1
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Milholland KL, Waddey BT, Velázquez-Marrero KG, Lihon MV, Danzeisen EL, Naughton NH, Adams TJ, Schwartz JL, Liu X, Hall MC. Cdc14 phosphatases use an intramolecular pseudosubstrate motif to stimulate and regulate catalysis. J Biol Chem 2024; 300:107644. [PMID: 39122012 DOI: 10.1016/j.jbc.2024.107644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024] Open
Abstract
Cdc14 phosphatases are related structurally and mechanistically to protein tyrosine phosphatases (PTPs) but evolved a unique specificity for phosphoSer-Pro-X-Lys/Arg sites primarily deposited by cyclin-dependent kinases. This specialization is widely conserved in eukaryotes. The evolutionary reconfiguration of the Cdc14 active site to selectively accommodate phosphoSer-Pro likely required modification to the canonical PTP catalytic cycle. While studying Saccharomyces cerevisiae Cdc14, we discovered a short sequence in the disordered C terminus, distal to the catalytic domain, which mimics an optimal substrate. Kinetic analyses demonstrated this pseudosubstrate binds the active site and strongly stimulates rate-limiting phosphoenzyme hydrolysis, and we named it "substrate-like catalytic enhancer" (SLiCE). The SLiCE motif is found in all Dikarya fungal Cdc14 orthologs and contains an invariant glutamine, which we propose is positioned via substrate-like contacts to assist orientation of the hydrolytic water, similar to a conserved active site glutamine in other PTPs that Cdc14 lacks. AlphaFold2 predictions revealed vertebrate Cdc14 orthologs contain a conserved C-terminal alpha helix bound to the active site. Although apparently unrelated to the fungal sequence, this motif also makes substrate-like contacts and has an invariant glutamine in the catalytic pocket. Altering these residues in human Cdc14A and Cdc14B demonstrated that it functions by the same mechanism as the fungal motif. However, the fungal and vertebrate SLiCE motifs were not functionally interchangeable, illuminating potential active site differences during catalysis. Finally, we show that the fungal SLiCE motif is a target for phosphoregulation of Cdc14 activity. Our study uncovered evolution of an unusual stimulatory pseudosubstrate motif in Cdc14 phosphatases.
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Affiliation(s)
| | - Benjamin T Waddey
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | | | - Michelle V Lihon
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Emily L Danzeisen
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Noelle H Naughton
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Timothy J Adams
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Jack L Schwartz
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA
| | - Xing Liu
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA; Center for Plant Biology, Purdue University, West Lafayette, Indiana, USA
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, Indiana, USA; Institute for Cancer Research, Purdue University, West Lafayette, Indiana, USA; Institute for Drug Discovery, Purdue University, West Lafayette, Indiana, USA; Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana, USA.
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2
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Dong J, Jassim BA, Milholland KL, Qu Z, Bai Y, Miao Y, Miao J, Ma Y, Lin J, Hall MC, Zhang ZY. Development of Novel Phosphonodifluoromethyl-Containing Phosphotyrosine Mimetics and a First-In-Class, Potent, Selective, and Bioavailable Inhibitor of Human CDC14 Phosphatases. J Med Chem 2024; 67:8817-8835. [PMID: 38768084 DOI: 10.1021/acs.jmedchem.4c00149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Together with protein tyrosine kinases, protein tyrosine phosphatases (PTPs) control protein tyrosine phosphorylation and regulate numerous cellular functions. Dysregulated PTP activity is associated with the onset of multiple human diseases. Nevertheless, understanding of the physiological function and disease biology of most PTPs remains limited, largely due to the lack of PTP-specific chemical probes. In this study, starting from a well-known nonhydrolyzable phosphotyrosine (pTyr) mimetic, phosphonodifluoromethyl phenylalanine (F2Pmp), we synthesized 7 novel phosphonodifluoromethyl-containing bicyclic/tricyclic aryl derivatives with improved cell permeability and potency toward various PTPs. Furthermore, with fragment- and structure-based design strategies, we advanced compound 9 to compound 15, a first-in-class, potent, selective, and bioavailable inhibitor of human CDC14A and B phosphatases. This study demonstrates the applicability of the fragment-based design strategy in creating potent, selective, and bioavailable PTP inhibitors and provides a valuable probe for interrogating the biological roles of hCDC14 phosphatases and assessing their potential for therapeutic interventions.
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Affiliation(s)
- Jiajun Dong
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Brenson A Jassim
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Kedric L Milholland
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zihan Qu
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yunpeng Bai
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yiming Miao
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jinmin Miao
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Yuan Ma
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Jianping Lin
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Mark C Hall
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
| | - Zhong-Yin Zhang
- Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
- Institute for Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, United States
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3
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Liang W, Krabill AD, Gallagher KS, Muli C, Qu Z, Trader D, Zhang ZY, Dai M. Natural Product-Inspired Molecules for Covalent Inhibition of SHP2 Tyrosine Phosphatase. Tetrahedron 2024; 156:133918. [PMID: 38618612 PMCID: PMC11008911 DOI: 10.1016/j.tet.2024.133918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Natural products have been playing indispensable roles in the development of lifesaving drug molecules. They are also valuable sources for covalent protein modifiers. However, they often are scarce in nature and have complex chemical structures, which are limiting their further biomedical development. Thus, natural product-inspired small molecules which still contain the essence of the parent natural products but are readily available and amenable for structural modification, are important and desirable in searching for lead compounds for various disease treatment. Inspired by the complex and diverse ent-kaurene diterpenoids with significant biological activities, we have created a synthetically accessible and focused covalent library by incorporating the bicyclo[3.2.1]octane α-methylene ketone, which is considered as the pharmacophore of ent-kaurene diterpenoids, as half of the structure, and replacing the other half with much less complex but more druglike scaffolds. From this library, we have identified and characterized selective covalent inhibitors of protein tyrosine phosphatase SHP2, an important anti-cancer therapeutic target. The success of this study demonstrated the importance of creating and evaluating natural product-inspired library as well as their application in targeting challenging disease targets.
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Affiliation(s)
- Weida Liang
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States
| | - Aaron D Krabill
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - Katelyn S Gallagher
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States
| | - Christine Muli
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - Zihan Qu
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
| | - Darci Trader
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, United States
| | - Zhong-Yin Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, United States
| | - Mingji Dai
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, United States
- Institute for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
- Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, United States
- Department of Chemistry, Emory University, Atlanta, GA 30322, United States
- Department of Pharmacology and Chemical Biology, Emory University, Atlanta, GA 30322, United States
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4
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Wu S, Coureuil M, Nassif X, Tautz L. Enzyme mechanistic studies of NMA1982, a protein tyrosine phosphatase and potential virulence factor in Neisseria meningitidis. Sci Rep 2023; 13:22015. [PMID: 38086986 PMCID: PMC10716126 DOI: 10.1038/s41598-023-49561-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 12/09/2023] [Indexed: 12/18/2023] Open
Abstract
Protein phosphorylation is an integral part of many cellular processes, not only in eukaryotes but also in bacteria. The discovery of both prokaryotic protein kinases and phosphatases has created interest in generating antibacterial therapeutics that target these enzymes. NMA1982 is a putative phosphatase from Neisseria meningitidis, the causative agent of meningitis and meningococcal septicemia. The overall fold of NMA1982 closely resembles that of protein tyrosine phosphatases (PTPs). However, the hallmark C(X)5R PTP signature motif, containing the catalytic cysteine and invariant arginine, is shorter by one amino acid in NMA1982. This has cast doubt about the catalytic mechanism of NMA1982 and its assignment to the PTP superfamily. Here, we demonstrate that NMA1982 indeed employs a catalytic mechanism that is specific to PTPs. Mutagenesis experiments, transition state inhibition, pH-dependence activity, and oxidative inactivation experiments all support that NMA1982 is a genuine PTP. Importantly, we show that NMA1982 is secreted by N. meningitidis, suggesting that this protein is a potential virulence factor. Future studies will need to address whether NMA1982 is indeed essential for N. meningitidis survival and virulence. Based on its unique active site conformation, NMA1982 may become a suitable target for developing selective antibacterial drugs.
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Affiliation(s)
- Shuangding Wu
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Mathieu Coureuil
- Université Paris CitéUFR de Médecine, 15 Rue de l'École de Médecine, 75006, Paris, France
- Institut Necker Enfants-MaladesInserm U1151, CNRS UMR 8253, 160 Rue de Vaugirard, 75015, Paris, France
| | - Xavier Nassif
- Université Paris CitéUFR de Médecine, 15 Rue de l'École de Médecine, 75006, Paris, France
- Institut Necker Enfants-MaladesInserm U1151, CNRS UMR 8253, 160 Rue de Vaugirard, 75015, Paris, France
| | - Lutz Tautz
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA, 92037, USA.
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5
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Wu S, Coureuil M, Nassif X, Tautz L. Enzyme Mechanistic Studies of NMA1982, a Protein Tyrosine Phosphatase and Potential Virulence Factor in Neisseria meningitidis. RESEARCH SQUARE 2023:rs.3.rs-3098138. [PMID: 37693380 PMCID: PMC10491346 DOI: 10.21203/rs.3.rs-3098138/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Protein phosphorylation is an integral part of many cellular processes, not only in eukaryotes but also in bacteria. The discovery of both prokaryotic protein kinases and phosphatases has created interest in generating antibacterial therapeutics that target these enzymes. NMA1982 is a putative phosphatase from Neisseria meningitidis, the causative agent of meningitis and meningococcal septicemia. The overall fold of NMA1982 closely resembles that of protein tyrosine phosphatases (PTPs). However, the hallmark C(X)5R PTP signature motif, containing the catalytic cysteine and invariant arginine, is shorter by one amino acid in NMA1982. This has cast doubt about the catalytic mechanism of NMA1982 and its assignment to the PTP superfamily. Here, we demonstrate that NMA1982 indeed employs a catalytic mechanism that is specific to PTPs. Mutagenesis experiments, transition state inhibition, pH-dependence activity, and oxidative inactivation experiments all support that NMA1982 is a genuine PTP. Importantly, we show that NMA1982 is secreted by N. meningitidis, suggesting that this protein is a potential virulence factor. Future studies will need to address whether NMA1982 is indeed essential for N. meningitidis survival and virulence. Based on its unique active site conformation, NMA1982 may become a suitable target for developing selective antibacterial drugs.
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Affiliation(s)
| | | | | | - Lutz Tautz
- Sanford Burnham Prebys Medical Discovery Institute
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6
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Wu S, Coureuil M, Nassif X, Tautz L. NMA1982 is a Novel Phosphatase and Potential Virulence Factor in Neisseria meningitidis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541968. [PMID: 37292688 PMCID: PMC10245925 DOI: 10.1101/2023.05.23.541968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein phosphorylation is an integral part of many cellular processes, not only in eukaryotes but also in bacteria. The discovery of both prokaryotic protein kinases and phosphatases has created interest in generating antibacterial therapeutics that target these enzymes. NMA1982 is a putative phosphatase from Neisseria meningitidis, the causative agent of meningitis and meningococcal septicemia. The overall fold of NMA1982 closely resembles that of protein tyrosine phosphatases (PTPs). However, the hallmark C(X)5R PTP signature motif, containing the catalytic cysteine and invariant arginine, is shorter by one amino acid in NMA1982. This has cast doubt about the catalytic mechanism of NMA1982 and its assignment to the PTP superfamily. Here, we demonstrate that NMA1982 indeed employs a catalytic mechanism that is specific to PTPs. Mutagenesis experiments, transition state inhibition, pH-dependence activity, and oxidative inactivation experiments all support that NMA1982 is a genuine phosphatase. Importantly, we show that NMA1982 is secreted by N. meningitidis, suggesting that this protein is a potential virulence factor. Future studies will need to address whether NMA1982 is indeed essential for N. meningitidis survival and virulence. Based on its unique active site conformation, NMA1982 may become a suitable target for developing selective antibacterial drugs.
