1
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Guerrero L, Ebrahim A, Riley BT, Kim M, Huang Q, Finke AD, Keedy DA. Pushed to extremes: distinct effects of high temperature versus pressure on the structure of STEP. Commun Biol 2024; 7:59. [PMID: 38216663 PMCID: PMC10786866 DOI: 10.1038/s42003-023-05609-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/20/2023] [Indexed: 01/14/2024] Open
Abstract
Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature versus. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Altogether, our work indicates that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.
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Affiliation(s)
- Liliana Guerrero
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
- PhD Program in Biochemistry, CUNY Graduate Center, New York, NY, 10016, USA
| | - Ali Ebrahim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
| | - Blake T Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
| | - Minyoung Kim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY, 14853, USA
| | - Aaron D Finke
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY, 14853, USA
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA.
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA.
- PhD Programs in Biochemistry, Biology, & Chemistry, CUNY Graduate Center, New York, NY, 10016, USA.
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2
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Zou F, Rao T, Chen W, Song T, Li T, Hu W, Li L, Yu W, Cheng F. DUSP2 affects bladder cancer prognosis by down-regulating MEK/ERK and P38 MAPK signaling pathways through PTPN7. Cell Signal 2023; 112:110893. [PMID: 37739277 DOI: 10.1016/j.cellsig.2023.110893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 09/17/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
BACKGROUND As one of the leading causes of cancer death worldwide, bladder cancer (BCa) ranks 12th in incidence rate. Dual Specific Phosphatase 2 (DUSP2) is a member of the bispecific protein phosphatase subfamily. DUSP2 is closely related to the prognosis of cancer, but the role of DUSP2 in bladder cancer is still unclear. This study aims to explore how DUSP2 affects the prognosis of bladder cancer and clarify the important mechanism in bladder cancer. METHODS Bioinformatics and experiments have detected the anti-tumor effect of DUSP2. Construct a DUSP2 overexpression cell model, and then use protein blotting experiments to verify the efficiency of transfection. The effects of DUSP2 on proliferation, metastasis, apoptosis, epithelial mesenchymal transition (EMT) and immune invasion of bladder cancer cells were detected in vitro or in vivo. In addition, the mechanism of DUSP2 regulating MEK/ERK through PTPN7 pathway and P38 MAPK inhibiting the progression of bladder cancer was also discussed. RESULTS The expression of DUSP2 was down regulated in bladder cancer samples and cell lines. The overexpression of DUSP2 inhibits the proliferation, metastasis and immune microenvironment of bladder cancer cells. In addition, we confirmed that DUSP2 regulates MEK/ERK and P38 MAPK through PTPN7 pathway to inhibit the progression of bladder cancer. CONCLUSION DUSP2 inhibits the progression of bladder cancer by regulating PTPN7. These results suggest that DUSP2/PTPN7/MEK/ERK pathway may become a new therapeutic target for bladder cancer.
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Affiliation(s)
- Fan Zou
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Ting Rao
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Wu Chen
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Tianbao Song
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Tongjie Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, 430026, China
| | - Weimin Hu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Linzhi Li
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Weimin Yu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China.
| | - Fan Cheng
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan 430060, China.
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3
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Bashore F, Annor-Gyamfi J, Du Y, Katis V, Nwogbo F, Flax RG, Frye SV, Pearce KH, Fu H, Willson TM, Drewry DH, Axtman AD. Fused Tetrahydroquinolines Are Interfering with Your Assay. J Med Chem 2023; 66:14434-14446. [PMID: 37874947 PMCID: PMC10641811 DOI: 10.1021/acs.jmedchem.3c01277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/12/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023]
Abstract
Tricyclic tetrahydroquinolines (THQs) have been repeatedly reported as hits across a diverse range of high-throughput screening (HTS) campaigns. The activities of these compounds, however, are likely due to reactive byproducts that interfere with the assay. As a lesser studied class of pan-assay interference compounds, the mechanism by which fused THQs react with protein targets remains largely unknown. During HTS follow-up, we characterized the behavior and stability of several fused tricyclic THQs. We synthesized key analogues to pinpoint the cyclopentene ring double bond as a source of reactivity of fused THQs. We found that these compounds degrade in solution under standard laboratory conditions in days. Importantly, these observations make it likely that fused THQs, which are ubiquitously found within small molecule screening libraries, are unlikely the intact parent compounds. We urge deprioritization of tricylic THQ hits in HTS follow-up and caution against the investment of resources to follow-up on these problematic compounds.
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Affiliation(s)
- Frances
M. Bashore
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Joel Annor-Gyamfi
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Yuhong Du
- Department
of Pharmacology and Chemical Biology, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
- Emory
Chemical Biology Discovery Center, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
| | - Vittorio Katis
- Alzheimer’s
Research UK Oxford Drug Discovery Institute, Centre for Medicines
Discovery, Nuffield Department of Medicine Research Building, Old
Road Campus, University of Oxford, Oxford OX3 7FZ, U.K.
| | - Felix Nwogbo
- UNC
Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal
Chemistry, Center for Integrative Chemical
Biology and Drug Discovery, Chapel
Hill, North Carolina 27599, United States
| | - Raymond G. Flax
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Stephen V. Frye
- UNC
Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal
Chemistry, Center for Integrative Chemical
Biology and Drug Discovery, Chapel
Hill, North Carolina 27599, United States
| | - Kenneth H. Pearce
- UNC
Eshelman School of Pharmacy, Division of Chemical Biology and Medicinal
Chemistry, Center for Integrative Chemical
Biology and Drug Discovery, Chapel
Hill, North Carolina 27599, United States
| | - Haian Fu
- Department
of Pharmacology and Chemical Biology, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
- Emory
Chemical Biology Discovery Center, Emory
University School of Medicine, Atlanta, Georgia 30322, United States
| | - Timothy M. Willson
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - David H. Drewry
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
- UNC Lineberger
Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Alison D. Axtman
- Structural
Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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4
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Wang X, Wu S, Sun L, Jin P, Zhang J, Liu W, Zhan Z, Wang Z, Liu X, He L. Pan-cancer analysis revealing that PTPN2 is an indicator of risk stratification for acute myeloid leukemia. Sci Rep 2023; 13:18372. [PMID: 37884566 PMCID: PMC10603079 DOI: 10.1038/s41598-023-44892-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
The non-receptor protein tyrosine phosphatases gene family (PTPNs) is involved in the tumorigenesis and development of many cancers, but the role of PTPNs in acute myeloid leukemia (AML) remains unclear. After a comprehensive evaluation on the expression patterns and immunological effects of PTPNs using a pan-cancer analysis based on RNA sequencing data obtained from The Cancer Genome Atlas, the most valuable gene PTPN2 was discovered. Further investigation of the expression patterns of PTPN2 in different tissues and cells showed a robust correlation with AML. PTPN2 was then systematically correlated with immunological signatures in the AML tumor microenvironment and its differential expression was verified using clinical samples. In addition, a prediction model, being validated and compared with other models, was developed in our research. The systematic analysis of PTPN family reveals that the effect of PTPNs on cancer may be correlated to mediating cell cycle-related pathways. It was then found that PTPN2 was highly expressed in hematologic diseases and bone marrow tissues, and its differential expression in AML patients and normal humans was verified by clinical samples. Based on its correlation with immune infiltrates, immunomodulators, and immune checkpoint, PTPN2 was found to be a reliable biomarker in the immunotherapy cohort and a prognostic predictor of AML. And PTPN2'riskscore can accurately predict the prognosis and response of cancer immunotherapy. These findings revealed the correlation between PTPNs and immunophenotype, which may be related to cell cycle. PTPN2 was differentially expressed between clinical AML patients and normal people. It is a diagnostic biomarker and potentially therapeutic target, providing targeted guidance for clinical treatment.
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Affiliation(s)
- Xuanyu Wang
- Department of Urology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Sanyun Wu
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Le Sun
- Department of Urology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China
| | - Peipei Jin
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jianmin Zhang
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Wen Liu
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Zhuo Zhan
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Zisong Wang
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, Hubei Province, China
| | - Xiaoping Liu
- Department of Pathology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China.
| | - Li He
- Department of Urology, Zhongnan Hospital of Wuhan University, 169 Donghu Road, Wuhan, 430071, China.
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
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5
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Bagwe PV, Deshpande RD, Juhasz G, Sathaye S, Joshi SV. Uncovering the Significance of STEP61 in Alzheimer's Disease: Structure, Substrates, and Interactome. Cell Mol Neurobiol 2023; 43:3099-3113. [PMID: 37219664 DOI: 10.1007/s10571-023-01364-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/15/2023] [Indexed: 05/24/2023]
Abstract
STEP (STriatal-Enriched Protein Tyrosine Phosphatase) is a brain-specific phosphatase that plays an important role in controlling signaling molecules involved in neuronal activity and synaptic development. The striatum is the main location of the STEP enzyme. An imbalance in STEP61 activity is a risk factor for Alzheimer's disease (AD). It can contribute to the development of numerous neuropsychiatric diseases, including Parkinson's disease (PD), schizophrenia, fragile X syndrome (FXS), Huntington's disease (HD), alcoholism, cerebral ischemia, and stress-related diseases. The molecular structure, chemistry, and molecular mechanisms associated with STEP61's two major substrates, Alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors (AMPAr) and N-methyl-D-aspartate receptors (NMDARs), are crucial in understanding the relationship between STEP61 and associated illnesses. STEP's interactions with its substrate proteins can alter the pathways of long-term potentiation and long-term depression. Therefore, understanding the role of STEP61 in neurological illnesses, particularly Alzheimer's disease-associated dementia, can provide valuable insights for possible therapeutic interventions. This review provides valuable insights into the molecular structure, chemistry, and molecular mechanisms associated with STEP61. This brain-specific phosphatase controls signaling molecules involved in neuronal activity and synaptic development. This review can aid researchers in gaining deep insights into the complex functions of STEP61.
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Affiliation(s)
- Pritam V Bagwe
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai, 400019, India
| | - Radni D Deshpande
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai, 400019, India
| | - Gabor Juhasz
- Clinical Research Unit (CRU Global Hungary Ltd.), Budapest, Hungary
| | - Sadhana Sathaye
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai, 400019, India.
| | - Shreerang V Joshi
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai, 400019, India.
