira-Halder CV, Fuhler GM. The role of phospho-tyrosine signaling in platelet biology and hemostasis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118927. [PMID: 33310067 DOI: 10.1016/j.bbamcr.2020.118927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/01/2020] [Accepted: 12/05/2020] [Indexed: 10/22/2022]
Abstract
Platelets are small enucleated cell fragments specialized in the control of hemostasis, but also playing a role in angiogenesis, inflammation and immunity. This plasticity demands a broad range of physiological processes. Platelet functions are mediated through a variety of receptors, the concerted action of which must be tightly regulated, in order to allow specific and timely responses to different stimuli. Protein phosphorylation is one of the main key regulatory mechanisms by which extracellular signals are conveyed. Despite the importance of platelets in health and disease, the molecular pathways underlying the activation of these cells are still under investigation. Here, we review current literature on signaling platelet biology and in particular emphasize the newly emerging role of phosphatases in these processes.
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Affiliation(s)
- Alessandra V S Faria
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center Rotterdam, NL-3000 CA Rotterdam, the Netherlands; Department of Biochemistry and Tissue Biology, University of Campinas, UNICAMP, Campinas, SP 13083-862, Brazil
| | | | - Maikel P Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center Rotterdam, NL-3000 CA Rotterdam, the Netherlands
| | - Carmen V Ferreira-Halder
- Department of Biochemistry and Tissue Biology, University of Campinas, UNICAMP, Campinas, SP 13083-862, Brazil
| | - Gwenny M Fuhler
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center Rotterdam, NL-3000 CA Rotterdam, the Netherlands.
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8
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Tripathi RKP, Ayyannan SR. Emerging chemical scaffolds with potential SHP2 phosphatase inhibitory capabilities - A comprehensive review. Chem Biol Drug Des 2020; 97:721-773. [PMID: 33191603 DOI: 10.1111/cbdd.13807] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/30/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022]
Abstract
The drug discovery panorama is cluttered with promising therapeutic targets that have been deserted because of inadequate authentication and screening failures. Molecular targets formerly tagged as "undruggable" are nowadays being more cautiously cross-examined, and whilst they stay intriguing, numerous targets are emerging more accessible. Protein tyrosine phosphatases (PTPs) excellently exemplifies a class of molecular targets that have transpired as druggable, with several small molecules and antibodies recently turned available for further development. In this respect, SHP2, a PTP, has emerged as one of the potential targets in the current pharmacological research, particularly for cancer, due to its critical role in various signalling pathways. Recently, few molecules with excellent potency have entered clinical trials, but none could reach the clinic. Consequently, search for novel, non-toxic, and specific SHP2 inhibitors are on purview. In this review, general aspects of SHP2 including its structure and mechanistic role in carcinogenesis have been presented. It also sheds light on the development of novel molecular architectures belonging to diverse chemical classes that have been proposed as SHP2-specific inhibitors along with their structure-activity relationships (SARs), stemming from chemical, mechanism-based and computer-aided studies reported since January 2015 to July 2020 (excluding patents), focusing on their potency and selectivity. The encyclopedic facts and discussions presented herein will hopefully facilitate researchers to design new ligands with better efficacy and selectivity against SHP2.
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Affiliation(s)
- Rati Kailash Prasad Tripathi
- Department of Pharmaceutical Science, Sushruta School of Medical and Paramedical Sciences, Assam University (A Central University), Silchar, Assam, India.,Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Senthil Raja Ayyannan
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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9
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LaMarche MJ, Acker M, Argintaru A, Bauer D, Boisclair J, Chan H, Chen CHT, Chen YN, Chen Z, Deng Z, Dore M, Dunstan D, Fan J, Fekkes P, Firestone B, Fodor M, Garcia-Fortanet J, Fortin PD, Fridrich C, Giraldes J, Glick M, Grunenfelder D, Hao HX, Hentemann M, Ho S, Jouk A, Kang ZB, Karki R, Kato M, Keen N, Koenig R, LaBonte LR, Larrow J, Liu G, Liu S, Majumdar D, Mathieu S, Meyer MJ, Mohseni M, Ntaganda R, Palermo M, Perez L, Pu M, Ramsey T, Reilly J, Sarver P, Sellers WR, Sendzik M, Shultz MD, Slisz J, Slocum K, Smith T, Spence S, Stams T, Straub C, Tamez V, Toure BB, Towler C, Wang P, Wang H, Williams SL, Yang F, Yu B, Zhang JH, Zhu S. Identification of TNO155, an Allosteric SHP2 Inhibitor for the Treatment of Cancer. J Med Chem 2020; 63:13578-13594. [PMID: 32910655 DOI: 10.1021/acs.jmedchem.0c01170] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
SHP2 is a nonreceptor protein tyrosine phosphatase encoded by the PTPN11 gene and is involved in cell growth and differentiation via the MAPK signaling pathway. SHP2 also plays an important role in the programed cell death pathway (PD-1/PD-L1). As an oncoprotein as well as a potential immunomodulator, controlling SHP2 activity is of high therapeutic interest. As part of our comprehensive program targeting SHP2, we identified multiple allosteric binding modes of inhibition and optimized numerous chemical scaffolds in parallel. In this drug annotation report, we detail the identification and optimization of the pyrazine class of allosteric SHP2 inhibitors. Structure and property based drug design enabled the identification of protein-ligand interactions, potent cellular inhibition, control of physicochemical, pharmaceutical and selectivity properties, and potent in vivo antitumor activity. These studies culminated in the discovery of TNO155, (3S,4S)-8-(6-amino-5-((2-amino-3-chloropyridin-4-yl)thio)pyrazin-2-yl)-3-methyl-2-oxa-8-azaspiro[4.5]decan-4-amine (1), a highly potent, selective, orally efficacious, and first-in-class SHP2 inhibitor currently in clinical trials for cancer.