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Affiliation(s)
- Shuangding Wu
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Mathieu Coureuil
- Université Paris Cité, UFR de Médecine, 15 Rue de l’École de Médecine, 75006 Paris, France
- Institut Necker Enfants-Malades, Inserm U1151, CNRS UMR 8253, 160 Rue de Vaugirard, 75015 Paris, France
| | - Xavier Nassif
- Université Paris Cité, UFR de Médecine, 15 Rue de l’École de Médecine, 75006 Paris, France
- Institut Necker Enfants-Malades, Inserm U1151, CNRS UMR 8253, 160 Rue de Vaugirard, 75015 Paris, France
| | - Lutz Tautz
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
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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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Solman M, Woutersen DTJ, den Hertog J. Modeling (not so) rare developmental disorders associated with mutations in the protein-tyrosine phosphatase SHP2. Front Cell Dev Biol 2022; 10:1046415. [PMID: 36407105 PMCID: PMC9672471 DOI: 10.3389/fcell.2022.1046415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
Src homology region 2 (SH2)-containing protein tyrosine phosphatase 2 (SHP2) is a highly conserved protein tyrosine phosphatase (PTP), which is encoded by PTPN11 and is indispensable during embryonic development. Mutations in PTPN11 in human patients cause aberrant signaling of SHP2, resulting in multiple rare hereditary diseases, including Noonan Syndrome (NS), Noonan Syndrome with Multiple Lentigines (NSML), Juvenile Myelomonocytic Leukemia (JMML) and Metachondromatosis (MC). Somatic mutations in PTPN11 have been found to cause cancer. Here, we focus on the role of SHP2 variants in rare diseases and advances in the understanding of its pathogenesis using model systems.
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Affiliation(s)
- Maja Solman
- Hubrecht Institute-KNAW, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Jeroen den Hertog
- Hubrecht Institute-KNAW, University Medical Center Utrecht, Utrecht, Netherlands
- Institute Biology Leiden, Leiden University, Leiden, Netherlands
- *Correspondence: Jeroen den Hertog,
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9
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Li Z, Meng L, Ma Q, Wang Z, Zhao Y, Luo D. Polyketides with IDH1 R132h and PTP1B inhibitory activities from the desert-plant-derived fungus Alternaria sp. HM 134. Front Microbiol 2022; 13:975579. [PMID: 36246217 PMCID: PMC9556845 DOI: 10.3389/fmicb.2022.975579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Five new polyketides named alternafurones A (1) and B (2), alternapyrones M-O (3–5), together with fourteen known ones (6–19), were isolated from the desert-plant-derived fungus Alternaria sp. HM 134. The structures of the new compounds were elucidated from spectroscopic data and ECD spectroscopic analyses. Alternafurones A and B represent polyketides with an unprecedented 6/5/6 skeleton core. Compounds 1, 2 and 4 showed definite inhibitory activities against isocitrate dehydrogenase 1 gene (IDH1 R132h) with IC50 values of 29.38, 19.41 and 14.14 μg/ml, respectively. Seven compounds (6, 7, 9–12, 14) showed potent protein tyrosine phosphatase 1B (PTP1B) inhibitory activity with IC50 values ranging from 0.97 μg/ml to 89.80 μg/ml.
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Affiliation(s)
- Zhuang Li
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Life Science, Hebei University, Baoding, China
| | - Lu Meng
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Life Science, Hebei University, Baoding, China
| | - Qingyun Ma
- Hainan Key Laboratory of Research and Development of Natural Product from Li Folk Medicine, Hainan Institute for Tropical Agricultural Resources, Institute of Tropical Bioscience and Biotechnology, CATAS, Haikou, China
| | - Zhen Wang
- Affiliated Hospital of Medical College, Hebei University of Engineering, Handan, China
- *Correspondence: Zhen Wang,
| | - Youxing Zhao
- Hainan Key Laboratory of Research and Development of Natural Product from Li Folk Medicine, Hainan Institute for Tropical Agricultural Resources, Institute of Tropical Bioscience and Biotechnology, CATAS, Haikou, China
- Youxing Zhao,
| | - Duqiang Luo
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Life Science, Hebei University, Baoding, China
- Duqiang Luo,
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10
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Prust N, van Breugel PC, Lemeer S. Widespread Arginine Phosphorylation in Staphylococcus aureus. Mol Cell Proteomics 2022; 21:100232. [PMID: 35421590 PMCID: PMC9112008 DOI: 10.1016/j.mcpro.2022.100232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 12/15/2021] [Accepted: 04/07/2022] [Indexed: 11/25/2022] Open
Abstract
Arginine phosphorylation was only recently discovered to play a significant and relevant role in the Gram-positive bacterium Bacillus subtilis. In addition, arginine phosphorylation was also detected in Staphylococcus aureus, suggesting a widespread role in bacteria. However, the large-scale analysis of protein phosphorylation, and especially those that involve a phosphoramidate bond, comes along with several challenges. The substoichiometric nature of protein phosphorylation requires proper enrichment strategies prior to LC-MS/MS analysis, and the acid instability of phosphoramidates was long thought to impede those enrichments. Furthermore, good spectral quality is required, which can be impeded by the presence of neutral losses of phosphoric acid upon higher energy collision–induced dissociation. Here we show that pArg is stable enough for commonly used Fe3+-IMAC enrichment followed by LC-MS/MS and that HCD is still the gold standard for the analysis of phosphopeptides. By profiling a serine/threonine kinase (Stk1) and phosphatase (Stp1) mutant from a methicillin-resistant S. aureus mutant library, we identified 1062 pArg sites and thus the most comprehensive arginine phosphoproteome to date. Using synthetic arginine phosphorylated peptides, we validated the presence and localization of arginine phosphorylation in S. aureus. Finally, we could show that the knockdown of Stp1 significantly increases the overall amount of arginine phosphorylation in S. aureus. However, our analysis also shows that Stp1 is not a direct protein-arginine phosphatase but only indirectly influences the arginine phosphoproteome. Extensive protein arginine phosphorylation in Staphylococcus aureus. pArg phosphorylation is stable under common phosphor enrichment conditions. Arginine phosphorylation is as widespread as threonine phosphorylation. Phosphatase Stp1 indirectly influences the pArg phosphoproteome in S. aureus.
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Affiliation(s)
- Nadine Prust
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Pieter C van Breugel
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands
| | - Simone Lemeer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands; Netherlands Proteomics Center, Utrecht, The Netherlands.
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11
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Shen R, Crean RM, Johnson SJ, Kamerlin SCL, Hengge AC. Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases. JACS AU 2021; 1:646-659. [PMID: 34308419 PMCID: PMC8297725 DOI: 10.1021/jacsau.1c00054] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Indexed: 05/08/2023]
Abstract
Catalysis by protein tyrosine phosphatases (PTPs) relies on the motion of a flexible protein loop (the WPD-loop) that carries a residue acting as a general acid/base catalyst during the PTP-catalyzed reaction. The orthogonal substitutions of a noncatalytic residue in the WPD-loops of YopH and PTP1B result in shifted pH-rate profiles from an altered kinetic pK a of the nucleophilic cysteine. Compared to wild type, the G352T YopH variant has a broadened pH-rate profile, similar activity at optimal pH, but significantly higher activity at low pH. Changes in the corresponding PTP1B T177G variant are more modest and in the opposite direction, with a narrowed pH profile and less activity in the most acidic range. Crystal structures of the variants show no structural perturbations but suggest an increased preference for the WPD-loop-closed conformation. Computational analysis confirms a shift in loop conformational equilibrium in favor of the closed conformation, arising from a combination of increased stability of the closed state and destabilization of the loop-open state. Simulations identify the origins of this population shift, revealing differences in the flexibility of the WPD-loop and neighboring regions. Our results demonstrate that changes to the pH dependency of catalysis by PTPs can result from small changes in amino acid composition in their WPD-loops affecting only loop dynamics and conformational equilibrium. The perturbation of kinetic pK a values of catalytic residues by nonchemical processes affords a means for nature to alter an enzyme's pH dependency by a less disruptive path than altering electrostatic networks around catalytic residues themselves.
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Affiliation(s)
- Ruidan Shen
- Department
of Chemistry and Biochemistry, Utah State
University, Logan, Utah 84322-0300, United States
| | - Rory M. Crean
- Science
for Life Laboratory, Department of Chemistry − BMC, Uppsala University, Box 576, S-751 23 Uppsala, Sweden
| | - Sean J. Johnson
- Department
of Chemistry and Biochemistry, Utah State
University, Logan, Utah 84322-0300, United States
| | - Shina C. L. Kamerlin
- Science
for Life Laboratory, Department of Chemistry − BMC, Uppsala University, Box 576, S-751 23 Uppsala, Sweden
| | - Alvan C. Hengge
- Department
of Chemistry and Biochemistry, Utah State
University, Logan, Utah 84322-0300, United States
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12
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Trichodermin Induces G0/G1 Cell Cycle Arrest by Inhibiting c-Myc in Ovarian Cancer Cells and Tumor Xenograft-Bearing Mice. Int J Mol Sci 2021; 22:ijms22095022. [PMID: 34065149 PMCID: PMC8126000 DOI: 10.3390/ijms22095022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/20/2021] [Accepted: 05/06/2021] [Indexed: 12/30/2022] Open
Abstract
Ovarian cancer is a fatal gynecological cancer because of a lack of early diagnosis, which often relapses as chemoresistant. Trichodermin, a trichothecene first isolated from Trichoderma viride, is an inhibitor of eukaryotic protein synthesis. However, whether trichodermin is able to suppress ovarian cancer or not was unclear. In this study, trichodermin (0.5 µM or greater) significantly decreased the proliferation of two ovarian cancer cell lines A2780/CP70 and OVCAR-3. Normal ovarian IOSE 346 cells were much less susceptible to trichodermin than the cancer cell lines. Trichodermin predominantly inhibited ovarian cancer cells by inducing G0/G1 cell cycle arrest rather than apoptosis. Trichodermin decreased the expression of cyclin D1, CDK4, CDK2, retinoblastoma protein, Cdc25A, and c-Myc but showed little effect on the expression of p21Waf1/Cip1, p27Kip1, or p16Ink4a. c-Myc was a key target of trichodermin. Trichodermin regulated the expression of Cdc25A and its downstream proteins via c-Myc. Overexpression of c-Myc attenuated trichodermin's anti-ovarian cancer activity. In addition, trichodermin decelerated tumor growth in BALB/c nude mice, proving its effectiveness in vivo. These findings suggested that trichodermin has the potential to contribute to the treatment of ovarian cancer.
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13
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The Phosphoarginine Phosphatase PtpB from Staphylococcus aureus Is Involved in Bacterial Stress Adaptation during Infection. Cells 2021; 10:cells10030645. [PMID: 33799337 PMCID: PMC8001253 DOI: 10.3390/cells10030645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 01/18/2023] Open
Abstract
Staphylococcus aureus continues to be a public health threat, especially in hospital settings. Studies aimed at deciphering the molecular and cellular mechanisms that underlie pathogenesis, host adaptation, and virulence are required to develop effective treatment strategies. Numerous host-pathogen interactions were found to be dependent on phosphatases-mediated regulation. This study focused on the analysis of the role of the low-molecular weight phosphatase PtpB, in particular, during infection. Deletion of ptpB in S. aureus strain SA564 significantly reduced the capacity of the mutant to withstand intracellular killing by THP-1 macrophages. When injected into normoglycemic C57BL/6 mice, the SA564 ΔptpB mutant displayed markedly reduced bacterial loads in liver and kidney tissues in a murine S. aureus abscess model when compared to the wild type. We also observed that PtpB phosphatase-activity was sensitive to oxidative stress. Our quantitative transcript analyses revealed that PtpB affects the transcription of various genes involved in oxidative stress adaptation and infectivity. Thus, this study disclosed first insights into the physiological role of PtpB during host interaction allowing us to link phosphatase-dependent regulation to oxidative bacterial stress adaptation during infection.
