1
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Zhang L, Ma W, Chen Y, Chen Z, Wang F, Xu Y. Design, synthesis, and biological evaluation of Pyrido[1,2-a]pyrimidin-4-one derivatives as novel allosteric SHP2 inhibitors. Bioorg Chem 2024; 151:107661. [PMID: 39067422 DOI: 10.1016/j.bioorg.2024.107661] [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: 05/27/2024] [Revised: 07/15/2024] [Accepted: 07/16/2024] [Indexed: 07/30/2024]
Abstract
SHP2 (Src homology-2-containing protein tyrosine phosphatase 2) plays an important role in cell proliferation, survival, migration by affecting RAS-ERK, PI3K-AKT, JAK-STAT signaling pathways and so on. Overexpression or gene mutation of SHP2 is closely linked with a variety of cancers, making it a potential therapeutic target for cancer disease. In this paper, 30 target compounds bearing pyrido[1,2-a]pyrimidin-4-one core were synthesized via two-round design strategy by means of scaffold hopping protocol. It was evaluated the in vitro enzymatic inhibition and cell antiproliferation assay of these targets. 13a, designed in the first round, presented relatively good inhibitory activity, but its molecular rigidity might limit further improvement by hindering the formation of the desired "bidentate ligand", as revealed by molecular docking studies. In our second-round design, S atom as a linker was inserted into the core and the 7-aryl group to enhance the flexibility of the structure. The screening result revealed that 14i could exhibit high enzymatic activity against full-length SHP2 (IC50 = 0.104 μM), while showing low inhibitory effect on SHP2-PTP (IC50 > 50 μM). 14i also demonstrated high antiproliferative activity against the Kyse-520 cells (IC50 = 1.06 μM) with low toxicity against the human brain microvascular endothelial cells HBMEC (IC50 = 30.75 μM). 14i also displayed stronger inhibitory activities on NCI-H358 and MIA-PaCa2 cells compared to that of SHP099. Mechanistic studies revealed that 14i could induce cell apoptosis, arrest the cell cycle at the G0/G1 phase and downregulate the phosphorylation levels of Akt and Erk1/2 in Kyse-520 cells. Molecular docking and molecular dynamics studies displayed more detailed information on the binding mode and binding mechanism of 14i and SHP2. These data suggest that 14i has the potential to be a promising lead compound for our further investigation of SHP2 inhibitors.
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Affiliation(s)
- Le Zhang
- School of Pharmaceutical Engineering, and Key Laboratory of Structure-Based Drug Design & Discovery (Ministry of Education), Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Wenchao Ma
- School of Pharmaceutical Engineering, and Key Laboratory of Structure-Based Drug Design & Discovery (Ministry of Education), Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Yu Chen
- Faculty of Functional Food and Wine, Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Zhijia Chen
- School of Pharmaceutical Engineering, and Key Laboratory of Structure-Based Drug Design & Discovery (Ministry of Education), Shenyang Pharmaceutical University, Shenyang 110016, PR China
| | - Fang Wang
- Faculty of Functional Food and Wine, Shenyang Pharmaceutical University, Shenyang 110016, PR China.
| | - Youjun Xu
- School of Pharmaceutical Engineering, and Key Laboratory of Structure-Based Drug Design & Discovery (Ministry of Education), Shenyang Pharmaceutical University, Shenyang 110016, PR China.
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2
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Guo Z, Duan Y, Sun K, Zheng T, Liu J, Xu S, Xu J. Advances in SHP2 tunnel allosteric inhibitors and bifunctional molecules. Eur J Med Chem 2024; 275:116579. [PMID: 38889611 DOI: 10.1016/j.ejmech.2024.116579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024]
Abstract
SHP2 is a non-receptor tyrosine phosphatase encoded by PTPN11, which performs the functions of regulating cell proliferation, differentiation, apoptosis, and survival through removing tyrosine phosphorylation and modulating various signaling pathways. The overexpression of SHP2 or its mutations is related to developmental diseases and several cancers. Numerous allosteric inhibitors with striking inhibitory potency against SHP2 allosteric pockets have recently been identified, and several SHP2 tunnel allosteric inhibitors have been applied in clinical trials to treat cancers. However, based on clinical results, the efficacy of single-agent treatments has been proven to be suboptimal. Most clinical trials involving SHP2 inhibitors have adopted drug combination strategies. This review briefly discusses the research progress on SHP2 allosteric inhibitors and pathway-dependent drug combination strategies for SHP2 in cancer therapy. In addition, we summarize the current bifunctional molecules of SHP2 and elaborate on the design and structural optimization strategies of these bifunctional molecules in detail, offering further direction for the research on novel SHP2 inhibitors.
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Affiliation(s)
- Zhichao Guo
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China
| | - Yiping Duan
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China
| | - Kai Sun
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China
| | - Tiandong Zheng
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China
| | - Jie Liu
- Department of Organic Chemistry, School of Science, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China.
| | - Shengtao Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China.
| | - Jinyi Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing, Jiangsu, 211198, China.
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3
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van Vlimmeren AE, Voleti R, Chartier CA, Jiang Z, Karandur D, Humphries PA, Lo WL, Shah NH. The pathogenic T42A mutation in SHP2 rewires the interaction specificity of its N-terminal regulatory domain. Proc Natl Acad Sci U S A 2024; 121:e2407159121. [PMID: 39012820 PMCID: PMC11287265 DOI: 10.1073/pnas.2407159121] [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: 04/09/2024] [Accepted: 06/19/2024] [Indexed: 07/18/2024] Open
Abstract
Mutations in the tyrosine phosphatase Src homology-2 domain-containing protein tyrosine phosphatase-2 (SHP2) are associated with a variety of human diseases. Most mutations in SHP2 increase its basal catalytic activity by disrupting autoinhibitory interactions between its phosphatase domain and N-terminal SH2 (phosphotyrosine recognition) domain. By contrast, some disease-associated mutations located in the ligand-binding pockets of the N- or C-terminal SH2 domains do not increase basal activity and likely exert their pathogenicity through alternative mechanisms. We lack a molecular understanding of how these SH2 mutations impact SHP2 structure, activity, and signaling. Here, we characterize five SHP2 SH2 domain ligand-binding pocket mutants through a combination of high-throughput biochemical screens, biophysical and biochemical measurements, and molecular dynamics simulations. We show that while some of these mutations alter binding affinity to phosphorylation sites, the T42A mutation in the N-SH2 domain is unique in that it also substantially alters ligand-binding specificity, despite being 8 to 10 Å from the specificity-determining region of the SH2 domain. This mutation exerts its effect on sequence specificity by remodeling the phosphotyrosine-binding pocket, altering the mode of engagement of both the phosphotyrosine and surrounding residues on the ligand. The functional consequence of this altered specificity is that the T42A mutant has biased sensitivity toward a subset of activating ligands and enhances downstream signaling. Our study highlights an example of a nuanced mechanism of action for a disease-associated mutation, characterized by a change in protein-protein interaction specificity that alters enzyme activation.
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Affiliation(s)
- Anne E. van Vlimmeren
- Department of Chemistry, Columbia University, New York, NY10027
- Department of Biological Sciences, Columbia University, New York, NY10027
| | - Rashmi Voleti
- Department of Chemistry, Columbia University, New York, NY10027
| | | | - Ziyuan Jiang
- Department of Chemistry, Columbia University, New York, NY10027
| | - Deepti Karandur
- Department of Biochemistry, Vanderbilt University, Nashville, TN37232
| | - Preston A. Humphries
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT84112
| | - Wan-Lin Lo
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT84112
| | - Neel H. Shah
- Department of Chemistry, Columbia University, New York, NY10027
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4
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van Vlimmeren AE, Voleti R, Chartier CA, Jiang Z, Karandur D, Humphries PA, Lo WL, Shah NH. The pathogenic T42A mutation in SHP2 rewires the interaction specificity of its N-terminal regulatory domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.10.548257. [PMID: 37502916 PMCID: PMC10369915 DOI: 10.1101/2023.07.10.548257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Mutations in the tyrosine phosphatase SHP2 are associated with a variety of human diseases. Most mutations in SHP2 increase its basal catalytic activity by disrupting auto-inhibitory interactions between its phosphatase domain and N-terminal SH2 (phosphotyrosine recognition) domain. By contrast, some disease-associated mutations located in the ligand-binding pockets of the N- or C-terminal SH2 domains do not increase basal activity and likely exert their pathogenicity through alternative mechanisms. We lack a molecular understanding of how these SH2 mutations impact SHP2 structure, activity, and signaling. Here, we characterize five SHP2 SH2 domain ligand-binding pocket mutants through a combination of high-throughput biochemical screens, biophysical and biochemical measurements, and molecular dynamics simulations. We show that, while some of these mutations alter binding affinity to phosphorylation sites, the T42A mutation in the N-SH2 domain is unique in that it also substantially alters ligand-binding specificity, despite being 8-10 Å from the specificity-determining region of the SH2 domain. This mutation exerts its effect on sequence specificity by remodeling the phosphotyrosine binding pocket, altering the mode of engagement of both the phosphotyrosine and surrounding residues on the ligand. The functional consequence of this altered specificity is that the T42A mutant has biased sensitivity toward a subset of activating ligands and enhances downstream signaling. Our study highlights an example of a nuanced mechanism of action for a disease-associated mutation, characterized by a change in protein-protein interaction specificity that alters enzyme activation.
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Affiliation(s)
- Anne E. van Vlimmeren
- Department of Chemistry, Columbia University, New York, NY 10027
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Rashmi Voleti
- Department of Chemistry, Columbia University, New York, NY 10027
| | | | - Ziyuan Jiang
- Department of Chemistry, Columbia University, New York, NY 10027
| | - Deepti Karandur
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232
| | - Preston A. Humphries
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Wan-Lin Lo
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Neel H. Shah
- Department of Chemistry, Columbia University, New York, NY 10027
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5
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Guo M, Li Z, Gu M, Gu J, You Q, Wang L. Targeting phosphatases: From molecule design to clinical trials. Eur J Med Chem 2024; 264:116031. [PMID: 38101039 DOI: 10.1016/j.ejmech.2023.116031] [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: 10/23/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
Phosphatase is a kind of enzyme that can dephosphorylate target proteins, which can be divided into serine/threonine phosphatase and tyrosine phosphatase according to its mode of action. Current evidence showed multiple phosphatases were highly correlated with diseases including various cancers, demonstrating them as potential targets. However, currently, targeting phosphatases with small molecules faces many challenges, resulting in no drug approved. In this case, phosphatases are even regarded as "undruggable" targets for a long time. Recently, a variety of strategies have been adopted in the design of small molecule inhibitors targeting phosphatases, leading many of them to enter into the clinical trials. In this review, we classified these inhibitors into 4 types, including (1) molecular glues, (2) small molecules targeting catalytic sites, (3) allosteric inhibition, and (4) bifunctional molecules (proteolysis targeting chimeras, PROTACs). These molecules with diverse strategies prove the feasibility of phosphatases as drug targets. In addition, the combination therapy of phosphatase inhibitors with other drugs has also entered clinical trials, which suggests a broad prospect. Thus, targeting phosphatases with small molecules by different strategies is emerging as a promising way in the modulation of pathogenetic phosphorylation.