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10
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Yuan X, Bu H, Zhou J, Yang CY, Zhang H. Recent Advances of SHP2 Inhibitors in Cancer Therapy: Current Development and Clinical Application. J Med Chem 2020; 63:11368-11396. [DOI: 10.1021/acs.jmedchem.0c00249] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Xinrui Yuan
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Hong Bu
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Jinpei Zhou
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Chao-Yie Yang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Huibin Zhang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
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11
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Hantani R, Hanawa S, Oie S, Umetani K, Sato T, Hantani Y. Identification of a New Inhibitor That Stabilizes Interleukin-2-Inducible T-Cell Kinase in Its Inactive Conformation. SLAS DISCOVERY 2019; 24:854-862. [PMID: 31247148 DOI: 10.1177/2472555219857542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Interleukin-2-inducible T-cell kinase (ITK) plays an important role in T-cell signaling and is considered a promising drug target. As the ATP binding sites of protein kinases are highly conserved, the design of selective kinase inhibitors remains a challenge. Targeting inactive kinase conformations can address the issue of kinase inhibitor selectivity. It is important for selectivity considerations to identify compounds that stabilize inactive conformations from the primary screen hits. Here we screened a library of 390,000 compounds with an ADP-Glo assay using dephosphorylated ITK. After a surface plasmon resonance (SPR) assay was used to filter out promiscuous inhibitors, 105 hits were confirmed. Next, we used a fluorescent biosensor to enable the detection of conformational changes to identify inactive conformation inhibitors. A single-cysteine-substituted ITK mutant was labeled with acrylodan, and fluorescence emission was monitored. Using a fluorescent biosensor assay, we identified 34 inactive conformation inhibitors from SPR hits. Among them, one compound was bound to a site other than the ATP pocket and exhibited excellent selectivity against a kinase panel. Overall, (1) biochemical screening using dephosphorylated kinase, (2) hit confirmation by SPR assay, and (3) fluorescent biosensor assay that can distinguish inactive compounds provide a useful platform and offer opportunities to identify selective kinase inhibitors.
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Affiliation(s)
- Rie Hantani
- 1 Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco, Takatsuki, Osaka, Japan
| | - Saya Hanawa
- 1 Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco, Takatsuki, Osaka, Japan
| | - Shohei Oie
- 1 Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco, Takatsuki, Osaka, Japan
| | - Kayo Umetani
- 1 Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco, Takatsuki, Osaka, Japan
| | - Toshihiro Sato
- 1 Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco, Takatsuki, Osaka, Japan
| | - Yoshiji Hantani
- 1 Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco, Takatsuki, Osaka, Japan
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12
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Sakamoto S, Kiyonaka S, Hamachi I. Construction of ligand assay systems by protein-based semisynthetic biosensors. Curr Opin Chem Biol 2019; 50:10-18. [PMID: 30875618 DOI: 10.1016/j.cbpa.2019.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/06/2019] [Accepted: 02/09/2019] [Indexed: 01/14/2023]
Abstract
Proteins as causative agents of diseases such as cancers, diabetes and neurological disorders are attractive drug targets. For developing chemicals selectively acting on key disease-causing proteins, one useful concept is the direct conversion of such target proteins into biosensors. This approach provides ligand-binding assay systems based on protein-based biosensors, which can quantitatively evaluate interactions between the protein and a specific ligand in many environments. Site-specific chemical modifications are used widely for the creation of protein-based semisynthetic biosensors in vitro. Notably, a few bio-orthogonal approaches capable of selectively modifying drug-targets have been developed, allowing conversion of specific target proteins into semisynthetic biosensors in live cells. These biosensors can be used for quantitative drug binding analyses in native environments. In this review, we discuss recent efforts for the construction of ligand assay systems using semisynthetic protein-based biosensors and their application to quantitative analysis and high-throughput screening of small molecules for drug discovery.
