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Bishop AC, Serbina A. Targeting Nonconserved and Pathogenic Cysteines of Protein Tyrosine Phosphatases with Small Molecules. Methods Mol Biol 2024; 2743:271-283. [PMID: 38147221 DOI: 10.1007/978-1-0716-3569-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Protein tyrosine phosphatases (PTPs) are important therapeutic targets for a range of human pathologies. However, the common architecture of PTP active sites impedes the discovery of selective PTP inhibitors. Our laboratory has recently developed methods to inhibit PTPs allosterically by targeting cysteine residues that either (i) are not conserved in the PTP family or (ii) result from pathogenic mutations. Here, we describe screening protocols for the identification of selective inhibitors that covalently engage such "rare" cysteines in target PTPs. Moreover, to elucidate the breadth of possible applications of our cysteine-directed screening protocols, we provide a brief overview of the nonconserved cysteines present in all human classical PTP domains.
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Affiliation(s)
| | - Anna Serbina
- Department of Chemistry, Amherst College, Amherst, MA, USA
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2
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Fujii J, Soma Y, Matsuda Y. Biological Action of Singlet Molecular Oxygen from the Standpoint of Cell Signaling, Injury and Death. Molecules 2023; 28:molecules28104085. [PMID: 37241826 DOI: 10.3390/molecules28104085] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Energy transfer to ground state triplet molecular oxygen results in the generation of singlet molecular oxygen (1O2), which has potent oxidizing ability. Irradiation of light, notably ultraviolet A, to a photosensitizing molecule results in the generation of 1O2, which is thought to play a role in causing skin damage and aging. It should also be noted that 1O2 is a dominant tumoricidal component that is generated during the photodynamic therapy (PDT). While type II photodynamic action generates not only 1O2 but also other reactive species, endoperoxides release pure 1O2 upon mild exposure to heat and, hence, are considered to be beneficial compounds for research purposes. Concerning target molecules, 1O2 preferentially reacts with unsaturated fatty acids to produce lipid peroxidation. Enzymes that contain a reactive cysteine group at the catalytic center are vulnerable to 1O2 exposure. Guanine base in nucleic acids is also susceptible to oxidative modification, and cells carrying DNA with oxidized guanine units may experience mutations. Since 1O2 is produced in various physiological reactions in addition to photodynamic reactions, overcoming technical challenges related to its detection and methods used for its generation would allow its potential functions in biological systems to be better understood.
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Affiliation(s)
- Junichi Fujii
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Yamagata University, Yamagata 990-9585, Japan
| | - Yuya Soma
- Graduate School of Nursing, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan
| | - Yumi Matsuda
- Graduate School of Nursing, Yamagata University Faculty of Medicine, Yamagata 990-9585, Japan
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Yarnall MT, Kim SH, Korntner S, Bishop AC. Destabilization of the SHP2 and SHP1 protein tyrosine phosphatase domains by a non-conserved "backdoor" cysteine. Biochem Biophys Rep 2022; 32:101370. [PMID: 36275931 PMCID: PMC9578986 DOI: 10.1016/j.bbrep.2022.101370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) are critical regulators of cellular signal transduction that catalyze the hydrolytic dephosphorylation of phosphotyrosine in substrate proteins. Among several conserved features in classical PTP domains are an active-site cysteine residue that is necessary for catalysis and a "backdoor" cysteine residue that can serve to protect the active-site cysteine from irreversible oxidation. Curiously, two biologically important phosphatases, Src homology domain-containing PTPs 2 and 1 (SHP2 and SHP1), each contain an additional backdoor cysteine residue at a position of the PTP domain that is occupied by proline in almost all other classical PTPs (position 333 in human SHP2 numbering). Here we show that the presence of cysteine 333 significantly destabilizes the fold of the PTP domains in the SHPs. We find that replacement of cysteine 333 with proline confers increased thermal stability on the SHP2 and SHP1 PTP domains, as measured by temperature-dependent activity assays and differential scanning fluorimetry. Conversely, we show that substantial destabilization of the PTP-domain fold is conferred by introduction of a non-natural cysteine residue in a non-SHP PTP that contains proline at the 333 position. It has previously been suggested that the extra backdoor cysteine of the SHP PTPs may work in tandem with the conserved backdoor cysteine to provide protection from irreversible oxidative enzyme inactivation. If so, our current results suggest that, during the course of mammalian evolution, the SHP proteins have developed extra protection from oxidation at the cost of the thermal instability that is conferred by the presence of their PTP domains' second backdoor cysteine.
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Affiliation(s)
| | - Sean H. Kim
- Amherst College, Department of Chemistry, Amherst, MA, 01002, USA
| | - Samuel Korntner
- Amherst College, Department of Chemistry, Amherst, MA, 01002, USA
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4
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Liu R, Zhang W, Gou P, Berthelet J, Nian Q, Chevreux G, Legros V, Moroy G, Bui LC, Wang L, Dupret JM, Deshayes F, Lima FR. Cisplatin causes covalent inhibition of protein-tyrosine phosphatase 1B (PTP1B) through reaction with its active site cysteine: Molecular, cellular and in vivo mice studies. Biomed Pharmacother 2022; 153:113372. [PMID: 35809481 DOI: 10.1016/j.biopha.2022.113372] [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: 04/11/2022] [Revised: 06/24/2022] [Accepted: 06/29/2022] [Indexed: 11/25/2022] Open
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a critical regulator of different signalling cascades such as the EGFR pathway. The biological importance of PTP1B is further evidenced by knockout mice studies and the identification of recurrent mutations/deletions in PTP1B linked to metabolic and oncogenic alterations. Cisplatin is among the most widely used anticancer drug. The biological effects of cisplatin are thought to arise primarily from DNA damaging events involving cisplatin-DNA adducts. However, increasing evidence indicate that the biological properties of cisplatin could also rely on the perturbation of other processes such as cell signalling through direct interaction with certain cysteine residues in proteins. Here, we provide molecular, cellular and in vivo evidence suggesting that PTP1B is a target of cisplatin. Mechanistic studies indicate that cisplatin inhibited PTP1B in an irreversible manner and binds covalently to the catalytic cysteine residue of the enzyme. Accordingly, experiments conducted in cells and mice exposed to cisplatin showed inhibition of endogenous PTP1B and concomitant increase in tyrosine phosphorylation of EGFR. These findings are consistent with previous studies showing tyrosine phosphorylation-dependent activation of the EGFR pathway by cisplatin and with recent studies suggesting PTP1B inhibition by cisplatin and other platinum complexes. Importantly, our work provides novel mechanistic evidence that PTP1B is a protein target of cisplatin and is inhibited by this drug at molecular, cellular and in vivo levels. In addition, our work may contribute to the understanding of the pathways undergoing modulation upon cisplatin administration beyond of the established genotoxic effect of cisplatin.
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Affiliation(s)
- Rongxing Liu
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Wenchao Zhang
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Panhong Gou
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Université Paris Cité, INSERM, Institut de RechercheSaint Louis, UMRS 1131, F-75010 Paris, France
| | - Jérémy Berthelet
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; Université Paris Cité, CNRS, Centre Epigénétique et Destin Cellulaire, F-75013 Paris, France
| | - Qing Nian
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France; Department of Blood Transfusion, Sichuan ProvincialPeople's Hospital, University of Electronic Science and Technology of China andChinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Guillaume Chevreux
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Véronique Legros
- Université Paris Cité, CNRS, Institut Jacques Monod, F-75013 Paris, France
| | - Gautier Moroy
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Linh-Chi Bui
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Li Wang
- Department of Hematology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jean-Marie Dupret
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Frédérique Deshayes
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France
| | - Fernando Rodrigues Lima
- Université Paris Cité, CNRS, Unité de Biologie Fonctionnelle et Adaptative, F-75013 Paris, France.
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5
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The role and therapeutic implication of protein tyrosine phosphatases in Alzheimer's disease. Biomed Pharmacother 2022; 151:113188. [PMID: 35676788 DOI: 10.1016/j.biopha.2022.113188] [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: 04/04/2022] [Revised: 05/16/2022] [Accepted: 05/22/2022] [Indexed: 11/24/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) are important regulator of neuronal signal transduction and a growing number of PTPs have been implicated in Alzheimer's disease (AD). In the brains of patients with AD, there are a variety of abnormally phosphorylated proteins, which are closely related to the abnormal expression and activity of PTPs. β-Amyloid plaques (Aβ) and hyperphosphorylated tau protein are two pathological hallmarks of AD, and their accumulation ultimately leads to neurodegeneration. Studies have shown that protein phosphorylation signaling pathways mediates intracellular accumulation of Aβ and tau during AD development and are involved in synaptic plasticity and other stress responses. Here, we summarized the roles of PTPs related to the pathogenesis of AD and analyzed their therapeutic potential in AD.
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Zhang Q, Kong W, Zhu T, Zhu G, Zhu J, Kong X, Du Y. Phase separation ability and phosphatase activity of the SHP1-R360E mutant. Biochem Biophys Res Commun 2022; 600:150-155. [DOI: 10.1016/j.bbrc.2022.02.070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/18/2022] [Indexed: 11/15/2022]
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Rocha RF, Martins PGA, D'Muniz Pereira H, Brandão-Neto J, Thiemann OH, Terenzi H, Menegatti ACO. Crystal structure of the Cys-NO modified YopH tyrosine phosphatase. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140754. [PMID: 34995802 DOI: 10.1016/j.bbapap.2022.140754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/21/2021] [Accepted: 01/01/2022] [Indexed: 06/14/2023]
Abstract
Protein tyrosine phosphatases (PTPs) are key virulence factors in pathogenic bacteria, consequently, they have become important targets for new approaches against these pathogens, especially in the fight against antibiotic resistance. Among these targets of interest YopH (Yersinia outer protein H) from virulent species of Yersinia is an example. PTPs can be reversibly inhibited by nitric oxide (NO) since the oxidative modification of cysteine residues may influence the protein structure and catalytic activity. We therefore investigated the effects of NO on the structure and enzymatic activity of Yersinia enterocolitica YopH in vitro. Through phosphatase activity assays, we observe that in the presence of NO YopH activity was inhibited by 50%, and that this oxidative modification is partially reversible in the presence of DTT. Furthermore, YopH S-nitrosylation was clearly confirmed by a biotin switch assay, high resolution mass spectrometry (MS) and X-ray crystallography approaches. The crystal structure confirmed the S-nitrosylation of the catalytic cysteine residue, Cys403, while the MS data provide evidence that Cys221 and Cys234 might also be modified by NO. Interestingly, circular dichroism spectroscopy shows that the S-nitrosylation affects secondary structure of wild type YopH, though to a lesser extent on the catalytic cysteine to serine YopH mutant. The data obtained demonstrate that S-nitrosylation inhibits the catalytic activity of YopH, with effects beyond the catalytic cysteine. These findings are helpful for designing effective YopH inhibitors and potential therapeutic strategies to fight this pathogen or others that use similar mechanisms to interfere in the signal transduction pathways of their hosts.