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14
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Tripathi RKP, Ayyannan SR. Emerging chemical scaffolds with potential SHP2 phosphatase inhibitory capabilities - A comprehensive review. Chem Biol Drug Des 2020; 97:721-773. [PMID: 33191603 DOI: 10.1111/cbdd.13807] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/30/2020] [Accepted: 11/05/2020] [Indexed: 12/13/2022]
Abstract
The drug discovery panorama is cluttered with promising therapeutic targets that have been deserted because of inadequate authentication and screening failures. Molecular targets formerly tagged as "undruggable" are nowadays being more cautiously cross-examined, and whilst they stay intriguing, numerous targets are emerging more accessible. Protein tyrosine phosphatases (PTPs) excellently exemplifies a class of molecular targets that have transpired as druggable, with several small molecules and antibodies recently turned available for further development. In this respect, SHP2, a PTP, has emerged as one of the potential targets in the current pharmacological research, particularly for cancer, due to its critical role in various signalling pathways. Recently, few molecules with excellent potency have entered clinical trials, but none could reach the clinic. Consequently, search for novel, non-toxic, and specific SHP2 inhibitors are on purview. In this review, general aspects of SHP2 including its structure and mechanistic role in carcinogenesis have been presented. It also sheds light on the development of novel molecular architectures belonging to diverse chemical classes that have been proposed as SHP2-specific inhibitors along with their structure-activity relationships (SARs), stemming from chemical, mechanism-based and computer-aided studies reported since January 2015 to July 2020 (excluding patents), focusing on their potency and selectivity. The encyclopedic facts and discussions presented herein will hopefully facilitate researchers to design new ligands with better efficacy and selectivity against SHP2.
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Affiliation(s)
- Rati Kailash Prasad Tripathi
- Department of Pharmaceutical Science, Sushruta School of Medical and Paramedical Sciences, Assam University (A Central University), Silchar, Assam, India.,Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Senthil Raja Ayyannan
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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15
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Luong NC, Abiko Y, Shibata T, Uchida K, Warabi E, Suzuki M, Noguchi T, Matsuzawa A, Kumagai Y. Redox cycling of 9,10-phenanthrenequinone activates epidermal growth factor receptor signaling through S-oxidation of protein tyrosine phosphatase 1B. J Toxicol Sci 2020; 45:349-363. [PMID: 32493877 DOI: 10.2131/jts.45.349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
9,10-Phenanthrenequinone (9,10-PQ) is a polycyclic aromatic hydrocarbon quinone contaminated in diesel exhaust particles and particulate matter 2.5. It is an efficient electron acceptor that induces redox cycling with electron donors, resulting in excessive reactive oxygen species and oxidized protein production in cells. The current study examined whether 9,10-PQ could activate epidermal growth factor receptor (EGFR) signaling in A431 cells through S-oxidation of its negative regulators such as protein tyrosine phosphatase (PTP) 1B. 9,10-PQ oxidized recombinant human PTP1B at Cys215 and inhibited its catalytic activity, an effect that was blocked by catalase (CAT), whereas cis-9,10-dihydroxy-9,10-dihydrophenanthrene (DDP), which lacks redox cycling activity, had no effect on PTP1B activity. Exposure of A431 cells to 9,10-PQ, but not DDP, activated signaling through EGFR and its downstream extracellular signal-regulated kinase 1/2 (ERK1/2), coupled with a decrease of cellular PTP activity. Immunoprecipitation and UPLC-MSE revealed that PTP1B easily undergoes oxidation during exposure of A431 cells to 9,10-PQ. Pretreatment with polyethylene glycol conjugated with CAT (PEG-CAT) abolished 9,10-PQ-generated H2O2 production and significantly blocked the activation of EGFR-ERK1/2 signaling by 9,10-PQ, indicating the involvement of H2O2 in the activation because scavenging agents for hydroxyl radicals had no effect on the redox signal activation. These results suggest that such an air pollutant producing H2O2, activates EGFR-ERK1/2 signaling, presumably through the S-oxidation of PTPs such as PTP1B, and activation of the signal cascade may contribute, at least in part, to cellular responses in A431 cells.
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Affiliation(s)
- Nho Cong Luong
- Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba.,Faculty of Pharmacy, Hue University of Medicine and Pharmacy, Hue University, Vietnam
| | - Yumi Abiko
- Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba.,Faculty of Medicine, University of Tsukuba
| | | | - Koji Uchida
- Graduate School of Bioagricultural Sciences, Nagoya University.,Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Eiji Warabi
- Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba.,Faculty of Medicine, University of Tsukuba
| | - Midori Suzuki
- Graduate School of Pharmaceutical Sciences, Tohoku University
| | - Takuya Noguchi
- Graduate School of Pharmaceutical Sciences, Tohoku University
| | | | - Yoshito Kumagai
- Doctoral Program in Biomedical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba.,Faculty of Medicine, University of Tsukuba
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16
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Phosphatase-independent functions of SHP2 and its regulation by small molecule compounds. J Pharmacol Sci 2020; 144:139-146. [PMID: 32921395 DOI: 10.1016/j.jphs.2020.06.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 06/03/2020] [Accepted: 06/08/2020] [Indexed: 12/13/2022] Open
Abstract
SHP2 is a non-receptor protein tyrosine phosphatase encoded by the PTPN11 gene in human. Clinically, SHP2 has been identified as a causal factor of several diseases, such as Noonan syndrome, LEOPARD syndrome as well as myeloid malignancies. Interestingly, both loss-of-function and gain-of-function mutations occur in the PTPN11 gene. Analyses by biochemical and cell biological means as well as probing with small molecule compounds have demonstrated that SHP2 has both phosphatase-dependent and independent functions. In comparison with its phosphatase activity, the non-phosphatase-like function of SHP2 has not been well introduced or summarized. This review mainly focuses on the phosphatase-independent functions and its regulation by small molecule compounds as well as their use for disease therapy.
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17
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Zhang X, Yu Y, Bai B, Wang T, Zhao J, Zhang N, Zhao Y, Wang X, Wang B. PTPN22 interacts with EB1 to regulate T-cell receptor signaling. FASEB J 2020; 34:8959-8974. [PMID: 32469452 DOI: 10.1096/fj.201902811rr] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 02/14/2020] [Accepted: 03/18/2020] [Indexed: 12/21/2022]
Abstract
The PTPN22 gene encoding the Lyp/Pep protein tyrosine phosphatase is a negative regulator of T-cell receptor (TCR) signaling. Recent studies have shown that phosphorylation of end-binding protein 1 (EB1) is associated with the TCR activation. In this study, using 2-hybrid and mass spectrometry analyses, we identified EB1 as a protein associated with PTPN22. Furthermore, we discovered that EB1 specifically bound to the P1 domain of PTPN22 by competing with CSK, and the variant PTPN22-R620W does not affect the association with EB1, which is instrumental with respect to the regulation of TCR signaling. In addition, PTPN22 dephosphorylates EB1 at tyrosine-247 (Y247), which decreases the expression of the T-cell activation markers CD25 and CD69 and the phosphorylation levels of the TCR molecules ZAP-70, LAT, and Erk, leading to the eventual downregulation of the transcription factor NFAT and reduced the levels of secreted IL-2. The findings of this study provide new insights into the TCR signaling and the T-cell immune response, which are important for clarifying the mechanism of PTPN22-related autoimmune diseases.
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Affiliation(s)
- Xiaonan Zhang
- Institute of Biochemistry and Molecular Biology, College of Life and Health Sciences, Northeastern University, Shenyang, P.R. China
| | - Yang Yu
- Institute of Biochemistry and Molecular Biology, College of Life and Health Sciences, Northeastern University, Shenyang, P.R. China
| | - Bin Bai
- Institute of Biochemistry and Molecular Biology, College of Life and Health Sciences, Northeastern University, Shenyang, P.R. China
| | - Tao Wang
- Institute of Biochemistry and Molecular Biology, College of Life and Health Sciences, Northeastern University, Shenyang, P.R. China
| | - Jiahui Zhao
- Institute of Biochemistry and Molecular Biology, College of Life and Health Sciences, Northeastern University, Shenyang, P.R. China
| | - Na Zhang
- Institute of Biochemistry and Molecular Biology, College of Life and Health Sciences, Northeastern University, Shenyang, P.R. China
| | - Yanjiao Zhao
- Institute of Biochemistry and Molecular Biology, College of Life and Health Sciences, Northeastern University, Shenyang, P.R. China
| | - Xipeng Wang
- Institute of Biochemistry and Molecular Biology, College of Life and Health Sciences, Northeastern University, Shenyang, P.R. China
| | - Bing Wang
- Institute of Biochemistry and Molecular Biology, College of Life and Health Sciences, Northeastern University, Shenyang, P.R. China
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18
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Wen Y, Yang S, Wakabayashi K, Svensson MND, Stanford SM, Santelli E, Bottini N. RPTPα phosphatase activity is allosterically regulated by the membrane-distal catalytic domain. J Biol Chem 2020; 295:4923-4936. [PMID: 32139509 DOI: 10.1074/jbc.ra119.011808] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/03/2020] [Indexed: 12/14/2022] Open
Abstract
Receptor-type protein tyrosine phosphatase α (RPTPα) is an important positive regulator of SRC kinase activation and a known promoter of cancer growth, fibrosis, and arthritis. The domain structure of RPTPs comprises an extracellular region, a transmembrane helix, and two tandem intracellular catalytic domains referred to as D1 and D2. The D2 domain of RPTPs is believed to mostly play a regulatory function; however, no regulatory model has been established for RPTPα-D2 or other RPTP-D2 domains. Here, we solved the 1.8 Å resolution crystal structure of the cytoplasmic region of RPTPα, encompassing D1 and D2, trapped in a conformation that revealed a possible mechanism through which D2 can allosterically inhibit D1 activity. Using a D2-truncation RPTPα variant and mutational analysis of the D1/D2 interfaces, we show that D2 inhibits RPTPα phosphatase activity and identified a 405PFTP408 motif in D1 that mediates the inhibitory effect of D2. Expression of the gain-of-function F406A/T407A RPTPα variant in HEK293T cells enhanced SRC activation, supporting the relevance of our proposed D2-mediated regulation mechanism in cell signaling. There is emerging interest in the development of allosteric inhibitors of RPTPs but a scarcity of validated allosteric sites for RPTPs. The results of our study not only shed light on the regulatory role of RPTP-D2 domains, but also provide a potentially useful tool for the discovery of chemical probes targeting RPTPα and other RPTPs.
