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Ruiz-Martín V, Marcos T, de Pereda JM, Sánchez-Crespo M, de la Fuente MA, Bayón Y, Alonso A. LYP regulates SLP76 and other adaptor proteins in T cells. Biol Res 2024; 57:69. [PMID: 39342392 PMCID: PMC11438317 DOI: 10.1186/s40659-024-00536-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 08/06/2024] [Indexed: 10/01/2024] Open
Abstract
BACKGROUND The LYP tyrosine phosphatase presents a SNP (1858C > T) that increases the risk of developing autoimmune diseases such as type I diabetes and arthritis. It remains unclear how this SNP affects LYP function and promotes the development of these diseases. The scarce information about LYP substrates is in part responsible for the poor understanding of LYP function. RESULTS In this study, we identify in T lymphocytes several adaptor proteins as potential substrates targeted by LYP, including FYB, SLP-76, HS-1, Vav, SKAP1 and SKAP2. We also show that LYP co-localizes with SLP76 in microclusters, upon TCR engagement. CONCLUSIONS These data indicate that LYP may modulate T cell activation by dephosphorylating several adaptor proteins, such as FYB, SLP-76, HS-1, Vav, SKAP1 and SKAP2 upon TCR engagement.
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Affiliation(s)
- Virginia Ruiz-Martín
- Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM), CSIC-Universidad de Valladolid, c/ Sanz y Forés 3, 47003, Valladolid, Spain
| | - Tamara Marcos
- Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM), CSIC-Universidad de Valladolid, c/ Sanz y Forés 3, 47003, Valladolid, Spain
| | - José María de Pereda
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC), CSIC-Universidad de Salamanca, Campus Unamuno, 37007, Salamanca, Spain
| | - Mariano Sánchez-Crespo
- Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM), CSIC-Universidad de Valladolid, c/ Sanz y Forés 3, 47003, Valladolid, Spain
| | - Miguel Angel de la Fuente
- Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM), CSIC-Universidad de Valladolid, c/ Sanz y Forés 3, 47003, Valladolid, Spain
| | - Yolanda Bayón
- Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM), CSIC-Universidad de Valladolid, c/ Sanz y Forés 3, 47003, Valladolid, Spain.
| | - Andrés Alonso
- Unidad de Excelencia Instituto de Biología y Genética Molecular (IBGM), CSIC-Universidad de Valladolid, c/ Sanz y Forés 3, 47003, Valladolid, Spain.
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2
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Degn SE, Tolar P. Towards a unifying model for B-cell receptor triggering. Nat Rev Immunol 2024:10.1038/s41577-024-01073-x. [PMID: 39256626 DOI: 10.1038/s41577-024-01073-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2024] [Indexed: 09/12/2024]
Abstract
Antibodies are exceptionally versatile molecules with remarkable flexibility in their binding properties. Their natural targets range from small-molecule toxins, across viruses of different sizes, to bacteria and large multicellular parasites. The molecular determinants bound by antibodies include proteins, peptides, carbohydrates, nucleic acids, lipids and even synthetic molecules that have never existed in nature. Membrane-anchored antibodies also serve as receptors on the surface of the B cells that produce them. Despite recent structural insights, there is still no unifying molecular mechanism to explain how antibody targets (antigens) trigger the activation of these B-cell receptors (BCRs). After cognate antigen encounter, somatic hypermutation and class-switch recombination allow BCR affinity maturation and immunoglobulin class-specific responses, respectively. This raises the fundamental question of how one receptor activation mechanism can accommodate a plethora of variant receptors and ligands, and how it can ensure that individual B cells remain responsive to antigen after somatic hypermutation and class switching. There is still no definite answer. Here we give a brief historical account of the different models proposed to explain BCR triggering and discuss their merit in the context of the current knowledge of the structure of BCRs, their dynamic membrane distribution, and recent biochemical and cell biological insights.
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Affiliation(s)
- Søren E Degn
- Laboratory for Lymphocyte Biology, Department of Biomedicine, Aarhus University, Aarhus, Denmark.
- Centre for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus, Denmark.
| | - Pavel Tolar
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
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3
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Bester SM, Linwood R, Kataoka R, Wu WI, Mou TC. Enhancing the apo protein tyrosine phosphatase non-receptor type 2 crystal soaking strategy through inhibitor-accessible binding sites. Acta Crystallogr F Struct Biol Commun 2024; 80:210-219. [PMID: 39177701 PMCID: PMC11376276 DOI: 10.1107/s2053230x24007866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 08/09/2024] [Indexed: 08/24/2024] Open
Abstract
Protein tyrosine phosphatase non-receptor type 2 (PTPN2) has recently been recognized as a promising target for cancer immunotherapy. Despite extensive structural and functional studies of other protein tyrosine phosphatases, there is limited structural understanding of PTPN2. Currently, there are only five published PTPN2 structures and none are truly unbound due to the presence of a mutation, an inhibitor or a loop (related to crystal packing) in the active site. In this report, a novel crystal packing is revealed that resulted in a true apo PTPN2 crystal structure with an unbound active site, allowing the active site to be observed in a native apo state for the first time. Key residues related to accommodation in the active site became identifiable upon comparison with previously published PTPN2 structures. Structures of PTPN2 in complex with an established PTPN1 active-site inhibitor and an allosteric inhibitor were achieved through soaking experiments using these apo PTPN2 crystals. The increased structural understanding of apo PTPN2 and the ability to soak in inhibitors will aid the development of future PTPN2 inhibitors.
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Affiliation(s)
| | - Rebecca Linwood
- Pfizer Boulder Research and Development, Boulder, CO 80301, USA
| | - Ryoko Kataoka
- Pfizer Boulder Research and Development, Boulder, CO 80301, USA
| | - Wen I Wu
- Pfizer Boulder Research and Development, Boulder, CO 80301, USA
| | - Tung Chung Mou
- Pfizer Boulder Research and Development, Boulder, CO 80301, USA
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4
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Perdikari A, Woods VA, Ebrahim A, Lawler K, Bounds R, Singh NI, Mehlman T(S, Riley BT, Sharma S, Morris JW, Keogh JM, Henning E, Smith M, Farooqi IS, Keedy DA. Structures of human PTP1B variants reveal allosteric sites to target for weight loss therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.603709. [PMID: 39149290 PMCID: PMC11326154 DOI: 10.1101/2024.08.05.603709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Protein Tyrosine Phosphatase 1B (PTP1B) is a negative regulator of leptin signaling whose disruption protects against diet-induced obesity in mice. We investigated whether structural characterization of human PTP1B variant proteins might reveal precise mechanisms to target for weight loss therapy. We selected 12 rare variants for functional characterization from exomes from 997 people with persistent thinness and 200,000 people from UK Biobank. Seven of 12 variants impaired PTP1B function by increasing leptin-stimulated STAT3 phosphorylation in cells. Using room-temperature X-ray crystallography, hydrogen-deuterium exchange mass spectrometry, and computational modeling, we determined that human variants modulate the 3-dimensional structure of PTP1B through distinct allosteric conduits that energetically link distal, highly ligandable structural regions to the active site. These studies inform the design of allosteric PTP1B inhibitors for the treatment of obesity.
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Affiliation(s)
- Aliki Perdikari
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - Virgil A. Woods
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
- PhD Program in Biochemistry, CUNY Graduate Center; New York, NY 10016, USA
| | - Ali Ebrahim
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
| | - Katherine Lawler
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - Rebecca Bounds
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - Nathanael I. Singh
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
| | - Tamar (Skaist) Mehlman
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
- PhD Program in Biochemistry, CUNY Graduate Center; New York, NY 10016, USA
| | - Blake T. Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
| | - Shivani Sharma
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
- PhD Program in Biology, CUNY Graduate Center; New York, NY 10016, USA
| | - Jackson W. Morris
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
| | - Julia M. Keogh
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - Elana Henning
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - Miriam Smith
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - I. Sadaf Farooqi
- University of Cambridge Metabolic Research Laboratories and NIHR Cambridge Biomedical Research Centre, Institute of Metabolic Science & Addenbrooke’s Hospital; Cambridge, CB2 0QQ, UK
| | - Daniel A. Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center; New York, NY 10031, USA
- Department of Chemistry and Biochemistry, City College of New York; New York, NY 10031, USA
- PhD Programs in Biochemistry, Biology, and Chemistry, CUNY Graduate Center; New York, NY 10016, USA
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5
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Coronell-Tovar A, Pardo JP, Rodríguez-Romero A, Sosa-Peinado A, Vásquez-Bochm L, Cano-Sánchez P, Álvarez-Añorve LI, González-Andrade M. Protein tyrosine phosphatase 1B (PTP1B) function, structure, and inhibition strategies to develop antidiabetic drugs. FEBS Lett 2024; 598:1811-1838. [PMID: 38724486 DOI: 10.1002/1873-3468.14901] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 08/13/2024]
Abstract
Tyrosine protein phosphatase non-receptor type 1 (PTP1B; also known as protein tyrosine phosphatase 1B) is a member of the protein tyrosine phosphatase (PTP) family and is a soluble enzyme that plays an essential role in different physiological processes, including the regulation of metabolism, specifically in insulin and leptin sensitivity. PTP1B is crucial in the pathogenesis of type 2 diabetes mellitus and obesity. These biological functions have made PTP1B validated as an antidiabetic and anti-obesity, and potentially anticancer, molecular target. Four main approaches aim to inhibit PTP1B: orthosteric, allosteric, bidentate inhibition, and PTPN1 gene silencing. Developing a potent and selective PTP1B inhibitor is still challenging due to the enzyme's ubiquitous expression, subcellular location, and structural properties. This article reviews the main advances in the study of PTP1B since it was first isolated in 1988, as well as recent contextual information related to the PTP family to which this protein belongs. Furthermore, we offer an overview of the role of PTP1B in diabetes and obesity, and the challenges to developing selective, effective, potent, bioavailable, and cell-permeable compounds that can inhibit the enzyme.
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Affiliation(s)
- Andrea Coronell-Tovar
- Laboratorio de Biosensores y Modelaje molecular, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Juan P Pardo
- Laboratorio de Biosensores y Modelaje molecular, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - Alejandro Sosa-Peinado
- Laboratorio de Biosensores y Modelaje molecular, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Luz Vásquez-Bochm
- Laboratorio de Biosensores y Modelaje molecular, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Patricia Cano-Sánchez
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Laura Iliana Álvarez-Añorve
- Laboratorio de Biosensores y Modelaje molecular, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Martin González-Andrade
- Laboratorio de Biosensores y Modelaje molecular, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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6
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Chartier CA, Woods VA, Xu Y, van Vlimmeren AE, Jovanovic M, McDermott AE, Keedy DA, Shah NH. Allosteric regulation of the tyrosine phosphatase PTP1B by a protein-protein interaction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603632. [PMID: 39071364 PMCID: PMC11275736 DOI: 10.1101/2024.07.16.603632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The rapid identification of protein-protein interactions has been significantly enabled by mass spectrometry (MS) proteomics-based methods, including affinity purification-MS, crosslinking-MS, and proximity-labeling proteomics. While these methods can reveal networks of interacting proteins, they cannot reveal how specific protein-protein interactions alter cell signaling or protein function. For instance, when two proteins interact, there can be emergent signaling processes driven purely by the individual activities of those proteins being co-localized. Alternatively, protein-protein interactions can allosterically regulate function, enhancing or suppressing activity in response to binding. In this work, we investigate the interaction between the tyrosine phosphatase PTP1B and the adaptor protein Grb2, which have been annotated as binding partners in a number of proteomics studies. This interaction has been postulated to co-localize PTP1B with its substrate IRS-1 by forming a ternary complex, thereby enhancing the dephosphorylation of IRS-1 to suppress insulin signaling. Here, we report that Grb2 binding to PTP1B also allosterically enhances PTP1B catalytic activity. We show that this interaction is dependent on the proline-rich region of PTP1B, which interacts with the C-terminal SH3 domain of Grb2. Using NMR spectroscopy and hydrogen-deuterium exchange mass spectrometry (HDX-MS) we show that Grb2 binding alters PTP1B structure and/or dynamics. Finally, we use MS proteomics to identify other interactors of the PTP1B proline-rich region that may also regulate PTP1B function similarly to Grb2. This work presents one of the first examples of a protein allosterically regulating the enzymatic activity of PTP1B and lays the foundation for discovering new mechanisms of PTP1B regulation in cell signaling. Significance Statement Protein-protein interactions are critical for cell signaling. The interaction between the phosphatase PTP1B and adaptor protein Grb2 co-localizes PTP1B with its substrates, thereby enhancing their dephosphorylation. We show that Grb2 binding also directly modulates PTP1B activity through an allosteric mechanism involving the proline-rich region of PTP1B. Our study reveals a novel mode of PTP1B regulation through a protein-protein interaction that is likely to be exploited by other cellular interactors of this important signaling enzyme.