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Affiliation(s)
- Mochen Guo
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Zekun Li
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Mingxiao Gu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Junrui Gu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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6
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Anselmi M, Hub JS. Atomistic ensemble of active SHP2 phosphatase. Commun Biol 2023; 6:1289. [PMID: 38129686 PMCID: PMC10739809 DOI: 10.1038/s42003-023-05682-5] [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: 07/05/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
SHP2 phosphatase plays an important role in regulating several intracellular signaling pathways. Pathogenic mutations of SHP2 cause developmental disorders and are linked to hematological malignancies and cancer. SHP2 comprises two tandemly-arranged SH2 domains, a catalytic PTP domain, and a disordered C-terminal tail. Under physiological, non-stimulating conditions, the catalytic site of PTP is occluded by the N-SH2 domain, so that the basal activity of SHP2 is low. Whereas the autoinhibited structure of SHP2 has been known for two decades, its active, open structure still represents a conundrum. Since the oncogenic mutant SHP2E76K almost completely populates the active, open state, this mutant has been extensively studied as a model for activated SHP2. By molecular dynamics simulations and accurate explicit-solvent SAXS curve predictions, we present the heterogeneous atomistic ensemble of constitutively active SHP2E76K in solution, encompassing a set of conformational arrangements and radii of gyration in agreement with experimental SAXS data.
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Affiliation(s)
- Massimiliano Anselmi
- Theoretical Physics and Center for Biophysics, Saarland University, 66123, Saarbrücken, Germany.
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, 66123, Saarbrücken, Germany.
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7
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Chan CH, Chu MF, Lam UP, Mok TM, Tam WC, Tomlinson B, Coelho R, Évora M. Case report: Distinctive cardiac features and phenotypic characteristics of Noonan syndrome with multiple lentigines among three generations in one family. Front Cardiovasc Med 2023; 10:1225667. [PMID: 37692036 PMCID: PMC10484218 DOI: 10.3389/fcvm.2023.1225667] [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: 05/19/2023] [Accepted: 08/08/2023] [Indexed: 09/12/2023] Open
Abstract
Noonan syndrome with multiple lentigines (NSML, formerly known as LEOPARD syndrome) is a variant of Noonan syndrome which is an autosomal dominant disorder. Most cases of NSML are secondary to mutations of the protein-tyrosine phosphatase nonreceptor type 11 (PTPN11). Hypertrophic cardiomyopathy (HCM) remains the most frequent and serious cardiac abnormality in this inherited syndrome, and it may lead to sudden cardiac death related to HCM-associated outflow obstruction and fatal arrhythmia. Beyond cardiac involvement, NSML may present with multiple lentigines, ocular hypertelorism, genital anomalies, short stature and deafness. Herein, we report three patients with NSML among three generations in one family, all presenting with multiple lentigines, HCM and other distinctive clinical and molecular features, including facial dysmorphism, deafness, family history of sudden death and PTPN11 mutations. This case series highlights the importance of early echocardiography examinations for patients with NSML. Careful family screening and genetic counselling are also necessary, especially in patients with diffuse lentigines or a history of sudden death among family members. We also discuss the distinctive cardiac features and phenotypic characteristics at different stages of NSML, including childhood, adulthood and elderhood.
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Affiliation(s)
- Chon-Hou Chan
- Department of Dermatology, Centro Hospitalar Conde São Januário, Macao, Macao SAR, China
| | - Man-Fong Chu
- Department of Cardiology, Centro Hospitalar Conde São Januário, Macao, Macao SAR, China
| | - U-Po Lam
- Department of Cardiology, Centro Hospitalar Conde São Januário, Macao, Macao SAR, China
| | - Toi-Meng Mok
- Department of Cardiology, Centro Hospitalar Conde São Januário, Macao, Macao SAR, China
| | - Weng-Chio Tam
- Department of Cardiology, Centro Hospitalar Conde São Januário, Macao, Macao SAR, China
| | - Brian Tomlinson
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Ricardo Coelho
- Department of Dermatology, Centro Hospitalar Conde São Januário, Macao, Macao SAR, China
| | - Màrio Évora
- Department of Cardiology, Centro Hospitalar Conde São Januário, Macao, Macao SAR, China
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8
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Rivero‐García P, Campuzano‐Estrada IDC, Hernandez‐Felix JH. Hypertrophic cardiomyopathy in an adult patient with Noonan syndrome with multiple lentigines. Clin Case Rep 2023; 11:e7607. [PMID: 37361648 PMCID: PMC10290193 DOI: 10.1002/ccr3.7607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/27/2023] [Accepted: 06/08/2023] [Indexed: 06/28/2023] Open
Abstract
Noonan syndrome with multiple lentigines (NSML) is a rare RASopathy caused by pathogenic variants (PV) predominantly in PTPN11 gene. We report a 54-year-old male with apical hypertrophic cardiomyopathy, who was diagnosed with NSML due to his short stature, multiple lentigines, winged neck, pectus excavatum, and a heterozygous PV in PTPN11 c.836A > ¡G.
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Affiliation(s)
- Pamela Rivero‐García
- División de Estudios de Posgrado de la Facultad de MedicinaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
- Departamento de GenéticaInstituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”Mexico CityMexico
| | - Isabel del Carmen Campuzano‐Estrada
- División de Estudios de Posgrado de la Facultad de MedicinaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
- Departamento de GenéticaInstituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”Mexico CityMexico
| | - Jorge Humberto Hernandez‐Felix
- División de Estudios de Posgrado de la Facultad de MedicinaUniversidad Nacional Autónoma de MéxicoMexico CityMexico
- Departamento de Medicina InternaInstituto Nacional de Ciencias Médicas y Nutrición “Salvador Zubirán”Mexico CityMexico
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9
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Welsh CL, Allen S, Madan LK. Setting sail: Maneuvering SHP2 activity and its effects in cancer. Adv Cancer Res 2023; 160:17-60. [PMID: 37704288 PMCID: PMC10500121 DOI: 10.1016/bs.acr.2023.03.003] [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: 09/15/2023]
Abstract
Since the discovery of tyrosine phosphorylation being a critical modulator of cancer signaling, proteins regulating phosphotyrosine levels in cells have fast become targets of therapeutic intervention. The nonreceptor protein tyrosine phosphatase (PTP) coded by the PTPN11 gene "SHP2" integrates phosphotyrosine signaling from growth factor receptors into the RAS/RAF/ERK pathway and is centrally positioned in processes regulating cell development and oncogenic transformation. Dysregulation of SHP2 expression or activity is linked to tumorigenesis and developmental defects. Even as a compelling anti-cancer target, SHP2 was considered "undruggable" for a long time owing to its conserved catalytic PTP domain that evaded drug development. Recently, SHP2 has risen from the "undruggable curse" with the discovery of small molecules that manipulate its intrinsic allostery for effective inhibition. SHP2's unique domain arrangement and conformation(s) allow for a truly novel paradigm of inhibitor development relying on skillful targeting of noncatalytic sites on proteins. In this review we summarize the biological functions, signaling properties, structural attributes, allostery and inhibitors of SHP2.
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Affiliation(s)
- Colin L Welsh
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Sarah Allen
- Department of Pediatrics, Darby Children's Research Institute, Medical University of South Carolina, Charleston, SC, United States
| | - Lalima K Madan
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, College of Medicine, Medical University of South Carolina, Charleston, SC, United States; Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States.
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10
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Design and synthesis of improved active-site SHP2 inhibitors with anti-breast cancer cell effects. Eur J Med Chem 2023; 247:115017. [PMID: 36584630 DOI: 10.1016/j.ejmech.2022.115017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
The Src homology containing phosphotyrosyl phosphatase 2 (SHP2) is a bona fide oncogene particularly in cancers driven by overexpression of receptor tyrosine kinases (RTKs). As such, there is a growing interest to target SHP2 in cancer. Based on these premises, several active site (type I) and allosteric site (type II) inhibitors have been developed, but no SHP2 targeting therapies have reached the clinic yet. In an effort to fill these gaps, we embarked on producing optimized versions of our parent active-site SHP2 inhibitor CNBDA. The objectives were to produce derivatives with increased inhibitory potential and improved selectivity. Accordingly, we designed derivatives around the CNBDA scaffold and predicted their binding property by in silico molecular modeling. Based on comparative differences in free energy of binding to the SHP2 versus the SHP1 active sites, ten were selected, chemically synthesized, and evaluated by NMR and mass spectroscopy for structural integrity. Among the ten derivatives, BPDA2 was found to be the most potent and highly selective compound, inhibiting the SHP2 enzyme activity with an IC50 of 92 nM when DiFMUP was used as a substrate and with an IC50 of 47 nM when pNPP was used as a substrate. Furthermore, enzyme kinetic analyses showed that BPDA2 is a competitive SHP2 inhibitor. Selectivity comparisons in a PTPase assay using DiFMUP as a substrate demonstrated that BPDA2 is more selective to SHP2 than to SHP1 and PTP1B by more than 369-fold and 442-fold, respectively. Evaluation with a cellular thermal shift assay (CETSA) confirmed that BPDA2 binds to wild-type SHP2 in a cellular context, and stabilizes it in solution. Treatment of cells with DBDA2 downregulates mitogenic and cell survival signaling and RTK expression in a concentration dependent manner. Furthermore, treatment of cells with BPDA2 suppresses anchorage independent growth and cancer stem cell properties of breast cancer cells. Overall, data described in this report show that BPDA2 is a more potent derivative of CNBDA with a highly improved selectivity for SHP2.
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11
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Bobone S, Storti C, Calligari P, Stella L. Fluorescence Anisotropy and Polarization in the Characterization of Biomolecular Association Processes and Their Application to Study SH2 Domain Binding Affinity. Methods Mol Biol 2023; 2705:93-112. [PMID: 37668971 DOI: 10.1007/978-1-0716-3393-9_6] [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: 09/06/2023]
Abstract
Fluorescence anisotropy (or polarization) is a powerful technique to study biomolecular association processes, by following the rotational motions of one of the two partners in the interaction, labeled with a fluorophore. It can be used to determine dissociation constants in solution, down to nM values, and unlabeled ligands can be characterized, too, by using competition experiments. In this chapter, we introduce the basic principles of the technique, compare it with other experimental approaches, and discuss the experimental details with specific examples regarding SH2 domain/phosphopeptide association processes. The experimental protocols to be used in binding experiments and displacement studies are described, as well as the caveats to be considered in performing accurate measurements.