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Affiliation(s)
- Ruth F Rocha
- Laboratório de Biologia Molecular Estrutural, Departamento de Bioquímica, CCB, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Brazil
| | - Priscila G A Martins
- Laboratório de Biologia Molecular Estrutural, Departamento de Bioquímica, CCB, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Brazil
| | | | - José Brandão-Neto
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot OX110DE, United Kingdom
| | - Otavio Henrique Thiemann
- São Carlos Institute of Physics, University of São Paulo, São Carlos, Brazil; Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, Brazil
| | - Hernán Terenzi
- Laboratório de Biologia Molecular Estrutural, Departamento de Bioquímica, CCB, Universidade Federal de Santa Catarina, Florianópolis 88040-900, Brazil.
| | - Angela C O Menegatti
- Department of Molecular Biology, Federal University of Paraiba, João Pessoa 58051-900, Brazil.
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Coles VE, Darveau P, Zhang X, Harvey H, Henriksbo BD, Yang A, Schertzer JD, Magolan J, Burrows LL. Exploration of BAY 11-7082 as a Potential Antibiotic. ACS Infect Dis 2022; 8:170-182. [PMID: 34860493 DOI: 10.1021/acsinfecdis.1c00522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Exposure of the Gram-negative pathogen Pseudomonas aeruginosa to subinhibitory concentrations of antibiotics increases the formation of biofilms. We exploited this phenotype to identify molecules with potential antimicrobial activity in a biofilm-based high-throughput screen. The anti-inflammatory compound BAY 11-7082 induced dose-dependent biofilm stimulation, indicative of antibacterial activity. We confirmed that BAY 11-7082 inhibits the growth of P. aeruginosa and other priority pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). We synthesized 27 structural analogues, including a series based on the related scaffold 3-(phenylsulfonyl)-2-pyrazinecarbonitrile (PSPC), 10 of which displayed increased anti-Staphylococcal activity. Because the parent molecule inhibits the NLR Family Pyrin Domain Containing 3 (NLRP3) inflammasome, we measured the ability of select analogues to reduce interleukin-1β (IL-1β) production in mammalian macrophages, identifying minor differences in the structure-activity relationship for the anti-inflammatory and antibacterial properties of this scaffold. Although we could evolve stably resistant MRSA mutants with cross-resistance to BAY 11-7082 and PSPC, their lack of shared mutations suggested that the two molecules could have multiple targets. Finally, we showed that BAY 11-7082 and its analogues synergize with penicillin G against MRSA, suggesting that this scaffold may serve as an interesting starting point for the development of antibiotic adjuvants.
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Affiliation(s)
- Victoria E. Coles
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West Hamilton, Ontario L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West Hamilton, Ontario L8S 4K1, Canada
| | - Patrick Darveau
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West Hamilton, Ontario L8S 4L8, Canada
| | - Xiong Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West Hamilton, Ontario L8S 4K1, Canada
| | - Hanjeong Harvey
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West Hamilton, Ontario L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West Hamilton, Ontario L8S 4K1, Canada
| | - Brandyn D. Henriksbo
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West Hamilton, Ontario L8S 4K1, Canada
| | - Angela Yang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West Hamilton, Ontario L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West Hamilton, Ontario L8S 4K1, Canada
| | - Jonathan D. Schertzer
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West Hamilton, Ontario L8S 4K1, Canada
| | - Jakob Magolan
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West Hamilton, Ontario L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West Hamilton, Ontario L8S 4K1, Canada
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West Hamilton, Ontario L8S 4L8, Canada
| | - Lori L. Burrows
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West Hamilton, Ontario L8S 4K1, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main Street West Hamilton, Ontario L8S 4K1, Canada
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A New Paradigm for KIM-PTP Drug Discovery: Identification of Allosteric Sites with Potential for Selective Inhibition Using Virtual Screening and LEI Analysis. Int J Mol Sci 2021; 22:ijms222212206. [PMID: 34830087 PMCID: PMC8624330 DOI: 10.3390/ijms222212206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/05/2021] [Accepted: 11/06/2021] [Indexed: 02/04/2023] Open
Abstract
The kinase interaction motif protein tyrosine phosphatases (KIM-PTPs), HePTP, PTPSL and STEP, are involved in the negative regulation of mitogen-activated protein kinase (MAPK) signalling pathways and are important therapeutic targets for a number of diseases. We have used VSpipe, a virtual screening pipeline, to identify a ligand cluster distribution that is unique to this subfamily of PTPs. Several clusters map onto KIM-PTP specific sequence motifs in contrast to the cluster distribution obtained for PTP1B, a classic PTP that mapped to general PTP motifs. Importantly, the ligand clusters coincide with previously reported functional and substrate binding sites in KIM-PTPs. Assessment of the KIM-PTP specific clusters, using ligand efficiency index (LEI) plots generated by the VSpipe, ascertained that the binders in these clusters reside in a more drug-like chemical-biological space than those at the active site. LEI analysis showed differences between clusters across all KIM-PTPs, highlighting a distinct and specific profile for each phosphatase. The most druggable cluster sites are unexplored allosteric functional sites unique to each target. Exploiting these sites may facilitate the delivery of inhibitors with improved drug-like properties, with selectivity amongst the KIM-PTPs and over other classical PTPs.
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Yu M, Xu C, Zhang H, Lun J, Wang L, Zhang G, Fang J. The tyrosine phosphatase SHP2 promotes proliferation and oxaliplatin resistance of colon cancer cells through AKT and ERK. Biochem Biophys Res Commun 2021; 563:1-7. [PMID: 34052504 DOI: 10.1016/j.bbrc.2021.05.068] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 05/19/2021] [Indexed: 02/05/2023]
Abstract
The SH2 domain-containing phosphatase 2 (SHP2) is a widely expressed protein tyrosine phosphatase, and it is proposed to act as an oncogenic protein. SHP2 is also engaged in drug resistance of a variety of cancers. However, the role of SHP2 in the proliferation and drug resistance of colon cancer cells remains elusive. In this work we determined the effect of SHP2 expression on colon cancer cell proliferation and resistance to oxaliplatin (L-OHP), a commonly used drug in the clinic. Our results show that knockdown of SHP2 decreased and overexpression of SHP2 increased the proliferation of SW480 cells, respectively. Knockdown of SHP2 increased, and overexpression of SHP2 decreased apoptosis of the cells. We selected oxaliplatin-resistant SW480(SW480/L-OHP) and HCT116(HCT116/L-OHP) cells and found that the SHP2 protein level was raised in these drug-resistant cells. The upregulated SHP2 contributed to oxaliplatin resistance of the cells, as knockdown of SHP2 decreased the IC50 of oxaliplatin and abated proliferation and survival of SW480/L-OHP and HCT116/L-OHP cells in the presence of oxaliplatin. Also, SW480/L-OHP and HCT116/L-OHP cells had increased phosphorylation of AKT and ERK. Inhibition of AKT, ERK, or SHP2 sensitized SW480/L-OHP and HCT116/L-OHP cells to oxaliplatin. Our results indicate that SHP2 contributes oxaliplatin resistance through AKT and ERK. These results also suggest that SHP2-targeting is a potential strategy for overcoming oxaliplatin resistance of colon cancer cells.
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Affiliation(s)
- Mengchao Yu
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao 266061, Qingdao Cancer Institute, Qingdao University, Qingdao 266061, China
| | - Chengzhen Xu
- Department of Chinese Medicine, Qingdao No. 6 People's Hospital, Qingdao, China
| | - Hongwei Zhang
- Shandong Provincial Maternal and Child Health Care Hospital, Jinan 250014, China
| | - Jie Lun
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao 266061, Qingdao Cancer Institute, Qingdao University, Qingdao 266061, China
| | - Lei Wang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao 266061, Qingdao Cancer Institute, Qingdao University, Qingdao 266061, China
| | - Gang Zhang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao 266061, Qingdao Cancer Institute, Qingdao University, Qingdao 266061, China
| | - Jing Fang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Qingdao 266061, Qingdao Cancer Institute, Qingdao University, Qingdao 266061, China.
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Zhu G, Xie J, Kong W, Xie J, Li Y, Du L, Zheng Q, Sun L, Guan M, Li H, Zhu T, He H, Liu Z, Xia X, Kan C, Tao Y, Shen HC, Li D, Wang S, Yu Y, Yu ZH, Zhang ZY, Liu C, Zhu J. Phase Separation of Disease-Associated SHP2 Mutants Underlies MAPK Hyperactivation. Cell 2020; 183:490-502.e18. [PMID: 33002410 DOI: 10.1016/j.cell.2020.09.002] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 04/19/2020] [Accepted: 08/31/2020] [Indexed: 02/08/2023]
Abstract
The non-receptor protein tyrosine phosphatase (PTP) SHP2, encoded by PTPN11, plays an essential role in RAS-mitogen-activated protein kinase (MAPK) signaling during normal development. It has been perplexing as to why both enzymatically activating and inactivating mutations in PTPN11 result in human developmental disorders with overlapping clinical manifestations. Here, we uncover a common liquid-liquid phase separation (LLPS) behavior shared by these disease-associated SHP2 mutants. SHP2 LLPS is mediated by the conserved well-folded PTP domain through multivalent electrostatic interactions and regulated by an intrinsic autoinhibitory mechanism through conformational changes. SHP2 allosteric inhibitors can attenuate LLPS of SHP2 mutants, which boosts SHP2 PTP activity. Moreover, disease-associated SHP2 mutants can recruit and activate wild-type (WT) SHP2 in LLPS to promote MAPK activation. These results not only suggest that LLPS serves as a gain-of-function mechanism involved in the pathogenesis of SHP2-associated human diseases but also provide evidence that PTP may be regulated by LLPS that can be therapeutically targeted.
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Affiliation(s)
- Guangya Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jingjing Xie
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wenna Kong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfei Xie
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yichen Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin Du
- Etern Biopharma Co. Ltd., Shanghai 201203, China
| | | | - Lin Sun
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
| | - Mingfeng Guan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Huan Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tianxin Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hao He
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenying Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xi Xia
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chen Kan
- Department of Pathophysiology, Anhui Medical University, Hefei 230032, China
| | - Youqi Tao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong C Shen
- Roche Innovation Center Shanghai, Roche Pharma Research & Early Development, Shanghai 201203, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Siying Wang
- Department of Pathophysiology, Anhui Medical University, Hefei 230032, China
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Zhi-Hong Yu
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research and Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research and Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Jidong Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.
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12
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Hou X, Sun JP, Ge L, Liang X, Li K, Zhang Y, Fang H. Inhibition of striatal-enriched protein tyrosine phosphatase by targeting computationally revealed cryptic pockets. Eur J Med Chem 2020; 190:112131. [PMID: 32078861 PMCID: PMC7163917 DOI: 10.1016/j.ejmech.2020.112131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 01/21/2020] [Accepted: 02/06/2020] [Indexed: 11/21/2022]
Abstract
Cryptic pockets, which are not apparent in crystallographic structures, provide promising alternatives to traditional binding sites for drug development. However, identifying cryptic pockets is extremely challenging and the therapeutic potential of cryptic pockets remains unclear. Here, we reported the discovery of novel inhibitors for striatal-enriched protein tyrosine phosphatase (STEP), a potential drug target for multiple neuropsychiatric disorders, based on cryptic pocket detection. By combining the use of molecular dynamics simulations and fragment-centric topographical mapping, we identified transiently open cryptic pockets and identified 12 new STEP inhibition scaffolds through structure-based virtual screening. Site-directed mutagenesis verified the binding of ST3 with the predicted cryptic pockets. Moreover, the most potent and selective inhibitors could modulate the phosphorylation of both ERK1/2 and Pyk2 in PC12 cells.