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7
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Huang X, Wu F, Ye J, Wang L, Wang X, Li X, He G. Expanding the horizons of targeted protein degradation: A non-small molecule perspective. Acta Pharm Sin B 2024; 14:2402-2427. [PMID: 38828146 PMCID: PMC11143490 DOI: 10.1016/j.apsb.2024.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/22/2023] [Accepted: 01/16/2024] [Indexed: 06/05/2024] Open
Abstract
Targeted protein degradation (TPD) represented by proteolysis targeting chimeras (PROTACs) marks a significant stride in drug discovery. A plethora of innovative technologies inspired by PROTAC have not only revolutionized the landscape of TPD but have the potential to unlock functionalities beyond degradation. Non-small-molecule-based approaches play an irreplaceable role in this field. A wide variety of agents spanning a broad chemical spectrum, including peptides, nucleic acids, antibodies, and even vaccines, which not only prove instrumental in overcoming the constraints of conventional small molecule entities but also provided rapidly renewing paradigms. Herein we summarize the burgeoning non-small molecule technological platforms inspired by PROTACs, including three major trajectories, to provide insights for the design strategies based on novel paradigms.
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Affiliation(s)
- Xiaowei Huang
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Fengbo Wu
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jing Ye
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-Related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lian Wang
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaoyun Wang
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-Related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiang Li
- Department of Urology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Gu He
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-Related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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8
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Hansen DT, Rueb NJ, Levinzon ND, Cheatham TE, Gaston R, Tanvir Ahmed K, Osburn-Staker S, Cox JE, Dudley GB, Barrios AM. The mechanism of covalent inhibition of LAR phosphatase by illudalic acid. Bioorg Med Chem Lett 2024; 104:129740. [PMID: 38599294 PMCID: PMC11057956 DOI: 10.1016/j.bmcl.2024.129740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/05/2024] [Accepted: 04/07/2024] [Indexed: 04/12/2024]
Abstract
Leukocyte antigen-related (LAR) phosphatase is a receptor-type protein tyrosine phosphatase involved in cellular signaling and associated with human disease including cancer and metabolic disorders. Selective inhibition of LAR phosphatase activity by well characterized and well validated small molecules would provide key insights into the roles of LAR phosphatase in health and disease, but identifying selective inhibitors of LAR phosphatase activity has been challenging. Recently, we described potent and selective inhibition of LAR phosphatase activity by the fungal natural product illudalic acid. Here we provide a detailed biochemical characterization of the adduct formed between LAR phosphatase and illudalic acid. A mass spectrometric analysis indicates that two cysteine residues are covalently labeled by illudalic acid and a related analog. Mutational analysis supports the hypothesis that inhibition of LAR phosphatase activity is due primarily to the adduct with the catalytic cysteine residue. A computational study suggests potential interactions between the illudalic acid moiety and the enzyme active site. Taken together, these data offer novel insights into the mechanism of inhibition of LAR phosphatase activity by illudalic acid.
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Affiliation(s)
- Daniel T Hansen
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Nicole J Rueb
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Nathan D Levinzon
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Robert Gaston
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Kh Tanvir Ahmed
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Sandra Osburn-Staker
- Mass Spectrometry and Proteomics Facility, University of Utah, Salt Lake City, UT 84112, USA
| | - James E Cox
- Mass Spectrometry and Proteomics Facility, University of Utah, Salt Lake City, UT 84112, USA
| | - Gregory B Dudley
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV 26506, USA
| | - Amy M Barrios
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, USA.
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9
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Ren J, Dai J, Chen Y, Wang Z, Sha R, Mao J, Mao Y. Hypoglycemic Activity of Rice Resistant-Starch Metabolites: A Mechanistic Network Pharmacology and In Vitro Approach. Metabolites 2024; 14:224. [PMID: 38668351 PMCID: PMC11052319 DOI: 10.3390/metabo14040224] [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: 03/04/2024] [Revised: 04/05/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Rice (Oryza sativa L.) is one of the primary sources of energy and nutrients needed by the body, and rice resistant starch (RRS) has been found to have hypoglycemic effects. However, its biological activity and specific mechanisms still need to be further elucidated. In the present study, 52 RRS differential metabolites were obtained from mouse liver, rat serum, canine feces, and human urine, and 246 potential targets were identified through a literature review and database analysis. A total of 151 common targets were identified by intersecting them with the targets of type 2 diabetes mellitus (T2DM). After network pharmacology analysis, 11 core metabolites were identified, including linolenic acid, chenodeoxycholic acid, ursodeoxycholic acid, deoxycholic acid, lithocholic acid, lithocholylglycine, glycoursodeoxycholic acid, phenylalanine, norepinephrine, cholic acid, and L-glutamic acid, and 16 core targets were identified, including MAPK3, MAPK1, EGFR, ESR1, PRKCA, FYN, LCK, DLG4, ITGB1, IL6, PTPN11, RARA, NR3C1, PTPN6, PPARA, and ITGAV. The core pathways included the neuroactive ligand-receptor interaction, cancer, and arachidonic acid metabolism pathways. The molecular docking results showed that bile acids such as glycoursodeoxycholic acid, chenodeoxycholic acid, ursodeoxycholic acid, lithocholic acid, deoxycholic acid, and cholic acid exhibited strong docking effects with EGFR, ITGAV, ITGB1, MAPK3, NR3C1, α-glucosidase, and α-amylase. In vitro hypoglycemic experiments further suggested that bile acids showed significant inhibitory effects on α-glucosidase and α-amylase, with CDCA and UDCA having the most prominent inhibitory effect. In summary, this study reveals a possible hypoglycemic pathway of RRS metabolites and provides new research perspectives to further explore the therapeutic mechanism of bile acids in T2DM.
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Affiliation(s)
- Jianing Ren
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China; (J.R.); (J.D.); (Y.C.); (Z.W.); (J.M.)
| | - Jing Dai
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China; (J.R.); (J.D.); (Y.C.); (Z.W.); (J.M.)
| | - Yue Chen
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China; (J.R.); (J.D.); (Y.C.); (Z.W.); (J.M.)
| | - Zhenzhen Wang
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China; (J.R.); (J.D.); (Y.C.); (Z.W.); (J.M.)
| | - Ruyi Sha
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China; (J.R.); (J.D.); (Y.C.); (Z.W.); (J.M.)
| | - Jianwei Mao
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou 310023, China; (J.R.); (J.D.); (Y.C.); (Z.W.); (J.M.)
| | - Yangchen Mao
- School of Medicine, University of Southampton, Southampton SO17 1BJ, UK;
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10
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Yuan Z, Zhang M, Chang L, Chen X, Ruan S, Shi S, Zhang Y, Zhu L, Li H, Li S. Discovery of a novel SHP2 allosteric inhibitor using virtual screening, FMO calculation, and molecular dynamic simulation. J Mol Model 2024; 30:131. [PMID: 38613643 DOI: 10.1007/s00894-024-05935-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/09/2024] [Indexed: 04/15/2024]
Abstract
CONTEXT SHP2 is a non-receptor protein tyrosine phosphatase to remove tyrosine phosphorylation. Functionally, SHP2 is an essential bridge to connect numerous oncogenic cell-signaling cascades including RAS-ERK, PI3K-AKT, JAK-STAT, and PD-1/PD-L1 pathways. This study aims to discover novel and potent SHP2 inhibitors using a hierarchical structure-based virtual screening strategy that combines molecular docking and the fragment molecular orbital method (FMO) for calculating binding affinity (referred to as the Dock-FMO protocol). For the SHP2 target, the FMO method prediction has a high correlation between the binding affinity of the protein-ligand interaction and experimental values (R2 = 0.55), demonstrating a significant advantage over the MM/PBSA (R2 = 0.02) and MM/GBSA (R2 = 0.15) methods. Therefore, we employed Dock-FMO virtual screening of ChemDiv database of ∼2,990,000 compounds to identify a novel SHP2 allosteric inhibitor bearing hydroxyimino acetamide scaffold. Experimental validation demonstrated that the new compound (E)-2-(hydroxyimino)-2-phenyl-N-(piperidin-4-ylmethyl)acetamide (7188-0011) effectively inhibited SHP2 in a dose-dependent manner. Molecular dynamics (MD) simulation analysis revealed the binding stability of compound 7188-0011 and the SHP2 protein, along with the key interacting residues in the allosteric binding site. Overall, our work has identified a novel and promising allosteric inhibitor that targets SHP2, providing a new starting point for further optimization to develop more potent inhibitors. METHODS All the molecular docking studies were employed to identify potential leads with Maestro v10.1. The protein-ligand binding affinities of potential leads were further predicted by FMO calculations at MP2/6-31G* level using GAMESS v2020 system. MD simulations were carried out with AmberTools18 by applying the FF14SB force field. MD trajectories were analyzed using VMD v1.9.3. MM/GB(PB)SA binding free energy analysis was carried out with the mmpbsa.py tool of AmberTools18. The docking and MD simulation results were visualized through PyMOL v2.5.0.
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Affiliation(s)
- Zhen Yuan
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Manzhan Zhang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Longfeng Chang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Xingyu Chen
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Shanshan Ruan
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Shanshan Shi
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Yiqing Zhang
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China
| | - Lili Zhu
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China.
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China.
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai, 200062, China.
- Lingang Laboratory, Shanghai, 200031, China.
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, State Key Laboratory of Bioreactor Engineering, School of Pharmacy, East China University of Science & Technology, Shanghai, China.
- Innovation Center for AI and Drug Discovery, East China Normal University, Shanghai, 200062, China.
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11
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Zhao L, Liu J, Li K, Zhang C, Chen T, Liu Z, Tang Y, Hu X, Shi A, Shu L, Huang S, Lian S, Zhang M, Li H, Sun J, Yu X, Zhang Z, Zhang Z, Xu Y. PTPN9 dephosphorylates FGFR2 pY656/657 through interaction with ACAP1 and ameliorates pemigatinib effect in cholangiocarcinoma. Hepatology 2024; 79:798-812. [PMID: 37505213 DOI: 10.1097/hep.0000000000000552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 07/06/2023] [Indexed: 07/29/2023]
Abstract
ABSTRACT AND AIM Cholangiocarcinoma (CCA) is a highly aggressive and lethal cancer that originates from the biliary epithelium. Systemic treatment options for CCA are currently limited, and the first targeted drug of CCA, pemigatinib, emerged in 2020 for CCA treatment by inhibiting FGFR2 phosphorylation. However, the regulatory mechanism of FGFR2 phosphorylation is not fully elucidated. APPROACH AND RESULTS Here we screened the FGFR2-interacting proteins and showed that protein tyrosine phosphatase (PTP) N9 interacts with FGFR2 and negatively regulates FGFR2 pY656/657 . Using phosphatase activity assays and modeling the FGFR2-PTPN9 complex structure, we identified FGFR2 pY656/657 as a substrate of PTPN9, and found that sec. 14p domain of PTPN9 interacts with FGFR2 through ACAP1 mediation. Coexpression of PTPN9 and ACAP1 indicates a favorable prognosis for CCA. In addition, we identified key amino acids and motifs involved in the sec. 14p-APCP1-FGFR2 interaction, including the "YRETRRKE" motif of sec. 14p, Y471 of PTPN9, as well as the PH and Arf-GAP domain of ACAP1. Moreover, we discovered that the FGFR2 I654V substitution can decrease PTPN9-FGFR2 interaction and thereby reduce the effectiveness of pemigatinib treatment. Using a series of in vitro and in vivo experiments including patient-derived xenografts (PDX), we showed that PTPN9 synergistically enhances pemigatinib effectiveness and suppresses CCA proliferation, migration, and invasion by inhibiting FGFR2 pY656/657 . CONCLUSIONS Our study identifies PTPN9 as a negative regulator of FGFR2 phosphorylation and a synergistic factor for pemigatinib treatment. The molecular mechanism, oncogenic function, and clinical significance of the PTPN9-ACAP1-FGFR2 complex are revealed, providing more evidence for CCA precision treatment.
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Affiliation(s)
- Liming Zhao
- Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Jialiang Liu
- Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Kangshuai Li
- Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Chao Zhang
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, Shandong, China
| | - Tianli Chen
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zengli Liu
- Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yongchang Tang
- Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Xiaoqiang Hu
- Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Anda Shi
- Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Lizhuang Shu
- Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Shaohui Huang
- Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Shuo Lian
- Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Minghui Zhang
- Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Hui Li
- Department of Pathology, The Second Hospital Affiliated to Shandong University, Jinan, China
| | - Jinpeng Sun
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, Shandong, China
| | - Xiao Yu
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Physiology, Shandong University School of Medicine, Jinan, Shandong, China
| | - Zhongyin Zhang
- Departments of Medicinal Chemistry and Molecular Pharmacology and Chemistry, Center for Cancer Research, Institute for Drug Discovery, Purdue University, West Lafayette, Indiana, USA
| | - Zongli Zhang
- Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Yunfei Xu
- Department of General Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
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12
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Chen L, Qian Z, Zheng Y, Zhang J, Sun J, Zhou C, Xiao H. Structural analysis of PTPN21 reveals a dominant-negative effect of the FERM domain on its phosphatase activity. SCIENCE ADVANCES 2024; 10:eadi7404. [PMID: 38416831 PMCID: PMC10901363 DOI: 10.1126/sciadv.adi7404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 01/24/2024] [Indexed: 03/01/2024]
Abstract
PTPN21 belongs to the four-point-one, ezrin, radixin, moesin (FERM) domain-containing protein tyrosine phosphatases (PTP) and plays important roles in cytoskeleton-associated cellular processes like cell adhesion, motility, and cargo transport. Because of the presence of a WPE loop instead of a WPD loop in the phosphatase domain, it is often considered to lack phosphatase activity. However, many of PTPN21's biological functions require its catalytic activity. To reconcile these findings, we have determined the structures of individual PTPN21 FERM, PTP domains, and a complex between FERM-PTP. Combined with biochemical analysis, we have found that PTPN21 PTP is weakly active and is autoinhibited by association with its FERM domain. Disruption of FERM-PTP interaction results in enhanced ERK activation. The oncogenic HPV18 E7 protein binds to PTP at the same location as PTPN21 FERM, indicating that it may act by displacing the FERM domain from PTP. Our results provide mechanistic insight into PTPN21 and benefit functional studies of PTPN21-mediated processes.