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Affiliation(s)
- Yutao Wen
- Department of Medicine, University of California, San Diego, La Jolla, California 92037.,Department of Biological Sciences, University of California, San Diego, La Jolla, California 92037
| | - Shen Yang
- Department of Medicine, University of California, San Diego, La Jolla, California 92037
| | - Kuninobu Wakabayashi
- Department of Medicine, University of California, San Diego, La Jolla, California 92037.,Division of Cellular Biology, La Jolla Institute for Immunology, La Jolla, California 92037
| | - Mattias N D Svensson
- Department of Medicine, University of California, San Diego, La Jolla, California 92037
| | - Stephanie M Stanford
- Department of Medicine, University of California, San Diego, La Jolla, California 92037.,Division of Cellular Biology, La Jolla Institute for Immunology, La Jolla, California 92037
| | - Eugenio Santelli
- Department of Medicine, University of California, San Diego, La Jolla, California 92037.,Division of Cellular Biology, La Jolla Institute for Immunology, La Jolla, California 92037
| | - Nunzio Bottini
- Department of Medicine, University of California, San Diego, La Jolla, California 92037 .,Division of Cellular Biology, La Jolla Institute for Immunology, La Jolla, California 92037
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19
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Deng H, Ke S, Callender R, Balakrishnan G, Spiro TG, May ER, Brooks CL. Computational Studies of Catalytic Loop Dynamics in Yersinia Protein Tyrosine Phosphatase Using Pathway Optimization Methods. J Phys Chem B 2019; 123:7840-7851. [PMID: 31437399 PMCID: PMC6752976 DOI: 10.1021/acs.jpcb.9b06759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Yersinia Protein Tyrosine Phosphatase (YopH) is the most efficient enzyme among all known PTPases and relies on its catalytic loop movements for substrate binding and catalysis. Fluorescence, NMR, and UV resonance Raman (UVRR) techniques have been used to study the thermodynamic and dynamic properties of the loop motions. In this study, a computational approach based on the pathway refinement methods nudged elastic band (NEB) and harmonic Fourier beads (HFB) has been developed to provide structural interpretations for the experimentally observed kinetic processes. In this approach, the minimum potential energy pathways for the loop open/closure conformational changes were determined by NEB using a one-dimensional global coordinate. Two dimensional data analyses of the NEB results were performed as an efficient method to qualitatively evaluate the energetics of transitions along several specific physical coordinates. The free energy barriers for these transitions were then determined more precisely using the HFB method. Kinetic parameters were estimated from the energy barriers using transition state theory and compared against experimentally determined kinetic parameters. When the calculated energy barriers are calibrated by a simple "scaling factor", as have been done in our previous vibrational frequency calculations to explain the ligand frequency shift upon its binding to protein, it is possible to make structural interpretations of several observed enzyme dynamic rates. For example, the nanosecond kinetics observed by fluorescence anisotropy may be assigned to the translational motion of the catalytic loop and microsecond kinetics observed in fluorescence T-jump can be assigned to the loop backbone dihedral angle flipping. Furthermore, we can predict that a Trp354 conformational conversion associated with the loop movements would occur on the tens of nanoseconds time scale, to be verified by future UVRR T-jump studies.
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Affiliation(s)
- Hua Deng
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Shan Ke
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | - Robert Callender
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461
| | | | - Thomas G. Spiro
- Department of Chemistry, University of Washington, Seattle, WA 98195
| | - Eric R. May
- Department of Molecular and Cell Biology, University of Connecticut, 91 N. Eagleville Rd, Storrs, CT, USA 06269
| | - Charles L. Brooks
- Department of Chemistry and Biophysics Program, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109
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20
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Backus KM, Cao J, Maddox SM. Opportunities and challenges for the development of covalent chemical immunomodulators. Bioorg Med Chem 2019; 27:3421-3439. [PMID: 31204229 DOI: 10.1016/j.bmc.2019.05.050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/24/2019] [Accepted: 05/31/2019] [Indexed: 02/06/2023]
Abstract
Compounds that react irreversibly with cysteines have reemerged as potent and selective tools for altering protein function, serving as chemical probes and even clinically approved drugs. The exquisite sensitivity of human immune cell signaling pathways to oxidative stress indicates the likely, yet still underexploited, general utility of covalent probes for selective chemical immunomodulation. Here, we provide an overview of immunomodulatory cysteines, including identification of electrophilic compounds available to label these residues. We focus our discussion on three protein classes essential for cell signaling, which span the 'druggability' spectrum from amenable to chemical probes (kinases), somewhat druggable (proteases), to inaccessible (phosphatases). Using existing inhibitors as a guide, we identify general strategies to guide the development of covalent probes for selected undruggable classes of proteins and propose the application of such compounds to alter immune cell functions.
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Affiliation(s)
- Keriann M Backus
- Departments of Biological Chemistry and Chemistry and Biochemistry, University of California Los Angeles, USA.
| | - Jian Cao
- Departments of Biological Chemistry and Chemistry and Biochemistry, University of California Los Angeles, USA
| | - Sean M Maddox
- Departments of Biological Chemistry and Chemistry and Biochemistry, University of California Los Angeles, USA
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21
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Gupta A, Brahmbhatt J, Syrlybaeva R, Bodnar C, Bodnar N, Bongard R, Pokkuluri PR, Sem DS, Ramchandran R, Rathore R, Talipov MR. Role of Conserved Histidine and Serine in the HCXXXXXRS Motif of Human Dual-Specificity Phosphatase 5. J Chem Inf Model 2019; 59:1563-1574. [PMID: 30835471 DOI: 10.1021/acs.jcim.8b00919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND The mitogen-activated protein kinase (MAPK) pathway is functionally generic and critical in maintaining physiological homeostasis and normal tissue development. This pathway is under tight regulation, which is in part mediated by dual-specific phosphatases (DUSPs), which dephosphorylate serine, threonine, and tyrosine residues of the ERK family of proteins. DUSP5 is of high clinical interest because of mutations we identified in this protein in patients with vascular anomalies. Unlike other DUSPs, DUSP5 has unique specificity toward substrate pERK1/2. Using molecular docking and simulation strategies, we previously showed that DUSP5 has two pockets, which are utilized in a specific fashion to facilitate specificity toward catalysis of its substrate pERK1/2. Remarkably, most DUSPs share high similarity in their catalytic sites. Studying the catalytic domain of DUSP5 and identifying amino acid residues that are important for dephosphorylating pERK1/2 could be critical in developing small molecules for therapies targeting DUSP5. RESULTS In this study, we utilized computational modeling to identify and predict the importance of two conserved amino acid residues, H262 and S270, in the DUSP5 catalytic site. Modeling studies predicted that catalytic activity of DUSP5 would be altered if these critical conserved residues were mutated. We next generated independent Glutathione-S-Transferase (GST)-tagged full-length DUSP5 mutant proteins carrying specific mutations H262F and S270A in the phosphatase domain. Biochemical analysis was performed on these purified proteins, and consistent with our computational prediction, we observed altered enzyme activity kinetic profiles for both mutants with a synthetic small molecule substrate (pNPP) and the physiological relevant substrate (pERK) when compared to wild type GST-DUSP5 protein. CONCLUSION Our molecular modeling and biochemical studies combined demonstrate that enzymatic activity of phosphatases can be manipulated by mutating specific conserved amino acid residues in the catalytic site (phosphatase domain). This strategy could facilitate generation of small molecules that will serve as agonists/antagonists of DUSP5 activity.
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Affiliation(s)
- Ankan Gupta
- Department of Pediatrics, Division of Neonatology, Children's Research Institute (CRI), Developmental Vascular Biology Program , Translational and Biomedical Research Center , 8701 Watertown Plank Road , P.O. Box 26509, Milwaukee , Wisconsin 53226 , United States
| | - Jaladhi Brahmbhatt
- BioTechnology Discovery Research, Lilly Research Laboratories , Eli Lilly and Company , Indianapolis , Indiana 46221 , United States
| | - Raulia Syrlybaeva
- Department of Chemistry & Biochemistry , New Mexico State University , 1175 N. Horseshoe Drive , Las Cruces , New Mexico 88003 , United States
| | - Catherine Bodnar
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences , Concordia University Wisconsin , 12800 North Lake Shore Drive , Mequon , Wisconsin 53907 , United States
| | - Natalia Bodnar
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences , Concordia University Wisconsin , 12800 North Lake Shore Drive , Mequon , Wisconsin 53907 , United States
| | - Robert Bongard
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences , Concordia University Wisconsin , 12800 North Lake Shore Drive , Mequon , Wisconsin 53907 , United States
| | - Phani Raj Pokkuluri
- Biosciences Division , Argonne National Laboratory , Lemont , Illinois 60439 United States
| | - Daniel S Sem
- Center for Structure-based Drug Design and Development, Department of Pharmaceutical Sciences , Concordia University Wisconsin , 12800 North Lake Shore Drive , Mequon , Wisconsin 53907 , United States
| | - Ramani Ramchandran
- Department of Pediatrics, Division of Neonatology, Children's Research Institute (CRI), Developmental Vascular Biology Program , Translational and Biomedical Research Center , 8701 Watertown Plank Road , P.O. Box 26509, Milwaukee , Wisconsin 53226 , United States.,Department of Obstetrics and Gynecology , 8701 Watertown Plank Road , P.O. Box 26509, Milwaukee , Wisconsin 53226 , United States
| | - Rajendra Rathore
- Department of Chemistry , Marquette University , Wehr Chemistry Building, P.O. Box 1881, 535 N. 14th Street , Milwaukee , Wisconsin 53201 , United States
| | - Marat R Talipov
- Department of Chemistry & Biochemistry , New Mexico State University , 1175 N. Horseshoe Drive , Las Cruces , New Mexico 88003 , United States
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22
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Bhattacharyya T, Sowdhamini R. Genome-Wide Search for Tyrosine Phosphatases in the Human Genome Through Computational Approaches Leads to the Discovery of Few New Domain Architectures. Evol Bioinform Online 2019; 15:1176934319840289. [PMID: 31007525 PMCID: PMC6457024 DOI: 10.1177/1176934319840289] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 03/04/2019] [Indexed: 11/24/2022] Open
Abstract
Reversible phosphorylation maintained by protein kinases and phosphatases is an integral part of intracellular signalling, and phosphorylation on tyrosine is extensively utilised in higher eukaryotes. Tyrosine phosphatases are enzymes that not only scavenge phosphotyrosine but are also involved in wide range of signalling pathways. As a result, mutations in these enzymes have been implicated in the pathogenesis of several diseases like cancer, autoimmune disorders, and muscle-related diseases. The genes that harbour phosphatase domain also display diversity in co-existing domains suggesting the recruitment of the catalytic machinery in diverse pathways. We have examined the current draft of the human genome, using a combination of 3 sequence search methods and validations, and identified 101 genes encoding tyrosine phosphatase-containing gene products, agreeing with previous reports. Such gene products adopt 37 unique domain architectures (DAs), including few new ones and harbouring few co-existing domains that have not been reported before. This semi-automated computational approach for detection of gene products belonging to a particular superfamily can now be easily applied at whole genome level on other mammalian genomes and for other protein domains as well.
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Affiliation(s)
- Teerna Bhattacharyya
- National Centre for Biological Sciences, Tata
Institute of Fundamental Research, Bangalore, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, Tata
Institute of Fundamental Research, Bangalore, India
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23
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Fatima S, Shukla S, Nazir A. C.el Phosphatome: A Catalogue of Actual and Pseudo Phosphatases Based on In-Silico Studies in Caenorhabditis elegans. Protein J 2018; 37:572-580. [PMID: 30242660 DOI: 10.1007/s10930-018-9794-6] [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] [Indexed: 11/26/2022]
Abstract
Phosphatases are well known to carry out important functions via counter activity of kinases and they serve as mechanism for dephosphorylating the monophosphate esters from the phosphorylated serine, threonine, tyrosine and histidine residues. The biological relevance of phosphatases could be explored further employing newer technologies and models. Caenorhabditis elegans is a powerful genetic model system that bears significant homology with humans, hence providing with a precious tool towards studying important signalling pathways. We carried out the present study to catalogue the C. elegans protein phosphatome, referred here as 'C.el phosphatome' and annotated the corresponding dataset. We further classified these phosphatases based on presence of catalytic conserved motif; GDxHG, GDxVDRG, GNHE, RxxD, DGxxG, DG, GxxDN for Ser/Thr phosphatases, HC(x)5 R for tyrosine phosphatases and DxDxT/V for aspartate based phosphatases. Bioinformatics tool DAVID was employed to decipher the biological relevance of phosphatases. Our findings show Ser/Thr phosphatases (114), Tyr phosphatases (121) and Asp phosphatases (0) in C. elegans genome based on the hallmark sequence identification. Amongst them, 34 and 57 Ser/Thr and Tyr phosphatases respectively contain the catalytic motif. This catalogue offers a precious tool for further studies towards understanding important biological processes and disease conditions.