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Affiliation(s)
- Xuben Hou
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmaceutical Science, Shandong University, Jinan, Shandong, 250012, China; Department of Chemistry, New York University, New York, NY, 10003, United States
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Lin Ge
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Xiao Liang
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmaceutical Science, Shandong University, Jinan, Shandong, 250012, China
| | - Kangshuai Li
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, School of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, NY, 10003, United States; NYU-ECNU Center for Computational Chemistry, New York University-Shanghai, Shanghai, 200122, China
| | - Hao Fang
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology of Natural Products (MOE), School of Pharmaceutical Science, Shandong University, Jinan, Shandong, 250012, China.
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13
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van den Bedem H, Wilson MA. Shining light on cysteine modification: connecting protein conformational dynamics to catalysis and regulation. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:958-966. [PMID: 31274417 PMCID: PMC6613112 DOI: 10.1107/s160057751900568x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/25/2019] [Indexed: 05/04/2023]
Abstract
Cysteine is a rare but functionally important amino acid that is often subject to covalent modification. Cysteine oxidation plays an important role in many human disease processes, and basal levels of cysteine oxidation are required for proper cellular function. Because reactive cysteine residues are typically ionized to the thiolate anion (Cys-S-), their formation of a covalent bond alters the electrostatic and steric environment of the active site. X-ray-induced photo-oxidation to sulfenic acids (Cys-SOH) can recapitulate some aspects of the changes that occur under physiological conditions. Here we propose how site-specific cysteine photo-oxidation can be used to interrogate ensuing changes in protein structure and dynamics at atomic resolution. Although this powerful approach can connect cysteine covalent modification to global protein conformational changes and function, careful biochemical validation must accompany all such studies to exclude misleading artifacts. New types of X-ray crystallography experiments and powerful computational methods are creating new opportunities to connect conformational dynamics to catalysis for the large class of systems that use covalently modified cysteine residues for catalysis or regulation.
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Affiliation(s)
- Henry van den Bedem
- Bioscience Division, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Mark A Wilson
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
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14
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Duval R, Bui LC, Mathieu C, Nian Q, Berthelet J, Xu X, Haddad I, Vinh J, Dupret JM, Busi F, Guidez F, Chomienne C, Rodrigues-Lima F. Benzoquinone, a leukemogenic metabolite of benzene, catalytically inhibits the protein tyrosine phosphatase PTPN2 and alters STAT1 signaling. J Biol Chem 2019; 294:12483-12494. [PMID: 31248982 DOI: 10.1074/jbc.ra119.008666] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/21/2019] [Indexed: 12/12/2022] Open
Abstract
Protein tyrosine phosphatase, nonreceptor type 2 (PTPN2) is mainly expressed in hematopoietic cells, where it negatively regulates growth factor and cytokine signaling. PTPN2 is an important regulator of hematopoiesis and immune/inflammatory responses, as evidenced by loss-of-function mutations of PTPN2 in leukemia and lymphoma and knockout mice studies. Benzene is an environmental chemical that causes hematological malignancies, and its hematotoxicity arises from its bioactivation in the bone marrow to electrophilic metabolites, notably 1,4-benzoquinone, a major hematotoxic benzene metabolite. Although the molecular bases for benzene-induced leukemia are not well-understood, it has been suggested that benzene metabolites alter topoisomerases II function and thereby significantly contribute to leukemogenesis. However, several studies indicate that benzene and its hematotoxic metabolites may also promote the leukemogenic process by reacting with other targets and pathways. Interestingly, alterations of cell-signaling pathways, such as Janus kinase (JAK)/signal transducer and activator of transcription (STAT), have been proposed to contribute to benzene-induced malignant blood diseases. We show here that 1,4-benzoquinone directly impairs PTPN2 activity. Mechanistic and kinetic experiments with purified human PTPN2 indicated that this impairment results from the irreversible formation (k inact = 645 m-1·s-1) of a covalent 1,4-benzoquinone adduct at the catalytic cysteine residue of the enzyme. Accordingly, cell experiments revealed that 1,4-benzoquinone exposure irreversibly inhibits cellular PTPN2 and concomitantly increases tyrosine phosphorylation of STAT1 and expression of STAT1-regulated genes. Our results provide molecular and cellular evidence that 1,4-benzoquinone covalently modifies key signaling enzymes, implicating it in benzene-induced malignant blood diseases.
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Affiliation(s)
- Romain Duval
- Université de Paris, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Linh-Chi Bui
- Université de Paris, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Cécile Mathieu
- Université de Paris, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Qing Nian
- Université de Paris, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | | | - Ximing Xu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Iman Haddad
- ESPCI Paris, PSL Université, USR 3149, CNRS, F-75005 Paris, France
| | - Joelle Vinh
- ESPCI Paris, PSL Université, USR 3149, CNRS, F-75005 Paris, France
| | | | - Florent Busi
- Université de Paris, BFA, UMR 8251, CNRS, F-75013 Paris, France
| | - Fabien Guidez
- Université de Paris, Institut de Recherche Saint-Louis, UMRS 1131, INSERM, F-75010 Paris, France
| | - Christine Chomienne
- Université de Paris, Institut de Recherche Saint-Louis, UMRS 1131, INSERM, F-75010 Paris, France; Service de Biologie Cellulaire, Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Saint Louis, F-75010 Paris, France
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15
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Pereira SB, Santos M, Leite JP, Flores C, Eisfeld C, Büttel Z, Mota R, Rossi F, De Philippis R, Gales L, Morais‐Cabral JH, Tamagnini P. The role of the tyrosine kinase Wzc (Sll0923) and the phosphatase Wzb (Slr0328) in the production of extracellular polymeric substances (EPS) by Synechocystis PCC 6803. Microbiologyopen 2019; 8:e00753. [PMID: 30675753 PMCID: PMC6562117 DOI: 10.1002/mbo3.753] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 11/10/2022] Open
Abstract
Many cyanobacteria produce extracellular polymeric substances (EPS) mainly composed of heteropolysaccharides with unique characteristics that make them suitable for biotechnological applications. However, manipulation/optimization of EPS biosynthesis/characteristics is hindered by a poor understanding of the production pathways and the differences between bacterial species. In this work, genes putatively related to different pathways of cyanobacterial EPS polymerization, assembly, and export were targeted for deletion or truncation in the unicellular Synechocystis sp. PCC 6803. No evident phenotypic changes were observed for some mutants in genes occurring in multiple copies in Synechocystis genome, namely ∆wzy (∆sll0737), ∆wzx (∆sll5049), ∆kpsM (∆slr2107), and ∆kpsM∆wzy (∆slr2107∆sll0737), strongly suggesting functional redundancy. In contrast, Δwzc (Δsll0923) and Δwzb (Δslr0328) influenced both the amount and composition of the EPS, establishing that Wzc participates in the production of capsular (CPS) and released (RPS) polysaccharides, and Wzb affects RPS production. The structure of Wzb was solved (2.28 Å), revealing structural differences relative to other phosphatases involved in EPS production and suggesting a different substrate recognition mechanism. In addition, Wzc showed the ATPase and autokinase activities typical of bacterial tyrosine kinases. Most importantly, Wzb was able to dephosphorylate Wzc in vitro, suggesting that tyrosine phosphorylation/dephosphorylation plays a role in cyanobacterial EPS production.
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Affiliation(s)
- Sara B. Pereira
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
| | - Marina Santos
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarPortoPortugal
| | - José P. Leite
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarPortoPortugal
| | - Carlos Flores
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarPortoPortugal
| | - Carina Eisfeld
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Present address:
Department of Water ManagementDelft University of TechnologyDelftThe Netherlands
| | - Zsófia Büttel
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Present address:
Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology InstituteUniversity of GroningenGroningenThe Netherlands
| | - Rita Mota
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
| | - Federico Rossi
- Department of Agrifood Production and Environmental SciencesUniversity of FlorenceFlorenceItaly
| | - Roberto De Philippis
- Department of Agrifood Production and Environmental SciencesUniversity of FlorenceFlorenceItaly
| | - Luís Gales
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarPortoPortugal
| | - João H. Morais‐Cabral
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
| | - Paula Tamagnini
- i3S ‐ Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversidade do PortoPortoPortugal
- Faculdade de Ciências, Departamento de BiologiaUniversidade do PortoPortoPortugal
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16
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Lack of CD45 in FLT3-ITD mice results in a myeloproliferative phenotype, cortical porosity, and ectopic bone formation. Oncogene 2019; 38:4773-4787. [DOI: 10.1038/s41388-019-0757-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 12/12/2018] [Accepted: 02/05/2019] [Indexed: 01/08/2023]
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17
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Morrell TE, Rafalska-Metcalf IU, Yang H, Chu JW. Compound Molecular Logic in Accessing the Active Site of Mycobacterium tuberculosis Protein Tyrosine Phosphatase B. J Am Chem Soc 2018; 140:14747-14752. [PMID: 30301350 DOI: 10.1021/jacs.8b08070] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein tyrosine phosphatase B (PtpB) from Mycobacterium tuberculosis (Mtb) extends the bacteria's survival in hosts and hence is a potential target for Mtb-specific drugs. To study how Mtb-specific sequence insertions in PtpB may regulate access to its active site through large-amplitude conformational changes, we performed free-energy calculations using an all-atom explicit solvent model. Corroborated by biochemical assays, the results show that PtpB's active site is controlled via an "either/or" compound conformational gating mechanism, an unexpected discovery that Mtb has evolved to bestow a single enzyme with such intricate logical operations. In addition to providing unprecedented insights for its active-site surroundings, the findings also suggest new ways of inactivating PtpB.
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Affiliation(s)
- Thomas E Morrell
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | | | - Haw Yang
- Department of Chemistry , Princeton University , Princeton , New Jersey 08544 , United States
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology, and Institute of Molecular Medicine and Bioengineering , National Chiao Tung University , Hsinchu , Taiwan 30068 , ROC
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18
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Junker S, Maaß S, Otto A, Hecker M, Becher D. Toward the Quantitative Characterization of Arginine Phosphorylations in Staphylococcus aureus. J Proteome Res 2018; 18:265-279. [PMID: 30358407 DOI: 10.1021/acs.jproteome.8b00579] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The Gram-positive bacterium Staphylococcus aureus plays an important role as an opportunistic pathogen and causative agent of nosocomial infections. As pathophysiological research gained insights into host-specific adaptation and a broad range of virulence mechanisms, S. aureus evolved as a model organism for human pathogens. Hence the investigation of staphylococcal proteome expression and regulation supports the understanding of the pathogenicity and relevant physiology of this organism. This study focused on the analysis of protein regulation by reversible protein phosphorylation, in particular, on arginine residues. Therefore, both proteome and phosphoproteome of S. aureus COL wild type were compared with the arginine phosphatase deletion mutant S. aureus COL ΔptpB under control and stress conditions in a quantitative manner. A gel-free approach, adapted to the special challenges of arginine phosphorylations, was applied to analyze the phosphoproteome of exponential growing cells after oxidative stress caused by sublethal concentrations of H2O2. Together with phenotypic characterization of S. aureus COL ΔptpB, this study disclosed first insights into the physiological role of arginine phosphorylations in Gram-positive pathogens. A spectral library based quantification of phosphopeptides finally allowed us to link arginine phosphorylation to staphylococcal oxidative stress response, amino acid metabolism, and virulence.