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Affiliation(s)
- Lu Chen
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Zijun Qian
- Department of Hematology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Yuyuan Zheng
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jie Zhang
- Department of Hematology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Jie Sun
- Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Chun Zhou
- Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Haowen Xiao
- Department of Hematology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
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13
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Gone GB, Go G, Nam G, Jeong W, Kim H, Lee S, Chung SJ. Exploring the Anti-Diabetic Potential of Quercetagitrin through Dual Inhibition of PTPN6 and PTPN9. Nutrients 2024; 16:647. [PMID: 38474775 DOI: 10.3390/nu16050647] [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: 01/29/2024] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Protein tyrosine phosphatases (PTPs) are pivotal contributors to the development of type 2 diabetes (T2DM). Hence, directing interventions towards PTPs emerges as a valuable therapeutic approach for managing type 2 diabetes. In particular, PTPN6 and PTPN9 are targets for anti-diabetic effects. Through high-throughput drug screening, quercetagitrin (QG) was recognized as a dual-target inhibitor of PTPN6 and PTPN9. We observed that QG suppressed the catalytic activity of PTPN6 (IC50 = 1 μM) and PTPN9 (IC50 = 1.7 μM) in vitro and enhanced glucose uptake by mature C2C12 myoblasts. Additionally, QG increased the phosphorylation of adenosine monophosphate-activated protein kinase (AMPK) and insulin-dependent phosphorylation of Akt in mature C2C12 myoblasts. It further promoted the phosphorylation of Akt in the presence of palmitic acid, suggesting the attenuation of insulin resistance. In summary, our results indicate QG's role as a potent inhibitor targeting both PTPN6 and PTPN9, showcasing its potential as a promising treatment avenue for T2DM.
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Affiliation(s)
- Geetanjali B Gone
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Geonhui Go
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Gibeom Nam
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Woojoo Jeong
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hyemin Kim
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Soah Lee
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Sang J Chung
- Department of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
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14
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Crean RM, Corbella M, Calixto AR, Hengge AC, Kamerlin SCL. Sequence - dynamics - function relationships in protein tyrosine phosphatases. QRB DISCOVERY 2024; 5:e4. [PMID: 38689874 PMCID: PMC11058592 DOI: 10.1017/qrd.2024.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/20/2023] [Accepted: 10/24/2023] [Indexed: 05/02/2024] Open
Abstract
Protein tyrosine phosphatases (PTPs) are crucial regulators of cellular signaling. Their activity is regulated by the motion of a conserved loop, the WPD-loop, from a catalytically inactive open to a catalytically active closed conformation. WPD-loop motion optimally positions a catalytically critical residue into the active site, and is directly linked to the turnover number of these enzymes. Crystal structures of chimeric PTPs constructed by grafting parts of the WPD-loop sequence of PTP1B onto the scaffold of YopH showed WPD-loops in a wide-open conformation never previously observed in either parent enzyme. This wide-open conformation has, however, been observed upon binding of small molecule inhibitors to other PTPs, suggesting the potential of targeting it for drug discovery efforts. Here, we have performed simulations of both enzymes and show that there are negligible energetic differences in the chemical step of catalysis, but significant differences in the dynamical properties of the WPD-loop. Detailed interaction network analysis provides insight into the molecular basis for this population shift to a wide-open conformation. Taken together, our study provides insight into the links between loop dynamics and chemistry in these YopH variants specifically, and how WPD-loop dynamic can be engineered through modification of the internal protein interaction network.
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Affiliation(s)
- Rory M. Crean
- Department of Chemistry – BMC, Uppsala University, Uppsala, Sweden
| | - Marina Corbella
- Department of Chemistry – BMC, Uppsala University, Uppsala, Sweden
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) & Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona, Spain
| | - Ana R. Calixto
- Department of Chemistry – BMC, Uppsala University, Uppsala, Sweden
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Alvan C. Hengge
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, USA
| | - Shina C. L. Kamerlin
- Department of Chemistry – BMC, Uppsala University, Uppsala, Sweden
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
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15
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Guerrero L, Ebrahim A, Riley BT, Kim M, Huang Q, Finke AD, Keedy DA. Pushed to extremes: distinct effects of high temperature versus pressure on the structure of STEP. Commun Biol 2024; 7:59. [PMID: 38216663 PMCID: PMC10786866 DOI: 10.1038/s42003-023-05609-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/20/2023] [Indexed: 01/14/2024] Open
Abstract
Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature versus. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Altogether, our work indicates that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.
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Affiliation(s)
- Liliana Guerrero
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
- PhD Program in Biochemistry, CUNY Graduate Center, New York, NY, 10016, USA
| | - Ali Ebrahim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
| | - Blake T Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
| | - Minyoung Kim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY, 14853, USA
| | - Aaron D Finke
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY, 14853, USA
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY, 10031, USA.
- Department of Chemistry and Biochemistry, City College of New York, New York, NY, 10031, USA.
- PhD Programs in Biochemistry, Biology, & Chemistry, CUNY Graduate Center, New York, NY, 10016, USA.
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16
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El Badaoui L, Barr AJ. Analysis of Receptor-Type Protein Tyrosine Phosphatase Extracellular Regions with Insights from AlphaFold. Int J Mol Sci 2024; 25:820. [PMID: 38255894 PMCID: PMC10815196 DOI: 10.3390/ijms25020820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
The receptor-type protein tyrosine phosphatases (RPTPs) are involved in a wide variety of physiological functions which are mediated via their diverse extracellular regions. They play key roles in cell-cell contacts, bind various ligands and are regulated by dimerization and other processes. Depending on the subgroup, they have been described as everything from 'rigid rods' to 'floppy tentacles'. Here, we review current experimental structural knowledge on the extracellular region of RPTPs and draw on AlphaFold structural predictions to provide further insights into structure and function of these cellular signalling molecules, which are often mutated in disease and are recognised as drug targets. In agreement with experimental data, AlphaFold predicted structures for extracellular regions of R1, and R2B subgroup RPTPs have an extended conformation, whereas R2B RPTPs are twisted, reflecting their high flexibility. For the R3 PTPs, AlphaFold predicts that members of this subgroup adopt an extended conformation while others are twisted, and that certain members, such as CD148, have one or more large, disordered loop regions in place of fibronectin type 3 domains suggested by sequence analysis.
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Affiliation(s)
| | - Alastair J. Barr
- School of Life Sciences, University of Westminster, 115 New Cavendish Street, London W1W 6UW, UK;
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17
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Gerritsen J, Rizzo S, Thévenin D, White FM. System-Level Analysis of the Effects of RPTPs on Cellular Signaling Networks. Methods Mol Biol 2024; 2743:153-163. [PMID: 38147214 PMCID: PMC10787581 DOI: 10.1007/978-1-0716-3569-8_10] [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: 12/27/2023]
Abstract
Tyrosine phosphorylation regulates signaling network activity downstream of receptor tyrosine kinase (RTK) activation. Receptor protein tyrosine phosphatases (RPTPs) serve to dephosphorylate RTKs and their proximal adaptor proteins, thus serving to modulate RTK activity. While the general function of RPTPs is well understood, the direct and indirect substrates for each RPTP are poorly characterized. Here we describe a method, quantitative phosphotyrosine phosphoproteomics, that enables the identification of specific phosphorylation sites whose phosphorylation levels are altered by the expression and activity of a given RPTP. In a proof-of-concept application, we use this method to highlight several direct or indirect substrate phosphorylation sites for PTPRJ, also known as DEP1, and show their quantitative phosphorylation in the context of wild-type PTPRJ compared to a mutant form of PTPRJ with increased activity, in EGF-stimulated cells. This method is generally applicable to define the signaling network effects of each RPTP in cells or tissues under different physiological conditions.
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Affiliation(s)
- Jacqueline Gerritsen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sophie Rizzo
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA
| | - Damien Thévenin
- Department of Chemistry, Lehigh University, Bethlehem, PA, USA
| | - Forest M White
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
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18
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Tiemann M, Rademann J. Identification and Optimization of Protein Tyrosine Phosphatase Inhibitors Via Fragment Ligation. Methods Mol Biol 2024; 2743:239-270. [PMID: 38147220 DOI: 10.1007/978-1-0716-3569-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Phosphotyrosine biomimetics are starting points for potent inhibitors of protein tyrosine phosphatases (PTPs) and, thus, crucial for drug development. Their identification, however, has been heavily driven by rational design, limiting the discovery of diverse, novel, and improved mimetics. In this chapter, we describe two screening approaches utilizing fragment ligation methods: one to identify new mimetics and the other to optimize existing mimetics into more potent and selective inhibitors.
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Affiliation(s)
- Markus Tiemann
- Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Jörg Rademann
- Institute of Pharmacy, Freie Universität Berlin, Berlin, Germany.
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19
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Bishop AC, Serbina A. Targeting Nonconserved and Pathogenic Cysteines of Protein Tyrosine Phosphatases with Small Molecules. Methods Mol Biol 2024; 2743:271-283. [PMID: 38147221 DOI: 10.1007/978-1-0716-3569-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Protein tyrosine phosphatases (PTPs) are important therapeutic targets for a range of human pathologies. However, the common architecture of PTP active sites impedes the discovery of selective PTP inhibitors. Our laboratory has recently developed methods to inhibit PTPs allosterically by targeting cysteine residues that either (i) are not conserved in the PTP family or (ii) result from pathogenic mutations. Here, we describe screening protocols for the identification of selective inhibitors that covalently engage such "rare" cysteines in target PTPs. Moreover, to elucidate the breadth of possible applications of our cysteine-directed screening protocols, we provide a brief overview of the nonconserved cysteines present in all human classical PTP domains.
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Affiliation(s)
| | - Anna Serbina
- Department of Chemistry, Amherst College, Amherst, MA, USA
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20
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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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21
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EswarKumar N, Yang CH, Tewary S, Peng WH, Chen GC, Yeh YQ, Yang HC, Ho MC. An integrative approach unveils a distal encounter site for rPTPε and phospho-Src complex formation. Structure 2023; 31:1567-1577.e5. [PMID: 37794594 DOI: 10.1016/j.str.2023.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/10/2023] [Accepted: 09/07/2023] [Indexed: 10/06/2023]
Abstract
The structure determination of protein tyrosine phosphatase (PTP): phospho-protein complexes, which is essential to understand how specificity is achieved at the amino acid level, remains a significant challenge for protein crystallography and cryoEM due to the transient nature of binding interactions. Using rPTPεD1 and phospho-SrcKD as a model system, we have established an integrative workflow to address this problem, by means of which we generate a protein:phospho-protein complex model using predetermined protein structures, SAXS and pTyr-tailored MD simulations. Our model reveals transient protein-protein interactions between rPTPεD1 and phospho-SrcKD and is supported by three independent experimental validations. Measurements of the association rate between rPTPεD1 and phospho-SrcKD showed that mutations on the rPTPεD1: SrcKD complex interface disrupts these transient interactions, resulting in a reduction in protein-protein association rate and, eventually, phosphatase activity. This integrative approach is applicable to other PTP: phospho-protein complexes and the characterization of transient protein-protein interface interactions.
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Affiliation(s)
- Nadendla EswarKumar
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan; Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cheng-Han Yang
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan; Department of Chemistry, Fu Jen Catholic University, New Taipei City 24205, Taiwan
| | - Sunilkumar Tewary
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan
| | - Wen-Hsin Peng
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan
| | - Guang-Chao Chen
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan
| | - Yi-Qi Yeh
- National Synchrotron Radiation Research Center, Hsin-Chu 300, Taiwan
| | - Hsiao-Ching Yang
- Department of Chemistry, Fu Jen Catholic University, New Taipei City 24205, Taiwan.
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei 115, Taiwan; Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.