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6
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Guerrero L, Ebrahim A, Riley BT, Kim M, Huang Q, Finke AD, Keedy DA. Pushed to extremes: distinct effects of high temperature vs. pressure on the structure of an atypical phosphatase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.538097. [PMID: 37205580 PMCID: PMC10187168 DOI: 10.1101/2023.05.02.538097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature vs. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes novel interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Together, our work argues that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.
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Affiliation(s)
- Liliana Guerrero
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- PhD Program in Biochemistry, CUNY Graduate Center, New York, NY 10016
| | - Ali Ebrahim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Blake T Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Minyoung Kim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853
| | - Aaron D Finke
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031
- PhD Programs in Biochemistry, Biology, & Chemistry, CUNY Graduate Center, New York, NY 10016
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7
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Chirgadze YN, Battaile KP, Likhachev IV, Balabaev NK, Gordon RD, Romanov V, Lin A, Karisch R, Lam R, Ruzanov M, Brazhnikov EV, Pai EF, Neel BG, Chirgadze NY. Signal transfer in human protein tyrosine phosphatase PTP1B from allosteric inhibitor P00058. J Biomol Struct Dyn 2022; 40:13823-13832. [PMID: 34705594 DOI: 10.1080/07391102.2021.1994879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein tyrosine phosphatases constitute a family of cytosolic and receptor-like signal transducing enzymes that catalyze the hydrolysis of phospho-tyrosine residues of phosphorylated proteins. PTP1B, encoded by PTPN1, is a key negative regulator of insulin and leptin receptor signaling, linking it to two widespread diseases: type 2 diabetes mellitus and obesity. Here, we present crystal structures of the PTP1B apo-enzyme and a complex with a newly identified allosteric inhibitor, 2-(2,5-dimethyl-pyrrol-1-yl)-5-hydroxy-benzoic acid, designated as P00058. The inhibitor binding site is located about 18 Å away from the active center. However, the inhibitor causes significant re-arrangements in the active center of enzyme: residues 45-50 of catalytic Tyr-loop are shifted at their Cα-atom positions by 2.6 to 5.8 Å. We have identified an event of allosteric signal transfer from the inhibitor to the catalytic area using molecular dynamic simulation. Analyzing change of complex structure along the fluctuation trajectory we have found the large Cα-atom shifts in external strand, residues 25-40, which occur at the same time with the shifts in adjacent catalytic p-Tyr-loop. Coming of the signal to this loop arises due to dynamic fluctuation of protein structure at about 4.0 nanoseconds after the inhibitor takes up its space. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Yuri N Chirgadze
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | | | - Ilya V Likhachev
- Institute of Mathematical Problems of Biology, Branch of Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Nikolay K Balabaev
- Institute of Mathematical Problems of Biology, Branch of Keldysh Institute of Applied Mathematics, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Roni D Gordon
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, ON, Canada
| | - Vladimir Romanov
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, ON, Canada
| | - Andres Lin
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, ON, Canada
| | - Robert Karisch
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, ON, Canada
| | - Robert Lam
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, ON, Canada
| | - Max Ruzanov
- Molecular Structure and Design, Molecular Discovery Technologies, Bristol-Myers Squibb Research & Development, Princeton, NJ, USA
| | - Evgeniy V Brazhnikov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Emil F Pai
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, ON, Canada.,Department of Biochemistry and Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Benjamin G Neel
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, ON, Canada.,Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, NYU Langone Health, NY, USA
| | - Nickolay Y Chirgadze
- Campbell Family Cancer Research Institute, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, ON, Canada.,X-CHIP Technologies Inc., Toronto, ON, Canada
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8
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Extracellular vesicles microRNA-592 of melanoma stem cells promotes metastasis through activation of MAPK/ERK signaling pathway by targeting PTPN7 in non-stemness melanoma cells. Cell Death Dis 2022; 8:428. [PMID: 36302748 PMCID: PMC9614017 DOI: 10.1038/s41420-022-01221-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 12/03/2022]
Abstract
Melanoma, one of the most aggressive malignancies, its high mortality and low survival rates are associated with effective metastatic colonization. Melanoma metastasis hinges on the bidirectional cell-cell communication within the complex metastatic microenvironments (MME). Extracellular vesicles (EVs) are recognized as a new class of molecular mediator in MME programing. Published studies show that melanoma EVs can educate MME stromal cells to acquire the pro-metastatic phenotype to enhance metastatic colonization. Whether EVs can mediate the interactions between heterogenous cancer cells within the MME that alter the course of metastasis has not been investigated at the mechanistic level. In this study, melanoma parental cells (MPCs) and paired derivative cancer stem cell line melanoma stem cells (MSCs) that were derived from melanoma cell line M14 were used. We demonstrate that the EVs-mediated crosstalk between the MSCs and the MPCs is a novel mechanism for melanoma metastasis. We characterized miR-592, a relatively novel microRNA of prognostic potential, in mediation of such intercellular crosstalk. EVs can encapsulate and deliver miR-592 to target MPCs. Upon entering, miR-592 inhibits the expression of its gene target protein tyrosine phosphatase non-receptor type7 (PTPN7), a phosphatase targeting MAPKs. This leads to the relief of the inhibitory effect of PTPN7 on MAPK/ERK signaling and consequently the augmentation of metastatic colonization of MPCs. Thus, via the extracellular vesicle miR-592/PTPN7/MAPK axis, melanoma-CSCs can transfer their metastatic ability to the low-metastatic non-CSC melanoma cells.
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9
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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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10
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Szedlacsek HS, Bajusz D, Badea RA, Pop A, Bică CC, Ravasz L, Mittli D, Mátyás D, Necula-Petrăreanu G, Munteanu CVA, Papp I, Juhász G, Hritcu L, Keserű GM, Szedlacsek SE. Designed Peptide Inhibitors of STEP Phosphatase-GluA2 AMPA Receptor Interaction Enhance the Cognitive Performance in Rats. J Med Chem 2021; 65:217-233. [PMID: 34962802 DOI: 10.1021/acs.jmedchem.1c01303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cognitive impairment and learning ability of the brain are directly linked to synaptic plasticity as measured in changes of long-term potentiation (LTP) and long-term depression (LTD) in animal models of brain diseases. LTD reflects a sustained reduction of the synaptic AMPA receptor content based on targeted clathrin-mediated endocytosis. AMPA receptor endocytosis is initiated by dephosphorylation of Tyr876 on the C-terminus of the AMPAR subunit GluA2. The brain-specific striatal-enriched protein tyrosine phosphatase (STEP) is responsible for this process. To identify new, highly effective inhibitors of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) internalization, we performed structure-based design of peptides able to inhibit STEP-GluA2-CT complex formation. Two short peptide derivatives were found as efficient in vitro inhibitors. Our in vivo experiments evidenced that both peptides restore the memory deficits and display anxiolytic and antidepressant effects in a scopolamine-treated rat model. The interference peptides identified and characterized here represent promising lead compounds for novel cognitive enhancers and/or behavioral modulators.
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Affiliation(s)
- Horea Stefan Szedlacsek
- Department of Enzymology, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - Dávid Bajusz
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary
| | - Rodica Aura Badea
- Department of Enzymology, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - Andreea Pop
- Department of Enzymology, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - Constantin Cătălin Bică
- Department of Enzymology, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - Lilla Ravasz
- CRU Hungary Kft, Thököly utca 15, 2131 Göd, Hungary
| | | | | | - Georgiana Necula-Petrăreanu
- Department of Enzymology, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - Cristian V A Munteanu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania
| | - Ildikó Papp
- CRU Hungary Kft, Thököly utca 15, 2131 Göd, Hungary
| | - Gábor Juhász
- CRU Hungary Kft, Thököly utca 15, 2131 Göd, Hungary
| | - Lucian Hritcu
- Department of Biology, Faculty of Biology, Alexandru Ioan Cuza University of Iasi, Bd. Carol I, No. 11, 700505 Iasi, Romania
| | - György Miklós Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary
| | - Stefan Eugen Szedlacsek
- Department of Enzymology, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031 Bucharest, Romania
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11
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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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12
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Abstract
Protein Tyrosine Phosphatases reverse cellular signals initiated by growth factors receptors and other tyrosine kinases by dephosphorylating phosphotyrosine on target proteins. The activity of these enzymes is crucial for maintaining cell homeostasis, yet these enzymes have been often dismissed as humble house-keeping proteins. Understandably, mutations and changes in expression patterns of Protein Tyrosine Phosphatases are implicated in tumorigenesis and various carcinomas. The conserved nature of their catalytic domains makes drug discovery a challenging pursuit. In this review, we focus on describing the various classes of Protein Tyrosine Phosphatases and their catalytic domains. We also summarize their role in cancer and neurodegenerative diseases using specific members as the model system. Finally, we explain the dichotomy in the biological role of catalytically active vs the pseudoenzyme forms of Protein Tyrosine Phosphatases in the context of their membrane bound receptor forms. This chapter aims to provide a current understanding of these proteins, in the background of their foundational past research.
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Affiliation(s)
- Colin L Welsh
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Preeti Pandey
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Lalima G Ahuja
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States.