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Affiliation(s)
- Sabryna Junker
- Institute for Microbiology , University of Greifswald , Greifswald 17487 , Germany
| | - Sandra Maaß
- Institute for Microbiology , University of Greifswald , Greifswald 17487 , Germany
| | - Andreas Otto
- Institute for Microbiology , University of Greifswald , Greifswald 17487 , Germany
| | - Michael Hecker
- Institute for Microbiology , University of Greifswald , Greifswald 17487 , Germany
| | - Dörte Becher
- Institute for Microbiology , University of Greifswald , Greifswald 17487 , Germany
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19
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Lountos GT, Raran-Kurussi S, Zhao BM, Dyas BK, Burke TR, Ulrich RG, Waugh DS. High-resolution crystal structures of the D1 and D2 domains of protein tyrosine phosphatase epsilon for structure-based drug design. Acta Crystallogr D Struct Biol 2018; 74:1015-1026. [PMID: 30289412 PMCID: PMC6173050 DOI: 10.1107/s2059798318011919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 08/22/2018] [Indexed: 11/10/2022] Open
Abstract
Here, new crystal structures are presented of the isolated membrane-proximal D1 and distal D2 domains of protein tyrosine phosphatase epsilon (PTPℇ), a protein tyrosine phosphatase that has been shown to play a positive role in the survival of human breast cancer cells. A triple mutant of the PTPℇ D2 domain (A455N/V457Y/E597D) was also constructed to reconstitute the residues of the PTPℇ D1 catalytic domain that are important for phosphatase activity, resulting in only a slight increase in the phosphatase activity compared with the native D2 protein. The structures reported here are of sufficient resolution for structure-based drug design, and a microarray-based assay for high-throughput screening to identify small-molecule inhibitors of the PTPℇ D1 domain is also described.
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Affiliation(s)
- George T. Lountos
- Basic Science Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Sreejith Raran-Kurussi
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Bryan M. Zhao
- The Oak Ridge Institute for Science and Education, Oak Ridge, TN 37831, USA
- Molecular and Translational Sciences Division, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Beverly K. Dyas
- Molecular and Translational Sciences Division, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - Terrence R. Burke
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Robert G. Ulrich
- Molecular and Translational Sciences Division, US Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702, USA
| | - David S. Waugh
- Macromolecular Crystallography Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
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20
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Hussein UK, Park HS, Bae JS, Kim KM, Chong YJ, Kim CY, Kwon KS, Chung MJ, Lee H, Kang MJ, Moon WS, Jang KY. Expression of oxidized protein tyrosine phosphatase and γH2AX predicts poor survival of gastric carcinoma patients. BMC Cancer 2018; 18:836. [PMID: 30126387 PMCID: PMC6102926 DOI: 10.1186/s12885-018-4752-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 08/14/2018] [Indexed: 11/25/2022] Open
Abstract
Background Oxidative stress induces various intracellular damage, which might be correlated with tumorigenesis. Accumulated oxidative stresses might inactivate protein tyrosine phosphatase (PTP) by oxidizing it, and inducing the phosphorylation of H2AX (γH2AX) in response to DNA damage. Methods We evaluated the clinical significance of the expression of oxidized-PTP and γH2AX in 169 gastric carcinomas. Results Immunohistochemical expression of nuclear oxidized-PTP, cytoplasmic oxidized-PTP, and γH2AX expression were significantly associated with each other, and their expressions predicted shorter survival of gastric carcinoma patients. In multivariate analysis, nuclear oxidized-PTP (overall survival; p < 0.001, relapse-free survival; P < 0.001) was an independent indicator of poor prognosis of gastric carcinoma patients. In addition, co-expression patterns of nuclear oxidized-PTP and γH2AX were independent indicators of poor prognosis of gastric carcinoma patients (overall survival; P < 0.001, relapse-free survival; P < 0.001). Conclusions This study suggests that oxidative stress-mediated oxidation of PTP might be involved in the progression of gastric carcinomas. In addition, this study suggests that individual and co-expression pattern of nuclear oxidized-PTP and γH2AX might be used as a prognostic marker of gastric carcinomas.
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Affiliation(s)
- Usama Khamis Hussein
- Department of Pathology, Chonbuk National University Medical School, Research Institute of Clinical Medicine of Chonbuk, National University-Biomedical Research Institute of Chonbuk National University Hospital, Jeonju, Republic of Korea.,Research Institute for Endocrine Sciences, Chonbuk National University Medical School, Jeonju, Republic of Korea.,Faculty of Science, Beni-Suef University, Beni-Suef, Egypt
| | - Ho Sung Park
- Department of Pathology, Chonbuk National University Medical School, Research Institute of Clinical Medicine of Chonbuk, National University-Biomedical Research Institute of Chonbuk National University Hospital, Jeonju, Republic of Korea.,Research Institute for Endocrine Sciences, Chonbuk National University Medical School, Jeonju, Republic of Korea
| | - Jun Sang Bae
- Department of Pathology, Chonbuk National University Medical School, Research Institute of Clinical Medicine of Chonbuk, National University-Biomedical Research Institute of Chonbuk National University Hospital, Jeonju, Republic of Korea.,Research Institute for Endocrine Sciences, Chonbuk National University Medical School, Jeonju, Republic of Korea
| | - Kyoung Min Kim
- Department of Pathology, Chonbuk National University Medical School, Research Institute of Clinical Medicine of Chonbuk, National University-Biomedical Research Institute of Chonbuk National University Hospital, Jeonju, Republic of Korea.,Research Institute for Endocrine Sciences, Chonbuk National University Medical School, Jeonju, Republic of Korea
| | - Yun Jo Chong
- Center for University-wide Research Facilities, Chonbuk National University, Jeonju, Republic of Korea
| | - Chan Young Kim
- Department of Surgery, Chonbuk National University Medical School, Jeonju, Republic of Korea
| | - Keun Sang Kwon
- Department of Preventive Medicine, Chonbuk National University Medical School, Jeonju, Republic of Korea
| | - Myoung Ja Chung
- Department of Pathology, Chonbuk National University Medical School, Research Institute of Clinical Medicine of Chonbuk, National University-Biomedical Research Institute of Chonbuk National University Hospital, Jeonju, Republic of Korea.,Research Institute for Endocrine Sciences, Chonbuk National University Medical School, Jeonju, Republic of Korea
| | - Ho Lee
- Department of Forensic Medicine, Chonbuk National University Medical School, Jeonju, Republic of Korea
| | - Myoung Jae Kang
- Department of Pathology, Chonbuk National University Medical School, Research Institute of Clinical Medicine of Chonbuk, National University-Biomedical Research Institute of Chonbuk National University Hospital, Jeonju, Republic of Korea.,Research Institute for Endocrine Sciences, Chonbuk National University Medical School, Jeonju, Republic of Korea
| | - Woo Sung Moon
- Department of Pathology, Chonbuk National University Medical School, Research Institute of Clinical Medicine of Chonbuk, National University-Biomedical Research Institute of Chonbuk National University Hospital, Jeonju, Republic of Korea.,Research Institute for Endocrine Sciences, Chonbuk National University Medical School, Jeonju, Republic of Korea
| | - Kyu Yun Jang
- Department of Pathology, Chonbuk National University Medical School, Research Institute of Clinical Medicine of Chonbuk, National University-Biomedical Research Institute of Chonbuk National University Hospital, Jeonju, Republic of Korea. .,Research Institute for Endocrine Sciences, Chonbuk National University Medical School, Jeonju, Republic of Korea.
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21
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Yu ZH, Zhang ZY. Regulatory Mechanisms and Novel Therapeutic Targeting Strategies for Protein Tyrosine Phosphatases. Chem Rev 2018; 118:1069-1091. [PMID: 28541680 PMCID: PMC5812791 DOI: 10.1021/acs.chemrev.7b00105] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An appropriate level of protein phosphorylation on tyrosine is essential for cells to react to extracellular stimuli and maintain cellular homeostasis. Faulty operation of signal pathways mediated by protein tyrosine phosphorylation causes numerous human diseases, which presents enormous opportunities for therapeutic intervention. While the importance of protein tyrosine kinases in orchestrating the tyrosine phosphorylation networks and in target-based drug discovery has long been recognized, the significance of protein tyrosine phosphatases (PTPs) in cellular signaling and disease biology has historically been underappreciated, due to a large extent to an erroneous assumption that they are largely constitutive and housekeeping enzymes. Here, we provide a comprehensive examination of a number of regulatory mechanisms, including redox modulation, allosteric regulation, and protein oligomerization, that control PTP activity. These regulatory mechanisms are integral to the myriad PTP-mediated biochemical events and reinforce the concept that PTPs are indispensable and specific modulators of cellular signaling. We also discuss how disruption of these PTP regulatory mechanisms can cause human diseases and how these diverse regulatory mechanisms can be exploited for novel therapeutic development.
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Affiliation(s)
- Zhi-Hong Yu
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907
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22
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Abstract
In higher eukaryotes, the Tyr phosphorylation status of cellular proteins results from the coordinated action of Protein Tyrosine Kinases (PTKs) and Protein Tyrosine Phosphatases (PTPs). PTPs have emerged as highly regulated enzymes with diverse substrate specificity, and proteins with Tyr-dephosphorylation or Tyr-dephosphorylation-like properties can be clustered as the PTPome. This includes proteins from the PTP superfamily, which display a Cys-based catalytic mechanism, as well as enzymes from other gene families (Asp-based phosphatases, His-based phosphatases) that have converged in protein Tyr-dephosphorylation-related functions by using non-Cys-based catalytic mechanisms. Within the Cys-based members of the PTPome, classical PTPs dephosphorylate specific phosphoTyr (pTyr) residues from protein substrates, whereas VH1-like dual-specificity PTPs dephosphorylate pTyr, pSer, and pThr residues, as well as nonproteinaceous substrates, including phosphoinositides and phosphorylated carbohydrates. In addition, several PTPs have impaired catalytic activity as a result of amino acid substitutions at their active sites, but retain regulatory functions related with pTyr signaling. As a result of their relevant biological activity, many PTPs are linked to human disease, including cancer, neurodevelopmental, and metabolic diseases, making these proteins important drug targets and molecular markers in the clinic. Here, a brief overview on the biochemistry and physiology of the different groups of proteins that belong to the mammalian PTPome is presented.