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22
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Molyneaux K, Laggner C, Brady‐Kalnay SM. A novel binding pocket in the D2 domain of protein tyrosine phosphatase mu (PTPmu) guides AI screen to identify small molecules that modulate tumour cell adhesion, growth and migration. J Cell Mol Med 2023; 27:3553-3564. [PMID: 37860940 PMCID: PMC10660673 DOI: 10.1111/jcmm.17973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 08/25/2023] [Accepted: 09/16/2023] [Indexed: 10/21/2023] Open
Abstract
Approximately 40% of people will get cancer in their lifetime in the US, and 20% are predicted to die from the condition when it is invasive and metastatic. Targeted screening for drugs that interact with proteins that drive cancer cell growth and migration can lead to new therapies. We screened molecular libraries with the AtomNet® AI-based drug design tool to identify compounds predicted to interact with the cytoplasmic domain of protein tyrosine phosphatase mu. Protein tyrosine phosphatase mu (PTPmu) is proteolytically downregulated in cancers such as glioblastoma generating fragments that stimulate cell survival and migration. Aberrant nuclear localization of PTPmu intracellular fragments drives cancer progression, so we targeted a predicted drug-binding site between the two cytoplasmic phosphatase domains we termed a D2 binding pocket. The function of the D2 domain is controversial with various proposed regulatory functions, making the D2 domain an attractive target for the development of allosteric drugs. Seventy-five of the best-scoring and chemically diverse computational hits predicted to interact with the D2 binding pocket were screened for effects on tumour cell motility and growth in 3D culture as well as in a direct assay for PTPmu-dependent adhesion. We identified two high-priority hits that inhibited the migration and glioma cell sphere formation of multiple glioma tumour cell lines as well as aggregation. We also identified one activator of PTPmu-dependent aggregation, which was able to stimulate cell migration. We propose that the PTPmu D2 binding pocket represents a novel regulatory site and that inhibitors targeting this region may have therapeutic potential for treating cancer.
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Affiliation(s)
- Kathleen Molyneaux
- Department of Molecular Biology & MicrobiologyCase Western Reserve UniversityClevelandOhioUSA
| | | | - Susann M. Brady‐Kalnay
- Department of Molecular Biology & MicrobiologyCase Western Reserve UniversityClevelandOhioUSA
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23
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Pass CG, Palzkill V, Tan J, Kim K, Thome T, Yang Q, Fazzone B, Robinson ST, O’Malley KA, Yue F, Scali ST, Berceli SA, Ryan TE. Single-Nuclei RNA-Sequencing of the Gastrocnemius Muscle in Peripheral Artery Disease. Circ Res 2023; 133:791-809. [PMID: 37823262 PMCID: PMC10599805 DOI: 10.1161/circresaha.123.323161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND Lower extremity peripheral artery disease (PAD) is a growing epidemic with limited effective treatment options. Here, we provide a single-nuclei atlas of PAD limb muscle to facilitate a better understanding of the composition of cells and transcriptional differences that comprise the diseased limb muscle. METHODS We obtained gastrocnemius muscle specimens from 20 patients with PAD and 12 non-PAD controls. Nuclei were isolated and single-nuclei RNA-sequencing was performed. The composition of nuclei was characterized by iterative clustering via principal component analysis, differential expression analysis, and the use of known marker genes. Bioinformatics analysis was performed to determine differences in gene expression between PAD and non-PAD nuclei, as well as subsequent analysis of intercellular signaling networks. Additional histological analyses of muscle specimens accompany the single-nuclei RNA-sequencing atlas. RESULTS Single-nuclei RNA-sequencing analysis indicated a fiber type shift with patients with PAD having fewer type I (slow/oxidative) and more type II (fast/glycolytic) myonuclei compared with non-PAD, which was confirmed using immunostaining of muscle specimens. Myonuclei from PAD displayed global upregulation of genes involved in stress response, autophagy, hypoxia, and atrophy. Subclustering of myonuclei also identified populations that were unique to PAD muscle characterized by metabolic dysregulation. PAD muscles also displayed unique transcriptional profiles and increased diversity of transcriptomes in muscle stem cells, regenerating myonuclei, and fibro-adipogenic progenitor cells. Analysis of intercellular communication networks revealed fibro-adipogenic progenitors as a major signaling hub in PAD muscle, as well as deficiencies in angiogenic and bone morphogenetic protein signaling which may contribute to poor limb function in PAD. CONCLUSIONS This reference single-nuclei RNA-sequencing atlas provides a comprehensive analysis of the cell composition, transcriptional signature, and intercellular communication pathways that are altered in the PAD condition.
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Affiliation(s)
- Caroline G. Pass
- Department of Applied Physiology and Kinesiology (C.G.P., V.P., J.T., K.K., T.T., Q.Y., T.E.R.), The University of Florida, Gainesville
| | - Victoria Palzkill
- Department of Applied Physiology and Kinesiology (C.G.P., V.P., J.T., K.K., T.T., Q.Y., T.E.R.), The University of Florida, Gainesville
| | - Jianna Tan
- Department of Applied Physiology and Kinesiology (C.G.P., V.P., J.T., K.K., T.T., Q.Y., T.E.R.), The University of Florida, Gainesville
| | - Kyoungrae Kim
- Department of Applied Physiology and Kinesiology (C.G.P., V.P., J.T., K.K., T.T., Q.Y., T.E.R.), The University of Florida, Gainesville
| | - Trace Thome
- Department of Applied Physiology and Kinesiology (C.G.P., V.P., J.T., K.K., T.T., Q.Y., T.E.R.), The University of Florida, Gainesville
| | - Qingping Yang
- Department of Applied Physiology and Kinesiology (C.G.P., V.P., J.T., K.K., T.T., Q.Y., T.E.R.), The University of Florida, Gainesville
| | - Brian Fazzone
- Department of Surgery, Division of Vascular Surgery and Endovascular Therapy (B.F., S.T.R., K.A.O., S.T.S., S.A.B.), The University of Florida, Gainesville
- Malcom Randall VA Medical Center, Gainesville, FL (B.F., S.T.R., K.A.O., S.T.S., S.A.B.)
| | - Scott T. Robinson
- Department of Surgery, Division of Vascular Surgery and Endovascular Therapy (B.F., S.T.R., K.A.O., S.T.S., S.A.B.), The University of Florida, Gainesville
- Malcom Randall VA Medical Center, Gainesville, FL (B.F., S.T.R., K.A.O., S.T.S., S.A.B.)
| | - Kerri A. O’Malley
- Department of Surgery, Division of Vascular Surgery and Endovascular Therapy (B.F., S.T.R., K.A.O., S.T.S., S.A.B.), The University of Florida, Gainesville
- Malcom Randall VA Medical Center, Gainesville, FL (B.F., S.T.R., K.A.O., S.T.S., S.A.B.)
| | - Feng Yue
- Department of Animal Sciences (F.Y.), The University of Florida, Gainesville
- Myology Institute (F.Y., T.E.R.), The University of Florida, Gainesville
| | - Salvatore T. Scali
- Department of Surgery, Division of Vascular Surgery and Endovascular Therapy (B.F., S.T.R., K.A.O., S.T.S., S.A.B.), The University of Florida, Gainesville
- Malcom Randall VA Medical Center, Gainesville, FL (B.F., S.T.R., K.A.O., S.T.S., S.A.B.)
| | - Scott A. Berceli
- Department of Surgery, Division of Vascular Surgery and Endovascular Therapy (B.F., S.T.R., K.A.O., S.T.S., S.A.B.), The University of Florida, Gainesville
- Malcom Randall VA Medical Center, Gainesville, FL (B.F., S.T.R., K.A.O., S.T.S., S.A.B.)
| | - Terence E. Ryan
- Department of Applied Physiology and Kinesiology (C.G.P., V.P., J.T., K.K., T.T., Q.Y., T.E.R.), The University of Florida, Gainesville
- Center for Exercise Science (T.E.R.), The University of Florida, Gainesville
- Myology Institute (F.Y., T.E.R.), The University of Florida, Gainesville
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24
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Bagwe PV, Deshpande RD, Juhasz G, Sathaye S, Joshi SV. Uncovering the Significance of STEP61 in Alzheimer's Disease: Structure, Substrates, and Interactome. Cell Mol Neurobiol 2023; 43:3099-3113. [PMID: 37219664 DOI: 10.1007/s10571-023-01364-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/15/2023] [Indexed: 05/24/2023]
Abstract
STEP (STriatal-Enriched Protein Tyrosine Phosphatase) is a brain-specific phosphatase that plays an important role in controlling signaling molecules involved in neuronal activity and synaptic development. The striatum is the main location of the STEP enzyme. An imbalance in STEP61 activity is a risk factor for Alzheimer's disease (AD). It can contribute to the development of numerous neuropsychiatric diseases, including Parkinson's disease (PD), schizophrenia, fragile X syndrome (FXS), Huntington's disease (HD), alcoholism, cerebral ischemia, and stress-related diseases. The molecular structure, chemistry, and molecular mechanisms associated with STEP61's two major substrates, Alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors (AMPAr) and N-methyl-D-aspartate receptors (NMDARs), are crucial in understanding the relationship between STEP61 and associated illnesses. STEP's interactions with its substrate proteins can alter the pathways of long-term potentiation and long-term depression. Therefore, understanding the role of STEP61 in neurological illnesses, particularly Alzheimer's disease-associated dementia, can provide valuable insights for possible therapeutic interventions. This review provides valuable insights into the molecular structure, chemistry, and molecular mechanisms associated with STEP61. This brain-specific phosphatase controls signaling molecules involved in neuronal activity and synaptic development. This review can aid researchers in gaining deep insights into the complex functions of STEP61.
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Affiliation(s)
- Pritam V Bagwe
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai, 400019, India
| | - Radni D Deshpande
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai, 400019, India
| | - Gabor Juhasz
- Clinical Research Unit (CRU Global Hungary Ltd.), Budapest, Hungary
| | - Sadhana Sathaye
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai, 400019, India.
| | - Shreerang V Joshi
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Matunga, Mumbai, 400019, India.
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25
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Yang X, Guo J, Li W, Li C, Zhu X, Liu Y, Wu X. PPM1H is down-regulated by ATF6 and dephosphorylates p-RPS6KB1 to inhibit progression of hepatocellular carcinoma. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:164-179. [PMID: 37456776 PMCID: PMC10345229 DOI: 10.1016/j.omtn.2023.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/15/2023] [Indexed: 07/18/2023]
Abstract
We have shown previously that polymorphism of activating transcription factor 6 (ATF6) is associated with susceptibility to hepatocellular carcinoma (HCC). Therefore, genes down-regulated by ATF6 might play a tumor-suppressing role. In the present study, we identified that expression of protein phosphatase magnesium- or manganous-dependent 1H (PPM1H) mRNA and protein can be inhibited by ATF6 in hepatoma cells and mice with liver Atf6 knockdown. Tumor tissues from 134 HCC patients were analyzed by immunohistochemistry, and PPM1H exhibited higher expression levels in adjacent para-cancer tissues than in HCC tissues. Therefore, patients with higher expression of PPM1H had a better prognosis. PPM1H inhibited proliferation, migration, and invasion of hepatoma cells. In addition, PPM1H inhibited induced HCC nodule formation as well as tumor xenograft growth in diethylnitrosamine/CCl4-induced HCC mouse model and nude mouse tumorigenicity assay, respectively. A 3D model of PPM1H was obtained by homology multi-template modeling, and ribosomal protein S6 kinase B1 (RPS6KB1) in the bone morphogenetic protein (BMP)/transforming growth factor β (TGF-β) pathway was screened out as the potential substrate of PPM1H by Rosetta. PPM1H could directly dephosphorylate p-RPS6KB1. To conclude, we discovered RPS6KB1 as a new PPM1H dephosphorylation substrate. PPM1H exhibited a suppressive effect on HCC progression by dephosphorylating p-RPS6KB1.