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13
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Xiao H, Lin S, Jiang D, Lin Y, Liu L, Zhang Q, He J, Chen Y. Association of Extracellular Signal-Regulated Kinase Genes With Myopia: A Longitudinal Study of Chinese Children. Front Genet 2021; 12:654869. [PMID: 34122509 PMCID: PMC8191505 DOI: 10.3389/fgene.2021.654869] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/27/2021] [Indexed: 11/13/2022] Open
Abstract
Objective The present study was designed to investigate whether the extracellular signal-regulated kinase (ERK) signaling pathway, a downstream component of dopamine signaling, is involved in myopia among Chinese children. Methods During a 3.5-year follow-up, 488 primary school students were enrolled in this study. Non-cycloplegic spherical equivalent refraction (SE) and other ocular parameters were assessed. Four variants of four genes in the ERK signaling pathway were selected: RASGRF1 rs6495367, PTPN5 rs1550870, PTPRR rs11178469, and PDGFRA rs6554163. SNPscan was used to genotype single-nucleotide polymorphisms (SNPs). PLINK software was used to assess the associations of the genetic variants with the occurrence or development of myopia, SE, and other ocular parameters. We created a protein-protein interaction (PPI) network and microRNA (miRNA)-gene network using String and Cytoscape and conducted enrichment analyses on the genes in these networks. Results In total, 426 children (baseline age: 7.28 ± 0.26 years; 236 (55.4%) boys and 190 girls) wereenrolled. After adjusting for confounding factors with 10,000 permutations, children with the CT or TT genotype of PTPN5 rs1550870 were more susceptible to myopia than those with the CC genotype (adjusted p = 0.011). Additionally, PTPN5 rs1550870 was correlated with significant myopic shift and increasing axial length (AL) and lens thickness (LT) but had a negative effect on central corneal thickness (CCT). RASGRF1 rs6495367 was negatively associated with myopic shift (additive: adjusted p = 0.034; dominant: adjusted p = 0.020), myopic SE and AL. PDGFRA rs6554163 TA or AA was negatively associated with increasing LT (adjusted p = 0.033). Evaluation of the effects of SNP-SNP combinations on incident myopia revealed a statistically significant one-locus model: PTPN5 rs1550870 [cross-validation consistency (CVC) = 10/10, adjusted p = 0.0107]. The genes in the PPI and miRNA-gene interaction networks were subjected to enrichment analyses, which suggested that these genes are involved mainly in eye development and dopaminergic synapse-related processes. Conclusion We identified genetic variants of crucial ERK signaling pathway genes that were significantly correlated with myopia and ocular parameter alterations in Chinese children. A combination of gene and miRNA functional analyses with enrichment analyses highlights the regulatory effects associated with ocular development and dopamine biological functions. This study offers novel clues to understand the role of dopamine in the molecular mechanisms of myopia.
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Affiliation(s)
- Haishao Xiao
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Shudan Lin
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Dandan Jiang
- The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yaoyao Lin
- The Eye Hospital, Wenzhou Medical University, Wenzhou, China
| | - Linjie Liu
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Qiqi Zhang
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Juan He
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Yanyan Chen
- The Eye Hospital, Wenzhou Medical University, Wenzhou, China
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14
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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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15
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Plaman BA, Chan WC, Bishop AC. Chemical activation of divergent protein tyrosine phosphatase domains with cyanine-based biarsenicals. Sci Rep 2019; 9:16148. [PMID: 31695052 PMCID: PMC6834593 DOI: 10.1038/s41598-019-52002-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/11/2019] [Indexed: 12/28/2022] Open
Abstract
Strategies for the direct chemical activation of specific signaling proteins could provide powerful tools for interrogating cellular signal transduction. However, targeted protein activation is chemically challenging, and few broadly applicable activation strategies for signaling enzymes have been developed. Here we report that classical protein tyrosine phosphatase (PTP) domains from multiple subfamilies can be systematically sensitized to target-specific activation by the cyanine-based biarsenical compounds AsCy3 and AsCy5. Engineering of the activatable PTPs (actPTPs) is achieved by the introduction of three cysteine residues within a conserved loop of the PTP domain, and the positions of the sensitizing mutations are readily identifiable from primary sequence alignments. In the current study we have generated and characterized actPTP domains from three different subfamilies of both receptor and non-receptor PTPs. Biarsenical-induced stimulation of the actPTPs is rapid and dose-dependent, and is operative with both purified enzymes and complex proteomic mixtures. Our results suggest that a substantial fraction of the classical PTP family will be compatible with the act-engineering approach, which provides a novel chemical-biological tool for the control of PTP activity and the study of PTP function.
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Affiliation(s)
- Bailey A Plaman
- Amherst College, Department of Chemistry, Amherst, Massachusetts, 01002, USA
| | - Wai Cheung Chan
- Amherst College, Department of Chemistry, Amherst, Massachusetts, 01002, USA.,Dana-Farber Cancer Institute, Department of Cancer Biology, Boston, MA, 02215, USA
| | - Anthony C Bishop
- Amherst College, Department of Chemistry, Amherst, Massachusetts, 01002, USA.
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16
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Park JS, Lee J, Jung ES, Kim MH, Kim IB, Son H, Kim S, Kim S, Park YM, Mook-Jung I, Yu SJ, Lee JH. Brain somatic mutations observed in Alzheimer's disease associated with aging and dysregulation of tau phosphorylation. Nat Commun 2019; 10:3090. [PMID: 31300647 PMCID: PMC6626023 DOI: 10.1038/s41467-019-11000-7] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 06/14/2019] [Indexed: 01/24/2023] Open
Abstract
The role of brain somatic mutations in Alzheimer’s disease (AD) is not well understood. Here, we perform deep whole-exome sequencing (average read depth 584×) in 111 postmortem hippocampal formation and matched blood samples from 52 patients with AD and 11 individuals not affected by AD. The number of somatic single nucleotide variations (SNVs) in AD brain specimens increases significantly with aging, and the rate of mutation accumulation in the brain is 4.8-fold slower than that in AD blood. The putatively pathogenic brain somatic mutations identified in 26.9% (14 of 52) of AD individuals are enriched in PI3K-AKT, MAPK, and AMPK pathway genes known to contribute to hyperphosphorylation of tau. We show that a pathogenic brain somatic mutation in PIN1 leads to a loss-of-function mutation. In vitro mimicking of haploinsufficiency of PIN1 aberrantly increases tau phosphorylation and aggregation. This study provides new insights into the genetic architecture underlying the pathogenesis of AD. The role of brain somatic mutations in neurodegenerative diseases such as Alzheimer’s disease (AD) is not well understood. Here the authors carry out high-depth exome sequencing ~500× on brain tissue from patients with AD and controls, and identify mutations in a number of genes that are known to contribute to phosphorylation and aggregation of tau, including PIN1.
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Affiliation(s)
- Jun Sung Park
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Junehawk Lee
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea
| | - Eun Sun Jung
- Department of Biochemistry and Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.,Neuroscience Research Institute, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Myeong-Heui Kim
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Il Bin Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyeonju Son
- Department of Biomedical Systems Informatics, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Sangwoo Kim
- Department of Biomedical Systems Informatics, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Sanghyeon Kim
- Laboratory of Brain Research, Stanley Medical Research Institute (SMRI), 9800 Medical Center Drive, Suite C-050, Rockville, MD, 20850, USA
| | - Young Mok Park
- Center for Cognition and Sociality, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - Inhee Mook-Jung
- Department of Biochemistry and Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.,Neuroscience Research Institute, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea
| | - Seok Jong Yu
- Center for Supercomputing Applications, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon, 34141, Republic of Korea.
| | - Jeong Ho Lee
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea. .,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
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17
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Tautermann CS, Binder F, Büttner FH, Eickmeier C, Fiegen D, Gross U, Grundl MA, Heilker R, Hobson S, Hoerer S, Luippold A, Mack V, Montel F, Peters S, Bhattacharya S, Vaidehi N, Schnapp G, Thamm S, Zeeb M. Allosteric Activation of Striatal-Enriched Protein Tyrosine Phosphatase (STEP, PTPN5) by a Fragment-like Molecule. J Med Chem 2018; 62:306-316. [PMID: 30207464 DOI: 10.1021/acs.jmedchem.8b00857] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Protein tyrosine phosphatase non-receptor type 5 (PTPN5, STEP) is a brain specific phosphatase that regulates synaptic function and plasticity by modulation of N-methyl-d-aspartate receptor (NMDAR) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) trafficking. Dysregulation of STEP has been linked to neurodegenerative and neuropsychiatric diseases, highlighting this enzyme as an attractive therapeutic target for drug discovery. Selective targeting of STEP with small molecules has been hampered by high conservation of the active site among protein tyrosine phosphatases. We report the discovery of the first small molecule allosteric activator for STEP that binds to the phosphatase domain. Allosteric binding is confirmed by both X-ray and 15N NMR experiments, and specificity has been demonstrated by an enzymatic test cascade. Molecular dynamics simulations indicate stimulation of enzymatic activity by a long-range allosteric mechanism. To allow the scientific community to make use of this tool, we offer to provide the compound in the course of an open innovation initiative.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Supriyo Bhattacharya
- Department of Molecular Immunology , Beckman Research Institute of the City of Hope , 1500, E. Duarte Road , Duarte , California 91010 , United States
| | - Nagarajan Vaidehi
- Department of Molecular Immunology , Beckman Research Institute of the City of Hope , 1500, E. Duarte Road , Duarte , California 91010 , United States
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18
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Witten MR, Wissler L, Snow M, Geschwindner S, Read JA, Brandon NJ, Nairn AC, Lombroso PJ, Käck H, Ellman JA. X-ray Characterization and Structure-Based Optimization of Striatal-Enriched Protein Tyrosine Phosphatase Inhibitors. J Med Chem 2017; 60:9299-9319. [PMID: 29116812 DOI: 10.1021/acs.jmedchem.7b01292] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Excessive activity of striatal-enriched protein tyrosine phosphatase (STEP) in the brain has been detected in numerous neuropsychiatric disorders including Alzheimer's disease. Notably, knockdown of STEP in an Alzheimer mouse model effected an increase in the phosphorylation levels of downstream STEP substrates and a significant reversal in the observed cognitive and memory deficits. These data point to the promising potential of STEP as a target for drug discovery in Alzheimer's treatment. We previously reported a substrate-based approach to the development of low molecular weight STEP inhibitors with Ki values as low as 7.8 μM. Herein, we disclose the first X-ray crystal structures of inhibitors bound to STEP and the surprising finding that they occupy noncoincident binding sites. Moreover, we utilize this structural information to optimize the inhibitor structure to achieve a Ki of 110 nM, with 15-60-fold selectivity across a series of phosphatases.
