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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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52
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Thareja S, Aggarwal S, Bhardwaj TR, Kumar M. Protein Tyrosine Phosphatase 1B Inhibitors: A Molecular Level Legitimate Approach for the Management of Diabetes Mellitus. Med Res Rev 2010; 32:459-517. [DOI: 10.1002/med.20219] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Suresh Thareja
- University Institute of Pharmaceutical Sciences; Panjab University; 160 014; Chandigarh; India
| | - Saurabh Aggarwal
- University Institute of Pharmaceutical Sciences; Panjab University; 160 014; Chandigarh; India
| | | | - Manoj Kumar
- University Institute of Pharmaceutical Sciences; Panjab University; 160 014; Chandigarh; India
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53
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Leone M, Barile E, Vazquez J, Mei A, Guiney D, Dahl R, Pellecchia M. NMR-based design and evaluation of novel bidentate inhibitors of the protein tyrosine phosphatase YopH. Chem Biol Drug Des 2010; 76:10-6. [PMID: 20456369 PMCID: PMC2905849 DOI: 10.1111/j.1747-0285.2010.00982.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We describe the use of a furanyl salicyl nitroxide derivative ('spin-labeled' compound), as a paramagnetic phosphotyrosine mimetic, to carry out a second-site screening by NMR against the PTPase YopH from Yersinia pestis. Using such a fragment-based screening approach we identified several small molecules targeting YopH that bind at sites adjacent to the spin-labeled compound. These second-site fragments were subsequently used to design and synthesize bidentate YopH inhibitors with submicromolar in vitro inhibition, selectivity against the human PTPase PTP1B, and cellular activity against Y. pseudotuberculosis. These initial compounds could result useful in elucidating the structural determinants necessary for YopH inhibition and may help in the design of even more active, selective and cell permeable compounds for the development of novel therapies against Yersiniae.
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Affiliation(s)
- Marilisa Leone
- Infectious and inflammatory Disease Center and Cancer Center, Sanford | Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
- Institute of Biostructures and Bioimaging-CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Elisa Barile
- Infectious and inflammatory Disease Center and Cancer Center, Sanford | Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
| | - Jesus Vazquez
- Infectious and inflammatory Disease Center and Cancer Center, Sanford | Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
| | - Angel Mei
- Infectious and inflammatory Disease Center and Cancer Center, Sanford | Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
| | - Donald Guiney
- Department of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Russel Dahl
- Infectious and inflammatory Disease Center and Cancer Center, Sanford | Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
| | - Maurizio Pellecchia
- Infectious and inflammatory Disease Center and Cancer Center, Sanford | Burnham Medical Research Institute, 10901 North Torrey Pines Rd, 92037 La Jolla, CA, USA
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54
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Zambuzzi WF, Milani R, Teti A. Expanding the role of Src and protein-tyrosine phosphatases balance in modulating osteoblast metabolism: lessons from mice. Biochimie 2010; 92:327-32. [PMID: 20083150 DOI: 10.1016/j.biochi.2010.01.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 01/06/2010] [Indexed: 10/20/2022]
Abstract
The widespread nature of protein phosphorylation/dephosphorylation underscores its key role in cell signaling metabolism, growth and differentiation. Tyrosine phosphorylation of cytoplasmic proteins is a critical event in the regulation of intracellular signaling pathways activated by external stimuli. An adequate balance in protein phosphorylation is a major factor in the regulation of osteoclast and osteoblast activities involved in bone metabolism. However, although phosphorylation is widely recognized as an important regulatory pathway in skeletal development and maintenance, the mechanisms involved are not fully understood. Among the putative protein-tyrosine kinases (ptk) and protein-tyrosine phosphatases (ptp) involved in this phenomenon there is increasing evidence that Src and low molecular weight-ptps play a central role in a range of osteoblast activities, from adhesion to differentiation. A role for Src in bone metabolism was first demonstrated in Src-deficient mice and has since been confirmed using low molecular weight Src inhibitors in animal models of osteoporosis. Several studies have shown that Src is important for cellular proliferation, adhesion and motility. In contrast, few studies have assessed the importance of the ptk/ptp balance in driving osteoblast metabolism. In this review, we summarize our current knowledge of the functional importance of the ptk/ptp balance in osteoblast metabolism, and highlight directions for future research that should improve our understanding of these critical signaling molecules.
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Affiliation(s)
- Willian F Zambuzzi
- Department of Biochemistry, University of Campinas, Campinas, SP, Brazil.