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Affiliation(s)
- Soobiya Fatima
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Central Drug Research Institute (CSIR-CDRI) Campus, Lucknow, India
- Laboratory of Functional Genomics and Molecular Toxicology, Division of Toxicology and Experimental Medicine, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
| | - Shikha Shukla
- Laboratory of Functional Genomics and Molecular Toxicology, Division of Toxicology and Experimental Medicine, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India
| | - Aamir Nazir
- Academy of Scientific and Innovative Research (AcSIR), CSIR-Central Drug Research Institute (CSIR-CDRI) Campus, Lucknow, India.
- Laboratory of Functional Genomics and Molecular Toxicology, Division of Toxicology and Experimental Medicine, CSIR-Central Drug Research Institute, Lucknow, Uttar Pradesh, 226031, India.
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24
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Ruddraraju KV, Zhang ZY. Covalent inhibition of protein tyrosine phosphatases. MOLECULAR BIOSYSTEMS 2018; 13:1257-1279. [PMID: 28534914 DOI: 10.1039/c7mb00151g] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein tyrosine phosphatases (PTPs) are a large family of 107 signaling enzymes that catalyze the hydrolytic removal of phosphate groups from tyrosine residues in a target protein. The phosphorylation status of tyrosine residues on proteins serve as a ubiquitous mechanism for cellular signal transduction. Aberrant function of PTPs can lead to many human diseases, such as diabetes, obesity, cancer, and autoimmune diseases. As the number of disease relevant PTPs increases, there is urgency in developing highly potent inhibitors that are selective towards specific PTPs. Most current efforts have been devoted to the development of active site-directed and reversible inhibitors for PTPs. This review summarizes recent progress made in the field of covalent inhibitors to target PTPs. Here, we discuss the in vivo and in vitro inactivation of various PTPs by small molecule-containing electrophiles, such as Michael acceptors, α-halo ketones, epoxides, and isothiocyanates, etc. as well as oxidizing agents. We also suggest potential strategies to transform these electrophiles into isozyme selective covalent PTP inhibitors.
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Affiliation(s)
- Kasi Viswanatharaju Ruddraraju
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907, USA.
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25
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Lec JC, Boutserin S, Mazon H, Mulliert G, Boschi-Muller S, Talfournier F. Unraveling the Mechanism of Cysteine Persulfide Formation Catalyzed by 3-Mercaptopyruvate Sulfurtransferases. ACS Catal 2018. [DOI: 10.1021/acscatal.7b02432] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jean-Christophe Lec
- Ingénierie
Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Bâtiment Biopole, Faculté de Médecine, Vandoeuvre-lès-Nancy 54506, France
| | - Séverine Boutserin
- Ingénierie
Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Bâtiment Biopole, Faculté de Médecine, Vandoeuvre-lès-Nancy 54506, France
| | - Hortense Mazon
- Ingénierie
Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Bâtiment Biopole, Faculté de Médecine, Vandoeuvre-lès-Nancy 54506, France
| | - Guillermo Mulliert
- Cristallographie,
Résonnance Magnétique et Modélisations (CRM2), UMR 7036 CNRS-Université de Lorraine, Vandoeuvre-lès-Nancy, 54506, France
| | - Sandrine Boschi-Muller
- Ingénierie
Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Bâtiment Biopole, Faculté de Médecine, Vandoeuvre-lès-Nancy 54506, France
| | - François Talfournier
- Ingénierie
Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS-Université de Lorraine, Bâtiment Biopole, Faculté de Médecine, Vandoeuvre-lès-Nancy 54506, France
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26
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Kargatov AM, Boshkova EA, Chirgadze YN. Novel approach for structural identification of protein family: glyoxalase I. J Biomol Struct Dyn 2017; 36:2699-2712. [PMID: 28805540 DOI: 10.1080/07391102.2017.1367330] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Glyoxalase is one of two enzymes of the glyoxalase detoxification system against methylglyoxal and other aldehydes, the metabolites derived from glycolysis. The glyoxalase system is found almost in all living organisms: bacteria, protozoa, plants, and animals, including humans, and is related to the class of 'life essential proteins'. The enzyme belongs to the expanded Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily. At present the GenBank contains about 700 of amino acid sequences of this enzyme type, and the Protein Data Bank includes dozens of spatial structures. We have offered a novel approach for structural identification of glyoxalase I protein family, which is based on the selecting of basic representative proteins with known structures. On this basis, six new subfamilies of these enzymes have been derived. Most populated subfamilies A1 and A2 were based on representative human Homo sapiens and bacterial Escherichia coli enzymes. We have found that the principle feature, which defines the subfamilies' structural differences, is conditioned by arrangement of N- and C-domains inside the protein monomer. Finely, we have deduced the structural classification for the glyoxalase I and assigned about 460 protein sequences distributed among six new subfamilies. Structural similarities and specific differences of all the subfamilies have been presented. This approach can be used for structural identification of thousands of the so-called hypothetical proteins with the known PDB structures allowing to identify many of already existing atomic coordinate entrees.
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Affiliation(s)
- Anton M Kargatov
- a Institute of Protein Research , Russian Academy of Sciences , Pushchino 142290 , Moscow Region , Russia
| | - Eugenia A Boshkova
- a Institute of Protein Research , Russian Academy of Sciences , Pushchino 142290 , Moscow Region , Russia
| | - Yuri N Chirgadze
- a Institute of Protein Research , Russian Academy of Sciences , Pushchino 142290 , Moscow Region , Russia
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27
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Gao L, Lee SS, Chen J, Sun H, Zhao Y, Chai Z, Hu Y. High-Throughput Screening of Substrate Specificity for Protein Tyrosine Phosphatases (PTPs) on Phosphopeptide Microarrays. Methods Mol Biol 2016; 1368:181-196. [PMID: 26614076 DOI: 10.1007/978-1-4939-3136-1_13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Phosphatases are a family of enzymes responsible for the dephosphorylation of biomolecules. Phosphatases play essential roles in cell cycle regulation, signal transduction, and cellular communication. In recent years, one type of phosphatases, protein tyrosine phosphatases (PTPs), emerges as important therapeutic targets for complex and devastating diseases. Nevertheless, the physiological roles, substrate specificity, and downstream targets for PTPs remain largely unknown. To demonstrate how microarrays can be applied to characterizing PTPs, we describe here a phosphopeptide microarray strategy for activity-based high-throughput screening of PTPs substrate specificity. This is followed by a kinetic microarray assay and microplate assay to determine the rate constants of dephosphorylation by PTPs. This microarray strategy has been successfully applied to identifying several potent and selective substrates against different PTPs. These substrates could be used to design potent and selective PTPs inhibitors in the future.
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Affiliation(s)
- Liqian Gao
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #04-01, Singapore, 138669, Singapore
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Singapore
| | - Su Seong Lee
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #04-01, Singapore, 138669, Singapore
| | - Jun Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Lab of Nuclear Radiation and Nuclear Energy Technology, Center for Multidisciplinary Research, Chinese Academy of Sciences (CAS), Institute of High Energy Physics, 19B Yuquan Road, Beijing, 100049, China
| | - Hongyan Sun
- Department of Biology and Chemistry, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon, Hong Kong, P.R. China.
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Lab of Nuclear Radiation and Nuclear Energy Technology, Center for Multidisciplinary Research, Chinese Academy of Sciences (CAS), Institute of High Energy Physics, 19B Yuquan Road, Beijing, 100049, China
| | - Zhifang Chai
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Lab of Nuclear Radiation and Nuclear Energy Technology, Center for Multidisciplinary Research, Chinese Academy of Sciences (CAS), Institute of High Energy Physics, 19B Yuquan Road, Beijing, 100049, China
| | - Yi Hu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Lab of Nuclear Radiation and Nuclear Energy Technology, Center for Multidisciplinary Research, Chinese Academy of Sciences (CAS), Institute of High Energy Physics, 19B Yuquan Road, Beijing, 100049, China.
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28
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SHP2 sails from physiology to pathology. Eur J Med Genet 2015; 58:509-25. [PMID: 26341048 DOI: 10.1016/j.ejmg.2015.08.005] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/24/2015] [Accepted: 08/30/2015] [Indexed: 02/08/2023]
Abstract
Over the two past decades, mutations of the PTPN11 gene, encoding the ubiquitous protein tyrosine phosphatase SHP2 (SH2 domain-containing tyrosine phosphatase 2), have been identified as the causal factor of several developmental diseases (Noonan syndrome (NS), Noonan syndrome with multiple lentigines (NS-ML), and metachondromatosis), and malignancies (juvenile myelomonocytic leukemia). SHP2 plays essential physiological functions in organism development and homeostasis maintenance by regulating fundamental intracellular signaling pathways in response to a wide range of growth factors and hormones, notably the pleiotropic Ras/Mitogen-Activated Protein Kinase (MAPK) and the Phosphoinositide-3 Kinase (PI3K)/AKT cascades. Analysis of the biochemical impacts of PTPN11 mutations first identified both loss-of-function and gain-of-function mutations, as well as more subtle defects, highlighting the major pathophysiological consequences of SHP2 dysregulation. Then, functional genetic studies provided insights into the molecular dysregulations that link SHP2 mutants to the development of specific traits of the diseases, paving the way for the design of specific therapies for affected patients. In this review, we first provide an overview of SHP2's structure and regulation, then describe its molecular roles, notably its functions in modulating the Ras/MAPK and PI3K/AKT signaling pathways, and its physiological roles in organism development and homeostasis. In the second part, we describe the different PTPN11 mutation-associated pathologies and their clinical manifestations, with particular focus on the biochemical and signaling outcomes of NS and NS-ML-associated mutations, and on the recent advances regarding the pathophysiology of these diseases.
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29
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Li Z, Wang Y. Effect of NADPH oxidase inhibitor-apocynin on the expression of Src homology-2 domain-containing phosphatase-1 (SHP-1) exposed renal ischemia/reperfusion injury in rats. Toxicol Rep 2015; 2:1111-1116. [PMID: 28962452 PMCID: PMC5598411 DOI: 10.1016/j.toxrep.2015.07.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 07/27/2015] [Accepted: 07/28/2015] [Indexed: 11/29/2022] Open
Abstract
This study was designed to evaluate whether NADPH oxidase inhibitor (apocynin) preconditioning induces expression of Src homology-2 domain-containing phosphatase-1 (SHP-1) to protect against renal ischemia/reperfusion (I/R) injury (RI/RI) in rats. Rats were pretreated with 50 mg/kg apocynin, then subjected to 45 min ischemia and 24 h reperfusion. The results indicated that apocynin preconditioning improved the recovery of renal function and nitroso-redox balance, reduced oxidative stress injury and inflammation damage, and upregulated expression of SHP-1 as compared to RI/RI group. Therefore our study demonstrated that apocynin preconditioning provided a protection to the kidney against I/R injury in rats partially through inducing expression of SHP-1.