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Affiliation(s)
- Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Shigeki Kiyonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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13
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Lu S, He X, Ni D, Zhang J. Allosteric Modulator Discovery: From Serendipity to Structure-Based Design. J Med Chem 2019; 62:6405-6421. [PMID: 30817889 DOI: 10.1021/acs.jmedchem.8b01749] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Shaoyong Lu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
- Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Xinheng He
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Duan Ni
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Clinical and Fundamental Research Center, Renji Hospital, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
- Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai 200025, China
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14
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Sarver P, Acker M, Bagdanoff JT, Chen Z, Chen YN, Chan H, Firestone B, Fodor M, Fortanet J, Hao H, Hentemann M, Kato M, Koenig R, LaBonte LR, Liu G, Liu S, Liu C, McNeill E, Mohseni M, Sendzik M, Stams T, Spence S, Tamez V, Tichkule R, Towler C, Wang H, Wang P, Williams SL, Yu B, LaMarche MJ. 6-Amino-3-methylpyrimidinones as Potent, Selective, and Orally Efficacious SHP2 Inhibitors. J Med Chem 2019; 62:1793-1802. [DOI: 10.1021/acs.jmedchem.8b01726] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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15
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Wolle P, Weisner J, Keul M, Landel I, Lategahn J, Rauh D. RASPELD to Perform High-End Screening in an Academic Environment toward the Development of Cancer Therapeutics. ChemMedChem 2018; 13:2065-2072. [DOI: 10.1002/cmdc.201800477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Patrik Wolle
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Jörn Weisner
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Marina Keul
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Ina Landel
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Jonas Lategahn
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
| | - Daniel Rauh
- Faculty of Chemistry and Chemical Biology; TU Dortmund University; Otto-Hahn-Strasse 4a 44227 Dortmund Germany
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16
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Kiyonaka S, Sakamoto S, Wakayama S, Morikawa Y, Tsujikawa M, Hamachi I. Ligand-Directed Chemistry of AMPA Receptors Confers Live-Cell Fluorescent Biosensors. ACS Chem Biol 2018; 13:1880-1889. [PMID: 29437380 DOI: 10.1021/acschembio.7b01042] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AMPA-type glutamate receptors (AMPARs) mediate fast excitatory synaptic transmission in the central nervous system. Dysregulation of AMPAR function is associated with many kinds of neurological, neurodegenerative, and psychiatric disorders. As a result, molecules capable of controlling AMPAR functions are potential therapeutic agents. Fluorescent semisynthetic biosensors have attracted considerable interest for the discovery of ligands selectively acting on target proteins. Given the large protein complex formation of AMPARs in live cells, biosensors using full-length AMPARs retaining original functionality are ideal for drug screening. Here, we demonstrate that fluorophore-labeled AMPARs prepared by ligand-directed acyl imidazole chemistry can act as turn-on fluorescent biosensors for AMPAR ligands in living cells. These biosensors selectively detect orthosteric ligands of AMPARs among the glutamate receptor family. Notably, the dissociation constants of agonists and antagonists for AMPARs were determined in live cells, which revealed that the ligand-binding properties of AMPARs to agonists are largely different in living cells, compared with noncellular conditions. We also show that these sensors can be applied to detecting allosteric modulators or subunit-selective ligands of AMPARs. Thus, our protein-based biosensors can be useful for discovering pharmaceutical agents to treat AMPAR-related neurological disorders.
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Affiliation(s)
- Shigeki Kiyonaka
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Sho Wakayama
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yuma Morikawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Muneo Tsujikawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
- CREST(Core Research for Evolutional Science and Technology, JST), Chiyodaku, Tokyo, 102-0075, Japan
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17
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Fodor M, Price E, Wang P, Lu H, Argintaru A, Chen Z, Glick M, Hao HX, Kato M, Koenig R, LaRochelle JR, Liu G, McNeill E, Majumdar D, Nishiguchi GA, Perez LB, Paris G, Quinn CM, Ramsey T, Sendzik M, Shultz MD, Williams SL, Stams T, Blacklow SC, Acker MG, LaMarche MJ. Dual Allosteric Inhibition of SHP2 Phosphatase. ACS Chem Biol 2018; 13:647-656. [PMID: 29304282 DOI: 10.1021/acschembio.7b00980] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
SHP2 is a cytoplasmic protein tyrosine phosphatase encoded by the PTPN11 gene and is involved in cell proliferation, differentiation, and survival. Recently, we reported an allosteric mechanism of inhibition that stabilizes the auto-inhibited conformation of SHP2. SHP099 (1) was identified and characterized as a moderately potent, orally bioavailable, allosteric small molecule inhibitor, which binds to a tunnel-like pocket formed by the confluence of three domains of SHP2. In this report, we describe further screening strategies that enabled the identification of a second, distinct small molecule allosteric site. SHP244 (2) was identified as a weak inhibitor of SHP2 with modest thermal stabilization of the enzyme. X-ray crystallography revealed that 2 binds and stabilizes the inactive, closed conformation of SHP2, at a distinct, previously unexplored binding site-a cleft formed at the interface of the N-terminal SH2 and PTP domains. Derivatization of 2 using structure-based design resulted in an increase in SHP2 thermal stabilization, biochemical inhibition, and subsequent MAPK pathway modulation. Downregulation of DUSP6 mRNA, a downstream MAPK pathway marker, was observed in KYSE-520 cancer cells. Remarkably, simultaneous occupation of both allosteric sites by 1 and 2 was possible, as characterized by cooperative biochemical inhibition experiments and X-ray crystallography. Combining an allosteric site 1 inhibitor with an allosteric site 2 inhibitor led to enhanced pharmacological pathway inhibition in cells. This work illustrates a rare example of dual allosteric targeted protein inhibition, demonstrates screening methodology and tactics to identify allosteric inhibitors, and enables further interrogation of SHP2 in cancer and related pathologies.