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55
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Vidović D, Schürer SC. Knowledge-based characterization of similarity relationships in the human protein-tyrosine phosphatase family for rational inhibitor design. J Med Chem 2009; 52:6649-59. [PMID: 19810703 DOI: 10.1021/jm9008899] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tyrosine phosphorylation, controlled by the coordinated action of protein-tyrosine kinases (PTKs) and protein-tyrosine phosphatases (PTPs), is a fundamental regulatory mechanism of numerous physiological processes. PTPs are implicated in a number of human diseases, and their potential as prospective drug targets is increasingly being recognized. Despite their biological importance, until now no comprehensive overview has been reported describing how all members of the human PTP family are related. Here we review the entire human PTP family and present a systematic knowledge-based characterization of global and local similarity relationships, which are relevant for the development of small molecule inhibitors. We use parallel homology modeling to expand the current PTP structure space and analyze the human PTPs based on local three-dimensional catalytic sites and domain sequences. Furthermore, we demonstrate the importance of binding site similarities in understanding cross-reactivity and inhibitor selectivity in the design of small molecule inhibitors.
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Affiliation(s)
- Dusica Vidović
- Center for Computational Science, University of Miami, Miami, Florida 33136, USA
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56
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Wu S, Vossius S, Rahmouni S, Miletic AV, Vang T, Vazquez-Rodriguez J, Cerignoli F, Arimura Y, Williams S, Hayes T, Moutschen M, Vasile S, Pellecchia M, Mustelin T, Tautz L. Multidentate small-molecule inhibitors of vaccinia H1-related (VHR) phosphatase decrease proliferation of cervix cancer cells. J Med Chem 2009; 52:6716-23. [PMID: 19888758 PMCID: PMC2790023 DOI: 10.1021/jm901016k] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Loss of VHR phosphatase causes cell cycle arrest in HeLa carcinoma cells, suggesting that VHR inhibition may be a useful approach to halt the growth of cancer cells. We recently reported that VHR is upregulated in several cervix cancer cell lines as well as in carcinomas of the uterine cervix. Here we report the development of multidentate small-molecule inhibitors of VHR that inhibit its enzymatic activity at nanomolar concentrations and exhibit antiproliferative effects on cervix cancer cells. Chemical library screening was used to identify hit compounds, which were further prioritized in profiling and kinetic experiments. SAR analysis was applied in the search for analogs with improved potency and selectivity, resulting in the discovery of novel inhibitors that are able to interact with both the phosphate-binding pocket and several distinct hydrophobic regions within VHR's active site. This multidentate binding mode was confirmed by X-ray crystallography. The inhibitors decreased the proliferation of cervix cancer cells, while growth of primary normal keratinocytes was not affected. These compounds may be a starting point to develop drugs for the treatment of cervical cancer.
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Affiliation(s)
- Shuangding Wu
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Sofie Vossius
- Immunology and Infectious Diseases Unit, GIGA-R, Liège University, Liège, Belgium
| | - Souad Rahmouni
- Immunology and Infectious Diseases Unit, GIGA-R, Liège University, Liège, Belgium
| | - Ana V. Miletic
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Torkel Vang
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Jesus Vazquez-Rodriguez
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Fabio Cerignoli
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Yutaka Arimura
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Scott Williams
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Tikva Hayes
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Michel Moutschen
- Immunology and Infectious Diseases Unit, GIGA-R, Liège University, Liège, Belgium
| | - Stefan Vasile
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Maurizio Pellecchia
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Tomas Mustelin
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Lutz Tautz
- Infectious and Inflammatory Disease Center and Cancer Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
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57
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Fridberg M, Servin A, Anagnostaki L, Linderoth J, Berglund M, Söderberg O, Enblad G, Rosén A, Mustelin T, Jerkeman M, Persson JL, Wingren AG. Protein expression and cellular localization in two prognostic subgroups of diffuse large B-cell lymphoma: Higher expression of ZAP70 and PKC-β II in the non-germinal center group and poor survival in patients deficient in nuclear PTEN. Leuk Lymphoma 2009; 48:2221-32. [DOI: 10.1080/10428190701636443] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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58
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Wu S, Bottini M, Rickert RC, Mustelin T, Tautz L. In silico screening for PTPN22 inhibitors: active hits from an inactive phosphatase conformation. ChemMedChem 2009; 4:440-4. [PMID: 19177473 DOI: 10.1002/cmdc.200800375] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A gain-of-function mutant of the lymphoid phosphatase Lyp (PTPN22) has recently been implicated in type 1 diabetes and other autoimmune diseases, suggesting that small-molecule inhibitors of Lyp could be useful for the treatment of autoimmunity. Virtual ligand screening (VLS) was applied in the search for hit compounds. Two different docking algorithms, FlexX and ICM, were used to screen a library of 'drug-like' molecules against two different 3D structures, representing the catalytic site of Lyp in both the inactive 'open' and active 'closed' conformations. The top-scoring compounds of each VLS run were tested for their inhibitory activity against recombinant Lyp. Interestingly, VLS with both active and inactive conformations yielded very potent hits, with IC(50) values in the sub- and low-micromolar range. Moreover, many of these hits showed high docking scores only with one conformation. For instance, this was the case with several 2-benzamidobenzoic acid derivatives, which specifically docked into the inactive open form. Tryptophan fluorescence measurements further support a binding mode in which these compounds seem to stabilize the phosphatase in its inactive conformation.