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23
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Computational Insight into Protein Tyrosine Phosphatase 1B Inhibition: A Case Study of the Combined Ligand- and Structure-Based Approach. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2017; 2017:4245613. [PMID: 29441120 PMCID: PMC5758944 DOI: 10.1155/2017/4245613] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 09/26/2017] [Indexed: 11/25/2022]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is an attractive target for treating cancer, obesity, and type 2 diabetes. In our work, the way of combined ligand- and structure-based approach was applied to analyze the characteristics of PTP1B enzyme and its interaction with competitive inhibitors. Firstly, the pharmacophore model of PTP1B inhibitors was built based on the common feature of sixteen compounds. It was found that the pharmacophore model consisted of five chemical features: one aromatic ring (R) region, two hydrophobic (H) groups, and two hydrogen bond acceptors (A). To further elucidate the binding modes of these inhibitors with PTP1B active sites, four docking programs (AutoDock 4.0, AutoDock Vina 1.0, standard precision (SP) Glide 9.7, and extra precision (XP) Glide 9.7) were used. The characteristics of the active sites were then described by the conformations of the docking results. In conclusion, a combination of various pharmacophore features and the integration information of structure activity relationship (SAR) can be used to design novel potent PTP1B inhibitors.
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Weddell JC, Chen S, Imoukhuede PI. VEGFR1 promotes cell migration and proliferation through PLCγ and PI3K pathways. NPJ Syst Biol Appl 2017; 4:1. [PMID: 29263797 PMCID: PMC5736688 DOI: 10.1038/s41540-017-0037-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 11/08/2017] [Accepted: 11/21/2017] [Indexed: 12/16/2022] Open
Abstract
The ability to control vascular endothelial growth factor (VEGF) signaling offers promising therapeutic potential for vascular diseases and cancer. Despite this promise, VEGF-targeted therapies are not clinically effective for many pathologies, such as breast cancer. VEGFR1 has recently emerged as a predictive biomarker for anti-VEGF efficacy, implying a functional VEGFR1 role beyond its classically defined decoy receptor status. Here we introduce a computational approach that accurately predicts cellular responses elicited via VEGFR1 signaling. Aligned with our model prediction, we show empirically that VEGFR1 promotes macrophage migration through PLCγ and PI3K pathways and promotes macrophage proliferation through a PLCγ pathway. These results provide new insight into the basic function of VEGFR1 signaling while offering a computational platform to quantify signaling of any receptor.
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Affiliation(s)
- Jared C. Weddell
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Si Chen
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - P. I. Imoukhuede
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
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25
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Zhang X, Yang S, Li X, Zhu P, Xie E, Li Z. Expression, purification, and characterization of a novel acid phosphatase that displays protein tyrosine phosphatases activity from Metarhizium anisopliae strain CQMa102. Biosci Biotechnol Biochem 2017; 81:2292-2300. [DOI: 10.1080/09168451.2017.1378087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Abstract
The protein tyrosine phosphatase (PTPase) plays an important role in insect immune system. Our group has purified a type of acid phosphatase that could specifically dephosphorylate trans-Golgi p230 in vitro. In order to study this phosphatase further, we have identified and cloned the phosphatase gene from a locust specific Metarhizium anisopliae Strain CQMa102. The CQMa102 phosphatase was expressed in Pichia pastoris to verify its protease activity. The molecular weight (MW) and the isoelectric point (pI) of the phosphatase were about 85 kDa and 6.15, respectively. Substrate specificity evaluation showed that the purified enzyme exhibited high activity on O-phospho-L-tyrosine. At its optimal pH of 6.5 and optimum temperature of 70 °C, the protein showed the highest activity respectively. It can be activated by Ca2+, Mg2+, Mn2+, Ba2+, Co2+ and phosphate analogs, but inhibited by Zn2+, Cu2+, fluoride, dithiothreitol, β-mercaptoethanol and N-ethylmaleimide.
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Affiliation(s)
- Xue Zhang
- Chongqing Key Laboratory of Soil Multi-scale Interfacial Process, College of Resources and Environment, Southwest University, Chongqing, China
| | - Shuiying Yang
- College of Plant Protection, Southwest University, Chongqing, China
| | - Xinqiang Li
- Chongqing Key Laboratory of Soil Multi-scale Interfacial Process, College of Resources and Environment, Southwest University, Chongqing, China
| | - Pei Zhu
- Chongqing Key Laboratory of Soil Multi-scale Interfacial Process, College of Resources and Environment, Southwest University, Chongqing, China
| | - Enyu Xie
- Chongqing Key Laboratory of Soil Multi-scale Interfacial Process, College of Resources and Environment, Southwest University, Chongqing, China
| | - Zhenlun Li
- Chongqing Key Laboratory of Soil Multi-scale Interfacial Process, College of Resources and Environment, Southwest University, Chongqing, China
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Sacchetti C, Bottini N. Protein Tyrosine Phosphatases in Systemic Sclerosis: Potential Pathogenic Players and Therapeutic Targets. Curr Rheumatol Rep 2017; 19:28. [PMID: 28397126 DOI: 10.1007/s11926-017-0655-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
PURPOSE OF REVIEW The pathogenesis of systemic sclerosis depends on a complex interplay between autoimmunity, vasculopathy, and fibrosis. Reversible phosphorylation on tyrosine residues, in response to growth factors and other stimuli, critically regulates each one of these three key pathogenic processes. Protein tyrosine kinases, the enzymes that catalyze addition of phosphate to tyrosine residues, are known players in systemic sclerosis, and tyrosine kinase inhibitors are undergoing clinical trials for treatment of this disease. Until recently, the role of tyrosine phosphatases-the enzymes that counteract the action of tyrosine kinases by removing phosphate from tyrosine residues-in systemic sclerosis has remained largely unknown. Here, we review the function of tyrosine phosphatases in pathways relevant to the pathogenesis of systemic sclerosis and their potential promise as therapeutic targets to halt progression of this debilitating rheumatic disease. RECENT FINDINGS Protein tyrosine phosphatases are emerging as important regulators of a multitude of signaling pathways and undergoing validation as molecular targets for cancer and other common diseases. Recent advances in drug discovery are paving the ways to develop new classes of tyrosine phosphatase modulators to treat human diseases. Although so far only few reports have focused on tyrosine phosphatases in systemic sclerosis, these enzymes play a role in multiple pathways relevant to disease pathogenesis. Further studies in this field are warranted to explore the potential of tyrosine phosphatases as drug targets for systemic sclerosis.
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Affiliation(s)
- Cristiano Sacchetti
- Division of Rheumatology, Allergy and Immunology, Department of Medicine, University of California, San Diego, 9500 Gilman Drive MC #0656, La Jolla, CA, 92093, USA
| | - Nunzio Bottini
- Division of Rheumatology, Allergy and Immunology, Department of Medicine, University of California, San Diego, 9500 Gilman Drive MC #0656, La Jolla, CA, 92093, USA.
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27
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Siqueira JD, Menegatti AC, Terenzi H, Pereira MB, Roman D, Rosso EF, Piquini PC, Iglesias BA, Back DF. Synthesis, characterization and phosphatase inhibitory activity of dioxidovanadium(V) complexes with Schiff base ligands derived from pyridoxal and resorcinol. Polyhedron 2017. [DOI: 10.1016/j.poly.2017.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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28
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Chicote JU, DeSalle R, García-España A. Phosphotyrosine phosphatase R3 receptors: Origin, evolution and structural diversification. PLoS One 2017; 12:e0172887. [PMID: 28257417 PMCID: PMC5336234 DOI: 10.1371/journal.pone.0172887] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 02/10/2017] [Indexed: 11/18/2022] Open
Abstract
Subtype R3 phosphotyrosine phosphatase receptors (R3 RPTPs) are single-spanning membrane proteins characterized by a unique modular composition of extracellular fibronectin repeats and a single cytoplasmatic protein tyrosine phosphatase (PTP) domain. Vertebrate R3 RPTPs consist of five members: PTPRB, PTPRJ, PTPRH and PTPRO, which dephosphorylate tyrosine residues, and PTPRQ, which dephosphorylates phophoinositides. R3 RPTPs are considered novel therapeutic targets in several pathologies such as ear diseases, nephrotic syndromes and cancer. R3 RPTP vertebrate receptors, as well as their known invertebrate counterparts from animal models: PTP52F, PTP10D and PTP4e from the fruitfly Drosophila melanogaster and F44G4.8/DEP-1 from the nematode Caenorhabditis elegans, participate in the regulation of cellular activities including cell growth and differentiation. Despite sharing structural and functional properties, the evolutionary relationships between vertebrate and invertebrate R3 RPTPs are not fully understood. Here we gathered R3 RPTPs from organisms covering a broad evolutionary distance, annotated their structure and analyzed their phylogenetic relationships. We show that R3 RPTPs (i) have probably originated in the common ancestor of animals (metazoans), (ii) are variants of a single ancestral gene in protostomes (arthropods, annelids and nematodes); (iii) a likely duplication of this ancestral gene in invertebrate deuterostomes (echinodermes, hemichordates and tunicates) generated the precursors of PTPRQ and PTPRB genes, and (iv) R3 RPTP groups are monophyletic in vertebrates and have specific conserved structural characteristics. These findings could have implications for the interpretation of past studies and provide a framework for future studies and functional analysis of this important family of proteins.
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Affiliation(s)
- Javier U. Chicote
- Hospital Universitari de Tarragona Joan XXIII, Institut d’Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Tarragona, Spain
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NewYork, United States of America
| | - Antonio García-España
- Hospital Universitari de Tarragona Joan XXIII, Institut d’Investigació Sanitària Pere Virgili, Universitat Rovira i Virgili, Tarragona, Spain
- * E-mail:
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29
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Schneble N, Müller J, Kliche S, Bauer R, Wetzker R, Böhmer FD, Wang ZQ, Müller JP. The protein-tyrosine phosphatase DEP-1 promotes migration and phagocytic activity of microglial cells in part through negative regulation of fyn tyrosine kinase. Glia 2016; 65:416-428. [DOI: 10.1002/glia.23100] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 10/28/2016] [Accepted: 10/31/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Nadine Schneble
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine (CMB), Jena University Hospital; Hans-Knöll-Straße 2 Jena Germany
- Leibniz Institute on Aging; Beutenberstraße 11 Jena Germany
| | - Julia Müller
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine (CMB), Jena University Hospital; Hans-Knöll-Straße 2 Jena Germany
| | - Stefanie Kliche
- Institute for Molecular and Clinical Immunology, Medical Faculty, Otto-von-Guericke-University; Leipziger Str. 44 Magdeburg Germany
| | - Reinhard Bauer
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine (CMB), Jena University Hospital; Hans-Knöll-Straße 2 Jena Germany
| | - Reinhard Wetzker
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine (CMB), Jena University Hospital; Hans-Knöll-Straße 2 Jena Germany
| | - Frank-D. Böhmer
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine (CMB), Jena University Hospital; Hans-Knöll-Straße 2 Jena Germany
| | - Zhao-Qi Wang
- Leibniz Institute on Aging; Beutenberstraße 11 Jena Germany
| | - Jörg P. Müller
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine (CMB), Jena University Hospital; Hans-Knöll-Straße 2 Jena Germany
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Sharma AK, Arora D, Singh LK, Gangwal A, Sajid A, Molle V, Singh Y, Nandicoori VK. Serine/Threonine Protein Phosphatase PstP of Mycobacterium tuberculosis Is Necessary for Accurate Cell Division and Survival of Pathogen. J Biol Chem 2016; 291:24215-24230. [PMID: 27758870 DOI: 10.1074/jbc.m116.754531] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Indexed: 02/06/2023] Open
Abstract
Protein phosphatases play vital roles in phosphorylation-mediated cellular signaling. Although there are 11 serine/threonine protein kinases in Mycobacterium tuberculosis, only one serine/threonine phosphatase, PstP, has been identified. Although PstP has been biochemically characterized and multiple in vitro substrates have been identified, its physiological role has not yet been elucidated. In this study, we have investigated the impact of PstP on cell growth and survival of the pathogen in the host. Overexpression of PstP led to elongated cells and partially compromised survival. We find that depletion of PstP is detrimental to cell survival, eventually leading to cell death. PstP depletion results in elongated multiseptate cells, suggesting a role for PstP in regulating cell division events. Complementation experiments performed with PstP deletion mutants revealed marginally compromised survival, suggesting that all of the domains, including the extracellular domain, are necessary for complete rescue. On the other hand, the catalytic activity of PstP is absolutely essential for the in vitro growth. Mice infection experiments establish a definitive role for PstP in pathogen survival within the host. Depletion of PstP from established infections causes pathogen clearance, indicating that the continued presence of PstP is necessary for pathogen survival. Taken together, our data suggest an important role for PstP in establishing and maintaining infection, possibly via the modulation of cell division events.