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Affiliation(s)
- Michael R Witten
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
| | - Lisa Wissler
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Gothenburg, Sweden
| | - Melanie Snow
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Macclesfield SK10 4TG, United Kingdom
| | - Stefan Geschwindner
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Gothenburg, Sweden
| | - Jon A Read
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Cambridge CB4 0WG, United Kingdom
| | - Nicholas J Brandon
- Neuroscience, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Cambridge, Massachusetts 02139, United States
| | - Angus C Nairn
- Department of Psychiatry, Yale University , New Haven, Connecticut 06520, United States
| | - Paul J Lombroso
- Department of Psychiatry, Yale University , New Haven, Connecticut 06520, United States.,Child Study Center, Yale University , New Haven, Connecticut 06520, United States
| | - Helena Käck
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Gothenburg, Sweden
| | - Jonathan A Ellman
- Department of Chemistry, Yale University , New Haven, Connecticut 06520, United States
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19
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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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20
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Sood RF, Arbabi S, Honari S, Gibran NS. Missense Variant in MAPK Inactivator PTPN5 Is Associated with Decreased Severity of Post-Burn Hypertrophic Scarring. PLoS One 2016; 11:e0149206. [PMID: 26872063 PMCID: PMC4752497 DOI: 10.1371/journal.pone.0149206] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/28/2016] [Indexed: 12/20/2022] Open
Abstract
Background Hypertrophic scarring (HTS) is hypothesized to have a genetic mechanism, yet its genetic determinants are largely unknown. The mitogen-activated protein kinase (MAPK) pathways are important mediators of inflammatory signaling, and experimental evidence implicates MAPKs in HTS formation. We hypothesized that single-nucleotide polymorphisms (SNPs) in MAPK-pathway genes would be associated with severity of post-burn HTS. Methods We analyzed data from a prospective-cohort genome-wide association study of post-burn HTS. We included subjects with deep-partial-thickness burns admitted to our center who provided blood for genotyping and had at least one Vancouver Scar Scale (VSS) assessment. After adjusting for HTS risk factors and population stratification, we tested MAPK-pathway gene SNPs for association with the four VSS variables in a joint regression model. In addition to individual-SNP analysis, we performed gene-based association testing. Results Our study population consisted of 538 adults (median age 40 years) who were predominantly White (76%) males (71%) admitted to our center from 2007–2014 with small-to-moderate-sized burns (median burn size 6% total body surface area). Of 2,146 SNPs tested, a rare missense variant in the PTPN5 gene (rs56234898; minor allele frequency 1.5%) was significantly associated with decreased severity of post-burn HTS (P = 1.3×10−6). In gene-based analysis, PTPN5 (P = 1.2×10−5) showed a significant association and BDNF (P = 9.5×10−4) a borderline-significant association with HTS severity. Conclusions We report PTPN5 as a novel genetic locus associated with HTS severity. PTPN5 is a MAPK inhibitor expressed in neurons, suggesting a potential role for neurotrophic factors and neuroinflammatory signaling in HTS pathophysiology.
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Affiliation(s)
- Ravi F. Sood
- Department of Surgery, UW Medicine Regional Burn Center, Harborview Medical Center, Seattle, WA, United States of America
- * E-mail:
| | - Saman Arbabi
- Department of Surgery, UW Medicine Regional Burn Center, Harborview Medical Center, Seattle, WA, United States of America
| | - Shari Honari
- Department of Surgery, UW Medicine Regional Burn Center, Harborview Medical Center, Seattle, WA, United States of America
| | - Nicole S. Gibran
- Department of Surgery, UW Medicine Regional Burn Center, Harborview Medical Center, Seattle, WA, United States of America
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21
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Inhibitor of the tyrosine phosphatase STEP reverses cognitive deficits in a mouse model of Alzheimer's disease. PLoS Biol 2014; 12:e1001923. [PMID: 25093460 PMCID: PMC4122355 DOI: 10.1371/journal.pbio.1001923] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 06/26/2014] [Indexed: 02/06/2023] Open
Abstract
STEP (STriatal-Enriched protein tyrosine Phosphatase) is a neuron-specific phosphatase that regulates N-methyl-D-aspartate receptor (NMDAR) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) trafficking, as well as ERK1/2, p38, Fyn, and Pyk2 activity. STEP is overactive in several neuropsychiatric and neurodegenerative disorders, including Alzheimer's disease (AD). The increase in STEP activity likely disrupts synaptic function and contributes to the cognitive deficits in AD. AD mice lacking STEP have restored levels of glutamate receptors on synaptosomal membranes and improved cognitive function, results that suggest STEP as a novel therapeutic target for AD. Here we describe the first large-scale effort to identify and characterize small-molecule STEP inhibitors. We identified the benzopentathiepin 8-(trifluoromethyl)-1,2,3,4,5-benzopentathiepin-6-amine hydrochloride (known as TC-2153) as an inhibitor of STEP with an IC50 of 24.6 nM. TC-2153 represents a novel class of PTP inhibitors based upon a cyclic polysulfide pharmacophore that forms a reversible covalent bond with the catalytic cysteine in STEP. In cell-based secondary assays, TC-2153 increased tyrosine phosphorylation of STEP substrates ERK1/2, Pyk2, and GluN2B, and exhibited no toxicity in cortical cultures. Validation and specificity experiments performed in wild-type (WT) and STEP knockout (KO) cortical cells and in vivo in WT and STEP KO mice suggest specificity of inhibitors towards STEP compared to highly homologous tyrosine phosphatases. Furthermore, TC-2153 improved cognitive function in several cognitive tasks in 6- and 12-mo-old triple transgenic AD (3xTg-AD) mice, with no change in beta amyloid and phospho-tau levels.
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22
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Francis DM, Page R, Peti W. Sequence-specific backbone ¹H, ¹³C and ¹⁵N assignments of the 34 kDa catalytic domain of PTPN5 (STEP). BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:185-188. [PMID: 23640000 DOI: 10.1007/s12104-013-9480-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 04/19/2013] [Indexed: 06/02/2023]
Abstract
PTPN5 is a protein tyrosine phosphatase that plays an integral role in regulating excitatory postsynaptic activity. The sequence-specific backbone assignments of the murine PTPN5 catalytic domain have been determined based on triple-resonance experiments using uniformly [(2)H,(13)C,(15)N]-labeled protein.
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Affiliation(s)
- Dana M Francis
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI, 02903, USA
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23
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Li R, Xie DD, Dong JH, Li H, Li KS, Su J, Chen LZ, Xu YF, Wang HM, Gong Z, Cui GY, Yu X, Wang K, Yao W, Xin T, Li MY, Xiao KH, An XF, Huo Y, Xu ZG, Sun JP, Pang Q. Molecular mechanism of ERK dephosphorylation by striatal-enriched protein tyrosine phosphatase. J Neurochem 2013; 128:315-329. [PMID: 24117863 DOI: 10.1111/jnc.12463] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 09/20/2013] [Accepted: 09/23/2013] [Indexed: 12/26/2022]
Abstract
Striatal-enriched tyrosine phosphatase (STEP) is an important regulator of neuronal synaptic plasticity, and its abnormal level or activity contributes to cognitive disorders. One crucial downstream effector and direct substrate of STEP is extracellular signal-regulated protein kinase (ERK), which has important functions in spine stabilisation and action potential transmission. The inhibition of STEP activity toward phospho-ERK has the potential to treat neuronal diseases, but the detailed mechanism underlying the dephosphorylation of phospho-ERK by STEP is not known. Therefore, we examined STEP activity toward para-nitrophenyl phosphate, phospho-tyrosine-containing peptides, and the full-length phospho-ERK protein using STEP mutants with different structural features. STEP was found to be a highly efficient ERK tyrosine phosphatase that required both its N-terminal regulatory region and key residues in its active site. Specifically, both kinase interaction motif (KIM) and kinase-specific sequence of STEP were required for ERK interaction. In addition to the N-terminal kinase-specific sequence region, S245, hydrophobic residues L249/L251, and basic residues R242/R243 located in the KIM region were important in controlling STEP activity toward phospho-ERK. Further kinetic experiments revealed subtle structural differences between STEP and HePTP that affected the interactions of their KIMs with ERK. Moreover, STEP recognised specific positions of a phospho-ERK peptide sequence through its active site, and the contact of STEP F311 with phospho-ERK V205 and T207 were crucial interactions. Taken together, our results not only provide the information for interactions between ERK and STEP, but will also help in the development of specific strategies to target STEP-ERK recognition, which could serve as a potential therapy for neurological disorders. Regulation of phospho-ERK by STEP underlies important neuronal activities. A detailed enzymologic characterisation and cellular studies of STEP revealed that specific residues in KIM and active site mediated ERK recognition. Structural differences between the KIM-ERK interfaces and the active site among different ERK phosphatases could be targeted to develop specific STEP inhibitor, which has therapeutic potential for neurological disorders. PKA, protein kinase A & NGF, nerve growth factor.
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Affiliation(s)
- Rong Li
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Di-Dong Xie
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Provincial Hospital affiliated to Shandong University, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Jun-Hong Dong
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China.,Weifang Medical University,Weifang, Shandong, 261042, China
| | - Hui Li
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Kang-Shuai Li
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Jing Su
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Lai-Zhong Chen
- School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, 250012, China
| | - Yun-Fei Xu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Hong-Mei Wang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Zheng Gong
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Weihai campus, Shandong University, Weihai, Shandong, 264209, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Guo-Ying Cui
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Xiao Yu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Kai Wang
- Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Wei Yao
- Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Tao Xin
- Provincial Hospital affiliated to Shandong University, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Min-Yong Li
- School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, 250012, China
| | - Kun-Hong Xiao
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Xiao-Fei An
- Drug Discovery Center, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China, 518055
| | - Yuqing Huo
- Vascular Biology Center, Department of Cellular Biology and Anatomy, Medical College of Georgia, Georgia Regents University, Augusta, GA 30912
| | - Zhi-Gang Xu
- Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China.,Shandong University, School of Life Sciences, Jinan, Shandong, 250021, China
| | - Jin-Peng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 250012, China.,Provincial Hospital affiliated to Shandong University, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
| | - Qi Pang
- Provincial Hospital affiliated to Shandong University, Jinan, Shandong, 250012, China.,Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, 250012, China
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24
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Francis DM, Kumar GS, Koveal D, Tortajada A, Page R, Peti W. The differential regulation of p38α by the neuronal kinase interaction motif protein tyrosine phosphatases, a detailed molecular study. Structure 2013; 21:1612-23. [PMID: 23932588 PMCID: PMC3769431 DOI: 10.1016/j.str.2013.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 06/24/2013] [Accepted: 07/02/2013] [Indexed: 10/26/2022]
Abstract
The MAP kinase p38α is essential for neuronal signaling. To better understand the molecular regulation of p38α we used atomistic and molecular techniques to determine the structural basis of p38α regulation by the two neuronal tyrosine phosphatases, PTPSL/PTPBR7 (PTPRR) and STEP (PTPN5). We show that, despite the fact that PTPSL and STEP belong to the same family of regulatory proteins, they interact with p38α differently and their distinct molecular interactions explain their different catalytic activities. Although the interaction of PTPSL with p38α is similar to that of the previously described p38α:HePTP (PTPN7) complex, STEP binds and regulates p38α in an unexpected manner. Using NMR and small-angle X-ray scattering data, we generated a model of the p38α:STEP complex and define molecular differences between its resting and active states. Together, these results provide insights into molecular regulation of p38α by key regulatory proteins.