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Affiliation(s)
- Michelle Fodor
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Edmund Price
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Ping Wang
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Hengyu Lu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Andreea Argintaru
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Zhouliang Chen
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Meir Glick
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Huai-Xiang Hao
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Mitsunori Kato
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Robert Koenig
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Jonathan R. LaRochelle
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School and Department of Cancer Biology, Dana−Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Gang Liu
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Eric McNeill
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Dyuti Majumdar
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Gisele A. Nishiguchi
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Lawrence B. Perez
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Gregory Paris
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Christopher M. Quinn
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Timothy Ramsey
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Martin Sendzik
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Michael David Shultz
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Sarah L. Williams
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Travis Stams
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Stephen C. Blacklow
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School and Department of Cancer Biology, Dana−Farber Cancer Institute, Boston, Massachusetts 02215, United States
| | - Michael G. Acker
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Matthew J. LaMarche
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, United States
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18
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Punthasee P, Laciak AR, Cummings AH, Ruddraraju KV, Lewis SM, Hillebrand R, Singh H, Tanner JJ, Gates KS. Covalent Allosteric Inactivation of Protein Tyrosine Phosphatase 1B (PTP1B) by an Inhibitor–Electrophile Conjugate. Biochemistry 2017; 56:2051-2060. [DOI: 10.1021/acs.biochem.7b00151] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Puminan Punthasee
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Adrian R. Laciak
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Andrea H. Cummings
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | | | - Sarah M. Lewis
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Roman Hillebrand
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Harkewal Singh
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - John J. Tanner
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
- Department
of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Kent S. Gates
- Department
of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
- Department
of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
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19
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Qi L, Zhang J, He T, Huo Y, Zhang ZQ. Probing interaction of a fluorescent ligand with HIV TAR RNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 173:93-98. [PMID: 27611591 DOI: 10.1016/j.saa.2016.08.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/15/2016] [Accepted: 08/29/2016] [Indexed: 06/06/2023]
Abstract
Trans-activator of Transcription (Tat) antagonists could block the interaction between Tat protein and its target, trans-activation responsive region (TAR) RNA, to inhibit Tat function and prevent human immunodeficiency virus type 1 (HIV-1) replication. For the first time, a small fluorescence ligand, ICR 191, was found to interact with TAR RNA at the Tat binding site and compete with Tat. It was also observed that the fluorescence of ICR 191 could be quenched when binding to TAR RNA and recovered when discharged via competition with Tat peptide or a well-known Tat inhibitor, neomycin B. The binding parameters of ICR 191 to TAR RNA were determined through theoretical calculations. Mass spectrometry, circular dichroism and molecular docking were used to further confirm the interaction of ICR 191 with TAR RNA. Inspired by these discoveries, a primary fluorescence model for the discovery of Tat antagonists was built using ICR 191 as a fluorescence indicator and the feasibility of this model was evaluated. This ligand-RNA interaction could provide a new strategy for research aimed at discovering Tat antagonists.
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MESH Headings
- Aminacrine/analogs & derivatives
- Aminacrine/chemistry
- Aminacrine/metabolism
- Aminacrine/pharmacology
- Binding, Competitive
- Circular Dichroism
- Drug Evaluation, Preclinical/methods
- Fluorescent Dyes/chemistry
- Fluorescent Dyes/metabolism
- Framycetin/chemistry
- Framycetin/metabolism
- HIV Long Terminal Repeat
- Models, Molecular
- Molecular Docking Simulation
- RNA, Viral/chemistry
- RNA, Viral/metabolism
- Spectrometry, Fluorescence
- Spectrometry, Mass, Electrospray Ionization
- tat Gene Products, Human Immunodeficiency Virus/antagonists & inhibitors
- tat Gene Products, Human Immunodeficiency Virus/chemistry
- tat Gene Products, Human Immunodeficiency Virus/metabolism
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Affiliation(s)
- Liang Qi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China; Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), Ministry of Education, Xi'an 710062, China
| | - Jing Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Tian He
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Yuan Huo
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China
| | - Zhi-Qi Zhang
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China; Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry (Shaanxi Normal University), Ministry of Education, Xi'an 710062, China.