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Affiliation(s)
- Xiaoshuang Yang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, P.R. China
- School of Basic Medicine, Peking Union Medical College, Beijing 100005, P.R. China
| | - Jianting Guo
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, P.R. China
- School of Basic Medicine, Peking Union Medical College, Beijing 100005, P.R. China
| | - Wei Li
- Department of Interventional Radiology, Affiliated Hospital of Qingdao University, Shandong 266003, P.R. China
| | - Chunrui Li
- Beijing Cloud Computing Key Technique and Application Key Laboratory, Beijing Computing Center, Beijing 100094, P.R. China
| | - Xilin Zhu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, P.R. China
- School of Basic Medicine, Peking Union Medical College, Beijing 100005, P.R. China
| | - Ying Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, P.R. China
- School of Basic Medicine, Peking Union Medical College, Beijing 100005, P.R. China
| | - Xiaopan Wu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Beijing 100005, P.R. China
- School of Basic Medicine, Peking Union Medical College, Beijing 100005, P.R. China
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26
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Rizzo S, Sikorski E, Park S, Im W, Vasquez‐Montes V, Ladokhin AS, Thévenin D. Promoting the activity of a receptor tyrosine phosphatase with a novel pH-responsive transmembrane agonist inhibits cancer-associated phenotypes. Protein Sci 2023; 32:e4742. [PMID: 37515426 PMCID: PMC10461461 DOI: 10.1002/pro.4742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/18/2023] [Accepted: 07/27/2023] [Indexed: 07/30/2023]
Abstract
Cell signaling by receptor protein tyrosine kinases (RTKs) is tightly controlled by the counterbalancing actions of receptor protein tyrosine phosphatases (RPTPs). Due to their role in attenuating the signal-initiating potency of RTKs, RPTPs have long been viewed as therapeutic targets. However, the development of activators of RPTPs has remained limited. We previously reported that the homodimerization of a representative member of the RPTP family (protein tyrosine phosphatase receptor J or PTPRJ) is regulated by specific transmembrane (TM) residues. Disrupting this interaction by single point mutations promotes PTPRJ access to its RTK substrates (e.g., EGFR and FLT3), reduces RTK's phosphorylation and downstream signaling, and ultimately antagonizes RTK-driven cell phenotypes. Here, we designed and tested a series of first-in-class pH-responsive TM peptide agonists of PTPRJ that are soluble in aqueous solution but insert as a helical TM domain in lipid membranes when the pH is lowered to match that of the acidic microenvironment of tumors. The most promising peptide reduced EGFR's phosphorylation and inhibited cancer cell EGFR-driven migration and proliferation, similar to the PTPRJ's TM point mutations. Developing tumor-selective and TM-targeting peptide binders of critical RPTPs could afford a potentially transformative approach to studying RPTP's selectivity mechanism without requiring less specific inhibitors and represent a novel class of therapeutics against RTK-driven cancers.
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Affiliation(s)
- Sophie Rizzo
- Department of ChemistryLehigh UniversityBethlehemPennsylvaniaUSA
| | - Eden Sikorski
- Department of ChemistryLehigh UniversityBethlehemPennsylvaniaUSA
| | - Soohyung Park
- Department of Biological SciencesLehigh UniversityBethlehemPennsylvaniaUSA
| | - Wonpil Im
- Department of ChemistryLehigh UniversityBethlehemPennsylvaniaUSA
- Department of Biological SciencesLehigh UniversityBethlehemPennsylvaniaUSA
| | - Victor Vasquez‐Montes
- Department of Biochemistry and Molecular BiologyThe University of Kansas Medical CenterKansas CityKansasUSA
| | - Alexey S. Ladokhin
- Department of Biochemistry and Molecular BiologyThe University of Kansas Medical CenterKansas CityKansasUSA
| | - Damien Thévenin
- Department of ChemistryLehigh UniversityBethlehemPennsylvaniaUSA
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27
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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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28
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Liechty ET, Hren A, Kramer L, Donovan G, Friedman AJ, Shirts MR, Fox JM. Analysis of neutral mutational drift in an allosteric enzyme. Protein Sci 2023; 32:e4719. [PMID: 37402140 PMCID: PMC10364584 DOI: 10.1002/pro.4719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/05/2023]
Abstract
Neutral mutational drift is an important source of biological diversity that remains underexploited in fundamental studies of protein biophysics. This study uses a synthetic transcriptional circuit to study neutral drift in protein tyrosine phosphatase 1B (PTP1B), a mammalian signaling enzyme for which conformational changes are rate limiting. Kinetic assays of purified mutants indicate that catalytic activity, rather than thermodynamic stability, guides enrichment under neutral drift, where neutral or mildly activating mutations can mitigate the effects of deleterious ones. In general, mutants show a moderate activity-stability tradeoff, an indication that minor improvements in the activity of PTP1B do not require concomitant losses in its stability. Multiplexed sequencing of large mutant pools suggests that substitutions at allosterically influential sites are purged under biological selection, which enriches for mutations located outside of the active site. Findings indicate that the positional dependence of neutral mutations within drifting populations can reveal the presence of allosteric networks and illustrate an approach for using synthetic transcriptional systems to explore these mutations in regulatory enzymes.
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Affiliation(s)
- Evan T. Liechty
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderColoradoUSA
| | - Andrew Hren
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderColoradoUSA
| | - Levi Kramer
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderColoradoUSA
| | - Gregory Donovan
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderColoradoUSA
| | - Anika J. Friedman
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderColoradoUSA
| | - Michael R. Shirts
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderColoradoUSA
| | - Jerome M. Fox
- Department of Chemical and Biological EngineeringUniversity of ColoradoBoulderColoradoUSA
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29
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Yao Z, Dong H, Zhu J, Du L, Luo Y, Liu Q, Liu S, Lin Y, Wang L, Wang S, Wei W, Zhang K, Huang Q, Yu X, Zhao W, Xu H, Qiu X, Pan Y, Huang X, Jim Yeung SC, Zhang D, Zhang H. Age-related decline in hippocampal tyrosine phosphatase PTPRO is a mechanistic factor in chemotherapy-related cognitive impairment. JCI Insight 2023; 8:e166306. [PMID: 37485875 PMCID: PMC10443805 DOI: 10.1172/jci.insight.166306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/31/2023] [Indexed: 07/25/2023] Open
Abstract
Chemotherapy-related cognitive impairment (CRCI) or "chemo brain" is a devastating neurotoxic sequela of cancer-related treatments, especially for the elderly individuals. Here we show that PTPRO, a tyrosine phosphatase, is highly enriched in the hippocampus, and its level is tightly associated with neurocognitive function but declined significantly during aging. To understand the protective role of PTPRO in CRCI, a mouse model was generated by treating Ptpro-/- female mice with doxorubicin (DOX) because Ptpro-/- female mice are more vulnerable to DOX, showing cognitive impairments and neurodegeneration. By analyzing PTPRO substrates that are neurocognition-associated tyrosine kinases, we found that SRC and EPHA4 are highly phosphorylated/activated in the hippocampi of Ptpro-/- female mice, with increased sensitivity to DOX-induced CRCI. On the other hand, restoration of PTPRO in the hippocampal CA3 region significantly ameliorate CRCI in Ptpro-/- female mice. In addition, we found that the plant alkaloid berberine (BBR) is capable of ameliorating CRCI in aged female mice by upregulating hippocampal PTPRO. Mechanistically, BBR upregulates PTPRO by downregulating miR-25-3p, which directly targeted PTPRO. These findings collectively demonstrate the protective role of hippocampal PTPRO against CRCI.
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Affiliation(s)
- Zhimeng Yao
- Department of Urology Surgery, and
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong, China
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Hongmei Dong
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Jianlin Zhu
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong, China
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Liang Du
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Yichen Luo
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Qing Liu
- Department of Pathology, The First People‘s Hospital of Foshan, Foshan, Guangdong, China
| | - Shixin Liu
- Department of Thoracic Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong, China
| | - Yusheng Lin
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
- Graduate School, Shantou University Medical College, Shantou, Guangdong, China
- Department of Hematology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Lu Wang
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Shuhong Wang
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Wei Wei
- Department of Pathophysiology, Key Laboratory of State Administration of Traditional Chinese Medicine of the People’s Republic of China, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | - Keke Zhang
- Department of Pathophysiology, Key Laboratory of State Administration of Traditional Chinese Medicine of the People’s Republic of China, School of Medicine, Jinan University, Guangzhou, Guangdong, China
| | | | - Xiaojun Yu
- National Key Disciplines, Department of Forensic and Pathology, and
| | - Weijiang Zhao
- Center for Neuroscience, Shantou University Medical College, Shantou, Guangdong, China
- Cell Biology Department, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Haiyun Xu
- Shantou University Mental Health Center
- The Affiliated Kangning Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaofu Qiu
- Department of Urology, Guangdong Second Provincial General Hospital, Guangzhou, Guangdong, China
| | - Yunlong Pan
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong, China
- Minister of Education Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou, Guangdong, China
| | - Xingxu Huang
- Gene Editing Center, School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
| | - Sai-Ching Jim Yeung
- Department of Emergency Medicine and Department of Endocrine Neoplasia and Hormonal Disorders, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dianzheng Zhang
- Department of Biomedical Sciences, Philadelphia College of Osteopathic Medicine, Philadelphia, Pennsylvania, USA
| | - Hao Zhang
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, Guangdong, China
- Institute of Precision Cancer Medicine and Pathology, School of Medicine, and Minister of Education Key Laboratory of Tumor Molecular Biology, Jinan University, Guangzhou, Guangdong, China
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30
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Asano W, Yamanaka K, Ohara Y, Uhara T, Doi S, Orita T, Iwanaga T, Adachi T, Fujioka S, Akaki T, Ikegashira K, Hantani Y. Fragment-Based Discovery of Novel VE-PTP Inhibitors Using Orthogonal Biophysical Techniques. Biochemistry 2023. [PMID: 37414577 DOI: 10.1021/acs.biochem.3c00079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Tyrosine phosphorylation is an essential post-translational modification that regulates various biological events and is implicated in many diseases including cancer and atherosclerosis. Vascular endothelial protein tyrosine phosphatase (VE-PTP), which plays an important role in vascular homeostasis and angiogenesis, is therefore an attractive drug target for these diseases. However, there are still no drugs targeting PTP including VE-PTP. In this paper, we report the discovery of a novel VE-PTP inhibitor, Cpd-2, by fragment-based screening combining various biophysical techniques. Cpd-2 is the first VE-PTP inhibitor with a weakly acidic structure and high selectivity, unlike known strongly acidic inhibitors. We believe that this compound represents a new possibility for the development of bioavailable VE-PTP inhibitors.
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Affiliation(s)
- Wataru Asano
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Kenji Yamanaka
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Yasunori Ohara
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Toru Uhara
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Satoki Doi
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Takuya Orita
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Tomoko Iwanaga
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Tsuyoshi Adachi
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Shingo Fujioka
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Tatsuo Akaki
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Kazutaka Ikegashira
- Chemical Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
| | - Yoshiji Hantani
- Biological/Pharmacological Research Laboratories, Central Pharmaceutical Research Institute, Japan Tobacco Inc., 1-1 Murasaki-cho, Takatsuki, Osaka 569-1125, Japan
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31
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Sendo S, Kiosses WB, Yang S, Wu DJ, Lee DWK, Liu L, Aschner Y, Vela AJ, Downey GP, Santelli E, Bottini N. Clustering of phosphatase RPTPα promotes Src signaling and the arthritogenic action of synovial fibroblasts. Sci Signal 2023; 16:eabn8668. [PMID: 37402225 PMCID: PMC10544828 DOI: 10.1126/scisignal.abn8668] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 06/15/2023] [Indexed: 07/06/2023]
Abstract
Receptor-type protein phosphatase α (RPTPα) promotes fibroblast-dependent arthritis and fibrosis, in part, by enhancing the activation of the kinase SRC. Synovial fibroblasts lining joint tissue mediate inflammation and tissue damage, and their infiltration into adjacent tissues promotes disease progression. RPTPα includes an ectodomain and two intracellular catalytic domains (D1 and D2) and, in cancer cells, undergoes inhibitory homodimerization, which is dependent on a D1 wedge motif. Through single-molecule localization and labeled molecule interaction microscopy of migrating synovial fibroblasts, we investigated the role of RPTPα dimerization in the activation of SRC, the migration of synovial fibroblasts, and joint damage in a mouse model of arthritis. RPTPα clustered with other RPTPα and with SRC molecules in the context of actin-rich structures. A known dimerization-impairing mutation in the wedge motif (P210L/P211L) and the deletion of the D2 domain reduced RPTPα-RPTPα clustering; however, it also unexpectedly reduced RPTPα-SRC association. The same mutations also reduced recruitment of RPTPα to actin-rich structures and inhibited SRC activation and cellular migration. An antibody against the RPTPα ectodomain that prevented the clustering of RPTPα also inhibited RPTPα-SRC association and SRC activation and attenuated fibroblast migration and joint damage in arthritic mice. A catalytically inactivating RPTPα-C469S mutation protected mice from arthritis and reduced SRC activation in synovial fibroblasts. We conclude that RPTPα clustering retains it to actin-rich structures to promote SRC-mediated fibroblast migration and can be modulated through the extracellular domain.