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Affiliation(s)
- Sara Bobone
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Claudia Storti
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Paolo Calligari
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy
| | - Lorenzo Stella
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, Rome, Italy.
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12
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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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13
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Solman M, Woutersen DTJ, den Hertog J. Modeling (not so) rare developmental disorders associated with mutations in the protein-tyrosine phosphatase SHP2. Front Cell Dev Biol 2022; 10:1046415. [PMID: 36407105 PMCID: PMC9672471 DOI: 10.3389/fcell.2022.1046415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
Src homology region 2 (SH2)-containing protein tyrosine phosphatase 2 (SHP2) is a highly conserved protein tyrosine phosphatase (PTP), which is encoded by PTPN11 and is indispensable during embryonic development. Mutations in PTPN11 in human patients cause aberrant signaling of SHP2, resulting in multiple rare hereditary diseases, including Noonan Syndrome (NS), Noonan Syndrome with Multiple Lentigines (NSML), Juvenile Myelomonocytic Leukemia (JMML) and Metachondromatosis (MC). Somatic mutations in PTPN11 have been found to cause cancer. Here, we focus on the role of SHP2 variants in rare diseases and advances in the understanding of its pathogenesis using model systems.
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Affiliation(s)
- Maja Solman
- Hubrecht Institute-KNAW, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Jeroen den Hertog
- Hubrecht Institute-KNAW, University Medical Center Utrecht, Utrecht, Netherlands
- Institute Biology Leiden, Leiden University, Leiden, Netherlands
- *Correspondence: Jeroen den Hertog,
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14
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Fauser J, Huyot V, Matsche J, Szynal BN, Alexeev Y, Kota P, Karginov AV. Dissecting protein tyrosine phosphatase signaling by engineered chemogenetic control of its activity. J Cell Biol 2022; 221:e202111066. [PMID: 35829702 PMCID: PMC9284425 DOI: 10.1083/jcb.202111066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/06/2022] [Accepted: 06/22/2022] [Indexed: 01/16/2023] Open
Abstract
Protein tyrosine phosphatases (PTPases) are critical mediators of dynamic cell signaling. A tool capable of identifying transient signaling events downstream of PTPases is essential to understand phosphatase function on a physiological time scale. We report a broadly applicable protein engineering method for allosteric regulation of PTPases. This method enables dissection of transient events and reconstruction of individual signaling pathways. Implementation of this approach for Shp2 phosphatase revealed parallel MAPK and ROCK II dependent pathways downstream of Shp2, mediating transient cell spreading and migration. Furthermore, we show that the N-SH2 domain of Shp2 regulates MAPK-independent, ROCK II-dependent cell migration. Engineered targeting of Shp2 activity to different protein complexes revealed that Shp2-FAK signaling induces cell spreading whereas Shp2-Gab1 or Shp2-Gab2 mediates cell migration. We identified specific transient morphodynamic processes induced by Shp2 and determined the role of individual signaling pathways downstream of Shp2 in regulating these events. Broad application of this approach is demonstrated by regulating PTP1B and PTP-PEST phosphatases.
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Affiliation(s)
- Jordan Fauser
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL
| | - Vincent Huyot
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL
| | - Jacob Matsche
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL
| | - Barbara N. Szynal
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL
| | | | - Pradeep Kota
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Andrei V. Karginov
- Department of Pharmacology and Regenerative Medicine, University of Illinois at Chicago, Chicago, IL
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15
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Song Y, Yang X, Wang S, Zhao M, Yu B. Crystallographic landscape of SHP2 provides molecular insights for SHP2 targeted drug discovery. Med Res Rev 2022; 42:1781-1821. [DOI: 10.1002/med.21890] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/17/2022] [Accepted: 05/04/2022] [Indexed: 12/31/2022]
Affiliation(s)
- Yihui Song
- School of Pharmaceutical Sciences Zhengzhou University 450001 Henan Zhengzhou China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment Zhengzhou University 450000 Henan Zhengzhou China
| | - Xinyu Yang
- School of Pharmaceutical Sciences Zhengzhou University 450001 Henan Zhengzhou China
| | - Shu Wang
- School of Pharmaceutical Sciences Zhengzhou University 450001 Henan Zhengzhou China
| | - Min Zhao
- School of Pharmaceutical Sciences Zhengzhou University 450001 Henan Zhengzhou China
| | - Bin Yu
- School of Pharmaceutical Sciences Zhengzhou University 450001 Henan Zhengzhou China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment Zhengzhou University 450000 Henan Zhengzhou China
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16
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Rydzanicz M, Glinkowski W, Walczak A, Koppolu A, Kostrzewa G, Gasperowicz P, Pollak A, Stawiński P, Płoski R. Postzygotic mosaicism of a novel PTPN11 mutation in monozygotic twins discordant for metachondromatosis. Am J Med Genet A 2022; 188:1482-1487. [PMID: 35112464 DOI: 10.1002/ajmg.a.62670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 12/16/2021] [Accepted: 01/11/2022] [Indexed: 01/05/2023]
Abstract
Genetic mosaicism caused by postzygotic mutations is of a great interest due to its role in human disease. Monozygotic twins arising from a single zygote are considered as genetically identical, and any differences likely to be caused by postzygotic events. Thus, phenotypically discordant monozygotic twins offer a unique opportunity to study genotype-phenotype correlation. Here, we present a three-generation family starting from a pair of monozygotic twins discordant for metachondromatosis due to postzygotic p.(Gln175His) variant in the PTPN11 gene. Both phenotypically discordant monozygotic twins harbor p.(Gln175His), however significant differences in mosaic ratio is observed not only between twins, but also within different tissue types within one individual. Phenotypic manifestation of p.(Gln175His) in examined family clearly depends on allele variant fraction (VAF). Individuals harboring constitutional mutation (VAF 50%) present typical metachondromatosis. Milder phenotype is observed in twin harboring high-level mosaicism in the tissue of ectodermal origin (VAF 45%), but not in a blood (VAF 5%). Finally, her twin sister harboring low-level mosaicism in blood (VAF 2%) and nonblood (VAF 12%) tissues is phenotypically normal. Our results provide insights into biological role of mosaicism in disease and further support the usefulness of nonblood tissues as an optimal source of DNA for the identification of postzygotic mutations in phenotypically discordant monozygotic twins.
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Affiliation(s)
| | - Wojciech Glinkowski
- Center of Excellence "TeleOrto" for Telediagnostics and Treatment of Disorders and Injuries of the Locomotor System, Department of Medical Informatics and Telemedicine, Medical University of Warsaw, Warsaw, Poland
| | - Anna Walczak
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Koppolu
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Grażyna Kostrzewa
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Gasperowicz
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Agnieszka Pollak
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Piotr Stawiński
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
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17
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Double-edged roles of protein tyrosine phosphatase SHP2 in cancer and its inhibitors in clinical trials. Pharmacol Ther 2021; 230:107966. [PMID: 34403682 DOI: 10.1016/j.pharmthera.2021.107966] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/09/2021] [Accepted: 07/20/2021] [Indexed: 12/13/2022]
Abstract
Phosphorylation is a reversible post-translational modification regulated by phosphorylase and dephosphorylase to mediate important cellular events. Src homology-2-containing protein tyrosine phosphatase 2 (SHP2) encoded by PTPN11 is the first identified oncogenic protein in protein tyrosine phosphatases family. Serving as a convergent node, SHP2 is involved in multiple cascade signaling pathways including Ras-Raf-MEK-ERK, PI3K-AKT, JAK-STAT and PD-1/PD-L1 pathways. Especially, the double-edged roles of SHP2 based on the substrate specificity in various biological contexts dramatically increase the effect complexity in different SHP2-associated diseases. Evidences suggest that by collaborating with other mutations in associated pathways, dysregulation of SHP2 contributes to the pathogenesis of different cancers, making SHP2 a promising therapeutic target for cancer treatment. SHP2 can either act as oncogenic factor or tumor suppressor in different diseases, and both the conserved catalytic dephosphorylation mechanism and the unique allosteric regulation mechanism of SHP2 provide opportunities for the development of SHP2 inhibitors and activators. To date, several small-molecule SHP2 inhibitors have advanced into clinical trials for mono- or combined therapy of cancers. Moreover, SHP2 activators and proteolysis-targeting chimera (PROTAC)-based degraders also display therapeutic promise. In this review, we comprehensively summarize the overall structures, regulation mechanisms, double-edged roles of SHP2 in both physiological and carcinogenic pathways, and SHP2 inhibitors in clinical trials. SHP2 activators and degraders are also briefly discussed. This review aims to provide in-depth understanding of the biological roles of SHP2 and highlight therapeutic potential of targeting SHP2.
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18
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Guo Y, Xu Y, Dong X, Zhang J. Cross the Undruggable Barrier, the Development of SHP2 Inhibitors: From Catalytic Site Inhibitors to Allosteric Inhibitors. ChemistrySelect 2021. [DOI: 10.1002/slct.202100186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yu Guo
- Hangzhou Institute of Innovative Medicine College of Pharmaceutical Sciences Zhejiang University Hangzhou 310058 P.R. China
| | - Yaping Xu
- Hangzhou Institute of Innovative Medicine College of Pharmaceutical Sciences Zhejiang University Hangzhou 310058 P.R. China
| | - Xiaowu Dong
- Hangzhou Institute of Innovative Medicine College of Pharmaceutical Sciences Zhejiang University Hangzhou 310058 P.R. China
| | - Jianjun Zhang
- Department of Pharmacy Institution The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine) Hangzhou 310006 P.R. China
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19
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The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation. Proc Natl Acad Sci U S A 2021; 118:2025107118. [PMID: 33888588 DOI: 10.1073/pnas.2025107118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The Src-homology-2 domain-containing phosphatase SHP2 is a critical regulator of signal transduction, being implicated in cell growth and differentiation. Activating mutations cause developmental disorders and act as oncogenic drivers in hematologic cancers. SHP2 is activated by phosphopeptide binding to the N-SH2 domain, triggering the release of N-SH2 from the catalytic PTP domain. Based on early crystallographic data, it has been widely accepted that opening of the binding cleft of N-SH2 serves as the key "allosteric switch" driving SHP2 activation. To test the putative coupling between binding cleft opening and SHP2 activation as assumed by the allosteric switch model, we critically reviewed structural data of SHP2, and we used extensive molecular dynamics (MD) simulation and free energy calculations of isolated N-SH2 in solution, SHP2 in solution, and SHP2 in a crystal environment. Our results demonstrate that the binding cleft in N-SH2 is constitutively flexible and open in solution and that a closed cleft found in certain structures is a consequence of crystal contacts. The degree of opening of the binding cleft has only a negligible effect on the free energy of SHP2 activation. Instead, SHP2 activation is greatly favored by the opening of the central β-sheet of N-SH2. We conclude that opening of the N-SH2 binding cleft is not the key allosteric switch triggering SHP2 activation.