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Affiliation(s)
- Zhiming Li
- Center for Information Technology, Hexi University, 846 Huancheng North Road, Zhangye 734000, PR China
- Department of Pharmacology, Medical College, Hexi University, 24 Danxia East Road, Zhangye 734000, PR China
| | - Yumei Wang
- Center for Information Technology, Hexi University, 846 Huancheng North Road, Zhangye 734000, PR China
- Department of Pharmacology, Medical College, Hexi University, 24 Danxia East Road, Zhangye 734000, PR China
- Corresponding author at: Department of Pharmacology, Medical College, Hexi University, 24 Danxia East Road, Zhangye,734000, PR China.
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30
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Harrison IP, Selemidis S. Understanding the biology of reactive oxygen species and their link to cancer: NADPH oxidases as novel pharmacological targets. Clin Exp Pharmacol Physiol 2015; 41:533-42. [PMID: 24738947 DOI: 10.1111/1440-1681.12238] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 04/01/2014] [Accepted: 04/02/2014] [Indexed: 12/18/2022]
Abstract
Reactive oxygen species (ROS), the cellular products of myriad physiological processes, have long been understood to lead to cellular damage if produced in excess and to be a causative factor in cancer through the oxidation and nitration of various macromolecules. Reactive oxygen species influence various hallmarks of cancer, such as cellular proliferation and angiogenesis, through the promotion of cell signalling pathways intrinsic to these processes and can also regulate the function of key immune cells, such as macrophages and regulatory T cells, which promote angiogenesis in the tumour environment. Herein we emphasize the family of NADPH oxidase enzymes as the most likely source of ROS, which promote angiogenesis and tumourigenesis through signalling pathways within endothelial, immune and tumour cells. In this review we focus on the pharmacological inhibitors of NADPH oxidases and suggest that, compared with traditional anti-oxidants, they are likely to offer better alternatives for suppression of tumour angiogenesis. Despite the emerging enthusiasm towards the use of NADPH oxidase inhibitors for cancer therapy, this field is still in its infancy; in particular, there is a glaring lack of knowledge of the roles of NADPH oxidases in in vivo animal models and in human cancers. Certainly a clearer understanding of the relevant signalling pathways influenced by NADPH oxidases during angiogenesis in cancer is likely to yield novel therapeutic approaches.
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Affiliation(s)
- Ian P Harrison
- Department of Pharmacology, Monash University, Melbourne, Vic., Australia
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31
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Hengge AC. Kinetic isotope effects in the characterization of catalysis by protein tyrosine phosphatases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:1768-75. [PMID: 25840000 DOI: 10.1016/j.bbapap.2015.03.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 03/09/2015] [Accepted: 03/23/2015] [Indexed: 11/30/2022]
Abstract
Although thermodynamically favorable, the uncatalyzed hydrolysis of phosphate monoesters is extraordinarily slow, making phosphatases among the most catalytically efficient enzymes known. Protein-tyrosine phosphatases (PTPs) are ubiquitous in biology, and kinetic isotope effects were one of the key mechanistic tools used to discern molecular details of their catalytic mechanism and the transition state for phosphoryl transfer. Later, the unique level of detail KIEs provided led to deeper questions about the potential role of protein motions in PTP catalysis. The recent discovery that such motions are responsible for different catalytic rates between PTPs arose from questions originating from KIE data showing that the transition states and chemical mechanisms are identical, combined with structural data demonstrating superimposable active sites. KIEs also reveal perturbations to the transition state as mutations are made to residues directly involved in chemistry, and to residues that affect protein motions essential for catalysis. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment.
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Affiliation(s)
- Alvan C Hengge
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA.
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32
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Xiao P, Wang X, Wang HM, Fu XL, Cui FA, Yu X, Wen SS, Bi WX, Sun JP. The second-sphere residue T263 is important for the function and catalytic activity of PTP1B via interaction with the WPD-loop. Int J Biochem Cell Biol 2014; 57:84-95. [PMID: 25450460 DOI: 10.1016/j.biocel.2014.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 09/21/2014] [Accepted: 10/04/2014] [Indexed: 10/24/2022]
Abstract
Protein tyrosine phosphatases have diverse substrate specificities and intrinsic activities that lay the foundations for the fine-tuning of a phosphorylation network to precisely regulate cellular signal transduction. All classical PTPs share common catalytic mechanisms, and the important catalytic residues in the first sphere of their active sites have been well characterized. However, little attention has been paid to the second-sphere residues that are potentially important in defining the intrinsic activity and substrate specificity of PTPs. Here, we find that a conserved second-sphere residue, Thr263, located in the surface Q-loop is important for both the function and activity of PTPs. Using PTP1B as a study model, we found that mutations of Thr263 impaired the negative regulation role of PTP1B in insulin signaling. A detailed mechanistic study utilizing steady-state kinetics, Brønsted analysis and pH dependence in the presence of pNPP or phosphopeptide substrates revealed that Thr263 is required for the stabilization of the leaving group during catalysis. Further crystallographic studies and structural comparison revealed that Thr263 regulates the general acid function through modulation of the WPD-loop by the T263:F182/Y/H interaction pair, which is conserved in 26 out of 32 classical PTPs. In addition, the hydrophobic interaction between Thr263 and Arg1159 of the insulin receptor contributes to the substrate specificity of PTP1B. Taken together, our findings demonstrate the general role of the second-sphere residue Thr263 in PTP catalysis. Our findings suggest that the second sphere residues of PTP active site may play important roles in PTP-mediated function in both normal and diseased states.
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Affiliation(s)
- Peng Xiao
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China; Shandong Provincial School Key Laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China
| | - Xiao Wang
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China; Shandong Provincial School Key Laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China
| | - Hong-Mei Wang
- Shandong Provincial School Key Laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China; Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, China
| | - Xiao-Lei Fu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China; Shandong Provincial School Key Laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China; Department of Public Health, Shandong University, School of Medicine, Jinan, Shandong, China
| | - Fu-ai Cui
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China
| | - Xiao Yu
- Shandong Provincial School Key Laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China; Department of Public Health, Shandong University, School of Medicine, Jinan, Shandong, China
| | - Shi-shuai Wen
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China; Shandong Provincial School Key Laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China
| | - Wen-Xiang Bi
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, 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, China; Shandong Provincial School Key Laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China; Provincial Hospital Affiliated to Shandong University, Jinan, Shandong, China.
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33
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Yu ZH, Zhang RY, Walls CD, Chen L, Zhang S, Wu L, Liu S, Zhang ZY. Molecular basis of gain-of-function LEOPARD syndrome-associated SHP2 mutations. Biochemistry 2014; 53:4136-51. [PMID: 24935154 PMCID: PMC4081049 DOI: 10.1021/bi5002695] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Src homology 2 (SH2) domain-containing protein tyrosine phosphatase 2 (SHP2) is a critical signal transducer downstream of growth factors that promotes the activation of the RAS-ERK1/2 cascade. In its basal state, SHP2 exists in an autoinhibited closed conformation because of an intramolecular interaction between its N-SH2 and protein tyrosine phosphatase (PTP) domains. Binding to pTyr ligands present on growth factor receptors and adaptor proteins with its N-SH2 domain localizes SHP2 to its substrates and frees the active site from allosteric inhibition. Germline mutations in SHP2 are known to cause both Noonan syndrome (NS) and LEOPARD syndrome (LS), two clinically similar autosomal dominant developmental disorders. NS-associated SHP2 mutants display elevated phosphatase activity, while LS-associated SHP2 mutants exhibit reduced catalytic activity. A conundrum in how clinically similar diseases result from mutations to SHP2 that have opposite effects on this enzyme's catalytic functionality exists. Here we report a comprehensive investigation of the kinetic, structural, dynamic, and biochemical signaling properties of the wild type as well as all reported LS-associated SHP2 mutants. The results reveal that LS-causing mutations not only affect SHP2 phosphatase activity but also induce a weakening of the intramolecular interaction between the N-SH2 and PTP domains, leading to mutants that are more readily activated by competing pTyr ligands. Our data also indicate that the residual phosphatase activity associated with the LS SHP2 mutant is required for enhanced ERK1/2 activation. Consequently, catalytically impaired SHP2 mutants could display gain-of-function properties because of their ability to localize to the vicinity of substrates for longer periods of time, thereby affording the opportunity for prolonged substrate turnover and sustained RAS-ERK1/2 activation.
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Affiliation(s)
- Zhi-Hong Yu
- Department
of Biochemistry and Molecular Biology, Indiana
University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Ruo-Yu Zhang
- Department
of Biochemistry and Molecular Biology, Indiana
University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Chad D. Walls
- Department
of Biochemistry and Molecular Biology, Indiana
University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Lan Chen
- Department
of Biochemistry and Molecular Biology, Indiana
University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States,Chemical
Genomics Core Facility, Indiana University
School of Medicine, 635
Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Sheng Zhang
- Department
of Biochemistry and Molecular Biology, Indiana
University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States,Chemical
Genomics Core Facility, Indiana University
School of Medicine, 635
Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Li Wu
- Department
of Biochemistry and Molecular Biology, Indiana
University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States,Chemical
Genomics Core Facility, Indiana University
School of Medicine, 635
Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Sijiu Liu
- Department
of Biochemistry and Molecular Biology, Indiana
University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States
| | - Zhong-Yin Zhang
- Department
of Biochemistry and Molecular Biology, Indiana
University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, United
States,E-mail:
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34
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Linford AS, Jiang NM, Edwards TE, Sherman NE, Van Voorhis WC, Stewart LJ, Myler PJ, Staker BL, Petri WA. Crystal structure and putative substrate identification for the Entamoeba histolytica low molecular weight tyrosine phosphatase. Mol Biochem Parasitol 2014; 193:33-44. [PMID: 24548880 DOI: 10.1016/j.molbiopara.2014.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2013] [Revised: 01/12/2014] [Accepted: 01/22/2014] [Indexed: 11/28/2022]
Abstract
Entamoeba histolytica is a eukaryotic intestinal parasite of humans, and is endemic in developing countries. We have characterized the E. histolytica putative low molecular weight protein tyrosine phosphatase (LMW-PTP). The structure for this amebic tyrosine phosphatase was solved, showing the ligand-induced conformational changes necessary for binding of substrate. In amebae, it was expressed at low but detectable levels as detected by immunoprecipitation followed by immunoblotting. A mutant LMW-PTP protein in which the catalytic cysteine in the active site was replaced with a serine lacked phosphatase activity, and was used to identify a number of trapped putative substrate proteins via mass spectrometry analysis. Seven of these putative substrate protein genes were cloned with an epitope tag and overexpressed in amebae. Five of these seven putative substrate proteins were demonstrated to interact specifically with the mutant LMW-PTP. This is the first biochemical study of a small tyrosine phosphatase in Entamoeba, and sets the stage for understanding its role in amebic biology and pathogenesis.
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Affiliation(s)
- Alicia S Linford
- Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, VA 22908, USA.
| | - Nona M Jiang
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Thomas E Edwards
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Emerald Bio, Bainbridge Island, WA 98110, USA
| | - Nicholas E Sherman
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA 22908, USA
| | - Wesley C Van Voorhis
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Lance J Stewart
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Emerald Bio, Bainbridge Island, WA 98110, USA
| | - Peter J Myler
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Seattle Biomedical Research Institute, Seattle, WA 98109, USA; Departments of Global Health and Medical Education & Biomedical Informatics, University of Washington, Seattle, WA 98195, USA
| | - Bart L Staker
- Seattle Structural Genomics Center for Infectious Disease (SSGCID), USA; Emerald Bio, Bainbridge Island, WA 98110, USA
| | - William A Petri
- Division of Infectious Diseases and International Health, University of Virginia Health System, Charlottesville, VA 22908, USA; Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA; Department of Pathology, University of Virginia, Charlottesville, VA 22908, USA.