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Affiliation(s)
- Aditya K Sharma
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India.,the Academy of Scientific and Innovative Research (AcSIR), CSIR-IGIB, Delhi-110025, India
| | - Divya Arora
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Lalit K Singh
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India
| | - Aakriti Gangwal
- the Department of Zoology, University of Delhi Delhi-110007, India
| | - Andaleeb Sajid
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India
| | - Virginie Molle
- the Laboratoire de Dynamique des Interactions Membranaires Normales et Pathologiques, Université Montpellier 2, CNRS, UMR 5235, Montpellier, France, and
| | - Yogendra Singh
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi-110007, India, .,the Department of Zoology, University of Delhi Delhi-110007, India
| | - Vinay Kumar Nandicoori
- From the National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi-110067, India,
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31
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Aurintricarboxylic acid structure modifications lead to reduction of inhibitory properties against virulence factor YopH and higher cytotoxicity. World J Microbiol Biotechnol 2016; 32:163. [PMID: 27562597 PMCID: PMC4999467 DOI: 10.1007/s11274-016-2123-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 08/08/2016] [Indexed: 01/14/2023]
Abstract
Yersinia sp. bacteria owe their viability and pathogenic virulence to the YopH factor, which is a highly active bacterial protein tyrosine phosphatase. Inhibition of YopH phosphatase results in the lack of Yersinia sp. pathogenicity. We have previously described that aurintricarboxylic acid inhibits the activity of YopH at nanomolar concentrations and represents a unique mechanism of YopH inactivation due to a redox process. This work is a continuation of our previous studies. Here we show that modifications of the structure of aurintricarboxylic acid reduce the ability to inactivate YopH and lead to higher cytotoxicity. In the present paper we examine the inhibitory properties of aurintricarboxylic acid analogues, such as eriochrome cyanine R (ECR) and pararosaniline. Computational docking studies we report here indicate that ATA analogues are not precluded to bind in the YopH active site and in all obtained binding conformations ECR and pararosaniline bind to YopH active site. The free binding energy calculations show that ECR has a stronger binding affinity to YopH than pararosaniline, which was confirmed by experimental YopH enzymatic activity studies. We found that ATA analogues can reversibly reduce the enzymatic activity of YopH, but possess weaker inhibitory properties than ATA. The ATA analogues induced inactivation of YopH is probably due to oxidative mechanism, as pretreatment with catalase prevents from inhibition. We also found that ATA analogues significantly decrease the viability of macrophage cells, especially pararosaniline, while ATA reveals only slight effect on cell viability.
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32
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Crystallization of PTP Domains. Methods Mol Biol 2016. [PMID: 27514806 DOI: 10.1007/978-1-4939-3746-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Protein crystallography is the most powerful method to obtain atomic resolution information on the three-dimensional structure of proteins. An essential step towards determining the crystallographic structure of a protein is to produce good quality crystals from a concentrated sample of purified protein. These crystals are then used to obtain X-ray diffraction data necessary to determine the 3D structure by direct phasing or molecular replacement if the model of a homologous protein is available. Here, we describe the main approaches and techniques to obtain suitable crystals for X-ray diffraction. We include tools and guidance on how to evaluate and design the protein construct, how to prepare Se-methionine derivatized protein, how to assess the stability and quality of the sample, and how to crystallize and prepare crystals for diffraction experiments. While general strategies for protein crystallization are summarized, specific examples of the application of these strategies to the crystallization of PTP domains are discussed.
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Aberrant protein phosphorylation in Alzheimer disease brain disturbs pro-survival and cell death pathways. Biochim Biophys Acta Mol Basis Dis 2016; 1862:1871-82. [PMID: 27425034 DOI: 10.1016/j.bbadis.2016.07.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 06/22/2016] [Accepted: 07/13/2016] [Indexed: 12/31/2022]
Abstract
Protein phosphorylation of serine, threonine, and tyrosine residues is one of the most prevalent post-translational modifications fundamental in mediating diverse cellular functions in living cells. Aberrant protein phosphorylation is currently recognized as a critical step in the pathogenesis and progression of Alzheimer disease (AD). Changes in the pattern of protein phosphorylation of different brain regions are suggested to promote AD transition from a presymptomatic to a symptomatic state in response to accumulating amyloid β-peptide (Aβ). Several experimental approaches have been utilized to profile alteration of protein phosphorylation in the brain, including proteomics. Among central pathways regulated by kinases/phosphatases those involved in the activation/inhibition of both pro survival and cell death pathways play a central role in AD pathology. We discuss in detail how aberrant phosphorylation could contribute to dysregulate p53 activity and insulin-mediated signaling. Taken together these results highlight that targeted therapeutic intervention, which can restore phosphorylation homeostasis, either acting on kinases and phosphatases, conceivably may prove to be beneficial to prevent or slow the development and progression of AD.
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Kuban-Jankowska A, Sahu KK, Niedzialkowski P, Gorska M, Tuszynski JA, Ossowski T, Wozniak M. Redox process is crucial for inhibitory properties of aurintricarboxylic acid against activity of YopH: virulence factor of Yersinia pestis. Oncotarget 2016; 6:18364-73. [PMID: 26286963 PMCID: PMC4621896 DOI: 10.18632/oncotarget.4625] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/09/2015] [Indexed: 01/14/2023] Open
Abstract
YopH is a bacterial protein tyrosine phosphatase, which is essential for the viability and pathogenic virulence of the plague-causing Yersinia sp. bacteria. Inactivation of YopH activity would lead to the loss of bacterial pathogenicity. We have studied the inhibitory properties of aurintricarboxylic acid (ATA) against YopH phosphatase and found that at nanomolar concentrations ATA reversibly decreases the activity of YopH. Computational docking studies indicated that in all binding poses ATA binds in the YopH active site. Molecular dynamics simulations showed that in the predicted binding pose, ATA binds to the essential Cys403 and Arg409 residues in the active site and has a stronger binding affinity than the natural substrate (pTyr). The cyclic voltammetry experiments suggest that ATA reacts remarkably strongly with molecular oxygen. Additionally, the electrochemical reduction of ATA in the presence of a negative potential from −2.0 to 2.5 V generates a current signal, which is observed for hydrogen peroxide. Here we showed that ATA indicates a unique mechanism of YopH inactivation due to a redox process. We proposed that the potent inhibitory properties of ATA are a result of its strong binding in the YopH active site and in situ generation of hydrogen peroxide near catalytic cysteine residue.
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Affiliation(s)
| | - Kamlesh K Sahu
- Department of Physics, University of Alberta, Edmonton, Canada.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Pawel Niedzialkowski
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Magdalena Gorska
- Department of Medical Chemistry, Medical University of Gdansk, Gdansk, Poland
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, Edmonton, Canada.,Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Canada
| | - Tadeusz Ossowski
- Department of Analytical Chemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Michal Wozniak
- Department of Medical Chemistry, Medical University of Gdansk, Gdansk, Poland
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35
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Li H, Li W, Liu F, Wang Z, Li G, Karamanos Y. Detection of Tumor Invasive Biomarker using a Peptamer of Signal Conversion and Signal Amplification. Anal Chem 2016; 88:3662-8. [PMID: 26938572 DOI: 10.1021/acs.analchem.5b04423] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Inspired by the structural and functional features of proteins in cell signaling, a switchable peptide is designed in this work. This switchable peptide is named a "peptamer," and it can react to ligand binding with conformational change and activation/deactivation of catalytic ability. The peptamer is constructed by elaborately integrating several different peptide motifs with targeting and catalytic abilities. Thus, targeted binding of the peptamer to an integrin can be regulated by a synthetic ligand. Moreover, the conformational rearrangement of the peptamer induced by both integrin and the synthetic ligand can resolve in altered affinity of the peptamer for a catalytic cofactor, cupric ion. This leads to greatly contrasted efficiency of catalysis in the presence/absence of integrin. This distinct switching on/off of catalytic activity also enables a bioassay of tissue integrin expression in clinical samples of thyroid carcinoma. Experimental results reveal that the detected integrin level parallels the state of lymph node metastasis. Therefore, this simple peptide model may help to understand the structural reconfiguration of proteins involved in cellular signal transduction, as well as to provide a new means to assess protein activity under pathological conditions such as cancer.