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Affiliation(s)
- Shuangding Wu
- Infectious and Inflammatory Disease Center, Burnham Institute for Medical Research, 10901 N. Torrey Pines Rd., La Jolla, CA 92037, USA
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59
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Panchal RG, Ulrich RL, Bradfute SB, Lane D, Ruthel G, Kenny TA, Iversen PL, Anderson AO, Gussio R, Raschke WC, Bavari S. Reduced expression of CD45 protein-tyrosine phosphatase provides protection against anthrax pathogenesis. J Biol Chem 2009; 284:12874-85. [PMID: 19269962 DOI: 10.1074/jbc.m809633200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The modulation of cellular processes by small molecule inhibitors, gene inactivation, or targeted knockdown strategies combined with phenotypic screens are powerful approaches to delineate complex cellular pathways and to identify key players involved in disease pathogenesis. Using chemical genetic screening, we tested a library of known phosphatase inhibitors and identified several compounds that protected Bacillus anthracis infected macrophages from cell death. The most potent compound was assayed against a panel of sixteen different phosphatases of which CD45 was found to be most sensitive to inhibition. Testing of a known CD45 inhibitor and antisense phosphorodiamidate morpholino oligomers targeting CD45 also protected B. anthracis-infected macrophages from cell death. However, reduced CD45 expression did not protect anthrax lethal toxin (LT) treated macrophages, suggesting that the pathogen and independently added LT may signal through distinct pathways. Subsequent, in vivo studies with both gene-targeted knockdown of CD45 and genetically engineered mice expressing reduced levels of CD45 resulted in protection of mice after infection with the virulent Ames B. anthracis. Intermediate levels of CD45 expression were critical for the protection, as mice expressing normal levels of CD45 or disrupted CD45 phosphatase activity or no CD45 all succumbed to this pathogen. Mechanism-based studies suggest that the protection provided by reduced CD45 levels results from regulated immune cell homeostasis that may diminish the impact of apoptosis during the infection. To date, this is the first report demonstrating that reduced levels of host phosphatase CD45 modulate anthrax pathogenesis.
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Affiliation(s)
- Rekha G Panchal
- United States Army Medical Research Institute of Infectious Diseases, Frederick, MD 21702-5011, USA.
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60
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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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61
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Biological Activity of Aminophosphonic Acids and Their Short Peptides. TOPICS IN HETEROCYCLIC CHEMISTRY 2009. [DOI: 10.1007/7081_2008_14] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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62
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Bakan A, Lazo JS, Wipf P, Brummond KM, Bahar I. Toward a molecular understanding of the interaction of dual specificity phosphatases with substrates: insights from structure-based modeling and high throughput screening. Curr Med Chem 2008; 15:2536-44. [PMID: 18855677 PMCID: PMC2764859 DOI: 10.2174/092986708785909003] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Dual-specificity phosphatases (DSPs) are important, but poorly understood, cell signaling enzymes that remove phosphate groups from tyrosine and serine/threonine residues on their substrate. Deregulation of DSPs has been implicated in cancer, obesity, diabetes, inflammation, and Alzheimer's disease. Due to their biological and biomedical significance, DSPs have increasingly become the subject of drug discovery high-throughput screening (HTS) and focused compound library development efforts. Progress in identifying selective and potent DSP inhibitors has, however, been restricted by the lack of sufficient structural data on inhibitor-bound DSPs. The shallow, almost flat, substrate binding sites in DSPs have been a major factor in hampering the rational design and the experimental development of active site inhibitors. Recent experimental and virtual HTS studies, as well as advances in molecular modeling, provide new insights into the potential mechanisms for substrate recognition and binding by this important class of enzymes. We present herein an overview of the progress, along with a brief description of applications to two types of DSPs: Cdc25 and MAP kinase phosphatase (MKP) family members. In particular, we focus on combined computational and experimental efforts for designing Cdc25B and MKP-1 inhibitors and understanding their mechanisms of interactions with their target proteins. These studies emphasize the utility of developing computational models and methods that meet the two major challenges currently faced in structure-based in silico design of lead compounds: the conformational flexibility of the target protein and the entropic contribution to the selection and stabilization of particular bound conformers.