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35
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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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36
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Kharitidi D, Manteghi S, Pause A. Pseudophosphatases: methods of analysis and physiological functions. Methods 2013; 65:207-18. [PMID: 24064037 DOI: 10.1016/j.ymeth.2013.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/20/2013] [Accepted: 09/11/2013] [Indexed: 01/27/2023] Open
Abstract
Protein tyrosine phosphatases (PTPs) are key enzymes in the regulation of cellular homeostasis and signaling pathways. Strikingly, not all PTPs bear enzymatic activity. A considerable fraction of PTPs are enzymatically inactive and are known as pseudophosphatases. Despite the lack of activity they execute pivotal roles in development, cell biology and human disease. The present review is focused on the methods used to identify pseudophosphatases, their targets, and physiological roles. We present a strategy for detailed enzymatic analysis of inactive PTPs, regulation of inactive PTP domains and identification of binding partners. Furthermore, we provide a detailed overview of human pseudophosphatases and discuss their regulation of cellular processes and functions in human pathologies.
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Affiliation(s)
- Dmitri Kharitidi
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, 3655, Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada.
| | - Sanaz Manteghi
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, 3655, Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada.
| | - Arnim Pause
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, 3655, Promenade Sir William Osler, Montreal, QC H3G 1Y6, Canada.
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37
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Fuhrmann J, Subramanian V, Thompson PR. Targeting the arginine phosphatase YwlE with a catalytic redox-based inhibitor. ACS Chem Biol 2013; 8:2024-32. [PMID: 23838530 DOI: 10.1021/cb4001469] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein phosphatases are critical regulators of cellular signaling in both eukaryotes and prokaryotes. The majority of protein phosphatases dephosphorylate phosphoserine/phosphothreonine or phosphotyrosine residues. Recently, however, YwlE, a member of the low-molecular weight protein tyrosine phosphatase (LMW-PTP) family, was shown to efficiently target phosphoarginine. YwlE shares several sequence motifs with this family including the C(X)4 CR(S/T) motif that is crucial for catalysis and redox regulation of the enzyme. Herein we confirm that Cys9 and Cys14 play important roles in YwlE catalysis and regulation. On the basis of these observations, we designed and synthesized a YwlE inhibitor, denoted cyc-SeCN-amidine, that irreversibly inhibits YwlE (kinact/KI = 310 M(-1) min(-1)) by inducing disulfide bond formation between the two active site cysteine residues. Interestingly, inactivation appears to be catalytic, since the compound is neither destroyed nor altered after enzyme inhibition. Although the exact mechanism of disulfide induction remains elusive, we propose several potential mechanisms accounting for the cyc-SeCN-amidine mediated inhibition of YwlE. These findings could stimulate the design of similar selenium-based compounds targeting other redox-sensitive enzymes.
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Affiliation(s)
- Jakob Fuhrmann
- Department
of Chemistry and ‡The Kellogg School of Science and Technology, The Scripps Research Institute, 130 Scripps Way, Jupiter,
Florida 33458, United States
| | - Venkataraman Subramanian
- Department
of Chemistry and ‡The Kellogg School of Science and Technology, The Scripps Research Institute, 130 Scripps Way, Jupiter,
Florida 33458, United States
| | - Paul R. Thompson
- Department
of Chemistry and ‡The Kellogg School of Science and Technology, The Scripps Research Institute, 130 Scripps Way, Jupiter,
Florida 33458, United States
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38
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Fuhrmann J, Mierzwa B, Trentini D, Spiess S, Lehner A, Charpentier E, Clausen T. Structural Basis for Recognizing Phosphoarginine and Evolving Residue-Specific Protein Phosphatases in Gram-Positive Bacteria. Cell Rep 2013; 3:1832-9. [DOI: 10.1016/j.celrep.2013.05.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/07/2013] [Accepted: 05/10/2013] [Indexed: 12/31/2022] Open
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Ponnusamy M, Ma L, Zhuang S. Necrotic renal epithelial cell inhibits renal interstitial fibroblast activation: role of protein tyrosine phosphatase 1B. Am J Physiol Renal Physiol 2013; 304:F698-709. [PMID: 23283996 DOI: 10.1152/ajprenal.00564.2012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Our recent studies showed that contents of necrotic renal proximal tubular cells (RPTC) from 2 × 10(6) cells/ml directly induced death of cultured renal interstitial fibroblasts. However, it remains unknown whether nonlethal number of necrotic RPTC would also alter the fate of renal interstitial fibroblasts. To address this issue, renal interstitial fibroblasts (NRK-49F) were exposed to necrotic RPTC supernatant (RPTC-Sup) obtained from 2 × 10(4) to 5 × 10(5) cells/ml. These concentrations of RPTC did not induce cell death, but led to inactivation of renal fibroblasts as indicated by reduced expression of α-smooth muscle actin and fibronectin, two hallmarks of activated fibroblasts. Concurrently, the same doses of necrotic RPTC-Sup suppressed phosphorylation of epidermal growth factor receptor (EGFR) and signal transducers and activators of transcription-3 (STAT3) in a time- and dose-dependent manner, but did not affect phosphorylation of platelet-derived growth factor receptor-β, AKT, and extracellular signal-regulated kinase 1/2. The presence of sodium orthovanadate, a general protein tyrosine phosphatase (PTP) inhibitor or TCS-401 (a selective PTP1B inhibitor), abrogated those effects of RPTC-Sup, whereas coincubation with the EGFR inhibitor (Gefitinib) or silencing of EGFR with siRNA preserved the ability of RPTC-Sup in suppressing renal fibroblast activation and STAT3 phosphorylation. Moreover, RPTC-Sup treatment induced PTP1B phosphorylation and its interaction with EGFR. Collectively, these results indicate that nonlethal necrotic RPTC-Sup can induce inactivation of renal interstitial fibroblasts, which occurs through a mechanism involved in PTP1B-mediated inhibition of EGFR signaling.
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Affiliation(s)
- Murugavel Ponnusamy
- Department of Medicine, Rhode Island Hospital and Alpert Medical School of Brown University, Providence, RI 02903, USA
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40
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Lountos GT, Tropea JE, Waugh DS. Structure of the Trypanosoma cruzi protein tyrosine phosphatase TcPTP1, a potential therapeutic target for Chagas' disease. Mol Biochem Parasitol 2013; 187:1-8. [PMID: 23137716 PMCID: PMC4197799 DOI: 10.1016/j.molbiopara.2012.10.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 10/22/2012] [Accepted: 10/26/2012] [Indexed: 12/26/2022]
Abstract
Chagas' disease, a neglected tropical affliction transmitted by the flagellated protozoan Trypanosoma cruzi, is prevalent in Latin America and affects nearly 18 million people worldwide, yet few approved drugs are available to treat the disease. Moreover, the currently available drugs exhibit severe toxicity or are poorly effective in the chronic phase of the disease. This limitation, along with the large population at risk, underscores the urgent need to discover new molecular targets and novel therapeutic agents. Recently, the T. cruzi protein tyrosine phosphatase TcPTP1 has been implicated in the cellular differentiation and infectivity of the parasite and is therefore a promising target for the design of novel anti-parasitic drugs. Here, we report the X-ray crystal structure of TcPTP1 refined to a resolution of 2.18 Å, which provides structural insights into the active site environment that can be used to initiate structure-based drug design efforts to develop specific TcPTP1 inhibitors. Potential strategies to develop such inhibitors are also discussed.
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Affiliation(s)
- George T. Lountos
- Basic Science Program, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
- Macromolecular Crystallography Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Joseph E. Tropea
- Macromolecular Crystallography Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - David S. Waugh
- Macromolecular Crystallography Laboratory, Center for Cancer Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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41
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Abstract
Massive evidence suggests that genetic abnormalities contribute to the development of lung cancer. These molecular abnormalities may serve as diagnostic, prognostic and predictive biomarkers for this deadly disease. It is imperative to search these biomarkers in different tumorigenesis pathways so as to provide the most appropriate therapy for each individual patient with lung malignancy. Phosphoproteomics is a promising technology for the identification of biomarkers and novel therapeutic targets for cancer. Thousands of proteins interact via physical and chemical association. Moreover, some proteins can covalently modify other proteins post-translationally. These post-translational modifications ultimately give rise to the emergent functions of cells in sequence, space and time. Phosphoproteomics clinical researches imply the comprehensive analysis of the proteins that are expressed in cells or tissues and can be employed at different stages. In addition, understanding the functions of phosphorylated proteins requires the study of proteomes as linked systems rather than collections of individual protein molecules. In fact, proteomics approaches coupled with affinity chromatography strategies followed by mass spectrometry have been used to elucidate relevant biological questions. This article will discuss the relevant clues of post-translational modifications, phosphorylated proteins, and useful proteomics approaches to identify molecular cancer signatures. The recent progress in phosphoproteomics research in lung cancer will be also discussed.
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Affiliation(s)
- Elena López
- Hospital Universitario Niño Jesús, Department of Oncohematology of Children, Madrid 28009, Spain; E-Mail:
| | - William C. S. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +852-295-854-41; Fax: +852-295-854-55
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42
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Khoontawad J, Laothong U, Roytrakul S, Pinlaor P, Mulvenna J, Wongkham C, Yongvanit P, Pairojkul C, Mairiang E, Sithithaworn P, Pinlaor S. Proteomic identification of plasma protein tyrosine phosphatase alpha and fibronectin associated with liver fluke, Opisthorchis viverrini, infection. PLoS One 2012; 7:e45460. [PMID: 23029023 PMCID: PMC3445495 DOI: 10.1371/journal.pone.0045460] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 08/22/2012] [Indexed: 12/02/2022] Open
Abstract
Opisthorchiasis caused by Opisthorchis viverrini induces periductal fibrosis via host immune/inflammatory responses. Plasma protein alteration during host-parasite interaction-mediated inflammation may provide potential diagnostic and/or prognostic biomarkers. To search for target protein changes in O. viverrini-infected hamsters, a 1-D PAGE gel band was trypsin-digested and analyzed by a LC-MS/MS-based proteomics approach in the plasma profile of infected hamsters, and applied to humans. Sixty seven proteins were selected for further analysis based on at least two unique tryptic peptides with protein ID score >10 and increased expression at least two times across time points. These proteins have not been previously identified in O. viverrini-associated infection. Among those, proteins involved in structural (19%), immune response (13%), cell cycle (10%) and transcription (10%) were highly expressed. Western blots revealed an expression level of protein tyrosine phosphatase alpha (PTPα) which reached a peak at 1 month and subsequently tended to decrease. Fibronectin significantly increased at 1 month and tended to increase with time, supporting proteomic analysis. PTPα was expressed in the cytoplasm of inflammatory cells, while fibronectin was observed mainly in the cytoplasm of fibroblasts and the extracellular matrix at periductal fibrosis areas. In addition, these protein levels significantly increased in the plasma of O. viverrini-infected patients compared to healthy individuals, and significantly decreased at 2-months post-treatment, indicating their potential as disease markers. In conclusion, our results suggest that plasma PTPα and fibronectin may be associated with opisthorchiasis and the hamster model provides the basis for development of novel diagnostic markers in the future.