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Affiliation(s)
- Dana May Francis
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence RI, 02912, USA
| | - Ganesan Senthil Kumar
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence RI, 02912, USA
| | - Dorothy Koveal
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence RI, 02912, USA
| | - Antoni Tortajada
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence RI, 02912, USA
| | - Rebecca Page
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence RI, 02912, USA
| | - Wolfgang Peti
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence RI, 02912, USA
- Department of Chemistry, Brown University, Providence RI, 02912, USA
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25
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A structural comparative approach to identifying novel antimalarial inhibitors. Comput Biol Chem 2013; 45:42-7. [DOI: 10.1016/j.compbiolchem.2013.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Revised: 04/16/2013] [Accepted: 04/18/2013] [Indexed: 11/22/2022]
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26
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Ozcan A, Olmez EO, Alakent B. Effects of protonation state of Asp181 and position of active site water molecules on the conformation of PTP1B. Proteins 2013; 81:788-804. [PMID: 23239271 DOI: 10.1002/prot.24234] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 10/19/2012] [Accepted: 12/05/2012] [Indexed: 12/11/2022]
Abstract
In protein tyrosine phosphatase 1B (PTP1B), the flexible WPD loop adopts a closed conformation (WPDclosed ) in the active state of PTP1B, bringing the catalytic Asp181 close to the active site pocket, while WPD loop is in an open conformation (WPDopen ) in the inactive state. Previous studies showed that Asp181 may be protonated at physiological pH, and ordered water molecules exist in the active site. In the current study, molecular dynamics simulations are employed at different Asp181 protonation states and initial positions of active site water molecules, and compared with the existing crystallographic data of PTP1B. In WPDclosed conformation, the active site is found to maintain its conformation only in the protonated state of Asp181 in both free and liganded states, while Asp181 is likely to be deprotonated in WPDopen conformation. When the active site water molecule network that is a part of the free WPDclosed crystal structure is disrupted, intermediate WPD loop conformations, similar to that in the PTPRR crystal structure, are sampled in the MD simulations. In liganded PTP1B, one active site water molecule is found to be important for facilitating the orientation of Cys215 and the phosphate ion, thus may play a role in the reaction. In conclusion, conformational stability of WPD loop, and possibly catalytic activity of PTP1B, is significantly affected by the protonation state of Asp181 and position of active site water molecules, showing that these aspects should be taken into consideration both in MD simulations and inhibitor design.
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Affiliation(s)
- Ahmet Ozcan
- Graduate Program in Computational Science and Engineering, Bogazici University, Bebek, Istanbul 34342, Turkey
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27
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Böhmer F, Szedlacsek S, Tabernero L, Ostman A, den Hertog J. Protein tyrosine phosphatase structure-function relationships in regulation and pathogenesis. FEBS J 2013; 280:413-31. [PMID: 22682070 DOI: 10.1111/j.1742-4658.2012.08655.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Protein phosphorylation on tyrosine residues is tightly controlled by protein tyrosine phosphatases (PTPs) at multiple levels: spatio-temporal expression, subcellular localization and post-translational modification. Structural and functional analysis of the PTP domains has provided insight into catalysis and regulatory mechanisms that control the enzymatic activity. Understanding the molecular basis of PTP regulation is of fundamental importance to dissect the pleiotropic effect of these enzymes in both health and disease. Here, we review recent insights into the regulation of receptor-like PTPs by extracellular ligands and into regulation by reversible oxidation that impairs catalysis directly. The physiological roles of PTPs are essential in homeostasis in eukaryotic cells and pertubation of their functional attributes causes different disease states. As an example, we discuss recent findings indicating how inappropriate oxidation of PTPs in cancer cells may contribute to cell transformation. On the other hand, PTPs from many pathogens are key virulence factors and manipulate signalling pathways in the host cells to promote invasion and survival of the microorganisms. This research area has received relatively little attention but has advanced remarkably. We review the structural features of pathogenic PTPs, their similarities and differences with eukaryotic PTPs, and the possible exploitation of this knowledge for therapeutic intervention.
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Affiliation(s)
- Frank Böhmer
- Center for Molecular Biomedicine, Jena University Hospital, Jena, Germany
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28
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Tautz L, Critton DA, Grotegut S. Protein tyrosine phosphatases: structure, function, and implication in human disease. Methods Mol Biol 2013; 1053:179-221. [PMID: 23860656 DOI: 10.1007/978-1-62703-562-0_13] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein tyrosine phosphorylation is a key regulatory mechanism in eukaryotic cell physiology. Aberrant expression or function of protein tyrosine kinases and protein tyrosine phosphatases can lead to serious human diseases, including cancer, diabetes, as well as cardiovascular, infectious, autoimmune, and neuropsychiatric disorders. Here, we give an overview of the protein tyrosine phosphatase superfamily with its over 100 members in humans. We review their structure, function, and implications in human diseases, and discuss their potential as novel drug targets, as well as current challenges and possible solutions to developing therapeutics based on these enzymes.
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Affiliation(s)
- Lutz Tautz
- Infectious and Inflammatory Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA
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29
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Johnson MA, Lombroso PJ. A common STEP in the synaptic pathology of diverse neuropsychiatric disorders. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2012; 85:481-90. [PMID: 23239949 PMCID: PMC3516890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Synaptic function is critical for proper cognition, and synaptopathologies have been implicated in diverse neuropsychiatric disorders. STriatal-Enriched protein tyrosine Phosphatase (STEP) is a brain-enriched tyrosine phosphatase that normally opposes synaptic strengthening by dephosphorylating key neuronal signaling molecules. STEP targets include N-methyl D-aspartate receptors (NMDARs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs), as well as extracellular signal-regulated kinase (ERK) and the tyrosine kinase Fyn. STEP-mediated dephosphorylation promotes the internalization of NMDARs and AMPARs and the inactivation of ERK and Fyn.Regulation of STEP is complex, and recent work has implicated STEP dysregulation in the pathophysiology of several neuropsychiatric disorders. Both high levels and low levels of STEP are found in a diverse group of illnesses. This review focuses on the role of STEP in three disorders in which STEP levels are elevated: Alzheimer's disease, fragile X syndrome, and schizophrenia. The presence of elevated STEP in all three of these disorders raises the intriguing possibility that cognitive deficits resulting from diverse etiologies may share a common molecular pathway.
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Affiliation(s)
- Micah A. Johnson
- Child Study Center, Yale School of Medicine, New Haven,
Connecticut,Department of Molecular Biophysics and Biochemistry,
Yale University, New Haven, Connecticut,Department of Psychology, Yale University, New Haven,
Connecticut,To whom all correspondence should be
addressed: Micah Johnson, Child Study Center, Yale School of Medicine, 230 South
Frontage Road, New Haven, CT 06520; Tele: 203-737-2224; Fax: 203-737-1118;
| | - Paul J. Lombroso
- Child Study Center, Yale School of Medicine, New Haven,
Connecticut,Departments of Neurobiology and Psychiatry, Yale School
of Medicine, New Haven, Connecticut
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30
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Hendriks WJAJ, Elson A, Harroch S, Pulido R, Stoker A, den Hertog J. Protein tyrosine phosphatases in health and disease. FEBS J 2012; 280:708-30. [DOI: 10.1111/febs.12000] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 08/17/2012] [Accepted: 08/28/2012] [Indexed: 01/06/2023]
Affiliation(s)
| | - Ari Elson
- Department of Molecular Genetics; The Weizmann Institute of Science; Rehovot; Israel
| | - Sheila Harroch
- Department of Neuroscience; Institut Pasteur; Paris; France
| | - Rafael Pulido
- Centro de Investigación Príncipe Felipe; Valencia; Spain
| | - Andrew Stoker
- Neural Development Unit; Institute of Child Health; University College London; UK
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31
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Sergienko E, Xu J, Liu WH, Dahl R, Critton DA, Su Y, Brown BT, Chan X, Yang L, Bobkova EV, Vasile S, Yuan H, Rascon J, Colayco S, Sidique S, Cosford NDP, Chung TDY, Mustelin T, Page R, Lombroso PJ, Tautz L. Inhibition of hematopoietic protein tyrosine phosphatase augments and prolongs ERK1/2 and p38 activation. ACS Chem Biol 2012; 7:367-77. [PMID: 22070201 DOI: 10.1021/cb2004274] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The hematopoietic protein tyrosine phosphatase (HePTP) is implicated in the development of blood cancers through its ability to negatively regulate the mitogen-activated protein kinases (MAPKs) ERK1/2 and p38. Small-molecule modulators of HePTP activity may become valuable in treating hematopoietic malignancies such as T cell acute lymphoblastic leukemia (T-ALL) and acute myelogenous leukemia (AML). Moreover, such compounds will further elucidate the regulation of MAPKs in hematopoietic cells. Although transient activation of MAPKs is crucial for growth and proliferation, prolonged activation of these important signaling molecules induces differentiation, cell cycle arrest, cell senescence, and apoptosis. Specific HePTP inhibitors may promote the latter and thereby may halt the growth of cancer cells. Here, we report the development of a small molecule that augments ERK1/2 and p38 activation in human T cells, specifically by inhibiting HePTP. Structure-activity relationship analysis, in silico docking studies, and mutagenesis experiments reveal how the inhibitor achieves selectivity for HePTP over related phosphatases by interacting with unique amino acid residues in the periphery of the highly conserved catalytic pocket. Importantly, we utilize this compound to show that pharmacological inhibition of HePTP not only augments but also prolongs activation of ERK1/2 and, especially, p38. Moreover, we present similar effects in leukocytes from mice intraperitoneally injected with the inhibitor at doses as low as 3 mg/kg. Our results warrant future studies with this probe compound that may establish HePTP as a new drug target for acute leukemic conditions.