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20
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Zhang J, Zhang Y, Qu B, Yang H, Hu S, Dong X. If small molecules immunotherapy comes, can the prime be far behind? Eur J Med Chem 2021; 218:113356. [PMID: 33773287 DOI: 10.1016/j.ejmech.2021.113356] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/15/2021] [Accepted: 02/28/2021] [Indexed: 02/07/2023]
Abstract
Anti-cancer immunotherapy, which includes cellular immunotherapy, immune checkpoint inhibitors and cancer vaccines, has transformed the treatment strategies of several malignancies in the past decades. Immune checkpoints blockade (ICB) is the most commonly tested therapy and has the potential to induce a durable immune response in different types of cancers. However, all approved immune checkpoint inhibitors (ICIs) are monoclonal antibodies (mAbs), which are fraught with disadvantages including lack of oral bioavailability, prolonged tissue retention and poor membrane permeability. Therefore, the research focus has shifted to developing small molecule inhibitors to obviate the limitations of mAbs. Given the complexity of the tumor micro-environment (TME), the combination of ICIs with various small molecule agonists/inhibitors are currently being tested in clinical trials to improve treatment outcomes and prevent tumor recurrence. In this review, we have summarized the mechanisms and therapeutic potential of several molecular targets, along with the current status of small molecule inhibitors.
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Affiliation(s)
- Jingyu Zhang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Yu Zhang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Bingxue Qu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China
| | - Haiyan Yang
- Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), PR China; Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, PR China
| | - Shengquan Hu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China.
| | - Xiaowu Dong
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, PR China; Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, 310058, PR China; Cancer Center of Zhejiang University, Hangzhou, 310058, PR China.
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21
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Yi JS, Perla S, Huang Y, Mizuno K, Giordano FJ, Vinks AA, Bennett AM. Low-dose Dasatinib Ameliorates Hypertrophic Cardiomyopathy in Noonan Syndrome with Multiple Lentigines. Cardiovasc Drugs Ther 2021; 36:589-604. [PMID: 33689087 PMCID: PMC9270274 DOI: 10.1007/s10557-021-07169-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/26/2021] [Indexed: 11/24/2022]
Abstract
Purpose Noonan syndrome with multiple lentigines (NSML) is an autosomal dominant disorder presenting with hypertrophic cardiomyopathy (HCM). Up to 85% of NSML cases are caused by mutations in the PTPN11 gene that encodes for the Src homology 2 (SH2) domain-containing protein tyrosine phosphatase 2 (SHP2). We previously showed that low-dose dasatinib protects from the development of cardiac fibrosis in a mouse model of NSML harboring a Ptpn11Y279C mutation. This study is performed to determine the pharmacokinetic (PK) and pharmacodynamic (PD) properties of a low-dose of dasatinib in NSML mice and to determine its effectiveness in ameliorating the development of HCM. Methods Dasatinib was administered intraperitoneally into NSML mice with doses ranging from 0.05 to 0.5 mg/kg. PK parameters of dasatinib in NSML mice were determined. PD parameters were obtained for biochemical analyses from heart tissue. Dasatinib-treated NSML mice (0.1 mg/kg) were subjected to echocardiography and assessment of markers of HCM by qRT-PCR. Transcriptome analysis was performed from the heart tissue of low-dose dasatinib-treated mice. Results Low-dose dasatinib exhibited PK properties that were linear across doses in NSML mice. Dasatinib treatment of between 0.05 and 0.5 mg/kg in NSML mice yielded an exposure-dependent inhibition of c-Src and PZR tyrosyl phosphorylation and inhibited AKT phosphorylation. We found that doses as low as 0.1 mg/kg of dasatinib prevented HCM in NSML mice. Transcriptome analysis identified differentially expressed HCM-associated genes in the heart of NSML mice that were reverted to wild type levels by low-dose dasatinib administration. Conclusion These data demonstrate that low-dose dasatinib exhibits desirable therapeutic PK properties that is sufficient for effective target engagement to ameliorate HCM progression in NSML mice. These data demonstrate that low-dose dasatinib treatment may be an effective therapy against HCM in NSML patients. Supplementary Information The online version contains supplementary material available at 10.1007/s10557-021-07169-z.
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Affiliation(s)
- Jae-Sung Yi
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA.
| | - Sravan Perla
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Yan Huang
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Kana Mizuno
- Division of Clinical Pharmacology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Frank J Giordano
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Alexander A Vinks
- Division of Clinical Pharmacology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, USA
| | - Anton M Bennett
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA.,Program in Integrative Cell Signaling and Neurobiology of Metabolism, Yale University School of Medicine, New Haven, CT, 06520, USA
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22
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Zhu G, Xie J, Kong W, Xie J, Li Y, Du L, Zheng Q, Sun L, Guan M, Li H, Zhu T, He H, Liu Z, Xia X, Kan C, Tao Y, Shen HC, Li D, Wang S, Yu Y, Yu ZH, Zhang ZY, Liu C, Zhu J. Phase Separation of Disease-Associated SHP2 Mutants Underlies MAPK Hyperactivation. Cell 2020; 183:490-502.e18. [PMID: 33002410 DOI: 10.1016/j.cell.2020.09.002] [Citation(s) in RCA: 132] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 04/19/2020] [Accepted: 08/31/2020] [Indexed: 02/08/2023]
Abstract
The non-receptor protein tyrosine phosphatase (PTP) SHP2, encoded by PTPN11, plays an essential role in RAS-mitogen-activated protein kinase (MAPK) signaling during normal development. It has been perplexing as to why both enzymatically activating and inactivating mutations in PTPN11 result in human developmental disorders with overlapping clinical manifestations. Here, we uncover a common liquid-liquid phase separation (LLPS) behavior shared by these disease-associated SHP2 mutants. SHP2 LLPS is mediated by the conserved well-folded PTP domain through multivalent electrostatic interactions and regulated by an intrinsic autoinhibitory mechanism through conformational changes. SHP2 allosteric inhibitors can attenuate LLPS of SHP2 mutants, which boosts SHP2 PTP activity. Moreover, disease-associated SHP2 mutants can recruit and activate wild-type (WT) SHP2 in LLPS to promote MAPK activation. These results not only suggest that LLPS serves as a gain-of-function mechanism involved in the pathogenesis of SHP2-associated human diseases but also provide evidence that PTP may be regulated by LLPS that can be therapeutically targeted.
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Affiliation(s)
- Guangya Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jingjing Xie
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Wenna Kong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfei Xie
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yichen Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin Du
- Etern Biopharma Co. Ltd., Shanghai 201203, China
| | | | - Lin Sun
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
| | - Mingfeng Guan
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Huan Li
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Tianxin Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Hao He
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenying Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xi Xia
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chen Kan
- Department of Pathophysiology, Anhui Medical University, Hefei 230032, China
| | - Youqi Tao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong C Shen
- Roche Innovation Center Shanghai, Roche Pharma Research & Early Development, Shanghai 201203, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Siying Wang
- Department of Pathophysiology, Anhui Medical University, Hefei 230032, China
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai 200092, China
| | - Zhi-Hong Yu
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research and Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Center for Cancer Research and Institute for Drug Discovery, Purdue University, West Lafayette, IN 47907, USA
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Jidong Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China; Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.
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23
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Kim JY, Plaman BA, Bishop AC. Targeting a Pathogenic Cysteine Mutation: Discovery of a Specific Inhibitor of Y279C SHP2. Biochemistry 2020; 59:3498-3507. [PMID: 32871078 PMCID: PMC7891893 DOI: 10.1021/acs.biochem.0c00471] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
An
intriguing challenge of drug discovery is targeting pathogenic
mutant proteins that differ from their wild-type counterparts by only
a single amino acid. In particular, pathogenic cysteine mutations
afford promising opportunities for mutant-specific drug discovery,
due to the unique reactivity of cysteine’s sulfhydryl-containing
side chain. Here we describe the first directed discovery effort targeting
a pathogenic cysteine mutant of a protein tyrosine phosphatase (PTP),
namely Y279C Src-homology-2-containing PTP 2 (SHP2), which has been
causatively linked to the developmental disorder Noonan syndrome with
multiple lentigines (NSML). Through a screen of commercially available
compounds that contain cysteine-reactive functional groups, we have
discovered a small-molecule inhibitor of Y279C SHP2 (compound 99; IC50 ≈ 6 μM) that has no appreciable
effect on the phosphatase activity of wild-type SHP2 or that of other
homologous PTPs (IC50 ≫ 100 μM). Compound 99 exerts its specific inhibitory effect through irreversible
engagement of Y279C SHP2’s pathogenic cysteine residue in a
manner that is time-dependent, is substrate-independent, and persists
in the context of a complex proteome. To the best of our knowledge, 99 is the first specific ligand of a disease-causing PTP mutant
to be identified. This study therefore provides both a starting point
for the development of NSML-directed therapeutic agents and a precedent
for the identification of mutant-specific inhibitors of other pathogenic
PTP mutants.
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Affiliation(s)
- Jenny Y Kim
- Department of Chemistry, Amherst College, Amherst, Massachusetts 01002, United States
| | - Bailey A Plaman
- Department of Chemistry, Amherst College, Amherst, Massachusetts 01002, United States
| | - Anthony C Bishop
- Department of Chemistry, Amherst College, Amherst, Massachusetts 01002, United States
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24
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Yi JS, Perla S, Enyenihi L, Bennett AM. Tyrosyl phosphorylation of PZR promotes hypertrophic cardiomyopathy in PTPN11-associated Noonan syndrome with multiple lentigines. JCI Insight 2020; 5:137753. [PMID: 32584792 PMCID: PMC7455087 DOI: 10.1172/jci.insight.137753] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 06/18/2020] [Indexed: 02/05/2023] Open
Abstract
Noonan syndrome with multiple lentigines (NSML) is a rare autosomal dominant disorder that presents with cardio-cutaneous-craniofacial defects. Hypertrophic cardiomyopathy (HCM) represents the major life-threatening presentation in NSML. Mutations in the PTPN11 gene that encodes for the protein tyrosine phosphatase (PTP), SHP2, represents the predominant cause of HCM in NSML. NSML-associated PTPN11 mutations render SHP2 catalytically inactive with an "open" conformation. NSML-associated PTPN11 mutations cause hypertyrosyl phosphorylation of the transmembrane glycoprotein, protein zero-related (PZR), resulting in increased SHP2 binding. Here we show that NSML mice harboring a tyrosyl phosphorylation-defective mutant of PZR (NSML/PZRY242F) that is defective for SHP2 binding fail to develop HCM. Enhanced AKT/S6 kinase signaling in heart lysates of NSML mice was reversed in NSML/PZRY242F mice, demonstrating that PZR/SHP2 interactions promote aberrant AKT/S6 kinase activity in NSML. Enhanced PZR tyrosyl phosphorylation in the hearts of NSML mice was found to drive myocardial fibrosis by engaging an Src/NF-κB pathway, resulting in increased activation of IL-6. Increased expression of IL-6 in the hearts of NSML mice was reversed in NSML/PZRY242F mice, and PZRY242F mutant fibroblasts were defective for IL-6 secretion and STAT3-mediated fibrogenesis. These results demonstrate that NSML-associated PTPN11 mutations that induce PZR hypertyrosyl phosphorylation trigger pathophysiological signaling that promotes HCM and cardiac fibrosis.