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20
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Discovery of allosteric modulators for GABAA receptors by ligand-directed chemistry. Nat Chem Biol 2016; 12:822-30. [DOI: 10.1038/nchembio.2150] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/17/2016] [Indexed: 12/26/2022]
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21
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Garcia Fortanet J, Chen CHT, Chen YNP, Chen Z, Deng Z, Firestone B, Fekkes P, Fodor M, Fortin PD, Fridrich C, Grunenfelder D, Ho S, Kang ZB, Karki R, Kato M, Keen N, LaBonte LR, Larrow J, Lenoir F, Liu G, Liu S, Lombardo F, Majumdar D, Meyer MJ, Palermo M, Perez L, Pu M, Ramsey T, Sellers WR, Shultz MD, Stams T, Towler C, Wang P, Williams SL, Zhang JH, LaMarche MJ. Allosteric Inhibition of SHP2: Identification of a Potent, Selective, and Orally Efficacious Phosphatase Inhibitor. J Med Chem 2016; 59:7773-82. [DOI: 10.1021/acs.jmedchem.6b00680] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Jorge Garcia Fortanet
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Christine Hiu-Tung Chen
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ying-Nan P. Chen
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Zhouliang Chen
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Zhan Deng
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Brant Firestone
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Peter Fekkes
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Michelle Fodor
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Pascal D. Fortin
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Cary Fridrich
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Denise Grunenfelder
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Samuel Ho
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Zhao B. Kang
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Rajesh Karki
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Mitsunori Kato
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Nick Keen
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Laura R. LaBonte
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jay Larrow
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Francois Lenoir
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Gang Liu
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Shumei Liu
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Franco Lombardo
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Dyuti Majumdar
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Matthew J. Meyer
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Mark Palermo
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Lawrence Perez
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Minying Pu
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Timothy Ramsey
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - William R. Sellers
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Michael D. Shultz
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Travis Stams
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Christopher Towler
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ping Wang
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Sarah L. Williams
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Ji-Hu Zhang
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Matthew J. LaMarche
- Global Discovery Chemistry, ‡Oncology Disease
Area, §Center
for Proteomic Chemistry, ∥Metabolism and Pharmacokinetics, Novartis Institutes
for Biomedical Research, and ⊥Chemical and Pharmaceutical Profiling, Novartis Pharmaceuticals, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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22
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Tautz L, Senis YA, Oury C, Rahmouni S. Perspective: Tyrosine phosphatases as novel targets for antiplatelet therapy. Bioorg Med Chem 2015; 23:2786-97. [PMID: 25921264 PMCID: PMC4451376 DOI: 10.1016/j.bmc.2015.03.075] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 03/27/2015] [Accepted: 03/29/2015] [Indexed: 11/26/2022]
Abstract
Arterial thrombosis is the primary cause of most cases of myocardial infarction and stroke, the leading causes of death in the developed world. Platelets, highly specialized cells of the circulatory system, are key contributors to thrombotic events. Antiplatelet drugs, which prevent platelets from aggregating, have been very effective in reducing the mortality and morbidity of these conditions. However, approved antiplatelet therapies have adverse side effects, most notably the increased risk of bleeding. Moreover, there remains a considerable incidence of arterial thrombosis in a subset of patients receiving currently available drugs. Thus, there is a pressing medical need for novel antiplatelet agents with a more favorable safety profile and less patient resistance. The discovery of novel antiplatelet targets is the matter of intense ongoing research. Recent findings demonstrate the potential of targeting key signaling molecules, including kinases and phosphatases, to prevent platelet activation and aggregation. Here, we offer perspectives to targeting members of the protein tyrosine phosphatase (PTP) superfamily, a major class of enzymes in signal transduction. We give an overview of previously identified PTPs in platelet signaling, and discuss their potential as antiplatelet drug targets. We also introduce VHR (DUSP3), a PTP that we recently identified as a major player in platelet biology and thrombosis. We review our data on genetic deletion as well as pharmacological inhibition of VHR, providing proof-of-principle for a novel and potentially safer VHR-based antiplatelet therapy.
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Affiliation(s)
- Lutz Tautz
- NCI-Designated Cancer Center, Sanford-Burnham Medical Research Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA.