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Affiliation(s)
- Jarinya Khoontawad
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Umawadee Laothong
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sittiruk Roytrakul
- Proteomics Research Laboratory, Genome Institute Biotechnology, Pathumthani, Thailand
| | - Porntip Pinlaor
- Centre for Research and Development in Medical Diagnostic Laboratory, Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Jason Mulvenna
- Department of Infectious Disease and Cancer, Faculty of Computational Biology, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Chaisiri Wongkham
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Puangrat Yongvanit
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Chawalit Pairojkul
- Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Eimorn Mairiang
- Department of Radiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Paiboon Sithithaworn
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Somchai Pinlaor
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- * E-mail:
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Liu J, Chen M, Li R, Yang F, Shi X, Zhu L, Wang HM, Yao W, Liu Q, Meng FG, Sun JP, Pang Q, Yu X. Biochemical and functional studies of lymphoid-specific tyrosine phosphatase (Lyp) variants S201F and R266W. PLoS One 2012; 7:e43631. [PMID: 22952725 PMCID: PMC3428364 DOI: 10.1371/journal.pone.0043631] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Accepted: 07/23/2012] [Indexed: 11/21/2022] Open
Abstract
The Lymphoid specific tyrosine phosphatase (Lyp) has elicited tremendous research interest due to the high risk of its missense mutation R620W in a wide spectrum of autoimmune diseases. While initially characterized as a gain-of-function mutant, R620W was thought to lead to autoimmune diseases through loss-of-function in T cell signaling by a recent study. Here we investigate the biochemical characters and T cell signaling functions of two uncharacterized Lyp variants S201F and R266W, together with a previously characterized Lyp variant R263Q, which had reduced risk in several autoimmune diseases, including systemic lupus erythematosus (SLE), ulcerative colitis (UC) and rheumatoid arthritis (RA). Our kinetic and functional studies of R263Q polymorphism basically reproduced previous findings that it was a loss-of-function mutant. The other variant S201F reduced Lyp phosphatase activity moderately and decreased Lyp function in T cell slightly, while R266W severely impaired phosphatase activity and was a loss-of-function variant in T cell signaling. A combined kinetic and structure analysis suggests that the R266W variant may decrease its phosphatase activity through perturbing either the Q-loop or the WPD loop of Lyp. As both R266W and R263Q significantly change their phosphatase activity and T cell functions, future work could be considered to evaluate these mutants in a broader spectrum of autoimmune diseases.
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Affiliation(s)
- Jing Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Ming Chen
- The 309 Hospital of PLA, Beijing, China
| | - Rong Li
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Fan Yang
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Xuanren Shi
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Lichao Zhu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Hong-Mei Wang
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Wei Yao
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Qiji Liu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
| | - Fan-Guo Meng
- Yangtze Delta Region Institute of Tsinghua University, Zhejiang, China
| | - Jin-Peng Sun
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
- Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
| | - Qi Pang
- Shandong Provincial Hospital, Shandong University, Jinan, Shandong, China
- * E-mail: (XY); (QP)
| | - Xiao Yu
- Key Laboratory for Experimental Teratology of the Ministry of Education, Shandong University School of Medicine, Jinan, Shandong, China
- * E-mail: (XY); (QP)
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44
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He R, Zeng LF, He Y, Zhang S, Zhang ZY. Small molecule tools for functional interrogation of protein tyrosine phosphatases. FEBS J 2012; 280:731-50. [PMID: 22816879 DOI: 10.1111/j.1742-4658.2012.08718.x] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The importance of protein tyrosine phosphatases (PTPs) in the regulation of cellular signalling is well established. Malfunction of PTP activity is also known to be associated with cancer, metabolic syndromes and autoimmune disorders, as well as neurodegenerative and infectious diseases. However, a detailed understanding of the roles played by the PTPs in normal physiology and in pathogenic conditions has been hampered by the absence of PTP-specific small molecule agents. In addition, the therapeutic benefits of modulating this target class are underexplored as a result of a lack of suitable chemical probes. Potent and specific PTP inhibitors could significantly facilitate functional analysis of the PTPs in complex cellular signal transduction pathways and may constitute valuable therapeutics in the treatment of several human diseases. We highlight the current challenges to and opportunities for developing PTP-specific small molecule agents. We also review available selective small molecule inhibitors developed for a number of PTPs, including PTP1B, TC-PTP, SHP2, lymphoid-specific tyrosine phosphatase, haematopoietic protein tyrosine phosphatase, CD45, PTPβ, PTPγ, PTPRO, Vaccinia H1-related phosphatase, mitogen-activated protein kinase phosphatase-1, mitogen-activated protein kinase phosphatase-3, Cdc25, YopH, mPTPA and mPTPB.
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Affiliation(s)
- Rongjun He
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Meng FG, Zhang ZY. Redox regulation of protein tyrosine phosphatase activity by hydroxyl radical. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:464-9. [PMID: 22819876 DOI: 10.1016/j.bbapap.2012.06.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 06/25/2012] [Accepted: 06/30/2012] [Indexed: 01/12/2023]
Abstract
Substantial evidence suggests that transient production of reactive oxygen species (ROS) such as hydrogen peroxide (H(2)O(2)) is an important signaling event triggered by the activation of various cell surface receptors. Major targets of H(2)O(2) include protein tyrosine phosphatases (PTPs). Oxidation of the active site Cys by H(2)O(2) abrogates PTP catalytic activity, thereby potentially furnishing a mechanism to ensure optimal tyrosine phosphorylation in response to a variety of physiological stimuli. Unfortunately, H(2)O(2) is poorly reactive in chemical terms and the second order rate constants for the H(2)O(2)-mediated PTP inactivation are ~10M(-1)s(-1), which is too slow to be compatible with the transient signaling events occurring at the physiological concentrations of H(2)O(2). We find that hydroxyl radical is produced from H(2)O(2) solutions in the absence of metal chelating agent by the Fenton reaction. We show that the hydroxyl radical is capable of inactivating the PTPs and the inactivation is active site directed, through oxidation of the catalytic Cys to sulfenic acid, which can be reduced by low molecular weight thiols. We also show that hydroxyl radical is a kinetically more efficient oxidant than H(2)O(2) for inactivating the PTPs. The second-order rate constants for the hydroxyl radical-mediated PTP inactivation are at least 2-3 orders of magnitude higher than those mediated by H(2)O(2) under the same conditions. Thus, hydroxyl radical generated in vivo may serve as a more physiologically relevant oxidizing agent for PTP inactivation. This article is part of a Special Issue entitled: Chemistry and mechanism of phosphatases, diesterases and triesterases.
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Affiliation(s)
- Fan-Guo Meng
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA
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Ke S, Ho MC, Zhadin N, Deng H, Callender R. Investigation of catalytic loop structure, dynamics, and function relationship of Yersinia protein tyrosine phosphatase by temperature-jump relaxation spectroscopy and X-ray structural determination. J Phys Chem B 2012; 116:6166-76. [PMID: 22564106 DOI: 10.1021/jp3037846] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Yersinia protein tyrosine phosphatase (YopH) is the most efficient enzyme among all PTPases. YopH is hyperactive compared to human PTPases, interfering with mammalian cellular pathways to achieve the pathogenicity of Yersinia. Two properties related to the catalytic loop structure differences have been proposed to affect its dynamics and enzyme efficiency. One is the ability of the loop to form stabilizing interactions to bound ligand after loop closure, which has long been recognized. In addition, the loop flexibility/mobility was suggested in a previous study to be a factor as well, based on the observation that incremental changes in PTPase loop structure by single point mutations to alanine often induce incremental changes in enzyme catalytic efficiency. In this study, the temperature jump relaxation spectroscopy (T-jump) has been used to discern the subtle changes of the loop dynamics due to point loop mutations. As expected, our results suggest a correlation between loop dynamics and the size of the residue on the catalytic loop. The stabilization of the enzyme-ligand complex is often enthalpy driven, achieved by formation of additional favorable hydrogen bonding/ionic interactions after loop closure. Interestingly, our T-jump and X-ray crystallography studies on YopH suggest that the elimination of some ligand-protein interactions by mutation does not necessarily destabilize the ligand-enzyme complex after loop closure, since the increased entropy in the forms of more mobile protein residues may be sufficient to compensate the free energy loss due to lost interactions and may even lead to enhanced efficiency of the enzyme catalysis. How these competing loop properties may affect loop dynamics and enzyme function are discussed.
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Affiliation(s)
- Shan Ke
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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Abstract
Reactive oxygen species (ROS), particularly hydrogen peroxide (H(2)O(2)), act as intracellular second messengers in many signaling pathways. Protein-tyrosine phosphatases (PTPs) are now believed to be important targets of ROS. PTPs contain a conserved catalytic cysteine with an unusually low pK(a). This property allows PTPs to execute nucleophilic attack on substrate phosphotyrosyl residues, but also renders them highly susceptible to oxidation. Reversible oxidation, which inactivates PTPs, is emerging as an important cellular regulatory mechanism and might contribute to human diseases, including cancer. Given their potential toxicity, it seems likely that ROS generation is highly controlled within cells to restrict oxidation to those PTPs that must be inactivated for signaling to proceed. Thus, identifying ROS-inactivated PTPs could be tantamount to finding the PTP(s) that critically regulate a specific signaling pathway. This article provides an overview of the methods currently available to identify and quantify PTP oxidation and outlines future challenges in redox signaling.
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Affiliation(s)
- Robert Karisch
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.
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Sobhia ME, Paul S, Shinde R, Potluri M, Gundam V, Kaur A, Haokip T. Protein tyrosine phosphatase inhibitors: a patent review (2002 – 2011). Expert Opin Ther Pat 2012; 22:125-53. [DOI: 10.1517/13543776.2012.661414] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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SHP2 is a target of the immunosuppressant tautomycetin. ACTA ACUST UNITED AC 2011; 18:101-10. [PMID: 21276943 DOI: 10.1016/j.chembiol.2010.10.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 09/23/2010] [Accepted: 10/29/2010] [Indexed: 02/02/2023]
Abstract
SHP2 phosphatase is a positive transducer of growth factor and cytokine signaling. SHP2 is also a bona fide oncogene; gain-of-function SHP2 mutations leading to increased phosphatase activity cause Noonan syndrome, as well as multiple forms of leukemia and solid tumors. We report that tautomycetin (TTN), an immunosuppressor in organ transplantation, and its engineered analog TTN D-1 are potent SHP2 inhibitors. TTN and TTN D-1 block T cell receptor-mediated tyrosine phosphorylation and ERK activation and gain-of-function mutant SHP2-induced hematopoietic progenitor hyperproliferation and monocytic differentiation. Crystal structure of the SHP2⋅TTN D-1 complex reveals that TTN D-1 occupies the SHP2 active site in a manner similar to that of a peptide substrate. Collectively, the data support the notion that SHP2 is a cellular target for TTN and provide a potential mechanism for the immunosuppressive activity of TTN. Moreover, the structure furnishes molecular insights upon which therapeutics targeting SHP2 can be developed on the basis of the TTN scaffold.
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Piovan L, Wu L, Zhang ZY, Andrade LH. Hypervalent organochalcogenanes as inhibitors of protein tyrosine phosphatases. Org Biomol Chem 2011; 9:1347-51. [PMID: 21240419 DOI: 10.1039/c0ob01050b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A series of organochalcogenanes was synthesized and evaluated as protein tyrosine phosphatases (PTPs) inhibitors. The results indicate that organochalcogenanes inactivate the PTPs in a time- and concentration-dependent fashion, most likely through covalent modification of the active site sulfur-moiety by the chalcogen atom. Consequently, organochalcogenanes represent a new class of mechanism-based probes to modulate the PTP-mediated cellular processes.
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Affiliation(s)
- Leandro Piovan
- Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, SP 05508-900, São Paulo, Brazil
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