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Affiliation(s)
- Sho Sendo
- Dept. of Medicine, University of California San Diego, La Jolla, CA 92093
| | - William B. Kiosses
- Dept. of Medicine, University of California San Diego, La Jolla, CA 92093
- La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Shen Yang
- Dept. of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Dennis J. Wu
- Dept. of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Daniel W. K. Lee
- Dept. of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Lin Liu
- Dept. of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Yael Aschner
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado, Aurora, Colorado
| | - Allison J. Vela
- Dept. of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Gregory P. Downey
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, National Jewish Health, Denver, Colorado
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado, Aurora, Colorado
- Department of Biomedical Research, National Jewish Health, Denver, Colorado
- Department of Immunology and Microbiology, University of Colorado, Aurora, Colorado
- Department of Pediatrics, National Jewish Health, Denver, Colorado
| | - Eugenio Santelli
- Dept. of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Nunzio Bottini
- Dept. of Medicine, University of California San Diego, La Jolla, CA 92093
- Department of Medicine, Kao Autoimmunity Institute, Cedars Sinai Medical Center, Los Angeles, CA, USA
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32
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Yeh CY, Izaguirre JA, Greisman JB, Willmore L, Maragakis P, Shaw DE. A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis. J Chem Inf Model 2023. [PMID: 37378552 DOI: 10.1021/acs.jcim.3c00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a negative regulator of the insulin and leptin signaling pathways, making it a highly attractive target for the treatment of type II diabetes. For PTP1B to perform its enzymatic function, a loop referred to as the "WPD loop" must transition between open (catalytically incompetent) and closed (catalytically competent) conformations, which have both been resolved by X-ray crystallography. Although prior studies have established this transition as the rate-limiting step for catalysis, the transition mechanism for PTP1B and other PTPs has been unclear. Here we present an atomically detailed model of WPD loop transitions in PTP1B based on unbiased, long-timescale molecular dynamics simulations and weighted ensemble simulations. We found that a specific WPD loop region─the PDFG motif─acted as the key conformational switch, with structural changes to the motif being necessary and sufficient for transitions between long-lived open and closed states of the loop. Simulations starting from the closed state repeatedly visited open states of the loop that quickly closed again unless the infrequent conformational switching of the motif stabilized the open state. The functional importance of the PDFG motif is supported by the fact that it is well conserved across PTPs. Bioinformatic analysis shows that the PDFG motif is also conserved, and adopts two distinct conformations, in deiminases, and the related DFG motif is known to function as a conformational switch in many kinases, suggesting that PDFG-like motifs may control transitions between structurally distinct, long-lived conformational states in multiple protein families.
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Affiliation(s)
- Christine Y Yeh
- D. E. Shaw Research, New York, New York 10036, United States
| | | | - Jack B Greisman
- D. E. Shaw Research, New York, New York 10036, United States
| | | | - Paul Maragakis
- D. E. Shaw Research, New York, New York 10036, United States
| | - David E Shaw
- D. E. Shaw Research, New York, New York 10036, United States
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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33
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Bajia D, Derwich K. An In Silico Study Investigating Camptothecin-Analog Interaction with Human Protein Tyrosine Phosphatase, SHP2 (PTPN11). Pharmaceuticals (Basel) 2023; 16:926. [PMID: 37513838 PMCID: PMC10386118 DOI: 10.3390/ph16070926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
The human PTPN11 gene encodes for the src tyrosine phosphatase protein (SHP2) is now gaining much attention in many disorders, particularly its oncogenic involvement in many types of cancer. Efforts in developing molecules targeting SHP2 with high efficacy are the future of drug discovery and chemotherapy. However, the interaction of a new camptothecin analog with the catalytic domain of SHP2 protein remains unknown. Therefore, this study aims to provide in silico rationale for the recognition and binding of FL118 and irinotecan with the catalytic domain of human protein tyrosine phosphatase-SHP2 (PTPc-SH2-SHP2, chain A). The docking interaction of the human SHP2 protein's catalytic domain as well as Y279C and R465G mutants with FL118 and irinotecan ligands were calculated and analyzed using the Autodock 4.2 programme, setting the docking grid to target the protein's active site. The camptothecin analog FL118 had the best lowest negative affinity energies with PTPc-SHP2 wildtype and SHP2-Y279C mutant model (-7.54 Kcal/mol and -6.94 Kcal/mol, respectively). Moreover, the protein-ligand complexes revealed several hydrogen bond interactions reflecting the degree of stability that each structure possesses, with the FL118-SHP2-wildtype forming the most stable complex among the structures. In addition, the FL118-SHP2 wildtype complex was validated for RMSD, RMSF, hydrogen bonds, and salt bridges. This revealed that the complex generated became stable over time. This in silico rationale identifies the novel FL118 camptothecin analog as a potent selective inhibitor of PTPc-SH2 domain of SHP2 protein, paving way for further in vitro investigations into the interactions and binding activity of analogs with SHP2 for potential therapeutic applications in PTPN11-associated disorders.
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Affiliation(s)
- Donald Bajia
- Department of Pediatric Oncology, Hematology and Transplantology, Poznan University of Medical Sciences, Ul. Fredry 10, 61701 Poznan, Poland
| | - Katarzyna Derwich
- Department of Pediatric Oncology, Hematology and Transplantology, Poznan University of Medical Sciences, Ul. Fredry 10, 61701 Poznan, Poland
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34
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Richards CE, Elamin YY, Carr A, Gately K, Rafee S, Cremona M, Hanrahan E, Smyth R, Ryan D, Morgan RK, Kennedy S, Hudson L, Fay J, O'Byrne K, Hennessy BT, Toomey S. Protein Tyrosine Phosphatase Non-Receptor 11 ( PTPN11/Shp2) as a Driver Oncogene and a Novel Therapeutic Target in Non-Small Cell Lung Cancer (NSCLC). Int J Mol Sci 2023; 24:10545. [PMID: 37445722 DOI: 10.3390/ijms241310545] [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: 05/03/2023] [Revised: 06/14/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
PTPN11 encodes the SHP2 protein tyrosine phosphatase that activates the mitogen-activated protein kinase (MAPK) pathway upstream of KRAS and MEK. PTPN11/Shp2 somatic mutations occur frequently in Juvenile myelomonocytic leukaemia (JMML); however, the role of mutated PTPN11 in lung cancer tumourigenesis and its utility as a therapeutic target has not been fully addressed. We applied mass-spectrometry-based genotyping to DNA extracted from the tumour and matched the normal tissue of 356 NSCLC patients (98 adenocarcinomas (LUAD) and 258 squamous cell carcinomas (LUSC)). Further, PTPN11 mutation cases were identified in additional cohorts, including TCGA, Broad, and MD Anderson datasets and the COSMIC database. PTPN11 constructs harbouring PTPN11 E76A, A72D and C459S mutations were stably expressed in IL-3 dependent BaF3 cells and NSCLC cell lines (NCI-H1703, NCI-H157, NCI-H1299). The MAPK and PI3K pathway activation was evaluated using Western blotting. PTPN11/Shp2 phosphatase activity was measured in whole-cell protein lysates using an Shp2 assay kit. The Shp2 inhibitor (SHPi) was assessed both in vitro and in vivo in a PTPN11-mutated cell line for improved responses to MAPK and PI3K targeting therapies. Somatic PTPN11 hotspot mutations occurred in 4/98 (4.1%) adenocarcinomas and 7/258 (2.7%) squamous cells of 356 NSCLC patients. Additional 26 PTPN11 hotspot mutations occurred in 23 and 3 adenocarcinomas and squamous cell carcinoma, respectively, across the additional cohorts. Mutant PTPN11 significantly increased the IL-3 independent survival of Ba/F3 cells compared to wildtype PTPN11 (p < 0.0001). Ba/F3, NCI-H1703, and NCI-H157 cells expressing mutant PTPN11 exhibited increased PTPN11/Shp2 phosphatase activity and phospho-ERK1/2 levels compared to cells expressing wildtype PTPN11. The transduction of the PTPN11 inactivating mutation C459S into NSCLC cell lines led to decreased phospho-ERK, as well as decreased phospho-AKT in the PTPN11-mutated NCI-H661 cell line. NCI-H661 cells (PTPN11-mutated, KRAS-wild type) were significantly more sensitive to growth inhibition by the PI3K inhibitor copanlisib (IC50: 13.9 ± 4.7 nM) compared to NCI-H1703 (PTPN11/KRAS-wild type) cells (IC50: >10,000 nM). The SHP2 inhibitor, in combination with the PI3K targeting therapy copanlisib, showed no significant difference in tumour development in vivo; however, this significantly prevented MAPK pathway induction in vitro (p < 0.0001). PTPN11/Shp2 demonstrated the in vitro features of a driver oncogene and could potentially sensitize NSCLC cells to PI3K inhibition and inhibit MAPK pathway activation following PI3K pathway targeting.
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Affiliation(s)
- Cathy E Richards
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, D09 YD60 Dublin, Ireland
| | - Yasir Y Elamin
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, D09 YD60 Dublin, Ireland
- Department of Thoracic Head and Neck Medical Oncology, Division of Cancer Medicine, M.D. Anderson Cancer Centre, Houston, TX 77030, USA
| | - Aoife Carr
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, D09 YD60 Dublin, Ireland
| | - Kathy Gately
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, Trinity College Dublin, St. James's Hospital, D08 NHY1 Dublin, Ireland
| | - Shereen Rafee
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, Trinity College Dublin, St. James's Hospital, D08 NHY1 Dublin, Ireland
| | - Mattia Cremona
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, D09 YD60 Dublin, Ireland
| | - Emer Hanrahan
- Department of Medical Oncology, St. Vincent's Hospital, D04 T6F4 Dublin, Ireland
| | - Robert Smyth
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, D09 YD60 Dublin, Ireland
| | - Daniel Ryan
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, D09 YD60 Dublin, Ireland
- Department of Respiratory Medicine, Beaumont Hospital, D09 V2N0 Dublin, Ireland
| | - Ross K Morgan
- Department of Respiratory Medicine, Beaumont Hospital, D09 V2N0 Dublin, Ireland
| | - Susan Kennedy
- Department of Pathology, St. Vincent's Hospital, D04 T6F4 Dublin, Ireland
| | - Lance Hudson
- Department of Surgery, Royal College of Surgeons in Ireland, D09 YD60 Dublin, Ireland
| | - Joanna Fay
- RCSI Biobank Service, Royal College of Surgeons in Ireland, D09 YD60 Dublin, Ireland
| | | | - Bryan T Hennessy
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, D09 YD60 Dublin, Ireland
| | - Sinead Toomey
- Medical Oncology Group, Department of Molecular Medicine, Royal College of Surgeons in Ireland, D09 YD60 Dublin, Ireland
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35
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Morris R, Keating N, Tan C, Chen H, Laktyushin A, Saiyed T, Liau NPD, Nicola NA, Tiganis T, Kershaw NJ, Babon JJ. Structure guided studies of the interaction between PTP1B and JAK. Commun Biol 2023; 6:641. [PMID: 37316570 DOI: 10.1038/s42003-023-05020-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/06/2023] [Indexed: 06/16/2023] Open
Abstract
Protein Tyrosine Phosphatase 1B (PTP1B) is the prototypical protein tyrosine phosphatase and plays an essential role in the regulation of several kinase-driven signalling pathways. PTP1B displays a preference for bisphosphorylated substrates. Here we identify PTP1B as an inhibitor of IL-6 and show that, in vitro, it can dephosphorylate all four members of the JAK family. In order to gain a detailed understanding of the molecular mechanism of JAK dephosphorylation, we undertook a structural and biochemical analysis of the dephosphorylation reaction. We identified a product-trapping PTP1B mutant that allowed visualisation of the tyrosine and phosphate products of the reaction and a substrate-trapping mutant with a vastly decreased off-rate compared to those previously described. The latter mutant was used to determine the structure of bisphosphorylated JAK peptides bound to the enzyme active site. These structures revealed that the downstream phosphotyrosine preferentially engaged the active site, in contrast to the analogous region of IRK. Biochemical analysis confirmed this preference. In this binding mode, the previously identified second aryl binding site remains unoccupied and the non-substrate phosphotyrosine engages Arg47. Mutation of this arginine disrupts the preference for the downstream phosphotyrosine. This study reveals a previously unappreciated plasticity in how PTP1B interacts with different substrates.
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Affiliation(s)
- Rhiannon Morris
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, VIC, Australia
| | - Narelle Keating
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, VIC, Australia
| | - Cyrus Tan
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, VIC, Australia
| | - Hao Chen
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, VIC, Australia
| | - Artem Laktyushin
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, VIC, Australia
| | - Tamanna Saiyed
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, VIC, Australia
| | - Nicholas P D Liau
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, VIC, Australia
| | - Nicos A Nicola
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, VIC, Australia
| | - Tony Tiganis
- Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
- Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Nadia J Kershaw
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, VIC, Australia
| | - Jeffrey J Babon
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, VIC, Australia.
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, VIC, Australia.