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Affiliation(s)
- Ahmet Bakan
- Department of Computational Biology, School of Medicine, University of Pittsburgh, 3064 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15213, USA
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63
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Abstract
Proper control of cell cycle progression requires the functionality of a small family of activating phosphatases termed Cdc25, which have been implicated in cancer and Alzheimer's disease. These protein tyrosine phosphatases are therefore recognized as attractive molecular targets for small molecules. We review the rationale, approaches, progress and challenges for developing small molecule inhibitors of the Cdc25 family. A number of potential chemical probes are discussed and their characteristics are summarized.
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Affiliation(s)
- John S Lazo
- Department of Pharmacology and Chemical Biology, Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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64
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Fridberg M, Kjellström S, Anagnostaki L, Skogvall I, Mustelin T, Wiebe T, Persson JL, Dictor M, Wingren AG. Immunohistochemical analyses of phosphatases in childhood B-cell lymphoma: lower expression of PTEN and HePTP and higher number of positive cells for nuclear SHP2 in B-cell lymphoma cases compared to controls. Pediatr Hematol Oncol 2008; 25:528-40. [PMID: 18728972 DOI: 10.1080/08880010802237054] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Although many pediatric B-cell lymphoma patients are being cured today, much is still unknown about the pathogenesis of this disease. Protein tyrosine phosphatases are involved in the control of survival, growth, and differentiation of cells. The authors have analyzed 26 pediatric B-cell lymphoma cases for the expression of a panel of phosphatases and report a statistically significant lower expression intensity of PTEN and HePTP and higher nuclear SHP2 expression in B-cell lymphoma cases compared to lymphoid tissue. Knowledge about the expression of key regulatory proteins in pediatric B-cell lymphomas is necessary for revealing the complex molecular background of this disease.
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Affiliation(s)
- Marie Fridberg
- Department of Tumor Biology, Lund University, Malmö University Hospital, Malmö, Sweden
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65
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Mitra S, Barrios AM. Identifying selective protein tyrosine phosphatase substrates and inhibitors from a fluorogenic, combinatorial peptide library. Chembiochem 2008; 9:1216-9. [PMID: 18412190 DOI: 10.1002/cbic.200800046] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sayantan Mitra
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
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66
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Lawrence HR, Pireddu R, Chen L, Luo Y, Sung SS, Szymanski AM, Yip MLR, Guida WC, Sebti SM, Wu J, Lawrence NJ. Inhibitors of Src homology-2 domain containing protein tyrosine phosphatase-2 (Shp2) based on oxindole scaffolds. J Med Chem 2008; 51:4948-56. [PMID: 18680359 DOI: 10.1021/jm8002526] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Screening of the NCI diversity set of compounds has led to the identification of 5 (NSC-117199), which inhibits the protein tyrosine phosphatase (PTP) Shp2 with an IC50 of 47 microM. A focused library incorporating an isatin scaffold was designed and evaluated for inhibition of Shp2 and Shp1 PTP activities. Several compounds were identified that selectively inhibit Shp2 over Shp1 and PTP1B with low to submicromolar activity. A model for the binding of the active compounds is proposed.
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Affiliation(s)
- Harshani R Lawrence
- Drug Discovery Program, Moffitt Cancer Center, 12901 Magnolia Drive, Tampa, Florida 33612, USA.
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67
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Ling Q, Huang Y, Zhou Y, Cai Z, Xiong B, Zhang Y, Ma L, Wang X, Li X, Li J, Shen J. Illudalic acid as a potential LAR inhibitor: synthesis, SAR, and preliminary studies on the mechanism of action. Bioorg Med Chem 2008; 16:7399-409. [PMID: 18579388 DOI: 10.1016/j.bmc.2008.06.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 06/08/2008] [Accepted: 06/10/2008] [Indexed: 11/30/2022]
Abstract
A novel synthesis of the human leukocyte common antigen-related (LAR) phosphatase inhibitor, illudalic acid, has been achieved by a route more amenable to structure modifications. A series of simpler analogues of illudalic acid was synthesized and evaluated for potency in inhibiting LAR. The structure-activity relationship (SAR) study has shown that the 5-formyl group and the hemi-acetal lactone are crucial for effective inhibition of LAR activity, and are the key pharmacophores of illudalic acid. The fused dimethylcyclopentene ring moiety evidently helps to enhance the potency of illudalic acid against LAR. A preliminary study of the mechanism of action of illudalic acid against LAR was conducted using electrospray ionization mass spectrometry (ESI-MS) and molecular docking techniques. The results are in full agreement with the described mechanism.