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Affiliation(s)
- Jae-Sung Yi
- Department of Pharmacology, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Sravan Perla
- Department of Pharmacology, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
| | - Liz Enyenihi
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
| | - Anton M. Bennett
- Department of Pharmacology, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
- Program in Integrative Cell Signaling and Neurobiology of Metabolism, Department of Comparative Medicine, Yale School of Medicine, Yale University, New Haven, Connecticut, USA
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25
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Yuan X, Bu H, Zhou J, Yang CY, Zhang H. Recent Advances of SHP2 Inhibitors in Cancer Therapy: Current Development and Clinical Application. J Med Chem 2020; 63:11368-11396. [DOI: 10.1021/acs.jmedchem.0c00249] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Xinrui Yuan
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Hong Bu
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Jinpei Zhou
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Chao-Yie Yang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee 38163, United States
| | - Huibin Zhang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
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26
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P 0-Related Protein Accelerates Human Mesenchymal Stromal Cell Migration by Modulating VLA-5 Interactions with Fibronectin. Cells 2020; 9:cells9051100. [PMID: 32365526 PMCID: PMC7290418 DOI: 10.3390/cells9051100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/16/2020] [Accepted: 04/24/2020] [Indexed: 12/22/2022] Open
Abstract
P0-related protein (PZR), a Noonan and LEOPARD syndrome target, is a member of the transmembrane Immunoglobulin superfamily. Its cytoplasmic tail contains two immune-receptor tyrosine-based inhibitory motifs (ITIMs), implicated in adhesion-dependent signaling and regulating cell adhesion and motility. PZR promotes cell migration on the extracellular matrix (ECM) molecule, fibronectin, by interacting with SHP-2 (Src homology-2 domain-containing protein tyrosine phosphatase-2), a molecule essential for skeletal development and often mutated in Noonan and LEOPARD syndrome patients sharing overlapping musculoskeletal abnormalities and cardiac defects. To further explore the role of PZR, we assessed the expression of PZR and its ITIM-less isoform, PZRb, in human bone marrow mesenchymal stromal cells (hBM MSC), and its ability to facilitate adhesion to and spreading and migration on various ECM molecules. Furthermore, using siRNA knockdown, confocal microscopy, and immunoprecipitation assays, we assessed PZR and PZRb interactions with β1 integrins. PZR was the predominant isoform in hBM MSC. Migrating hBM MSCs interacted most effectively with fibronectin and required the association of PZR, but not PZRb, with the integrin, VLA-5(α5β1), leading to modulation of focal adhesion kinase phosphorylation and vinculin levels. This raises the possibility that dysregulation of PZR function may modify hBM MSC migratory behavior, potentially contributing to skeletal abnormalities.
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27
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Athota JP, Bhat M, Nampoothiri S, Gowrishankar K, Narayanachar SG, Puttamallesh V, Farooque MO, Shetty S. Molecular and clinical studies in 107 Noonan syndrome affected individuals with PTPN11 mutations. BMC MEDICAL GENETICS 2020; 21:50. [PMID: 32164556 PMCID: PMC7068896 DOI: 10.1186/s12881-020-0986-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 02/25/2020] [Indexed: 02/08/2023]
Abstract
Background Noonan syndrome (NS), an autosomal dominant developmental genetic disorder, is caused by germline mutations in genes associated with the RAS / mitogen-activated protein kinase (MAPK) pathway. In several studies PTPN11 is one of the genes with a significant number of pathogenic variants in NS-affected patients. Therefore, clinically diagnosed NS individuals are initially tested for pathogenic variants in PTPN11 gene to confirm the relationship before studying genotype–phenotype correlation. Methods Individuals (363) with clinically diagnosed NS from four hospitals in South India were recruited and the exons of PTPN11 gene were sequenced. Results Thirty-two previously described pathogenic variants in eight different exons in PTPN11 gene were detected in 107 patients, of whom 10 were familial cases. Exons 3, 8 and 13 had the highest number of pathogenic variants. The most commonly identified pathogenic variants in this series were in exon 8 (c.922A > G, c.923A > G), observed in 22 of the affected. Congenital cardiac anomalies were present in 84% of the mutation-positive cohort, the majority being defects in the right side of the heart. The most common facial features were downward-slanting palpebral fissures, hypertelorism and low-set posteriorly rotated ears. Other clinical features included short stature (40%), pectus excavatum (54%) and, in males, unilateral or bilateral cryptorchidism (44%). Conclusion The clinical features and mutational spectrum observed in our cohort are similar to those reported in other large studies done worldwide. This is the largest case series of NS-affected individuals with PTPN11 mutations described till date from India.
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Affiliation(s)
| | - Meenakshi Bhat
- Molecular Genetics, Centre for Human Genetics, Bengaluru, 560100, India.,Pediatric Genetics, Indira Gandhi Institute of Child Health, Bengaluru, 560029, India
| | - Sheela Nampoothiri
- Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre (AIMS), Kochi, 682041, India
| | | | | | | | | | - Swathi Shetty
- Molecular Genetics, Centre for Human Genetics, Bengaluru, 560100, India.
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28
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Therapeutic potential of targeting SHP2 in human developmental disorders and cancers. Eur J Med Chem 2020; 190:112117. [PMID: 32061959 DOI: 10.1016/j.ejmech.2020.112117] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 02/03/2020] [Accepted: 02/03/2020] [Indexed: 02/06/2023]
Abstract
Src homology 2 (SH2)-containing protein tyrosine phosphatase 2 (SHP2), encoded by PTPN11, regulates cell proliferation, differentiation, apoptosis and survival via releasing intramolecular autoinhibition and modulating various signaling pathways, such as mitogen-activated protein kinase (MAPK) pathway. Mutations and aberrant expression of SHP2 are implicated in human developmental disorders, leukemias and several solid tumors. As an oncoprotein in some cancers, SHP2 represents a rational target for inhibitors to interfere. Nevertheless, its tumor suppressive effect has also been uncovered, indicating the context-specificity. Even so, two types of SHP2 inhibitors including targeting catalytic pocket and allosteric sites have been developed associated with resolved cocrystal complexes. Herein, we describe its structure, biological function, deregulation in human diseases and summarize recent advance in development of SHP2 inhibitors, trying to give an insight into the therapeutic potential in future.
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29
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Niogret C, Birchmeier W, Guarda G. SHP-2 in Lymphocytes' Cytokine and Inhibitory Receptor Signaling. Front Immunol 2019; 10:2468. [PMID: 31708921 PMCID: PMC6823243 DOI: 10.3389/fimmu.2019.02468] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/03/2019] [Indexed: 02/06/2023] Open
Abstract
Somewhat counterintuitively, the tyrosine phosphatase SHP-2 (SH2 domain-containing protein tyrosine phosphatase-2) is crucial for the activation of extracellular signal-regulated kinase (ERK) downstream of various growth factor receptors, thereby exerting essential developmental functions. This phosphatase also deploys proto-oncogenic functions and specific inhibitors have recently been developed. With respect to the immune system, the role of SHP-2 in the signaling of cytokines relevant for myelopoiesis and myeloid malignancies has been intensively studied. The function of this phosphatase downstream of cytokines important for lymphocytes is less understood, though multiple lines of evidence suggest its importance. In addition, SHP-2 has been proposed to mediate the suppressive effects of inhibitory receptors (IRs) that sustain a dysfunctional state in anticancer T cells. Molecules involved in IR signaling are of potential pharmaceutical interest as blockade of these inhibitory circuits leads to remarkable clinical benefit. Here, we discuss the dichotomy in the functions ascribed to SHP-2 downstream of cytokine receptors and IRs, with a focus on T and NK lymphocytes. Further, we highlight the importance of broadening our understanding of SHP-2′s relevance in lymphocytes, an essential step to inform on side effects and unanticipated benefits of its therapeutic blockade.
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Affiliation(s)
- Charlène Niogret
- Department of Biochemistry, University of Lausanne, Épalinges, Switzerland
| | - Walter Birchmeier
- Max-Delbrueck-Center for Molecular Medicine (MDC) in the Helmholtz Society, Berlin, Germany
| | - Greta Guarda
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
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30
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Mechanism of activating mutations and allosteric drug inhibition of the phosphatase SHP2. Nat Commun 2018; 9:4507. [PMID: 30375376 PMCID: PMC6207724 DOI: 10.1038/s41467-018-06814-w] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 09/20/2018] [Indexed: 01/01/2023] Open
Abstract
Protein tyrosine phosphatase SHP2 functions as a key regulator of cell cycle control, and activating mutations cause several cancers. Here, we dissect the energy landscape of wild-type SHP2 and the oncogenic mutation E76K. NMR spectroscopy and X-ray crystallography reveal that wild-type SHP2 exchanges between closed, inactive and open, active conformations. E76K mutation shifts this equilibrium toward the open state. The previously unknown open conformation is characterized, including the active-site WPD loop in the inward and outward conformations. Binding of the allosteric inhibitor SHP099 to E76K mutant, despite much weaker, results in an identical structure as the wild-type complex. A conformational selection to the closed state reduces drug affinity which, combined with E76K’s much higher activity, demands significantly greater SHP099 concentrations to restore wild-type activity levels. The differences in structural ensembles and drug-binding kinetics of cancer-associated SHP2 forms may stimulate innovative ideas for developing more potent inhibitors for activated SHP2 mutants. The protein tyrosine phosphatase SHP2 is a key regulator of cell cycle control. Here the authors combine NMR measurements and X-ray crystallography and show that wild-type SHP2 dynamically exchanges between a closed inactive conformation and an open activated form and that the oncogenic E76K mutation shifts the equilibrium to the open state, which is reversed by binding of the allosteric inhibitor SHP099.