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36
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Windheim M, Reubold TF, Aichane K, Gaestel M, Burgert HG. Enforced Dimerization of CD45 by the Adenovirus E3/49K Protein Inhibits T Cell Receptor Signaling. J Virol 2023; 97:e0189822. [PMID: 37125921 PMCID: PMC10231199 DOI: 10.1128/jvi.01898-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/07/2023] [Indexed: 05/02/2023] Open
Abstract
Human adenoviruses (HAdVs) are widespread pathogens that generally cause mild infections in immunocompetent individuals but severe or even fatal diseases in immunocompromised patients. In order to counteract the host immune defenses, HAdVs encode various immunomodulatory proteins in the early transcription unit 3 (E3). The E3/49K protein is a highly glycosylated type I transmembrane protein uniquely expressed by species D HAdVs. Its N-terminal ectodomain sec49K is released by metalloprotease-mediated shedding at the cell surface and binds to the receptor-like protein tyrosine phosphatase CD45, a critical regulator of leukocyte activation and functions. It remained elusive which domains of CD45 and E3/49K are involved in the interaction and whether such an interaction can also occur on the cell surface with membrane-anchored full-length E3/49K. Here, we show that the two extracellular domains R1 and R2 of E3/49K bind to the same site in the domain d3 of CD45. This interaction enforces the dimerization of CD45, causing the inhibition of T cell receptor signaling. Intriguingly, the membrane-anchored E3/49K appears to be designed like a "molecular fishing rod" using an extended disordered region of E3/49K as a "fishing line" to bridge the distance between the plasma membrane of infected cells and the CD45 binding site on T cells to effectively position the domains R1 and R2 as baits for CD45 binding. This design strongly suggests that both secreted sec49K as well as membrane-anchored full-length E3/49K have immunomodulatory functions. The forced dimerization of CD45 may be applied as a therapeutic strategy in chronic inflammatory disorders and cancer. IMPORTANCE The battle between viruses and their hosts is an ongoing arms race. Whereas the host tries to detect and eliminate the virus, the latter counteracts such antiviral measures to replicate and spread. Adenoviruses have evolved various mechanisms to evade the human immune response. The E3/49K protein of species D adenoviruses mediates the inhibition of immune cell function via binding to the protein tyrosine phosphatase CD45. Here, we show that E3/49K triggers the dimerization of CD45 and thereby inhibits its phosphatase activity. Intriguingly, the membrane-anchored E3/49K seems to be designed like a "molecular fishing rod" with the two CD45 binding domains of E3/49K as baits positioned at the end of an extended disordered region reminiscent of a fishing line. The adenoviral strategy to inhibit CD45 activity by forced dimerization may be used for therapeutic intervention in autoimmune diseases or to prevent graft rejection after transplantation.
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Affiliation(s)
- Mark Windheim
- Institute of Cell Biochemistry, Hannover Medical School, Hannover, Germany
| | - Thomas F. Reubold
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Khadija Aichane
- Institute of Cell Biochemistry, Hannover Medical School, Hannover, Germany
| | - Matthias Gaestel
- Institute of Cell Biochemistry, Hannover Medical School, Hannover, Germany
| | - Hans-Gerhard Burgert
- Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Freiburg, Germany
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37
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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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38
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Hong SH, Xi SY, Johns AC, Tang LC, Li A, Hum MN, Chartier CA, Jovanovic M, Shah NH. Mapping the Chemical Space of Active-Site Targeted Covalent Ligands for Protein Tyrosine Phosphatases. Chembiochem 2023; 24:e202200706. [PMID: 36893077 PMCID: PMC10192133 DOI: 10.1002/cbic.202200706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 03/10/2023]
Abstract
Protein tyrosine phosphatases (PTPs) are an important class of enzymes that modulate essential cellular processes through protein dephosphorylation and are dysregulated in various disease states. There is demand for new compounds that target the active sites of these enzymes, for use as chemical tools to dissect their biological roles or as leads for the development of new therapeutics. In this study, we explore an array of electrophiles and fragment scaffolds to investigate the required chemical parameters for covalent inhibition of tyrosine phosphatases. Our analysis juxtaposes the intrinsic electrophilicity of these compounds with their potency against several classical PTPs, revealing chemotypes that inhibit tyrosine phosphatases while minimizing excessive, potentially non-specific reactivity. We also assess sequence divergence at key residues in PTPs to explain their differential susceptibility to covalent inhibition. We anticipate that our study will inspire new strategies to develop covalent probes and inhibitors for tyrosine phosphatases.
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Affiliation(s)
- Suk ho Hong
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Sarah Y. Xi
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Andrew C. Johns
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Lauren C. Tang
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Allyson Li
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Madeleine N. Hum
- Department of Chemistry, Columbia University, New York, NY 10027
| | | | - Marko Jovanovic
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Neel H. Shah
- Department of Chemistry, Columbia University, New York, NY 10027
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39
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Guerrero L, Ebrahim A, Riley BT, Kim M, Huang Q, Finke AD, Keedy DA. Pushed to extremes: distinct effects of high temperature vs. pressure on the structure of an atypical phosphatase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.02.538097. [PMID: 37205580 PMCID: PMC10187168 DOI: 10.1101/2023.05.02.538097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Protein function hinges on small shifts of three-dimensional structure. Elevating temperature or pressure may provide experimentally accessible insights into such shifts, but the effects of these distinct perturbations on protein structures have not been compared in atomic detail. To quantitatively explore these two axes, we report the first pair of structures at physiological temperature vs. high pressure for the same protein, STEP (PTPN5). We show that these perturbations have distinct and surprising effects on protein volume, patterns of ordered solvent, and local backbone and side-chain conformations. This includes novel interactions between key catalytic loops only at physiological temperature, and a distinct conformational ensemble for another active-site loop only at high pressure. Strikingly, in torsional space, physiological temperature shifts STEP toward previously reported active-like states, while high pressure shifts it toward a previously uncharted region. Together, our work argues that temperature and pressure are complementary, powerful, fundamental macromolecular perturbations.
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Affiliation(s)
- Liliana Guerrero
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- PhD Program in Biochemistry, CUNY Graduate Center, New York, NY 10016
| | - Ali Ebrahim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Blake T Riley
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
| | - Minyoung Kim
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Qingqiu Huang
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853
| | - Aaron D Finke
- Cornell High Energy Synchrotron Source (CHESS), Cornell University, Ithaca, NY 14853
| | - Daniel A Keedy
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031
- Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031
- PhD Programs in Biochemistry, Biology, & Chemistry, CUNY Graduate Center, New York, NY 10016
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40
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Regulation of Cell Plasticity by Bromodomain and Extraterminal Domain (BET) Proteins: A New Perspective in Glioblastoma Therapy. Int J Mol Sci 2023; 24:ijms24065665. [PMID: 36982740 PMCID: PMC10055343 DOI: 10.3390/ijms24065665] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 03/18/2023] Open
Abstract
BET proteins are a family of multifunctional epigenetic readers, mainly involved in transcriptional regulation through chromatin modelling. Transcriptome handling ability of BET proteins suggests a key role in the modulation of cell plasticity, both in fate decision and in lineage commitment during embryonic development and in pathogenic conditions, including cancerogenesis. Glioblastoma is the most aggressive form of glioma, characterized by a very poor prognosis despite the application of a multimodal therapy. Recently, new insights are emerging about the glioblastoma cellular origin, leading to the hypothesis that several putative mechanisms occur during gliomagenesis. Interestingly, epigenome dysregulation associated with loss of cellular identity and functions are emerging as crucial features of glioblastoma pathogenesis. Therefore, the emerging roles of BET protein in glioblastoma onco-biology and the compelling demand for more effective therapeutic strategies suggest that BET family members could be promising targets for translational breakthroughs in glioblastoma treatment. Primarily, “Reprogramming Therapy”, which is aimed at reverting the malignant phenotype, is now considered a promising strategy for GBM therapy.
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Adisornkanj P, Chanprasit R, Eliason S, Fons JM, Intachai W, Tongsima S, Olsen B, Arold ST, Ngamphiw C, Amendt BA, Tucker AS, Kantaputra P. Genetic Variants in Protein Tyrosine Phosphatase Non-Receptor Type 23 Are Responsible for Mesiodens Formation. BIOLOGY 2023; 12:393. [PMID: 36979085 PMCID: PMC10045488 DOI: 10.3390/biology12030393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
A mesiodens is a supernumerary tooth located in the midline of the premaxilla. To investigate the genetic cause of mesiodens, clinical and radiographic examination were performed on 23 family members of a two-generation Hmong family. Whole exome sequencing (WES) or Sanger sequencing were performed in 22 family members and two unrelated Thai patients with mesiodens. WES in the Hmong family revealed a missense mutation (c.1807G>A;p.Glu603Lys) in PTPN23 in seven affected members and six unaffected members. The mode of inheritance was autosomal dominance with incomplete penetrance (53.84%). Two additional mutations in PTPN23, c.2248C>G;p.Pro750Ala and c.3298C>T;p.Arg1100Cys were identified in two unrelated patients with mesiodens. PTPN23 is a regulator of endosomal trafficking functioning to move activated membrane receptors, such as EGFR, from the endosomal sorting complex towards the ESCRT-III complex for multivesicular body biogenesis, lysosomal degradation, and subsequent downregulation of receptor signaling. Immunohistochemical study and RNAscope on developing mouse embryos showed broad expression of PTPN23 in oral tissues, while immunofluorescence showed that EGFR was specifically concentrated in the midline epithelium. Importantly, PTPN23 mutant protein was shown to have reduced phosphatase activity. In conclusion, mesiodens were associated with genetic variants in PTPN23, suggesting that mesiodens may form due to defects in endosomal trafficking, leading to disrupted midline signaling.
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Affiliation(s)
- Ploy Adisornkanj
- Center of Excellence in Medical Genetics Research, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
- Division of Pediatric Dentistry, Department of Orthodontics and Pediatric Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Rajit Chanprasit
- Dental Department, Wiang Kaen Hospital, Wiang Kaen, Chiang Rai 57310, Thailand
| | - Steven Eliason
- Department of Anatomy and Cell Biology and the Craniofacial Anomalies Research Center, The University of Iowa, Iowa City, IA 52242, USA
| | - Juan M. Fons
- Centre for Craniofacial and Regenerative Biology, King’s College London, Floor 27 Guy’ Hospital, London Bridge, London SE1 9RT, UK
| | - Worrachet Intachai
- Center of Excellence in Medical Genetics Research, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Sissades Tongsima
- National Biobank of Thailand, National Science and Technology Development Agency, Thailand Science Park, Pathum Thani 12120, Thailand
| | - Bjorn Olsen
- Department of Developmental Biology, Harvard School of Dental Medicine, Harvard University, Boston, MA 02115, USA
| | - Stefan T. Arold
- Computational Bioscience Research Center, Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Center for Structural Biology, National Institute of Health and Medical Research, National Centre for Scientific Research, University of Montpellier, 34090 Montpellier, France
| | - Chumpol Ngamphiw
- National Biobank of Thailand, National Science and Technology Development Agency, Thailand Science Park, Pathum Thani 12120, Thailand
| | - Brad A. Amendt
- Department of Anatomy and Cell Biology and the Craniofacial Anomalies Research Center, The University of Iowa, Iowa City, IA 52242, USA
- Iowa Institute of Oral Health Research, University of Iowa, Iowa City, IA 52242, USA
| | - Abigail S. Tucker
- Centre for Craniofacial and Regenerative Biology, King’s College London, Floor 27 Guy’ Hospital, London Bridge, London SE1 9RT, UK
| | - Piranit Kantaputra
- Center of Excellence in Medical Genetics Research, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
- Division of Pediatric Dentistry, Department of Orthodontics and Pediatric Dentistry, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
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42
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Chen YL, Hsieh CC, Chu PM, Chen JY, Huang YC, Chen CY. Roles of protein tyrosine phosphatases in hepatocellular carcinoma progression (Review). Oncol Rep 2023; 49:48. [PMID: 36660927 PMCID: PMC9887465 DOI: 10.3892/or.2023.8485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/15/2022] [Indexed: 01/20/2023] Open
Abstract
Hepatocellular carcinoma (HCC) represents almost 80% of all liver cancers, is the sixth most common cancer and is the second‑highest cause of cancer‑related deaths worldwide. Protein tyrosine phosphatases (PTPs), which are encoded by the largest family of phosphatase genes, play critical roles in cellular responses and are implicated in various signaling pathways. Moreover, PTPs are dysregulated and involved in various cellular processes in numerous cancers, including HCC. Kinases and phosphatases are coordinators that modulate cell activities and regulate signaling responses. There are multiple interacting signaling networks, and coordination of these signaling networks in response to a stimulus determines the physiological outcome. Numerous issues, such as drug resistance and inflammatory reactions in the tumor microenvironment, are implicated in cancer progression, and the role of PTPs in these processes has not been well elucidated. Therefore, the present review focused on discussing the relationship of PTPs with inflammatory cytokines and chemotherapy/targeted drug resistance, providing detailed information on how PTPs can modulate inflammatory reactions and drug resistance to influence progression in HCC.