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Affiliation(s)
- Hao Li
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, China
| | - Weiwei Li
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, China
| | - Fengzhen Liu
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University , Nanjing 210011, China
| | - Zhaoxia Wang
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University , Nanjing 210011, China
| | - Genxi Li
- State Key Laboratory of Pharmaceutical Biotechnology and Collaborative Innovation Center of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University , Nanjing 210093, China.,Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University , Shanghai 200444, China
| | - Yannis Karamanos
- Laboratoire de la Barrière Hémato-encéphalique, Faculté des Sciences, Université d'Artois , rue Souvraz SP18, 62307 CEDEX Lens, France
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36
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Cook NL, Moeke CH, Fantoni LI, Pattison DI, Davies MJ. The myeloperoxidase-derived oxidant hypothiocyanous acid inhibits protein tyrosine phosphatases via oxidation of key cysteine residues. Free Radic Biol Med 2016; 90:195-205. [PMID: 26616646 DOI: 10.1016/j.freeradbiomed.2015.11.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 11/13/2015] [Accepted: 11/20/2015] [Indexed: 12/31/2022]
Abstract
Phosphorylation of protein tyrosine residues is critical to cellular processes, and is regulated by kinases and phosphatases (PTPs). PTPs contain a redox-sensitive active site Cys residue, which is readily oxidized. Myeloperoxidase, released from activated leukocytes, catalyzes thiocyanate ion (SCN(-)) oxidation by H2O2 to form hypothiocyanous acid (HOSCN), an oxidant that targets Cys residues. Dysregulated phosphorylation and elevated MPO levels have been associated with chronic inflammatory diseases where HOSCN can be generated. Previous studies have shown that HOSCN inhibits isolated PTP1B and induces cellular dysfunction in cultured macrophage-like cells. The present study extends this previous work and shows that physiologically-relevant concentrations of HOSCN alter the activity and structure of other members of the wider PTP family (including leukocyte antigen-related PTP, PTP-LAR; T-cell PTP, TC-PTP; CD45 and Src homology phosphatase-1, Shp-1) by targeting Cys residues. Isolated PTP activity, and activity in lysates of human monocyte-derived macrophages (HMDM) was inhibited by 0-100 µM HOSCN with this being accompanied by reversible oxidation of Cys residues, formation of sulfenic acids or sulfenyl-thiocyanates (detected by Western blotting, and LC-MS as dimedone adducts), and structural changes. LC-MS/MS peptide mass-mapping has provided data on the modified Cys residues in PTP-LAR. This study indicates that inflammation-induced oxidants, and particularly myeloperoxidase-derived species, can modulate the activity of multiple members of the PTP superfamily via oxidation of Cys residues to sulfenic acids. This alteration of the balance of PTP/kinase activity may perturb protein phosphorylation and disrupt cell signaling with subsequent induction of apoptosis at sites of inflammation.
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Affiliation(s)
- Naomi L Cook
- The Heart Research Institute, Newtown, Sydney, NSW 2042, Australia
| | - Cassidy H Moeke
- The Heart Research Institute, Newtown, Sydney, NSW 2042, Australia; Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Luca I Fantoni
- The Heart Research Institute, Newtown, Sydney, NSW 2042, Australia
| | - David I Pattison
- The Heart Research Institute, Newtown, Sydney, NSW 2042, Australia; Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Michael J Davies
- The Heart Research Institute, Newtown, Sydney, NSW 2042, Australia; Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia; Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Building 4.5, Blegdamsvej 3, DK-2200 Copenhagen, Denmark.
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37
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Alonso A, Pulido R. The extended human PTPome: a growing tyrosine phosphatase family. FEBS J 2015; 283:1404-29. [PMID: 26573778 DOI: 10.1111/febs.13600] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 10/02/2015] [Accepted: 11/13/2015] [Indexed: 12/13/2022]
Abstract
Tyr phosphatases are, by definition, enzymes that dephosphorylate phospho-Tyr (pTyr) from proteins. This activity is found in several structurally diverse protein families, including the protein Tyr phosphatase (PTP), arsenate reductase, rhodanese, haloacid dehalogenase (HAD) and His phosphatase (HP) families. Most of these families include members with substrate specificity for non-pTyr substrates, such as phospho-Ser/phospho-Thr, phosphoinositides, phosphorylated carbohydrates, mRNAs, or inorganic moieties. A Cys is essential for catalysis in PTPs, rhodanese and arsenate reductase enzymes, whereas this work is performed by an Asp in HAD phosphatases and by a His in HPs, via a catalytic mechanism shared by all of the different families. The category that contains most Tyr phosphatases is the PTP family, which, although it received its name from this activity, includes Ser, Thr, inositide, carbohydrate and RNA phosphatases, as well as some inactive pseudophosphatase proteins. Here, we propose an extended collection of human Tyr phosphatases, which we call the extended human PTPome. The addition of new members (SACs, paladin, INPP4s, TMEM55s, SSU72, and acid phosphatases) to the currently categorized PTP group of enzymes means that the extended human PTPome contains up to 125 proteins, of which ~ 40 are selective for pTyr. We set criteria to ascribe proteins to the extended PTPome, and summarize the more important features of the new PTPome members in the context of their phosphatase activity and their relationship with human disease.
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Affiliation(s)
- Andrés Alonso
- Instituto de Biología y Genética Molecular (IBGM), CSIC-Universidad de Valladolid, Valladolid, Spain
| | - Rafael Pulido
- Biocruces Health Research Institute, Barakaldo, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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Varughese EA, Kasper S, Anneken EM, Yadav JS. SHP-2 Mediates Cryptosporidium parvum Infectivity in Human Intestinal Epithelial Cells. PLoS One 2015; 10:e0142219. [PMID: 26556238 PMCID: PMC4640876 DOI: 10.1371/journal.pone.0142219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/19/2015] [Indexed: 01/17/2023] Open
Abstract
The parasite, Cryptosporidium parvum, induces human gastroenteritis through infection of host epithelial cells in the small intestine. During the initial stage of infection, C. parvum is reported to engage host mechanisms at the host cell-parasite interface to form a parasitophorous vacuole. We determined that upon infection, the larger molecular weight proteins in human small intestinal epithelial host cells (FHs 74 Int) appeared to globally undergo tyrosine dephosphorylation. In parallel, expression of the cytoplasmic protein tyrosine phosphatase Src homology-2 domain-containing phosphatase 2 (SHP-2) increased in a time-dependent manner. SHP-2 co-localized with the C. parvum sporozoite and this interaction increased the rate of C. parvum infectivity through SH2-mediated SHP-2 activity. Furthermore, we show that one potential target that SHP-2 acts upon is the focal adhesion protein, paxillin, which undergoes moderate dephosphorylation following infection, with inhibition of SHP-2 rescuing paxillin phosphorylation. Importantly, treatment with an inhibitor to SHP-2 and with an inhibitor to paxillin and Src family kinases, effectively decreased the multiplicity of C. parvum infection in a dose-dependent manner. Thus, our study reveals an important role for SHP-2 in the pathogenesis of C. parvum. Furthermore, while host proteins can be recruited to participate in the development of the electron dense band at the host cell-parasite interface, our study implies for the first time that SHP-2 appears to be recruited by the C. parvum sporozoite to regulate infectivity. Taken together, these findings suggest that SHP-2 and its down-stream target paxillin could serve as targets for intervention.
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Affiliation(s)
- Eunice A. Varughese
- Division of Environmental Genetics and Molecular Toxicology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- National Exposure Research Laboratory, United States Environmental Protection Agency, Cincinnati, Ohio, United States of America
- * E-mail: (EAV); (JSY)
| | - Susan Kasper
- Division of Environmental Genetics and Molecular Toxicology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Emily M. Anneken
- National Exposure Research Laboratory, United States Environmental Protection Agency, Cincinnati, Ohio, United States of America
| | - Jagjit S. Yadav
- Division of Environmental Genetics and Molecular Toxicology, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- * E-mail: (EAV); (JSY)
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Romá-Mateo C, Aguado C, García-Giménez JL, Knecht E, Sanz P, Pallardó FV. Oxidative stress, a new hallmark in the pathophysiology of Lafora progressive myoclonus epilepsy. Free Radic Biol Med 2015; 88:30-41. [PMID: 25680286 DOI: 10.1016/j.freeradbiomed.2015.01.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 01/16/2015] [Accepted: 01/28/2015] [Indexed: 12/12/2022]
Abstract
Lafora disease (LD; OMIM 254780, ORPHA501) is a devastating neurodegenerative disorder characterized by the presence of glycogen-like intracellular inclusions called Lafora bodies and caused, in most cases, by mutations in either the EPM2A or the EPM2B gene, encoding respectively laforin, a phosphatase with dual specificity that is involved in the dephosphorylation of glycogen, and malin, an E3-ubiquitin ligase involved in the polyubiquitination of proteins related to glycogen metabolism. Thus, it has been reported that laforin and malin form a functional complex that acts as a key regulator of glycogen metabolism and that also plays a crucial role in protein homeostasis (proteostasis). Regarding this last function, it has been shown that cells are more sensitive to ER stress and show defects in proteasome and autophagy activities in the absence of a functional laforin-malin complex. More recently, we have demonstrated that oxidative stress accompanies these proteostasis defects and that various LD models show an increase in reactive oxygen species and oxidative stress products together with a dysregulated antioxidant enzyme expression and activity. In this review we discuss possible connections between the multiple defects in protein homeostasis present in LD and oxidative stress.
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Affiliation(s)
- Carlos Romá-Mateo
- Fundación Investigación Clinico de Valencia, Instituto de Investigación Sanitaria, Valencia, Spain; Department of Physiology, School of Medicine and Dentistry, University of Valencia, E46010 Valencia, Spain
| | - Carmen Aguado
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain; Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - José Luis García-Giménez
- Fundación Investigación Clinico de Valencia, Instituto de Investigación Sanitaria, Valencia, Spain; Department of Physiology, School of Medicine and Dentistry, University of Valencia, E46010 Valencia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain
| | - Erwin Knecht
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain; Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Pascual Sanz
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain; Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Federico V Pallardó
- Fundación Investigación Clinico de Valencia, Instituto de Investigación Sanitaria, Valencia, Spain; Department of Physiology, School of Medicine and Dentistry, University of Valencia, E46010 Valencia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain.
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Martins PGA, Mori M, Chiaradia-Delatorre LD, Menegatti ACO, Mascarello A, Botta B, Benítez J, Gambino D, Terenzi H. Exploring Oxidovanadium(IV) Complexes as YopH Inhibitors: Mechanism of Action and Modeling Studies. ACS Med Chem Lett 2015; 6:1035-40. [PMID: 26617957 PMCID: PMC4641580 DOI: 10.1021/acsmedchemlett.5b00267] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/31/2015] [Indexed: 12/13/2022] Open
Abstract
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YopH
tyrosine phosphatase, a virulence factor produced by pathogenic species
of Yersinia, is an attractive drug target. In this
work, three oxidovanadium(IV) complexes were assayed against recombinant
YopH and showed strong inhibition of the enzyme in the nanomolar range.
Molecular modeling indicated that their binding is reinforced by H-bond,
cation−π, and π–π interactions conferring
specificity toward YopH. These complexes are thus interesting lead
molecules for phosphatase inhibitor drug discovery.