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31
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Sun YZ, Chen XB, Wang RR, Li WY, Ma Y. Exploring the effect of N308D mutation on protein tyrosine phosphatase-2 cause gain-of-function activity by a molecular dynamics study. J Cell Biochem 2018; 120:5949-5961. [PMID: 30304563 DOI: 10.1002/jcb.27883] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 09/19/2018] [Indexed: 01/27/2023]
Abstract
One of the most common protein tyrosine phosphatase-2 (SHP2) mutations in Noonan syndrome is the N308D mutation, and it increases the activity of the protein. However, the molecular basis of the activation of N308D mutation on SHP2 conformations is poorly understood. Here, molecular dynamic simulations were performed on SHP2 and SHP2-N308D to explore the effect of N308D mutation on SHP2 cause gain of function activity, respectively. The principal component analysis, dynamic cross-correlation map, secondary structure analysis, residue interaction networks, and solvent accessible surface area analysis suggested that the N308D mutation distorted the residues interactions network between the allosteric site (residue Gly244-Gly246) and C-SH2 domain, including the hydrogen bond formation and the binding energy. Meanwhile, the activity of catalytic site (residue Gly503-Val505) located in the Q-loop in mutant increased due to this region's high fluctuations. Therefore, the substrate had more chances to access to the catalytic activity site of the precision time protocol domain of SHP2-N308D, which was easy to be exposed. In addition, we had speculated that the Lys244 located in the allosteric site was the key residue which lead to the protein conformation changes. Consequently, overall calculations presented in this study ultimately provide a useful understanding of the increased activity of SHP2 caused by the N308D mutation.
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Affiliation(s)
- Ying-Zhan Sun
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Xiu-Bo Chen
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China.,Eye Hospital, Tianjin Medical University, School of Optometry and Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Rui-Rui Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Wei-Ya Li
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Ying Ma
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
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32
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Tajan M, Paccoud R, Branka S, Edouard T, Yart A. The RASopathy Family: Consequences of Germline Activation of the RAS/MAPK Pathway. Endocr Rev 2018; 39:676-700. [PMID: 29924299 DOI: 10.1210/er.2017-00232] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 06/13/2018] [Indexed: 12/13/2022]
Abstract
Noonan syndrome [NS; Mendelian Inheritance in Men (MIM) #163950] and related syndromes [Noonan syndrome with multiple lentigines (formerly called LEOPARD syndrome; MIM #151100), Noonan-like syndrome with loose anagen hair (MIM #607721), Costello syndrome (MIM #218040), cardio-facio-cutaneous syndrome (MIM #115150), type I neurofibromatosis (MIM #162200), and Legius syndrome (MIM #611431)] are a group of related genetic disorders associated with distinctive facial features, cardiopathies, growth and skeletal abnormalities, developmental delay/mental retardation, and tumor predisposition. NS was clinically described more than 50 years ago, and disease genes have been identified throughout the last 3 decades, providing a molecular basis to better understand their physiopathology and identify targets for therapeutic strategies. Most of these genes encode proteins belonging to or regulating the so-called RAS/MAPK signaling pathway, so these syndromes have been gathered under the name RASopathies. In this review, we provide a clinical overview of RASopathies and an update on their genetics. We then focus on the functional and pathophysiological effects of RASopathy-causing mutations and discuss therapeutic perspectives and future directions.
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Affiliation(s)
- Mylène Tajan
- INSERM UMR 1048, Institute of Cardiovascular and Metabolic Diseases (I2MC), University of Toulouse Paul Sabatier, Toulouse, France
| | - Romain Paccoud
- INSERM UMR 1048, Institute of Cardiovascular and Metabolic Diseases (I2MC), University of Toulouse Paul Sabatier, Toulouse, France
| | - Sophie Branka
- INSERM UMR 1048, Institute of Cardiovascular and Metabolic Diseases (I2MC), University of Toulouse Paul Sabatier, Toulouse, France
| | - Thomas Edouard
- Endocrine, Bone Diseases, and Genetics Unit, Children's Hospital, Toulouse University Hospital, Toulouse, France
| | - Armelle Yart
- INSERM UMR 1048, Institute of Cardiovascular and Metabolic Diseases (I2MC), University of Toulouse Paul Sabatier, Toulouse, France
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33
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Yu ZH, Zhang ZY. Regulatory Mechanisms and Novel Therapeutic Targeting Strategies for Protein Tyrosine Phosphatases. Chem Rev 2018; 118:1069-1091. [PMID: 28541680 PMCID: PMC5812791 DOI: 10.1021/acs.chemrev.7b00105] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An appropriate level of protein phosphorylation on tyrosine is essential for cells to react to extracellular stimuli and maintain cellular homeostasis. Faulty operation of signal pathways mediated by protein tyrosine phosphorylation causes numerous human diseases, which presents enormous opportunities for therapeutic intervention. While the importance of protein tyrosine kinases in orchestrating the tyrosine phosphorylation networks and in target-based drug discovery has long been recognized, the significance of protein tyrosine phosphatases (PTPs) in cellular signaling and disease biology has historically been underappreciated, due to a large extent to an erroneous assumption that they are largely constitutive and housekeeping enzymes. Here, we provide a comprehensive examination of a number of regulatory mechanisms, including redox modulation, allosteric regulation, and protein oligomerization, that control PTP activity. These regulatory mechanisms are integral to the myriad PTP-mediated biochemical events and reinforce the concept that PTPs are indispensable and specific modulators of cellular signaling. We also discuss how disruption of these PTP regulatory mechanisms can cause human diseases and how these diverse regulatory mechanisms can be exploited for novel therapeutic development.
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Affiliation(s)
- Zhi-Hong Yu
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907
| | - Zhong-Yin Zhang
- Department of Medicinal Chemistry and Molecular Pharmacology, Department of Chemistry, Center for Cancer Research, and Institute for Drug Discovery, Purdue University, 720 Clinic Drive, West Lafayette, IN 47907
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34
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Machado LSF, Critton DA, Page R, Peti W. Redox Regulation of a Gain-of-Function Mutation (N308D) in SHP2 Noonan Syndrome. ACS OMEGA 2017; 2:8313-8318. [PMID: 29214238 PMCID: PMC5709778 DOI: 10.1021/acsomega.7b01318] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/10/2017] [Indexed: 06/07/2023]
Abstract
SHP2 (Src homology 2 domain-containing protein tyrosine phosphatase 2; PTPN11) is a ubiquitous multidomain, nonreceptor protein tyrosine phosphatase (PTP) that plays an important role in diseases such as cancer, diabetes, and Noonan syndrome (NS). NS is one of the most common genetic disorders associated with congenital heart disease, and approximately half of the patients with Noonan syndrome have gain-of-function mutations in SHP2. One of the most common NS mutations is N308D. The activity of SHP2, like that of most PTPs, is reversibly inactivated by reactive oxygen species (ROS). However, the molecular basis of this inactivation and the consequences of NS-related mutations in PTPN11 on ROS-mediated inhibition are poorly understood. Here, we investigated the mechanistic and structural details of the reversible oxidation of the NS variant SHP2N308D. We show that SHP2N308D is more sensitive to oxidation when compared with wild-type SHP2. We also show that although the SHP2N308D catalytic domain can be reactivated by dithiothreitol as effectively as the wild-type, full-length SHP2N308D is only poorly reactivated by comparison. To understand the mechanism of oxidation at a molecular level, we determined the crystal structure of oxidized SHP2N308D. The structure shows that the catalytic Cys459 residue forms a disulfide bond with Cys367, which confirms that Cys367 functions as the "backdoor" cysteine in SHP2. Together, our data suggest that the reversible oxidation of SHP2 contributes negligibly, if at all, to the symptoms associated with NS.
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Affiliation(s)
- Luciana
E. S. F. Machado
- Department
of Chemistry and Biochemistry, University
of Arizona, Tucson, Arizona 85721, United
States
| | - David A. Critton
- Department
of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Rebecca Page
- Department
of Chemistry and Biochemistry, University
of Arizona, Tucson, Arizona 85721, United
States
| | - Wolfgang Peti
- Department
of Chemistry and Biochemistry, University
of Arizona, Tucson, Arizona 85721, United
States
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35
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Chitranshi N, Dheer Y, Gupta V, Abbasi M, Mirzaei M, You Y, Chung R, Graham SL, Gupta V. PTPN11 induces endoplasmic stress and apoptosis in SH-SY5Y cells. Neuroscience 2017; 364:175-189. [PMID: 28947394 DOI: 10.1016/j.neuroscience.2017.09.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/13/2017] [Accepted: 09/14/2017] [Indexed: 12/25/2022]
Abstract
PTPN11 is associated with regulation of growth factor signaling pathways in neuronal cells. Using SH-SY5Y neuroblastoma cells, we showed that adeno-associated virus (AAV)-mediated PTPN11 upregulation was associated with TrkB antagonism, reduced neuritogenesis and enhanced endoplasmic reticulum (ER) stress response leading to apoptotic changes. Genetic knock-down of PTPN11 on the other hand leads to increased TrkB phosphorylation in SH-SY5Y cells. ER stress response induced by PTPN11 upregulation was alleviated pharmacologically by a TrkB agonist. Conversely the enhanced ER stress response induced by TrkB receptor antagonism was ameliorated by PTPN11 suppression, providing evidence of cross-talk of PTPN11 effects with TrkB actions. BDNF treatment of neuronal cells with PTPN11 upregulation also resulted in reduced expression of ER stress protein markers. This study provides evidence of molecular interactions between PTPN11 and the TrkB receptor in SH-SY5Y cells. The results reinforce the role played by PTPN11 in regulating neurotrophin protective signaling in neuronal cells and highlight that PTPN11 dysregulation promotes apoptotic activation. Based on these findings we suggest that blocking PTPN11 could have potential beneficial effects to limit the progression of neuronal loss in neurodegenerative disorders.
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Affiliation(s)
- Nitin Chitranshi
- Faculty of Medicine and Health Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia.
| | - Yogita Dheer
- Faculty of Medicine and Health Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Veer Gupta
- School of Medical Sciences, Edith Cowan University, Perth, Australia
| | - Mojdeh Abbasi
- Faculty of Medicine and Health Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Mehdi Mirzaei
- Faculty of Medicine and Health Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia; Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW 2109, Australia
| | - Yuyi You
- Save Sight Institute, Sydney University, Sydney, NSW 2000, Australia
| | - Roger Chung
- Faculty of Medicine and Health Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia
| | - Stuart L Graham
- Faculty of Medicine and Health Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia; Save Sight Institute, Sydney University, Sydney, NSW 2000, Australia
| | - Vivek Gupta
- Faculty of Medicine and Health Sciences, Macquarie University, F10A, 2 Technology Place, North Ryde, NSW 2109, Australia
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36
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Elson A. Stepping out of the shadows: Oncogenic and tumor-promoting protein tyrosine phosphatases. Int J Biochem Cell Biol 2017; 96:135-147. [PMID: 28941747 DOI: 10.1016/j.biocel.2017.09.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/15/2017] [Accepted: 09/16/2017] [Indexed: 12/18/2022]
Abstract
Protein tyrosine phosphorylation is critical for proper function of cells and organisms. Phosphorylation is regulated by the concerted but generically opposing activities of tyrosine kinases (PTKs) and tyrosine phosphatases (PTPs), which ensure its proper regulation, reversibility, and ability to respond to changing physiological situations. Historically, PTKs have been associated mainly with oncogenic and pro-tumorigenic activities, leading to the generalization that protein dephosphorylation is anti-oncogenic and hence that PTPs are tumor-suppressors. In many cases PTPs do suppress tumorigenesis. However, a growing body of evidence indicates that PTPs act as dominant oncogenes and drive cell transformation in a number of contexts, while in others PTPs support transformation that is driven by other oncogenes. This review summarizes the known transforming and tumor-promoting activities of the classical, tyrosine specific PTPs and highlights their potential as drug targets for cancer therapy.