| | - Yotis A Senis
- Centre for Cardiovascular Sciences, Institute of Biomedical Research, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Cécile Oury
- Laboratory of Thrombosis and Haemostasis, GIGA-Cardiovascular Sciences, University of Liège, Liège, Belgium
| | - Souad Rahmouni
- Immunology and Infectious Diseases Unit, GIGA-Signal Transduction, University of Liège, Liège, Belgium
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23
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Mayer-Wrangowski SC, Rauh D. Monitoring Ligand-Induced Conformational Changes for the Identification of Estrogen Receptor Agonists and Antagonists. Angew Chem Int Ed Engl 2015; 54:4379-82. [DOI: 10.1002/anie.201410148] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Indexed: 01/12/2023]
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24
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Mayer-Wrangowski SC, Rauh D. Detektion ligandeninduzierter Konformationsänderungen im Östrogenrezeptor. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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25
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Fang Z, Simard JR, Plenker D, Nguyen HD, Phan T, Wolle P, Baumeister S, Rauh D. Discovery of inter-domain stabilizers-a novel assay system for allosteric akt inhibitors. ACS Chem Biol 2015; 10:279-88. [PMID: 24959717 DOI: 10.1021/cb500355c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In addition to the catalytically active kinase domain, most kinases feature regulatory domains that govern their activity. Modulating and interfering with these interdomain interactions presents a major opportunity for understanding biological systems and developing novel therapeutics. Therefore, small molecule inhibitors that target these interactions through an allosteric mode of action have high intrinsic selectivity, as these interactions are often unique to a single kinase or kinase family. Here we report the development of iFLiK (interface-Fluorescent Labels in Kinases), a fluorescence-based assay that can monitor such interdomain interactions. Using iFLiK, we have demonstrated selective detection of allosteric Akt inhibitors that induce an inactive closed conformation unique to Akt. This methodology easily distinguished small molecule allosteric inhibitors from classic ATP-competitive inhibitors. Screening an in-house compound library with iFLiK, we were able to identify novel compounds with a scaffold that has not been previously described for allosteric Akt inhibitors.
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Affiliation(s)
- Zhizhou Fang
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
| | - Jeffrey R. Simard
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
| | - Dennis Plenker
- University of Cologne, Medical Faculty, Department
of Translational Genomics, Weyertal 115b, 50931 Cologne, Germany
| | - Hoang D. Nguyen
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
| | - Trang Phan
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
| | - Patrik Wolle
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Stefan Baumeister
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Daniel Rauh
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
- Chemical
Genomics
Centre of the Max Planck Society, Otto-Hahn-Strasse
15, 44227 Dortmund, Germany
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26
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Tamura T, Hamachi I. Recent progress in design of protein-based fluorescent biosensors and their cellular applications. ACS Chem Biol 2014; 9:2708-17. [PMID: 25317665 DOI: 10.1021/cb500661v] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein-based fluorescent biosensors have emerged as key bioanalytical tools to visualize and quantify a wide range of biological substances and events in vitro, in cells, and even in vivo. On the basis of the construction method, the protein-based fluorescent biosensors can be principally classified into two classes: (1) genetically encoded fluorescent biosensors harnessing fluorescent proteins (FPs) and (2) semisynthetic biosensors comprised of protein scaffolds and synthetic fluorophores. Recent advances in protein engineering and chemical biology not only allowed the further optimization of conventional biosensors but also facilitated the creation of novel biosensors based on unique strategies. In this review, we survey the recent studies in the development and improvement of protein-based fluorescent biosensors and highlight the successful applications to live cell and in vivo imaging. Furthermore, we provide perspectives on possible future directions of the technique.
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Affiliation(s)
- Tomonori Tamura
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
| | - Itaru Hamachi
- Department
of Synthetic Chemistry and Biological Chemistry, Graduate School of
Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
- Core
Research for Evolutional Science and Technology, Japan Science and Technology Agency, 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
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27
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Li S, Zhang J, Lu S, Huang W, Geng L, Shen Q, Zhang J. The mechanism of allosteric inhibition of protein tyrosine phosphatase 1B. PLoS One 2014; 9:e97668. [PMID: 24831294 PMCID: PMC4022711 DOI: 10.1371/journal.pone.0097668] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 04/09/2014] [Indexed: 11/24/2022] Open
Abstract
As the prototypical member of the PTP family, protein tyrosine phosphatase 1B (PTP1B) is an attractive target for therapeutic interventions in type 2 diabetes. The extremely conserved catalytic site of PTP1B renders the design of selective PTP1B inhibitors intractable. Although discovered allosteric inhibitors containing a benzofuran sulfonamide scaffold offer fascinating opportunities to overcome selectivity issues, the allosteric inhibitory mechanism of PTP1B has remained elusive. Here, molecular dynamics (MD) simulations, coupled with a dynamic weighted community analysis, were performed to unveil the potential allosteric signal propagation pathway from the allosteric site to the catalytic site in PTP1B. This result revealed that the allosteric inhibitor compound-3 induces a conformational rearrangement in helix α7, disrupting the triangular interaction among helix α7, helix α3, and loop11. Helix α7 then produces a force, pulling helix α3 outward, and promotes Ser190 to interact with Tyr176. As a result, the deviation of Tyr176 abrogates the hydrophobic interactions with Trp179 and leads to the downward movement of the WPD loop, which forms an H-bond between Asp181 and Glu115. The formation of this H-bond constrains the WPD loop to its open conformation and thus inactivates PTP1B. The discovery of this allosteric mechanism provides an overall view of the regulation of PTP1B, which is an important insight for the design of potent allosteric PTP1B inhibitors.