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Affiliation(s)
| | | | | | | | - David A. Critton
- Department
of Molecular Biology,
Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Rebecca Page
- Department
of Molecular Biology,
Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
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32
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Xu J, Kurup P, Nairn AC, Lombroso PJ. Striatal-enriched protein tyrosine phosphatase in Alzheimer's disease. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2012; 64:303-25. [PMID: 22840751 PMCID: PMC3740556 DOI: 10.1016/b978-0-12-394816-8.00009-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Alzheimer's disease (AD) is the most common form of dementia among the elderly, affecting millions of people worldwide and representing a substantial economic burden. AD is a progressive disease associated with memory loss and impaired cognitive function. The neuropathology is characterized by cortical accumulation of amyloid plaques and neurofibrillary tangles (NFTs). Amyloid plaques are small, aggregated peptides called beta amyloid (Aβ) and NFTs are aggregates of hyperphosphorylated Tau protein. Because Aβ disrupts multiple intracellular signaling pathways, resulting in some of the clinical symptoms of AD, understanding the underlying molecular mechanisms has implications for the diagnosis and treatment of AD. Recent studies have demonstrated that Aβ regulates striatal-enriched protein tyrosine phosphatase (STEP) (PTPN5). Aβ accumulation is associated with increases in STEP levels and activity that in turn disrupts glutamate receptor trafficking to and from the neuronal membrane. These findings indicate that modulating STEP levels or inhibiting its activity may have beneficial effects for patients with AD, making it an important target for drug discovery. This article reviews the biology of STEP and its role in AD as well as the potential clinical applications.
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Affiliation(s)
- Jian Xu
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA
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33
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Goebel-Goody SM, Baum M, Paspalas CD, Fernandez SM, Carty NC, Kurup P, Lombroso PJ. Therapeutic implications for striatal-enriched protein tyrosine phosphatase (STEP) in neuropsychiatric disorders. Pharmacol Rev 2011; 64:65-87. [PMID: 22090472 DOI: 10.1124/pr.110.003053] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Striatal-enriched protein tyrosine phosphatase (STEP) is a brain-specific phosphatase that modulates key signaling molecules involved in synaptic plasticity and neuronal function. Targets include extracellular-regulated kinase 1 and 2 (ERK1/2), stress-activated protein kinase p38 (p38), the Src family tyrosine kinase Fyn, N-methyl-D-aspartate receptors (NMDARs), and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs). STEP-mediated dephosphorylation of ERK1/2, p38, and Fyn leads to inactivation of these enzymes, whereas STEP-mediated dephosphorylation of surface NMDARs and AMPARs promotes their endocytosis. Accordingly, the current model of STEP function posits that it opposes long-term potentiation and promotes long-term depression. Phosphorylation, cleavage, dimerization, ubiquitination, and local translation all converge to maintain an appropriate balance of STEP in the central nervous system. Accumulating evidence over the past decade indicates that STEP dysregulation contributes to the pathophysiology of several neuropsychiatric disorders, including Alzheimer's disease, schizophrenia, fragile X syndrome, epileptogenesis, alcohol-induced memory loss, Huntington's disease, drug abuse, stroke/ischemia, and inflammatory pain. This comprehensive review discusses STEP expression and regulation and highlights how disrupted STEP function contributes to the pathophysiology of diverse neuropsychiatric disorders.
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Affiliation(s)
- Susan M Goebel-Goody
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut, USA
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34
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Sheriff S, Beno BR, Zhai W, Kostich WA, McDonnell PA, Kish K, Goldfarb V, Gao M, Kiefer SE, Yanchunas J, Huang Y, Shi S, Zhu S, Dzierba C, Bronson J, Macor JE, Appiah KK, Westphal RS, O’Connell J, Gerritz SW. Small Molecule Receptor Protein Tyrosine Phosphatase γ (RPTPγ) Ligands That Inhibit Phosphatase Activity via Perturbation of the Tryptophan–Proline–Aspartate (WPD) Loop. J Med Chem 2011; 54:6548-62. [DOI: 10.1021/jm2003766] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Steven Sheriff
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Brett R. Beno
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Weixu Zhai
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Walter A. Kostich
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Patricia A. McDonnell
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Kevin Kish
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Valentina Goldfarb
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Mian Gao
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Susan E. Kiefer
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Joseph Yanchunas
- Bristol-Myers Squibb Research and Development, P.O. Box 4000, Princeton, New Jersey 08543-4000, United States
| | - Yanling Huang
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Shuhao Shi
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Shirong Zhu
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Carolyn Dzierba
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Joanne Bronson
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - John E. Macor
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Kingsley K. Appiah
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Ryan S. Westphal
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Jonathan O’Connell
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
| | - Samuel W. Gerritz
- Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
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35
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Protein tyrosine phosphatases as drug targets: strategies and challenges of inhibitor development. Future Med Chem 2011; 2:1563-76. [PMID: 21426149 DOI: 10.4155/fmc.10.241] [Citation(s) in RCA: 217] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Several 'classical' protein tyrosine phosphatases are attractive therapeutic targets, including PTP1B for obesity and Type II diabetes; SHP2 for cancer and Lyp for rheumatoid arthritis. Progress has been made in identifying a broad range of chemically distinct inhibitors; however, developing selective and cell-permeable clinically useful compounds has proved challenging. Here the ongoing challenges and recent significant advances in the field are reviewed. Key novel compounds are highlighted and a perspective on the future of phosphatase inhibitor development is presented.
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Critton DA, Tautz L, Page R. Visualizing active-site dynamics in single crystals of HePTP: opening of the WPD loop involves coordinated movement of the E loop. J Mol Biol 2010; 405:619-29. [PMID: 21094165 DOI: 10.1016/j.jmb.2010.11.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 11/09/2010] [Accepted: 11/10/2010] [Indexed: 10/18/2022]
Abstract
Phosphotyrosine hydrolysis by protein tyrosine phosphatases (PTPs) involves substrate binding by the PTP loop and closure over the active site by the WPD loop. The E loop, located immediately adjacent to the PTP and WPD loops, is conserved among human PTPs in both sequence and structure, yet the role of this loop in substrate binding and catalysis is comparatively unexplored. Hematopoietic PTP (HePTP) is a member of the kinase interaction motif (KIM) PTP family. Compared to other PTPs, KIM-PTPs have E loops that are unique in both sequence and structure. In order to understand the role of the E loop in the transition between the closed state and the open state of HePTP, we identified a novel crystal form of HePTP that allowed the closed-state-to-open-state transition to be observed within a single crystal form. These structures, which include the first structure of the HePTP open state, show that the WPD loop adopts an 'atypically open' conformation and, importantly, that ligands can be exchanged at the active site, which is critical for HePTP inhibitor development. These structures also show that tetrahedral oxyanions bind at a novel secondary site and function to coordinate the PTP, WPD, and E loops. Finally, using both structural and kinetic data, we reveal a novel role for E-loop residue Lys182 in enhancing HePTP catalytic activity through its interaction with Asp236 of the WPD loop, providing the first evidence for the coordinated dynamics of the WPD and E loops in the catalytic cycle, which, as we show, is relevant to multiple PTP families.
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Affiliation(s)
- David A Critton
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA
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Kim TI, Jeong M, Chung S, Kim Y. An Iminocoumarin-Based Fluorescent Probe for the Selective Detection of Dual-Specific Protein Tyrosine Phosphatases. Chemistry 2010; 16:5297-300. [DOI: 10.1002/chem.201000154] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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38
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Menigatti M, Cattaneo E, Sabates-Bellver J, Ilinsky VV, Went P, Buffoli F, Marquez VE, Jiricny J, Marra G. The protein tyrosine phosphatase receptor type R gene is an early and frequent target of silencing in human colorectal tumorigenesis. Mol Cancer 2009; 8:124. [PMID: 20015382 PMCID: PMC2801661 DOI: 10.1186/1476-4598-8-124] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Accepted: 12/16/2009] [Indexed: 12/19/2022] Open
Abstract
Background Tumor development in the human colon is commonly accompanied by epigenetic changes, such as DNA methylation and chromatin modifications. These alterations result in significant, inheritable changes in gene expression that contribute to the selection of tumor cells with enhanced survival potential. Results A recent high-throughput gene expression analysis conducted by our group identified numerous genes whose transcription was markedly diminished in colorectal tumors. One of these, the protein-tyrosine phosphatase receptor type R (PTPRR) gene, was dramatically downregulated from the earliest stages of cellular transformation. Here, we show that levels of both major PTPRR transcript variants are markedly decreased (compared with normal mucosal levels) in precancerous and cancerous colorectal tumors, as well in colorectal cancer cell lines. The expression of the PTPRR-1 isoform was inactivated in colorectal cancer cells as a result of de novo CpG island methylation and enrichment of transcription-repressive histone-tail marks, mainly H3K27me3. De novo methylation of the PTPRR-1 transcription start site was demonstrated in 29/36 (80%) colorectal adenomas, 42/44 (95%) colorectal adenocarcinomas, and 8/8 (100%) liver metastases associated with the latter tumors. Conclusions Epigenetic downregulation of PTPRR seems to be an early alteration in colorectal cell transformation, which is maintained during the clonal selection associated with tumor progression. It may represent a preliminary step in the constitutive activation of the RAS/RAF/MAPK/ERK signalling, an effect that will later be consolidated by mutations in genes encoding key components of this pathway.
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Affiliation(s)
- Mirco Menigatti
- Institute of Molecular Cancer Research, University of Zurich, Switzerland.