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Affiliation(s)
- Ari Elson
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, 76100, Israel.
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Noonan Syndrome: An Underestimated Cause of Severe to Profound Sensorineural Hearing Impairment. Which Clues to Suspect the Diagnosis? Otol Neurotol 2017; 38:1081-1084. [PMID: 28742629 DOI: 10.1097/mao.0000000000001509] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To highlight Noonan syndrome as a clinically recognizable cause of severe to profound sensorineural hearing impairment. STUDY DESIGN New clinical cases and review. SETTING Patients evaluated for etiological diagnosis by a medical geneticist in a reference center for hearing impairment. PATIENTS Five patients presenting with confirmed Noonan syndrome and profound sensorineural hearing impairment. INTERVENTIONS Diagnostic and review of the literature. RESULTS Five patients presented with profound sensorineural hearing impairment and molecularly confirmed Noonan syndrome. Sensorineural hearing impairment has been progressive for three patients. Cardiac echography identified pulmonary stenosis in two patients and was normal for the three other patients. Short stature was found in two patients. Mild intellectual disability was found in one patient. Inconspicuous clinical features as facial dysmorphism, cryptorchidism, or easy bruising were of peculiar interest to reach the diagnosis of Noonan syndrome. CONCLUSION Profound sensorineural hearing impairment can be the main feature of Noonan syndrome. Associated features are highly variable; thus, detailed medical history and careful physical examination are mandatory to consider the diagnosis in case of a sensorineural hearing impairment.
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38
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Chen C, Liang F, Chen B, Sun Z, Xue T, Yang R, Luo D. Identification of demethylincisterol A 3 as a selective inhibitor of protein tyrosine phosphatase Shp2. Eur J Pharmacol 2017; 795:124-133. [DOI: 10.1016/j.ejphar.2016.12.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 12/06/2016] [Accepted: 12/07/2016] [Indexed: 11/29/2022]
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39
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Yi JS, Huang Y, Kwaczala AT, Kuo IY, Ehrlich BE, Campbell SG, Giordano FJ, Bennett AM. Low-dose dasatinib rescues cardiac function in Noonan syndrome. JCI Insight 2016; 1:e90220. [PMID: 27942593 DOI: 10.1172/jci.insight.90220] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Noonan syndrome (NS) is a common autosomal dominant disorder that presents with short stature, craniofacial dysmorphism, and cardiac abnormalities. Activating mutations in the PTPN11 gene encoding for the Src homology 2 (SH2) domain-containing protein tyrosine phosphatase-2 (SHP2) causes approximately 50% of NS cases. In contrast, NS with multiple lentigines (NSML) is caused by mutations that inactivate SHP2, but it exhibits some overlapping abnormalities with NS. Protein zero-related (PZR) is a SHP2-binding protein that is hyper-tyrosyl phosphorylated in the hearts of mice from NS and NSML, suggesting that PZR and the tyrosine kinase that catalyzes its phosphorylation represent common targets for these diseases. We show that the tyrosine kinase inhibitor, dasatinib, at doses orders of magnitude lower than that used for its anticancer activities inhibited PZR tyrosyl phosphorylation in the hearts of NS mice. Low-dose dasatinib treatment of NS mice markedly improved cardiomyocyte contractility and functionality. Remarkably, a low dose of dasatinib reversed the expression levels of molecular markers of cardiomyopathy and reduced cardiac fibrosis in NS and NSML mice. These results suggest that PZR/SHP2 signaling is a common target of both NS and NSML and that low-dose dasatinib may represent a unifying therapy for the treatment of PTPN11-related cardiomyopathies.
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Affiliation(s)
| | | | | | | | | | | | | | - Anton M Bennett
- Department of Pharmacology.,Program in Integrative Cell Signaling and Neurobiology of Metabolism, Yale School of Medicine, New Haven, Connecticut, USA
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40
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Lauriol J, Cabrera JR, Roy A, Keith K, Hough SM, Damilano F, Wang B, Segarra GC, Flessa ME, Miller LE, Das S, Bronson R, Lee KH, Kontaridis MI. Developmental SHP2 dysfunction underlies cardiac hypertrophy in Noonan syndrome with multiple lentigines. J Clin Invest 2016; 126:2989-3005. [PMID: 27348588 PMCID: PMC4966304 DOI: 10.1172/jci80396] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 05/09/2016] [Indexed: 11/17/2022] Open
Abstract
Hypertrophic cardiomyopathy is a common cause of mortality in congenital heart disease (CHD). Many gene abnormalities are associated with cardiac hypertrophy, but their function in cardiac development is not well understood. Loss-of-function mutations in PTPN11, which encodes the protein tyrosine phosphatase (PTP) SHP2, are implicated in CHD and cause Noonan syndrome with multiple lentigines (NSML), a condition that often presents with cardiac hypertrophic defects. Here, we found that NSML-associated hypertrophy stems from aberrant signaling mechanisms originating in developing endocardium. Trabeculation and valvular hyperplasia were diminished in hearts of embryonic mice expressing a human NSML-associated variant of SHP2, and these defects were recapitulated in mice expressing NSML-associated SHP2 specifically in endothelial, but not myocardial or neural crest, cells. In contrast, mice with myocardial- but not endothelial-specific NSML SHP2 expression developed ventricular septal defects, suggesting that NSML-associated mutations have both cell-autonomous and nonautonomous functions in cardiac development. However, only endothelial-specific expression of NSML-associated SHP2 induced adult-onset cardiac hypertrophy. Further, embryos expressing the NSML-associated SHP2 mutation exhibited aberrant AKT activity and decreased downstream forkhead box P1 (FOXP1)/FGF and NOTCH1/EPHB2 signaling, indicating that SHP2 is required for regulating reciprocal crosstalk between developing endocardium and myocardium. Together, our data provide functional and disease-based evidence that aberrant SHP2 signaling during cardiac development leads to CHD and adult-onset heart hypertrophy.
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Affiliation(s)
- Jessica Lauriol
- Department of Medicine, Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Janel R. Cabrera
- Department of Medicine, Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Ashbeel Roy
- Department of Medicine, Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Kimberly Keith
- Department of Medicine, Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Sara M. Hough
- Department of Medicine, Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Federico Damilano
- Department of Medicine, Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Bonnie Wang
- Department of Medicine, Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Gabriel C. Segarra
- Department of Pediatrics and Department of Obstetrics and Gynecology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Meaghan E. Flessa
- Department of Pediatrics and Department of Obstetrics and Gynecology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Lauren E. Miller
- Department of Pediatrics and Department of Obstetrics and Gynecology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Saumya Das
- Department of Medicine, Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | | | - Kyu-Ho Lee
- Department of Pediatrics and Department of Obstetrics and Gynecology, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Maria I. Kontaridis
- Department of Medicine, Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA
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41
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LaRochelle JR, Fodor M, Xu X, Durzynska I, Fan L, Stams T, Chan HM, LaMarche MJ, Chopra R, Wang P, Fortin PD, Acker MG, Blacklow SC. Structural and Functional Consequences of Three Cancer-Associated Mutations of the Oncogenic Phosphatase SHP2. Biochemistry 2016; 55:2269-77. [PMID: 27030275 DOI: 10.1021/acs.biochem.5b01287] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The proto-oncogene PTPN11 encodes a cytoplasmic protein tyrosine phosphatase, SHP2, which is required for normal development and sustained activation of the Ras-MAPK signaling pathway. Germline mutations in SHP2 cause developmental disorders, and somatic mutations have been identified in childhood and adult cancers and drive leukemia in mice. Despite our knowledge of the PTPN11 variations associated with pathology, the structural and functional consequences of many disease-associated mutants remain poorly understood. Here, we combine X-ray crystallography, small-angle X-ray scattering, and biochemistry to elucidate structural and mechanistic features of three cancer-associated SHP2 variants harboring single point mutations within the N-SH2:PTP interdomain autoinhibitory interface. Our findings directly compare the impact of each mutation on autoinhibition of the phosphatase and advance the development of structure-guided and mutation-specific SHP2 therapies.
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Affiliation(s)
- Jonathan R LaRochelle
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States.,Department of Cancer Biology, Dana-Farber Cancer Institute , Boston, Massachusetts 02215, United States
| | | | - Xiang Xu
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States.,Department of Cancer Biology, Dana-Farber Cancer Institute , Boston, Massachusetts 02215, United States
| | - Izabela Durzynska
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States.,Department of Cancer Biology, Dana-Farber Cancer Institute , Boston, Massachusetts 02215, United States
| | - Lixin Fan
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research , Frederick, Maryland 21702, United States
| | | | | | | | | | | | | | | | - Stephen C Blacklow
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School , Boston, Massachusetts 02115, United States.,Department of Cancer Biology, Dana-Farber Cancer Institute , Boston, Massachusetts 02215, United States
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42
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Radha V. Use of Dominant-Negative/Substrate Trapping PTP Mutations to Search for PTP Interactors/Substrates. Methods Mol Biol 2016; 1447:243-65. [PMID: 27514810 DOI: 10.1007/978-1-4939-3746-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Phosphorylation of proteins on tyrosine residues is the consequence of coordinated action of tyrosine kinases (TKs), and protein tyrosine phosphatases (PTPs). Together, they regulate intermolecular interactions, subcellular localization, and activity of a variety of proteins. The level of total protein-associated tyrosine phosphorylation in eukaryotic cells is only a small fraction of the total phosphorylation. PTPs, which have high specific activity compared to tyrosine kinases, play an important role in maintaining the tyrosine phosphorylation state of proteins and regulate signal transduction pathways and cellular responses. PTPs depend on specific invariant residues that enable binding to substrates phosphorylated at tyrosine and aid catalytic activity. Identification of PTP substrates has helped understand their role in distinct intracellular signaling pathways. Because of their high specific activity, the interaction between tyrosine phosphatases and their substrates is often very transient in the cellular context, and therefore identification of physiological substrates has been difficult. Single-site mutations in the enzymes stabilize interaction between the enzyme and its targets and have been used extensively to identify substrates. The mutations are either of the catalytic cysteine (Cys) residue or other invariant residues and have been classified as substrate-trapping mutants (STMs). These mutants often serve as dominant negatives that can inactivate effector functions of a specific PTP within cells. Considering their association with human disorders, inhibiting specific PTPs is important therapeutically. Since the catalytic domains are largely conserved, developing small-molecule inhibitors to a particular enzyme has proven difficult and therefore alternate strategies to block functions of individual enzymes are seriously being investigated. We provide a description of methods that will be useful to design strategies of using dominant-negative and substrate-trapping mutants for identifying novel interacting partners and substrates of PTPs.