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Affiliation(s)
- Qing Ling
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, PR China
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68
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Vang T, Miletic AV, Arimura Y, Tautz L, Rickert RC, Mustelin T. Protein tyrosine phosphatases in autoimmunity. Annu Rev Immunol 2008; 26:29-55. [PMID: 18303998 DOI: 10.1146/annurev.immunol.26.021607.090418] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein tyrosine phosphatases (PTPs) are important regulators of many cellular functions and a growing number of PTPs have been implicated in human disease conditions, such as developmental defects, neoplastic disorders, and immunodeficiency. Here, we review the involvement of PTPs in human autoimmunity. The leading examples include the allelic variant of the lymphoid tyrosine phosphatase (PTPN22), which is associated with multiple autoimmune diseases, and mutations that affect the exon-intron splicing of CD45 (PTPRC). We also find it likely that additional PTPs are involved in susceptibility to autoimmune and inflammatory diseases. Finally, we discuss the possibility that PTPs regulating the immune system may serve as therapeutic targets.
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Affiliation(s)
- Torkel Vang
- Burnham Institute for Medical Research, La Jolla, California 92037, USA.
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69
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Bertini I, Fragai M, Luchinat C, Talluri E. Water-Based Ligand Screening for Paramagnetic Metalloproteins. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200800327] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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70
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Bertini I, Fragai M, Luchinat C, Talluri E. Water-Based Ligand Screening for Paramagnetic Metalloproteins. Angew Chem Int Ed Engl 2008; 47:4533-7. [DOI: 10.1002/anie.200800327] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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71
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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: 110] [Impact Index Per Article: 6.9] [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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72
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Berman-Golan D, Granot-Attas S, Elson A. Protein tyrosine phosphatase epsilon and Neu-induced mammary tumorigenesis. Cancer Metastasis Rev 2008; 27:193-203. [DOI: 10.1007/s10555-008-9124-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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73
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Tautz L, Mustelin T. Strategies for developing protein tyrosine phosphatase inhibitors. Methods 2007; 42:250-60. [PMID: 17532512 DOI: 10.1016/j.ymeth.2007.02.014] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2007] [Accepted: 02/15/2007] [Indexed: 10/23/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) play vital roles in numerous cellular processes and are implicated in a growing number of human diseases, ranging from cancer to cardiovascular, immunological, infectious, neurological, and metabolic diseases. Here we present methods for developing small molecule inhibitors for these enzymes, starting with how to set up a high throughput chemical library screening for PTP inhibitors, how to confirm and prioritize hits, and how to circumnavigate possible pitfalls. Next, we present the relatively new hit generating method of in silico or virtual screening. We give an overview of existing software tools, describe how to choose and generate protein target structures and illustrate the procedure with examples. We then discuss how three-dimensional PTP structures can be analyzed in terms of their potential to bind small molecule inhibitors selectively over homologous proteins and how computer tools can be applied for lead optimization efforts. We finish with a perspective of how well these PTP inhibitors might perform as future drugs to treat human disease.
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Affiliation(s)
- Lutz Tautz
- Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
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74
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Bishop AC, Zhang XY, Lone AM. Generation of inhibitor-sensitive protein tyrosine phosphatases via active-site mutations. Methods 2007; 42:278-88. [PMID: 17532515 PMCID: PMC1950444 DOI: 10.1016/j.ymeth.2007.02.005] [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] [Received: 01/09/2007] [Accepted: 02/14/2007] [Indexed: 01/23/2023] Open
Abstract
Protein tyrosine phosphatases (PTPs) catalyze the dephosphorylation of phosphotyrosine, a central control element in mammalian signal transduction. Small-molecule inhibitors that are specific for each cellular PTP would be valuable tools in dissecting phosphorylation networks and for validating PTPs as therapeutic targets. However, the common architecture of PTP active sites impedes the discovery of selective PTP inhibitors. Our laboratory has recently used enzyme/inhibitor-interface engineering to generate selective PTP inhibitors. The crux of the strategy resides in the design of "inhibitor-sensitized" PTPs through protein engineering of a novel binding pocket in the target PTP. "Allele-specific" inhibitors that selectively target the sensitized PTP can be synthesized by modifying broad-specificity inhibitors with bulky chemical groups that are incompatible with wild-type PTP active sites; alternatively, specific inhibitors that serendipitously recognize the sensitized PTP's non-natural pocket may be discovered from panels of "non-rationally" designed compounds. In this review, we describe the current state of the PTP-sensitization strategy, with emphases on the methodology of identifying PTP-sensitizing mutations and synthesizing the compounds that have been found to target PTPs in an allele-specific manner. Moreover, we discuss the scope of PTP sensitization in regard to the potential application of the approach across the family of classical PTPs.
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Affiliation(s)
- Anthony C Bishop
- Department of Chemistry, Amherst College, Amherst, MA 01002, USA.