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Johnston PA, Foster CA, Tierno MB, Shun TY, Shinde SN, Paquette WD, Brummond KM, Wipf P, Lazo JS. Cdc25B dual-specificity phosphatase inhibitors identified in a high-throughput screen of the NIH compound library. Assay Drug Dev Technol 2009; 7:250-65. [PMID: 19530895 DOI: 10.1089/adt.2008.186] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The University of Pittsburgh Molecular Library Screening Center (Pittsburgh, PA) conducted a screen with the National Institutes of Health compound library for inhibitors of in vitro cell division cycle 25 protein (Cdc25) B activity during the pilot phase of the Molecular Library Screening Center Network. Seventy-nine (0.12%) of the 65,239 compounds screened at 10 muM met the active criterion of > or =50% inhibition of Cdc25B activity, and 25 (31.6%) of these were confirmed as Cdc25B inhibitors with 50% inhibitory concentration (IC(50)) values <50 microM. Thirteen of the Cdc25B inhibitors were represented by singleton chemical structures, and 12 were divided among four clusters of related structures. Thirteen (52%) of the Cdc25B inhibitor hits were quinone-based structures. The Cdc25B inhibitors were further characterized in a series of in vitro secondary assays to confirm their activity, to determine their phosphatase selectivity against two other dual-specificity phosphatases, mitogen-activated protein kinase phosphatase (MKP)-1 and MKP-3, and to examine if the mechanism of Cdc25B inhibition involved oxidation and inactivation. Nine Cdc25B inhibitors did not appear to affect Cdc25B through a mechanism involving oxidation because they did not generate detectable amounts of H(2)O(2) in the presence of dithiothreitol, and their Cdc25B IC(50) values were not significantly affected by exchanging the dithiothreitol for beta-mercaptoethanol or reduced glutathione or by adding catalase to the assay. Six of the nonoxidative hits were selective for Cdc25B inhibition versus MKP-1 and MKP-3, but only the two bisfuran-containing hits, PubChem substance identifiers 4258795 and 4260465, significantly inhibited the growth of human MBA-MD-435 breast and PC-3 prostate cancer cell lines. To confirm the structure and biological activity of 4260465, the compound was resynthesized along with two analogs. Neither of the substitutions to the two analogs was tolerated, and only the resynthesized hit 26683752 inhibited Cdc25B activity in vitro (IC(50) = 13.83 +/- 1.0 microM) and significantly inhibited the growth of the MBA-MD-435 breast and PC-3 prostate cancer cell lines (IC(50) = 20.16 +/- 2.0 microM and 24.87 +/- 2.25 microM, respectively). The two bis-furan-containing hits identified in the screen represent novel nonoxidative Cdc25B inhibitor chemotypes that block tumor cell proliferation. The availability of non-redox active Cdc25B inhibitors should provide valuable tools to explore the inhibition of the Cdc25 phosphatases as potential mono- or combination therapies for cancer.
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Affiliation(s)
- Paul A Johnston
- University of Pittsburgh Drug Discovery Institute, Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA.
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Abstract
The large-scale structural biology projects that target human proteins focus predominantly on the catalytic domains of potential therapeutic targets and the domains of human proteins that mediate protein-protein and protein-small-molecule interactions. Their main scientific objective is to elucidate the molecular basis for specificity and selectivity of function within large protein families of therapeutic interest, such as kinases, phosphatases, and proteins involved in epigenetic regulation. Half of the unique human protein structures determined in the past three years derive from these initiatives.
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Affiliation(s)
- Aled Edwards
- Banting and Best Department of Medical Research, University of Toronto, Ontario M5G 1L6, Canada
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41
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Balasu MC, Spiridon LN, Miron S, Craescu CT, Scheidig AJ, Petrescu AJ, Szedlacsek SE. Interface analysis of the complex between ERK2 and PTP-SL. PLoS One 2009; 4:e5432. [PMID: 19424502 PMCID: PMC2675061 DOI: 10.1371/journal.pone.0005432] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2009] [Accepted: 03/27/2009] [Indexed: 01/13/2023] Open
Abstract
The activity of ERK2, an essential component of MAP-kinase pathway, is under the strict control of various effector proteins. Despite numerous efforts, no crystal structure of ERK2 complexed with such partners has been obtained so far. PTP-SL is a major regulator of ERK2 activity. To investigate the ERK2–PTP-SL complex we used a combined method based on cross-linking, MALDI-TOF analysis, isothermal titration calorimetry, molecular modeling and docking. Hence, new insights into the stoichiometry, thermodynamics and interacting regions of the complex are obtained and a structural model of ERK2-PTP-SL complex in a state consistent with PTP-SL phosphatase activity is developed incorporating all the experimental constraints available at hand to date. According to this model, part of the N-terminal region of PTP-SL has propensity for intrinsic disorder and becomes structured within the complex with ERK2. The proposed model accounts for the structural basis of several experimental findings such as the complex-dissociating effect of ATP, or PTP-SL blocking effect on the ERK2 export to the nucleus. A general observation emerging from this model is that regions involved in substrate binding in PTP-SL and ERK2, respectively are interacting within the interface of the complex.
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Affiliation(s)
- Mihaela C. Balasu
- Department of Enzymology, Institute of Biochemistry, Bucharest, Romania
- Department of Organic Chemistry , University POLITEHNICA, Bucharest, Romania
| | - Laurentiu N. Spiridon
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry, Bucharest, Romania
| | - Simona Miron
- Institut Curie Centre de Recherche, Orsay, France
- INSERM U759, Orsay, France
| | | | - Axel J. Scheidig
- Zoologisches Institut, Strukturbiologie/ZBM, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Andrei-Jose Petrescu
- Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry, Bucharest, Romania
| | - Stefan E. Szedlacsek
- Department of Enzymology, Institute of Biochemistry, Bucharest, Romania
- * E-mail:
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42
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Barr AJ, Ugochukwu E, Lee WH, King ON, Filippakopoulos P, Alfano I, Savitsky P, Burgess-Brown NA, Müller S, Knapp S. Large-scale structural analysis of the classical human protein tyrosine phosphatome. Cell 2009; 136:352-63. [PMID: 19167335 PMCID: PMC2638020 DOI: 10.1016/j.cell.2008.11.038] [Citation(s) in RCA: 358] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Revised: 09/15/2008] [Accepted: 11/20/2008] [Indexed: 02/05/2023]
Abstract
Protein tyrosine phosphatases (PTPs) play a critical role in regulating cellular functions by selectively dephosphorylating their substrates. Here we present 22 human PTP crystal structures that, together with prior structural knowledge, enable a comprehensive analysis of the classical PTP family. Despite their largely conserved fold, surface properties of PTPs are strikingly diverse. A potential secondary substrate-binding pocket is frequently found in phosphatases, and this has implications for both substrate recognition and development of selective inhibitors. Structural comparison identified four diverse catalytic loop (WPD) conformations and suggested a mechanism for loop closure. Enzymatic assays revealed vast differences in PTP catalytic activity and identified PTPD1, PTPD2, and HDPTP as catalytically inert protein phosphatases. We propose a “head-to-toe” dimerization model for RPTPγ/ζ that is distinct from the “inhibitory wedge” model and that provides a molecular basis for inhibitory regulation. This phosphatome resource gives an expanded insight into intrafamily PTP diversity, catalytic activity, substrate recognition, and autoregulatory self-association.
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Affiliation(s)
- Alastair J. Barr
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
- Corresponding author
| | - Emilie Ugochukwu
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Wen Hwa Lee
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Oliver N.F. King
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Panagis Filippakopoulos
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Ivan Alfano
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Pavel Savitsky
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Nicola A. Burgess-Brown
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Susanne Müller
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Stefan Knapp
- University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
- University of Oxford, Department of Clinical Pharmacology, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
- Corresponding author
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Critton DA, Tortajada A, Stetson G, Peti W, Page R. Structural basis of substrate recognition by hematopoietic tyrosine phosphatase. Biochemistry 2009; 47:13336-45. [PMID: 19053285 DOI: 10.1021/bi801724n] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hematopoietic tyrosine phosphatase (HePTP) is one of three members of the kinase interaction motif (KIM) phosphatase family which also includes STEP and PCPTP1. The KIM-PTPs are characterized by a 15 residue sequence, the KIM, which confers specific high-affinity binding to their only known substrates, the MAP kinases Erk and p38, an interaction which is critical for their ability to regulate processes such as T cell differentiation (HePTP) and neuronal signaling (STEP). The KIM-PTPs are also characterized by a unique set of residues in their PTP substrate binding loops, where 4 of the 13 residues are differentially conserved among the KIM-PTPs as compared to more than 30 other class I PTPs. One of these residues, T106 in HePTP, is either an aspartate or asparagine in nearly every other PTP. Using multiple techniques, we investigate the role of these KIM-PTP specific residues in order to elucidate the molecular basis of substrate recognition by HePTP. First, we used NMR spectroscopy to show that Erk2-derived peptides interact specifically with HePTP at the active site. Next, to reveal the molecular details of this interaction, we solved the high-resolution three-dimensional structures of two distinct HePTP-Erk2 peptide complexes. Strikingly, we were only able to obtain crystals of these transient complexes using a KIM-PTP specific substrate-trapping mutant, in which the KIM-PTP specific residue T106 was mutated to an aspartic acid (T106D). The introduced aspartate side chain facilitates the coordination of the bound peptides, thereby stabilizing the active dephosphorylation complex. These structures establish the essential role of HePTP T106 in restricting HePTP specificity to only those substrates which are able to interact with KIM-PTPs via the KIM (e.g., Erk2, p38). Finally, we describe how this interaction of the KIM is sufficient for overcoming the otherwise weak interaction at the active site of KIM-PTPs.
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Affiliation(s)
- David A Critton
- Department of Molecular Biology, Brown University, Providence, Rhode Island 02912, USA
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44
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Jeeves M, McClelland DM, Barr AJ, Overduin M. Sequence-specific 1H, 13C and 15N backbone resonance assignments of the 34 kDa catalytic domain of human PTPN7. BIOMOLECULAR NMR ASSIGNMENTS 2008; 2:101-103. [PMID: 19636879 DOI: 10.1007/s12104-008-9095-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Accepted: 05/06/2008] [Indexed: 05/28/2023]
Abstract
PTPN7 is a protein tyrosine phosphatase responsible for inactivation of MAPK in leukocytes. Here we report the backbone resonance assignments of the 34 kDa phosphatase domain of human PTPN7, which is amplified in myeloid malignancies and deleted in lymphoproliferative disorders.