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Affiliation(s)
- Vegesna Radha
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, 500 007, India.
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43
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SHP2 sails from physiology to pathology. Eur J Med Genet 2015; 58:509-25. [PMID: 26341048 DOI: 10.1016/j.ejmg.2015.08.005] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 07/24/2015] [Accepted: 08/30/2015] [Indexed: 02/08/2023]
Abstract
Over the two past decades, mutations of the PTPN11 gene, encoding the ubiquitous protein tyrosine phosphatase SHP2 (SH2 domain-containing tyrosine phosphatase 2), have been identified as the causal factor of several developmental diseases (Noonan syndrome (NS), Noonan syndrome with multiple lentigines (NS-ML), and metachondromatosis), and malignancies (juvenile myelomonocytic leukemia). SHP2 plays essential physiological functions in organism development and homeostasis maintenance by regulating fundamental intracellular signaling pathways in response to a wide range of growth factors and hormones, notably the pleiotropic Ras/Mitogen-Activated Protein Kinase (MAPK) and the Phosphoinositide-3 Kinase (PI3K)/AKT cascades. Analysis of the biochemical impacts of PTPN11 mutations first identified both loss-of-function and gain-of-function mutations, as well as more subtle defects, highlighting the major pathophysiological consequences of SHP2 dysregulation. Then, functional genetic studies provided insights into the molecular dysregulations that link SHP2 mutants to the development of specific traits of the diseases, paving the way for the design of specific therapies for affected patients. In this review, we first provide an overview of SHP2's structure and regulation, then describe its molecular roles, notably its functions in modulating the Ras/MAPK and PI3K/AKT signaling pathways, and its physiological roles in organism development and homeostasis. In the second part, we describe the different PTPN11 mutation-associated pathologies and their clinical manifestations, with particular focus on the biochemical and signaling outcomes of NS and NS-ML-associated mutations, and on the recent advances regarding the pathophysiology of these diseases.
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44
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Hu ZQ, Ma R, Zhang CM, Li J, Li L, Hu ZT, Gao QI, Li WM. Expression and clinical significance of tyrosine phosphatase SHP2 in thyroid carcinoma. Oncol Lett 2015; 10:1507-1512. [PMID: 26622699 DOI: 10.3892/ol.2015.3479] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 05/07/2015] [Indexed: 12/19/2022] Open
Abstract
Protein-tyrosine phosphatase SHP2 is encoded by the gene PTPN11. SHP2 is hypothesized to have a critical role in cancer, via the activation of mutations that have been detected in several types of leukaemia and in certain solid tumours, including liver, breast, gastric and cervical cancer. However, to the best of our knowledge, there have been no previous reports evaluating the significance of SHP2 expression in thyroid cancer. The present study evaluated SHP2 expression in 65 thyroid cancer specimens, 40 specimens of self-matched adjacent peritumour tissues and 40 specimens of normal thyroid tissue, using immunohistochemical and western blot analyses with an anti-SHP2 antibody. Western blotting was also used to assess SHP2 expression in thyroid cancer cell lines (SW579, IHH-4, FTC-133, TPC-1, DRO, TA-K, and ML-1) and Nthy-ori3-1 normal thyroid cells. In addition, SHP2 antisense oligonucleotides were used to block SHP2 expression in SW579 cells, and growth inhibition assays were conducted. Increased SHP2 expression was detected in the tumour tissues compared with that of the normal thyroid tissues (P<0.05). SHP2 expression was significantly correlated with poor tumour differentiation (P<0.05), late TNM stage (P<0.05) and lymph node metastasis (P<0.05), suggesting that SHP2 may represent a potential target for thyroid cancer therapy.
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Affiliation(s)
- Zhong-Qian Hu
- Department of Ultrasound, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Rui Ma
- Department of Cardiology, Jinling Hospital, Nanjing, Jiangsu 210002, P.R. China
| | - Chi-Min Zhang
- Department of Ultrasound, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Jia Li
- Department of Ultrasound, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Ling Li
- Department of Ultrasound, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Zhong-Ting Hu
- Department of Cardiology, Jinling Hospital, Nanjing, Jiangsu 210002, P.R. China
| | - Q I Gao
- Department of Ultrasound, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Wei-Min Li
- Department of Ultrasound, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
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45
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Chio CM, Cheng KW, Bishop AC. Direct Chemical Activation of a Rationally Engineered Signaling Enzyme. Chembiochem 2015; 16:1735-9. [PMID: 26063205 DOI: 10.1002/cbic.201500245] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Indexed: 11/08/2022]
Abstract
Few chemical strategies for activating enzymes have been developed. Here we show that a biarsenical compound (FlAsH) can directly activate a rationally engineered protein tyrosine phosphatase (Shp2 PTP) by disrupting autoinhibitory interactions between Shp2's N-terminal SH2 domain and its PTP domain. We found that introducing a tricysteine motif at a loop of Shp2's N-SH2 domain confers affinity for FlAsH; binding of FlAsH to the cysteine-enriched loop relieves Shp2's inhibitory interdomain interaction and substantially increases the enzyme's PTP activity. Activation of engineered Shp2 is substrate independent and is observed in the contexts of both purified enzyme and complex proteomes. A chemical means for activating Shp2 could be useful for investigating its roles in signaling and oncogenesis, and the loop-targeting strategy described herein could provide a blueprint for the development of target-specific activators of other autoinhibited enzymes.
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Affiliation(s)
- Cynthia M Chio
- Department of Chemistry, Amherst College, Amherst, MA 01002 (USA)
| | - Karen W Cheng
- Department of Chemistry, Amherst College, Amherst, MA 01002 (USA)
| | - Anthony C Bishop
- Department of Chemistry, Amherst College, Amherst, MA 01002 (USA).
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46
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Ramos-Geldres T, Dávila-Seijo P, Duat-Rodríguez A, Noguera-Morel L, Ezquieta-Zubicaray B, Rosón-López E, Hernández-Martín A, Torrelo-Fernández A. LEOPARD Syndrome Without Hearing Loss or Pulmonary Stenosis: A Report of 2 Cases. ACTAS DERMO-SIFILIOGRAFICAS 2015. [DOI: 10.1016/j.adengl.2015.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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47
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Síndrome LEOPARD sin sordera ni estenosis pulmonar: a propósito de 2 casos. ACTAS DERMO-SIFILIOGRAFICAS 2015; 106:e19-22. [DOI: 10.1016/j.ad.2014.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/31/2014] [Accepted: 11/06/2014] [Indexed: 11/19/2022] Open
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48
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Lauriol J, Jaffré F, Kontaridis MI. The role of the protein tyrosine phosphatase SHP2 in cardiac development and disease. Semin Cell Dev Biol 2014; 37:73-81. [PMID: 25256404 DOI: 10.1016/j.semcdb.2014.09.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 09/09/2014] [Accepted: 09/15/2014] [Indexed: 02/06/2023]
Abstract
Congenital heart disease is the most common human developmental disorder, affecting ∼1:100 newborns, and is the primary cause of birth-defect related deaths worldwide. As a major regulator of receptor tyrosine kinase (RTK), cytokine and G-protein coupled receptor signaling, the non-receptor protein tyrosine phosphatase SHP2 plays a critical role in normal cardiac development and function. Indeed, SHP2 participates in a wide variety of cellular functions, including proliferation, survival, differentiation, migration, and cell-cell communication. Moreover, human activating and inactivating mutations of SHP2 are responsible for two related developmental disorders called Noonan and LEOPARD Syndromes, respectively, which are both characterized, in part, by congenital heart defects. Structural, enzymologic, biochemical, and SHP2 mouse model studies have together greatly enriched our knowledge of SHP2 and, as such, have also uncovered the diverse roles for SHP2 in cardiac development, including its contribution to progenitor cell specification, cardiac morphogenesis, and maturation of cardiac valves and myocardial chambers. By delineating the precise mechanisms by which SHP2 is involved in regulating these processes, we can begin to better understand the pathogenesis of cardiac disease and find more strategic and effective therapies for treatment of patients with congenital heart disorders.
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Affiliation(s)
- Jessica Lauriol
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Fabrice Jaffré
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, United States
| | - Maria I Kontaridis
- Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, United States; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, United States.
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49
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Targeting protein tyrosine phosphatase SHP2 for therapeutic intervention. Future Med Chem 2014; 6:1423-37. [DOI: 10.4155/fmc.14.88] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Protein tyrosine phosphatases have been the focus of considerable research efforts aimed at developing novel therapeutics; however, these targets are often characterized as being ‘undruggable’ due to the challenge of achieving selectivity, potency and cell permeability. More recently, there has been renewed interest in developing inhibitors of the tyrosine phosphatase SHP2 (PTPN11) in the light of its broad role in cancer, specifically juvenile myelomonocytic leukemia, and recent studies that implicate SHP2 as a key factor in breast cancer progression. Recent significant advances in the field of SHP2 inhibitor development raise the question: are we on the verge of a new era of protein tyrosine phosphatase-directed therapeutics? This article critically appraises recent developments, assesses ongoing challenges and presents a perspective on possible future directions.
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50
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PZR coordinates Shp2 Noonan and LEOPARD syndrome signaling in zebrafish and mice. Mol Cell Biol 2014; 34:2874-89. [PMID: 24865967 DOI: 10.1128/mcb.00135-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Noonan syndrome (NS) is an autosomal dominant disorder caused by activating mutations in the PTPN11 gene encoding Shp2, which manifests in congenital heart disease, short stature, and facial dysmorphia. The complexity of Shp2 signaling is exemplified by the observation that LEOPARD syndrome (LS) patients possess inactivating PTPN11 mutations yet exhibit similar symptoms to NS. Here, we identify "protein zero-related" (PZR), a transmembrane glycoprotein that interfaces with the extracellular matrix to promote cell migration, as a major hyper-tyrosyl-phosphorylated protein in mouse and zebrafish models of NS and LS. PZR hyper-tyrosyl phosphorylation is facilitated in a phosphatase-independent manner by enhanced Src recruitment to NS and LS Shp2. In zebrafish, PZR overexpression recapitulated NS and LS phenotypes. PZR was required for zebrafish gastrulation in a manner dependent upon PZR tyrosyl phosphorylation. Hence, we identify PZR as an NS and LS target. Enhanced PZR-mediated membrane recruitment of Shp2 serves as a common mechanism to direct overlapping pathophysiological characteristics of these PTPN11 mutations.
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