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75
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Hsu EC, Lin YC, Hung CS, Huang CJ, Lee MY, Yang SC, Ting LP. Suppression of hepatitis B viral gene expression by protein-tyrosine phosphatase PTPN3. J Biomed Sci 2007; 14:731-44. [PMID: 17588219 DOI: 10.1007/s11373-007-9187-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Accepted: 06/03/2007] [Indexed: 10/23/2022] Open
Abstract
Protein-tyrosine phosphatase PTPN3 is a membrane-associated non-receptor protein-tyrosine phosphatase. PTPN3 contains a N-terminal FERM domain, a middle PDZ domain, and a C-terminal phosphatase domain. Upon co-expression of PTPN3, the level of human hepatitis B viral (HBV) RNAs, 3.5 kb, 2.4/2.1 kb, and 0.7 kb transcribed from a replicating HBV expression plasmid is significantly reduced in human hepatoma HuH-7 cells. When the expression of endogenous PTPN3 protein is diminished by specific small interfering RNA, the expression of HBV genes is enhanced, indicating that the endogenous PTPN3 indeed plays a suppressive role on HBV gene expression. PTPN3 can interact with HBV core protein. The interaction is mediated via the PDZ domain of PTPN3 and the carboxyl-terminal last four amino acids of core. Either deletion of PDZ domain of PTPN3 or substitution of PDZ ligand in core has no effect on PTPN3-mediated suppression. These results clearly show that the interaction of PTPN3 with core is not required for PTPN3 suppressive effect. Mutation of (359)serine and (835)serine of 14-3-3beta binding sites to alanine, which slightly reduces the interaction with 14-3-3beta, does not influence the PTPN3 effect. In contrast, mutation of the invariant (842)cysteine residue in phosphatase domain to serine, which makes the phosphatase activity inactive, does not change its subcellular localization and interaction with core or 14-3-3beta, but completely abolishes PTPN3-mediated suppression. Furthermore, deletion of FERM domain does not affect the phosphatase activity or interaction with 14-3-3beta, but changes the subcellular localization from cytoskeleton-membrane interface to cytoplasm and nucleus, abolishes binding to core, and diminishes the PTPN3 effect on HBV gene expression. Taken together, these results demonstrate that the phosphatase activity and FERM domain of PTPN3 are essential for its suppression of HBV gene expression.
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MESH Headings
- Carcinoma, Hepatocellular/metabolism
- Cells, Cultured
- Fluorescent Antibody Technique
- Gene Expression Regulation, Viral
- Gene Silencing
- Genes, Viral
- Hepatitis B virus/genetics
- Hepatitis B virus/metabolism
- Humans
- Liver Neoplasms/metabolism
- Protein Structure, Tertiary
- Protein Tyrosine Phosphatase, Non-Receptor Type 3/analysis
- Protein Tyrosine Phosphatase, Non-Receptor Type 3/genetics
- Protein Tyrosine Phosphatase, Non-Receptor Type 3/metabolism
- Suppression, Genetic
- Transfection
- Tumor Cells, Cultured
- Viral Core Proteins/genetics
- Viral Core Proteins/metabolism
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Affiliation(s)
- En-Chi Hsu
- Institute of Microbiology and Immunology, School of Life Science, National Yang-Ming University, Pei-Tou, Taipei 11221, Taiwan, ROC
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76
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Vazquez J, Tautz L, Ryan JJ, Vuori K, Mustelin T, Pellecchia M. Development of molecular probes for second-site screening and design of protein tyrosine phosphatase inhibitors. J Med Chem 2007; 50:2137-43. [PMID: 17394300 PMCID: PMC2615387 DOI: 10.1021/jm061481l] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report on the design, synthesis, and evaluation of a series of furanyl-salicyl-nitroxide derivatives as effective chemical probes for second-site screening against phosphotyrosine phosphatases (PTPs) using NMR-based techniques. The compounds have been tested against a panel of PTPs to assess their ability to inhibit a broad spectrum of these phosphatases. The utility of the derived compounds is illustrated with the phosphatase YopH, a bacterial toxin from Yersinia pestis. Novel chemical fragments were identified during an NMR-based screen for compounds that are capable of binding on the surface of YopH in regions adjacent the catalytic site in the presence of the spin-labeled compounds. Our data demonstrate the value of the derived chemical probes for NMR-based second-site screening in PTPs.
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Affiliation(s)
| | | | | | | | | | - Maurizio Pellecchia
- *To whom correspondence should be addressed: Maurizio Pellecchia. Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, California, 92037., Phone: (858) 646-3159. Fax: (858) 713-9925. E-mail:
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77
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McCulloch CA, Downey GP, El-Gabalawy H. Signalling platforms that modulate the inflammatory response: new targets for drug development. Nat Rev Drug Discov 2006; 5:864-76. [PMID: 17016427 DOI: 10.1038/nrd2109] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Therapeutically controlling inflammation is essential for the clinical management of many high-prevalence human diseases. Drugs that block the pro-inflammatory cytokines tumour-necrosis factor-alpha and interleukin-1 (IL-1) can improve outcomes for rheumatoid arthritis and other inflammatory diseases but many patients remain refractory to treatment. Here we explore the need for developing new types of anti-inflammatory drugs and the emergence of novel drug targets based on the clustering of IL-1 receptors into multi-protein aggregates associated with cell adhesions. Interference with receptor aggregation into multi-protein complexes effectively abrogates IL-1 signalling. The exploration of the crucial molecules required for receptor clustering, and therefore signal transduction, offers new targets and scope for anti-inflammatory drug development.