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Affiliation(s)
- Shuai Li
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine (SJTU-SM), Shanghai, China
| | - Jingmiao Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine (SJTU-SM), Shanghai, China
| | - Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine (SJTU-SM), Shanghai, China
| | - Wenkang Huang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine (SJTU-SM), Shanghai, China
| | - Lv Geng
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine (SJTU-SM), Shanghai, China
| | - Qiancheng Shen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine (SJTU-SM), Shanghai, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai JiaoTong University, School of Medicine (SJTU-SM), Shanghai, China
- Medicinal Bioinformatics Center, Shanghai JiaoTong University, School of Medicine, Shanghai, China
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28
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Abstract
Allostery is the most direct and efficient way for regulation of biological macromolecule function, ranging from the control of metabolic mechanisms to signal transduction pathways. Allosteric modulators target to allosteric sites, offering distinct advantages compared to orthosteric ligands that target to active sites, such as greater specificity, reduced side effects, and lower toxicity. Allosteric modulators have therefore drawn increasing attention as potential therapeutic drugs in the design and development of new drugs. In recent years, advancements in our understanding of the fundamental principles underlying allostery, coupled with the exploitation of powerful techniques and methods in the field of allostery, provide unprecedented opportunities to discover allosteric proteins, detect and characterize allosteric sites, design and develop novel efficient allosteric drugs, and recapitulate the universal features of allosteric proteins and allosteric modulators. In the present review, we summarize the recent advances in the repertoire of allostery, with a particular focus on the aforementioned allosteric compounds.
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Affiliation(s)
- Shaoyong Lu
- Department of Pathophysiology, Chemical Biology Division of Shanghai Universities E-Institutes, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao-Tong University School of Medicine (SJTU-SM), Shanghai, China
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29
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Krueger AB, Drasin DJ, Lea WA, Patrick AN, Patnaik S, Backos DS, Matheson CJ, Hu X, Barnaeva E, Holliday MJ, Blevins MA, Robin TP, Eisenmesser EZ, Ferrer M, Simeonov A, Southall N, Reigan P, Marugan J, Ford HL, Zhao R. Allosteric inhibitors of the Eya2 phosphatase are selective and inhibit Eya2-mediated cell migration. J Biol Chem 2014; 289:16349-61. [PMID: 24755226 DOI: 10.1074/jbc.m114.566729] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Eya proteins are essential co-activators of the Six family of transcription factors and contain a unique tyrosine phosphatase domain belonging to the haloacid dehalogenase family of phosphatases. The phosphatase activity of Eya is important for the transcription of a subset of Six1-target genes, and also directs cells to the repair rather than apoptosis pathway upon DNA damage. Furthermore, Eya phosphatase activity has been shown to mediate transformation, invasion, migration, and metastasis of breast cancer cells, making it a potential new drug target for breast cancer. We have previously identified a class of N-arylidenebenzohydrazide compounds that specifically inhibit the Eya2 phosphatase. Herein, we demonstrate that these compounds are reversible inhibitors that selectively inhibit the phosphatase activity of Eya2, but not Eya3. Our mutagenesis results suggest that this class of compounds does not bind to the active site and the binding does not require the coordination with Mg(2+). Moreover, these compounds likely bind within a site on the opposite face of the active site, and function as allosteric inhibitors. We also demonstrate that this class of compounds inhibits Eya2 phosphatase-mediated cell migration, setting the foundation for these molecules to be developed into chemical probes for understanding the specific function of the Eya2 phosphatase and to serve as a prototype for the development of Eya2 phosphatase specific anti-cancer drugs.
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Affiliation(s)
- Aaron B Krueger
- From the Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - David J Drasin
- the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Wendy A Lea
- the National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Aaron N Patrick
- the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Samarjit Patnaik
- the National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Donald S Backos
- the Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, Colorado 80045
| | - Christopher J Matheson
- the Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, Colorado 80045
| | - Xin Hu
- the National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Elena Barnaeva
- the National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Michael J Holliday
- From the Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Melanie A Blevins
- From the Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Tyler P Robin
- the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Elan Z Eisenmesser
- From the Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045
| | - Marc Ferrer
- the National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Anton Simeonov
- the National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Noel Southall
- the National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Philip Reigan
- the Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado School of Pharmacy, Aurora, Colorado 80045
| | - Juan Marugan
- the National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Heide L Ford
- the Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045,
| | - Rui Zhao
- From the Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado 80045,
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30
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Albers HMHG, Kuijl C, Bakker J, Hendrickx L, Wekker S, Farhou N, Liu N, Blasco-Moreno B, Scanu T, den Hertog J, Celie P, Ovaa H, Neefjes J. Integrating chemical and genetic silencing strategies to identify host kinase-phosphatase inhibitor networks that control bacterial infection. ACS Chem Biol 2014; 9:414-22. [PMID: 24274083 PMCID: PMC3934374 DOI: 10.1021/cb400421a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
Every
year three million people die as a result of bacterial infections,
and this number may further increase due to resistance to current
antibiotics. These antibiotics target almost all essential bacterial
processes, leaving only a few new targets for manipulation. The host
proteome has many more potential targets for manipulation in order
to control bacterial infection, as exemplified by the observation
that inhibiting the host kinase Akt supports the elimination of different
intracellular bacteria including Salmonella and M. tuberculosis. If host kinases are involved in the control
of bacterial infections, phosphatases could be as well. Here we present
an integrated small interference RNA and small molecule screen to
identify host phosphatase-inhibitor combinations that control bacterial
infection. We define host phosphatases inhibiting intracellular growth
of Salmonella and identify corresponding inhibitors
for the dual specificity phosphatases DUSP11 and 27. Pathway analysis
places many kinases and phosphatases controlling bacterial infection
in an integrated pathway centered around Akt. This network controls
host cell metabolism, survival, and growth and bacterial survival
and reflect a natural host cell response to bacterial infection. Inhibiting
two enzyme classes with opposite activities–kinases and phosphatases–may
be a new strategy to overcome infections by antibiotic-resistant bacteria.