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Affiliation(s)
- Priscila G. A. Martins
- Centro
de Biologia Molecular Estrutural−CEBIME, Universidade Federal de Santa Catarina, Campus Trindade, 88040-900 Florianópolis, Santa Catarina, Brasil
| | - Mattia Mori
- Center
for Life NanoScience@Sapienza, Istituto Italiano di Tecnologia, viale Regina Elena 291, 00161 Roma, Italy
| | - Louise D. Chiaradia-Delatorre
- Centro
de Biologia Molecular Estrutural−CEBIME, Universidade Federal de Santa Catarina, Campus Trindade, 88040-900 Florianópolis, Santa Catarina, Brasil
| | - Angela C. O. Menegatti
- Centro
de Biologia Molecular Estrutural−CEBIME, Universidade Federal de Santa Catarina, Campus Trindade, 88040-900 Florianópolis, Santa Catarina, Brasil
| | - Alessandra Mascarello
- Centro
de Biologia Molecular Estrutural−CEBIME, Universidade Federal de Santa Catarina, Campus Trindade, 88040-900 Florianópolis, Santa Catarina, Brasil
- Dipartimento di Chimica
e Tecnologia del Farmaco, Sapienza, Università di Roma, Piazzale Aldo
Moro 5, 00185 Roma, Italy
| | - Bruno Botta
- Dipartimento di Chimica
e Tecnologia del Farmaco, Sapienza, Università di Roma, Piazzale Aldo
Moro 5, 00185 Roma, Italy
| | - Julio Benítez
- Cátedra de Química Inorgánica,
Facultad de Química, Universidad de la República, Gral. Flores 2124, 11800 Montevideo, Uruguay
| | - Dinorah Gambino
- Cátedra de Química Inorgánica,
Facultad de Química, Universidad de la República, Gral. Flores 2124, 11800 Montevideo, Uruguay
| | - Hernán Terenzi
- Centro
de Biologia Molecular Estrutural−CEBIME, Universidade Federal de Santa Catarina, Campus Trindade, 88040-900 Florianópolis, Santa Catarina, Brasil
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McLauchlan CC, Peters BJ, Willsky GR, Crans DC. Vanadium–phosphatase complexes: Phosphatase inhibitors favor the trigonal bipyramidal transition state geometries. Coord Chem Rev 2015. [DOI: 10.1016/j.ccr.2014.12.012] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Samofalova DA, Karpov PA, Blume YB. Bioinformatic comparison of human and higher plant phosphatomes. CYTOL GENET+ 2015. [DOI: 10.3103/s0095452715040088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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A RP-UFLC Assay for Protein Tyrosine Phosphatases: Focus on Protein Tyrosine Phosphatase Non-Receptor Type 2 (PTPN2). Sci Rep 2015; 5:10750. [PMID: 26040922 PMCID: PMC4455150 DOI: 10.1038/srep10750] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/30/2015] [Indexed: 11/08/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) are involved in numerous signaling pathways and dysfunctions of certain of these enzymes have been linked to several human diseases including cancer and autoimmune diseases. PTPN2 is a PTP mainly expressed in hematopoietic cells and involved in growth factor and JAK/STAT signaling pathways. Loss of function analyses in patients with mutation/deletion of the PTPN2 gene and knock-out mouse models indicate that PTPN2 acts as a tumor suppressor in T-cell malignancies and as a regulator of inflammation and immunity. The use of sensitive and quantitative assays is of prime importance to better characterize the biochemical properties of PTPN2 and its biological roles. We report a highly sensitive non-radioactive assay that allows the measurement of the activity of purified PTPN2 and of endogenous PTPN2 immunoprecipitated on agarose beads. The assay relies on separation and quantitation by reverse-phase ultra fast liquid chromatography (RP-UFLC) of a fluorescein-labeled phosphotyrosine peptide substrate derived from the sequence of STAT1. The applicability and reliability of this approach is supported by kinetic and mechanistic studies using PTP inhibitors. More broadly, our PTPN2 assay provides the basis for the design of flexible methods for the measurement of other PTPs.
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Kant S, Agarwal S, Pancholi P, Pancholi V. TheStreptococcus pyogenesorphan protein tyrosine phosphatase, SP-PTP, possesses dual specificity and essential virulence regulatory functions. Mol Microbiol 2015; 97:515-40. [DOI: 10.1111/mmi.13047] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2015] [Indexed: 01/06/2023]
Affiliation(s)
- Sashi Kant
- Department of Pathology; The Ohio State University College of Medicine; Wexner Medical Center; Columbus OH USA
| | - Shivani Agarwal
- Department of Pathology; The Ohio State University College of Medicine; Wexner Medical Center; Columbus OH USA
| | - Preeti Pancholi
- Department of Pathology; The Ohio State University College of Medicine; Wexner Medical Center; Columbus OH USA
| | - Vijay Pancholi
- Department of Pathology; The Ohio State University College of Medicine; Wexner Medical Center; Columbus OH USA
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45
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Zhen XL, Yin WH, Tian X, Ma ZJ, Fan SM, Han JR, Liu S. Synthesis and biological evaluation of open-chain analogs of cyclic peptides as inhibitors of cellular Shp2 activity. Bioorg Med Chem 2015; 23:2562-7. [DOI: 10.1016/j.bmc.2015.03.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 11/26/2022]
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46
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Victorino VJ, Mencalha AL, Panis C. Post-translational modifications disclose a dual role for redox stress in cardiovascular pathophysiology. Life Sci 2015; 129:42-7. [DOI: 10.1016/j.lfs.2014.11.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 11/03/2014] [Accepted: 11/11/2014] [Indexed: 02/07/2023]
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47
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Defelipe LA, Lanzarotti E, Gauto D, Marti MA, Turjanski AG. Protein topology determines cysteine oxidation fate: the case of sulfenyl amide formation among protein families. PLoS Comput Biol 2015; 11:e1004051. [PMID: 25741692 PMCID: PMC4351059 DOI: 10.1371/journal.pcbi.1004051] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 11/17/2014] [Indexed: 02/07/2023] Open
Abstract
Cysteine residues have a rich chemistry and play a critical role in the catalytic activity of a plethora of enzymes. However, cysteines are susceptible to oxidation by Reactive Oxygen and Nitrogen Species, leading to a loss of their catalytic function. Therefore, cysteine oxidation is emerging as a relevant physiological regulatory mechanism. Formation of a cyclic sulfenyl amide residue at the active site of redox-regulated proteins has been proposed as a protection mechanism against irreversible oxidation as the sulfenyl amide intermediate has been identified in several proteins. However, how and why only some specific cysteine residues in particular proteins react to form this intermediate is still unknown. In the present work using in-silico based tools, we have identified a constrained conformation that accelerates sulfenyl amide formation. By means of combined MD and QM/MM calculation we show that this conformation positions the NH backbone towards the sulfenic acid and promotes the reaction to yield the sulfenyl amide intermediate, in one step with the concomitant release of a water molecule. Moreover, in a large subset of the proteins we found a conserved beta sheet-loop-helix motif, which is present across different protein folds, that is key for sulfenyl amide production as it promotes the previous formation of sulfenic acid. For catalytic activity, in several cases, proteins need the Cysteine to be in the cysteinate form, i.e. a low pKa Cys. We found that the conserved motif stabilizes the cysteinate by hydrogen bonding to several NH backbone moieties. As cysteinate is also more reactive toward ROS we propose that the sheet-loop-helix motif and the constraint conformation have been selected by evolution for proteins that need a reactive Cys protected from irreversible oxidation. Our results also highlight how fold conservation can be correlated to redox chemistry regulation of protein function. Cysteine oxidation is emerging as a relevant regulatory mechanism of enzymatic function in the cell. Many proteins are protected from over oxidation by reactive oxygen species by the formation of a cyclic sulfenyl amide. Understanding how cyclic sulfenyl amide is formed and its dependence on protein structure is not only a basic question but necessary to predict which proteins may auto protect from over oxidation We describe a structural motif, which includes cysteine residues with a constrained conformation in a “forbidden” region of the Ramachandran plot plus a Beta-Cys-loop-helix motif, which has a reactive low pKa Cysteine and also enables to form the cyclic sulfenyl amide with a low activation barrier. Our QM/MM computations show that the cyclization reaction only occurs if the “forbidden” conformation is acquired by the Cysteine residue. This structural motif was identified at least in 7 PFAM families and 145 proteins with solved structure, showing that a large number of proteins could have the ability to go through such cyclic product preventing irreversible oxidation.
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Affiliation(s)
- Lucas A. Defelipe
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- INQUIMAE/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Buenos Aires, Argentina
| | - Esteban Lanzarotti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Diego Gauto
- INQUIMAE/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Buenos Aires, Argentina
| | - Marcelo A. Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- INQUIMAE/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Buenos Aires, Argentina
- * E-mail: (MAM); (AGT)
| | - Adrián G. Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
- INQUIMAE/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Buenos Aires, Argentina
- * E-mail: (MAM); (AGT)
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Alexander SPH, Benson HE, Faccenda E, Pawson AJ, Sharman JL, Spedding M, Peters JA, Harmar AJ. The Concise Guide to PHARMACOLOGY 2013/14: catalytic receptors. Br J Pharmacol 2014; 170:1676-705. [PMID: 24528241 PMCID: PMC3892291 DOI: 10.1111/bph.12449] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The Concise Guide to PHARMACOLOGY 2013/14 provides concise overviews of the key properties of over 2000 human drug targets with their pharmacology, plus links to an open access knowledgebase of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. The full contents can be found at http://onlinelibrary.wiley.com/doi/10.1111/bph.12444/full. Catalytic receptors are one of the seven major pharmacological targets into which the Guide is divided, with the others being G protein-coupled receptors, ligand-gated ion channels, ion channels, nuclear hormone receptors, transporters and enzymes. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. A new landscape format has easy to use tables comparing related targets. It is a condensed version of material contemporary to late 2013, which is presented in greater detail and constantly updated on the website www.guidetopharmacology.org, superseding data presented in previous Guides to Receptors and Channels. It is produced in conjunction with NC-IUPHAR and provides the official IUPHAR classification and nomenclature for human drug targets, where appropriate. It consolidates information previously curated and displayed separately in IUPHAR-DB and the Guide to Receptors and Channels, providing a permanent, citable, point-in-time record that will survive database updates.
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Affiliation(s)
- Stephen P H Alexander
- School of Life Sciences, University of Nottingham Medical School, Nottingham, NG7 2UH, UK
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Lee H, Yi JS, Lawan A, Min K, Bennett AM. Mining the function of protein tyrosine phosphatases in health and disease. Semin Cell Dev Biol 2014; 37:66-72. [PMID: 25263013 DOI: 10.1016/j.semcdb.2014.09.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 09/21/2014] [Indexed: 12/31/2022]
Abstract
Protein tyrosine phosphatases (PTPs) play a crucial role in the regulation of human health and it is now clear that PTP dysfunction is causal to a variety of human diseases. Research in the PTP field has accelerated dramatically over the last decade fueled by cutting-edge technologies in genomic and proteomic techniques. This system-wide non-biased approach when applied to the discovery of PTP function has led to the elucidation of new and unanticipated roles for the PTPs. These discoveries, driven by genomic and proteomic approaches, have uncovered novel PTP findings that range from those that describe fundamental cell signaling mechanisms to implications for PTPs as novel therapeutic targets for the treatment of human disease. This review will discuss how new PTP functions have been uncovered through studies that have utilized genomic and proteomic technologies and strategies.
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Affiliation(s)
- Hojin Lee
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Jae-Sung Yi
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Ahmed Lawan
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Kisuk Min
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA
| | - Anton M Bennett
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, USA; Program in Integrative Cell Signaling and Neurobiology of Metabolism, Yale University School of Medicine, New Haven, CT, USA.
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Pantazaka E, Papadimitriou E. Chondroitin sulfate-cell membrane effectors as regulators of growth factor-mediated vascular and cancer cell migration. Biochim Biophys Acta Gen Subj 2014; 1840:2643-50. [DOI: 10.1016/j.bbagen.2014.01.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 01/02/2014] [Accepted: 01/03/2014] [Indexed: 12/18/2022]
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