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78
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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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79
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Ferreira CV, Justo GZ, Souza ACS, Queiroz KCS, Zambuzzi WF, Aoyama H, Peppelenbosch MP. Natural compounds as a source of protein tyrosine phosphatase inhibitors: application to the rational design of small-molecule derivatives. Biochimie 2006; 88:1859-73. [PMID: 17010496 DOI: 10.1016/j.biochi.2006.08.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2006] [Accepted: 08/25/2006] [Indexed: 12/21/2022]
Abstract
Reversible phosphorylation of tyrosine residues is a key regulatory mechanism for numerous cellular events. Protein tyrosine kinases and protein tyrosine phosphatases (PTPs) have a pivotal role in regulating both normal cell physiology and pathophysiology. Accordingly, deregulated activity of both protein tyrosine kinases and PTPs is involved in the development of numerous congenitically inherited and acquired human diseases, prompting obvious pharmaceutical and academic research interest. The development of compound libraries with higher selective PTP inhibitory activity has been bolstered by the realization that many natural products have such activity and thus are interesting biologically lead compounds, which properties are widely exploited. In addition, more rational approaches have focused on the incorporation of phosphotyrosine mimetics into specific peptide templates (peptidomimetic backbones). Additional factors furthering discovery as well as therapeutic application of new bioactive molecules are the integration of functional genomics, cell biology, structural biology, drug design, molecular screening and chemical diversity. Together, all these factors will lead to new avenues to treat clinical disease based on PTP inhibition.
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Affiliation(s)
- Carmen V Ferreira
- Laboratory of Cell Signaling, Departamento de Bioquímica, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), CP 6109, CEP 13083-970, Campinas, Sao Paulo, Brazil.
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80
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Abstract
The discovery that a single amino acid substitution in the PTPN22 protein tyrosine phosphatase can predispose to so many autoimmune diseases (see chapters 2 and 3), even when present in a single copy, raises many questions regarding the broader significance of this observation. Is there something unique about PTPN22 or are genetic variants of other protein tyrosine phosphatases likely also associated with autoimmune disease? If so, will polymorphisms in other phosphatases be found in the same spectrum of diseases? Are protein tyrosine phosphatases like PTPN22 good drug targets for the treatment of human autoimmunity? In this review, I offer some basis for thinking about these questions.
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Affiliation(s)
- Tomas Mustelin
- Program on Inflammatory Disease Research Infectious and Inflammatory Disease Center, The Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
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81
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Barr AJ, Debreczeni JE, Eswaran J, Knapp S. Crystal structure of human protein tyrosine phosphatase 14 (PTPN14) at 1.65-A resolution. Proteins 2006; 63:1132-6. [PMID: 16534812 DOI: 10.1002/prot.20958] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Alastair J Barr
- Structural Genomics Consortium, University of Oxford, Botnar Research Centre, Oxford, United Kingdom.
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82
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Sim ATR, Ludowyke RI, Verrills NM. Mast cell function: regulation of degranulation by serine/threonine phosphatases. Pharmacol Ther 2006; 112:425-39. [PMID: 16790278 DOI: 10.1016/j.pharmthera.2006.04.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2006] [Accepted: 04/26/2006] [Indexed: 01/28/2023]
Abstract
Mast cells play both effector and modulatory roles in a range of allergic and immune responses. The principal function of these cells is the release of inflammatory mediators from mast cells by degranulation, which involves a complex interplay of signalling molecules. Understanding the molecular architecture underlying mast cell signalling has attracted renewed interest as the capacity for therapeutic intervention through controlling mast cell degranulation is now accepted as a viable proposition. The dynamic regulation of signalling by protein phosphorylation is a well-established phenomenon and many of the early events involved in mast cell activation are well understood. Less well understood however are the events further downstream of receptor activation that allow movement of granules through the cytoskeletal barrier and docking and fusion of granules with the plasma membrane. Whilst a potential role for the protein phosphatase family of signalling enzymes in mast cell function has been accepted for some time, the evidence has largely been derived from the use of broad specificity pharmacological inhibitors and results often depend upon the experimental conditions, leading to conflicting views. In this review, we present and discuss the pharmacological and recent molecular evidence that protein phosphatases, and in particular the protein phosphatase serine/threonine phosphatase type 2A (PP2A), have major regulatory roles to play and may be potential targets for the design of new therapeutic agents.