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Affiliation(s)
- Mark Jeeves
- Cancer Research UK Institute for Cancer Studies, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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45
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Tabernero L, Aricescu AR, Jones EY, Szedlacsek SE. Protein tyrosine phosphatases: structure-function relationships. FEBS J 2008; 275:867-82. [PMID: 18298793 DOI: 10.1111/j.1742-4658.2008.06251.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structural analysis of protein tyrosine phosphatases (PTPs) has expanded considerably in the last several years, producing more than 200 structures in this class of enzymes (from 35 different proteins and their complexes with ligands). The small-medium size of the catalytic domain of approximately 280 residues plus a very compact fold makes it amenable to cloning and overexpression in bacterial systems thus facilitating crystallographic analysis. The low molecular weight PTPs being even smaller, approximately 150 residues, are also perfect targets for NMR analysis. The availability of different structures and complexes of PTPs with substrates and inhibitors has provided a wealth of information with profound effects in the way we understand their biological functions. Developments in mammalian expression technology recently led to the first crystal structure of a receptor-like PTP extracellular region. Altogether, the PTP structural work significantly advanced our knowledge regarding the architecture, regulation and substrate specificity of these enzymes. In this review, we compile the most prominent structural traits that characterize PTPs and their complexes with ligands. We discuss how the data can be used to design further functional experiments and as a basis for drug design given that many PTPs are now considered strategic therapeutic targets for human diseases such as diabetes and cancer.
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46
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Structural genomics and drug discovery: all in the family. Curr Opin Chem Biol 2008; 12:32-9. [PMID: 18282486 DOI: 10.1016/j.cbpa.2008.01.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 01/23/2008] [Accepted: 01/28/2008] [Indexed: 11/22/2022]
Abstract
Structural genomics is starting to have an impact on the early stages of drug discovery and target validation through the contribution of new structures of known and potential drug targets, their complexes with ligands and protocols and reagents for additional structural work within a drug discovery program. Recent progress includes structures of targets from bacterial, viral and protozoan human pathogens, and human targets from known or potential druggable protein families such as, kinases, phosphatases, dehydrogenases/oxidoreductases, sulfo-, acetyl- and methyl-transferases, and a number of other key metabolic enzymes. Importantly, many of these structures contained ligands in the active sites, including for example, the first structures of target-bound therapeutics. Structural genomics of protein families combined with ligand discovery holds particular promise for advancing early stage discovery programs.
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47
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Thalmeier A, Dickmann M, Giegling I, Schneider B, M Hartmann A, Maurer K, Schnabel A, Kauert G, Möller HJ, Rujescu D. Gene expression profiling of post-mortem orbitofrontal cortex in violent suicide victims. Int J Neuropsychopharmacol 2008; 11:217-28. [PMID: 17608962 DOI: 10.1017/s1461145707007894] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The neurobiological basis of suicidal behaviour is multifactorial and complex. Several lines of evidence indicate that environmental factors as well as multiple genes and interactions of both are implicated in its aetiology. The aim of this study was to establish the transcriptomic expression profile of post-mortem brain tissue of suicide victims in order to identify new candidate genes and biological patterns for suicidal behaviour. Post-mortem orbitofrontal cortex tissue was derived from 11 suicide victims and 10 non-psychiatric controls carefully selected from a brain bank of over 150 brains, and the expression of more than 23000 messenger RNAs was assessed in this case-control study. Validation experiments were carried out using quantitative RT-PCR as an independent method. A classification of the differentially expressed genes according to their biological function and statistical analyses of the data were performed in order to identify biological pathways that are over-represented in the suicide group. In total, 124 transcripts demonstrated significant changes (fold changes > or = 1.3, p value < or = 0.01), with 59 showing under-, and 65 over-expression in the suicide group. The results could be validated for nine particularly interesting transcripts (CDCA7L, CDH12, EFEMP1, MLC1, PCDHB5, PTPRR, S100A13, SCN2B, and ZFP36). The pathway analysis showed that the Gene Ontology categories 'central nervous system development', 'homophilic cell adhesion', 'regulation of cell proliferation' and 'transmission of nerve impulse' were significantly enriched. The differentially expressed genes and significant biological processes might be involved in the pathophysiology of suicide and warrant further attention.
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Affiliation(s)
- Andreas Thalmeier
- Department of Psychiatry, Ludwig Maximilians University, Munich, Germany
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48
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Nordle AKL, Rios P, Gaulton A, Pulido R, Attwood TK, Tabernero L. Functional assignment of MAPK phosphatase domains. Proteins 2007; 69:19-31. [PMID: 17596826 DOI: 10.1002/prot.21477] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Mitogen-activated protein kinase (MAPK) pathways are well conserved in most organisms, from yeast to humans. The principal components of these pathways are MAP kinases whose activity is regulated by phosphorylation, implicating various MAPK protein effectors-in particular, protein phosphatases that inactivate MAPKs by dephosphorylation. The molecular basis of binding specificity of such regulatory phosphatases to MAPKs is poorly understood. To try to pinpoint potential functional regions within the sequences and to help identify new family members, we have applied a multimotif pattern-recognition approach to characterize two MAPK phosphatase subfamilies (tyrosine-specific and dual specificity) that are crucial in the regulation of MAPKs. We built "fingerprints" for these two subfamilies that are unique to, and highly discriminatory for, each group of proteins. The fingerprints were used in a genome-wide screen, identifying more than 80 MAPK phosphatase domains, several of which were in partial sequences or unclassified proteins. We confirmed experimentally that one predicted MAPK phosphatase orthologue in Xenopus binds to ERK1/2, suggesting a role in MAPK signaling and thus supporting our functional predictions. Further analysis, mapping the fingerprints on the three-dimensional structure of MAPK phosphatases, revealed that some of the fingerprint motifs reside in the N-terminal noncatalytic regions coinciding with reported MAPK binding sites, while others lie within the catalytic phosphatase domain. These results also suggest the presence of putative allosteric sites in the catalytic region for modulation of protein-protein interactions, and provide a framework for future experimental validation.
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Affiliation(s)
- Anna K L Nordle
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
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49
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Johnston PA, Foster CA, Shun TY, Skoko JJ, Shinde S, Wipf P, Lazo JS. Development and Implementation of a 384-Well Homogeneous Fluorescence Intensity High-Throughput Screening Assay to Identify Mitogen-Activated Protein Kinase Phosphatase-1 Dual-Specificity Protein Phosphatase Inhibitors. Assay Drug Dev Technol 2007; 5:319-32. [PMID: 17638532 DOI: 10.1089/adt.2007.066] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We report here the miniaturization, development, and implementation of a homogeneous 384-well fluorescence intensity high-throughput screening (HTS) assay for identifying mitogen-activated protein kinase (MAPK) phosphatase-1 (MKP-1) dual-specificity phosphatase inhibitors. As part of the National Institutes of Health (NIH) Molecular Libraries Screening Center Network (MLSCN), the MKP-1 assay was utilized to screen an NIH diversity library of 65,239 compounds for inhibitors of MKP-1 activity at 10 microM and was also used to confirm the concentration dependence of active agents identified in the primary screen. We observed 100 (0.15%) compounds that inhibited MKP-1 in vitro by > or =50% at 10 microM in the primary assay, and 46 of the 100 compounds were confirmed as concentration-dependent inhibitors of MKP-1 with 50% inhibitory concentration (IC(50)) values of <50 microM; four exhibited IC(50) values <1.0 microM, six produced IC(50) values in the 1-10 microM range, and 36 produced IC(50) values in the 10-50 microM range. A clustering and classification analysis of the compound structures of the 46 confirmed MKP-1 inhibitors produced 29 singleton structures and seven clusters of related structures. Some MKP-1 inhibitors were members of structural classes or contained substructure pharmacophores that previously were reported to inhibit either MKP-1 or other protein tyrosine phosphatases, validating the HTS assay. Importantly, we have identified several attractive and novel MKP-1 inhibitor structures that warrant further investigation as potential probes to study the biology of MKP-1 and its role in controlling the amplitude and/or duration of MAPK signaling, cell survival, and tumor progression.
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Affiliation(s)
- Paul A Johnston
- Pittsburgh Molecular Libraries Screening Center, Department of Pharmacology, University of Pittsburgh Drug Discovery Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
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50
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Barr AJ, Knapp S. MAPK-specific tyrosine phosphatases: new targets for drug discovery? Trends Pharmacol Sci 2006; 27:525-30. [PMID: 16919785 DOI: 10.1016/j.tips.2006.08.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2006] [Revised: 07/11/2006] [Accepted: 08/03/2006] [Indexed: 10/24/2022]
Abstract
Protein tyrosine phosphatases (PTPs) have key roles in a diverse range of cellular processes, and their dysregulation is associated with several human diseases. Many PTPs are recognized as potential drug targets; however, inhibitor development has focused only on a small number of enzymes, most notably PTP1B for type II diabetes and obesity, and MKP1 and CDC25 for cancer. The future challenge of selective-inhibitor development for PTPs will be significantly facilitated by the recent rapid progress in the structural biology of the 'PTPome'. In this article, we focus on the family of mitogen-activated protein kinase (MAPK)-specific tyrosine phosphatases--PTPN5 [also called striatal-enriched phosphatase (STEP)], PTPN7 (also called hematopoietic PTP) and PTPRR (also called PC12 PTP or STEP-like PTP)--and discuss approaches for achieving selectivity for the MAPK-PTPs at the molecular level using recently determined high-resolution X-ray crystal structures. We believe that the development of specific inhibitors would provide a valuable set of experimental pharmacological tools for investigating the physiological role of these phosphatases and exploring their emerging role in human disease.
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Affiliation(s)
- Alastair J Barr
- Structural Genomics Consortium, University of Oxford, Botnar Research Centre, Oxford, OX3 7LD, UK.
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