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Affiliation(s)
- Yi-Li Chen
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, R.O.C
| | - Ching-Chuan Hsieh
- Division of General Surgery, Chang Gung Memorial Hospital, Chiayi 613, Taiwan, R.O.C
| | - Pei-Ming Chu
- Department of Anatomy, School of Medicine, Chung Shan Medical University, Taichung 40201, Taiwan, R.O.C
| | - Jing-Yi Chen
- Department of Medical Laboratory Science, College of Medicine, I‑Shou University, Kaohsiung 82445, Taiwan, R.O.C
| | - Yu-Chun Huang
- Aging and Diseases Prevention Research Center, Fooyin University, Kaohsiung 83102, Taiwan, R.O.C
| | - Cheng-Yi Chen
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan, R.O.C
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43
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Seong CS, Huang C, Boese AC, Hou Y, Koo J, Mouw JK, Rupji M, Joseph G, Johnston HR, Claussen H, Switchenko JM, Behera M, Churchman M, Kolesar JM, Arnold SM, Kerrigan K, Akerley W, Colman H, Johns MA, Arciero C, Zhou W, Marcus AI, Ramalingam SS, Fu H, Gilbert-Ross M. Loss of the endocytic tumor suppressor HD-PTP phenocopies LKB1 and promotes RAS-driven oncogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525772. [PMID: 36747658 PMCID: PMC9900931 DOI: 10.1101/2023.01.26.525772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Oncogenic RAS mutations drive aggressive cancers that are difficult to treat in the clinic, and while direct inhibition of the most common KRAS variant in lung adenocarcinoma (G12C) is undergoing clinical evaluation, a wide spectrum of oncogenic RAS variants together make up a large percentage of untargetable lung and GI cancers. Here we report that loss-of-function alterations (mutations and deep deletions) in the gene that encodes HD-PTP (PTPN23) occur in up to 14% of lung cancers in the ORIEN Avatar lung cancer cohort, associate with adenosquamous histology, and occur alongside an altered spectrum of KRAS alleles. Furthermore, we show that in publicly available early-stage NSCLC studies loss of HD-PTP is mutually exclusive with loss of LKB1, which suggests they restrict a common oncogenic pathway in early lung tumorigenesis. In support of this, knockdown of HD-PTP in RAS-transformed lung cancer cells is sufficient to promote FAK-dependent invasion. Lastly, knockdown of the Drosophila homolog of HD-PTP (dHD-PTP/Myopic) synergizes to promote RAS-dependent neoplastic progression. Our findings highlight a novel tumor suppressor that can restrict RAS-driven lung cancer oncogenesis and identify a targetable pathway for personalized therapeutic approaches for adenosquamous lung cancer.
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Affiliation(s)
- Chang-Soo Seong
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA USA
| | - Chunzi Huang
- Cancer Animal Models Shared Resource, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Austin C. Boese
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA USA
- Cancer Biology Graduate Program, Laney Graduate School, Emory University, Atlanta, GA, USA
| | - Yuning Hou
- Cancer Animal Models Shared Resource, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Junghui Koo
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA USA
| | - Janna K. Mouw
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA USA
| | - Manali Rupji
- Biostatistics Shared Resource, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Greg Joseph
- Data and Technology Applications Shared Resource, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | | | - Henry Claussen
- Emory Integrated Computational Core, Emory University, Atlanta, GA
| | - Jeffrey M. Switchenko
- Biostatistics Shared Resource, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Madhusmita Behera
- Data and Technology Applications Shared Resource, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | | | - Jill M. Kolesar
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | | | - Katie Kerrigan
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Wallace Akerley
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Howard Colman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | | | - Cletus Arciero
- Department of Surgery, Emory University School of Medicine, Atlanta, GA USA
| | - Wei Zhou
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA USA
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Adam I. Marcus
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA USA
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Suresh S. Ramalingam
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA USA
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Haian Fu
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA USA
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA, USA
| | - Melissa Gilbert-Ross
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, GA USA
- Winship Cancer Institute of Emory University, Atlanta, GA, USA
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44
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Hendriks WJAJ, van Cruchten RTP, Pulido R. Hereditable variants of classical protein tyrosine phosphatase genes: Will they prove innocent or guilty? Front Cell Dev Biol 2023; 10:1051311. [PMID: 36755664 PMCID: PMC9900141 DOI: 10.3389/fcell.2022.1051311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life-if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest 'guilt by association' for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.
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Affiliation(s)
- Wiljan J. A. J. Hendriks
- Department of Cell Biology, Radboud University Medical Centre, Nijmegen, The Netherlands,*Correspondence: Wiljan J. A. J. Hendriks,
| | | | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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45
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Yarnall MT, Kim SH, Korntner S, Bishop AC. Destabilization of the SHP2 and SHP1 protein tyrosine phosphatase domains by a non-conserved "backdoor" cysteine. Biochem Biophys Rep 2022; 32:101370. [PMID: 36275931 PMCID: PMC9578986 DOI: 10.1016/j.bbrep.2022.101370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) are critical regulators of cellular signal transduction that catalyze the hydrolytic dephosphorylation of phosphotyrosine in substrate proteins. Among several conserved features in classical PTP domains are an active-site cysteine residue that is necessary for catalysis and a "backdoor" cysteine residue that can serve to protect the active-site cysteine from irreversible oxidation. Curiously, two biologically important phosphatases, Src homology domain-containing PTPs 2 and 1 (SHP2 and SHP1), each contain an additional backdoor cysteine residue at a position of the PTP domain that is occupied by proline in almost all other classical PTPs (position 333 in human SHP2 numbering). Here we show that the presence of cysteine 333 significantly destabilizes the fold of the PTP domains in the SHPs. We find that replacement of cysteine 333 with proline confers increased thermal stability on the SHP2 and SHP1 PTP domains, as measured by temperature-dependent activity assays and differential scanning fluorimetry. Conversely, we show that substantial destabilization of the PTP-domain fold is conferred by introduction of a non-natural cysteine residue in a non-SHP PTP that contains proline at the 333 position. It has previously been suggested that the extra backdoor cysteine of the SHP PTPs may work in tandem with the conserved backdoor cysteine to provide protection from irreversible oxidative enzyme inactivation. If so, our current results suggest that, during the course of mammalian evolution, the SHP proteins have developed extra protection from oxidation at the cost of the thermal instability that is conferred by the presence of their PTP domains' second backdoor cysteine.
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Affiliation(s)
| | - Sean H. Kim
- Amherst College, Department of Chemistry, Amherst, MA, 01002, USA
| | - Samuel Korntner
- Amherst College, Department of Chemistry, Amherst, MA, 01002, USA
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46
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Schwarz M, Rizzo S, Paz WE, Kresinsky A, Thévenin D, Müller JP. Disrupting PTPRJ transmembrane-mediated oligomerization counteracts oncogenic receptor tyrosine kinase FLT3 ITD. Front Oncol 2022; 12:1017947. [PMID: 36452504 PMCID: PMC9701752 DOI: 10.3389/fonc.2022.1017947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/25/2022] [Indexed: 11/15/2022] Open
Abstract
The receptor protein tyrosine phosphatase (RPTP) PTPRJ (also known as DEP-1) has been identified as a negative regulator of the receptor tyrosine kinase FLT3 signalling in vitro. The inactivation of the PTPRJ gene in mice expressing the constitutively active, oncogenic receptor tyrosine kinase FLT3 ITD aggravated known features of leukaemogenesis, revealing PTPRJ's antagonistic role. FLT3 ITD mutations resulting in constitutively kinase activity and cell transformation frequently occur in patients with acute myeloid leukaemia (AML). Thus, in situ activation of PTPRJ could be used to abrogate oncogenic FLT3 signalling. The activity of PTPRJ is suppressed by homodimerization, which is mediated by transmembrane domain (TMD) interactions. Specific Glycine-to-Leucine mutations in the TMD disrupt oligomerization and inhibit the Epidermal Growth Factor Receptor (EGFR) and EGFR-driven cancer cell phenotypes. To study the effects of PTPRJ TMD mutant proteins on FLT3 ITD activity in cell lines, endogenous PTPRJ was inactivated and replaced by stable expression of PTPRJ TMD mutants. Autophosphorylation of wild-type and ITD-mutated FLT3 was diminished in AML cell lines expressing the PTPRJ TMD mutants compared to wild-type-expressing cells. This was accompanied by reduced FLT3-mediated global protein tyrosine phosphorylation and downstream signalling. Further, PTPRJ TMD mutant proteins impaired the proliferation and in vitro transformation of leukemic cells. Although PTPRJ's TMD mutant proteins showed impaired self-association, the specific phosphatase activity of immunoprecipitated proteins remained unchanged. In conclusion, this study demonstrates that the destabilization of PTPRJ TMD-mediated self-association increases the activity of PTPRJ in situ and impairs FLT3 activity and FLT3-driven cell phenotypes of AML cells. Thus, disrupting the oligomerization of PTPRJ in situ could prove a valuable therapeutic strategy to restrict oncogenic FLT3 activity in leukemic cells.
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Affiliation(s)
- Marie Schwarz
- Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Jena, Germany
| | - Sophie Rizzo
- Department of Chemistry, Lehigh University, Bethlehem, PA, United States
| | | | - Anne Kresinsky
- Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Jena, Germany,Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Damien Thévenin
- Department of Chemistry, Lehigh University, Bethlehem, PA, United States
| | - Jörg P. Müller
- Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Jena, Germany,*Correspondence: Jörg P. Müller,
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47
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In Silico Discovery of Anticancer Peptides from Sanghuang. Int J Mol Sci 2022; 23:ijms232213682. [PMID: 36430160 PMCID: PMC9693127 DOI: 10.3390/ijms232213682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/24/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022] Open
Abstract
Anticancer peptide (ACP) is a short peptide with less than 50 amino acids that has been discovered in a variety of foods. It has been demonstrated that traditional Chinese medicine or food can help treat cancer in some cases, which suggests that ACP may be one of the therapeutic ingredients. Studies on the anti-cancer properties of Sanghuangporus sanghuang have concentrated on polysaccharides, flavonoids, triterpenoids, etc. The function of peptides has not received much attention. The purpose of this study is to use computer mining techniques to search for potential anticancer peptides from 62 proteins of Sanghuang. We used mACPpred to perform sequence scans after theoretical trypsin hydrolysis and discovered nine fragments with an anticancer probability of over 0.60. The study used AlphaFold 2 to perform structural modeling of the first three ACPs discovered, which had blast results from the Cancer PPD database. Using reverse docking technology, we found the target proteins and interacting residues of two ACPs with an unknown mechanism. Reverse docking results predicted the binding modes of the ACPs and their target protein. In addition, we determined the active part of ACPs by quantum chemical calculation. Our study provides a framework for the future discovery of functional peptides from foods. The ACPs discovered have the potential to be used as drugs in oncology clinical treatment after further research.
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48
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Ryan A, Janosko CP, Courtney TM, Deiters A. Engineering SHP2 Phosphatase for Optical Control. Biochemistry 2022; 61:2687-2697. [DOI: 10.1021/acs.biochem.2c00387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Amy Ryan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Chasity P. Janosko
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Taylor M. Courtney
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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Structural insights into the pSer/pThr dependent regulation of the SHP2 tyrosine phosphatase in insulin and CD28 signaling. Nat Commun 2022; 13:5439. [PMID: 36114179 PMCID: PMC9481563 DOI: 10.1038/s41467-022-32918-5] [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: 10/04/2021] [Accepted: 08/23/2022] [Indexed: 11/09/2022] Open
Abstract
Serine/threonine phosphorylation of insulin receptor substrate (IRS) proteins is well known to modulate insulin signaling. However, the molecular details of this process have mostly been elusive. While exploring the role of phosphoserines, we have detected a direct link between Tyr-flanking Ser/Thr phosphorylation sites and regulation of specific phosphotyrosine phosphatases. Here we present a concise structural study on how the activity of SHP2 phosphatase is controlled by an asymmetric, dual phosphorylation of its substrates. The structure of SHP2 has been determined with three different substrate peptides, unveiling the versatile and highly dynamic nature of substrate recruitment. What is more, the relatively stable pre-catalytic state of SHP2 could potentially be useful for inhibitor design. Our findings not only show an unusual dependence of SHP2 catalytic activity on Ser/Thr phosphorylation sites in IRS1 and CD28, but also suggest a negative regulatory mechanism that may also apply to other tyrosine kinase pathways as well. SHP2 is an important human tyrosine phosphatase with key roles in cancer, immune responses and insulin signaling. Here, the authors explore its substrate recognition mechanism in molecular detail and uncover a complex regulatory mechanism for this enzyme that marks specific target sites for dephosphorylation.
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50
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Computational Methods in Cooperation with Experimental Approaches to Design Protein Tyrosine Phosphatase 1B Inhibitors in Type 2 Diabetes Drug Design: A Review of the Achievements of This Century. Pharmaceuticals (Basel) 2022; 15:ph15070866. [PMID: 35890163 PMCID: PMC9322956 DOI: 10.3390/ph15070866] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 02/04/2023] Open
Abstract
Protein tyrosine phosphatase 1B (PTP1B) dephosphorylates phosphotyrosine residues and is an important regulator of several signaling pathways, such as insulin, leptin, and the ErbB signaling network, among others. Therefore, this enzyme is considered an attractive target to design new drugs against type 2 diabetes, obesity, and cancer. To date, a wide variety of PTP1B inhibitors that have been developed by experimental and computational approaches. In this review, we summarize the achievements with respect to PTP1B inhibitors discovered by applying computer-assisted drug design methodologies (virtual screening, molecular docking, pharmacophore modeling, and quantitative structure–activity relationships (QSAR)) as the principal strategy, in cooperation with experimental approaches, covering articles published from the beginning of the century until the time this review was submitted, with a focus on studies conducted with the aim of discovering new drugs against type 2 diabetes. This review encourages the use of computational techniques and includes helpful information that increases the knowledge generated to date about PTP1B inhibition, with a positive impact on the route toward obtaining a new drug against type 2 diabetes with PTP1B as a molecular target.
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