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Affiliation(s)
- Alistair T R Sim
- School of Biomedical Sciences and Hunter Medical Research Institute, Faculty of Health, The University of Newcastle, Callaghan, NSW, Australia.
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83
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Eswaran J, von Kries J, Marsden B, Longman E, Debreczeni J, Ugochukwu E, Turnbull A, Lee W, Knapp S, Barr A. Crystal structures and inhibitor identification for PTPN5, PTPRR and PTPN7: a family of human MAPK-specific protein tyrosine phosphatases. Biochem J 2006; 395:483-91. [PMID: 16441242 PMCID: PMC1462698 DOI: 10.1042/bj20051931] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Revised: 01/20/2006] [Accepted: 01/30/2006] [Indexed: 11/17/2022]
Abstract
Protein tyrosine phosphatases PTPN5, PTPRR and PTPN7 comprise a family of phosphatases that specifically inactivate MAPKs (mitogen-activated protein kinases). We have determined high-resolution structures of all of the human family members, screened them against a library of 24000 compounds and identified two classes of inhibitors, cyclopenta[c]quinolinecarboxylic acids and 2,5-dimethylpyrrolyl benzoic acids. Comparative structural analysis revealed significant differences within this conserved family that could be explored for the design of selective inhibitors. PTPN5 crystallized, in two distinct crystal forms, with a sulphate ion in close proximity to the active site and the WPD (Trp-Pro-Asp) loop in a unique conformation, not seen in other PTPs, ending in a 3(10)-helix. In the PTPN7 structure, the WPD loop was in the closed conformation and part of the KIM (kinase-interaction motif) was visible, which forms an N-terminal aliphatic helix with the phosphorylation site Thr66 in an accessible position. The WPD loop of PTPRR was open; however, in contrast with the structure of its mouse homologue, PTPSL, a salt bridge between the conserved lysine and aspartate residues, which has been postulated to confer a more rigid loop structure, thereby modulating activity in PTPSL, does not form in PTPRR. One of the identified inhibitor scaffolds, cyclopenta[c]quinoline, was docked successfully into PTPRR, suggesting several possibilities for hit expansion. The determined structures together with the established SAR (structure-activity relationship) propose new avenues for the development of selective inhibitors that may have therapeutic potential for treating neurodegenerative diseases in the case of PTPRR or acute myeloblastic leukaemia targeting PTPN7.
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Key Words
- crystal structure
- phosphatase inhibitor
- protein tyrosine phosphatase
- ptpn5
- ptpn7
- ptprr
- difmup, 6,8-difluoro-4-methylumbelliferyl phosphate
- dtt, dithiothreitol
- erk, extracellular-signal-regulated kinase
- gst, glutathione s-transferase
- kim, kinase-interaction motif
- mapk, mitogen-activated protein kinase
- peg, poly(ethylene glycol)
- pnpp, p-nitrophenyl phosphate
- ptp, protein tyrosine phosphatase
- sar, structure–activity relationship
- tcep, tris-(2-carboxyethyl)phosphine
- tev, tobacco etch virus
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Affiliation(s)
- Jeyanthy Eswaran
- *Structural Genomics Consortium, University of Oxford, Botnar Research Centre, Oxford OX3 7LD, U.K
| | - Jens Peter von Kries
- †Screening Unit, Forschunginstitut für Molekulare Pharmakologie, Robert-Roessle Strasse 10, 13125 Berlin, Germany
| | - Brian Marsden
- *Structural Genomics Consortium, University of Oxford, Botnar Research Centre, Oxford OX3 7LD, U.K
| | - Emma Longman
- *Structural Genomics Consortium, University of Oxford, Botnar Research Centre, Oxford OX3 7LD, U.K
| | - Judit É. Debreczeni
- *Structural Genomics Consortium, University of Oxford, Botnar Research Centre, Oxford OX3 7LD, U.K
| | - Emilie Ugochukwu
- *Structural Genomics Consortium, University of Oxford, Botnar Research Centre, Oxford OX3 7LD, U.K
| | - Andrew Turnbull
- *Structural Genomics Consortium, University of Oxford, Botnar Research Centre, Oxford OX3 7LD, U.K
| | - Wen Hwa Lee
- *Structural Genomics Consortium, University of Oxford, Botnar Research Centre, Oxford OX3 7LD, U.K
| | - Stefan Knapp
- *Structural Genomics Consortium, University of Oxford, Botnar Research Centre, Oxford OX3 7LD, U.K
| | - Alastair J. Barr
- *Structural Genomics Consortium, University of Oxford, Botnar Research Centre, Oxford OX3 7LD, U.K
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