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Affiliation(s)
| | | | | | | | | | | | | | - Bernat Blasco-Moreno
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Doctor Aiguader, 88, 08003 Barcelona, Spain
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31
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Eren D, Alakent B. Frequency response of a protein to local conformational perturbations. PLoS Comput Biol 2013; 9:e1003238. [PMID: 24086121 PMCID: PMC3784495 DOI: 10.1371/journal.pcbi.1003238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 08/11/2013] [Indexed: 11/18/2022] Open
Abstract
Signals created by local perturbations are known to propagate long distances through proteins via backbone connectivity and nonbonded interactions. In the current study, signal propagation from the flexible ligand binding loop to the rest of Protein Tyrosine Phosphatase 1B (PTP1B) was investigated using frequency response techniques. Using restrained Targeted Molecular Dynamics (TMD) potential on WPD and R loops, PTP1B was driven between its crystal structure conformations at different frequencies. Propagation of the local perturbation signal was manifested via peaks at the fundamental frequency and upper harmonics of 1/f distributed spectral density of atomic variables, such as Cα atoms, dihedral angles, or polar interaction distances. Frequency of perturbation was adjusted high enough (simulation length >∼10×period of a perturbation cycle) not to be clouded by random diffusional fluctuations, and low enough (<∼0.8 ns(-1)) not to attenuate the propagating signal and enhance the contribution of the side-chains to the dissipation of the signals. Employing Discrete Fourier Transform (DFT) to TMD simulation trajectories of 16 cycles of conformational transitions at periods of 1.2 to 5 ns yielded Cα displacements consistent with those obtained from crystal structures. Identification of the perturbed atomic variables by statistical t-tests on log-log scale spectral densities revealed the extent of signal propagation in PTP1B, while phase angles of the filtered trajectories at the fundamental frequency were used to cluster collectively fluctuating elements. Hydrophobic interactions were found to have a higher contribution to signal transduction between side-chains compared to the role of polar interactions. Most of in-phase fluctuating residues on the signaling pathway were found to have high identity among PTP domains, and located over a wide region of PTP1B including the allosteric site. Due to its simplicity and efficiency, the suggested technique may find wide applications in identification of signaling pathways of different proteins.
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Affiliation(s)
- Dilek Eren
- Department of Chemical Engineering, Bogazici University, Bebek, Istanbul, Turkey
| | - Burak Alakent
- Department of Chemical Engineering, Bogazici University, Bebek, Istanbul, Turkey
- * E-mail:
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32
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Schneider R, Gohla A, Simard JR, Yadav DB, Fang Z, van Otterlo WAL, Rauh D. Overcoming compound fluorescence in the FLiK screening assay with red-shifted fluorophores. J Am Chem Soc 2013; 135:8400-8. [PMID: 23672540 DOI: 10.1021/ja403074j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In the attempt to discover novel chemical scaffolds that can modulate the activity of disease-associated enzymes, such as kinases, biochemical assays are usually deployed in high-throughput screenings. First-line assays, such as activity-based assays, often rely on fluorescent molecules by measuring a change in the total emission intensity, polarization state, or energy transfer to another fluorescent molecule. However, under certain conditions, intrinsic compound fluorescence can lead to difficult data analysis and to false-positive, as well as false-negative, hits. We have reported previously on a powerful direct binding assay called fluorescent labels in kinases ('FLiK'), which enables a sensitive measurement of conformational changes in kinases upon ligand binding. In this assay system, changes in the emission spectrum of the fluorophore acrylodan, induced by the binding of a ligand, are translated into a robust assay readout. However, under the excitation conditions of acrylodan, intrinsic compound fluorescence derived from highly conjugated compounds complicates data analysis. We therefore optimized this method by identifying novel fluorophores that excite in the far red, thereby avoiding compound fluorescence. With this advancement, even rigid compounds with multiple π-conjugated ring systems can now be measured reliably. This study was performed on three different kinase constructs with three different labeling sites, each undergoing distinct conformational changes upon ligand binding. It may therefore serve as a guideline for the establishment of novel fluorescence-based detection assays.
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Affiliation(s)
- Ralf Schneider
- Chemical Genomics Centre of the Max-Planck-Society , Otto-Hahn-Strasse 15, 44137 Dortmund, Germany
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